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| Status |
Public on Jan 25, 2022 |
| Title |
15C_WT_3 |
| Sample type |
SRA |
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| Source name |
In vitro bacteria culture
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| Organism |
Xylella fastidiosa subsp. fastidiosa |
| Characteristics |
strain: Stag's Leap
genotype: wild type
growth temperature: 15°C
age: 7 days post inoculation
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bacteria cells were scraped off PD3 agar plates and flash frozen on dry ice. RNA was purified using Trizol reagent. Oxford Nanopore direct cDNA sequencing kit was was used with 250ng of rRNA depleted RNA for the construction of sequencing libraries.
Nanopre direct cDNA sequencing library
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
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| Data processing |
Guppy, A neural network basecaller that converts Nanopore electronic raw signal from sequencer into bases.
Deepbinner, A signal-level demultiplexer for Oxford Nanopore reads.
Porechop, An adapter trimmer for Oxford Nanopore reads.
Minimap2, A pairwise reads aligner for genomic and spliced nucleotide sequences
Salmon, A transcript quantification tool for RNA-Seq data
Tximport, Imports transcript-level estimates and summarizes abundances, counts, and transcript lengths to the gene-level
DESeq2, Provides methods to test for differential gene expression based on the negative binomial distribution
Supplementary_files_format_and_content: Summary of gene-level abundances, including gene ID and transcipts per million (TMP) values for each sample.
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| Submission date |
Jan 22, 2022 |
| Last update date |
Jan 26, 2022 |
| Contact name |
Lindsey Burbank |
| E-mail(s) |
lindsey.burbank@ars.usda.gov
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| Phone |
5595962714
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| Organization name |
USDA-ARS
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| Street address |
9611 S Riverbend Ave
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| City |
Parlier |
| State/province |
California |
| ZIP/Postal code |
93648 |
| Country |
USA |
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| Platform ID |
GPL30664 |
| Series (1) |
| GSE184594 |
Using next generation sequencing to compare gene expression of wild type and Δcsp1 mutant of bacterial plant pathogen Xylella fastidiosa strain Stag's Leap |
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| Relations |
| BioSample |
SAMN25182178 |
| SRA |
SRX13867585 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5830727_15C_WT_3.txt.gz |
13.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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