{"canonical":"https://abierto.us/opportunities/36c24e25q0045","key":"36C24E25Q0045","url":"https://abierto.us/opportunities/36c24e25q0045","title":"Q301--Advanced Genetic Sequencing (Research Support)","solicitation_number":"36C24E25Q0045","notice_type":"k","open":false,"response_deadline":"2025-09-12T15:59:00Z","first_posted":"2025-06-04","last_posted":"2025-09-12","department":"VETERANS AFFAIRS, DEPARTMENT OF","subagency":"VETERANS AFFAIRS, DEPARTMENT OF","office":"RPO EAST (36C24E)","naics":"541715","psc":"Q301","set_aside":null,"place_state":"KS","place_county":"20143","place_county_name":"Ottawa County","place_city":"2047075","place_city_name":"Minneapolis","winner":null,"award_amount":null,"publications":[{"notice_id":"f6b762e43cb5470b95334ecd1c8e4f6d","title":"Q301--Advanced Genetic Sequencing (Research Study Support)","solicitation_number":"36C24E25Q0045","notice_type":"k","base_type":"k","posted":"2025-06-04","posted_at":null,"due_at":"2025-06-11T15:59:00Z","due_date":"2025-06-11","cancelled":null,"archived":null,"archive_date":"2025-07-11","award_number":null,"awardee_name":null,"amount":null,"link_sam":"https://sam.gov/workspace/contract/opp/f6b762e43cb5470b95334ecd1c8e4f6d/view","enriched":false,"history":[]},{"notice_id":"454050f45f9141fd8f24f53bce863b10","title":"Q301--Modification - Q & A for Advanced Genetic Sequencing","solicitation_number":"36C24E25Q0045","notice_type":"k","base_type":"k","posted":"2025-06-11","posted_at":null,"due_at":"2025-06-16T15:59:00Z","due_date":"2025-06-16","cancelled":null,"archived":null,"archive_date":"2025-07-16","award_number":null,"awardee_name":null,"amount":null,"link_sam":"https://sam.gov/workspace/contract/opp/454050f45f9141fd8f24f53bce863b10/view","enriched":false,"history":[]},{"notice_id":"e76bab3278c3482384f3335638ee75ee","title":"Q301--Modification - Q & A for Advanced Genetic Sequencing","solicitation_number":"36C24E25Q0045","notice_type":"k","base_type":"k","posted":"2025-06-23","posted_at":null,"due_at":"2025-06-30T15:59:00Z","due_date":"2025-06-30","cancelled":null,"archived":null,"archive_date":"2025-07-30","award_number":null,"awardee_name":null,"amount":null,"link_sam":"https://sam.gov/workspace/contract/opp/e76bab3278c3482384f3335638ee75ee/view","enriched":false,"history":[]},{"notice_id":"0889a728b3ef4245b8ca17437aad202a","title":"Q301--Modification - Q & A for Advanced Genetic Sequencing","solicitation_number":"36C24E25Q0045","notice_type":"k","base_type":"k","posted":"2025-06-24","posted_at":null,"due_at":"2025-06-26T15:59:00Z","due_date":"2025-06-26","cancelled":null,"archived":null,"archive_date":"2025-07-26","award_number":null,"awardee_name":null,"amount":null,"link_sam":"https://sam.gov/workspace/contract/opp/0889a728b3ef4245b8ca17437aad202a/view","enriched":false,"history":[]},{"notice_id":"529a97ea52a74be1be645c8a43533879","title":"Q301--Modification - Q & A for Advanced Genetic Sequencing","solicitation_number":"36C24E25Q0045","notice_type":"k","base_type":"k","posted":"2025-08-13","posted_at":null,"due_at":"2025-06-26T15:59:00Z","due_date":"2025-06-26","cancelled":null,"archived":null,"archive_date":"2025-10-10","award_number":null,"awardee_name":null,"amount":null,"link_sam":"https://sam.gov/workspace/contract/opp/529a97ea52a74be1be645c8a43533879/view","enriched":false,"history":[]},{"notice_id":"962ca8bb31a24986b1a140ee7218378d","title":"Q301--Advanced Genetic Sequencing (Research Support)","solicitation_number":"36C24E25Q0045","notice_type":"k","base_type":"k","posted":"2025-08-13","posted_at":null,"due_at":"2025-08-20T15:59:00Z","due_date":"2025-08-20","cancelled":null,"archived":null,"archive_date":"2025-10-19","award_number":null,"awardee_name":null,"amount":null,"link_sam":"https://sam.gov/workspace/contract/opp/962ca8bb31a24986b1a140ee7218378d/view","enriched":false,"history":[]},{"notice_id":"b39fc859ce5b444c81ac4b024d377a7c","title":"Q301--Advanced Genetic Sequencing (Research Support)","solicitation_number":"36C24E25Q0045","notice_type":"k","base_type":"k","posted":"2025-09-12","posted_at":null,"due_at":"2025-09-12T15:59:00Z","due_date":"2025-09-12","cancelled":null,"archived":null,"archive_date":"2025-09-27","award_number":null,"awardee_name":null,"amount":null,"link_sam":"https://sam.gov/workspace/contract/opp/b39fc859ce5b444c81ac4b024d377a7c/view","enriched":false,"history":[]}],"latest_notice_id":"b39fc859ce5b444c81ac4b024d377a7c","first_type":"k","notices":[{"dates":{"posted":"2025-06-04","response_deadline":{"raw":"2025-06-11T11:59:00-04:00","utc":"2025-06-11T15:59:00Z","date":"2025-06-11","time":"11:59:00","utc_offset_seconds":-14400}},"links":{"sam":"https://sam.gov/workspace/contract/opp/f6b762e43cb5470b95334ecd1c8e4f6d/view"},"naics":{"codes":["541715"],"primary":"541715"},"title":"Q301--Advanced Genetic Sequencing (Research Study Support)","agency":{"office":{"code":"36C24E","name":"RPO EAST (36C24E)"},"subtier":{"code":"3600","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"department":{"code":"036","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"office_address":{"zip":"15212","city":"PITTSBURGH","state":"PA","country":"USA"},"organization_type":"OFFICE"},"status":{"active":false,"archive_date":"2025-07-11","archive_type":"auto_custom"},"contacts":[{"name":"Ms. Millicent Covert","role":"primary","email":"millicent.covert@va.gov","phone":"(Phone calls will not be taken)","title":"Contracting Officer"}],"base_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"notice_id":"f6b762e43cb5470b95334ecd1c8e4f6d","provenance":{"extract":{"url":"https://s3.amazonaws.com/falextracts/Contract%20Opportunities/Archived%20Data/FY2025_archived_opportunities.csv","etag":"\"d47226e3d2c6545974b252e103f82b34-139\"","fetched_at":"2026-09-16T17:45:50.850439Z","row_sha256":"64296054fbdd55a7dfde2ad3cd8c2629205143f4ef8f959206927e845e2c3c8e","last_modified":"2026-09-13T14:49:20Z"},"updated_at":"2026-09-16T17:45:50.850439Z","first_seen_at":"2026-09-16T17:45:50.850439Z"},"description":{"text":"This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6 in conjunction with Part 13 of Federal Acquisition Regulation (FAR), as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will not be issued. This Solicitation is issued as a Request for Quote (RFQ), and the solicitation number is 36C24E25Q0045. The government anticipates awarding a firm-fixed price contract will be awarded resulting from this combined synopsis/solicitation. This solicitation is issued as a Full and Open Competition concern. This solicitation and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2025-03. It is the responsibility of the contractor to be familiar with the applicable clauses and provisions. The clauses may be accessed in full text at www.acquisition.gov. The associated NAICS Code for this procurement is 541715 Research and Development in the Physical, Engineering, and Life Sciences (except Nanotechnology and Biotechnology) and the business size standard is 1,000 employees. The FSC/PSC is Q301. **NOTE: RFQ 36C24E25Q0045 hereby replaces RFQ 36C24E25Q0034** STATEMENT OF NEED (SON) CONTRACT DESCRIPTION AND REQUIREMENTS: The Regional Procurement Office (RPO) - East has a requirement to purchase specialized genetic sequencing services for the Research Department at the Minneapolis VA Health Care System. These services are required for the VA-funded research study Impact of Obesity on Brain Immune Response and Cognition . A firm-fixed price contract will be awarded for the purchase of services in accordance with all terms, conditions, provisions, specifications, and schedule of this solicitation herein. Quotes shall contain the Offeror s best terms for cost/price and technical capabilities of the requirement. The government reserves the right to award without discussions. All work shall be completed in accordance with the Statement of Work, included as Attachment 1 to this solicitation. The contract resulting from this solicitation will be a Firm Fixed Price contract. Period of Performance will be 5 years. Anticipated start