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Sample GSM7880908 Query DataSets for GSM7880908
Status Public on May 01, 2024
Title WT_MC38, IRF1, ChIP-seq, 2
Sample type SRA
 
Source name MC38
Organism Mus musculus
Characteristics cell line: MC38
cell type: Mouse Colon Adeno Carcinoma
genotype: WT
treatment: untreated
Treatment protocol IFN-y (Peprotech #315-05) at a concentration 100 units per milli liter was used to stimulate WT or Irf1-/- MC38 cells in large 15 cm plate.
Growth protocol MC38 cell line was maintained in DMEM with 10% fetal bovine serum, 2mM L- glutamine (Gibco, #25030-081), 0.1 mM non-essential amino acids (Gibco, #11140-050), 1 mM sodium pyruvate (Gibco, #11360-070), 10 mM Hepes (Gibco, #15630-080), and 1X pen/strep (Gibco, #15140-122)
Extracted molecule genomic DNA
Extraction protocol Purified nuclei from untreated or IFN-y stimulated WT or Irf1-/- MC 38 cells were lysed and chromatin was sheared using a Bioraptor (Diagenode) sonicator for 20 cycles prior to immunoprecipitation with anti-IRF1, or anti-STAT1 antibodies
libraries were constructed using Kapa's LTP Library Preparation kit according to manufactuer's instruction.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Data processing ChIP-seq libraries were sequenced, single end 50bp on an Illumina HiSeq 3000.
ChIP-seq fastq files were mapped using Hisat2. Only the uniquely mapped reads were kept for further analysis.
Uniquely aligned reads were peak-called using the Homer suite with a FDR threshold of 0.01.
Called peaks were annotated to the nearest Refseq ID, mm9 build
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample was generated using Homer and represent the read coverage at each genomic position
Supplementary files format and content: Peak files for each sample versus respective input was generated using Homer where peaks were generated considering peak type as transcription factor ( -style factor)
 
Submission date Nov 02, 2023
Last update date May 01, 2024
Contact name Prabhat Kumar Purbey
E-mail(s) ppurbey@gmail.com
Phone 3102064946
Organization name UCLA
Department MIMG
Lab Stephen T. Smale
Street address 675 Charles E. Young Drive South
City los angeles
State/province California
ZIP/Postal code 90095
Country USA
 
Platform ID GPL21493
Series (1)
GSE246923 Opposing tumor cell-intrinsic and -extrinsic roles of the IRF1 transcription factor in anti-tumor immunity
Relations
BioSample SAMN38083803
SRA SRX22361138

Supplementary file Size Download File type/resource
GSM7880908_1b_WT_0h_anti-IRF1_rep2.ucsc.bedGraph.gz 156.3 Mb (ftp)(http) BEDGRAPH
GSM7880908_1b_WT_0h_anti-IRF1_rep2_peaks.txt.gz 28.0 Kb (ftp)(http) TXT
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Raw data are available in SRA

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