|
| Status |
Public on Jan 27, 2023 |
| Title |
5_Amnios_1x |
| Sample type |
SRA |
| |
|
| Source name |
Brain tissue
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: Brain tissue
treatment: Mixture 1x-treated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNAqueous-microkit from Thermofisher. Libraries are made from 50 ng of total RNA based on Qubit assays.
The transcriptome libraries were prepared from total RNA using Illumina TruSeq Stranded mRNA Sample Preparation kits (Illumina Inc., USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were first cleaned by removing PCR bias conserving one copy per cluster of duplicated reads (python script).
Then, reads were trimmed for the first 11 and last 1 nucleotides (fastx-trimmer from fastx-toolkit version 0.0.13.2) to remove adapter remnants. Reads 64bp long were specifically selected (cutadapt version 1.15). The global quality of the reads was checked using the FastQC (version 0.11.2).
Bowtie2 (v2.2.4) was used to map the clean reads against the Xenopus laevis genome (release 9.2) downloaded from XenBase (https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/, accessed on 19 January 2023) only conserving uniquely mapped reads.
Reads were counted on gene annotations was accomplished by HTSeq-count (v0.9.1) in union mode.
Assembly: Xenbase: https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/, accessed on 19 January 2023)
Supplementary files format and content: tab-delimited text files included raw read counts
|
| |
|
| Submission date |
Jan 26, 2023 |
| Last update date |
Jan 27, 2023 |
| Contact name |
Evelyne Duvernois-Berthet |
| E-mail(s) |
evelyne.duvernois@mnhn.fr
|
| Organization name |
Museum national d'Histoire naturelle
|
| Department |
AVIV
|
| Lab |
UMR7221
|
| Street address |
43 rue Cuvier
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL21248 |
| Series (1) |
| GSE223829 |
A mixture of chemicals found in human amniotic fluid disrupts brain gene expression and behavior in Xenopus laevis |
|
| Relations |
| BioSample |
SAMN32934458 |
| SRA |
SRX19194109 |
