Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Kidney
Cell type
HKC8
NA
NA

Attributes by original data submitter

Sample

source_name
human kidney proximal tubule cells (HKC8 cells)
cells
HKC8 cells
antibodies
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HKC8 cell were collected when it reached to 80% confluence. Media were changed before fixing the cells to remove the dead cells. Cells were cross-linked with formaldehyde in a final concentration of 1% for 10 mins at room temperature. A final concentration of 0.125M glycine was used in room temperature for 10 minutes to stop the reaction. Cells were scraped with ice cold PBS containing protease inhibitor. The chromatin immunoprecipitation procedure was done with Invitrogen MAGnify™ Chromatin immunoprecipitation System following the manufacturer's protocols. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Illumina). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
66778297
Reads aligned (%)
57.8
Duplicates removed (%)
6.6
Number of peaks
1357 (qval < 1E-05)

hg19

Number of total reads
66778297
Reads aligned (%)
56.9
Duplicates removed (%)
7.1
Number of peaks
962 (qval < 1E-05)

Base call quality data from DBCLS SRA