75N95023Q00366

Post Date/ Solicitation Issue Date

June 7, 2023 12:00 pm

Closing Response Date

June 17, 2023 12:00 pm

Proposed Award Date

June 30, 2023 12:00 pm

Project Title

Bioinformatic analysis of bulk and single cell data for iPSCs and iPSC-derived cell types

Contracting Office

National Center for Advancing Translational Sciences (NCATS)

Small Business Size Standard

$19M

Estimated Period of Performance

17 weeks (8hrs/week for 17 weeks(

Competition Status

Competitive

Background/Description of Requirement

ELECTRONIC REQUEST FOR QUOTATION (E-RFQ)

Bioinformatic analysis of bulk and single cell data for iPSCs and iPSC-derived cell types

REQUEST NUMBER: 75N95023Q00366

 

DATE ISSUED: June 7, 2023

ISSUED BY CONTRACTING OFFICE:  Department of Health and Human Services / National Institutes of Health / National Institute on Drug Abuse (NIDA)/ OA / 301 N Stonestreet Ave, Bethesda, MD 20892

FOR INFORMATION CONTACT:  Claudia Ventola / claudia.ventola@nih.gov / 301-496-0870

NORTH AMERICAN CLASSIFICATION SYSTEM (NAICS) CODE:   541690 – Others Scientific and Technical Consulting Services

USINESS SIZE STANDARD: $19M.  

SET-ASIDE STATUS: Not set-aside restriction applicable

Competition Status:  This requirement is competitive

Non-Competitive (Single-sole Source (Including brand-name)) Determination:

N/A

DATE QUOTATION DUE:

All responses to this RFQ must be received by 12:00 PM EST, on June 17, 2023 and must reference the request number cited above. Responses must be submitted electronically to the contact person cited above. Fax responses will not be accepted.

IMPORTANT: This is a request for quotations. If you are unable to quote, please so indicate in a reply email to the contract specialist cited herein.  This request does not commit the Government to pay any costs incurred in the preparation of the submission of this quotation or to contract for supplies or service. Supplies are of domestic origin unless otherwise indicated by quoter. Any representations and/or certifications attached to this Request for Quotation must be completed by the quoter.

Purchase Description:

Bulk, Single cell RNA-Seq, and Spatial Transcriptomics Bioinformatic Analysis – Advances in single cell technologies have led to rapid generation of large biological data sets which require informatics approaches to analyze. Single cell resolution of -omics data sets holds tremendous promise for advancing swaths of biology but to fully utilize the data sets, marriage of biological and computational knowledge is required. This kind of transdisciplinary work requires a firm partnership with constant interaction.

These services will be utilized by the SCTL to obtain expertise in explaining results and translating biological questions into computational pipelines with dedication and involvement in each project to obtain top tier analysis. The data obtained from this study will be used for publication.

Salient characteristics

Single cell RNA sequencing analysis:

Experimental design for single cell RNA sequencing including technology selection, hashing, power analysis, and coordiation with local facilities for library construction and sequencing parameters. Alignment including custom genome annotations and other preprocessing necessary for 10X, BioRad, Parse, and homebrew techniques like SmartSeq2, DropSeq, inDrop, and SeqWell. Sample level quality control including examination of sequencing quality and visualization and filtering of UMI count, feature count, and mitochondrial gene content. Batch quality control and batch effect correction if applicable. Clustering with visualization of marker genes and differentially expressed genes for cluster identification. Differential expression and gene set analyses for all comparison groups of interest. RNA velocity and pseudotime analyses including visualization of velocities, construction of pseudotime trajectories, and identification of genes driving differentiation by trajectory. Customized intercellular signaling analysis linking transcriptional changes with putative signaling pathways. Data set specific analyses such as copy-number variation, transfer learning, and gene regulatory network analysis. Generation of files and instructions for interactive data viewing with the CellXGene platform.

Spatial transcriptomics analysis:

All services available for single cell RNA sequencing as presented above. Region of interest selection and downstream analyses (these can include ANY services available for single cell RNA sequencing as well). Label transfer to identify spots enriched for specific clusters identified from other single cell RNA sequencing data sets.

Bulk RNA sequencing analysis:

Power calculations, experimental planning, and coordination with your local core facility or sequencing service provider for improved turn-around times. Quality control and visualization of raw data. Alignment including custom genome annotations where necessary. Sample and batch level quality control including visualization and filtration on number of reads, proportion of reads aligning to the transcriptome, and correlation and PCA based outlier identification. Differential expression and gene set analyses accounting for complex experimental design, clinical data, and/or batch effect issues if present. Cell type deconvolution to estimate cellular composition of samples. Data set specific analyses such as copy number variation, TCR repertoire estimation, repeat element expression, and others.

