|
Status |
Public on May 23, 2023 |
Title |
LU_m97 |
Sample type |
SRA |
|
|
Source name |
PLBS338
|
Organism |
Bacillus subtilis |
Characteristics |
tissue: Lung genotype: Wild type treatment: IL6IL10_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 |
SAMN32973154 |
SRA |
SRX19229359 |