|
| Status |
Public on Feb 13, 2017 |
| Title |
Blue_2 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA extracted from Rho prion-containing cells
|
| Organism |
Escherichia coli |
| Characteristics |
growth protocol: Log-phase culture (LB broth, Miller formulation) inoculated with one blue colony and grown for 5 hr at 37 degrees celsius
phenotype: Blue colony-color (prion-containing)
parent strain: BW27785
|
| Growth protocol |
Log-phase cultures (LB broth, Miller formulation) inoculated with either blue or pale colonies were grown for 5 hr at 37 degrees celsius. Cells were pelleted by centrifugation and flash frozen on dry ice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell pellets with TRI Reagent (MRC). RNA was precipitated, resuspended in DNase Reaction Buffer (Invitrogen) for 30 min at room temperature. DNase-treated samples were subsequently purified with an Rneasy Plus Mini Kit (Qiagen).
Purified total RNA was depleted of rRNA using a Ribo-Zero (Bacteria) rRNA Removal Kit (Illumina). cDNA libraries were constructed and sequenced on an Illumina NextSeq 500 sequencer at the Harvard Biopolymers Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Total RNA isolated from cells descended from a blue (Rho prion-containing) colony.
Blue_2.fastq (see "Data processing" Supplementary_files_format_and_content)
|
| Data processing |
All data analysis was performed using Rockhopper (McClure et al., 2013) and Escherichia coli str. K-12 substr. MG1655 as the reference genome.
Specifically, data were treated as two experiments constituting either two ("blue" cell transcriptomes) or three ("pale" cell transcriptomes) biological replicates.
Data were visualized in the Rockhopper IGV genome browser (McClure et al., 2013) and TreeView 3.0 (Saldana et al., 2004).
Genome_build: ASM584v2
Supplementary_files_format_and_content: Tab-delimited text file includes Rockhopper (McClure et al., 2013) normalized transcript abundance measurements (Expression), transcript abundance ratios (Expression Ratio), and qValues (qValue) for raw data that were treated as two experiments constituting either two ("blue" cell transcriptomes; Blue_1.fastq, Blue_2.fastq) or three ("pale" cell transcriptomes; Pale_1.fastq, Pale_2.fastq, Pale_3.fastq) biological replicates. Gene annotation, gene product description, and strand information is also included.
|
| |
|
| Submission date |
Nov 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ann Hochschild |
| E-mail(s) |
ann_hochschild@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Microbiology and Immunobiology
|
| Lab |
Hochschild Lab
|
| Street address |
4 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE90485 |
A bacterial global regulator forms a prion |
|
| Relations |
| BioSample |
SAMN06052192 |
| SRA |
SRX2372724 |
