Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Others
Cell type
5637
Primary Tissue
Bladder
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
5637 bladder cancer cell line
cell type
bladder cancer cell line 5637
chip antibody
H3K27ac (Abcam, catalog# ab4729, lot# GR132150-1)

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
34099807
Reads aligned (%)
99.2
Duplicates removed (%)
5.8
Number of peaks
52185 (qval < 1E-05)

hg19

Number of total reads
34099807
Reads aligned (%)
99.0
Duplicates removed (%)
6.0
Number of peaks
52411 (qval < 1E-05)

Base call quality data from DBCLS SRA