Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Kidney
Cell type
UM-RC-6
Primary Tissue
Kidney
Tissue Diagnosis
Carcinoma Renal Cell

Attributes by original data submitter

Sample

source_name
UMRC6, WT
cell line
UMRC6
antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation was performed using the SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003) following the instructions of the manufacturer. 20 μg of chromatin was incubated overnight with 5 μl H2Aub antibody (Cell Signaling Technology, 8240). 100 ng fly chromatin and 0.5 μg H2Av antibody (ActiveMotif, 61686) was added in each tube as spike-in control. Purified ChIP-DNA was verified by agarose gel to make sure properly fragmented and sent to Sequencing and Microarray Facility at MD Anderson Cancer Center for ChIP-seq. ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
37378268
Reads aligned (%)
98.0
Duplicates removed (%)
2.8
Number of peaks
901 (qval < 1E-05)

hg19

Number of total reads
37378268
Reads aligned (%)
97.2
Duplicates removed (%)
4.2
Number of peaks
853 (qval < 1E-05)

Base call quality data from DBCLS SRA