|
Status |
Public on Feb 18, 2022 |
Title |
N2_L2_2_S11 |
Sample type |
SRA |
|
|
Source name |
C. elegans whole animal
|
Organism |
Caenorhabditis elegans |
Characteristics |
developmental stage: L2 larval stage tissue: whole animal genotype: WT
|
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 |
N2_2
|
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 |
SAMN14996067 |
SRA |
SRX8379834 |