Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Kidney
Cell type
G-401
Primary Tissue
Kidney
Tissue Diagnosis
Wilms' tumor

Attributes by original data submitter

Sample

source_name
ChIP-seq_G401_Dox
cell line
G401
cell type
kidney rhabdoid tumor derived cell line
treatment/condition
Doxycycline induced SMARCB1 reexpresion
chip antibody
H3K4me3 (Millipore, 07-473)

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

hg38

Number of total reads
25477708
Reads aligned (%)
98.0
Duplicates removed (%)
12.7
Number of peaks
28184 (qval < 1E-05)

hg19

Number of total reads
25477708
Reads aligned (%)
97.5
Duplicates removed (%)
13.1
Number of peaks
28209 (qval < 1E-05)

Base call quality data from DBCLS SRA