 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 25, 2021 |
| Title |
TuMV-Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Nicotiana benthamiana |
| Characteristics |
treatment: TuMV infection
genotype: wild type
tissue: leaves
|
| Treatment protocol |
N. benthamiana leaves were infiltrated with Agrobacterium tumefaciens carrying the TuMV-GFP vector.
|
| Growth protocol |
N. benthamiana plants were grown in a greenhouse under a 16 h light/8 h dark regime at 25±2 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
TU63_TU=TuMV-Rep3
|
| Data processing |
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: transcriptome built with Trinity, FASTA on series record.
Supplementary_files_format_and_content: The file <transcript_expression_all> provides <transcript_ID> of each transcript. The sequence of each transcript are provided in the file <Trinity_transcript>.
|
| |
|
| Submission date |
Feb 24, 2021 |
| Last update date |
Feb 25, 2021 |
| Contact name |
Xinyang Wu |
| E-mail(s) |
[email protected]
|
| Organization name |
Ningbo University
|
| Street address |
818# Fenghua Road
|
| City |
Ningbo |
| State/province |
Zhejiang |
| ZIP/Postal code |
315211 |
| Country |
China |
| |
|
| Platform ID |
GPL29766 |
| Series (1) |
| GSE167415 |
Transcriptome sequencing from Nicotiana benthamiana leaves non-infected and infected with Turnip mosaic virus (TuMV) |
|
| Relations |
| BioSample |
SAMN18048851 |
| SRA |
SRX10162828 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
