Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ATF4

Cell type

Cell type Class
Blood
Cell type
HUDEP-2
NA
NA

Attributes by original data submitter

Sample

source_name
HUDEP2-ATF4
cell line
HUDEP2
tissue
Immortalized Human Erythroid Progenitor
cell type
Erythroid cells
differentiation
Undifferentiated
chip antibody
ATF4 (Cell Signaling Technology, 11815S, lot 4)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight. Libraries were prepared using TruSeq ChIP-seq Sample Preparation Kit (Part# IP-202-1012) according to Illumina's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
34607618
Reads aligned (%)
78.3
Duplicates removed (%)
17.7
Number of peaks
2351 (qval < 1E-05)

hg38

Number of total reads
34607618
Reads aligned (%)
81.0
Duplicates removed (%)
15.6
Number of peaks
2737 (qval < 1E-05)

Base call quality data from DBCLS SRA