SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	individual: healthy child PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	disease state: control PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	carbon source: Glycerol PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	replicate: 1 PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
SRR6449111	GSE108846	GSM2914317	GPL16085	PMID_29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	contact_name	Samuel,,Miller PGCGROWTHCONDITIONS