|
| Status |
Public on May 29, 2019 |
| Title |
N2 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
tissue: Whole animal
age: Day 1 adult
genotype: wild-type
|
| Growth protocol |
All strains were maintained at 20˚C on nematode growth medium (NGM) plates seeded with E. coli (OP50 strain). Unhatched eggs were age-synchronized and after 3 days, day 1 adult worms were harvested for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent (Thermo Fisher) was used to extract total RNA from ~1,000 age-synchronized day 1 adult worms (three biological replicates per genotype). DNase-treatment was performed using TURBO DNA-free kit (Themo Fisher). mRNA was isolated from the DNase-treated total RNA using oligo(dT) and cDNA was synthesized by reverse transcription using TruSeq RNA Library Prep Kit v2 (Illumina).
The samples were end-repaired, poly(A)-tailed, ligated to barcoded oligo adapters (Illumina) and PCR-amplified using Apollo 324 library preparation system (Wafergen Bio-systems) to prepare non-stranded poly(A)-based cDNA libraries with 120 bp insert size.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_41028
|
| Data processing |
Basecalling was performed using HiSeq Control Software (Illumina)
Quality control of raw RNA-Seq reads was performed using FastQC
Tuxedo Suite was used for alignment, differential expression analysis and post-analysis diagnostics
RNA-Seq reads were aligned to the C. elegans reference transcriptome (WS220 release) using Bowtie 2
Transcript splicing junctions were mapped using TopHat
FastQC was used for post-alignment quality control to ensure high quality of input data for subsequent analysis steps
Cufflinks was used to assemble the aligned reads, estimate abundance of transcripts and calculate FPKM values
Transcripts that were differentially expressed relative to wild-type were determined using CuffDiff 2 using the following two criteria: false discovery rate (FDR)-adjusted p value < 0.05 and fold-change ≥ 1.5
Genome_build: C. elegans reference transcriptome WS220 release
Supplementary_files_format_and_content: Text file with mapped read counts
|
| |
|
| Submission date |
Sep 14, 2018 |
| Last update date |
May 29, 2019 |
| Contact name |
Richard C McEachin |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Department |
DCM&B
|
| Street address |
2800 Plymouth Road
|
| City |
Ann Arbor |
| State/province |
United States |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE119993 |
Comparison of gene expression in the long-lived hsb-1 mutant and hsf-1 overexpression C. elegans strains |
|
| Relations |
| BioSample |
SAMN10063986 |
| SRA |
SRX4683271 |
