Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BCL11B

Cell type

Cell type Class
Blood
Cell type
Thymus
NA
NA

Attributes by original data submitter

Sample

source_name
thymus
cell type
CD34+
replicate
1
chip antibody
BCL11B

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
CD34+ (19-29×106 cells) or CD34- (60×106 cells) cells were treated with 1% formaldehyde for 10 minutes, which was followed by chromatin shearing with micrococcal nuclease to an average size of 150 base pairs. An aliquot of precleared chromatin was incubated with 1µg of anti-Bcl11b (IP) or 1µg of isotype control (control) antibody (antibodies from Cell Signaling) followed by hybridization to 30μl of Protein G Magnetic Beads for 3 hours. The protein-DNA complexes were eluted, and incubated with proteinase K to digest protein. The eluate was reverse crosslinked by incubation at 65°C for 2 hours. DNA was purified with a DNA purification kit (Cell Signaling). Libraries were made with the Next Ultra™ DNA Library Prep Kit (NEB) (input=5 ng of ChIP DNA) Libraries were sequenced on Illumina Nextseq500 (paired end 75 base pair sequencing)

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
25679866
Reads aligned (%)
175.2
Duplicates removed (%)
2.9
Number of peaks
1198 (qval < 1E-05)

hg38

Number of total reads
25679866
Reads aligned (%)
177.7
Duplicates removed (%)
2.3
Number of peaks
1539 (qval < 1E-05)

Base call quality data from DBCLS SRA