Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Kidney
Cell type
Renal cell carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
ccRCC cell line
histone
Input
chip antibody
none
source
Non-targeting control (Dharmacon, D-001810-01)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
One million cells were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Cells were washed 3 times with TBSE buffer. Pelleted cells were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). Sonicated DNA was normalized for each pair of cells with and without wildtype VHL before immuno-precipitation. The total volume of immunoprecipitation was 1 ml and the amount of antibody used was 2 µg. The input DNA was precleared with protein G Dynabeads (Life Technologies) for 1 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 3 times with cold wash buffer. Whole-genome-amplification was performed on ChIP DNA and input using the WGA4 kit (Sigma-Aldrich). The amplified DNA was used with NEBNext ChIP-Seq library prep reagent set.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
28835104
Reads aligned (%)
90.9
Duplicates removed (%)
19.7
Number of peaks
1357 (qval < 1E-05)

hg19

Number of total reads
28835104
Reads aligned (%)
90.1
Duplicates removed (%)
20.3
Number of peaks
1206 (qval < 1E-05)

Base call quality data from DBCLS SRA