|
| Status |
Public on Jan 17, 2018 |
| Title |
Ctcf_NP_ChIP-Seq_1 |
| Sample type |
SRA |
| |
|
| Source name |
nephron progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: CFW
developing stage: E16.5
antibody: CTCF (D31H2) XP® Rabbit mAb
|
| 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 NextSeq 500 |
| |
|
| Description |
genotype: wild-type
|
| 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: mm10
Supplementary_files_format_and_content: txt files containing peak coordinates; BigWig files containing UCSC genome browser visualization tracks
|
| |
|
| Submission date |
Nov 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew P McMahon |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE90016 |
Mapping of transcription factor binding sites in mouse nephron progenitor cells |
| GSE90017 |
Transcriptional and cistromic profiling of mouse nephron progenitor cells |
|
| Relations |
| BioSample |
SAMN08106041 |
| SRA |
SRX3427396 |