date will be June 30, 2025, and run through June 29, 2030. Offerors are requested to quote Firm Fixed Price for any and all of the line items on the Schedule of Supplies and Services attached to this solicitation. The Schedule of Supplies and Services is included as Attachment 2 to this solicitation. Any award resulting from this solicitation will be issued on a Standard Form 1449. NOTE: To receive an award resulting from this solicitation, offerors MUST be registered in the System for Award Management (SAM) database IAW FAR 52.212-(k). Registration may be done online at: www.acquisition.gov or www.sam.gov. Instructions to the Offeror Award will be based upon a comparative evaluation of quotes in accordance with the Simplified Acquisition Procedures of FAR 13. Comparative evaluation is the side by side pairwise comparison of quotes based on factors resulting in a Contracting Officer decision for the quote most favorable to the Government. Comparative Evaluation of Quotes will be used, in accordance with FAR 13.106-2. The following are the decision factors: Factor 1 - Technical Capabilities All offerors must meet or exceed all requirements and salient features as listed in the Statement of Need. Factor 2 - Past Performance - Past Performance will be based on the most current CPARS Report. A lack of relevant past performance will be graded as neutral during evaluation. Factor 3 Price 13.106-2 Evaluation of Quotations or Offers The Government intends to award one purchase order as a result of this Request for Quote to the responsible offeror whose quote conforms to the solicitation requirements and will be most advantageous to the Government, considering price, technical capability and past performance of the service offered. Offerors must be determined responsible according to the standards of FAR Part 9 to be eligible for award. The Government is not limited to the Past Performance Record information provided above, but reserves the right to independently seek past performance information through open market contracts, government systems, and other government agencies. The Contracting Officer does anticipate adequate price competition for this RFQ. Should that not happen, the Contracting Officer may need to ask for Data Other than Certified Cost and Price Data to assist with the determination of price reasonableness. Vendors are advised that submitting an unrealistically low price may be grounds for eliminating a quote from competition. This could be on the basis that the vendor does not understand the requirement or has made an incautious quote. The following FAR provision and clauses apply to this solicitation and are incorporated by reference. The solicitation document, incorporated provision and clauses are those in effect through the Federal Acquisition Circular (FAC) 2025-03, Effective 01/17/2025. It is the responsibility of the contractor to be familiar with the applicable clauses and provisions. The clauses may be accessed in full text at www.acquistion.gov. This contract incorporates one or more clauses by reference, with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. FAR 52.212-1 Instructions to Offerors Commercial FAR 52.212-2 Evaluation- Commercial Items FAR 52.212-3 Offeror Representations and Certifications** (SAM registration is required to be complete at time of submission of response) Offerors must complete annual representations and certifications electronically via thein accordance with FAR 52.212-3, Offerors Representations and Certifications Commercial Products and Commercial Services. If paragraph (j) of the provision is applicable, a written submission is required) FAR 52.212-4 Contract Terms and Conditions FAR 52.212-5 Contract Terms and Conditions Required to Implement Statutes or Executive Orders -- Commercial Items (JAN 2025) (DEVIATION FEB 2025) applies to this solicitation. The additional FAR clauses cited in 52.212-5 are applicable to this acquisition. In paragraph (a) the following clauses apply: 52.209-10, Prohibition on Contracting with Inverted Domestic Corporations (NOV 2015) 52.233-3, Protest After Award (AUG 1996) 52.233-4, Applicable Law for Breach of Contract Claim (OCT 2004) In paragraph (b) the following clauses apply: 52.203-6, Restrictions on Subcontractor Sales to the Government (JUN 2020), with Alternate I (NOV 2021) 52.204-10, Reporting Executive Compensation and First-Tier Subcontract Awards (JUN 2020) 52.209-6, Protecting the Government s Interest When Subcontracting with Contractors Debarred, Suspended, or Proposed for Debarment Protecting the Government s Interest When Subcontracting with Contractors Debarred, Suspended, Proposed for Debarment, or Voluntarily Excluded. (JAN 2025) 52.219-8, Utilization of Small Business Concerns (JAN 2025 52.219-28, Post Award Small Business Program Representation Postaward Small Business Program Rerepresentation (JAN 2025) 52.222-3, Convict Labor (JUNE 2003) 52.222-35, Equal Opportunity for Veterans (JUN 2020) 52.222-36, Equal Opportunity for Workers with Disabilities (JUN 2020) 52.222-50, Combating Trafficking in Persons (NOV 2021) (22 U.S.C. chapter 78 and E.O. 13627) 52.222-54, Employment Eligibility Verification (JAN 2025). (E.O. 12989) 52.225-13, Restrictions on Certain Foreign Purchases (FEB 2021) 52.232-33, Payment by Electronic Funds Transfer System for Award Management (OCT 2018) Under paragraph (c) the following clauses apply: 52.222-41, Service Contract Labor Standards (MAY 2014) 52.222-42, Statement of Equivalent Rates for Federal Hires (MAY 2014) Employee Class Monetary Wage Fringe Benefits 12130 - Medical Laboratory Technician 30.2999252 - Laboratory 52.222-44, Fair Labor Standards Act and Service Contract Labor Standards Price Adjustment (May 2014) 52.222-55, Minimum Wages for Contractor Workers Under Executive Order 14026 (JAN 2022) 52.222-62, Paid Sick Leave Under Executive Order 13706 (JAN 2022) All clauses under paragraph (d) and (e) as applicable (End of Clause) FAR 52.219-8 Utilization of Small Business Concerns (JAN 2025) FAR 52.219-14 Limitations on Subcontracting (Oct 2022) FAR 52.233-3 Protest After Award (Aug 1996) VAAR 852.233-70 Protest Content/Alternative Dispute Resolution (SEP 2018) FAR 52.252-1 Solicitation Provisions Incorporated by Reference (FEB 1998) FAR 52.252-5 Authorized Deviations in Provisions (APR 1984) FAR 52.209-5 Representation by Corporations Regarding an Unpaid Tax Liability or a Felony Conviction Under any Federal Law (MAR 2012) (DEVIATION) FAR 52.216-1 Type of Contract (APR 1984) The award will be made to the response most advantageous to the Government. Responses should contain your best terms, conditions. Offerors are advised that any and all questions concerning this solicitation must be sent in writing via email to Ms. Millicent Covert at millicent.covert@va.gov. No questions will be answered after Friday, June 6, 2025. Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive. All offers must be received by 11:59 EST, Wednesday, June 11, 2025. Quote Submission Instructions: Quotes shall be sent electronically via e-mail. All quotes shall include one (1) separate copy of each of the items listed below. Submission of a quote that does not contain all items requested below may result in elimination from consideration of award. Offerors must submit each item of quote in a separate electronic attachment clearly identified as described below. No price information shall be included in the technical or past performance section. Offerors are responsible for including sufficient details to permit a complete and accurate evaluation of each quote. First Attachment - Volume 1 1. Completed Schedule of Supplies and Services (Attachment 2 to this solicitation). Completed CLIN price information in the Schedule of Supplies/Services. *Offerors must use the CLINs specified in the Schedule of Supplies/Services. It is not permissible for offerors to use offeror created CLINs or SUBCLINs. 