|
| Status |
Public on Aug 01, 2021 |
| Title |
met2cd_eemb_20°C_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
met2cd_eemb_20°C_rep2
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: met-2(gw1660) III
tissue: early embryo
|
| Treatment protocol |
as indicated worm cultures were either maintained at 20°C, or exposed to a 1hr heatstress at 37°C prior to RNA extraction.
|
| Growth protocol |
RNA was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in three independent biological replicates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using Trizol and further purified using the RNA Clean & Concentrator kit (Zymo Research R1015) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.
Libraries were prepared using the TruSeq Total RNA-seq (stranded-high input) Library Prep Kit (Illumina, San Diego, CA, USA).
|
| |
|
| 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.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (WormbaseID), following columns contain raw counts of reads overlapping each gene for each sample.
|
| |
|
| Submission date |
Mar 15, 2021 |
| Last update date |
Aug 01, 2021 |
| 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 (2) |
| GSE168924 |
A structural role for histone methyltransferase MET-2 represses transcription independent of H3K9me catalysis [RNA-seq] |
| GSE168925 |
A structural role for histone methyltransferase MET-2 represses transcription independent of H3K9me catalysis |
|
| Relations |
| BioSample |
SAMN18313026 |
| SRA |
SRX10342557 |
