|
| Status |
Public on May 04, 2014 |
| Title |
control20-5 |
| Sample type |
SRA |
| |
|
| Source name |
Control selected_pooled L1 tissue
|
| Organism |
Caenorhabditis remanei |
| Characteristics |
strain: Control selected, derived from PX443
developmental stage: L1
temperature: 20°C
batch: D
|
| Treatment protocol |
Populations were age-synchronized during the embryonic stage via a standard bleaching procedure. Embryos were incubated at either 20°C or 30°C in liquid buffer without food for 20 hours. Pooled L1 larvae were passed through a 20 micron filter immediately prior to tissue collection.
|
| Growth protocol |
Worms were maintained on NGM-lite seeded with E. coli strain OP50 at 20°C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Approximately 100,000 individuals per replicate were flash frozen in Trizol. Total RNA was extracted using a standard Trizol extraction protocol. Poly-A mRNA was isolated from total RNA using the Dynabeads mRNA purification kit (Ambion).
mRNA was sheared to 200-600nt fragments using a buffered zinc solution (RNA fragmentation kit; Ambion). cDNA was synthesized from fragments using Superscript III, and barcoded sequencing adaptors were added to enable multiplexing of samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calls were performed using Illumina software
Initial processing was performed using the process_shortreads component of Stacks. In short, reads were demultiplexed, and the barcodes were removed. Reads with ambiguous barcodes were rescued if there were fewer than 2 mismatches, and discarded otherwise. Reads failing the Illumina chastity filter were also removed.
Filtered reads were aligned to the C. remanei genome using GSNAP version 2013-03-31 with parameters -N 1 -s -w 10000 --pairmax-RNA 10000
Reads aligning to genes were counted using htseq-count with parameters -m union -s no
Genome_build: C_remanei-15.0.1; ASM14951v1
Supplementary_files_format_and_content: tab-delimited text files with read counts per gene
|
| |
|
| Submission date |
Apr 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick C. Phillips |
| E-mail(s) |
pphil@uoregon.edu
|
| Organization name |
University of Oregon
|
| Department |
Institute of Ecology and Evolution
|
| Street address |
5289 University of Oregon
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403 |
| Country |
USA |
| |
|
| Platform ID |
GPL16141 |
| Series (1) |
| GSE56510 |
Rapid evolution of phenotypic plasticity and shifting thresholds of genetic assimilation in the nematode Caenorhabditis remanei |
|
| Relations |
| Reanalyzed by |
GSM1534367 |
| BioSample |
SAMN02719398 |
| SRA |
SRX511002 |
