|
| Status |
Public on Jan 17, 2018 |
| Title |
Six2-BF_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
developing kidneys
|
| Organism |
Mus musculus |
| Characteristics |
strain: CFW
developing stage: E16.5
antibody: FLAG (Sigma, #F1804)
genotype: Six2DE-Six2BF
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen MinElute PCR Purification kit (#28004)
Rubicon ThruPlex genomic DNA library kit (#R400429)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Fastq files were aligned using Novoalign
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; BigWig files were generated using Wig2BigWig published by UCSC genome browser
Genome_build: mm9
Supplementary_files_format_and_content: txt files containing peak coordinates; BigWig files containing UCSC genome browser visualization tracks
|
| |
|
| Submission date |
Nov 17, 2016 |
| Last update date |
May 15, 2019 |
| 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 |
GPL13112 |
| Series (2) |
| GSE90016 |
Mapping of transcription factor binding sites in mouse nephron progenitor cells |
| GSE90017 |
Transcriptional and cistromic profiling of mouse nephron progenitor cells |
|
| Relations |
| BioSample |
SAMN06034609 |
| SRA |
SRX2357484 |
