|
| Status |
Public on Jun 30, 2020 |
| Title |
Fraction_19 |
| Sample type |
SRA |
| |
|
| Source name |
Clarified whole cell lysate
|
| Organism |
Escherichia coli |
| Characteristics |
strain: MG1655
growth phase: Early stationary (OD 2.0)
genotype: wild type
|
| Growth protocol |
Escherichia coli MG1655 was streaked on LB plates and grown overnight at 37°C. Overnight cultures of single colonies were grown in 2 ml LB at 37°C with shaking at 220 rpm. The next day, 1:100 dilutions in fresh LB of the overnight cultures were used to start the cultures for the experiments and grown to an OD600 nm of 2.0 (early stationary phase) at 37°C with shaking at 220 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Clarified lysates were centrifuged on a glycerol gradient, which was subsequently fractionated and the RNA extracted by P/C/I extraction. Input control was isolated using TRIzol reagent.
RNA was fragmented, and the 3' TruSeq adapter ligated to the 3' end. Following cDNA synthesis, the 5' TruSeq adapter was ligated to the 3' end and the resulting cDNA amplified by PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Fraction_19
|
| Data processing |
Adaptor clipping:cutadapt
Read mapping:READemption align and segemehl
coverage calculationREADemption coverage
Genome_build: NC_000913.3
Supplementary_files_format_and_content: wiggle
|
| |
|
| Submission date |
Jun 22, 2020 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
[email protected]
|
| Organization name |
ZB MED - Information Centre for Life Sciences
|
| Department |
Information Services
|
| Lab |
Förstner Lab
|
| Street address |
Gleueler Str. 60
|
| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE152974 |
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli |
|
| Relations |
| BioSample |
SAMN15340522 |
| SRA |
SRX8595110 |
