|
| Status |
Public on Apr 19, 2024 |
| Title |
Curtobacterium_Grass_32_T1_R2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial isolate
|
| Organism |
Curtobacterium |
| Characteristics |
cell type: Bacterial isolate
strain: Grass_32
clade: IV
timepoint: T1
days: 1
replicate: R2
|
| Treatment protocol |
They were then centrifuged at 2808 rcf for 15 minutes, washed twice in 0.9% saline, and resuspended in 0.9% saline. They were subjected to up to 32 days inside a desiccation chamber on glass slides. Saline was added to the slides to remove the cells, and they were added to a ZymoBiomics ZR Bashing Bead Tube and flash frozen in liquid nitrogen, and then stored in the freezer (-80C)
|
| Growth protocol |
Isolates were streaked from frozen (-80C) glycerol stock and then grown in Luria Broth and harvested at mid-log phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We used the ZymoBiomics Quick-RNA Fungal/Bacterial Kit. We lysed the cells by bead beating for 5 min at 6.5 m/sec in a MPBio FastPrep bead beater and in the final protocol step eluted into 10µL DNase/RNase free water
9 µL of total RNA was mixed with 1 µL 10x Turbo DNase Buffer and 1 µL of Turbo DNase Enzyme. The enzymatic digestion proceeded for 30 minutes at 37C in a PCR machine. We inactivated the reaction by mixing in 2 µL of DNase Inactivation buffer. Subsequently, we followed the Kapa RNA Hyper Prep Protocol. For fragmentation we incubated the total RNA with the Fragment Prime Elute Buffer for 6 minutes at 85°C
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
there are two sets of paired-end reads for each sample, for increased depth. These are technical replicates and can be combined
|
| Data processing |
Raw reads were QC'ed and low quality reads were removed using trimmomatic.
Bowtie2 was used to remove rRNA by mapping the reads to the SILVA v0.2 ssRNA database
Fully closed reference genomes were annotated using PROKKA
Salmon was used to map mRNA to the reference genome
DESeq was used in R for differential abundance testing
Assembly: GCA_001864975.1
Supplementary files format and content: The processed data file is one combined DESeq differential abundance table for all the strains. Day 0 was used as the control, representing the unstressed mid-log cells, and the two constasts are day 1 vs day 0 and day 32 vs day 0
Supplementary files format and content: The DESeq output underwent the LFC processing step as recommended in their manual
|
| |
|
| Submission date |
Apr 21, 2023 |
| Last update date |
Apr 19, 2024 |
| Contact name |
Nicholas C Scales |
| E-mail(s) |
[email protected]
|
| Organization name |
UC Irvine
|
| Department |
Ecology & Evolutionary Biology
|
| Street address |
321 Steinhaus Hall
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL33356 |
| Series (1) |
| GSE230266 |
Desiccation induces varied responses within a soil bacterial genus |
|
| Relations |
| BioSample |
SAMN34284178 |
| SRA |
SRX20044742 |
