|
| Status |
Public on Dec 31, 2019 |
| Title |
D1119_OP_2h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole body
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole body
strain: Wild type (N2)
treatment: E. coli OP50
timepoint: 2 h
medium: mNGM
temperature: 20 degrees Celsius
|
| Treatment protocol |
Worms were exposed to OP50 and BT at the stage L4. The experiments with BT were performed at 20°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
BT_counts_table.txt
sample name:
D1119
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using STAR-2.5.3a
Read counts per gene is extracted via STAR-2.5.3a
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text files include Raw reads counts for each Sample ...
|
| |
|
| Submission date |
Aug 20, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Hinrich Schulenburg |
| E-mail(s) |
hschulenburg@zoologie.uni-kiel.de
|
| Organization name |
Christian-Albrechts-Universitaet zu Kiel
|
| Department |
Evolutionary Ecology and Genetics, Zoological Institute
|
| Lab |
Schulenburg Group
|
| Street address |
Am Botanischen Garten 1-9
|
| City |
Kiel |
| ZIP/Postal code |
24118 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE136058 |
Transcriptome of the nematode Caenorhabditis elegans infected by Bacillus thuringiensis |
|
| Relations |
| BioSample |
SAMN12608749 |
| SRA |
SRX6743833 |
