Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Rag1

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
thymocytes
cell type
thymocytes
genotype
cR1
strain
C57BL/6
chip antibody
RAG1
age
4 weeks
Sex
female

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cells were crosslinked with 1% HCHO, quenched with 0.125 M glycine, washed and resuspended in RIPA buffer (10 mM Tris pH 7.4, 1 mM EDTA, 1% tritonX-100, 0.1% sodium deoxycholate, 0.1% SDS) containing 0.8 M NaCl and sonicated using a water bath sonicator (Diagenode) to obtain DNA of ≈ 300–500 bp. libraries were prepared and sequenced following standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
21686333
Reads aligned (%)
59.7
Duplicates removed (%)
45.3
Number of peaks
12567 (qval < 1E-05)

mm9

Number of total reads
21686333
Reads aligned (%)
59.6
Duplicates removed (%)
45.4
Number of peaks
12569 (qval < 1E-05)

Base call quality data from DBCLS SRA