Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ascl2

Cell type

Cell type Class
Blood
Cell type
CD4+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
CD4+ T cells
strain
C57BL/6
cell type
CD4+ T cells
genotype/variation
empty vector transfected
chip antibody
Ascl2 mAb (clone, 7E2, Millipore, lot# 2066321)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA or protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Sorted T cells were fixed by 1% paraformaldehyde, and followed with digestion with Mnase cocktail (Active motif). Chromatin from 5x106 cells was used for each ChIP experiment. Antibodies against H3K4me3 (Cat# 07-473, Millipore), H3K27me3 (Cat# 07-449, Millipore), and Ascl2 mAb (clone, 7E2, Millipore) were used. The pull-down DNA fragments were blunt-ended ligated with Solexa adaptors, and amplified for sequencing. The DNA fragments were sequenced with Illumina 1G Analyzer at the Institute for System Biology.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

mm10

Number of total reads
30943133
Reads aligned (%)
98.0
Duplicates removed (%)
7.7
Number of peaks
200 (qval < 1E-05)

mm9

Number of total reads
30943133
Reads aligned (%)
97.9
Duplicates removed (%)
7.7
Number of peaks
219 (qval < 1E-05)

Base call quality data from DBCLS SRA