Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Others
Cell type
Bladder cancer
NA
NA

Attributes by original data submitter

Sample

source_name
Primary bladder cancer
tissue
FFPE
antibody
H3K4me3 (Diagenode C15410003)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIPseq:ThruPLEX-FD kits (Rubicon Genomics) was used and 75 bp single-end reads were sequenced on a NextSeq 500 instrument (Illumina). For RNAseq: TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
72698373
Reads aligned (%)
83.5
Duplicates removed (%)
39.9
Number of peaks
9220 (qval < 1E-05)

hg19

Number of total reads
72698373
Reads aligned (%)
83.1
Duplicates removed (%)
40.7
Number of peaks
8930 (qval < 1E-05)

Base call quality data from DBCLS SRA