|
| Status |
Public on Feb 12, 2019 |
| Title |
DM_TR_2 |
| Sample type |
SRA |
| |
|
| Source name |
whole worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole worm
treatment: Ad Libitum
fraction: polysome bound RNA
strain/genotype: daf-2;rsks-1
|
| Treatment protocol |
Starting at day one of adults hood, worms were fed OP50 at 10^11 CFU for well fed treatment or at 10^9 CFU for dietary restriction.
|
| Growth protocol |
Worms were raised at 20°C on nematode growth media with OP50 as the food source
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After lysis total RNA was isolated using Trizol as recommended by the manufacturer, polysomal bound RNA was collected using polysomal profiling with 10-50% sucrose gradients.
TruSeq RNA kit, unstranded
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base call (.bcl) files for each cycle of sequencing are generated by Illumina Real Time Analysis (RTA) software. The base call files and run folders are streamed to servers maintained at the Minnesota Supercomputing Institute. Primary analysis and de-multiplexing are performed using Illumina’s bcl2fastq v2.20. The end result of the bcl2fastq workflow is de-multiplexed FASTQ files that are released to client accounts for subsequent analysis by the mapping software and aligner of their own choosing.
w
Aligned reads were counted per gene using the python script HTseq version 0.6.1 with the parameters: --stranded=no -a 0
Calculation of normalized counts per million (cpm) was performed using edgeR version 3.0. The dataset was normalized using the trimmed mean of M-values method with the calcNormFactors() command and tagwise dispersion was estimated using the estimateGLMTagwiseDisp() command. CPM values were exported using the command cpm() with the parameters: count=y,log=F,prior.count=0.03,normalized.lib.sizes=T.
Genome_build: Ensemble version 66
Supplementary_files_format_and_content: A single tab delimited file, CPM.txt contains the CPM for each gene.id for each sample submitted
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Jarod Alton Rollins |
| E-mail(s) |
jrollins@mdibl.org
|
| Phone |
20728889880
|
| Organization name |
MDI Biological Laboratory
|
| Lab |
Rollins Lab
|
| Street address |
159 Old Bar Harbor Rd
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE119485 |
Polysome profiling and mRNA-seq to quantify translational gene regulation in dietary restricted C. elegans and in a long-lived daf-2:rsks-1 double mutant. |
|
| Relations |
| BioSample |
SAMN09976733 |
| SRA |
SRX4643652 |
