|
| Status |
Public on Nov 11, 2020 |
| Title |
N2 EDL933 |
| Sample type |
SRA |
| |
|
| Source name |
N2 WT C. elegans whole cells
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype/variation: wild type
treatment: fed with EDL933 for 6 hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All worms were collected, flash frozen on dry ice, and 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 |
| |
|
| Data processing |
Basecalls performed using Illumina GA Pipeline v1.3
Raw reads produced from sequencing machines contain dirty reads which contain adapters, unknown or low quality bases. These data will negatively affect following bioinformatics analysis. Therefore, dirty raw reads are discarded.
Reads after filtering dirty raw reads, on which all following analysis are based.
The calculation of Unigene expression uses RPKM method (Reads Per kb per Million reads) (Mortazavi, Williams et al. 2008)
Genome_build: ce6
Supplementary_files_format_and_content: xls files include RPKM values for each Sample
|
| |
|
| Submission date |
Dec 22, 2019 |
| Last update date |
Nov 12, 2020 |
| Contact name |
Cheng-Rung Huang |
| E-mail(s) |
[email protected]
|
| Phone |
886928547266
|
| Organization name |
National Cheng Kung University
|
| Street address |
University Road
|
| City |
Tainan |
| ZIP/Postal code |
701 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE142507 |
CDK1-formin signal confers microvillar effacement by an attaching and effacing (A/E) pathogen |
|
| Relations |
| BioSample |
SAMN13670855 |
| SRA |
SRX7431047 |
