|
| 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 |
