|
| Status |
Public on Dec 31, 2017 |
| Title |
Scale E9 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
tarsometatarsal skin, E9, H3K27ac ChIP
|
| Organism |
Gallus gallus |
| Characteristics |
breed: White Leghorn
tissue: tarsometatarsal skin
developmental stage: H&H 35 (E9)
chip antibody: H3K27ac (Abcam ab4729)
|
| Treatment protocol |
Untreated
|
| Growth protocol |
Fertilized eggs.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP; see the supplementary file 'Chip_protocol_Chuong_lab.pdf'.
NEBNext® Ultra™ DNA Library Prep Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
This GEO Sample represents 2 replicates.
|
| Data processing |
Alignment of reads (Bowtie2, UCSC galGal4) was done in Partek Flow.
Only unique reads are used for peak calling.
MACS was used for peak calling.
The replicates of each sample group are combined to perform peak calling.
BigWig files were generated using deepTools.
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: BigWig files
|
| |
|
| Submission date |
Sep 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ping Wu |
| E-mail(s) |
pingwu@usc.edu
|
| Phone |
6264979629
|
| Organization name |
University of Southern California
|
| Department |
Pathology
|
| Street address |
2011 Zonal Ave HMR313A
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL16133 |
| Series (2) |
| GSE87248 |
ChIP-seq for embryonic chicken feather and scale samples |
| GSE87250 |
Multiple regulatory modules are required for scale-to-feather conversion |
|
| Relations |
| BioSample |
SAMN05806343 |
| SRA |
SRX2186319 |