Intercellular signaling analyses:

Customized, in-house intercellular signaling package based on Domino, a previously published software package developed by our founder and the only scRNAseq intercellular signaling packages capable of identifying ligand-receptor pairs and their transcription factor targets. Package applicable to single cell RNA sequencing, spatial transcriptomics, and high-sample bulk RNA sequencing data sets. Global inter-group signaling overview quantifying all estimated intercellular signaling between groups. Visualization of top ligand-receptor-transcription factor pathways between each specific pair of groups. Activation and expression of each ligand, receptor, and transcription factor

Quantity:

1

Delivery/Warranty

The period of performance will commence immediately after receipt of order (ARO) and last 17 weeks (8hrs/week for 17 weeks) from receipt of data intended for analysis.

Contract Type:

A Fixed-Price type of Purchase Order award not exceeding the Simplified Acquisition Threshold is anticipated for any contract resulting from this requirement. The anticipated award date is June 30, 2023.

QUOTER TERMS AND CONDITIONS (to be filled out by the Offeror):

1. Period of Performance OR Delivery Date After Receipt of Order:
2. Shipping Point (F.O.B. OR Destination):
3. Payment Discount Terms:
4. Select One: Open Market; GSA FSS Contract Number; Other Government Agency (OGA) Contract Number, Government-wide Agency (GWAC) Contract Number; or National Institute of Health (NIH) Blanket Purchase Agreement (BPA) Number:
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6. Name of Company:
7. Street Address, City, State, Zip code:
8. Name of Person Authorized to Provide Quote:
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ADDITIONAL TERMS AND CONDITIONS, PROVISIONS, AND REPRESENTATIONS

The FAR Clauses are incorporated by reference and are provided in full text at https://www.acquisition.gov/

1. 1. 1. 1. The provisions of FAR Clause 52.212-1 Instructions to Offerors—Commercial Items (OCT 2018) is applicable to this solicitation.
         2. The provisions of FAR Clause 52.212.2 Evaluation—Commercial Items (Oct 2014) is applicable to this solicitation. The Government will evaluate quotations or offers in accordance with FAR 13.106-2 and award a purchase order from this solicitation to the responsible offeror whose quote conforming to the solicitation will be most advantageous to the Government, price and other factors considered. The following factors shall be used to evaluate quotes:
            1. 1. 1. 1. Technical capability of the item offered to meet the Government requirement;
                     2. Price; and
                     3. Past performance [see FAR 13.106-2(b)(3)].
         3. The provisions of FAR Clause 52.212-3, Offeror Representations and Certifications—Commercial Items (Feb 2021), is applicable to this solicitation.
         4. The provisions of FAR Clause 52.212-4, Contract Terms and Conditions—Commercial Items (OCT 2018) with Addenda: Stop Work Order, FAR Clause 52.242-15 (August 1989) is applicable to this solicitation.
         5. The provisions of FAR clause at 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders—Commercial Items (Jul 2021) is applicable to this solicitation:

52.222-3 Convict Labor (June 2003)

52.222-19 Child Labor-Cooperation With Authorities and Remedies (Jan 2018)

52.222-21 Prohibition of Segregated Facilities (Apr 2015)

52.222-26 Equal Opportunity (Sep 2016)

52.222-36 Equal Opportunity for Workers With Disabilities (Jul 2014)

52.222-50 Combating Trafficking in Persons (Mar 2015)

52.223-18 Encouraging Contractor Policies to Ban Text Messaging While Driving (Aug 2011)

52.232-33 Payment by Electronic Funds Transfer-- System for Award Management (Jul 2013)

 

In addition, the following FAR provisions are applicable to this solicitation and incorporated by reference: 52.204-7 System for Award Management (Oct 2018),

52.204-13 System for Award Management Maintenance (Oct 2018),

52.204-16 Commercial and Government Entity Code Reporting (Jul 2016),

52.204-18 Commercial and Government Entity Code Maintenance (Jul 2016).

The following provisions and clauses apply to this acquisition:

NIH Invoice and Payment Provisions (4/2022)

SUMMARY STATEMENT:

Responses to this notice must include sufficient information to establish the interested parties’ bona-fide capabilities of providing the product or service.  The response shall include a QUOTATION that includes: unit price, list price, total price, any shipping and handling costs, delivery days after contract award, delivery terms, prompt payment discount terms, F.O.B. Point (Destination or Origin), product or catalog number(s); product description; and any other information or factors that may be considered in the award decision.  Such factors may include: past performance; special features required for effective program performance; trade-in considerations; probable life of the item selected as compared with that of a comparable item; warranty considerations; maintenance availability; and environmental and energy efficiency considerations.