Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Blood
Cell type
CD34+
NA
NA

Attributes by original data submitter

Sample

source_name
CD34 Culture
individual
Don001
gender
female
cell type
Erythroid
target
CTCF
chip antibody
MP 07-729

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde (Sigma) by the addition of 1 ml 10x crosslinking buffer (50 mM HEPES, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 10 % formaldehyde) to 10E7 cells in 9 ml of media and incubation at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS before snap freezing pelleted cells. Fixed material was stored at -80 ºC for less than 12 months. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 10E7 cells were lysed by incubation on ice with 130 µl lysis buffer for 15 minutes. Lysed cells were transferred to Covaris microtubes and sonicated on the Covaris S220 (Duty cycle: 2 %, Intensity: 3, Cycles per burst: 200, Power mode: Frequency sweeping, Duration: 480 sec, Temp.: 6 ºC) to generate 200-400 bp fragments. Insoluble material was removed by centrifugation (15,000 rcf, 15 min, 4 ºC) and soluble material was diluted to 4 ml with dilution buffer. Immunoprecipitation was performed by incubation of 2 ml diluted chromatin (equivalent to 5x10E6 input cells) with antibodies for Gata-1 (7 µg ab11852, lot: GR290167-7; AbCam), H3K4me3 (1 µl 07-473, lot: 2664283; Millipore), H3K27ac (0.3 µg ab4729, lot: GR3205523-1; AbCam), or CTCF (10 µl 07-729, lot: 2836929; Millipore) overnight. Chromatin binding to Protein A/agarose slurry, washes and elution were performed according to the manufacturer's instructions. DNA was purified by phenol-chloroform extraction with PhaseLock tubes (5Prime) and ethanol precipitation with NaOAc, and 2 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
71267787
Reads aligned (%)
177.9
Duplicates removed (%)
6.0
Number of peaks
51412 (qval < 1E-05)

hg38

Number of total reads
71267787
Reads aligned (%)
179.8
Duplicates removed (%)
5.8
Number of peaks
51209 (qval < 1E-05)

Base call quality data from DBCLS SRA