|
| Status |
Public on Mar 23, 2020 |
| Title |
Ea1: WT |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Erwinia amylovora |
| Characteristics |
strain: Ea1189
genotype: wild-type
|
| Treatment protocol |
Bacterial cells of WT and (p)ppGpp mutant were adjusted to 2 x 10^8 cfu/ml in 5 mL of hrp-inducing minimal media and incubated 3hr at 18 °C.
|
| Growth protocol |
Overnight cultures of wild-type and mutant strains grown in LB were harvested and washed twice with hrp-inducing minimal media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cells were harvested, and RNA was isolated using Qiagen RNeasy bacteria Mini kit
The stranded RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)
Sequenced reads were trimmed for adaptor sequence, then mapped to Erwinia amylovora CFBP1430 whole genome using bowtie v0.12.7 with parameters -t --sam -v 2 -B 1 -3 20 --best
The number of reads mapped to CDS of Erwinia amylovora CFBP1430 were counted using bedtools 2.17.0
Normalization and statistical analysis were carried out using the R package DESeq2 as described in Love et al. Genome biology, 2014.
Genome_build: bowtieNC_013961
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample ('p' in file name denotes plasmid abundance measurements; no 'p' in file name denotes genomic abundance measurements)
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Mar 25, 2020 |
| Contact name |
Frank Zhao |
| E-mail(s) |
frankzhao55@gmail.com
|
| Phone |
2172659822
|
| Organization name |
University of Illinois
|
| Department |
Crop Sciences
|
| Street address |
1201 W. Gregory Dr.
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL26279 |
| Series (1) |
| GSE143324 |
The stringent response regulator (p)ppGpp mediates virulence gene expression and survival in Erwinia amylovora |
|
| Relations |
| BioSample |
SAMN13780910 |
| SRA |
SRX7523770 |
