|
| Status |
Public on Apr 03, 2024 |
| Title |
Paerugionsa Capture Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Pseudomonas aeruginosa PA14 |
| Characteristics |
cell type: bacterial cell
genotype: WT
media condition: chemically defined media
fraction: captured s4u-containing RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation with Trizol reagent, precipitation with GlycoBlue
Sequencing libraries were prepared from inputs and captured s4u-containing RNA. 3’ end adaptors (Table 6) were ligated 100 ng of RNA in an overnight reaction at 16C (250 nM adaptor, 1x T4 RNA ligase buffer, 1 ml of T4 RNA Ligase 1 (ssRNA Ligase), High Concentration (M0437M), 50 mM DTT (Sigma 43816-10mL), 6 ml of 50% PEG 8000 (NEB B1004A), 40 units of Ribolock RNase inhibitor EO0382). All samples were then gel purified on a denaturing 10% polyacrylamide gel (National Diagnostics, EC-829). Gels were cut between 60 to 200 nt and purified via crush and soak overnight tumble at 4C (crush gel through needle punched bottom of 500 ml tubes into 1.7 mL Eppendorf tubes, soak in 10 mM Tris pH 7.5 (15567-027), 500 mM NaCl (AM9759), 1 mM EDTA (AM9261), 0.1% SDS (351-032-101). Gel buffer mix is then transferred to SpinX columns (CLS8162-96EA) to remove remaining gel. Three volumes of 100% ethanol are added to the RNA-containing buffer for precipitation.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
WT_Paeruginosa_MTSEA-Capture_collated_processed.csv
|
| Data processing |
Raw fastqs were mapped using bowtie2 2.5.1
samtools 1.17 was used to extract tRNA reads containing the 3'CCA
Assembly: Custom transcriptomes for E. Coli and P. Aeruginosa
Supplementary files format and content: Mapped and subsetted BAM files containing mature tRNA reads
|
| |
|
| Submission date |
Jul 06, 2023 |
| Last update date |
Apr 03, 2024 |
| Contact name |
Pedro J Batista |
| E-mail(s) |
pedro.batista@nih.gov
|
| Phone |
3014356294
|
| Organization name |
National Institutes of Health
|
| Department |
National Cancer Institute
|
| Lab |
Cell Biology
|
| Street address |
37 Convent Street Bldg 37
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL30881 |
| Series (1) |
| GSE236676 |
The modification landscape of P. aeruginosa tRNAs |
|
| Relations |
| BioSample |
SAMN36344965 |
| SRA |
SRX20928219 |
