 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 03, 2024 |
| Title |
Medaka_SEDL Knockout #1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Oryzias latipes |
| Characteristics |
developmental stage: Stage 40
tissue: embryo
gender: not determined
|
| Growth protocol |
The Cab-strain of medaka fish (Oryzias latipes) was maintained as described in Avellino et al., 2013. Embryos were staged according to the method proposed by Iwamatsu (Iwamatsu, 2004). All studies on fish were conducted in strict accordance with the institutional guidelines for animal research and approved by the Italian Ministry of Health; Department of Public Health, Animal Health, Nutrition and Food Safety in accordance to the law on animal experimentation (D.Lgs. 26/2014). Furthermore, all animal treatments were reviewed and approved in advance by the Ethics Committee at the TIGEM Institute, (Pozzuoli (NA), Italy).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was quantified and mixed at 10ng/µl
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq500 (Illumina) with a read length of 100 bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Transcriptome profile of a wild type 40 Oryzias latipes (Medaka) embryo KO for SEDL, biological rep1
|
| Data processing |
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
|
| |
|
| Submission date |
Jan 13, 2020 |
| Last update date |
May 05, 2024 |
| Contact name |
Rossella De Cegli |
| E-mail(s) |
decegli@tigem.it
|
| Phone |
08119230692
|
| Organization name |
Tigem
|
| Street address |
Via Campi Flegrei 34
|
| City |
Pozzuoli |
| ZIP/Postal code |
80078 |
| Country |
Italy |
| |
|
| Platform ID |
GPL27992 |
| Series (2) |
| GSE143538 |
Transcriptome profile of Stage 40 Oryzias latipes (Medaka) embryos |
| GSE143540 |
Transcriptome profile of wildtype and SEDL knockdown Medaka embryos and Human ARPE-19 cells |
|
| Relations |
| BioSample |
SAMN13836629 |
| SRA |
SRX7546944 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4261604_S263_20190517143845_5_unique_counts.txt.gz |
72.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
