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Sample GSM4123836 Query DataSets for GSM4123836
Status Public on Apr 03, 2020
Title naive_CD4_NCOR1_WT2 (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 WT2
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 SAMN13038858
SRA SRX7004439

Supplementary file Size Download File type/resource
GSM4123836_naive_CD4_NCOR1_WT2_S42909_gp38posCD31neg_CM_input_S23970_peaks.tsv.gz 188.0 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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