2. Completed certifications and representations located at FAR 52.212-3, or an indication that said certifications and representations are current and located in the SAM database. 3. Signed Certifications that may be included as Addenda to FAR 52.212-1. 4. Signed acknowledgements of amendments (SF30). Applicable only if any amendments are issued against this solicitation. Second Attachment - Volume 2 Offerors shall provide a narrative (including any descriptive literature and/or certifications) which demonstrates the offeror s ability to meet the technical credentials and capability stated in the Statement of Work (SOW). The narrative shall not exceed ten (10) pages and address the requirements within Item 3 Major Requirements and Item 10 under A. General Information in the SOW. Third Attachment - Volume 3 Past Performance Record: Vendors shall provide information on Past Performance Record. This information is used in determining the level of confidence the Government has for a successful performance based upon the vendor s actions under previously awarded and/or relevant contracts. The information provided in Volume 3 will be utilized to evaluate the Vendor s Past Performance. To be considered part of the Past Performance record, we ask to provide two (2) or more relevant contracts in the last five (5) years. If a vendor or its major subcontractor determines that they have no relevant past performance data, they shall provide the following statement in lieu of the information provided below: (Insert vendor or major subcontractor s name) has determined that they possess no relevant past performance information in accordance with the RFQ. To be compliant with this factor, vendors shall provide the following information for both the vendor and proposed major subcontractors: (1) A list of Previous Contract Data for the vendor. Please provide two (2) PRIME contracts and relevant subcontracts that the vendor is currently performing or has completed during the last 5 years. The list shall include: - Contractor name - Name of customer/agency - Contract/Purchase Order Number - Customer points of contact (minimum of two; provide name, telephone number, fax number and e-mail addresses) - Length of contract - Period of Performance (dates) - Initial Contract Price - Description of product/service provided (include sufficient detail to demonstrate similarities/dissimilarities to the requirements of this solicitation) (2) A list of Previous Contract Data for all minor subcontractors containing the information listed in (1) above as it relates to relevant Prime and Subcontracts that the major subcontractor is currently performing or has completed during the last 5 years. (3) The Government may utilize the Contractor Performance Assessment Reporting System (CPARS), responses from the Performance Risk Assessment Questionnaire, data submitted by the vendor, and any other information available to determine the quality and relevance of the vendor s past performance. Fourth Attachment Volume 4 Contractors are required to include a copy of the FAR provision 52.212-3 Offeror Representations and Certifications Commercial Items with its proposal or may indicate completion of the representations and certifications on the internet at http://sam.gov. Failure to include the certifications along with the price proposal or complete certifications on the internet may result in elimination from consideration for award. To facilitate the award process, all quotes must include a statement regarding the terms and conditions herein as follows: \"The terms and conditions in the solicitation are acceptable to be included in the award document without modification, deletion, or addition.\" OR \"The terms and conditions in the solicitation are acceptable to be included in the award document with the exception, deletion, or addition of the following:\" Quoters shall list exception(s) and rationale for the exception(s), if any. Offerors are advised that any and all questions concerning this solicitation must be sent in writing via email to Ms. Millicent Covert at millicent.covert@va.gov. No questions will be answered after Friday, June 6, 2025. Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive. All offers must be received by 11:59 EST, Wednesday, June 11, 2025.","origin":"extract"},"notice_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"schema_version":1,"solicitation_number":"36C24E25Q0045","place_of_performance":{"street":"Vendor's facility"},"product_service_code":"Q301"},{"dates":{"posted":"2025-06-11","response_deadline":{"raw":"2025-06-16T11:59:00-04:00","utc":"2025-06-16T15:59:00Z","date":"2025-06-16","time":"11:59:00","utc_offset_seconds":-14400}},"links":{"sam":"https://sam.gov/workspace/contract/opp/454050f45f9141fd8f24f53bce863b10/view"},"naics":{"codes":["541715"],"primary":"541715"},"title":"Q301--Modification - Q & A for Advanced Genetic Sequencing","agency":{"office":{"code":"36C24E","name":"RPO EAST (36C24E)"},"subtier":{"code":"3600","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"department":{"code":"036","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"office_address":{"zip":"15212","city":"PITTSBURGH","state":"PA","country":"USA"},"organization_type":"OFFICE"},"status":{"active":false,"archive_date":"2025-07-16","archive_type":"auto_custom"},"contacts":[{"name":"Ms. Millicent Covert","role":"primary","email":"millicent.covert@va.gov","phone":"(Telephone call shall not be accepted)","title":"Contracting Officer"}],"base_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"notice_id":"454050f45f9141fd8f24f53bce863b10","provenance":{"extract":{"url":"https://s3.amazonaws.com/falextracts/Contract%20Opportunities/Archived%20Data/FY2025_archived_opportunities.csv","etag":"\"d47226e3d2c6545974b252e103f82b34-139\"","fetched_at":"2026-09-16T17:45:50.850439Z","row_sha256":"d760ab306cdc9f7ed91cea9b2972528211f01cb00e12bf7e16c6d18927e1d2e6","last_modified":"2026-09-13T14:49:20Z"},"updated_at":"2026-09-16T17:45:50.850439Z","first_seen_at":"2026-09-16T17:45:50.850439Z"},"description":{"text":"RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer **Quote submission is extended from Wednesday, June 11, 2025, to no later than 11:59 EST, Monday, June 16, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive. _______________________________________________________________________ 1. For the \"spatially segregated mouse brain and lung\" samples, please clarify their processing prior to shipment. Specifically, will they be fresh-frozen (snap-frozen) or fixed-frozen (e.g., briefly fixed and then frozen)? The spatially segregated phrase refers to dissection of brain and lung regions prior to dissociation. No spatial transcriptomic techniques will be performed. Tissues are enzymatically dissociated into single-cell suspensions, then fixed and frozen in cryovials using Parse Biosciences methanol-based fixation protocol. 2. If able, can you also comment on: a) Tissue Details: Expected section thickness, mounting method, and clarity on section orientation (e.g., anatomical landmarks, images). Not applicable, no sectioning or mounting will be involved. Only single-cell suspensions will be used. b) Quality & Shipping: Anticipated RNA Integrity Number (RIN), detailed shipping conditions (e.g., dry ice amount, packaging), and frequency of shipments. Cells are fixed at our facility prior to shipment using Parse Evercode protocols. Shipping: Frozen in cryovials on dry ice using validated shippers. Shipments are expected 2 3 times per year, based on project progress. c) Histology: Will accompanying H&E stained slides or images be provided for morphological context? N/A Morphological context (e.g., H&E slides or images) may be provided separately for selected samples, but is not required for scRNA-seq processing. 