Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

Cell type Class
Kidney
Cell type
TTC-1240
NA
NA

Attributes by original data submitter

Sample

source_name
TTC1240 (MRT)
agent
DMSO
cell line
TTC1240
chip antibody
Abcam (EPNCIR111A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was performed using standard protocols (Millipore, Billerica, MA). Specifically, cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 10min at 37C and quenched with 125mM glycine for 5min at 37C. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. ChIP-sequencing libraries were prepared with the Rubicon Thruplex DNAseq prep kit using standard protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
32074909
Reads aligned (%)
52.1
Duplicates removed (%)
38.0
Number of peaks
4666 (qval < 1E-05)

hg38

Number of total reads
32074909
Reads aligned (%)
53.7
Duplicates removed (%)
36.7
Number of peaks
4368 (qval < 1E-05)

Base call quality data from DBCLS SRA