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Sample GSM3383360

Query DataSets for GSM3383360

Status

Public on Feb 14, 2019

Title

Tcf1-deficient CD4 T cells

Sample type

SRA

Source name

all CD4 T cells

Organism

Mus musculus

Characteristics

genotype: Tcf1 deficient
tissue: effector CD4 T cells
cell phenotype: TCRb+, CD4+
antibody: anti-Tcf1

Extracted molecule

genomic DNA

Extraction protocol

Conventional or regulatory CD4+ T cells were sort-purified from WT Foxp3-cre-GFP mice, and the Tcf1-deficient CD4+ T cells were sorted from CD4-Cre+ Tcf1 fl/fl mice. The cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with antiserum against Tcf1, which were then properly washed and immunoprecipitated DNA extracted.
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2000

Data processing

The sequencing quality of ChIP-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.3.4.1, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm10 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ChIP-Seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of enrichment of four-fold or more, a P value of < 1E-5 and false-discovery rate of < 5% and thus identified Tcf1 binding peaks.
Genome_build: mm10

Submission date

Sep 10, 2018

Last update date

Feb 14, 2019

Contact name

Weiqun Peng

E-mail(s)

[email protected]

Organization name

The George Washington University

Street address

1918 F Street, NW , DC