Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
CD8+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
CD8 T cells
genotype
wild type
tissue
mature thymocytes
cell phenotype
TCRbeta high, CD69–, CD24–, CD8+
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Mature CD4 or CD8 thymocytes were sort-purified for WT or Tcf1/Lef1-deficient mice, the cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with antibodies against H3K4me3, H3K27me3, H3K27Ac, H3K9Ac, or Tcf1, which were then properly washed and immunoprecipitated DNA extracted. Splenic CD8 T cells were sort-purified for WT or Tcf1-deficient mice, the cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with a Tcf1 antiserum, 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. For Histone Marks: ChIPseq, single end, 51 nucleotide sequencing. For several samples we did the high throughput sequencing for a second time to improve the coverage, and the other sequencing strategy is: ChIPseq, single end, 101 nucleotide sequencing. For Tcf1: ChIPseq, single end, 50 nucleotide sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
19817236
Reads aligned (%)
98.3
Duplicates removed (%)
58.2
Number of peaks
408 (qval < 1E-05)

mm9

Number of total reads
19817236
Reads aligned (%)
98.0
Duplicates removed (%)
58.4
Number of peaks
415 (qval < 1E-05)

Base call quality data from DBCLS SRA