Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H1
NA
NA

Attributes by original data submitter

Sample

source_name
BAF47-targeting shRNA D2
cell line
H1 hESCs (WA01)
cell type
human embryonic stem cells
genotype/variation
BAF47-targeting shRNA
treatment
none
molecule subtype
T5-tagmented DNA

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were collected in Gentle Cell Disociation Reagent (StemCell Technologies) and resuspended in cold PBS to 1e6 cells /ml Cells were subjected to the ATACseq protocol as described by Buenrostro, et al. 2015, with the following parameters (Buenrostro et al., 2015). Buffer: CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100). Transposase volume/25 µl cell suspension: 5 µl.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
106678260
Reads aligned (%)
61.8
Duplicates removed (%)
22.7
Number of peaks
77683 (qval < 1E-05)

hg19

Number of total reads
106678260
Reads aligned (%)
61.6
Duplicates removed (%)
22.8
Number of peaks
77381 (qval < 1E-05)

Base call quality data from DBCLS SRA