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Sample GSM2326153 Query DataSets for GSM2326153
Status Public on Dec 31, 2017
Title Scale E11 input
Sample type SRA
Source name tarsometatarsal skin, E11, input
Organism Gallus gallus
Characteristics breed: White Leghorn
tissue: tarsometatarsal skin
developmental stage: H&H 37 (E11)
chip antibody: none
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
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
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
BioSample SAMN05806348
SRA SRX2186322

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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