|
| Status |
Public on Jul 20, 2019 |
| Title |
M1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Xenopus tropicalis |
| Characteristics |
common name: tropical clawed frog
treatment: exposed to mixture
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each biological replicate, total RNA was extracted from 15 mg of liver using the RNAqueous®-4PCR Kit (Ambion, USA), according to the manufacturer's instructions. Total RNA quality and quantity were controlled on an Agilent 2100 Bioanalyzer (Agilent, USA). RNA-seq libraries were prepared using the TruSeq Stranded mRNA sample Prep kit (Illumina) and sequenced on an Illumina GAIIx sequencer as 75 bp reads by Hybrigenics-Helixio (Clermont-Ferrand, France).
TruSeq Stranded mRNA sample Prep kit
|
| |
|
| 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 (JGI4.2 assembly) with Ensembl annotations (release 79) using Bowtie-0.12.7 / TopHat 2 (v0.6) software (81) (http://tophat.cbcb.umd.edu) (with a maximum intron size of 250,000 bp to discover novel junctions between exons).
The Cufflinks (v0.0.7) tool was applied to TopHat alignments to enumerate the number of short reads overlapping the Ensembl annotated genes, for each library
Genome_build: (JGI4.2 assembly)
Supplementary_files_format_and_content: GTF file from cufflink including gene ID, gene name and FPKM valuesfor gene expression
|
| |
|
| Submission date |
Jul 19, 2019 |
| Last update date |
Jul 20, 2019 |
| 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) |
| GSE134545 |
Using RNAseq for identifying hepatic genes involved in the response to chronic endocrine disruptor exposure in Xenopus tropicalis. |
|
| Relations |
| BioSample |
SAMEA19978168 |
| SRA |
ERX1817560 |
