Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Setdb1

Cell type

Cell type Class
Blood
Cell type
Pro-B cells
NA
NA

Attributes by original data submitter

Sample

source_name
pro-B cells
strain
C57BL/6
genotype
Rag2-/-
chip antibody
Setdb1 Santa Cruz SC-66884X

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit / phenol-chloroform extraction 2-5 ng of cDNA, ChIP-precipitated DNA were 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 the following sizes were selected for the different experiments: 200–350 bp for ChIPseq and 150–700 bp for RNA-seq. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were modified with uracil-N-glycosylase (New England Biolabs) unable to generate second strand. The barcode containing adaptor was used for tagging and PCR amplification. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit. library construction protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
62812160
Reads aligned (%)
92.6
Duplicates removed (%)
16.3
Number of peaks
2763 (qval < 1E-05)

mm9

Number of total reads
62812160
Reads aligned (%)
92.4
Duplicates removed (%)
16.8
Number of peaks
2755 (qval < 1E-05)

Base call quality data from DBCLS SRA