|
| Status |
Public on Oct 03, 2018 |
| Title |
5_CK07_30S_1 |
| Sample type |
SRA |
| |
|
| Source name |
CK07_30S
|
| Organism |
Escherichia coli |
| Characteristics |
genotype/variation: {delta}7prrn-BBB
dms concentration: 100 mM
treatment time: 4 minutes
molecule subtype: Purified ribosomes; 30S ribosomal RNA
|
| Treatment protocol |
Ribosomes were treated for 4 min with 100mM DMS, and quenched with βME buffer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Modified ribosomes were isopropanol precipitated, phenol extracted, reprecipitated.
rRNA was fragmented with Zinc Chloride for 5' @ 94C. 3' ends were resolved by treatment with T4 PNK, and RNA was size-selected by gel for ~60-70nt fragments.Preadenylated IDT miRNA cloning linker 2 was ligated with T4 PNK, and the ligated products gel purified. RT was performed with TGIRTIII RT @ 60C for 1 hour, and full-length RT products were gel purified. cDNA was circularized with circ ligase, and amplified by 11-13 cycles of PCR.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
library strategy: DMS-MapSeq
adaptor removed with cutadapt
first 3 nt trimmed with FASTX trimmer
low quality bases trimmed (ShapeMapper)
Reads mapped to rRNA with Bowtie2 (ShapeMapper)
Coverage and mutations computed for each read (ShapeMapper)
Genome_build: E.coli rRNA operons B or H
Supplementary_files_format_and_content: tab-seperated text file of mutation rates (#mutations/coverage), a proxy for extent of DMS modification, for each nucleotide in each dataset.
|
| |
|
| Submission date |
Oct 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Boris Zinshteyn |
| E-mail(s) |
zinshteyn.boris@gmail.com
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Molecular Biology and Genetics
|
| Lab |
Green
|
| Street address |
725 N Wolfe St, PCTB 714
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL14548 |
| Series (1) |
| GSE105112 |
Structural characterization of ribosome variants |
|
| Relations |
| BioSample |
SAMN07809641 |
| SRA |
SRX3294628 |
