|
| Status |
Public on Dec 17, 2018 |
| Title |
RCC033 |
| Sample type |
SRA |
| |
|
| Source name |
Rap-3
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: Bristow N2
tissue: Whole body
age: Day 6
genotype: wild type
|
| Treatment protocol |
Drug treatment from day 4 to day 6
|
| Growth protocol |
Solid Nematode Growth Medium (NGM)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nematodes were collected at day 6 and RNA was harvested using Qiagen RNAeasy micro kit. Illumina HiSeq4000 RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The RNAseq reads from each sample were mapped to the reference C. elegans transcriptome (WBcel235) with kallisto using 100 bootstrap samples and sequence based bias correction.
The estimated counts were imported from kallisto to the R environment (v3.3.2) and summarized to gene-level using the tximport package.
The DESeq2 package followed by the EdgeR package were then used to normalized and replaced outliers culminating on the counts per million (CPM) matrix table.
Genome_build: WBcel235
Supplementary_files_format_and_content: .csv file of the matrix table of CPM of all the genes (wormbase IDs) for every sample.
|
| |
|
| Submission date |
Dec 19, 2017 |
| Last update date |
Dec 17, 2018 |
| Contact name |
Jan Gruber |
| E-mail(s) |
yncjg@nus.edu.sg
|
| Phone |
65-90084510
|
| Organization name |
Yale-NUS College / NUS
|
| Department |
Science/ Biochemistry
|
| Lab |
Nematode Ageing Lab
|
| Street address |
5 Engineering Drive 1
|
| City |
Singapore |
| ZIP/Postal code |
130013 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE108263 |
Drug synergy slows ageing and improves healthspan through IGF and SREBP lipid signaling |
|
| Relations |
| BioSample |
SAMN08202548 |
| SRA |
SRX3481986 |
