|
| Status |
Public on Oct 30, 2021 |
| Title |
F12O1, liver, RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Xenopus tropicalis |
| Characteristics |
common name: tropical clawed frog
generation and f0-treatment: F1 generation control
Sex: female
|
| Treatment protocol |
F0 generation exposure from the tadpole to the mature adult stage at a concentration (50 ng.L-1). Females from F1 and F2 generation were not exposed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each biological replicate, the RNAqueous®-4PCR Kit (Ambion, Austin USA) was used to extract the total RNA from 15 mg of liver according to manufacturer instructions
RNA-seq libraries were prepared using the TruSeq Stranded mRNA sample Prep kit (Illumina, San Diego, USA) and sequenced on an Illumina GAIIx sequencer as 75 bp reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Reads were filtered based on their length, pairing, and quality using Trimmomatic (v0.32.1)
Cleaned reads were mapped to the Xenopus genome (10.0 assembly) using HISAT2.
The Cufflinks (v0.0.7) tool was applied to HISAT2 alignments to enumerate the number of short reads overlapping the Ensembl annotated genes, for each library
The Cuffmerge (v0.0.6) toll was used to merge transcriptome
Cuffdiff (v0.0.7) toll was used for differential gene expression analysis. Control mRNAseq data have been have been deposited on NCBI Gene Expression Omnibus (GEO) (accession no GSE150911).
Supplementary_files_format_and_content: Cuffdiff file.txt
|
| |
|
| Submission date |
Jul 01, 2021 |
| Last update date |
Oct 30, 2021 |
| Contact name |
Stéphane REYNAUD |
| E-mail(s) |
stephane.reynaud@univ-grenoble-alpes.fr
|
| Phone |
04 76 51 46 80
|
| Organization name |
Grenoble-Alpes University
|
| Lab |
Laboratory of alpine ecology
|
| Street address |
2233 rue de la piscine
|
| City |
Saint Martin d'Hères |
| ZIP/Postal code |
38400 |
| Country |
France |
| |
|
| Platform ID |
GPL24898 |
| Series (1) |
| GSE179257 |
Using RNAseq for identifying hepatic genes involved in multi- (F1 generation) and transgenerational (F2 generation) responses to chronic benzo[a]pyrene (BaP) and triclosan (TCS) mixture exposure (F0 generation) in Xenopus tropicalis. |
|
| Relations |
| Reanalysis of |
GSM4560793 |
| BioSample |
SAMN19987918 |
| SRA |
SRX11326463 |
