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Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), Pseudomonas putida KT2440 genome (NCBI:txid160488) and Acinetobacter baylyi ADP1 genome (NCBI:txid62977) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene. Overall design: Bacterial mRNA profiles of E. coli K-12 LE392, P.putida KT2440 and A.baylyi ADP1 in response to 0 mg/L (control), 10 mg/L Duloxetine, 1 and 10 mg/L Sertraline, 50 mg/L Escitalopram, 10 mg/L Fluoxetine, 100 mg/L Bupropion and 50 mg/L Agomelatine for 2 h, in triplicate, using Illumina HiSeq 2500"],"repository":["ENA"],"description_synonyms":["High-Throughput RNA, Thymoleptics., Bacterium coli, High Throughput DNA Sequencing, Transcriptome, Nucleotide Sequencing, determination, Transcriptome Profile, Massively-Parallel, Expression Profiles, High-Throughput DNA Sequencing, Gene Expression Profile, Gene, High-Throughput DNA, Profiles, Antidepressant Drug, Medication, Antidepressive Agent, Illumina, Next-Generation Sequencing, Agent, Gene Expression, High-Throughput RNA Sequencing, Ion Torrent Sequencing, thymoanaleptics, Bacillus coli, Deep, DNA Sequencing, Massively-Parallel Sequencing, Expression Signatures, chemical analysis, Gene Expression Signatures, Thymoanaleptic, Next-Generation, Antidepressant Medication, Ion Torrent, Gene Expression Signature, Enterococcus coli, Massively Parallel Sequencing, Expression Profile, Next Generation Sequencing, Deep Sequencing, Transcriptome Profiles, Antidepressive, Antidepressant, thymoleptic drugs, antidepressant drugs, Ion Proton Sequencing, Escherichia/Shigella coli, thymoleptics, Illumina Sequencing, Profile, Thymoanaleptics, Antidepressants, Pyrosequencing, Signatures, Sequencing, E. coli, High Throughput Sequencing, Drug, Thymoleptic, High Throughput RNA Sequencing, Bacterium coli commune, High-Throughput Sequencing, Expression Signature, antidepressants, Gene Expression Profiles, Transcriptomes, High-Throughput, RNA Sequencing, High Throughput Nucleotide Sequencing, assay, Signature, Antidepressant Drugs, Ion Proton, High-Throughput Nucleotide"],"name_synonyms":["High-Throughput RNA, Thymoleptics., Bacterium coli, High Throughput DNA Sequencing, Transcriptome, Nucleotide Sequencing, determination, Transcriptome Profile, Massively-Parallel, Expression Profiles, High-Throughput DNA Sequencing, Gene Expression Profile, Gene, High-Throughput DNA, Profiles, Antidepressant Drug, Medication, Antidepressive Agent, Illumina, Next-Generation Sequencing, Agent, Gene Expression, High-Throughput RNA Sequencing, Ion Torrent Sequencing, thymoanaleptics, Bacillus coli, Deep, DNA Sequencing, Massively-Parallel Sequencing, Expression Signatures, chemical analysis, Gene Expression Signatures, Thymoanaleptic, Next-Generation, Antidepressant Medication, Ion Torrent, Gene Expression Signature, Enterococcus coli, Massively Parallel Sequencing, Expression Profile, Next Generation Sequencing, Deep Sequencing, Transcriptome Profiles, Antidepressive, Antidepressant, thymoleptic drugs, antidepressant drugs, Ion Proton Sequencing, Escherichia/Shigella coli, thymoleptics, Illumina Sequencing, Profile, Thymoanaleptics, Antidepressants, Pyrosequencing, Signatures, Sequencing, E. coli, High Throughput Sequencing, Drug, Thymoleptic, High Throughput RNA Sequencing, Bacterium coli commune, High-Throughput Sequencing, Expression Signature, antidepressants, Gene Expression Profiles, Transcriptomes, High-Throughput, RNA Sequencing, High Throughput Nucleotide Sequencing, assay, Signature, Antidepressant Drugs, Ion Proton, High-Throughput Nucleotide"],"additional_accession":[]},"is_claimable":false,"name":"Next Generation Sequencing Facilitates Quantitative Analysis of E. coli K-12 LE392, P. putida KT2440, and Acinetobacter baylyi ADP1 Transcriptomes under various antidepressant exposure","description":"Next Generation Sequencing Facilitates Quantitative Analysis of E. coli K-12 LE392, P. putida KT2440, and Acinetobacter baylyi ADP1 Transcriptomes under various antidepressant exposure","dates":{"last_updated":"2023-05-19","first_public":"2022-10-07"},"accession":"PRJNA753825","cross_references":{"GEO":["GSE181900"],"PubMed":["36054646"]}}