Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Biotin

Cell type

Cell type Class
Blood
Cell type
Thymocytes
MeSH Description
HEMATOPOIETIC PROGENITOR CELLS that have migrated to the THYMUS where they differentiate into T-LYMPHOCYTES. Thymocytes are classified into maturational stages based on the expression of CELL SURFACE ANTIGENS.

Attributes by original data submitter

Sample

source_name
Total Thymocytes
strain background
C57BL/6
genotype/variation
Tcf3(Bio/Bio) Rosa26(BirA/BirA)
cell type
total thymocytes
chip antibody
Streptavidin (BioChIP using a Streptavidin pulldown; PMID:21552207)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
E2A-Bio bound DNA was isolated with Streptavidin coupled beads and purified through phenol-chloroform extraction. About 5 ng of ChIP-precipitated DNA was used as starting material for the generation of single-end sequencing libraries as described by Illumina’s ChIP Sequencing sample preparation protocol. DNA fragments of 200–350 bp were selected. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit. Cluster generation and sequencing was performed by using the Illumina/Solexa Genome Analyzer II and IIx systems according to the manufacturer’s guidelines.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
20103396
Reads aligned (%)
95.7
Duplicates removed (%)
23.1
Number of peaks
3633 (qval < 1E-05)

mm9

Number of total reads
20103396
Reads aligned (%)
95.5
Duplicates removed (%)
23.3
Number of peaks
3634 (qval < 1E-05)

Base call quality data from DBCLS SRA