Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Kidney
Cell type
Nephrectomy sample
NA
NA

Attributes by original data submitter

Sample

source_name
Nephrectomy sample
tissue
kidney
tissue type
uninvolved kidney
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to ActiveMotif instructions; ChIP and input DNAs were prepared at ActiveMotif (Carlsbad, CA) by converting overhangs into phosphorylated blunt ends, the addition of an adenine to the 3’ ends, and the addition of Illumina adaptors. The library was size-selected (175-225 base pairs [bp]) and amplified for 18 cycles.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
41734531
Reads aligned (%)
98.9
Duplicates removed (%)
19.7
Number of peaks
1159 (qval < 1E-05)

hg19

Number of total reads
41734531
Reads aligned (%)
98.1
Duplicates removed (%)
20.9
Number of peaks
1306 (qval < 1E-05)

Base call quality data from DBCLS SRA