Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SIX1

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 embryonic kidney cortex
developmental stage
16 weeks
strain
NA
chip antibody
SIX1 antibidy (Cell Signaling; 12891S)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cortex of human embryonic kidneys were micro-dissected and fixed in crosslinking buffer containing 1% PFA for 30 min, then homogenized, followed by chromatin extraction and sonication. Sonicated chromatin was then immuno-precipitated with the indicated antibodies. The precipitated DNA was subsequently collected with Qiagen PCR product purification kit. Mouse embryonic kidneys were processed in a similar way. Libraries were constructed using ThruPLEX-FD Prep Kit (Rubicon Genomics), and subsequently sequenced by Illumina HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
26053066
Reads aligned (%)
84.1
Duplicates removed (%)
13.2
Number of peaks
1007 (qval < 1E-05)

hg38

Number of total reads
26053066
Reads aligned (%)
85.5
Duplicates removed (%)
12.4
Number of peaks
886 (qval < 1E-05)

Base call quality data from DBCLS SRA