|
| Status |
Public on Nov 21, 2018 |
| Title |
WT_9 |
| Sample type |
SRA |
| |
|
| Source name |
Whole worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole worm
developmental stage: prefertile young adult
sequencing batch: 2
|
| Growth protocol |
NGM plates, 20 degrees Celsius, OP50 bacteria
|
| Extracted molecule |
total RNA |
| Extraction protocol |
See Schaar et al. 2015 PLoS Genetics for RNA isolation protocol
Sequencing libraries were prepared using the Kapa Biosystems stranded mRNA-Seq kit for the Illumina platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Libraries were sequenced using 1x75 bp sequencing on the Illumina NextSeq 500 platform at the Van Andel Research Institute. Data were demultplexed using bcl2fastq v 2.18.
Read quality was assessed using FASTQC v. 0.11.5 and aligned first to the E. coli K-12 genome to assess contamination, then one-pass aligned to WBcel235 C. elegans genome using STAR v. 2.5.2b with default parameters and --outReadsUnmapped None. The STAR genome index was generated with the corresponding Ensembl WBcel235 build 89 GTF annotations integrated.
Transcript abundances were quantified using the --quantMode GeneCounts option enabled during alignment. Differential gene expression analysis was performed using the quasi-likelihood framework in edgeR package v. 3.20.1 in R v. 3.4.1. The model used for DGE accounts for sequencing batch and genotype and is as follows: design <- model.matrix(~seqbatch + genotype). Gene names, gene IDs, and predicted function annotations were downloaded using the biomaRt package v. 2.34.0.
Filtered CPM were filtered keeping genes that had CPM > 2 in at least 3 samples. Raw CPM are unfiltered.
Genome_build: WBcel235
Supplementary_files_format_and_content: Text file containing filtered gene counts per million matrix (CPM) from all samples.
|
| |
|
| Submission date |
Feb 22, 2018 |
| Last update date |
Jul 12, 2021 |
| Contact name |
Jeremy Michael Van Raamsdonk |
| Organization name |
McGill University
|
| Department |
Neurology and Neurosurgery
|
| Street address |
1001 Decarie Boulevard
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H4A3J1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE110984 |
Role of mitochondrial unfolded protein response transcription fatcor ATFS-1 in lifespan of long-lived mitochondrial mutants |
|
| Relations |
| BioSample |
SAMN08580400 |
| SRA |
SRX3733477 |