3. For the single-cell suspensions, please provide details on: Single-Cell Suspensions a) Cell State & Handling: Pre-fixation viability: 85% Target cell concentration: 1 million cells/mL Total cells per sample: 50,000 100,000 Suspension buffer: PBS + 0.04% BSA b) Fixation: Will cells be provided as fresh suspensions (requiring our lab to fix them upon receipt) or will they be pre-fixed by the VA? If pre-fixed, please specify the fixation protocol/reagents. Cells will be pre-fixed by the VA using Parse Biosciences recommended Evercode protocol (methanol-based). c) Shipping: Specific shipping conditions (e.g., frozen in cryovials on dry ice). Cryovials shipped on dry ice; each vial contains fixed single-cell suspensions. 4. Finally, to plan the project effectively: a) Metadata: What specific metadata will accompany each sample? Sample ID, tissue type (brain/lung), treatment group, sex, genotype, age, fixation date, cell counts, and batch number. b) Bioinformatics: Beyond raw and processed sequencing data, are specific downstream analyses or visualizations expected (e.g., cell clustering, differential gene expression)? Required analyses include: Demultiplexing and UMI deduplication Alignment (mouse genome mm10) Unsupervised clustering (Seurat/Scanpy) Differential gene expression analysis Pathway analysis (GO, KEGG, GSEA) Visualizations: UMAP, heatmaps, volcano plots c) Timeline: What is the needed turnaround time for processing and data delivery once samples are received? 6 8 weeks from receipt of samples to delivery of final data and reports. 5) How many cells the VA wants processed along with how many reads per cells. The SOW mentions 100M read per samples, but with single-cell seq, reads are on a per cell level instead of a per sample level. Cell and Read Depth Targets: Targeting 50,000 100,000 cells per sample 30,000 50,000 reads per cell, as recommended for high-quality gene expression profiling using the Parse platform. __________________________________________ Section 3 states: Contractor shall provide start-to-finish advanced genetic sequencing and quantitation services tailored to the analysis of single-cells. Start-to-finish includes the comprehensive workflow required for single-cell RNA sequencing using the PARSE platform, to include RNA tagging, library construction, sequencing, and bioinformatics. However, Section 8 (Report/Deliverables section) Statement of Work notes pre-made libraries and only requires pricing for sequencing (a portion of the workflow):Â Pre-made libraries lane sequencing (NovaSeq X Plus 25B PE150) .Â Â Â Â Â Â Â Â Thus, we respectfully ask: Is the scope to provide the entire single cell workflow (i.e. receipt of frozen mouse tissue from VA and the start to finish Parse single cell workflow), or will we receive pre-made libraries requiring sequencing only? The scope includes the entire Parse single-cell workflow from receipt of fixed single-cell suspensions, through barcoding, library prep, sequencing, and bioinformatics. Pre-made libraries will not be provided. Pre-made libraries will not be supplied; all samples will be delivered as fixed single-cell suspensions, and the contractor is expected to perform library preparation. What is the sequencing depth required per cell? Sequencing Depth per Cell: 30,000 50,000 paired-end reads (150 bp) per cell on the NovaSeq X Plus or equivalent. How many samples (or pre-made libraries) will be provided per batch (since the contract states 4-20 samples per year? Sample Throughput: 4 20 samples per year, sent in batches of 2 6 samples depending on study progress. For the Parse kit does the VA want to use the Parse WT or MEGA kit?Â We need to know how many cells per sample are needed and if they will be shared across a WT (100K kit) or 1M cells (MEGA kit). Kit Selection: Parse WT kit (up to 100K cells) will be used for most studies. The MEGA kit (up to 1M cells) may be used when pooling samples or scaling up. The number of cells per kit will be provided prior to shipment. Please define the bioinformatics needed. Required bioinformatics deliverables include: Demultiplexing and UMI deduplication Alignment to reference genome (mouse: mm10) Quality control metrics Dimensionality reduction (e.g., PCA, UMAP) Clustering of cell populations Differential gene expression analysis between experimental groups Pathway enrichment analysis (GO, KEGG, GSEA) Visualizations: UMAP plots, heatmaps, and volcano plots Exported count matrices and metadata for downstream analysis All data must be provided in formats compatible with Seurat and/or Scanpy pipelines. The specification notes single cell sequencing (scRNA).Â Â If we cannot recover enough live/healthy cells from the frozen mouse tissue provided by the VA, should be process the tissue for single nuclei (snRNA) instead? Â Yes, if cell viability is compromised or cell recovery is insufficient, processing for single-nucleus RNA sequencing (snRNA-seq) using Parse-compatible protocols is an acceptable contingency. This should be discussed and approved by the VA before proceeding with snRNA processing. _____________________________________________ 1.Â This SOW mentioned using Parse technology for single-cell RNAseq. Are you sending in plates? if so, how many samples in each plate?Â Based on the plates, number of samples, cell count, the type of Parse kit will vary and sequencing strategies. Additional Clarifications Scope: The scope includes the entire Parse single-cell workflow from receipt of fixed single-cell suspensions, through barcoding, library prep, sequencing, and bioinformatics. Pre-made libraries will not be provided. Sequencing Depth per Cell: 30,000 50,000 paired-end reads (150 bp) per cell on the NovaSeq X Plus or equivalent. Sample Throughput: 4 20 samples per year, sent in batches of 2 6 samples depending on study progress. Kit Selection: Parse WT kit (up to 100K cells) will be used for most studies. The MEGA kit (up to 1M cells) may be used when pooling samples or scaling up. The number of cells per kit will be provided prior to shipment. snRNA Contingency: If viable single-cell recovery from frozen tissues is inadequate, tissue will be reprocessed for single-nucleus RNA-seq (snRNA) using Parse-compatible protocols, with prior discussion. Plates: No plates will be sent. Samples will be shipped as fixed suspensions in cryovials only. **See Updated SOW Attachment 1** __________________________________________________________ RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer **Quote submission is extended from Wednesday, June 11, 2025, to no later than 11:59 EST, Monday, June 16, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive.","origin":"extract"},"notice_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"schema_version":1,"solicitation_number":"36C24E25Q0045","place_of_performance":{"street":"Vendor's facility"},"product_service_code":"Q301"},{"dates":{"posted":"2025-06-23","response_deadline":{"raw":"2025-06-30T11:59:00-04:00","utc":"2025-06-30T15:59:00Z","date":"2025-06-30","time":"11:59:00","utc_offset_seconds":-14400}},"links":{"sam":"https://sam.gov/workspace/contract/opp/e76bab3278c3482384f3335638ee75ee/view"},"naics":{"codes":["541715"],"primary":"541715"},"title":"Q301--Modification - Q & A for Advanced Genetic Sequencing","agency":{"office":{"code":"36C24E","name":"RPO EAST (36C24E)"},"subtier":{"code":"3600","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"department":{"code":"036","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"office_address":{"zip":"15212","city":"PITTSBURGH","state":"PA","country":"USA"},"organization_type":"OFFICE"},"status":{"active":false,"archive_date":"2025-07-30","archive_type":"auto_custom"},"contacts":[{"name":"Ms. Millicent Covert","role":"primary","email":"millicent.covert@va.gov","phone":"(Telephone call shall not be accepted)","title":"Contracting Officer"}],"base_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"notice_id":"e76bab3278c3482384f3335638ee75ee","provenance":{"extract":{"url":"https://s3.amazonaws.com/falextracts/Contract%20Opportunities/Archived%20Data/FY2025_archived_opportunities.csv","etag":"\"d47226e3d2c6545974b252e103f82b34-139\"","fetched_at":"2026-09-16T17:45:50.850439Z","row_sha256":"184861fc1a732a62015ed83af9c8c13cc33defa66e9a7fcb0f892295f35c2419","last_modified":"2026-09-13T14:49:20Z"},"updated_at":"2026-09-16T17:45:50.850439Z","first_seen_at":"2026-09-16T17:45:50.850439Z"},"description":{"text":"RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 