|
| Status |
Public on Jul 27, 2018 |
| Title |
LC14_Ctrl_starved |
| Sample type |
SRA |
| |
|
| Source name |
control_starved_24hr
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
developmental stage: L1 larvae
fed or starved: starved
ancestral conditions: control
batch: 1
|
| Treatment protocol |
After 18 hr of feeding or 24 hr of starvation as L1 larvae, worms were spun down for collection. Fed worms were washed quickly 3-4X with S-basal to remove bacteria, and starved worms were washed 0-1X. Samples were flash frozen in liquid nitrogen and stored at -80C until RNA extraction.
|
| Growth protocol |
N2 worms were maintained well fed for at least 3 generations. Gravid adults were hypochlorite treated to obtain emrbyos, which were put in liquid culture under control or dauer-forming conditions. After control, short-term dauer, or long-term dauer, worms were recovered on plated and maintained well fed. F1 and F2 adults were bleached to obtain embryos for the next generations. F3 embryos were set up in liquid cultures as either fed or starved, and these F3 samples were collected for RNA-seq.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
LC14_Ctrl_24hr
RC-L22_S31_L005
|
| Data processing |
Bowtie version 1.1.2 was used to map reads to the WS210 version of the genome.
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210.
edgeR exact test was used on normalized count tables for differential expression analysis. Genes with counts per million (CPM) >4 in all libraries were included in the analysis. LC4_49d_Dauer_starved sample was not included in subsequent differential expression analysis because it did not cluster with other starved samples. The other 38 samples were used.
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries).
|
| |
|
| Submission date |
Apr 22, 2018 |
| Last update date |
Jul 27, 2018 |
| Contact name |
Amy K Webster |
| E-mail(s) |
awebst10@uoregon.edu
|
| Organization name |
University of Oregon
|
| Street address |
Institute of Ecology and Evolution
|
| City |
Eugene |
| State/province |
Oregon |
| ZIP/Postal code |
97703 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE113500 |
mRNA of fed and starved C. elegans L1 larvae 3 generations following control, short-term dauer or long-term dauer conditions |
|
| Relations |
| BioSample |
SAMN08969136 |
| SRA |
SRX3985525 |
