Bulk (RNA, ATAC, CHIP), Whole Geneome Bisulfate and single cell Sequencing

This is a Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding the availability and capability of all qualified sources to perform a potential requirement.

This notice is issued to help determine the availability of qualified companies technically capable of meeting the Government requirement and to determine the method of acquisition.  It is not to be construed as a commitment by the Government to issue a solicitation or ultimately award a contract.  Responses will not be considered as proposals or quotes.  No award will be made as a result of this notice.  The Government will NOT be responsible for any costs incurred by the respondents to this notice.  This notice is strictly for research and information purposes only.

Background:  The analysis of DNA methylation state of heterochromatin in B, CD4+T and myeloid cells is best done by WGBS.  WGBS is an especially complex form of whole genome sequencing because many cytosine associated with CG pairs get converted to thymines, leading to imbalance of C/G versus A/T ratios in the genome.  Because of lack of experience within the NIA/IRP in this form of sequencing, this project is best done with an outside source. 

The proposed bulk RNA-seq, ATACseq and ChIPseq experiments are designed to evaluate changes in  in chromatin structure and gene expression in developing pro- and pre-B cells in the bone marrow in genetically mutated strains of mice, and to evaluate heterogeneity of activation responses in B and T lymphocytes, especially with regard to NF-kB-dependent gene expression and function of different subunits of NF-kB accessed via specific genetic mutations.

The proposed sc RNA-seq experiments are designed to evaluate a mouse model of Parkinson’s disease in which the disease time course can be followed temporally.  These experiments will be carried in WT C57/Bl6 mice, in mice that lack specific immune cells, and in mice here the transcription factor NF-kB will be specifically manipulated in microglia.  The sc libraries generated and sequenced here will provide a great deal of insight as to the function of NFKB in dementia.

Purpose and Objectives: We have a need to hire a contractor to perform the following:

• Whole Geneome Bisulfate Sequencing (WGBS) in mouse samples to examine the development of immune senescence in aging.
• Sequencing of bulk 1)RNA-seq, 2)ATACseq and 3) ChIPseq libraries are required to generate knowledge of the gene expression and transcriptional regulation both at the chromatin and chromosomal level. We require high throughput sequencing  performed on a NextSeq to acheive the correct level of inquiry depth.
• The proposed sc RNA-seq experiment libraries are designed to evaluate changes in microglial composition and immune cell subsets in the brain, especially with regard to expression of inflammation-related genes, specifically NFKB.

Project requirements: The contractor shall generate WGBS libraries and sequence them.

The contractor shall sequence the bulk libraries provided by the government to obtain specified sequencing reads per sample on Illumina Novaseq machine.  The contractor shall then provide FASTQ files as a resultant read out of the libraries provided.

The contractor shall sequence the single cell libraries provided by the government to obtain specified sequencing reads per sample on Illumina Novaseq machine.  The contractor shall then provide FASTQ files as a resultant read out of the libraries provided.

The contractor shall generate WGBS mouse libraries from 58 samples provided by the government.  These 58 libraries will then be subsequently sequenced on an Illumina platform to 100Gb data per sample.  The contractor shall then provide FASTQ files as a resultant read out of the libraries provided.

Illumina NextSeq instrument shall be utilized to sequence prepared bulk 1)RNA-seq, 2)ATACseq and 3) ChIPseq libraries. We are requsting the depth per library to be 400 million reads per run for RNAseq, ChIPseq libraries at 75 cycle sequencing and 130 million reads per library for ATACseq samples at 2X75 bp cycles.  Once the libraries are sequenced, both the run details and the FATQ files will be delivered.  To maintain uniformity with past experiments that is essential for rigorous data interpretation we need to use the same facility for future studies.

Illumina NovaSeq instrument shall be utilized to sequence prepared single cell RNA  (scRNA) libraries. We are requsting the depth to be 500 million reads per sample for 3’ libraries and 200 million reads per sample for 5’ libraries in combination with 50 million reads for VDJ libraries.  Once the libraries are sequenced, both the run details and the FATQ files will be delivered.  To maintain uniformity with past experiments that is essential for rigorous data interpretation we need to use the same facility for future studies.

Anticipated period of performance: September 15, 2020 – August 30, 2021

Capability statement /information sought. Respondents must provide, as part of their responses, a capability statement that includes:  

• respondents’ opinions about the difficulty and/or feasibility of the potential requirement or proposed acquisition, possible solutions and approaches that may currently exist in the marketplace, and information regarding innovative ideas or concepts; and

• information regarding respondents’: (a) staff expertise, including their availability, experience, and formal and other training; (b) current in-house capability and capacity to perform the work; (c) prior completed projects of similar nature; (d) corporate experience and management capability; and (e) examples of prior completed Government contracts, references, and other related information.

The respondent must also provide their  DUNS number, organization name, address, point of contact, and size and type of business (e.g., 8(a), HubZone, etc., pursuant to the applicable NAICS code and any other information that may be helpful in developing or finalizing the acquisition requirements.

One (1) copy of the response is required and must be in Microsoft Word or Adobe PDF format using 11-point or 12-point font, 8-1/2” x 11” paper size, with 1” top, bottom, left and right margins, and with single or double spacing.

The information submitted must be in an outline format that addresses each of the elements of the project requirement and in the capability statement /information sought paragraphs stated herein.  A cover page and an executive summary may be included but is not required.

The response is limited to ten (10) page limit.  The 10-page limit does not include the cover page, executive summary, or references, if requested.

The response must include the respondents’ technical and administrative points of contact, including names, titles, addresses, telephone and fax numbers, and e-mail addresses.

All responses to this notice must be submitted electronically to the Contracting Officer.  Facsimile responses are NOT accepted.

The response must be submitted to Karen Mahon, Contracting Officer, at e-mail address Karen.Mahon@nih.gov

The response must be received on or before August 21, 2020 at 10:00 am, Eastern Time.

 “Disclaimer and Important Notes:  This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization’s qualifications to perform the work.

Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a presolicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation.

Confidentiality: No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).”