|
| Status |
Public on Jul 26, 2017 |
| Title |
CN3_12 |
| Sample type |
SRA |
| |
|
| Source name |
whole adult animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole adult animal
Stage: Control animals
strain: N2
mutation: wt
|
| Treatment protocol |
All infection assays were carried out at 25 °C on nematode growth medium seeded with 50 ul of OP50 E. coli culture. Infection assays were carried out in triplicates and consisted of 50 animals being transferred onto plates containing 3 infected animals, or onto control plates devoid of pathogen.
|
| Growth protocol |
The strains used in this study were cultured and handled according to standard protocols (Brenner, 1974). Animals for infection assays were synchronized to L4 by bleaching gravid hermaphrodites.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from a total of 50 infected and control animals after 12 hrs and 24 hrs post-exposure to pathogen using TRIzol ® reagent and the Direct-zolTM RNA extraction kit (Zymo Research), according to the manufacturer’s instructions. The quality and quantity of RNA was determined using the Agilent® RNA ScreenType System on an Agilent ® 2100 Bioanalyzer.
The library preparation was done using the Illumina TruSeq RNA stranded mRNA library prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
12 hrs post L4
|
| Data processing |
Reads aligned to a custom transcriptome dataset having built this as a genome using bowtie2 in paired end mode
The alignments were converted to count files using bedtools coverageBed module using the options -s and -counts.
Genome_build: WS190
Supplementary_files_format_and_content: tab-delimited text file with raw counts
Supplementary_files_format_and_content: tab-delimited text file with DESeq2 normalized counts
|
| |
|
| Submission date |
Jul 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Michalis Barkoulas |
| E-mail(s) |
m.barkoulas@imperial.ac.uk
|
| Phone |
+44 2075945227
|
| Organization name |
Imperial College London
|
| Department |
Life Sciences
|
| Lab |
Michalis Barkoulas's lab
|
| Street address |
South Kensington Campus
|
| City |
London |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE101647 |
Transcriptomic analysis of control and Myzocytiopsis humicola-infected C. elegans |
|
| Relations |
| BioSample |
SAMN07370618 |
| SRA |
SRX3020093 |
