 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 26, 2023 |
| Title |
worms_7day_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole body
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole body
age: 7 days
sexe: NA
feeding: AL
genotype: N2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TruSeq stranded total RNA (Illumina) protocol
RNeasy mini Kit and Trizol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
worms_7day_rep3
Replicate 3
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic version 0.33 ILLUMINACLIP:(TruSeq3-PE.fa:2:30:10 or TruSeq3-SE.fa:2:30:10) LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:45 then mapped using STAR version 2.5.1b ‘--outFilterType BySJout --outWigNorm None
Isoform abundancy estimated using Kallisto version 0.42.5
Differential gene expression obtained using DESeq2 version 1.8.2 with RUVr normalization on gene counts obtained by summing kallisto isoform abundancy
Genome_build: hg19,rn5,mm10,dm6,ce10
Supplementary_files_format_and_content: tab-delimited text files with gene counts and differential expression analysis for each contrast
|
| |
|
| Submission date |
Aug 11, 2017 |
| Last update date |
Jan 26, 2023 |
| Contact name |
Antonios Papadakis |
| E-mail(s) |
apapada1@uni-koeln.de
|
| Phone |
01724565854
|
| Organization name |
CECAD
|
| Street address |
Fürvelser Str. 15
|
| City |
Köln |
| ZIP/Postal code |
51069 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE102537 |
Ageing-associated changes in transcription and splicing efficiency influence longevity |
|
| Relations |
| BioSample |
SAMN07498576 |
| SRA |
SRX3088140 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
