|
| Status |
Public on Sep 14, 2023 |
| Title |
WT, DMS, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
MG1655
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
cell line: MG1655
genotype: WT
treatment: DMS
|
| Treatment protocol |
Samples were treated with DMS at a final concentration of 40 mM or EDC at a final concentration of 35 mM by adding chemical to the growth media for 5 min, then reaction was quenched with DTT. Control samples had an equivalent amount of DTT added.
|
| Growth protocol |
Escherichia coli MG1655 cells were grown to mid-exponential phase in a shaking water bath at 37 °C. 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) and immediately plunging on ice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy MINI kit (Qiagen) and then ribosomal RNA was depleted using RiboMinus (Thermo Fisher)
Structure-seq2 libraries were prepared by reverse transcription with a random hexamer primer, 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 |
Read trimming using fastq_trimmer.py in StructureFold2 with Cutadapt 3.5
Read mapping using fastq_mapper.py in StructureFold2 with Bowtie 2.4.4
Read filtering using sam_filter.py in StructureFold2 with Samtools 1.16
Stop counting using sam_to_rtsc.py
Depth was calculated with Samtools 1.16
Assembly: NCBI: U00096.2, NCBI: GSE52059
Supplementary files format and content: rtsc files: contains rt stop count per nucleotide
Supplementary files format and content: depth T files: contains read depth as described in citation
Library strategy: Structure-seq2
|
| |
|
| Submission date |
May 26, 2023 |
| Last update date |
Sep 14, 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 |
GPL33080 |
| Series (1) |
| GSE233607 |
In vivo-like nearest neighbor parameters accurately predict fractional RNA base-pairing in cells |
|
| Relations |
| BioSample |
SAMN35440817 |
| SRA |
SRX20526534 |
