Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

Cell type Class
Lung
Cell type
HS-SY-II
Primary Tissue
Lung
Tissue Diagnosis
Sarcoma Synovial

Attributes by original data submitter

Sample

source_name
HA tagged HS-SY-II cell line
cell line/type
Human Synovial sarcoma cells (HS-SY-II)
genotype/variation
HA tagged HS-SY-II cell line
condition/shrna
REN. 713
chip antibody
BRG1 (Abcam, Ab110641)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For HA-tag, BRG1 and KDM2B ChIP 60-100 million cells were collected, pre-fixed with ethylene glycol bis(succinimidyl succinate) (EGS) for 30 min, and crosllinked with 1% formaldehyde for 15 min. For H3K27me3 ChIP about 10-20 million cells were crosslinkined with 1% formaldehyde for 15 min. Libraries were constructed using NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina accordingly with manufactor instructions. 6-10 samples were pooled per sequencing lane in order to generate 20-40 million reads per sample

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
11318104
Reads aligned (%)
98.1
Duplicates removed (%)
0.2
Number of peaks
1362 (qval < 1E-05)

hg38

Number of total reads
11318104
Reads aligned (%)
98.5
Duplicates removed (%)
0.1
Number of peaks
1299 (qval < 1E-05)

Base call quality data from DBCLS SRA