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Sample GSM2875477 Query DataSets for GSM2875477
Status Public on May 21, 2018
Title A234T1_E11G
Sample type SRA
Source name E11 male gonads
Organism Gallus gallus
Characteristics breed: JA57
tissue: Male gonads
developmental stage: E11
Growth protocol Fertilized eggs incubated at 37oC at 60% humidity to desired date
Extracted molecule total RNA
Extraction protocol Total RNA samples are extracted via TRIzol reagent according to according to manufacturers’ instructions.
Strand-specific library was constructed following Illumina TruSeq stranded total RNA sample preparation kit according to manufacture's instruction
Library strategy ssRNA-seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description strand-specific
Data processing Adapter trimmed RNAs are aligned to gga5 genome assembly using tophat2, with options: -G galGal5.refseq.gtf --library-type fr-firststrand
Reference guided sequence assembly on RNA-seq samples using Cufflinks (v2.2.1), with options: --GTF-guide galGal5.refseq.gtf --frag-bias-correct galGal5.fa --multi-read-correct --library-type fr-firststrand --max-mle-iterations 500 --no-effective-length-correction --min-isoform-fraction 0.4 --pre-mrna-fraction 0.4 --min-frags-per-transfrag 100 --min-intron-length 20 --max-multiread-fraction 0.3 --3-overhang-tolerance 0 --intron-overhang-tolerance 0
Cuffmerge assemble the Cufflinks results of each RNA-seq samples, with option: --min-isoform-fraction 0.7
Cuffnorm for gene and novel transcript expression calculation on the RNA-seq samples, with reference to Cuffmerge results, with options: --library-type fr-firststrand
Supplementary_files_format_and_content: Cuffnorm normalized transcript expressions, for RNA-seq samples
Submission date Dec 04, 2017
Last update date May 15, 2019
Contact name Shau-Ping Lin
Organization name National Taiwan University
Department Institute of Biotechnology
Street address No. 81, Chang-Xing St.
City Taipei City
ZIP/Postal code 10672
Country Taiwan
Platform ID GPL16133
Series (1)
GSE98005 Oxidation treated small RNA-seq for studying roles of chicken piRNAs in germ cell development
BioSample SAMN08129760
SRA SRX3442475

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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