|
| Status |
Public on Aug 02, 2019 |
| Title |
t2160_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
nxf-1 (t2160)_rep3
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
age: adults worms grown at 15C
treatment: shifted to 25 C for 16 hours before collected
genotype: ts allele
|
| Treatment protocol |
16 hours at 25 C after one day adult stage
|
| Growth protocol |
Synchronized wild type and nxf-1(t2160) worms were grown at 15˚C until adult stage in standart conditions
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA, Rneasy Mini kit Qiagen, following manufacturer's recommendations
TruSeq mRNA (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Quality analysis of raw reads with FastQC
Sequenced reads were trimmed for adaptor sequence and masked for low-quality sequence with Trim-Galore software
Quality analysis of clean reads with FastQC
Clean reads were mapped against the reference genome with Tophat2 software
Resulting mapping files (bam files) were sorted and indexed with the Samtools software
Quality analysis of Bam files with Qualimap tool
FeatureCounts tools was used to obtain raw counts over gene features.
Differential expression analysis with DESeq2 and edgeR Bioconductor packages
Resulting tables annotated with Biomart, WormBase and org.Ce.eg.db databases in R platform
Common up- and down- regulated genes from both statistical protocols were used for the wnrichment analysis for GO, Kegg and Reactome terms/pathways.
Genome_build: Ensemble version of C. elegans WBcel235.85
Supplementary_files_format_and_content: raw counts obtained from FeatureCounts
|
| |
|
| Submission date |
Jul 06, 2018 |
| Last update date |
Aug 02, 2019 |
| Contact name |
María de Toro |
| E-mail(s) |
mthernando@riojasalud.es
|
| Organization name |
Centro de Investigación Biomédica de La Rioja
|
| Department |
Genomics & Bioinformatics Core Facility
|
| Street address |
C/Piqueras 98
|
| City |
Logrono |
| State/province |
La Rioja |
| ZIP/Postal code |
26006 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15716 |
| Series (1) |
| GSE116737 |
mRNA profiles of nxf-1 (t2160) and wild type C. elegans in adult stage |
|
| Relations |
| BioSample |
SAMN09623514 |
| SRA |
SRX4348319 |
