Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Polymerase Error Rates by PacBio Sequencing

ABSTRACT: Polymerase Specific Error Rates and Profiles Identified by PacBio Single Molecule Sequencing

PROVIDER: PRJEB12175 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Taq Polymerase Error Rate by PacBio Sequencing

Project description:Taq Polymerase Error Rate and Profile Determined by High Coverage Single Molecule Amplicon Sequencing

| PRJEB12157 | ENA

RNA-seq (Illumina and PacBio) of hESC

Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data. PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.

2013-10-30 | E-GEOD-51861 | biostudies-arrayexpress

Analysis and comprehensive comparison of Pacbio and Nanopore-based RNA-sequencing in Arabidopsis transcriptome

Project description:Rapidly increased studies by third-generation sequencing [Pacific Biosciences (Pacbio) and Oxford Nanopore Technologies (ONT)] have been used in all kinds of research areas. Among them, the plant full-length single-molecule transcriptome studies were most used by Pacbio while ONT was rarely used. Therefore, in this study, we developed ONT RNA-sequencing methods in plants. We performed a detailed evaluation of reads from Pacbio and Nanopore PCR cDNA (ONT Pc) sequencing in plants (Arabidopsis), including the characteristics of raw data and identification of transcripts. We aimed to provide a valuable reference for applications of ONT in plant transcriptome analysis.

2019-12-15 | GSE141641 | GEO

Exploring the Respective Contributions of DNA Polymerase Proofreading and Mismatch Repair in the Shaping of Spontaneous Mutation Rates.

Project description:The spontaneous mutation rate is a crucial parameter in molecular evolution which is maintained very low. To better characterize how proofreading activity of the DNA polymerase and Mismatch repair (MMR) which are ubiquitous in all kingdoms of life shape a mutational landscape we built B. subtilis 168-derived strains allowing conditional inactivation of either one or both of these two error reparation mechanisms. In practice, we used an IPTG-inducible promoter to control the expression of mutant alleles selected for their ability to displace by competition their functional counterparts. The first allele, denoted here mutL*, has a mutation in the ATP hydrolysis active site of MutL. The second allele, denoted here polC* encodes an exonuclease-deficient variant of PolC. Fluctuation tests and Mutation Accumulation experiments confirmed extremely high mutation rates, upon IPTG-induction, in the strain that combine these two deficient alleles in a synthetic operon (mutL*//polC*). The purpose of this transcritomic study was to better characterize this inducible system. Analysis of the data did not reveal specific transcriptional responses of the bacterium to IPTG addition and extreme mutations rates.

2024-03-25 | GSE239804 | GEO

Made in error

Project description:Made in error

| PRJEB31468 | ENA

RNA-seq (Illumina and PacBio) of hESC

Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data.

2013-10-30 | GSE51861 | GEO

Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates

Project description:Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates

| PRJNA561141 | ENA

PacBio Iso-Seq transcriptome sequencing data of multiplexed maize cDNA

Project description:Full-Length cDNA transcriptome (Iso-Seq) data sequenced on the PacBio Sequel system using 2.1 chemistry. Multiplexed cDNA library of 12 samples (3 tissues x 4 strains). Tissues: root, embryo, endosperm. Strains: B73, Ki11, B73xKi11, Ki11xB73.

2020-02-25 | E-MTAB-7837 | biostudies-arrayexpress

Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates

Project description:Transcription elongation rates influence RNA processing, but sequence-specific regulation is poorly understood. We addressed this in vivo, analyzing RNAPI in S. cerevisiae. Mapping RNAPI by Miller chromatin spreads or UV crosslinking revealed 5′ enrichment and strikingly uneven local polymerase occupancy along the rDNA, indicating substantial variation in transcription speed. Two features of the nascent transcript correlated with RNAPI distribution: folding energy and GC content in the transcription bubble. In vitro experiments confirmed that strong RNA structures close to the polymerase promote forward translocation and limit backtracking, whereas high GC in the transcription bubble slows elongation. A mathematical model for RNAPI elongation confirmed the importance of nascent RNA folding in transcription. RNAPI from S. pombe was similarly sensitive to transcript folding, as were S. cerevisiae RNAPII and RNAPIII. For RNAPII, unstructured RNA, which favors slowed elongation, was associated with faster cotranscriptional splicing and proximal splice site use, indicating regulatory significance for transcript folding.

2020-06-24 | GSE136056 | GEO

NEI Refractive Error Collaboration (KORA)

Project description:NEI Refractive Error Collaboration (KORA)

| PRJNA75817 | ENA