|
| Status |
Public on Aug 13, 2020 |
| Title |
met2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
met-2 (n4256)_whole worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: met-2 (n4256)
developmental stage: starved L1
growth temperature: 25°C
tissue: whole worm
sample id: rCG084
|
| Growth protocol |
Synchronized adults grown in liquid culture using standard S-basal medium with HB101 E. coli at 20°C were bleached to isolate embryos, the eggs were hatched at 25°C in M9 buffer, and starved L1s were sucrose floated and collected 20-22 hours following hatching by flash freezing in liquid nitrogen. The efl-1 mutants were hatched at 26°C to ensure that the gene was inactivated post early-embryogenesis.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TriPure (Roche) and further purified using an RNeasy column (Qiagen).
RNA-seq libraries were prepared from 100-1000 ng of total RNA using the Illumina TruSeq RNA kit according to the manufacturers’ instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
met2.rCG084
|
| Data processing |
RNA-seq reads were aligned using STAR (Dobin et al., 2013) with the two-pass mode using the C. elegans gene annotation from Wormbase (version WS260) as a guide (after removing any gene annotation from the mitochondrial DNA).
BigWig tracks were generated using the wigToBigWig tool downloaded from the UCSC website (http://hgdownload.soe.ucsc.edu/).
Genome_build: ce11
Supplementary_files_format_and_content: Forward and reverse-strand genome-wide read coverage in RPM (reads per million of mapped reads)
|
| |
|
| Submission date |
Jul 27, 2020 |
| Last update date |
Aug 13, 2020 |
| Contact name |
Francesco Nicola Carelli |
| E-mail(s) |
fr.carelli@gmail.com
|
| Organization name |
University of Cambridge
|
| Lab |
Julie Ahringer
|
| Street address |
Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18730 |
| Series (2) |
| GSE155190 |
DREAM represses distinct targets by cooperating with different THAP domain proteins [RNA-seq] |
| GSE155191 |
DREAM represses distinct targets by cooperating with different THAP domain proteins |
|
| Relations |
| BioSample |
SAMN15651177 |
| SRA |
SRX8831872 |
