|
| Status |
Public on Sep 07, 2021 |
| Title |
DMSO #1 |
| Sample type |
SRA |
| |
|
| Source name |
L. crescens BT-1, DMSO
|
| Organism |
Liberibacter crescens BT-1 |
| Characteristics |
treatment: DMSO
|
| Growth protocol |
L. crescens BT-1 cells were grown with 10 μM tolfenamic acid (in 0.05% dimethyl sulfoxide) while the control was grown with 0.05% DMSO. L. crescens BT-1 cells were collected at OD600= 0.3 (mid-exponential phase) by centrifugation at 8000 rpm, at 4 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RiboPure-Bacteria (Life Technologies) kit following the manufacturer’s protocol. The quality of isolated RNA samples was examined in an Agilent 2100 Bioanalyzer. The rRNA was depleted using the MICROBExpress Bacterial mRNA enrichment kit (Life Technologies) according to the manufacturer’s instructions.
Single end RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and followed by sequencing using a HiSeq2500 system. RNA sequencing was performed by the Genome Sciences Facility at Penn State University in Hershey, PA. The assays were performed in duplicates, and approximately 2million reads were obtained for each library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
FP40
|
| Data processing |
Raw sequences were modified to trim the Illumina sequencing adapter using Cutadapt.
Sequence processing using the Sickle tool to verify the quality of the samples prior to further analyses.
Sequences were mapped against the genome of L. crescens BT-1 using Bowtie2.
The mapped mRNA sequences were aligned using Samtools.
mRNA sequences were counted using the HTseq tool.
Genome_build: Liberibacter crescens BT-1 (NC_019907.1)
Supplementary_files_format_and_content: Processed data files are in the form of an Htseq .txt file with gene counts.
Supplementary_files_format_and_content: DESeq2_results.txt: Processed data file is in the form of an DESeq2 results file in a .txt file with differential expression data.
|
| |
|
| Submission date |
Aug 16, 2021 |
| Last update date |
Sep 07, 2021 |
| Contact name |
Kaylie Padgett-Pagliai |
| E-mail(s) |
[email protected]
|
| Phone |
3525380181
|
| Organization name |
University of Florida
|
| Street address |
2033 Mowry Road, Lab 325 CGRC
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL30517 |
| Series (1) |
| GSE182163 |
PrbP modulates biofilm formation in Liberibacter crescens |
|
| Relations |
| SRA |
SRX11765070 |
| BioSample |
SAMN20834973 |
