|
| Status |
Public on Sep 15, 2013 |
| Title |
DH5_N2_44 |
| Sample type |
SRA |
| |
|
| Source name |
wild-type (N2) at 20C: 44 hrs
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
temperature: 20C
|
| Growth protocol |
Embryos of wild-type (N2) and mutant nematodes were isolated by hypochlorite treatment and hatched larvae were synchronized by starvation. L1-arrested animals in starvation medium were spotted onto NGM plates with food (OP50 E. coli strain) and cultured at 20C or 25C, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from synchronized larval populations using Trizol (Invitrogen). Each sample underwent 3 rounds of freeze-thaw cycles for enhanced efficiency.
Poly(A)+ RNA libraries were prepared from total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
whole worm poly(A)-extracted mRNA library
|
| Data processing |
Debarcoding of samples.
Sequencing reads for each sample and timepoint were seperately mapped to the transcriptome using bwa (version 0.5.9) with default parameters.
Reads were aggregated across all isoforms of a given gene.
Aggregated reads were converted to reads per million mapped reads per kilobase of transcript length (RPKM).
Genome_build: WS190
Supplementary_files_format_and_content: data_rpkm.txt: Tab separated data file listing all genes (rows) and expression data in RPKM for all samples and all time points. Column name indicates sample, strain and time point, separated by an underscore. The first two columns indicate the wormbase gene symbol and gene name, respectively.
|
| |
|
| Submission date |
Jul 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Dominic Grün |
| E-mail(s) |
gruen@ie-freiburg.mpg.de
|
| Phone |
+491791073352
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Street address |
Stübeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE49043 |
Dampening of expression oscillations by synchronous regulation of a microRNA and its target |
|
| Relations |
| BioSample |
SAMN02261047 |
| SRA |
SRX326736 |
