|
| Status |
Public on Jul 27, 2020 |
| Title |
RNAseq_tm548_23h |
| Sample type |
SRA |
| |
|
| Source name |
synchronized population
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: blmp-1(tm548) mutant
developmental stage: 23 h after plating L1-arrested C. elegans larvae
|
| Growth protocol |
a population of L1 synchronized by egg prep and M9 incubation was grown on OP50 containing agar plates at 25 degrees. Worms were collected hourly by washing of worms with M9 and washing 3 times in M9.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol and conventional Phenol / Chlorophorm extraction.
Illumina TruSeq mRNA-Seq Sample Prep Kit (Stranded - high input), followed by the Hiseq50 Cycle Single-end reads on HiSeq2500 protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
tm548_TP23_2139F47
tm548_timepoint_23
|
| Data processing |
3' adapters are trimmed with cutadapt=2.3 (--error-rate = 0.1, --minimum-length = 15, --overlap = 3)
RNA-seq data were mapped to the C. elegans ce10 genome using STAR with default parameters (version 2.7.0f)
reads are counted using htseq-count (version = 0.11.2)
Genome_build: ce10
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (Wormbase identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample.
|
| |
|
| Submission date |
Mar 23, 2020 |
| Last update date |
Jul 27, 2020 |
| Contact name |
Helge Grosshans |
| E-mail(s) |
helge.grosshans@fmi.ch
|
| Organization name |
Friedriche Miescher Institute for Biomedical Research (FMI)
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18245 |
| Series (2) |
| GSE133576 |
State transitions of a developmental oscillator |
| GSE147388 |
mRNA sequencing time course of C. elegans samples at time point 1 hours until time point 24 hours at 25 degree [blmp-1(tm548) mutant] |
|
| Relations |
| BioSample |
SAMN14426687 |
| SRA |
SRX7971172 |
