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Sample GSM1904605 Query DataSets for GSM1904605
Status Public on Jan 31, 2016
Title mSix2_ChIPSeq
Sample type SRA
Source name mouse embryonic kidney
Organism Mus musculus
Characteristics developmental stage: 16.5 days
strain: Swiss Webster
chip antibody: Six2 antibody (Proteintech,11562-1-AP)
Treatment protocol NA
Growth protocol NA
Extracted molecule genomic DNA
Extraction 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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing 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
Genome_build: hg19/mm9
Supplementary_files_format_and_content: wiggle files represents ChIP-Seq tags; peak files
Submission date Oct 08, 2015
Last update date May 15, 2019
Contact name Andrew P McMahon
Phone 323-442-7847
Organization name University of Southern California
Department Stem Cell Biol & Regen Med
Lab Andrew McMahon
Street address 1425 San Pablo St, BCC 312
City Los Angeles
State/province California
ZIP/Postal code 90033
Country USA
Platform ID GPL13112
Series (2)
GSE73865 Genome-wide map of SIX2 and SIX1 binding in human embryonic kidney cortex
GSE73867 Nephron endowment
BioSample SAMN04156941
SRA SRX1318627

Supplementary file Size Download File type/resource
GSM1904605_mSix2_ChIPSeq_chr1.wig.gz 97.8 Mb (ftp)(http) WIG
GSM1904605_mSix2_ChIPSeq_chr12.wig.gz 59.6 Mb (ftp)(http) WIG
GSM1904605_mSix2_ChIPSeq_chr17.wig.gz 50.3 Mb (ftp)(http) WIG
GSM1904605_mSix2_ChIPSeq_fe60.bed.gz 108.8 Kb (ftp)(http) BED
GSM1904605_mSix2_ChIPSeq_fe60.humanized.bed.gz 81.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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