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Transcriptome profiling of Mesoplasma florum strain L1 using RNA sequencing (RNA-Seq) and genome-wide 5'-rapid amplification of cDNA ends (5'-RACE)

ABSTRACT: Mesoplasma florum is a near-minimal bacterium belonging to the Mollicutes class particularly characterized by its small genome, fast growth rate, and lack of pathogenic potential. Here, we report the first genome-wide transcriptomic analysis of this microorganism using directional RNA sequencing (RNA-Seq) and 5'-rapid amplification of cDNA ends (5'-RACE). 5'-RACE sequencing reads were used to identify 605 putative transcription start sites (TSSs), of which more than 400 could be associated to a conserved promoter sequence. Along with terminator predictions, these TSSs allowed the reconstruction of M. florum transcription units, covering more than 90% of annotated genes. We evaluated the expression level of all M. florum protein coding genes using paired-end RNA-Seq reads according to the number of fragments per kilobase per million of mapped reads (FPKM). FPKM values were converted to absolute transcript abundances using biomass quantification data. These efforts aim at reaching a deep understanding of global cellular mechanisms in M. florum and will guide future genome engineering projects in this simple organism.

ORGANISM(S): Mesoplasma florum

PROVIDER: GSE152985 | GEO | 2020/11/02

REPOSITORIES: GEO

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Project description:Transcriptional profiling by high throughput sequencing of RACE-PCR-amplified human brain and testis samples to determine lncRNA transcript 5' and 3'-ends (GENCODE Batch VIII a) As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. In the current phase of ENCODE we have found strong evidence that many lncRNAs transcript termini are still unknown. This experiment aims to set up an experimental validation strategy to accurately determine the 5' and 3' ends of transcripts, which is based on semi-nested RACE extensions of annotated 5' and 3' ends followed by high throughput sequencing. A total of 400 highly expressed lncRNA transcript models from Gencode 7 which did not have any CAGE/PET support were selected as the test set whereas 25 transcripts with transcript start site (TSS) supported by CAGE tags and transcript termination site (TTS) supported by PET ditags formed the positive control set. Transcript ends were amplified by RACE-PCR from brain and testis RNA samples and sequenced using the Roche 454 platform. The sequencing was performed at the Andalusian Human Genome Sequencing Centre (CASEGH), Seville, Spain. ArrayExpress Release Date: 2012-08-31 Person Roles: submitter Person Last Name: Gonzalez Person First Name: Jose Person Mid Initials: M Person Email: jmg@sanger.ac.uk Person Phone: -498006 Person Address: Wellcome Trust Genome Campus, Hinxton, UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: investigator Person Last Name: Hubbard Person First Name: Tim Person Mid Initials: Person Email: th@sanger.ac.uk Person Phone: -498055 Person Address: Wellcome Trust Genome Campus, Hinxton, UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: investigator Person Last Name: Reymond Person First Name: Alexandre Person Mid Initials: Person Email: Alexandre.Reymond@unil.ch Person Phone: Person Address: Lausanne, Switzerland Person Affiliation: University of Lausanne Person Roles: investigator Person Last Name: Guigo Person First Name: Roderic Person Mid Initials: Person Email: roderic.guigo@crg.cat Person Phone: Person Address: Barcelona, Spain Person Affiliation: Centre for Genomic Regulation (CRG) Person Roles: investigator Person Last Name: Santoyo Person First Name: Javier Person Mid Initials: Person Email: jsantoyo@bioinfomgp.org Person Phone: Person Address: Seville, Spain Person Affiliation: Andalusian Human Genome Sequencing Centre (CASEGH) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Project description:Transcriptional profiling by high throughput sequencing of RACE-PCR-amplified human brain and testis samples to determine lncRNA transcript 5' and 3'-ends (GENCODE Batch VIII b) As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. In the current phase of ENCODE we have found strong evidence that many lncRNAs transcript termini are still unknown. This experiment aims to set up an experimental validation strategy to accurately determine the 5' and 3' ends of transcripts, which is based on semi-nested RACE extensions of annotated 5' and 3' ends followed by high throughput sequencing. A total of 400 highly expressed lncRNA transcript models from Gencode 7 which did not have any CAGE/PET support were selected as the test set whereas 25 transcripts with transcript start site (TSS) supported by CAGE tags and transcript termination site (TTS) supported by PET ditags formed the positive control set. Transcript ends were amplified by RACE-PCR from brain and testis RNA samples and sequenced using the Roche 454 platform. The sequencing was performed at the Centre for Genomic Regulation (CRG), Barcelona, Spain. ArrayExpress Release Date: 2012-08-31 Person Roles: submitter Person Last Name: Gonzalez Person First Name: Jose Person Mid Initials: M Person Email: jmg@sanger.ac.uk Person Phone: -498006 Person Address: Wellcome Trust Genome Campus, Hinxton, UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: investigator Person Last Name: Hubbard Person First Name: Tim Person Mid Initials: Person Email: th@sanger.ac.uk Person Phone: -498055 Person Address: Wellcome Trust Genome Campus, Hinxton, UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: investigator Person Last Name: Reymond Person First Name: Alexandre Person Mid Initials: Person Email: Alexandre.Reymond@unil.ch Person Phone: Person Address: Lausanne, Switzerland Person Affiliation: University of Lausanne Person Roles: investigator Person Last Name: Guigo Person First Name: Roderic Person Mid Initials: Person Email: roderic.guigo@crg.cat Person Phone: Person Address: Barcelona, Spain Person Affiliation: Centre for Genomic Regulation (CRG) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Dataset Information

Transcriptome profiling of Mesoplasma florum strain L1 using RNA sequencing (RNA-Seq) and genome-wide 5'-rapid amplification of cDNA ends (5'-RACE)

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