|
Status |
Public on Mar 01, 2016 |
Title |
ChIPseq_WT_NHS_MM |
Sample type |
SRA |
|
|
Source name |
MEFs_WT_NHS
|
Organism |
Mus musculus |
Characteristics |
strain background: 129Sv.BALB/c genotype/variation: wild type cell type: Mouse embryonic fibroblasts (MEFs) time point: before heat shock chip antibody: gift from Morimoto lab (MM)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Nuclei were isolated for PRO-seq and run-on reactions were performed with biotinylated nucleotides. For ChIP-seq, isolated nuclei were sonicated to shear chromatin and IPed with two different antibodies (CS and MM) and non-specific IgG. Input DNA was also sequenced for each condition. PRO-seq libraries were performed according to the paper: Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013 Feb 22;339(6122):950-3. PMID: 23430654. ChIP-seq libraries were prepared the standard way using Illumnia TRU-seq adpapters.
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
PRO-seq: adapters were removed and the reads were trimmed to 36bp. Reverse complement of reads were generated. PRO-seq: reads were first mapped to ribosomal genome and anything that did not map to ribosomal genome were mapped to rest of the genome using mm10. The bedgraph files were normalized with the custom normalization approach as discribed in the paper and the bigWig files were generated from the normalized bedgraph files. ChIP-seq: adapters were removed and the reads were trimmed to 36bp. The trimmed reads were mapped to the mouse genome mm10. ChIP-seq: Using MACS, peaks were called against IgG and Input. p-value threshold of 1e-04 was used. Overlapping peaks from two different antibodies (CS and MM) were combind using fisher's method of combining p-value. The resulting peaks were selected against any peaks called in HSF1-/- lines. Genome_build: mm10 Supplementary_files_format_and_content: peak.txt file of HSF1 peaks for ChIP-seq and normalized bigWig for PRO-seq
|
|
|
Submission date |
Aug 04, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Dig Bijay Mahat |
E-mail(s) |
dbm222@cornell.edu
|
Organization name |
Cornell University
|
Department |
Molecular Biology & Genetics
|
Lab |
John Lis
|
Street address |
526 campus Rd
|
City |
Ithaca |
State/province |
NY |
ZIP/Postal code |
14853 |
Country |
USA |
|
|
Platform ID |
GPL13112 |
Series (1) |
GSE71708 |
Mammalian Heat Shock Response And Mechanisms Underlying Its Genome-wide Transcriptional Regulation |
|
Relations |
BioSample |
SAMN03956257 |
SRA |
SRX1132772 |