Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCC1

Cell type

Cell type Class
Neural
Cell type
SK-N-MC
Primary Tissue
Brain
Site of Extraction
Brain
Tissue Diagnosis
neuroepithelioma

Attributes by original data submitter

Sample

source_name
SKNMC
chip antibody
aa924-1004; C-terminus)
source_type
cell line

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment. ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
75003930
Reads aligned (%)
35.8
Duplicates removed (%)
61.7
Number of peaks
1339 (qval < 1E-05)

hg38

Number of total reads
75003930
Reads aligned (%)
37.5
Duplicates removed (%)
60.3
Number of peaks
1348 (qval < 1E-05)

Base call quality data from DBCLS SRA