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Sample GSM4294430 Query DataSets for GSM4294430
Status Public on Feb 04, 2021
Title AF_35W rep3
Sample type SRA
 
Source name abdominal fat_35 weeks
Organism Cairina moschata
Characteristics common name: Muscovy duck
age: 35 weeks
tissue: abdominal fat
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 2-A3_GTGAAA_L004
AF3_35W_FPKM
Data processing Raw data (raw reads) were processed using fastx(version:0.0.13). The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using tophat(version:2.0.9).
FPKM value of each gene was calculated using cufflinks(version:2.1.1).
and the read counts of each gene were obtained.
DEGs were identified using the cufflinks Cuffdiff functions FoldChange and Fisher-test.
Genome_build: Anas_platyrhynchos.BGI_duck_1.0
Supplementary_files_format_and_content: FPKM values for each Sample with gene_id @ http://asia.ensembl.org/index.html
 
Submission date Feb 04, 2020
Last update date Feb 04, 2021
Contact name Xingyong Chen
Organization name Anhui Agricultural University
Department College of Animal Science and Technology
Street address 130 Changjiangxilu
City Hefei
State/province Anhui
ZIP/Postal code 230036
Country China
 
Platform ID GPL28113
Series (1)
GSE144727 Abdominal fat mRNA transcriptome of Muscovy duck
Relations
BioSample SAMN13978982
SRA SRX7670058

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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