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Status |
Public on Dec 31, 2017 |
Title |
Feather dorsal E9 input |
Sample type |
SRA |
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Source name |
dorsal skin, E9, input
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Organism |
Gallus gallus |
Characteristics |
breed: White Leghorn tissue: dorsal skin developmental stage: H&H 35 (E9) chip antibody: none
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Treatment protocol |
Untreated
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Growth protocol |
Fertilized eggs.
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Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP; see the supplementary file 'Chip_protocol_Chuong_lab.pdf'. NEBNext® Ultra™ DNA Library Prep Kit.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Sep 22, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Ping Wu |
E-mail(s) |
pingwu@usc.edu
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Phone |
6264979629
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Organization name |
University of Southern California
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Department |
Pathology
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Street address |
2011 Zonal Ave HMR313A
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City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90033 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN05806344 |
SRA |
SRX2186318 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data not applicable for this record |
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