2 **Quote submission is extended to no later than 11:59AM EST, Thursday, June 26, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive. ___________________________________________________________ Response to Question 1: Scope, Library Prep, and Sequencing Capacity We appreciate your request for clarification and have refined the expectations to ensure alignment with the full Statement of Work (SOW). The following applies: 1. Workflow Scope – Full Single-Cell RNA-seq Services Required The requirement includes complete execution of the Parse Biosciences single-cell RNA-seq pipeline, starting from fixed single-cell suspensions. This encompasses: - Sample intake and QC - Cell barcoding and library preparation using Parse WT or MEGA kits - Library quality control - High-throughput sequencing on NovaSeq X Plus PE150 (25B lanes) - Full bioinformatics pipeline (alignment, clustering, DEG, pathway analysis) Pre-made libraries are not in scope, and the contractor must have demonstrated experience handling Parse Biosciences workflows end-to-end, including immediate sequencing upon library completion without outsourcing. 2. Library QC and Kit Considerations Library QC is embedded within the full workflow and must be included in the price per library. The contractor should have: - Infrastructure and staffing to process up to 20 libraries/year in multiple independent batches (2–6 per shipment) - Access to and experience with Parse WT and MEGA kits, with the ability to scale per batch and adjust based on submission schedule without delays or combining batches 3. Sequencing Specifications and Lane Requirements Sequencing must reach 30,000–50,000 PE150 reads per cell in line with Parse’s UMI-based design. The contractor should be able to independently: - Assess and balance sample pools - Perform high-throughput sequencing using NovaSeq X Plus - Deliver per-library and per-cell metrics, not only per-lane summaries Contractor must control both library prep and sequencing in-house, ensuring minimal sample handoff and continuity of sample metadata. Response to Question 2: Misalignment Between Pricing Table and Deliverables We acknowledge that the originally provided table structure may have introduced ambiguity. To ensure it accurately reflects the technical and operational deliverables, we recommend the pricing table be realigned to match the complete workflow. Recommended Table Format (Reflecting SOW) Line Item Qty Description 0001 Fixed Sample Receipt & Batch Intake 20 Intake, logging, and QC of methanol-fixed single-cell suspensions 0002 Parse Library Prep (WT or MEGA) + QC 20 Barcoding, cDNA synthesis, library prep, Bioanalyzer/Qubit QC 0003 Sequencing – NovaSeq X Plus PE150 TBD Based on UMI complexity and required depth (30–50K reads per cell) 0004 Data Processing & Bioinformatics 20 UMI alignment, cell clustering, DEG, GSEA, UMAPs, raw & processed outputs Summary of Key Requirements To ensure scientific success, the vendor must: - Handle full Parse Evercode single-cell RNA-seq pipeline internally - Have proven experience with Parse kits (WT, MEGA) and NovaSeq X Plus - Support batch-level flexibility (2–6 samples), not pooled 20-sample prep - Deliver complete sequencing + bioinformatics per sample - Ensure end-to-end traceability and QC without third-party outsourcing __________________________________________________________________ RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 2 **Quote submission is extended to no later than 11:59AM EST, Thursday, June 26, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive.","origin":"extract"},"notice_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"schema_version":1,"solicitation_number":"36C24E25Q0045","place_of_performance":{"street":"Vendor's facility"},"product_service_code":"Q301"},{"dates":{"posted":"2025-06-24","response_deadline":{"raw":"2025-06-26T11:59:00-04:00","utc":"2025-06-26T15:59:00Z","date":"2025-06-26","time":"11:59:00","utc_offset_seconds":-14400}},"links":{"sam":"https://sam.gov/workspace/contract/opp/0889a728b3ef4245b8ca17437aad202a/view"},"naics":{"codes":["541715"],"primary":"541715"},"title":"Q301--Modification - Q & A for Advanced Genetic Sequencing","agency":{"office":{"code":"36C24E","name":"RPO EAST (36C24E)"},"subtier":{"code":"3600","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"department":{"code":"036","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"office_address":{"zip":"15212","city":"PITTSBURGH","state":"PA","country":"USA"},"organization_type":"OFFICE"},"status":{"active":false,"archive_date":"2025-07-26","archive_type":"auto_custom"},"contacts":[{"name":"Ms. Millicent Covert","role":"primary","email":"millicent.covert@va.gov","phone":"(Telephone calls shall not be accepted)","title":"Contracting Officer"}],"base_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"notice_id":"0889a728b3ef4245b8ca17437aad202a","provenance":{"extract":{"url":"https://s3.amazonaws.com/falextracts/Contract%20Opportunities/Archived%20Data/FY2025_archived_opportunities.csv","etag":"\"d47226e3d2c6545974b252e103f82b34-139\"","fetched_at":"2026-09-16T17:45:50.850439Z","row_sha256":"2e41bf59f88adedd0718050bd0b13ed542db53d3ce5d7f3df899921a486dfded","last_modified":"2026-09-13T14:49:20Z"},"updated_at":"2026-09-16T17:45:50.850439Z","first_seen_at":"2026-09-16T17:45:50.850439Z"},"description":{"text":"RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 2 **Quote submission is extended to no later than 11:59AM EST, Thursday, June 26, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive. ___________________________________________________________ Response to Question 1: Scope, Library Prep, and Sequencing Capacity We appreciate your request for clarification and have refined the expectations to ensure alignment with the full Statement of Work (SOW). The following applies: 1. Workflow Scope – Full Single-Cell RNA-seq Services Required The requirement includes complete execution of the Parse Biosciences single-cell RNA-seq pipeline, starting from fixed single-cell suspensions. This encompasses: - Sample intake and QC - Cell barcoding and library preparation using Parse WT or MEGA kits - Library quality control - High-throughput sequencing on NovaSeq X Plus PE150 (25B lanes) - Full bioinformatics pipeline (alignment, clustering, DEG, pathway analysis) Pre-made libraries are not in scope, and the contractor must have demonstrated experience handling Parse Biosciences workflows end-to-end, including immediate sequencing upon library completion without outsourcing. 2. Library QC and Kit Considerations Library QC is embedded within the full workflow and must be included in the price per library. The contractor should have: - Infrastructure and staffing to process up to 20 libraries/year in multiple independent batches (2–6 per shipment) - Access to and experience with Parse WT and MEGA kits, with the ability to scale per batch and adjust based on submission schedule without delays or combining batches 3. Sequencing Specifications and Lane Requirements Sequencing must reach 30,000–50,000 PE150 reads per cell in line with Parse’s UMI-based design. The contractor should be able to independently: - Assess and balance sample pools - Perform high-throughput sequencing using NovaSeq X Plus - Deliver per-library and per-cell metrics, not only per-lane summaries Contractor must control both library prep and sequencing in-house, ensuring minimal sample handoff and continuity of sample metadata. Response to Question 2: Misalignment Between Pricing Table and Deliverables We acknowledge that the originally provided table structure may have introduced ambiguity. To ensure it accurately reflects the technical and operational deliverables, we recommend the pricing table be realigned to match the complete workflow. Recommended