|
| Status |
Public on Oct 01, 2021 |
| Title |
wt_4 |
| Sample type |
SRA |
| |
|
| Source name |
intestine
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: wild-type
age: 5 days old
sample id: 8695
|
| Growth protocol |
worms were bleached onto OP50-seeded NGM plates and grown for 5 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
worms were placed in M9 and 20 intestines per sample were dissected out and flash frozen in 1mL Qiazol. Total RNA was extracted using the miRNeasy Micro kit (Qiagen) according to manufacturer’s protocol.
Smart-seq2 was used for the generation of non-strand-specific, full transcript sequencing libraries using standard reagents and procedures as previously described (Picelli et al, 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Libraries were quantified using the Qubit hs dsDNA assay and library fragment size distribution was determined using the D1000 assay on a Tapestation 4200 system (Agilent).
Samples were pooled and clustered at 1.4pM on a NextSeq500 system (Illumina) to generate ~10M single end reads per sample using High Output v2.5 chemistry.
Sequencing data was demultiplexed using bcl2fastq2 v2.20 and pseudo aligned to Caenorhabditis elegans.
WBcel235.98 transcriptome using kallisto v.0.44.0.
Data analysis was performed using Shiny-Seq.
Genome_build: WBcel235.98
Supplementary_files_format_and_content: abundance measurements for each sample and a matrix table integrating all replicates across three different strains
|
| |
|
| Submission date |
Mar 08, 2021 |
| Last update date |
Oct 01, 2021 |
| Contact name |
Daniele Bano |
| Organization name |
DZNE
|
| Street address |
Sigmund-Freud-Strasse 27
|
| City |
Bonn |
| ZIP/Postal code |
53127 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19757 |
| Series (2) |
| GSE168501 |
CEST-2.2 stimulates lipid metabolism and promotes longevity in mitochondrial mutant animals (RNA-Seq) |
| GSE168502 |
CEST-2.2 stimulates lipid metabolism and promotes longevity in mitochondrial mutant animals |
|
| Relations |
| BioSample |
SAMN18210908 |
| SRA |
SRX10274899 |
