|
| Status |
Public on Oct 30, 2019 |
| Title |
CD4+ T cells: Tox2:HA - ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen+Lymph nodes
age: 7-8 wk
genotype: wild type
|
| Treatment protocol |
Naive CD4+ T cells were activated and infected with retrovirus Tox2:HA-RV-GFP under neutral condition, after which GFP+ cells were sorted and cultured in Tfh-like conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP assay was performed using Active Motif’s ChIP assay kit (53035) according to manufacturer’s instructions with slight modifications.
ChIP-seq DNA library was constructed for deep sequencing by BGI Genomics.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4
Clean reads were aligned to mm10 by Bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.01
The uniquely mapped reads were used to call peak with MACS2 using a q value cutoff 0.01
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each RNAseq Sample and bigwig file with quantitative data for Chip Sample
|
| |
|
| Submission date |
Aug 28, 2019 |
| Last update date |
Oct 31, 2019 |
| Contact name |
Chen Dong |
| Organization name |
Tsinghua University
|
| Department |
Institute for Immunology and School of Medicine
|
| Lab |
Dongchen's lab
|
| Street address |
Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE136539 |
Genome binding/occupancy profiling of Tox2 in Tfh-like cells |
|
| Relations |
| BioSample |
SAMN12646163 |
| SRA |
SRX6769601 |