Table Format (Reflecting SOW) Line Item Qty Description 0001 Fixed Sample Receipt & Batch Intake 20 Intake, logging, and QC of methanol-fixed single-cell suspensions 0002 Parse Library Prep (WT or MEGA) + QC 20 Barcoding, cDNA synthesis, library prep, Bioanalyzer/Qubit QC 0003 Sequencing – NovaSeq X Plus PE150 TBD Based on UMI complexity and required depth (30–50K reads per cell) 0004 Data Processing & Bioinformatics 20 UMI alignment, cell clustering, DEG, GSEA, UMAPs, raw & processed outputs Summary of Key Requirements To ensure scientific success, the vendor must: - Handle full Parse Evercode single-cell RNA-seq pipeline internally - Have proven experience with Parse kits (WT, MEGA) and NovaSeq X Plus - Support batch-level flexibility (2–6 samples), not pooled 20-sample prep - Deliver complete sequencing + bioinformatics per sample - Ensure end-to-end traceability and QC without third-party outsourcing __________________________________________________________________ RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 2 **Quote submission is extended to no later than 11:59AM EST, Thursday, June 26, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive.","origin":"extract"},"notice_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"schema_version":1,"solicitation_number":"36C24E25Q0045","place_of_performance":{"city":{"name":"Minneapolis"},"state":{"code":"KS"},"street":"Vendor's facility","country":{"code":"USA"}},"product_service_code":"Q301"},{"dates":{"posted":"2025-08-13","response_deadline":{"raw":"2025-06-26T11:59:00-04:00","utc":"2025-06-26T15:59:00Z","date":"2025-06-26","time":"11:59:00","utc_offset_seconds":-14400}},"links":{"sam":"https://sam.gov/workspace/contract/opp/529a97ea52a74be1be645c8a43533879/view"},"naics":{"codes":["541715"],"primary":"541715"},"title":"Q301--Modification - Q & A for Advanced Genetic Sequencing","agency":{"office":{"code":"36C24E","name":"RPO EAST (36C24E)"},"subtier":{"code":"3600","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"department":{"code":"036","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"office_address":{"zip":"15212","city":"PITTSBURGH","state":"PA","country":"USA"},"organization_type":"OFFICE"},"status":{"active":false,"archive_date":"2025-10-10","archive_type":"auto_custom"},"contacts":[{"name":"Ms. Millicent Covert","role":"primary","email":"millicent.covert@va.gov","phone":"(Telephone calls shall not be accepted)","title":"Contracting Officer"}],"base_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"notice_id":"529a97ea52a74be1be645c8a43533879","provenance":{"extract":{"url":"https://s3.amazonaws.com/falextracts/Contract%20Opportunities/Archived%20Data/FY2025_archived_opportunities.csv","etag":"\"d47226e3d2c6545974b252e103f82b34-139\"","fetched_at":"2026-09-16T17:45:50.850439Z","row_sha256":"9b8709e1245452672a672effc236c04dc1cc944577624f368cae41c00998cc72","last_modified":"2026-09-13T14:49:20Z"},"updated_at":"2026-09-16T17:45:50.850439Z","first_seen_at":"2026-09-16T17:45:50.850439Z"},"description":{"text":"RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 2 **Quote submission is extended to no later than 11:59AM EST, Thursday, June 26, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive. ___________________________________________________________ Response to Question 1: Scope, Library Prep, and Sequencing Capacity We appreciate your request for clarification and have refined the expectations to ensure alignment with the full Statement of Work (SOW). The following applies: 1. Workflow Scope – Full Single-Cell RNA-seq Services Required The requirement includes complete execution of the Parse Biosciences single-cell RNA-seq pipeline, starting from fixed single-cell suspensions. This encompasses: - Sample intake and QC - Cell barcoding and library preparation using Parse WT or MEGA kits - Library quality control - High-throughput sequencing on NovaSeq X Plus PE150 (25B lanes) - Full bioinformatics pipeline (alignment, clustering, DEG, pathway analysis) Pre-made libraries are not in scope, and the contractor must have demonstrated experience handling Parse Biosciences workflows end-to-end, including immediate sequencing upon library completion without outsourcing. 2. Library QC and Kit Considerations Library QC is embedded within the full workflow and must be included in the price per library. The contractor should have: - Infrastructure and staffing to process up to 20 libraries/year in multiple independent batches (2–6 per shipment) - Access to and experience with Parse WT and MEGA kits, with the ability to scale per batch and adjust based on submission schedule without delays or combining batches 3. Sequencing Specifications and Lane Requirements Sequencing must reach 30,000–50,000 PE150 reads per cell in line with Parse’s UMI-based design. The contractor should be able to independently: - Assess and balance sample pools - Perform high-throughput sequencing using NovaSeq X Plus - Deliver per-library and per-cell metrics, not only per-lane summaries Contractor must control both library prep and sequencing in-house, ensuring minimal sample handoff and continuity of sample metadata. Response to Question 2: Misalignment Between Pricing Table and Deliverables We acknowledge that the originally provided table structure may have introduced ambiguity. To ensure it accurately reflects the technical and operational deliverables, we recommend the pricing table be realigned to match the complete workflow. Recommended Table Format (Reflecting SOW) Line Item Qty Description 0001 Fixed Sample Receipt & Batch Intake 20 Intake, logging, and QC of methanol-fixed single-cell suspensions 0002 Parse Library Prep (WT or MEGA) + QC 20 Barcoding, cDNA synthesis, library prep, Bioanalyzer/Qubit QC 0003 Sequencing – NovaSeq X Plus PE150 TBD Based on UMI complexity and required depth (30–50K reads per cell) 0004 Data Processing & Bioinformatics 20 UMI alignment, cell clustering, DEG, GSEA, UMAPs, raw & processed outputs Summary of Key Requirements To ensure scientific success, the vendor must: - Handle full Parse Evercode single-cell RNA-seq pipeline internally - Have proven experience with Parse kits (WT, MEGA) and NovaSeq X Plus - Support batch-level flexibility (2–6 samples), not pooled 20-sample prep - Deliver complete sequencing + bioinformatics per sample - Ensure end-to-end traceability and QC without third-party outsourcing __________________________________________________________________ RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 2 **Quote submission is extended to no later than 11:59AM EST, Thursday, June 26, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered nonresponsive.","origin":"extract"},"notice_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"schema_version":1,"solicitation_number":"36C24E25Q0045","place_of_performance":{"city":{"name":"Minneapolis"},"state":{"code":"KS"},"street":"Vendor's facility","country":{"code":"USA"}},"product_service_code":"Q301"},{"dates":{"posted":"2025-08-13","response_deadline":{"raw":"2025-08-20T11:59:00-04:00","utc":"2025-08-20T15:59:00Z","date":"2025-08-20","time":"11:59:00","utc_offset_seconds":-14400}},"links":{"sam":"https://sam.gov/workspace/contract/opp/962ca8bb31a24986b1a140ee7218378d/view"},"naics":{"codes":["541715"],"primary":"541715"},"title":"Q301--Advanced Genetic Sequencing (Research Support)","agency":{"office":{"code":"36C24E","name":"RPO EAST (36C24E)"},"subtier":{"code":"3600","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"department":{"code":"036","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"office_address":{"zip":"15212","city":"PITTSBURGH","state":"PA","country":"USA"},"organization_type":"OFFICE"},"status":{"active":false,"archive_date":"2025-10-19","archive_type":"auto_custom"},"contacts":[{"name":"Ms. Millicent Covert","role":"primary","email":"millicent.covert@va.gov","phone":"(Phone calls will not be taken)","title":"Contracting