|
| Status |
Public on Jun 27, 2023 |
| Title |
Acetate, DMS, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
DSM 2834
|
| Organism |
Methanosarcina acetivorans C2A |
| Characteristics |
strain: C2A
cell type: DSM 2834
genotype: WT
treatment: DMS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pelleted cells were resuspended in 1 mL of Trizol, and the RNA was extracted according to the Direct-zol RNA MiniPrep kit (Zymo Research).
DMS-treated total RNA is reverse transcribed using a random hexamer primer to generate cDNA that is prepared for sequencing by ligating a hairpin adapter and then PCR amplifying products while incorporating Illumina sequencing primers. Libraries are size-selected on a denaturing PAGE gel between 200-600 nucleotides and then submitted for sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
All data processing steps were done using StrutureFold2
Library strategy: Structure-seq2
|
| |
|
| Submission date |
Apr 12, 2023 |
| Last update date |
Jun 27, 2023 |
| Contact name |
Elizabeth Jolley |
| E-mail(s) |
[email protected]
|
| Phone |
8148633109
|
| Organization name |
Pennsylvania State University
|
| Lab |
Bevilacqua
|
| Street address |
239 Chemistry Bldg, Pennsylvania State University
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL33336 |
| Series (1) |
| GSE229536 |
In vivo structure probing of RNA in Archaea: Novel insights into the ribosome structure of Methanosarcina acetivorans |
|
| Relations |
| SRA |
SRX19947869 |
| BioSample |
SAMN34159596 |
