|
| Status |
Public on Oct 17, 2020 |
| Title |
F1 Fe2O3 rep1 GW2 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Paracentrotus lividus |
| Characteristics |
time post fertilization: 24h
tissue: embryo
|
| Treatment protocol |
Sea urchin fertilized eggs were exposed for 24h to Fe2O3 (5.0 10-5M, [Fe]=4mg/L) and ZnO ENPs (10-5M, [Zn]=0,8mg/L) or the equivalent metal concentration of corresponding ions Fe3+ (FeCl3, 6H2O) or Zn2+ (ZnSO4, 7H2O).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos (about 6000) were harvested 24h p.f., briefly centrifuged and the pellet was suspended in 200 µl Thioglycerol/homogeneization solution. RNA was extracted with Maxwell 16 LEV simply RNA kit (Promega) in Maxwell 16 instrument. Purified total RNA were collected in 50 µL RNase-free water and kept afterwards at -80°C. RNA integrity (RIN>9) was estimated with a Bioanalyzer.
RNA libraries were prepared for sequencing by Genewiz LLC (www.genewiz.com) using standard Illumina protocols and via poly A selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
GW2-Sample 3
|
| Data processing |
adapters were removed with trim_galore version 0.4.0 using standard parameters
the reads were assembled with Drap version 1.7 to produce the contigs file
the reads were aligned on the contigs using bwa mem version 0.7.12-r1039 with standard parameters and the bam files were sorted, compressed and indexed with samtools version 1.3.1 using standard parameters
the expression was quantified using samtools idxstats and merged in the expression file using unix command lines
Genome_build: de novo reference transcriptome. FASTA file with transcript sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample
|
| |
|
| Submission date |
Nov 21, 2019 |
| Last update date |
Oct 17, 2020 |
| Contact name |
Anne-M Marie GENEVIERE |
| Organization name |
CNRS
|
| Department |
BIOM
|
| Lab |
Observatoire Océanaologique Banyuls
|
| Street address |
Avenue Pierre Fabre
|
| City |
Banyuls-sur-mer |
| ZIP/Postal code |
66650 |
| Country |
France |
| |
|
| Platform ID |
GPL27788 |
| Series (1) |
| GSE140784 |
The sea urchin larval response to metaloxide nanoparticule exposure |
|
| Relations |
| BioSample |
SAMN13343787 |
| SRA |
SRX7198259 |
