|
| Status |
Public on Feb 18, 2022 |
| Title |
sma-6-1_S1 |
| Sample type |
SRA |
| |
|
| Source name |
C. elegans whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L2 larval stage
tissue: whole animal
genotype: sma-6
|
| Growth protocol |
Worms were grown on standard NGM plates and fed with E. coli bacteria at 20 degrees celsius
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with TRIZOL
RNA was poly-A selected using oligo dT magnetic beads, fragmented and library prepared using TruSeq stranded kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sma-6-1
|
| Data processing |
Fastq files generated by bcl2fastq with adapter trimming
Map R1 to WBcel235 as single-end using STAR v2.5.2b
Assign uniquely-mapping read-pairs to transcript exons and splice-junctions using Featurecounts v1.5.2
Filter out genes not accruing 10 reads in at least 1 library
Call differentially expressed genes using Limma Voom with TMM normalization
Genome_build: WBcel235
Supplementary_files_format_and_content: Sma_mutants_Protein_Coding_Only.csv; comma-separated values format; contains Degust-generated gene-count matrix for samples and Limma-voom estimates for expression levels and significance
|
| |
|
| Submission date |
May 21, 2020 |
| Last update date |
Feb 18, 2022 |
| Contact name |
Stuart Kenneth Archer |
| Organization name |
Monash University
|
| Department |
Monash Bioinformatics Platform
|
| Street address |
15 Innovation Walk, Monash University
|
| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE151035 |
Gene expression profile of sma-3 mutant Caenorhabditis elegans |
|
| Relations |
| BioSample |
SAMN14996073 |
| SRA |
SRX8379843 |
