|
| Status |
Public on Mar 27, 2023 |
| Title |
whole animal, 25 degrees, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole animal
genotype: lin-15(n765ts); Is[ttx-1p::EGFP::rpl1a + lin-15(+)]
treatment: 25 degrees celsius overnight
|
| Treatment protocol |
At the L4 stage, animals were shifted to either 15 or 25 degrees celsius overnight (~16 hours) and then collected (flash frozen) as adults.
|
| Growth protocol |
Animals were synchronized by bleaching then plated as L1s on HB101 bacteria and grown at 20 degrees celsius to the L4 stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
AFD-specific RNA was obtained using Translating Ribosome Affinity Purification. Briefly, frozen worms samples were lysed by grinding. The lysates were either used in an anti-EGFP ribosome immunoprecipitation followed by Trizol extraction (AFD samples) or RNA was extracted directly from lysates using Trizol (whole animal samples). 10 ng of RNA was used for library construction.
Libraries were generated using the Smart-Seq v4 Ultra Low Input RNA kit followed by Nextera XT DNA Library Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
total RNA
whole_25_2
|
| Data processing |
Cutadapt 1.12, quality cutoff=20, minimum length=50
Mapping with STAR with GeneCounts option. Reference genome was WBcel235/ce11.
Assembly: WBcel235/ce11
Supplementary files format and content: tab-delimited text files include raw per gene read counts for each sample
|
| |
|
| Submission date |
Jan 05, 2023 |
| Last update date |
Mar 27, 2023 |
| Contact name |
Nathan Harris |
| E-mail(s) |
nathanharris@brandeis.edu
|
| Organization name |
Brandeis University
|
| Street address |
415 South Street
|
| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
02454 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE222226 |
Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity |
|
| Relations |
| BioSample |
SAMN32600510 |
| SRA |
SRX18943662 |
