"growth protocol: Log-phase culture (LB broth, Miller formulation) inoculated with one blue colony and grown for 5 hr at 37 degrees celsius"	"characteristics_ch1.1"
"phenotype: Blue colony-color (prion-containing)"	"characteristics_ch1.2"
"parent strain: BW27785"	"characteristics_ch1.3"
"All data analysis was performed using Rockhopper (McClure et al., 2013) and Escherichia coli str. K-12 substr. MG1655 as the reference genome."	"data_processing.1"
"Specifically, data were treated as two experiments constituting either two (\"blue\" cell transcriptomes) or three (\"pale\" cell transcriptomes) biological replicates."	"data_processing.2"
"Data were visualized in the Rockhopper IGV genome browser (McClure et al., 2013) and TreeView 3.0 (Saldana et al., 2004)."	"data_processing.3"
"Genome_build: ASM584v2"	"data_processing.4"
"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."	"data_processing.5"
"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)."	"extract_protocol_ch1.1"
"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."	"extract_protocol_ch1.2"
"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."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Total RNA extracted from Rho prion-containing cells"	"source_name_ch1.1"
"Blue_2"	"title.1"
"RNA-Seq"	"library_strategy.1"
"growth protocol: Log-phase culture (LB broth, Miller formulation) inoculated with one blue colony and grown for 5 hr at 37 degrees celsius"	"characteristics_ch1.1"
"phenotype: Blue colony-color (prion-containing)"	"characteristics_ch1.2"
"parent strain: BW27785"	"characteristics_ch1.3"
"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."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Total RNA extracted from Rho prion-containing cells"	"source_name_ch1.1"