|
| Status |
Public on Feb 26, 2024 |
| Title |
wild type young adult experiment 1rep3 |
| Sample type |
SRA |
| |
|
| Source name |
wild type
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: sKM222
cell line: N2
cell type: young adult
tissue: wild type
cell line: wild type
cell type: hermaphrodite
genotype: whole animal
|
| Growth protocol |
Nematode culture was performed on NGM plates seeded with OP50. Worms were maintained at 20°C except where otherwise noted. Embryo samples were harvested by hypochlorite treatment. For L4 and young adult samples, L1s were hatched overnight in M9 supplemented with cholesterol, then grown on NGM with OP50 for 48h at 20°C (for L4s) or for 44h at 25°C (for young adults).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were snap frozen, then resuspended in Trizol and vortexed for 15 minutes at room temperature. Thereafter, total RNA was purified according to the Trizol manufacturer’s instructions (ThermoFisher).
TruSeq Stranded Total RNA Library Prep kit (Total RNA sequencing) - prepped by Psomagen
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
TruSeq Stranded Total RNA Library Prep kit (Total RNA sequencing) - prepped by Psomagen
|
| Data processing |
Low quality bases and adaptors were trimmed from sequence reads using Cutadapt v2.7 with parameters “–q 20 -minimum-length 25” (122). Resulting reads were mapped to WS277 using HISAT2 v2.1.0 with default parameters (127). Aligned reads were counted using subread featureCounts v1.6.4 with default parameters, except that “-s” option was used to specify appropriate strands (128). Differential expression analysis was done with DESeq2 v1.22.1 (ref4) in v3.5.1 R version (126).
Assembly: WS277
Supplementary files format and content: feature counts for annotated transcripts
|
| |
|
| Submission date |
Feb 23, 2024 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Katherine McJunkin |
| E-mail(s) |
mcjunkin@nih.gov
|
| Phone |
3048811944
|
| Organization name |
National Institutes of Health
|
| Street address |
50 South Drive, Building 50 Room 3148
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL26672 |
| Series (1) |
| GSE256488 |
Catalytic residues of microRNA Argonautes play a modest role in microRNA star strand destabilization in C. elegans |
|
| Relations |
| BioSample |
SAMN32677661 |
| SRA |
SRX19003386 |
