|Public on Jan 31, 2016
|human embryonic kidney cortex
|developmental stage: 17 weeks
chip antibody: H3K27ac antibody (Abcam, ab4729)
|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.
|Illumina HiSeq 2000
|Base call by bcl2fastq v. 2.17
Fastq files were aligned using Novoalign. Human data was aligned to hg19, and mouse data was aligned to mm9.
ChIP-Seq peaks were called using QuEST (Valouev et al., 2008).
peak files were generated by extracting the chromosome numbers coordinates and QuEST enrichment score from QuEST.out files
wig profiles were generated using QuEST
Supplementary_files_format_and_content: wiggle files represents ChIP-Seq tags; peak files
|Oct 08, 2015
|Last update date
|May 15, 2019
|Andrew P McMahon
|University of Southern California
|Stem Cell Biol & Regen Med
|1425 San Pablo St, BCC 312
|Genome-wide map of SIX2 and SIX1 binding in human embryonic kidney cortex