|
| Status |
Public on Apr 03, 2020 |
| Title |
naive_CD4_NCOR1_WT1 (ChIP-seq) |
| Sample type |
SRA |
| |
|
| Source name |
spleen, lymph nodes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: naive CD4+ T cells
genotype: wild-type
chip antibody: NCOR1 antibody (Cell Signaling Technology, #5948S)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
WT and NCOR1f/f,Cd4Cre naive CD4+ T cell samples were prepared according to the ChIPmentation protocol (doi:10.1038/nmeth.3542, doi:10.1186/s12864-018-5299-0) by using a NCOR1 antibody from Cell Signaling Technology (#5948S).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
WT1
|
| Data processing |
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquistion on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing was performed with custom programs based on Picard tools (v2.18.11, http://broadinstitute.github.io/picard/).
NGS reads passing vendor quality filtering were aligned with Bowtie2 (version 2.2.5) to teh UCSC mm10 flavour of the GRCm38 assembly.
The MACS2 program (2.1.2, http://www.ncbi.nlm.nih.gov/pubmed/18798982) was used for peak calling and signal track generation.
Bioconductor DiffBind (2.12.10, http://www.ncbi.nlm.nih.gov/pubmed/22217937) was used in a differntual binding analysis.
Genome_build: GRCm38 (UCSC mm10)
Supplementary_files_format_and_content: tab-separated value peak list obtained by MACS2.
|
| |
|
| Submission date |
Oct 16, 2019 |
| Last update date |
Apr 04, 2020 |
| Contact name |
Wilfried Ellmeier |
| E-mail(s) |
wilfried.ellmeier@meduniwien.ac.at
|
| Organization name |
Medical University of Vienna
|
| Department |
Institute of Immunology
|
| Street address |
Lazarettgase 19
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE138930 |
NCOR1 ChIP-seq analysis of WT naive CD4+ T cells |
| GSE138934 |
Role of NCOR1 in CD4+ T cells |
|
| Relations |
| BioSample |
SAMN13038859 |
| SRA |
SRX7004438 |
