Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Others
Cell type
J82
Primary Tissue
Bladder
Tissue Diagnosis
Carcinoma Transitional Cell

Attributes by original data submitter

Sample

source_name
J82 bladder cancer cell line
cell type
bladder cancer cell line J82
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin lysates were isolated from sonicated nuclei (from a 10-cm plate containing 1-2 x 106 cells) and histone-DNA interactions were extracted using an antibody against H3K27ac Libraries were prepared at Global Biologics (Missouri) using the Illumina ChIP-seq kit, beginning with 20-30ng of pooled DNA sample (from replicates). Barcodes were used to multiplex the sequencing run and the barcodes used were the following: CGATGT, TGACCA, ACAGTG, GCCAAT, CAGATC, CTTGTA. Libraries were sequenced on the HiSeq2000 according to the manufacturer's protocols at the University of Delaware

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
28960844
Reads aligned (%)
93.4
Duplicates removed (%)
3.8
Number of peaks
1057 (qval < 1E-05)

hg19

Number of total reads
28960844
Reads aligned (%)
92.6
Duplicates removed (%)
5.1
Number of peaks
1012 (qval < 1E-05)

Base call quality data from DBCLS SRA