|
| Status |
Public on Jan 31, 2016 |
| Title |
input_mDNA_new2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic kidney
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: 16.5 days
strain: Swiss Webster
chip antibody: NA
|
| 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 NextSeq 500 |
| |
|
| 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 |
| 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) |
| GSE73865 |
Genome-wide map of SIX2 and SIX1 binding in human embryonic kidney cortex |
| GSE73867 |
Nephron endowment |
|
| Relations |
| BioSample |
SAMN04156952 |
| SRA |
SRX1318638 |
