Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

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

Attributes by original data submitter

Sample

source_name
Splenic CD4+ T cells
tissue
spleen
cell type
CD4+ T cells
strain
AND
peptide
No Peptide
timepoint
24 hours
chip antibody
H3K27Ac (Abcam, cat. no. ab4729)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Quoted from GSE42147: "Native chromatin was prepared by lysing CD4+ cells in low salt buffer and digesting with Micrococcal nuclease. Lysates were then sonicated to assist in recovery of oligonucleosomes and adjusted to RIPA immunoprecipitation buffer conditions. Extracts were then incubated overnight with specific antisera prior to immunoprecipitation with protein A & G beads, and recovery of bound DNA using silica column purification." Sodium butyrate added, and library prep as in Gosselin ChIP-Seq. CD4+ cells were re-isolated from the culture using the Miltenyi MACS system.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
18099865
Reads aligned (%)
99.0
Duplicates removed (%)
5.2
Number of peaks
5762 (qval < 1E-05)

mm9

Number of total reads
18099865
Reads aligned (%)
98.9
Duplicates removed (%)
5.3
Number of peaks
5751 (qval < 1E-05)

Base call quality data from DBCLS SRA