Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Gamma delta T cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse thymocytes
strain
C57BL/6
genotype
TCRbeta KO.Sox13tg+.Sox13 ECFP KI/+
cell type
sorted gd T thymocytes
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
1 million cells for TCF1 ChIPseq were sorted (gd+, CD24+ and CFPlo/-), crosslinked with 1% formaldehyde, sonicated, and then subjected to chromatin immunoprecipitation with anti-TCF1 antibody. 300-500 bp DNA fragments were obtained after reverse-cross linking. The TCF1 ChIP DNA fragments were processed for ChIPseq with Illumina adapters and Illumina primers (Primer1.1 and Primer2.1). After adapter ligation, DNAs were PCR-amplified for 17 cycles and library fragments of 300-500 bp were extracted from an agarose gel.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
96028898
Reads aligned (%)
98.8
Duplicates removed (%)
12.5
Number of peaks
2127 (qval < 1E-05)

mm9

Number of total reads
96028898
Reads aligned (%)
98.5
Duplicates removed (%)
12.4
Number of peaks
2198 (qval < 1E-05)

Base call quality data from DBCLS SRA