|
| Status |
Public on Dec 31, 2020 |
| Title |
C48B |
| Sample type |
SRA |
| |
|
| Source name |
Control_48h post L4
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype/variation: WT
developmental stage: L4 stage animal
treatment: Control
timepoint: 48h post L4
|
| Treatment protocol |
Extract treatment was carried out at 20 °C on nematode growth medium seeded with 200 ml of OP50 E. coli culture. 300 ml of M. humicola extract was added on bacterial lawn prior to additon of animals. Same amount of water was added to control plates. The experiment was performed in triplicates and consisted of 200 animals on each plate. For infection set up, 50 L4 stage animals were added onto a plate with and without (control) 3 previously infected animals with M. humicola on a small bacterial lawn (100 ml) (Osman et al., Curr Biol 2018)
|
| Growth protocol |
The strains used in this study were cultured and handled according to standard protocols (Brenner, 1974). Gravid adults were bleached to obtain synchronized L4 stage animals which were then treated with M. humicola extract or infected with the pathogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The animals were collected by washing with M9 at respective time points and RNA was extracted using TRIzol ® reagent. The quality and quantity of RNA was determined respectively using agarose gel electrophoresis and Qubit fluorometer.
The library preparation was done using PE100 strand-specific library preparation protocol as previously described (Zhu et al., Plant Methods 2018)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
C48B
|
| Data processing |
Pseudoalignment was performed using Kallisto (Bray et al., Nat Biotechnol 2016) and the WS235 transcriptome from Wormbase
Analysis of counts was performed using Sleuth using the Wald test for two sample comparison (Pimentel et al., Nat Methods 2017)
Genome_build: WS235
Supplementary_files_format_and_content: abundance.h5 is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.
|
| |
|
| Submission date |
May 08, 2020 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Michalis Barkoulas |
| E-mail(s) |
m.barkoulas@imperial.ac.uk
|
| Organization name |
Imperial College London
|
| Street address |
SAF Building, South Kensington
|
| City |
London |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL25145 |
| Series (1) |
| GSE150135 |
Transcriptomic analysis of C. elegans infected with Myzocytiopsis humicola or treated with its extract |
|
| Relations |
| BioSample |
SAMN14856543 |
| SRA |
SRX8294553 |
