|
| Status |
Public on Mar 04, 2019 |
| Title |
RET_BWK |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BWK
treatment: Retapamulin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosome protected fragments were isolated as described in Oh et al. 2011
Libraries were generated as described in Oh et al. 2011
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
library strategy: Ribo-seq
Reads were trimmed with Cutadapt 1.1.a
Reads were first aligned to a ncRNA fasta file and the unmapped reads were subsequently mapped to the respective genomes with Bowtie 1.1.2
P-sites of the ribosomes were mapped as 15 nts away from the 3prime end of the read and used to calculate nucleotide rpm
Genome_build: U00096, CP001509_3
Supplementary_files_format_and_content: wig, rpm values of the calculated ribosmal P-site
|
| |
|
| Submission date |
Nov 04, 2018 |
| Last update date |
Oct 10, 2019 |
| Contact name |
Alexander Mankin |
| E-mail(s) |
shura@uic.edu
|
| Organization name |
University of Illinois at Chicago
|
| Department |
Pharmacognosy
|
| Street address |
900 S. Ashland Avenue Room 3056
|
| City |
Chicago |
| State/province |
Illinois (IL) |
| ZIP/Postal code |
60607 |
| Country |
USA |
| |
|
| Platform ID |
GPL14548 |
| Series (1) |
| GSE122129 |
Retapamulin-assisted Ribo-seq reveals the alternative bacterial proteome |
|
| Relations |
| BioSample |
SAMN10373503 |
| SRA |
SRX4976959 |
