Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Kidney
Cell type
Renal cell carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
Patient x750 ccRCC Tumor Tissue
chip antibody
H3K27me3 (Active Motif, 39155)
tissue
Clear cell renal cell carcinoma tumor

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Flash-frozen minced tissue was thawed in cell culture medium (Gibco® Keratinocyte-SFM (1X) Catalog #17005-042) with 1% formaldehyde for 10 minutes under rotation for cross-linking, which was then quenched with 2M Glycine (final concentration of 100mM). Minced tissue was then washed twice with ice-cold PBS with Protease Inhibitor Cocktail (PIC) and resuspended in 1mL ChIP Lysis Buffer (1% SDS, 50mM Tris HCl pH 8.1, 10mM EDTA) with PIC. The suspension was ground in a dounce homogenizer 10-15 times and then passed through a 40µM filter and checked for lysis with Trypan Blue under a microscope. The nuclei were then sonicated using a probe sonicator (Branson Sonifier® Cell Disruptor 185, 4.5 Output Control, 12 cycles, 10 seconds ON/30 seconds OFF) and centrifuged at 12,000rpm for 10 minutes at 4°C. Libraries were constructed using the KAPA DNA library preparation kit (KK8230)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
36532878
Reads aligned (%)
96.0
Duplicates removed (%)
5.0
Number of peaks
1112 (qval < 1E-05)

hg19

Number of total reads
36532878
Reads aligned (%)
95.3
Duplicates removed (%)
6.4
Number of peaks
1143 (qval < 1E-05)

Base call quality data from DBCLS SRA