|
| Status |
Public on Mar 05, 2018 |
| Title |
nhr1 |
| Sample type |
SRA |
| |
|
| Source name |
nhr-49(nr2041), No treatment
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: nhr-49(nr2041)
Stage: L4
treatment: No treatment
|
| Treatment protocol |
L4 stage worms were exposed to 7.5 mM tBOOH for 4 hours, while the control remained untreated
|
| Growth protocol |
We allowed N2 and nhr-49(nr2041) worms to grow on OP50 until they reached L4 stage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol
ribosomal RNA removed using the RiboGone - Mammalian—Low Input Ribosomal RNA Removal Kit for Human, Mouse and Rat Samples (Takara #634847). Ribosomal RNA depletion and RNA integrity were verified on a Bioanalyzer with the RNA 6000 Pico kit (Agilent #5067-1513). We constructed cDNA libraries with the SMARTer Universal Low Input RNA Kit (Takara #634900), and measured adapter-ligated concentrations with the High Sensitivity DNA Analysis Kit (Agilent #5067-4626) and by qPCR standard-curve quantitation using the KAPA Library Quantification Kit Illumina Platforms (KK4824).
RNA-seq was done on an Illumina Nextseq 500 using 76bp x2 paired-end reads, using the NextSeq 500/550 High Output Kit v2 (150 cycles).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Single-end reads were aligned to the C. elegans UCSC ce10 reference genome using an RNA-seq alignment app from Illumina, which uses STAR aligner to map reads
we used edgeR to convert raw gene counts into counts per million (CPM) and log2-counts per million (log-CPM).
Weakly expressed genes were removed by only including genes with counts per million (CPM) >1 across two libraries. Gene expression distributions were normalized by the method of trimmed mean of M-values (TMM) in edgeR
Genome_build: C. elegans UCSC ce10
Supplementary_files_format_and_content: tab-delimited text files with raw counts and normalized CPM values for each sample
|
| |
|
| Submission date |
Dec 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Forum Bhanshali |
| E-mail(s) |
[email protected]
|
| Organization name |
Centre for Molecular Medicine and Therapeutics, UBC
|
| Department |
Medical genetics
|
| Lab |
Taubert Lab
|
| Street address |
950 west 28th avenue
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z4H4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE107799 |
NHR-49/HNF4 integrates regulation of fatty acid metabolism with a protective transcriptional response to oxidative stress and fasting |
|
| Relations |
| BioSample |
SAMN08142851 |
| SRA |
SRX3453158 |
