Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCB1

Cell type

Cell type Class
Gonad
Cell type
RMG-I
Primary Tissue
Ovary
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
RMG1 cell line, ARID1A CRISPR
cell line
RMG1
arid1a
KO
factor
SNF5
chip antibody
rabbit anti-SNF5 (Bethyl, cat. no. A301-087A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. The reaction was quenched by 0.125 M glycine for 5 min. Fixed cells were lysated with ChIP lysis buffer 1 (50 mM HEPES-KOH, pH7.5, 140 mM NaCl, 1 mM EDTA, pH8.0, 1% Triton X-100, 0.1% DOC) on ice and lysis buffer 2 (10 mM Tris pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) at room temperature. Chromatin was digested with MNase (Cell Signaling) in digestion buffer (10 mM Tris 8.0, 1 mM CaCl2, 0.2% Triton X-100) at 37°C for 15 min. The nucleus was broken down by one pulse of bioruptor with high output. Chromatin were incubated overnight at 4°C and protein A+G Dynabeads were added to the reaction for another 1.5 hour. Magnetic beads were washed and chromatin was eluted. Eluted DNA was treated with proteinase K at 55°C for 45 min and decrosslinked at 65°C overnight. Zymo ChIP DNA clean and concentrator kit (zymo, cat. no. D5205) was used to purify the ChIP DNA 10 ng ChIP DNA was used for library construction. NEBNext Ultra DNA Library Prep Kit (NEB, E7645) was used to prepare sequencing library

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
36560578
Reads aligned (%)
89.7
Duplicates removed (%)
5.4
Number of peaks
669 (qval < 1E-05)

hg38

Number of total reads
36560578
Reads aligned (%)
91.7
Duplicates removed (%)
4.0
Number of peaks
864 (qval < 1E-05)

Base call quality data from DBCLS SRA