|
| Status |
Public on May 01, 2022 |
| Title |
RNAseq.stg16.WT 4 |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryos
|
| Organism |
Oryzias latipes |
| Characteristics |
developmental stage: Stg 16
tag: wild type
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 |
SAMN27934756 |
| SRA |
SRX15039550 |
