|
| Status |
Public on Jun 20, 2017 |
| Title |
m_2dps_2 |
| Sample type |
SRA |
| |
|
| Source name |
Ventricle
|
| Organism |
Oryzias latipes |
| Characteristics |
hours/days after injury: 2d
operation: sham operation
|
| Treatment protocol |
WT zebrafish (AB strain) and medaka (Cab strain) from 6-9 month old with similar body size were anethesized and operated (untouched, sham operation, or cryoinjurd) as previously described (Gonzalez-Rosa et al., 2011, Chablais et al., 2011, Schnabel et al., 2011). Fish were recovered after operation, and lived until specified time points of sample collection.
|
| Growth protocol |
Zebrafish were raised and handled in compliance with local animal welfare legislation and maintained according to standard protocols (zfin.org). All animals were maintained at 28 °C in a re-circulating system and fish at >6 months of age were used in the experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, RNA was isolated from medaka and zebrafish ventricles using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer).
500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read quality trimming with Trimmomatic version 0.33 (java -jar trimmomatic-0.33.jar PE ... LEADING:3 TRAILING:3 SLIDINGWINDOW:5:15 CROP:500 MINLEN:30)
Mapping of reads versus zebrafish genome assembly 10 (Danio rerio GRCz10) and medaka assembly 1 (Oryzias latipes MEDAKA1) using STAR 2.4.0a (--outFilterMismatchNoverLmax 0.1)
Read counting per gene with featureCounts 1.4.5-p1 from the Subread package using default parameters
Raw gene counts for both organisms were joined to a common matrix based on gene homology (BioMart) resulting in 15292 genes
The common matrix of gene counts was normalized with DESeq
Genome_build: Danio rerio GRCz10, Oryzias latipes MEDAKA1
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all homologous genes
|
| |
|
| Submission date |
Feb 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shih-Lei Ben Lai |
| E-mail(s) |
ben.s.lai@gmail.com
|
| Organization name |
Max Planck Institute for Heart and Lung Research
|
| Department |
Developmental Genetics
|
| Lab |
Stainier lab
|
| Street address |
Ludwigstraße 43
|
| City |
Bad Nauheim |
| State/province |
Hessen |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23039 |
| Series (1) |
| GSE94617 |
Comparative transcriptome profiling of zebrafish and medaka hearts following cardiac cryoinjury |
|
| Relations |
| BioSample |
SAMN06309956 |
| SRA |
SRX2542715 |
