|
| Status |
Public on Jun 17, 2019 |
| Title |
N2_empty vector_cadmium_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
N2_empty vector_cadmium, whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
treatment: 300um Cadmium (12h)
genotype: wildtype
tissue: whole animal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using the RNAqueous Total RNA Isolation Kit
Standard Illumina protocols with oligo-dT beads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
emptyvector_control&cadmium
EC_4
|
| Data processing |
HISAT2 2.1.0-beta used for mapping to the C. elegans reference genome
HTSeq V0.6.1 used for Quantification
rMATS 3.0.8 used for Alternative Splicing analysis
cufflinks 2.1.1 used for novel gene prediction.
DEGSeq 1.12.0 used for differential expression analysis
Genome_build: WS220
Supplementary_files_format_and_content: Processed data files (in Excel format) include readcounts, differential gene expression and alternative splicing for each file.
The data are exported with the standard rMATS format:
IC refers to number of reads mapped to the exon inclusion isoform.
SC refers to number of reads mapped to the exon skipping isoform.
Sample_1 always refers to the experimental group on the name of the processed data file (e.g. cadmium, ints-4 RNAi, ints-4 RNAi + cadmium, etc.)
Sample_2 always refers to the control value (empty vector + control) that is used for all processed files.
|
| |
|
| Submission date |
Apr 17, 2019 |
| Last update date |
Jun 17, 2019 |
| Contact name |
Cheng-Wei Wu |
| E-mail(s) |
[email protected]
|
| Phone |
306-966-7672
|
| Organization name |
University of Saskatchewan
|
| Street address |
52 Campus Drive
|
| City |
Saskatoon |
| State/province |
SK |
| ZIP/Postal code |
S7N 5B4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE129970 |
Effects of cadmium and integrator complex knockdown on gene expression and mRNA splicing |
|
| Relations |
| BioSample |
SAMN11456594 |
| SRA |
SRX5704694 |