Officer"}],"base_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"notice_id":"962ca8bb31a24986b1a140ee7218378d","provenance":{"extract":{"url":"https://s3.amazonaws.com/falextracts/Contract%20Opportunities/Archived%20Data/FY2025_archived_opportunities.csv","etag":"\"d47226e3d2c6545974b252e103f82b34-139\"","fetched_at":"2026-09-16T17:45:50.850439Z","row_sha256":"e1be4d27f051917d657cf46a52edb9be6aee6e4e27279a092d9c8e8f3a3da72b","last_modified":"2026-09-13T14:49:20Z"},"updated_at":"2026-09-16T17:45:50.850439Z","first_seen_at":"2026-09-16T17:45:50.850439Z"},"description":{"text":"RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 3 **Quote submission is extended to no later than 11:59AM EST, Wednesday, August 20, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered non-responsive. ______________________________________________________________________ This project requires high-throughput, high-quality single-cell RNA sequencing (scRNA-seq) services compatible with Parse Biosciences library preparation technology for murine brain tissue samples. The sequencing provider must meet specific technical requirements necessary for data quality, compatibility, and compliance with VA standards. These include the ability to accommodate Parse's unique chemistry, ensure precise read configurations, and deliver data in a timely and secure manner. Our specifications are designed to eliminate ambiguity, ensure an equitable vendor comparison, and reflect scientifically justified parameters aligned with our research goals. Technical Requirements 1. Specialized Sequencing Compatibility Parse Biosciences uses a non-standard read configuration: Read 1: 28 bp (cell barcode + UMI) Read 2: 91 100 bp (transcript) Index i7: 8 bp (sample index) The sequencing provider must demonstrate prior experience or validated capability with Parse Biosciences libraries and must support these custom read configurations on Illumina platforms. 2. High-Throughput Capacity with Fast Turnaround For each sample consisting of 10,000 nuclei sequenced at 75,000 reads per cell, ~750 million paired-end reads are required. The provider must offer access to NovaSeq S1 or S2 lanes and the ability to sequence multiple samples per run. Turnaround time must be no more than 10 15 business days from receipt of libraries. 3. Cost Efficiency with Fixed Project Design To enable precise cost estimates and avoid ambiguity: Number of Samples: 20 Batch Size: Fixed at 4 samples per batch (5 total batches) Sequencing Depth: Fixed at 75,000 paired-end 150 bp reads per cell Target Cells per Sample: 10,000 nuclei Library Format: Parse Biosciences Evercode WT v2 Midi kits (supports 4 8 samples) This fixed structure balances scientific rigor with cost-effective use of reagents and sequencing lanes, and eliminates the variability introduced by a range of read depths or batch sizes. 4. Validated Quality Control and Data Delivery Infrastructure The provider must deliver raw FASTQ files and associated QC metrics compatible with Parse's cloud-based or command-line pipelines. Services must include demultiplexing, base calling, and sequencing documentation suitable for regulatory compliance and publication. 5. Data Security and Regulatory Compliance Sequencing services must be performed within the United States. Data transfer must occur through secure, encrypted platforms. No biological samples or raw data may be transferred internationally, in alignment with VA requirements. Scientific and Operational Requirements Summary Requirement Specification Compatibility with Parse Biosciences Required; including support for custom read layout Sequencing platform Illumina NovaSeq 6000 Number of samples 20 Batch size 4 samples per batch, 5 total batches Required read depth 75,000 reads per cell Target cell number per sample 10,000 nuclei Read configuration PE150 (R1: 28 bp, R2: 91 100 bp, Index: 8 bp) Turnaround time 10 15 business days Bioinformatics compatibility FASTQ format compatible with Parse/Seurat pipelines Data security U.S.-based, secure upload/download infrastructure The above technical requirements reflect essential capabilities needed to meet the scientific aims of our VA-funded research project. The ability to support Parse Biosciences chemistry, deliver high-throughput sequencing at fixed and justifiable specifications, ensure domestic sample handling, and provide compatible bioinformatics output are critical. These parameters have been established to ensure technical quality, cost transparency, and regulatory compliance. Any vendor responding must fully meet these defined specifications. ______________________________________________________________________ RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 3 **Quote submission is extended to no later than 11:59AM EST, Wednesday, August 20, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered non-responsive. **Quote Submission Instructions** Quotes shall be sent electronically via e-mail. All quotes shall include one (1) separate copy of each of the items listed below. Submission of a quote that does not contain all items requested below may result in elimination from consideration of award. Offerors must submit each item of quote in a separate electronic attachment clearly identified as described below. No price information shall be included in the technical or past performance section. Offerors are responsible for including sufficient details to permit a complete and accurate evaluation of each quote. First Attachment - Volume 1 1. Completed Schedule of Supplies and Services (Attachment 2 to this solicitation). Completed CLIN price information in the Schedule of Supplies/Services. *Offerors must use the CLINs specified in the Schedule of Supplies/Services. It is not permissible for offerors to use offeror created CLINs or SUBCLINs. 2. Completed certifications and representations located at FAR 52.212-3, or an indication that said certifications and representations are current and located in the SAM database. 3. Certifications that may be included as Addenda to FAR 52.212-1. 4. Signed acknowledgements of amendments (SF30). Applicable only if any amendments are issued against this solicitation. Amendments 001 and 002 shall be acknowledged. Second Attachment - Volume 2 Offerors shall provide a narrative (including any descriptive literature and/or certifications) which demonstrates the offeror s ability to meet the technical credentials and capability stated in the Statement of Work (SOW). The narrative shall not exceed ten (10) pages and address the requirements within Item 3 Major Requirements and Item 10 under A. General Information in the SOW. Third Attachment - Volume 3 Past Performance Record: Vendors shall provide information on Past Performance Record. This information is used in determining the level of confidence the Government has for a successful performance based upon the vendor s actions under previously awarded and/or relevant contracts. The information provided in Volume 3 will be utilized to evaluate the Vendor s Past Performance. To be considered part of the Past Performance record, we ask to provide two (2) or more relevant contracts in the last five (5) years. If a vendor or its major subcontractor determines that they have no relevant past performance data, they shall provide the following statement in lieu of the information provided below: (Insert vendor or major subcontractor s name) has determined that they possess no relevant past performance information in accordance with the RFQ. To be compliant with this factor, vendors shall provide the following information for both the vendor and proposed major subcontractors: (1) A list of Previous Contract Data for the vendor. Please provide two (2) PRIME contracts and relevant subcontracts that the vendor is currently performing or has completed during the last 5 years. The list shall include: - Contractor name - Name of customer/agency - Contract/Purchase Order Number - Customer points of contact (minimum of two; provide name, telephone number, fax number and e-mail addresses) - Length