|
| Status |
Public on Dec 06, 2017 |
| Title |
RPF MG1655 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: K12 MG1655
genotype: wild type
|
| Treatment protocol |
Samples were treated with 100ug/ml choramphenicol for 2 minutes, quick chilled on ice, washed, and frozen with liquid nitrogen
|
| Growth protocol |
Strains were grown in LB media to mid-exponential phase (OD600 = 0.5)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were thawed, lysed with bead beating, and treated with micrococcal nuclease to release single monosomes. Ribosomes were isolated by ultracentrifuging lysate over a sucrose cushion. Ribosome protected fragments (RPF) were extracted from the pelleted ribosomes with miRNeasy RNA Extraction Kit (Qiagen) and size selected between 20 and 35 bases with denaturing PAGE.
RNA samples were ligated to a 3' adaptor and reverse transcribed. The cDNA was circularized to add a 5' adaptor then PCR amplified to add sample specific barcodes.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Ribosome protected fragments (RPF)
EC_1
|
| Data processing |
Library strategy: Ribosome profiling
Basecalls were made with Casava…
Reads were trimmed to remove adaptor sequences and reads shorter than 12 bases were discarded. Reads were aligned to the E. coli rRNA sequences with bowtie with default parameters and unaligned reads were retained
Reads were aligned to the E. coli genome with bowtie using default parameters.
Read counts per gene were calculated with Htseq Count
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Raw count matrix
|
| |
|
| Submission date |
Aug 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anastasia Haley Potts |
| E-mail(s) |
anastasi@ufl.edu
|
| Organization name |
University of Florida
|
| Department |
Department of Microbiology and Cell Science
|
| Lab |
Dr. Tony Romeo
|
| Street address |
1355 Museum Drive, Bldg. 981
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32611 |
| Country |
USA |
| |
|
| Platform ID |
GPL15010 |
| Series (2) |
| GSE102385 |
The contribution of the post-transcriptional regulator CsrA to translation |
| GSE102386 |
The contribution of the post-transcriptional regulator CsrA to RNA stability and translation and identification of binding partners |
|
| Relations |
| BioSample |
SAMN07469441 |
| SRA |
SRX3073834 |
