Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCB1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
SAH
cell type
induced pluripotent stem cell line
cell line
SAH
genotype
wild type
chip antibody
SMARCB1/BAF47 (Cell Signaling Tech., 91735S (D8M1X), lot: 1)
time
day 0

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. All ChIP-seq was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. RNA was collected in biological duplicate using the RNeasy Mini Kit (QIAGEN). All RNA was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. ATAC-seq libraries were prepared in biological replicates using standard protocol (Buenrostro et al., Current Protocols (2013)) with 12 cycles of amplification. ATAC-seq samples were sequenced on Nex-seq 500 using 37 bp, 37 bp pair-end sequencing parameters. ChIP-sequencing libraries were prepared with Illumina's NEBNext Ultra II DNA library Prep Kit using standard protocols. RNA-seq libraries were prepared with Illumina's TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
24026964
Reads aligned (%)
85.1
Duplicates removed (%)
11.4
Number of peaks
12310 (qval < 1E-05)

hg38

Number of total reads
24026964
Reads aligned (%)
86.0
Duplicates removed (%)
10.9
Number of peaks
12385 (qval < 1E-05)

Base call quality data from DBCLS SRA