|
| Status |
Public on Dec 02, 2021 |
| Title |
Wildtype 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Erwinia amylovora |
| Characteristics |
strain: Ea1189
genotype: wild-type
|
| Treatment protocol |
Bacterial cells were adjusted to 2 x 10^8 cfu/ml in 5 mL of hrp-inducing minimal media and incubated for 6 h at 18 °C.
|
| Growth protocol |
Overnight cultures of wild-type and mutant strain 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 Ea1189 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 Ea1189 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
|
| |
|
| Submission date |
Nov 24, 2020 |
| Last update date |
Dec 02, 2021 |
| 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) |
| GSE162090 |
Transcriptomic analysis of the rpoN mutant in Erwinia amylovora |
|
| Relations |
| BioSample |
SAMN16882221 |
| SRA |
SRX9568653 |
