NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6071597 Query DataSets for GSM6071597
Status Public on May 01, 2022
Title RNAseq.stg16.YAPd 1
Sample type SRA
 
Source name Whole embryos
Organism Oryzias latipes
Characteristics developmental stage: Stg 16
tag: yap-/- yap1b-/-
tissue: whole embryos
Growth protocol Medaka embryos were raised in E3 medium at 28ºC.
Extracted molecule total RNA
Extraction protocol RNA and gDNA fractions from stage 16 medaka embryos were extracted using TRIzol (Ambion). Possible DNA contamination was eliminated treating the RNA samples with TURBO DNAse-free (Ambion). Each embryo was genotyped using its DNA fraction following a previously published approach (Vázquez-Marín et al., 2019). RNA from embryos with the same genotype were pooled together in up to four replicates and sent to sequence (Illumina Hiseq 2500).
cDNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Raw reads were pre-processed using Trimmomatic (HEADCROP:12 MINLEN:50 AVGQUAL:20)
Potential rRNA contaminating sequences were removed using Sortmerna.
Reads were mapped against the latest medaka genome assembly (ASM223467) using Hisat2.
Reads with low quality scores (-q 60) were filtered out using samtools.
Reads per gene were count using Htseq-count (GTF file from Ensembl version 99).
Subsequent analysis was performed using DEBrowser v1.14.2 (RowMeans < 10). Data was normalized using the RLE method and batch effects were removed using ComBat. Differential gene expression was carried out using DESeq2).
Assembly: ASM223467 (Oryzias latipes)
Supplementary files format and content: Tab-limited TXT files showing unnormalized counts for each gene, genotype and replicate. BW files containing read coordinated for each sample and replicate (mapped against the OryLat2 genome build)
 
Submission date Apr 28, 2022
Last update date May 01, 2022
Contact name Javier Vázquez-Marín
E-mail(s) jvazmar89@gmail.com, javier.vazquez@cos.uni-heidelberg.de
Organization name Heidelberg University
Department Centre for Organismal Studies (COS)
Street address Im Neuenheimer Feld 230, 5th floor
City Heidelberg
State/province Baden-Württemberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL23308
Series (1)
GSE201791 A Yap-dependent transcriptional program directs cell migration for embryo axis assembly
Relations
BioSample SAMN27934743
SRA SRX15039554

Supplementary file Size Download File type/resource
GSM6071597_YAPd_R1_RNAseq.bw 75.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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