GEO DataSets

(Submitter supplied) We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. more...

Organism:

Pseudomonas putida KT2440; Escherichia coli K-12; Plasmid RP4

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

15 Samples

Download data: XLSX

(Submitter supplied) The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of E. coli K-12 LE392, P. putida KT2440 and Acinetobacter baylyi ADP1 in response to various antidepressant concentrations for 2 h, in triplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. more...

Organism:

Escherichia coli; Acinetobacter baylyi; Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30502

24 Samples

Download data: XLS

(Submitter supplied) The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid in response to 0, 0.02, 20 and 2000 μg/L triclosan for 2 h, in duplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24570

8 Samples

Download data: XLSX

(Submitter supplied) The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid in response to 0 and 1 μg/L AgNPs or silver ion for 2 h, in duplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. more...

Organism:

Pseudomonas putida KT2440; Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26298

9 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Plasmid RP4; Escherichia coli K-12; Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

30 Samples

Download data

(Submitter supplied) The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of CuO NPs and Cu2+. The concentrations were 5 μmol/L for CuO NPs and Cu2+. The group without dosing CuO NPs or Cu2+ was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these CuO NPs and Cu2+ on transcriptional levels can be revealed. more...

Organism:

Plasmid RP4; Escherichia coli K-12; Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

9 Samples

Download data: XLSX

(Submitter supplied) The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of six non-antibiotic pharmaceuticals, including ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and iopromide. The concentrations were 0.5 mg/L for ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and 1.0 mg/L for iopromide. more...

Organism:

Plasmid RP4; Escherichia coli K-12; Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

21 Samples

Download data: XLSX

(Submitter supplied) Antibiotic resistance is exacerbated by the exchange of antibiotic resistance genes (ARGs) between microbes from diverse habitats. Plasmids are important ARGs mobile elements and are spread by horizontal gene transfer (HGT). In this study, we demonstrated the presence of multi-resistant plasmids from inhalable particulate matter (PM) and its effect on gene horizontal transfer. Three transferable multi-resistant plasmids were identified from PM in a hospital, using conjugative mating assays and nanopore sequencing. more...

Organism:

Escherichia coli HB101

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29268

1 Sample

Download data: TXT