Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Others
Cell type
Bladder micropapillary carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
FFPE micropapillary carcinoma
tissue type
bladder
biopsy year
2010
storage years
9
sample collection
cores
chip antibody
H3K27Ac (Diagenode, cat. no. C15410196, lot no. A1723-0041D)

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
51613279
Reads aligned (%)
76.6
Duplicates removed (%)
43.0
Number of peaks
17716 (qval < 1E-05)

hg19

Number of total reads
51613279
Reads aligned (%)
76.0
Duplicates removed (%)
43.7
Number of peaks
17380 (qval < 1E-05)

Base call quality data from DBCLS SRA