Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RAG1

Cell type

Cell type Class
Blood
Cell type
Thymus
NA
NA

Attributes by original data submitter

Sample

source_name
thymocytes
cell type
thymocytes
genotype
n/a
strain
n/a
chip antibody
RAG1
age
Mixture: 4 months or 1.5 years
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

hg19

Number of total reads
25938187
Reads aligned (%)
64.4
Duplicates removed (%)
8.4
Number of peaks
436 (qval < 1E-05)

hg38

Number of total reads
25938187
Reads aligned (%)
65.9
Duplicates removed (%)
7.3
Number of peaks
349 (qval < 1E-05)

Base call quality data from DBCLS SRA