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| Status |
Public on May 12, 2023 |
| Title |
CK |
| Sample type |
SRA |
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| Source name |
seedlings
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| Organism |
Nicotiana benthamiana |
| Characteristics |
genotype: wild type
tissue: seedlings
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| Growth protocol |
Nicotiana benthamiana seeds were surface sterilized with 70% (w/v) ethanol for 30 s and 5% (v/v) H2O2 for 30 min, then washed with sterile H2O and planted on Murashige and Skoog (MS) medium for germination under a 16 h light/8 h dark cycle at 26°C in a growth chamber. The seedlings of N. benthamiana were transferred to the soil mix and grown under greenhouse conditions.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from N. benthamiana plant tissue using a TransZol Plant RNA Kit (TransGen Biotech, Beijing, China).
The cDNA libraries were generated using NEBNext? Ultra? RNA Library Prep Kit for (Illumina, USA) according to manufacturer's recommendations.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
polyA RNA isolated
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| Data processing |
Clean reads were filtered by removing reads containing ploy-N, reads containing adapter, and low-quality reads from the raw data. The filtered clean reads were aligned to the N. benthamiana reference genome using Hisat2 v2.0.4 with default parameters. The expression level for each transcript was normalized and estimated using the fragments per kilobases per million reads (FPKM) method (Trapnell et al., 2010).
Genome_build: Niben101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Nov 19, 2021 |
| Last update date |
May 12, 2023 |
| Contact name |
Xuncheng Wang |
| E-mail(s) |
[email protected]
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| Organization name |
Peiking University
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| Street address |
5 Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL29766 |
| Series (1) |
| GSE189162 |
A woody plant degrading pathogen effector targets host glucose signaling protein VvRHIP1 to promote virulence |
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| Relations |
| BioSample |
SAMN23297167 |
| SRA |
SRX13171647 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5695581_CK.txt.gz |
607.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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