|
| Status |
Public on Apr 14, 2022 |
| Title |
Hfx med: Panarchaea - rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Archaeal cells
|
| Organism |
Haloferax mediterranei |
| Characteristics |
strain: ATCC33500
genotype: <delta>pyrE
|
| Growth protocol |
Cells (3-4 biological replicates) were precultured to stationary phase, and then diluted back to a starting OD. These cultures were then grown to mid-log phase in appropriate rich media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
~3-5mL of cells in mid-log phase were flash-frozen in Liq N2 and stored at -80C. Total RNA was extracted from cell pellets using the Agilent Absolutely RNA Miniprep kit. RNA was measured using Nanodrop and quality-checked using Bioanalyzer.
1-10ng of total RNA was used as input for rRNA removal by the various kits tested here. The kit protocol included creation of a dsDNA library from the depleted RNA as template. This library was quality-checked using DNA High Sensitivity chip on the Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Total RNA depleted using siTools Panarchaea kit
HFX_pyrE_pan_1
ΔpyrE
|
| Data processing |
50bp paired reads were quality checked using FastQC, adapter sequences trimmed using Trim Galore and Cutadapt.
Result sequences were aligned to the Hbt sal genome (GCF_000006805.1), Hfx vol (GCF_000025685.1_ASM2568v1), Hca his (GCF_000223905.1_ASM22390v1), or Hfx med (GCF_000306765.2_ASM30676v2) genomes (as appropriate) using Bowtie2.
BAM files were generated using samtools, they were inputs to generate count files using HTSeq (count files associated with each sample are included in this GEO dataset). Note that these BAM files are sorted by name, not by read.
Counts mapping to rRNA genes as a percentage of counts mapping to all genes were obtained and reported.
Supplementary files format and content: *.count: Tab-delimited text files include raw counts.
|
| |
|
| Submission date |
Apr 13, 2022 |
| Last update date |
Apr 14, 2022 |
| Contact name |
Amy K Schmid |
| E-mail(s) |
amy.schmid@duke.edu
|
| Organization name |
Duke University
|
| Department |
Biology
|
| Lab |
Schmid
|
| Street address |
125 Science Dr.
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27707 |
| Country |
USA |
| |
|
| Platform ID |
GPL32167 |
| Series (1) |
| GSE200776 |
Testing different rRNA removal methods in 4 species of model halophilic archaea |
|
| Relations |
| BioSample |
SAMN27571599 |
| SRA |
SRX14847220 |
