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Sample GSM2897996 Query DataSets for GSM2897996
Status Public on Jan 17, 2018
Title E16.5_Six2+_ATAC_Seq_2
Sample type SRA
 
Source name developing kidneys
Organism Mus musculus
Characteristics strain: CFW
developmental stage: E16.5
cell type: Six2+
genotype: genotype: Six2TGC/+
Treatment protocol NA
Growth protocol NA
Extracted molecule genomic DNA
Extraction protocol ATAC-Seq (Buenrostro et al, 2013)
ATAC-Seq (Buenrostro et al, 2013)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Fastq files were aligned using Bowtie2
ATAC-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; BigWig files were generated using Wig2BigWig published by UCSC genome browser
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing peak coordinates; BigWig files containing UCSC genome browser visualization tracks
 
Submission date Dec 22, 2017
Last update date Jan 24, 2018
Contact name Andrew P McMahon
E-mail(s) amcmahon@med.usc.edu
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 GPL19057
Series (2)
GSE90017 Transcriptional and cistromic profiling of mouse nephron progenitor cells
GSE108424 Mapping open chromatin in mouse nephron progenitor cells
Relations
BioSample SAMN08225844
SRA SRX3504243

Supplementary file Size Download File type/resource
GSM2897996_E16.5_Six2+_ATAC_Seq_2.peak.txt.gz 375.6 Kb (ftp)(http) TXT
GSM2897996_E16.5_Six2+_ATAC_Seq_2_normalized.bw 2.6 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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