|
| Status |
Public on Nov 01, 2016 |
| Title |
N2-control |
| Sample type |
SRA |
| |
|
| Source name |
whole body
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
bacteria strain: pQE9 in E. coli OP50
genotype: wild type
treatment: control (pQE9 in E. coli OP50) for 3 hours
|
| Treatment protocol |
Worms were treated with control(pQE9 in E. coli OP50) or Cry5B(pQE9-Cry5B in E. coli OP50) for 3 hours.
|
| Growth protocol |
All worms were fed with E. coli OP50 for 44 hours to reached L4 stage, and ready for Cry5B treatment.
|
| 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 MiSeq |
| |
|
| Description |
N2CvsN2P_score.xlsx
30PvsN2P_score.xlsx
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: worm base
Supplementary_files_format_and_content: xlsx files include RPKM values, Fold change values and P-values for each Sample.
|
| |
|
| Submission date |
Mar 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Huan-Da Chen |
| E-mail(s) |
adaisgzl@gmail.com
|
| Organization name |
National Cheng Kung University
|
| Street address |
No.1, University Road
|
| City |
Tainan |
| ZIP/Postal code |
701 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL15716 |
| Series (1) |
| GSE78878 |
HLH-30/TFEB-mediated autophagy functions in a cell-autonomous manner for epithelium intrinsic cellular defense against bacterial pore-forming toxin in C. elegans |
|
| Relations |
| BioSample |
SAMN04531128 |
| SRA |
SRX1613096 |
