|
| Status |
Public on Sep 01, 2016 |
| Title |
Pancreas-inputDNA |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: pancreas
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with Ptf1a antibodies.
Standard Illumina ChIP-seq
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq reads were aligned by using bowtie -v --best -p -q
Peaks were called using HOMER with the following setting: Enrichment Fold (4), Poisson, pValue = 1e-4 .
Peaks of replicates were merged by using SAMTOOLS intersectBed command with default setup (at least 1 bp overlap between 2 peaks)
Genes associated with peaks were defined by using GREAT
Genome_build: mm9
Supplementary_files_format_and_content: .txt Bedtool output of merged peak coordinates.
|
| |
|
| Submission date |
Aug 31, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Galvin Swift |
| E-mail(s) |
galvin.swift@utsouthwestern.edu
|
| Organization name |
U TX Southwestern Medical Center
|
| Department |
Molecular Biology
|
| Lab |
Ray MacDonald
|
| Street address |
6000 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9148 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE86262 |
Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation and Homeostasis by PTF1A [ChIP-Seq] |
| GSE86263 |
Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation and Homeostasis by PTF1A |
|
| Relations |
| BioSample |
SAMN05717686 |
| SRA |
SRX2069640 |
