|
| Status |
Public on May 23, 2023 |
| Title |
LU_m114 |
| Sample type |
SRA |
| |
|
| Source name |
PLBS338
|
| Organism |
Bacillus subtilis |
| Characteristics |
tissue: Lung
genotype: Wild type
treatment: IFNgIL18_d0.5
growth media: LB
|
| Treatment protocol |
Samples treated with DMS had a final concentration of 50 mM DMS added to the growth media for 5 min, then reaction was quenched with DTT. Control samples had an equivalent amount of DTT added.
|
| Growth protocol |
Bacillus subtilis PLBS338 cells were grown to mid-exponential phase in a shaking water bath at one of four temperatures, 23C, 30C, 37C, or 42C. Growth was stopped by using frozen slurry killing buffer (containing 10 mM Tris-HCl, 5 mM MgCl2, 25 mM NaN3, 1.5 mM chloramphenicol, and 12.5% ethanol)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted and frozen, and RNA was extracted using RNeasy Mini Kit, then ribosomal RNA was depleted with Ribo-Zero rRNA Removal Kit
Structure-seq2 libraries were prepared using reverse transcription with a random hexamer, ligation of a hairpin adapter, and then amplification incorporating Illumina-specific primers.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Cutadapt (1.16)
Bowtie (2.3.4.1)
StructureFold2 modules
Assembly: custom build as described in citation
Supplementary files format and content: processed data files are provided as rtsc files containing reverse transcription stop count on each nucleotide
Library strategy: Structure-seq2
|
| |
|
| Submission date |
Jan 31, 2023 |
| Last update date |
Nov 29, 2023 |
| Contact name |
Elizabeth Jolley |
| E-mail(s) |
eaj19@psu.edu
|
| 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 |
GPL32426 |
| Series (1) |
| GSE224126 |
Transcriptome-wide probing of RNA in Bacillus subtilis identified RNA thermometers that regulate translation of two glycerol permease genes |
|
| Relations |
| BioSample |
SAMN32973139 |
| SRA |
SRX19229374 |
