Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Stat3

Cell type

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

Attributes by original data submitter

Sample

source_name
Pre-activated CD4+ T cells
strain
C57BL/6
tissue
Spleen
cell type
Pre-activated CD4+ T cells
genotype
WT
chip antibody
STAT3 (Invitrogen, 13-7000)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, Cells were fixed with 1% formaldehyde at 37°C for 10 min, and chromatin from 2.5 x 107 cells was sonicated for 20 cycles (15 sec on/45 sec off) to produce 250-450 bp fragments. STAT3-linked chromatin was immunoprecipitated using anti-STAT3 (13-7000, Invitrogen) antibody bound to Dynabeads. The ends of isolated DNA were repaired using the DNA END-Repair kit (Epicentre Biotechnologies), and a 3’ “A” nucleotide was added with Taq polymerase. Two mixed Solexa adaptors (Illumina) were ligated to DNA ends and primers complementary to these adaptors (PE 1.0 and 2.0, Illumina) were used to amplify the DNA for 18 cycles. DNA fragments of 250-450 bp were purified from 2% E-gels and used for cluster generation and sequencing. For RNA-Seq, Total RNA was isolated, and 5 μg per sample were used for mRNA purification using Dynal oligo(dT) beads (Invitrogen). Double-stranded cDNA was synthesized with random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (Invitrogen) and fragmented by Bioraptor. After end repair (Epicentre DNA END-Repair kit) and the addition of an “A” nucleotide to the 3’ ends with Taq DNA polymerase, two mixed Solexa adaptors (Illumina) were ligated to DNA ends using T4 DNA ligase (New England Biolabs). 250-450 bp fragments were isolated on 2% E-Gels (Invitrogen) and amplified for 18 cycles using PE 1.0 and 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs). PCR products were run on a gel, and 250-450 bp fragments were purified PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
52459212
Reads aligned (%)
63.3
Duplicates removed (%)
86.5
Number of peaks
1027 (qval < 1E-05)

mm9

Number of total reads
52459212
Reads aligned (%)
63.2
Duplicates removed (%)
86.6
Number of peaks
1007 (qval < 1E-05)

Base call quality data from DBCLS SRA