|
| Status |
Public on Nov 01, 2018 |
| Title |
L1-DR-C |
| Sample type |
SRA |
| |
|
| Source name |
L1 larvae
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
parental diet: DR
strain: N2
|
| Treatment protocol |
After 24 hr, L1 larvae were collected. Samples were flash frozen in liquid nitrogen and stored at -80C until RNA extraction.
|
| Growth protocol |
The wild-type N2 strain was maintained well-fed at 20C on E. coli OP50 on standard NGM plates prior to setting up the experiment. Worms were then bleached, and embryos were placed in liquid culture at 1 embryo/ 100 uL under AL (25 mg/mL HB101) or DR (3.1 ml/mL HB101) conditions with S-complete. After 96 hr, AL/DR adults were bleached and embryos were resuspended in S-basal at 1 embryo / uL.
|
| 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. 12 cycles of PCR were used to amplify libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| 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) >1 in at least 3 libraries were included in the analysis.
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 |
May 09, 2018 |
| Last update date |
Nov 01, 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 (2) |
| GSE114271 |
mRNA-seq comparison of C. elegans L1 larvae with parents experiencing dietary restriction or ad libitum conditions |
| GSE129089 |
Insulin/IGF signaling and vitellogenin provisioning mediate intergenerational adaptation to nutrient stress |
|
| Relations |
| BioSample |
SAMN09101808 |
| SRA |
SRX4061797 |
