Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Kidney
Cell type
RPTEC
Tissue
epithelium
Description
renal proximal tubule epithelial cells

Attributes by original data submitter

Sample

source_name
normal primary renal proximal tubule epithelial cells
histone
H3K4me3
chip antibody
H3K4me3 (07-473, Millipore)
source
PCS-400 (ATCC PCS-400-010)

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). 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
24595472
Reads aligned (%)
94.6
Duplicates removed (%)
44.5
Number of peaks
34720 (qval < 1E-05)

hg19

Number of total reads
24595472
Reads aligned (%)
94.2
Duplicates removed (%)
44.9
Number of peaks
34541 (qval < 1E-05)

Base call quality data from DBCLS SRA