|
| Status |
Public on Feb 04, 2020 |
| Title |
Sample_I17_48h_50mG_E8 |
| Sample type |
SRA |
| |
|
| Source name |
entire embryos
|
| Organism |
Danio rerio |
| Characteristics |
tissue: entire embryos
genetic background: AB
developmental stage: 48h
irradiation batch: I17
dose rate in mgy/h: 50mG
|
| Treatment protocol |
External continuous irradiation to gamma radiation (137Cs) at 0.5mGy/h, 5mGy/h 50mGy/h or non-exposed controls
|
| Growth protocol |
Zebrafish eggs were collected just after fertlization and grown in 9mm Petri dishes with embryo medium (60mg/L Instant Ocean, 0.01 % (w/v) of methylene blue). Eggs were grown in Panasonic incubator (MIRE) at 28°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction with trizol no DNaseI treatment, followed by two rounds of mRNA extraction with illumina magnetic Beads
Stranded mRNAseq v2 Illumina with dual UDT indexes
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Exposed
|
| Data processing |
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.4.2
Mapping with 2PASS STAR v020201 against GRCz11 zebrafish reference genome and Ensembl v95 exon-exon junctions
Quantification and normalization with Desq2 v1.22.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw reads in fastq
Supplementary_files_format_and_content: Read count files from RNAstar
|
| |
|
| Submission date |
Jul 22, 2019 |
| Last update date |
Feb 04, 2020 |
| Contact name |
olivier ARMANT |
| E-mail(s) |
olivier.armant@irsn.fr
|
| Organization name |
IRSN
|
| Department |
SERIS
|
| Lab |
LECO
|
| Street address |
Cadarache BP3
|
| City |
Saint Paul lez Durance |
| ZIP/Postal code |
13115 |
| Country |
France |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE134634 |
A system biology approach reveals neuronal and muscles developmental defects after chronic exposure to ionising radiation |
|
| Relations |
| BioSample |
SAMN12335433 |
| SRA |
SRX6486158 |
