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Status |
Public on May 01, 2024 |
Title |
WT_MC38, IRF1, ChIP-seq, 2 |
Sample type |
SRA |
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Source name |
MC38
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Organism |
Mus musculus |
Characteristics |
cell line: MC38 cell type: Mouse Colon Adeno Carcinoma genotype: WT treatment: untreated
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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.
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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)
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 3000 |
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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)
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Submission date |
Nov 02, 2023 |
Last update date |
May 01, 2024 |
Contact name |
Prabhat Kumar Purbey |
E-mail(s) |
ppurbey@gmail.com
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Phone |
3102064946
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Organization name |
UCLA
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Department |
MIMG
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Lab |
Stephen T. Smale
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Street address |
675 Charles E. Young Drive South
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City |
los angeles |
State/province |
California |
ZIP/Postal code |
90095 |
Country |
USA |
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Platform ID |
GPL21493 |
Series (1) |
GSE246923 |
Opposing tumor cell-intrinsic and -extrinsic roles of the IRF1 transcription factor in anti-tumor immunity |
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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 |
SRA Run Selector |
Raw data are available in SRA |
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