|
| Status |
Public on Jan 25, 2023 |
| Title |
N2 8 days after return to ground Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
group: 8 days after return to ground
tissue: whole organism
strain: N2
developmental stage: Mixed stage
|
| Growth protocol |
After bleaching the adult worms, L1 worms were cultured in ground conditions in CeHR medium for three weeks. Then, the worms were exposed to clinostat-simulated microgravity for four days and the maintained impacts were observed at four, eight, and twelve days after placing the worms back to ground conditions All animals were grown at room temperature.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from mixed stage C. elegans were isolated with a modified TRIzol protocol and recovered by alcohol precipitation. Total RNA was further purified by PureLink ™ RNA Mini Kit (Life Technologies).
Two micrograms of total RNA were used for library preparations using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RGC8
|
| Data processing |
Quality control was implemented on the raw sequence data with FASTQC software (version 0.11.2).
The raw reads were mapped to the reference genome (WBCel235), obtained from Ensembl along with the annotation file, by using TopHat.
The Tuxedo pipeline was employed to find differential gene expressions with default parameters.
Genome_build: WBCel235
Supplementary_files_format_and_content: format: cuffdiff; output: fold changes for the gene expressions among the conditions
|
| |
|
| Submission date |
Nov 04, 2018 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Irem Celen |
| E-mail(s) |
irem@udel.edu
|
| Organization name |
University of Delaware
|
| Street address |
15 Innovation Way
|
| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19711 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE122125 |
Comparative Transcriptomic Signature of the Simulated Microgravity Response in C. elegans |
|
| Relations |
| BioSample |
SAMN10372225 |
| SRA |
SRX4975906 |
