|
| Status |
Public on Aug 30, 2017 |
| Title |
isp-1_3 |
| Sample type |
SRA |
| |
|
| Source name |
isp-1 mutant_whole worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: isp-1 mutant
developmental stage: prefertile young adult
pooling: none
tissue: whole worm
|
| 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 2.17.1.14.
Read quality was assessed using FASTQC v. 0.11.3 and aligned first to the E. coli K-12 genome to assess contamination, then aligned to the WBcel235 C. elegans genome assembly using Subread v. 1.5.0 with default parameters.
Transcript abundances were quantified using featureCounts v. 1.4.6 with strand specific read counting.
Differential gene expression analysis was performed using the edgeR package v. 3.14.0 in R v. 3.3.0.
Genome_build: WBcel235
Supplementary_files_format_and_content: Text file containing raw counts per million matrix (CPM) from WT, isp-1, isp-1;sod-3, and isp-1;sod-5 samples.
|
| |
|
| Submission date |
Feb 23, 2017 |
| 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) |
| GSE95240 |
RNA-sequencing of C.elegans isp-1 mutant and superoxide dismutase-isp-1 double mutants |
|
| Relations |
| BioSample |
SAMN06434208 |
| SRA |
SRX2583501 |
