|
| Status |
Public on Mar 10, 2015 |
| Title |
efp_mops_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cell cultures
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype/variation: efp
media: MOPS
monosome purification: sucrose gradient
|
| Growth protocol |
400 mL cultures were grown to OD600 of 0.4, filtered, and flash frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were lysed in a freezer mill, clarified, digested with MNase, and monosomes were purified over a sucrose gradient (except cw31).
RNA fragments 20 - 40 nt in length were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA: ribosome footprints
|
| Data processing |
Reads with N bases or Phred < 20 were dropped. The linker sequence was trimmed, and reads mapping to rRNA or tRNA sequences were subtracted.
Remaining reads were mapped to the E coli K12 MG1655 genome using bowtie.
Genome_build: NC_000913ver2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, with 3'-assignment method, normalized by number of reads.
|
| |
|
| Submission date |
Dec 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Allen R Buskirk |
| E-mail(s) |
buskirk@jhmi.edu
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Molecular Biology and Genetics
|
| Street address |
725 N. Wolfe St
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL18956 |
| Series (1) |
| GSE64488 |
High Precision Analysis of Translational Pausing in Bacteria Lacking EFP by Ribosome Profiling |
|
| Relations |
| BioSample |
SAMN03272892 |
| SRA |
SRX823694 |
