Loren Data's SAM Daily™

FBO DAILY ISSUE OF JANUARY 20, 2011 FBO #3344
MODIFICATION

B -- Sequence ChIP-Seq, MeDIP-Seq and RNA-Seq experiments followed by quantitative informatic analysis - Contractor's Questions

Notice Date

1/18/2011
 

Notice Type

Modification/Amendment
 

NAICS

541712 — Research and Development in the Physical, Engineering, and Life Sciences (except Biotechnology)
 

Contracting Office

Other Defense Agencies, Uniformed Services University of the Health Sciences, Directorate of Contracting, 4301 Jones Bridge Road, Bethesda, Maryland, 20814-4799
 

ZIP Code

20814-4799
 

Solicitation Number

HU00011366
 

Point of Contact

Christina Johnson, Phone: 3012953069, Zamora Olin, Phone: 301-295-3922
 

E-Mail Address

cjohnson@usuhs.mil, Zamora.Olin@usuhs.mil
(cjohnson@usuhs.mil, Zamora.Olin@usuhs.mil)
 

Small Business Set-Aside

N/A
 

Description

Addressing contractor's questions. The purpose of this amendment is to address the following contractor's questions. Please see the attached file. The purpose of this amendment is to address the following contractor's questions: 1. Just to confirm, the work required is the sequencing and delivery of the data only. The IP work would be done elsewhere, as well as the RNA extraction from tissues. Is this correct? Can you provide additional information about these requirements. Yes, USUHS will perform all IP (chromatin immunoprecipitation) assays and RNA extraction from tissues. The contractor is expected to perform quality check of the samples, all steps of sequencing, initial data analysis including the alignment with the reference genome and final delivery of the data. 2. Upon completion of the processing of each sample batch, as provided by the USUHS, the Contractor shall provide a briefing or report synopsis to the designated USUHS point of contact along with the results of each sample batch. Can you provide additional information on the format and detail required for these reports? Upon completion of the processing of each sample batch, the contractor is expected to provide the QC (quality check) data [e.g. files generated showing the quality (RIN values for RNA), quantity of the samples as well as base pair size distribution of fragments especially for the CHIP samples]. Apart from these, the contractor is expected to provide the raw sequence files, quality reports, as well as data files generated after alignment with the reference genome. 3. The Contractor shall also provide all necessary research support to ensure the successful completion of the project. Can you provide additional information about the extent of the contractor's responsibility? Presumably, it would be limited to the provision of high-quality data. The contractor is expected to help us generate the best high quality data. This will include providing scientific suggestions and support to facilitate the sample preparation of best quality as well the final data analysis comprising quality assessment of the sequence data, normalization, gene expression analysis, novel miRNA exploration, defining peaks and final ratiometric comparison of experimental to control samples to identify true binding sites. 4. There are three applications in this project, which are ChIP-Seq, MeDIP-Seq and RNA-seq. For each application, do your PIs have any specific requirement for sequencing design, such as sequence read length, single read or paired end read. We would like to run our samples using Illumina sequencers and single read fragment libraries using the latest development in sample indexing. The read depth can be adjusted based upon contractors experience and our preliminary results. We need flexibility/high-sequencing capacity of the contractor so that the project can be finished in a timely manner. 5. In the request, you specifically mentioned pooling samples. For pooling samples, sample numbers in each pool will vary based on application type and data throughput requirement. Do you have any requirement on sample pooling strategy? Or we should based on your preliminary study to design sample pooling. Yes, we understand that the sample numbers in each pool will vary based on application type and data throughput requirement. We would be interested in pooling the number of samples recommended by the contractor based on contractor prior published experience and knowledge and also based on our preliminary study data to finally achieve high quality sequencing data with adequate read depth. 6. For methylation seq, is this is whole genome scale? Or just portion of genome. For methylation seq, we are interested to perform whole genome MeDIP sequencing. 7. Beyond aligning the sequence data to the reference genome how much analysis is required, if any? Is differential expression analysis between sample sets part of this project or will it be handled internally? What specific types of analysis are you looking and how will that data be summarized and managed? After the alignment with the reference genome, we will perform multiple set of data analysis related to different applications mentioned in the proposed contract. This will be handled internally (but require scientific support and suggestions from the contractor) and mainly include: a) differential expression analysis between treated and untreated samples for RNASeq b) peak finding, % input and final calculation of differential fold occupancy of the protein of interest between treated and untreated samples for ChIPSeq c) estimate the methylation levels of different regions throughout the genome between treated and untreated samples All data relevant to the project will be stored on a Dell T7500 work station and external UNIX servers. Secondary analysis will be performed using specialized statistical and bioinformatic analysis tools suggested by the contractor based on contractor prior experience in data analysis. 8. What is the expected deliverable with respect to data format, type, summary reports etc. The expected deliverable is the raw sequencing reads in a FASTA format and the associated sequence quality files in.fastq or a suitable format. Alignment of reads with the reference genome in SAM format will be expected. Apart from this, we require the basic QC files to check the quality of the samples submitted for sequencing. The data format is liable to change based on our discussion, prior experience, and knowledge of the contractor. All quotes are still due on January 25, 2011 at 12:00 pm (est).
 

Web Link

FBO.gov Permalink
(https://www.fbo.gov/spg/ODA/USUHS/BethesdaMD/HU00011366/listing.html)
 

Place of Performance

Address: Bethesda, Maryland, 20814, United States

Zip Code: 20814
 

Record

SN02361670-W 20110120/110118233927-08e5d9452d8c0c84c4f0e7b5fc42dc96 (fbodaily.com)
 

Source

FedBizOpps Link to This Notice
(may not be valid after Archive Date)

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