Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Others
Cell type
Urothelial cell carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
FFPE urothelial cell carcinoma
tissue type
bladder
biopsy year
2010
storage years
9
sample collection
full section
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
FFPE blocks were histologically examined and accordingly sectioned, macrodissected or cored. Samples were deparaffinized, rehydrated and homogenized by heating at 65C in 1% SDS detergent buffer overnight. Next samples were sonicated and solubilized chromatin was immunoprecipitated following a low-input protocol. Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) or SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA Inc), amplified for 14 cycles.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
35613674
Reads aligned (%)
65.2
Duplicates removed (%)
20.5
Number of peaks
2435 (qval < 1E-05)

hg19

Number of total reads
35613674
Reads aligned (%)
62.7
Duplicates removed (%)
22.9
Number of peaks
1238 (qval < 1E-05)

Base call quality data from DBCLS SRA