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Sample GSM1843451 Query DataSets for GSM1843451
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.
 
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

Supplementary file Size Download File type/resource
GSM1843451_ChIPseq_WT_NHS_MM_vs_IgG_peaks.txt.gz 9.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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