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| Status |
Public on Apr 26, 2023 |
| Title |
50_D5_Th17_STAT5cKO2_Ets1 |
| Sample type |
SRA |
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| Source name |
CD4 T cell
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| Organism |
Mus musculus |
| Characteristics |
strain: activated CD4 T cells
tissue: spleen and lymph nodes
genotype: wild-type
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| Treatment protocol |
Naïve cells were activated under Th17 culture conditions (20 ng/ml IL-6; 5 ng/ml human TGFb; 10 ng/ml IL-1b, 10 ug/ml anti-IL-4, and 10 ug/ml anti-IFNg) for 5 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells (5-20 x 106) were cross-linked for 10 min with 1% formaldehyde, quenched with Glycine, and washed. Cell pellets were resuspended in lysis buffer, and homogenized. Nuclei were resuspended in RIPA buffer and sonicated to a size range of 200-600 bp using Qsonica. Cells were pelleted, and RIPA buffer was added to supernatant to 1 ml. Appropriate antibody coupled to Dynabeads M-280 Sheep anti-rabbit IgG was added to the mix. The immunocomplexes were washed 5X with LiCl solution. Supernatants were collected, incubated at 65C overnight, and immunoprecipiated DNA were purified using MinElute columns (Qiagen)
Immunoprecipiated DNA was used to prepare library using NEBNext Ultra II DNA library prep kit and NEBNext Multiplex Oligos for Illumina (NEB). ChIP-seq libraries were sequenced with single-end 50 bp using Illumina HiSeq 2500.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
49_D5_Th17_STAT5cKO_Ets1.bw
Ets1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)
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| Data processing |
fastq QC
remove adapter: trim_galore v0.4.1
mapping: Bowtie1 (v1.1.2)
filter/remove duplicates: samtools v0.1.19
peak-calling: MACS2 v.2.1.0
normalization/tagcount/bedgraph: HOMER v4.9.0
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using HOMER
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| Submission date |
Feb 24, 2021 |
| Last update date |
Apr 26, 2023 |
| Contact name |
Min Gao |
| E-mail(s) |
[email protected]
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| Organization name |
University of Alabama at Birmingham
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| Street address |
1900 University Blvd, THT Building Suite #130G
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| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE167417 |
Batf stabilizes Th17 cell development via limiting STAT5 signaling pathway (ChIP-Seq) |
| GSE167420 |
Batf stabilizes Th17 cell development via limiting STAT5 signaling pathway |
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| Relations |
| BioSample |
SAMN18050382 |
| SRA |
SRX10162866 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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