NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2875481 Query DataSets for GSM2875481
Status Public on May 21, 2018
Title A234T5_BC
Sample type SRA
 
Source name Blastodermal cells
Organism Gallus gallus
Characteristics breed: JA57
tissue: Blastodermal cells
developmental stage: fresh fertilized eggs
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
E-mail(s) shaupinglin@ntu.edu.tw
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
Relations
BioSample SAMN08129762
SRA SRX3442479

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap