|
| Status |
Public on Feb 22, 2018 |
| Title |
TRIM28KO Input for p300 |
| Sample type |
SRA |
| |
|
| Source name |
Th17 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Th17 differentiated in vitro for 3 days
genotype: TRIM28fl/flxCD4cre
chip antibody: None
|
| Treatment protocol |
Naive CD4+ T cells were cultured under Th17 differentiation conditions for 3 days
|
| Growth protocol |
RPMI-1640 medium with 10% FBS, 0.5ng/ml TGFβ and 20ng/ml IL-6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted from cells by Trizol. ChIP-seq was performed from crosslinked and MNase digested nuclear lysates; protein-DNA complexes were pulled down by indicated antibodies; after reverse-crosslinking, DNA was purified by phenol-chloroform.
RNA libraries were prepared by the BerryGenomics company and only mRNA was used. ChIP libraries were constructed following the protocol of NEXTflex ChIP-Seq DNA Sequencing Kit(Bioo Scientific, 5143) described in the paper.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using bcl2fastq Conversion Software v1.8.4
RNA-seq reads were aligned to the mm10 genome using SOAP2.
Reads count were calculated using htseq-count.
ChIP-seq reads were aligned to the mm10 genome using bowtie.
peaks were called using SICER version 1.1.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using SICER version 1.1; tdf files were converted using igvtools.
|
| |
|
| Submission date |
May 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Huiping Lu |
| E-mail(s) |
luhuiping1@hotmail.com
|
| Phone |
010-62797352
|
| Organization name |
Tsinghua university
|
| Street address |
Tsinghua university
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE98427 |
Epigenetic activation during Th17 cell differentiation is impaired after TRIM28 deletion |
|
| Relations |
| BioSample |
SAMN06859065 |
| SRA |
SRX2775262 |
