|
| Status |
Public on Oct 05, 2022 |
| Title |
RARα TG, 10nM RA (H3k27ac) |
| Sample type |
SRA |
| |
|
| Source name |
CD4 T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD4 T cells
culture conditions: 16h w/ 10nM RA
strain: C57BL/6
genotype: RAR{alpha} TG
chip antibody: H3k27ac
|
| Treatment protocol |
Cells were cultured with or without RA at 10nM for the 16h of culture.
|
| Growth protocol |
Naïve CD4 T cells (>95% pure) were cultured in cRPMI (w/charcoal-stripped FBS) and activated with anti-CD3 and anti-CD28 in the presence of mIL-6 (20 ng/mL), mIL-1β (10 ng/mL), mIL-21 (10 ng/mL), mIL-23 (10 ng/mL), mTNFα (5 ng/mL), hTGFβ-1 (5 ng/mL), anti-IFNγ (10 μg/mL), and anti-IL-4 (10 μg/mL) for 16h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. Samples were Mnase treated for 6 minutes and sonicated to achieve desired chromatin banding of 150-900bp. IP was performed overnight with clone D5E4 for H3k27ac using the magnetic SimpleChIP kit (Cell Signaling)
Indexed libraries were generated using the ThruPLEX DNA-seq kit (Takara; Mountain View, CA) with 13 cycles of amplification
ChIPseq. 1 x 50 bp sequencing was performed on a NovaSeq 6000 (Illumina; San Diego, CA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were quality trimmed and Illumina adapter sequences were removed.
Alignment of reads to the GRCm38 mm10 Ensembl mouse genome was performed with Bowtie.
ChIP-seq coverage plots in bigWig files were created with bins of 100bp and normalized to reads per million.
Differences in H3k27ac enriched signal by subtracting normalized input with bigwigCompare.
Peaks were called uing MACS2
Assembly: mm10
Supplementary files format and content: bigWig files containing H3K27ac signal - input signal
|
| |
|
| Submission date |
Apr 27, 2022 |
| Last update date |
Oct 05, 2022 |
| Contact name |
Chang Kim |
| Organization name |
University of Michigan
|
| Street address |
109 Zina Pitcher
|
| City |
Ann Arbor |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE201728 |
CD4 T cell ChIPseq (H3k27ac) and RARα |
|
| Relations |
| BioSample |
SAMN27923157 |
| SRA |
SRX15036235 |
