|
| Status |
Public on Apr 21, 2025 |
| Title |
ZMC-Vab3A-5-2 |
| Sample type |
SRA |
| |
|
| Source name |
whole worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole worm
strain: N2
Sex: hermaphrodite
age: 5 days
treatment: RNAi Vab3 isof A/N2
|
| Treatment protocol |
Synchronized young adult worms were treated with empty vector (L4440), vab-3a and vab-3c RNAis and collected at 5 days of adulthood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol–chloroform (isoamyl pH4) extraction method (Phenol:Chloroform:Iso-amyl alcohol (125:24:1), Sigma).
Libraries were prepared using the TruSeq RNA library preparation kit v2 (Illumina) following the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence information was converted to FASTQ format using bcl2fastq v1.8.4
FastQ files were mapped using Tophat v.2.1.0 (parameters: -x 1 --no-coverage-search --no-convert-bam --no-novel-juncs --no-novel-indels -T –transcriptome-index=$TRANSCRIPTOME_INDEX $REFERENCE_DNA_TOPLEVEL)
Counting of reads per gene was done using featureCounts: v1.5.0 (parameters: -s 0 -a $ANNOTATION)
RPKMs were calculated based on the gene length given by featureCounts.
Assembly: Ensembl (WBcel235.85)
Supplementary files format and content: Excel sheet (xlsx) containing counts, RPMs and RPKMs
|
| |
|
| Submission date |
Apr 21, 2022 |
| Last update date |
Apr 21, 2025 |
| Contact name |
Marco Groth |
| E-mail(s) |
cfngs@leibniz-fli.de
|
| Organization name |
Leibniz Institute on Aging - FLI
|
| Department |
Core Facility - Next Generation Sequencing
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| ZIP/Postal code |
07747 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE201211 |
Gene expression analysis after RNAi treatment of different isoforms of vab-3 in C.elegans |
|
| Relations |
| BioSample |
SAMN27714279 |
| SRA |
SRX14949420 |
