Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SIX2

Cell type

Cell type Class
Kidney
Cell type
Kidney Cortex
MeSH Description
The outer zone of the KIDNEY, beneath the capsule, consisting of KIDNEY GLOMERULUS; KIDNEY TUBULES, DISTAL; and KIDNEY TUBULES, PROXIMAL.

Attributes by original data submitter

Sample

source_name
Human kidney ChIP SIX2-16wk
genotype
wild type
tissue
renal cortex
age
16 weeks 2 days
Stage
Fetal 17wk
Sex
unknown
pooled sample
no

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Human fetal kidney tissue was microdissected to remove the cortex and incubated for 30 minutes at room temperature in crosslink buffer. Crosslinking was stopped by the addition of glycine. Tissue was washed with PBS containing protease inhibitors, homogenized, pelleted, and lysed in ChIP lysis buffer with the aid of a B dounce homogenizer. Processing of the samples from this point was carried forward using the mouse ChIP protocol (see Park et al, 2012; PMID: 22902740 for experimental conditions and buffer components). Sequencing libraries were made using the ThruPLEX-FD Prep Kit (Rubicon Genomics) according to manufacturer’s instructions. In brief 10-50ng of DNA was end repaired, A-tailed and ligated with adapters, amplified with indexing reagents, and DNA libraries purified using Ampure magnetic beads. Libraries were submitted to the USC Epigenome Center for sequencing on the Illumina HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
35525754
Reads aligned (%)
92.3
Duplicates removed (%)
4.4
Number of peaks
14791 (qval < 1E-05)

hg38

Number of total reads
35525754
Reads aligned (%)
94.1
Duplicates removed (%)
3.4
Number of peaks
14890 (qval < 1E-05)

Base call quality data from DBCLS SRA