Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Blood
Cell type
CD34 Hematopoietic stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
Human CD34+ HSPCs
tissue
Cord Blood
cell type
CD34+ hematopoietic stem cells (HSPCs)
input
CD34_CTCF_INPUT
chip antibody
CTCF
chip antibody vendor
Cell signaling

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
CD34+ cells were cross linked with 1% formaldehyde at room temperature for 10 min, and the reaction was stopped by 0.125M glycine at RT 5 min. Cross linked cells were lysed in 50μl lysis buffer (10 mM Tris pH 7.5, 1mM EDTA, 1% SDS), then diluted with 150 μl of PBS/PIC, and sonicated using Bioruptor (Diagenode) 30sec on 30 sec off 7 cycles to 200-500 bp fragments. ChIP-qualified CTCF (Cell signaling #2899), H3K27ac (abcam #ab4729) and H3K27me3 (Millipore #07-449) antibodies were added to the sonicated chromatin and incubated at 4°C overnight. Previously washed 10 μl of protein A magnetic beads (Invitrogen #88846) were added and incubated for additional 2 hours at 4°C. Immunoprecipitated complexes were washed three times with RIPA buffer and twice with TE (10 mM Tris pH 8.0/1 mM EDTA) buffer. Following transfer into new 1.5 ml collection tube, genomic DNA was eluted for 2 hours at 68 °C in 100 µl Complete Elution Buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 µg/ml proteinase K), and combined with a second elution of 100 µl Elution Buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl) for 10 min at 68 °C. ChIPed DNA was purified by MinElute Purification Kit (Qiagen #28006) and eluted in 12 µl elution buffer. Chip-Seq libraries was constructed using Rubicon Genomics ThruPLEX® DNA-seq Kit

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
13998436
Reads aligned (%)
104.0
Duplicates removed (%)
39.0
Number of peaks
28459 (qval < 1E-05)

hg38

Number of total reads
13998436
Reads aligned (%)
105.8
Duplicates removed (%)
38.4
Number of peaks
28559 (qval < 1E-05)

Base call quality data from DBCLS SRA