|
| Status |
Public on Mar 15, 2024 |
| Title |
L4_CK1441;CK1943-1 |
| Sample type |
SRA |
| |
|
| Source name |
whole body lysate
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole body lysate
Stage: L4
|
| Growth protocol |
C. elegans worms were grown on NGM agar plates at 20°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from L2 and L4 snap-frozen C. elegans pellets using TRIzol Reagent (Thermo Fisher Scientific, Inc.) per manufacturer’s protocol. RNA was resuspended in 50 µL sterile water and concentration was assessed using NanoPhotometer® NP80 spectrophotometer (Implen GmbH).
1000ng of RNA isolated from age synchronized L2 and L4 C. elegans was used for RNA sequencing library prep using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina) as per manufacturer’s protocol. RNA libraries from each sample were individually barcoded and pooled in batches of 16 stage-matched samples (L2 or L4 stage). Library quality was assessed using a Bioanalyzer (Agilent 2100) prior to sequencing
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing was outsourced to University of Washington Northwest Genomics Center. Samples were sequenced with a target sequencing depth of 50-60 million reads per sample using NovaSeq S2 platform (Illumina) to generate 150bp paired end reads. NWGC provided us with paired .fastq files separated by each barcoded sample with the illumina adaptors trimmed.
paired .fastq files were aligned to the Caenorhabditis elegans.WBcel235 transcriptome using RNA-Star (default parameters) on Galaxy to produce sample .bam and .bai files
For differential expression analysis, reads were mapped and counted using salmon (default settings). Resulting files were imported and analyzed using DESeq2 on Galaxy.
Assembly: Ensemble C elegans genome WBcel235
Supplementary files format and content: .sf (salmon) transcript quantification
|
| |
|
| Submission date |
Dec 05, 2023 |
| Last update date |
Mar 15, 2024 |
| Contact name |
Nicole Liachko |
| E-mail(s) |
nliachko@uw.edu
|
| Organization name |
VA Puget Sound Health Care System
|
| Department |
GRECC
|
| Street address |
1660 Columbian Way S.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98108 |
| Country |
USA |
| |
|
| Platform ID |
GPL26672 |
| Series (1) |
| GSE249339 |
Transcriptomic evaluation of tau and TDP-43 synergism shows tauopathy predominates. |
|
| Relations |
| BioSample |
SAMN38658660 |
| SRA |
SRX22754737 |
