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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 30, 2023 |
| Title |
WT1 |
| Sample type |
SRA |
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| Source name |
Bacterial cells
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| Organism |
Xanthomonas citri pv. glycines |
| Characteristics |
strain: Strain 12-2
genotype: wild-type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each strain was isolated using an RNeasy® Mini Kit (QIAGEN) and contaminating DNA was removed using TURBO DNA-free™ Kit (Ambion, Austin, TX, U.S.A.).
Libraries were prepared using Ribo-Zero rRNA Removal Kit (Bacteria), TruSeq RNA Sample Prep Kit v2 following the Illumina manufacturer’s instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Sequenced reads were trimmed for adaptor sequence, and then mapped to Xanthomonas citri pv.glycines 12-2 whole genome using Bioconductor Rsubread package with parameter align(index=" Xag12-2index ",readfile1="XagWT2_1.fastq.gz", readfile2="XagWT2_2.fastq.gz",output_file="WT2alignResults.BAM")
Genome_build: Xag12-2index
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample ...
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| Submission date |
Jan 17, 2022 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Tiyakhon Chatnaparat |
| E-mail(s) |
[email protected]
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| Organization name |
Kasetsart University
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| Department |
Plant Pathology
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| Lab |
Phytobacteriology
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| Street address |
50 Ngamwongwan Rd. Ladyao, Chatuchak
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| City |
Bangkok |
| ZIP/Postal code |
10900 |
| Country |
Thailand |
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| Platform ID |
GPL31233 |
| Series (1) |
| GSE193787 |
Global gene expression profiles of phoB and phoU mutants of X. citri pv. glycines 12-2 conducted under phosphate limitation conditions in vitro using RNA-seq |
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| Relations |
| BioSample |
SAMN25042800 |
| SRA |
SRX13811073 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5821094_WT1countsnew.txt.gz |
31.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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