|
| Status |
Public on Jul 01, 2017 |
| Title |
wt_2H_C |
| Sample type |
SRA |
| |
|
| Source name |
wild type
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: wild type
starvation timepoint: 2h
|
| Treatment protocol |
Nematodes were starved for 0, 1, 2, 3, 4, 6, or 16 hours by transfering them to empty NMG plates.
|
| Growth protocol |
Nematodes were grown at 20C on NGM plates seeded with OP50 bacteria when not starved.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nematodes were harvested, flash frozen with liquid nitrogen, and RNA was harvested using Isol-RNA Lysis Reagent (Ref #2302700 5 PRIME), RNA was further cleaned using Qiagen RNeasy Protect Mini kit (Qiagen). Illumina TruSeq RNA Sample Prep kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA-seq: Libraries were prepared from purified RNA (TruSeq Illumina mRNA prep kit) and sequenced according to the manufacturer’s instructions (HiSeq v4 Illumina SR sequencing kit).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
mRNA-seq reads were aligned to the ce6 genome by STAR (Dobin et al., 2013) and differentially expressed genes were identified by HOMER (Heinz et al., 2010) and EdgeR (Robinson et al., 2010)
Genome_build: ce6
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
May 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Susanne Mandrup |
| E-mail(s) |
s.mandrup@bmb.sdu.dk
|
| Phone |
+45 6550 2340
|
| Organization name |
University of Southern Denmark
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
Campusvej 55
|
| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL18730 |
| Series (1) |
| GSE98919 |
Global proteomic- and transcriptomic analyses of starvation responses reveal a central role for lipoprotein metabolism in acute starvation survival in C. elegans |
|
| Relations |
| BioSample |
SAMN07124473 |
| SRA |
SRX2823937 |
