{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jose Losa"],"organism":["Escherichia coli K-12"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15217"],"description":["The goal of this analysis was to perform transcriptome-wide quantification of genes expressed in E.coli BW25113 when it is grown in M9 with 2.2 g/L glycerol, M9 + 3.3 g/L sodium pyruvate, or M9 + 2.2 g/L glycerol + 2 g/L casamino acids. With this data, we aimed to determine the fractional abundance of certain transcripts, and relate that to the fractional abundance of the proteins they code for (see proteomics data in Schmidt et al 2016)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - E.coli cells were inoculated in M9 + 2.2 g/L glycerol; M9 + 3.3 g/L sodium pyruvate or M9 + 2.2 g/L glycerol + 2 g/L casamino acids. After the first overnight growth (to saturation), cells were diluted two additional times into pre-heated medium with the same composition: between the 1st and 2nd dilution, the incubation period was ~8hours; between the 2nd dilution and sample collection, the incubation period was ~15h.","Library Construction - dsDNA was tagmented using the Illumina Nextera XT kit, as per manufacturer instructions.","Nucleic Acid Extraction - For reverse transcription, 2 µg of total RNA were mixed with 1 µL 20 µM random 9N primers, 1 µL TGIRT-III RT (InGex), 4 µL 5X RT Buffer (250 mM Tris pH 8.3, 375 mM KCl, 15 mM MgCl2), 1 µL dithiothreitol 0.1 M and1 µL dNTPs (10 mM each), in a total reaction volume of 20 µL and incubated at 25 °C for 10 min, 57 °C for 1 h. To convert the RNA-DNA hybrid to dsDNA, the TGIRT-III enzyme was first degraded by addition of 1 µg Proteinase K, incubating at 37 °C for 20 min. Then Proteinase K was inactivated by addition of 0.5 µL of Sigma Aldrich Protease Inhibitor Cocktail. The reaction was used as input for the NEBNext Second Strand Module, and second strand synthesis was performed at 16 °C for 1 h, as per manufacturer instructions.","Sequencing - Samples were sequenced on a Illumina NextSeq 1000.","Sample Collection - Cells were collected in the exponential growth phase, while at a concentration of ~1.5x10^8 cells/mL. The collection was performed by centrifugation in a microcentrifuge at 20 000 rpm, for 1 min. The supernatant was discarded and the cell pellets flash-frozen in liquid N2."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads were mapped to a transcriptome reference (U00096.3) containing all E. coli genes, plus the 16S and 23S rRNAs using Bowtie2. Gene counts were then computed from BAM files and normalized to RPKM."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 1000"],"study_type":["RNA-seq of coding RNA"],"species":["Escherichia coli K-12"],"pubmed_title":["Condition-dependent, amorphous protein agglomerates control cytoplasmic rheology"],"pubmed_authors":["Jose Losa","Matthias Heinemann"],"additional_accession":[]},"is_claimable":false,"name":"E. coli BW25113 grown on minimal medium with different carbon sources","description":"The goal of this analysis was to perform transcriptome-wide quantification of genes expressed in E.coli BW25113 when it is grown in M9 with 2.2 g/L glycerol, M9 + 3.3 g/L sodium pyruvate, or M9 + 2.2 g/L glycerol + 2 g/L casamino acids. With this data, we aimed to determine the fractional abundance of certain transcripts, and relate that to the fractional abundance of the proteins they code for (see proteomics data in Schmidt et al 2016).","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:46.987Z","creation":"2025-06-11T11:58:43.987Z"},"accession":"E-MTAB-15217","cross_references":{"ENA":["ERP173356"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}