Long non-coding RNA and small RNA sequencing of human endothelial cells with and without Radiation

Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Room 1E132, Bethesda, MD 20892, UNITED STATES Description The U.S. Department of Health and Human Services, National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research (CCR), Radiation Oncology Branch (ROB), Office of Acquisitions (OA) plans to procure on a sole source basis with Novogene Corporate Inc, 823 Anchorage Place Chula Vista, CA 91914 services to identify lncRNA and microRNA profiles which are regulated in a radiation responsive manner in human endothelial cells. This acquisition will be processed under FAR Part 12 - Acquisition for Commercial Items and will be made pursuant to the authority in FAR Part 13.106-1 (b) (1) using simplified acquisition procedures for commercial acquisitions. The North American Industry Classification System Code is 541990 and the business size standard is 500 employees. Only one award will be made as a result of this solicitation. This will be awarded as a non-severable firm fixed price type contract. The period of performance shall be 90 days after award. It has been determined there are no opportunities to acquire green products or services for this procurement. The NCI/ROB are interested in identifying radiation responsive RNAs in endothelial cells. Endothelial cells are at the centre of the radiation damage to different organs. Knowing that several RNAs (lncRNA and miRNA) are central to the radiation response, it is interesting to look at the RNA profiles in these cells in response to radiation. Several studies have proposed that endothelial cell damage is the primary cause of organ failure in case of lethal and sub-lethal exposure to external radiation sources. Endothelial cells line all the blood vessels and are influenced by the niche in which blood vessels reside. These cells release exosomes which are shed directly into the circulation. Long non-coding RNA and microRNA play crucial roles in DNA damage response sustained by radiation which can be detected in the blood. It is necessary to identify RNA expression changes occurring in the endothelial cells in response to radiation which could be released into the circulation. To that end the NCI have designed this study to explore both long non-coding and small microRNAs which change in response to radiation using high throughput NGS sequencing platforms. The primary objective is to identify lncRNA and microRNA profiles which are regulated in a radiation responsive manner in human endothelial cells. The Contractor shall perform all the tasks listed below: 1. RNA quality control and library preparation 2. lncRNA and small RNA sequencing using Illumina sequencers 3. Data acquisition and analysis Library prep- LncRNA (250-300 bp insert strand specific library with rRNA removal (Ribo-zeroTM magnetic Kit) Bioinformatics- Standard analysis a) LncRNA Standard Analysis QC 1. Data Quality Control: filtering reads containing adapter or with low quality 2. Statistics of Data Production and Quality 3. Alignment with reference genome lncRNA prediction 1. Reference based reconstruction of transcripts 2. Filtering of candidate lncRNA Structure analysis 1. Alternative splicing analysis 2. SNP/Indel calling 3. LncRNA target gene prediction Expression quantification analysis 1. Expression quantification analysis for mRNA and lncRNA (two or more groups of samples) 2. Correlation analysis (For biological replicates only) 3. Differential expression analysis for mRNA and lncRNA (two or more groups of samples) 4. GO enrichment analysis of differentially expressed coding genes 5. KEGG enrichment analysis differentially expressed coding genes 6. Network analysis of protein-protein interactions of differential mRNA 7. Enrichment analysis of differentially expressed lncRNA target genes lncRNA mRNA comparative analysis 1. Structural comparison between lncRNA and mRNA 2. Expression comparison between lncRNA and mRNA 3. Conservation comparison between lncRNA and mRNA (For a few animal species only) 4. lncRNA-mRNA network analysis b) Small RNA smallRNA-18-40 insert sRNA library 1. Standard Analysis 2. Data Quality Control: filtering reads containing adapter or with low quality 3. Summarize the length distribution of small RNA 4. Analyze common and specific sequences between two samples 5. Align small RNA to reference genome 6. Identify known miRNA 7. Identify rRNA, tRNA, snRNA, snoRNA and Non-coding RNA 8. Identify repeat associated small RNAs (repeat annotation information of the reference genome should be provided) 9. Align small RNA to mRNA, exon and intron 10. Predict novel miRNAs and their secondary structures by Mireap from unannotated small RNAs 11. Analyze the expression pattern of known miRNAs 12. Analyze the base bias of miRNA 13. Classify and annotate of small RNAs NCI has determined that Novogene Corporate Inc is uniquely qualified to deliver on this project and have already delivered on a previous project using smaller sample sets. For the aforementioned reason, it is not advantageous to the NCI/ROB to change Contractors to avoid introducing any variability in the data processing and analysis, which would result in the Government spending unnecessary additional funds and time. CLAUSES AND PROVISIONS The following FAR Clauses/Provisions are incorporate as required by the John S. McCain National Defense Authorization Act (NDAA) for FY 2019, Public Law 115-232, Section 889(a)(1)(A). The following FAR Clauses/Provisions are hereby added in full text. FAR 52.204-24 - Representation Regarding Certain Telecommunications and Video Surveillance Services or Equipment NOTE: Offerors are required to have an authorized individual self-certify and return attachment from FAR 52.204-24 along with the quote. FAR 52.204-25 - Prohibition on Contracting for Certain Telecommunications and Video Surveillance Services or Equipment. FAR 52.212-5 - Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial. This notice is not a request for competitive quotation. However, if any interested party, especially small businesses, believes it can meet the above requirement, it may submit a capability statement, proposal, or quotation, which shall be considered by the agency. The statement of capabilities and any other information furnished must be in writing and must contain material in sufficient detail to allow NCI to determine if the party can perform the requirement. Responses must be received in the contracting office by 4:00 PM EST, on September 3, 2019. All responses and questions can be emailed to Ronette Collins, Contract Specialist via electronic mail at ronette.collins@nih.gov. A determination by the Government not to compete this proposed requirement based upon responses to this notice is solely within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. In order to receive an award, contractors must be registered and have valid certification in the System for Award Management (SAM) through sam.gov. Reference: 75N91019Q00106 on all correspondence.