|
| Status |
Public on Dec 01, 2018 |
| Title |
TRV |
| Sample type |
SRA |
| |
|
| Source name |
inflorescences
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
tissue: Inflorescences
age: 6-weeks-old (14dpi)
agent: Tobacco rattle virus
|
| Treatment protocol |
Arabidopsis plants were inoculated on rosette leaves using fresh inoculum prepared from Nicotiana benthamiana leaves systemically infected with an infectious TRV-GFP clone
|
| Growth protocol |
Arabidopsis thaliana plants were were grown in controlled environment chambers under 16 h/8 h of light/dark at 22ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Inflorescences were collected at 14dpi and frozen on liquid nitrogen, and total RNA was extracted using Trizol reagent. For mock-samples, the same procedure was performed at 6-weeks-old Arabidopsis plants.
Library construction and Illumina sequencing using HiSeq2000 were done by BGI-Tech (Pipeline version 5.0).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
TV_FPKM
|
| Data processing |
Illumina GA Pipeline v15 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then used BWA to map clean reads to Arabidopsis genome (TAIR 10) and used Bowtie to gene reference.
FPKM 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: TAIR 10 Arabidopsis genome
Supplementary_files_format_and_content: Chepelev et al., Nucleic Acids Research, 2009
Supplementary_files_format_and_content: Clean Data Assess
Supplementary_files_format_and_content: Mapping Assess
Supplementary_files_format_and_content: all.gene.FPKM.xls
|
| |
|
| Submission date |
Jul 20, 2018 |
| Last update date |
Dec 01, 2018 |
| Contact name |
Virginia Ruiz-Ferrer |
| E-mail(s) |
vruizferrer@cib.csic.es
|
| Phone |
+34 91 837 31 12
|
| Organization name |
CSIC
|
| Department |
Environmental Biology
|
| Lab |
Stress and Gene Regulation
|
| Street address |
Ramiro de Maeztu, 9
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE117417 |
Next Generation Sequencing Facilitates Quantitative Analysis of mock and tobacco ratle virus (TRV) Arabidopsis inflorescences Transcriptome [RNA-Seq] |
| GSE117419 |
Next Generation Sequencing Facilitates Quantitative Analysis of mock and tobacco ratle virus (TRV) Arabidopsis inflorescences Transcriptome |
|
| Relations |
| BioSample |
SAMN09694917 |
| SRA |
SRX4410939 |
