|
| Status |
Public on Feb 27, 2015 |
| Title |
N2, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole animals, N2
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/background: N2
developmental stage: L4 larva
tissue: whole body
|
| Growth protocol |
Gravid adults grown at 20¡C on 100 mm NG plates seeded with OP50-1 E. coli were collected and treated with hypochlorite to release eggs. Eggs were incubated overnight in M9 media to obtain L1 synchronized populations. One thousand L1 larvae were grown on a 100 mm NG plate seeded with OP50-1 E. coli.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Worms were harvested for RNA extraction when L4 larval stage was reached. Animals were collected and washed extensively with M9 media to remove bacteria. Worms were then snap frozen in liquid nitrogen. RNA was extracted by five freeze/thaw cycles in Qiazol then purified by RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA quality was checked using an Agilent Technologies 2100 Bioanalyzer. All samples had an RNA integrity number of 10. cDNA libraries were prepared from 4 μgs of total RNA using the TruSeq RNA Sample Preparation v2 kit (Illumina).
50-cycle paired-end sequencing was performed on an Illumina HiSeq 2000 by the Harvard Biopolymer Core.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
TRA00009038
Poly-A selected RNA
Processed data file: N2norm.txt
|
| Data processing |
Basecalls performed with CASAVA version 1.8.2.
Adapter sequences and poor quality bases (<20) were trimmed and filtered with CUTADAPT.
Reads (50b paired-end) were aligned to the Caernohadbitis elegans reference genome (ce6, WS238) using TopHat version 2.0.8 (Kim et al., 2013), with a median 35 million reads mapped in proper pairs.
The number of reads mapping to each gene was counted with htseq-count. Genes with less than 1 Count Per Million Reads (CPM) were discarded from further analysis. Counts were normalized for sequencing depth and RNA composition across all samples with edgeR. Genes were tested for differential expression between each mutant strain and wild-type using edgeR's glm method. For each comparison, genes with less than 5 CPM were filtered and those with at least 50% change and FDR of 1% or less were considered differentially expressed.
Genome_build: ce6
Supplementary_files_format_and_content: Tab-delimited text files with normalized expression measurements in all replicates for a strain.
|
| |
|
| Submission date |
Jun 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ana Rodrigues Grant |
| E-mail(s) |
anapcr@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Computational Medicine & Bioinformatics
|
| Street address |
100 Washtenaw Avenue
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE58931 |
Neuronal CRTC-1 governs systemic mitochondrial metabolism and lifespan via a catecholamine signal |
|
| Relations |
| BioSample |
SAMN02898127 |
| SRA |
SRX641435 |