of contract - Period of Performance (dates) - Initial Contract Price - Description of product/service provided (include sufficient detail to demonstrate similarities/dissimilarities to the requirements of this solicitation) (2) A list of Previous Contract Data for all minor subcontractors containing the information listed in (1) above as it relates to relevant Prime and Subcontracts that the major subcontractor is currently performing or has completed during the last 5 years. (3) The Government may utilize the Contractor Performance Assessment Reporting System (CPARS), responses from the Performance Risk Assessment Questionnaire, data submitted by the vendor, and any other information available to determine the quality and relevance of the vendor s past performance. Fourth Attachment Volume 4 Contractors are required to include a copy of the FAR provision 52.212-3 Offeror Representations and Certifications Commercial Items with its proposal or may indicate completion of the representations and certifications on the internet at http://sam.gov. Failure to include the certifications along with the price proposal or complete certifications on the internet may result in elimination from consideration for award. To facilitate the award process, all quotes must include a statement regarding the terms and conditions herein as follows: \"The terms and conditions in the solicitation are acceptable to be included in the award document without modification, deletion, or addition.\" OR \"The terms and conditions in the solicitation are acceptable to be included in the award document with the exception, deletion, or addition of the following:\" Quoters shall list exception(s) and rationale for the exception(s), if any. ______________________________________________________________________ RFQ 36C24E25Q0045 Advanced Genetic Sequencing Solicitation Clarification and Question & Answer, PART 3 **Quote submission is extended to no later than 11:59AM EST, Wednesday, August 20, 2025.** Quotes shall be submitted via email to millicent.covert@va.gov. Offerors must reference Solicitation 36C24E25Q0045 in the subject line of the email. No telephone requests for information will be considered. Incomplete packages will be considered non-responsive.","origin":"extract"},"notice_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"schema_version":1,"solicitation_number":"36C24E25Q0045","place_of_performance":{"street":"Vendor's facility"},"product_service_code":"Q301"},{"dates":{"posted":"2025-09-12","response_deadline":{"raw":"2025-09-12T11:59:00-04:00","utc":"2025-09-12T15:59:00Z","date":"2025-09-12","time":"11:59:00","utc_offset_seconds":-14400}},"links":{"sam":"https://sam.gov/workspace/contract/opp/b39fc859ce5b444c81ac4b024d377a7c/view"},"naics":{"codes":["541715"],"primary":"541715"},"title":"Q301--Advanced Genetic Sequencing (Research Support)","agency":{"office":{"code":"36C24E","name":"RPO EAST (36C24E)"},"subtier":{"code":"3600","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"department":{"code":"036","name":"VETERANS AFFAIRS, DEPARTMENT OF"},"office_address":{"zip":"15212","city":"PITTSBURGH","state":"PA","country":"USA"},"organization_type":"OFFICE"},"status":{"active":false,"archive_date":"2025-09-27","archive_type":"auto_custom"},"contacts":[{"name":"Ms. Millicent Covert","role":"primary","email":"millicent.covert@va.gov","phone":"(Calls shall not be accepted)","title":"Contracting Officer"}],"base_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"notice_id":"b39fc859ce5b444c81ac4b024d377a7c","provenance":{"extract":{"url":"https://s3.amazonaws.com/falextracts/Contract%20Opportunities/Archived%20Data/FY2025_archived_opportunities.csv","etag":"\"d47226e3d2c6545974b252e103f82b34-139\"","fetched_at":"2026-09-16T17:45:50.850439Z","row_sha256":"31d41238573972c7ffd0a3b5d7e57acb036d9979fd13624af9797724ef185bf5","last_modified":"2026-09-13T14:49:20Z"},"updated_at":"2026-09-16T17:45:50.850439Z","first_seen_at":"2026-09-16T17:45:50.850439Z"},"description":{"text":"Please be advised that Solicitation 36C24E25Q0045 is hereby cancelled. Requirement may be reposted at a later date.","origin":"extract"},"notice_type":{"code":"k","label":"Combined Synopsis/Solicitation"},"schema_version":1,"solicitation_number":"36C24E25Q0045","product_service_code":"Q301"}],"due_at":"2025-09-12T15:59:00Z","due_date":"2025-09-12","closes_at":"2025-09-12T15:59:00Z","awardable":true,"dept_key":"d-036","dept_name":"VETERANS AFFAIRS, DEPARTMENT OF","sub_key":"s-3600","sub_name":"VETERANS AFFAIRS, DEPARTMENT OF","office_key":"o-36C24E","office_name":"RPO EAST (36C24E)","state":"KS","county":"20143","county_name":"Ottawa County","city":"2047075","city_name":"Minneapolis","country":"USA","winner_key":null,"amount":null,"linked_awards":0,"cancelled":false,"archived":false,"updated_at":"2026-09-16T21:18:12.857524Z","principal_notice_id":"b39fc859ce5b444c81ac4b024d377a7c","description":{"text":"Please be advised that Solicitation 36C24E25Q0045 is hereby cancelled. Requirement may be reposted at a later date.","html":null,"origin":"extract"},"contacts":[{"name":"Ms. Millicent Covert","role":"primary","email":"millicent.covert@va.gov","phone":"(Calls shall not be accepted)","title":"Contracting Officer"}],"place_of_performance":null,"office_address":{"zip":"15212","city":"PITTSBURGH","state":"PA","country":"USA"},"naics_codes":["541715"],"award":null,"attachments":[],"awards":[],"related":[{"key":"36C24E26Q0108","latest_notice_id":"4f4fc6a59e9f4929bac5bd6086bd9fa2","title":"6515--Textiles - Towels and Washcloths","solicitation_number":"36C24E26Q0108","notice_type":"r","first_type":"r","first_posted":"2026-08-21","last_posted":"2026-09-14","notices":2,"due_at":"2026-09-17T19:00:00Z","due_date":"2026-09-17","closes_at":"2026-09-17T19:00:00Z","awardable":true,"open":true,"dept_key":"d-036","dept_name":"VETERANS AFFAIRS, DEPARTMENT OF","sub_key":"s-3600","sub_name":"VETERANS AFFAIRS, DEPARTMENT OF","office_key":"o-36C24E","office_name":"RPO EAST (36C24E)","naics":"339113","psc":"6515","set_aside":null,"state":null,"county":null,"county_name":null,"city":null,"city_name":null,"country":null,"winner":null,"winner_key":null,"amount":null,"linked_awards":0,"cancelled":false,"archived":false,"updated_at":"2026-09-16T21:18:12.857524Z"},{"key":"36C24E26Q0091","latest_notice_id":"d6ed0fd8634e4d2ba85aa4eb03958b49","title":"Research Equip (LAMb) - Cage and Rack Washer Replacement - CLEVE | EDA: 9/25/26","solicitation_number":"36C24E26Q0091","notice_type":"k","first_type":"k","first_posted":"2026-09-15","last_posted":"2026-09-15","notices":1,"due_at":"2026-09-21T20:00:00Z","due_date":"2026-09-21","closes_at":"2026-09-21T20:00:00Z","awardable":true,"open":true,"dept_key":"d-036","dept_name":"VETERANS AFFAIRS, DEPARTMENT OF","sub_key":"s-3600","sub_name":"VETERANS AFFAIRS, DEPARTMENT OF","office_key":"o-36C24E","office_name":"RPO EAST (36C24E)","naics":"339112","psc":"6515","set_aside":null,"state":null,"county":null,"county_name":null,"city":null,"city_name":null,"country":null,"winner":null,"winner_key":null,"amount":null,"linked_awards":0,"cancelled":false,"archived":false,"updated_at":"2026-09-16T21:18:12.857524Z"},{"key":"36C24E26Q0058","latest_notice_id":"b1b590da28f645f091497d8374cbbf44","title":"MSPV Q4 FY26 Open Market","solicitation_number":"36C24E26Q0058","notice_type":"k","first_type":"k","first_posted":"2026-09-15","last_posted":"2026-09-15","notices":1,"due_at":"2026-10-15T21:00:00Z","due_date":"2026-10-15","closes_at":"2026-10-15T21:00:00Z","awardable":true,"open":true,"dept_key":"d-036","dept_name":"VETERANS AFFAIRS, DEPARTMENT OF","sub_key":"s-3600","sub_name":"VETERANS AFFAIRS, DEPARTMENT OF","office_key":"o-36C24E","office_name":"RPO EAST (36C24E)","naics":"339113","psc":"6515","set_aside":"VSA","state":null,"county":null,"county_name":null,"city":null,"city_name":null,"country":"USA","winner":null,"winner_key":null,"amount":null,"linked_awards":0,"cancelled":false,"archived":false,"updated_at":"2026-09-16T21:18:12.857524Z"}]}