NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4546563 Query DataSets for GSM4546563
Status Public on Jun 16, 2020
Title st32-2_RNA
Sample type SRA
 
Source name whole embryo
Organism Oryzias latipes
Characteristics strain: Hd-rR
tissue: embryo
developmental stages: stage32
Extracted molecule total RNA
Extraction protocol RNA extraction using both TRIzol and Qiagen RNeasy Micro Kit
Illumina TruSeq stranded mRNA library preparation protocol for RNA-seq samples
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description Illumina TruSeq stranded RNA-seq
Data processing for TPM.tab file: genome mapping using hisat2(2.1.0), default parameters
for TPM.tab file: gene expression quantification using stringtie(v1.3.3b), default parameters
for fasta file: gene model built from pacbio data and generate transcript sequance
Genome_build: medaka ASM223467v1
Supplementary_files_format_and_content: Two TPM.tab files are plain text(quantification count matrix by TPM, rows are genes and columns are samples), fasta file is transcript sequence use for quantification.
 
Submission date May 11, 2020
Last update date Jun 16, 2020
Contact name Qiang Tu
E-mail(s) qtu@genetics.ac.cn
Organization name Institute of Genetics and Developmental Biology
Street address No.1 West Beichen Road,Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL25587
Series (1)
GSE136018 Transcriptome profiling of medaka timecourse embryonic samples and adult tissues samples.
Relations
BioSample SAMN14891101
SRA SRX8325514

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