|
| Status |
Public on Dec 06, 2022 |
| Title |
MG_B |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Xanthomonas campestris pv. campestris str. 8004 |
| Characteristics |
genotype: Xcc 8004 pilG (XC_1183) deletion mutant
|
| Growth protocol |
RNA isolated from cultures of Xcc strains grown to an OD600 of 1.0 in NYGB medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from Xcc strains grown to OD600 of 1.0 in NYGB medium using Omega’s RNA kit
RNA sample were prepared for sequencing using IlluminaTruseqTM RNAsampleprepKit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw data of fastq format were firstly prosessed in-house perl scripts. In this step, clean data were obtained by software SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle(https://github.com/najoshi/sickle)
Compare with the reference genome by software Bowtie2（http://www.bowtie-bio.sourceforge.net/bowtie2/manual）
Expression analysis was built using RSEM（http://deweylab.github.io/RSEM/）
FPKM of gene was calculated based on the length of the gene and reads count mapped to this gene.
The different expressed genes between mutant and wild type were calculated using edgeR（http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html）
Genome_build: Xanthomonas campestris pv. campestris 8004（CP000050.1）
Supplementary_files_format_and_content: Excel files include FPKM values for each sample
|
| |
|
| Submission date |
Dec 06, 2019 |
| Last update date |
Dec 06, 2022 |
| Contact name |
Yan-Hua Qi |
| E-mail(s) |
[email protected]
|
| Organization name |
Guangxi university
|
| Street address |
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of L
|
| City |
Nanning |
| State/province |
China |
| ZIP/Postal code |
530004 |
| Country |
China |
| |
|
| Platform ID |
GPL25598 |
| Series (1) |
| GSE141596 |
Transcriptomic analysis of Xanthomonas campestris pv. campestris wild type vs two mutant |
|
| Relations |
| BioSample |
SAMN13499971 |
| SRA |
SRX7283165 |
