|
| Status |
Public on Feb 07, 2024 |
| Title |
DMSO_1_S1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole organism
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole organism
pair (batch): 1
treatment: DMSO
|
| Treatment protocol |
24-hour exposure to either DMSO alone (0.1%) or DEET dissolved in DMSO (0.1M)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples of 1,000 col-121 worms each following 24-hour exposure to either DMSO alone (0.1%) or DEET dissolved in DMSO (0.1M) were collected in 500 ml of Trizol (Invitrogen) and prepared using the Direct-zol RNA miniprep kit (Zymo Research) by following the manufacturer’s instructions. Four independent biological repeats per condition were used for Illumina NextSeq High 2x38 using Kapa mRNA HyperPrep kit (Roche).
RNA libraries for RNA-seq were prepared using Kapa mRNA HyperPrep kit (Roche).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
raw_counts.csv
tpm_counts.csv
|
| Data processing |
Sequenced reads were assessed for low-quality sequence, then mapped against the WBcel235 transcriptome where reads were quantified at the transcript level using Salmon
Transcript-level abundance estimates from Salmon were collapsed to gene-leve estimates and converted to raw count values using the R Bioconductor package tximport
Differentially expressed genes were identified using the R Bioconductor package DESeq2
Assembly: Wormbase assembly WBcel235, Annotation Version WS272
Supplementary files format and content: comma separated file of raw count matrix where columns correspond to samples and rows correspond to genes;
Supplementary files format and content: comma separated file of transcript per million counts where columns correspond to samples and rows correspond to genes
|
| |
|
| Submission date |
Sep 07, 2023 |
| Last update date |
Feb 07, 2024 |
| Contact name |
VICTOR BARRERA BURGOS |
| Organization name |
Harvard School of Public Health
|
| Department |
Biostatistics
|
| Lab |
Bioinformatics Core
|
| Street address |
Landmark 401 Park Drive 3 East
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE242682 |
Altered gene expression linked to germline dysfunction following exposure to environmentally relevant level of DEET |
|
| Relations |
| BioSample |
SAMN37319481 |
| SRA |
SRX21666791 |
