|
| Status |
Public on Jul 19, 2024 |
| Title |
pre-Auxin_DCW447_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
intestine
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: intestine
strain: DCW447
genotype: qzIs15[rpoa-2p::degron1(TIR1)::GFP::rpoa-2] I; ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR+Cbr-unc-119(+)] II
treatment: 0 mM Auxin
time: 0h
|
| Treatment protocol |
For dissected tissues, RNA was purified from lysed intestinal cells cells following the instructions of the Norgen Single Cell RNA Purification Kit (51800, Norgen Biotek). Libraries were produced using the Smart-Seq2 mRNA sequencing kit (Illumina).
|
| Growth protocol |
RNA was isolated from dissected intesties from synchronized L1 larvae grown at 20°C for the indicated amount of time on Auxin containing plates in 4 independent biological replicates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). For isolated tissues, RNA was purified from lysed muscle or seam cells following the instructions of the Norgen Single Cell RNA Purification Kit (51800, Norgen Biotek).
Libraries were produced using the Smart-Seq2 mRNA sequencing kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS220 annotations downloaded from UCSC. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Assembly: Genome_build: ce10 (WS220)
Supplementary files format and content: Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (Wormbase identifiers) and width of genes, following columns contain raw counts of reads overlapping each gene for each sample.
|
| |
|
| Submission date |
Jun 03, 2024 |
| Last update date |
Jul 19, 2024 |
| Contact name |
Jan Padeken |
| E-mail(s) |
j.padeken@imb-mainz.de
|
| Organization name |
Institute of Molecular Biology
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE268974 |
Effect of RNA Polymerase I (RPOA-2) degradation on transcription in intestinal cells dissected from adult C. elegans |
|
| Relations |
| BioSample |
SAMN41659260 |
| SRA |
SRX24787135 |
