Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCC1

Cell type

Cell type Class
Liver
Cell type
MRT TTC549
Tissue
liver
Lineage
missing
Description
Malignant Hepatic Rhabdoid tumor line

Attributes by original data submitter

Sample

source_name
ChIP-seq_TTC549_Dox
cell line
TTC549
cell type
liver rhabdoid tumor derived cell line
treatment/condition
Doxycycline induced SMARCB1 reexpresion
chip antibody
SMARCC1/BAF155 (Santa Cruz, R-8, sc-9746)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Cat.# IP-202-1012)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
24217011
Reads aligned (%)
93.3
Duplicates removed (%)
5.3
Number of peaks
9853 (qval < 1E-05)

hg38

Number of total reads
24217011
Reads aligned (%)
94.9
Duplicates removed (%)
4.2
Number of peaks
9675 (qval < 1E-05)

Base call quality data from DBCLS SRA