Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Longread Sequencing for Wild Type E. coli Transcriptomes using SMRT-Cappable-seq

ABSTRACT: Next Generation Longread Sequencing for Wild Type E. coli Transcriptomes using SMRT-Cappable-seq

PROVIDER: PRJNA481586 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

SMRT-Cappable-seq reveals complex operon variants in bacteria

Project description:We develop a method SMRT-Cappable-seq that combines the isolation of unfragmented bacterial primary transcripts with the longread sequencing using PacBio. This method allows the identification and phasing of the transcrription start sites and the termination sites, thereby revealing the operon structure and the regulation of gene experession in bacteria. Applied to E.coli, our method results in an unprecedented definition of the transcriptome with 34% of the known operons from RegulonDB database being extended by at least one gene, and identifies a total of 2300 operons from which around 900 are novel.

2018-07-22 | GSE117273 | GEO

SMRT-Cappable-seq reveals complex operon variants in bacteria.

Project description: Not available

| S-EPMC6131387 | biostudies-literature

Refining the transcriptional maps of Pseudomonas aeruginosa phages using ONT-cappable-seq

Project description:The global transcriptional profiles of Pseudomonas aeruginosa phages LUZ19, LUZ24, YuA, PAK_P3, 14-1 and phiKZ was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units.

2024-03-13 | GSE231702 | GEO

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Project description: Not available

| S-EPMC3233386 | biostudies-literature

Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing.

Project description: Not available

| S-EPMC3880972 | biostudies-literature

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NS-DADm mice myocardium Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived heart transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: myocardium mRNA profiles of 6-week-old wild-type (WT) and whole-body knock-in mutations in DADs of both NCOR and SMRT (NS-DADm) mice were generated by Agilent 2100 Bio analyzer. we filter the low quality reads (More than 20% of the bases qualities are lower than 10),reads with adaptors and reads with unknown bases (N bases more than 5%)to get the clean reads. Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP &INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis andfunctional annotations Results: Using an optimized data analysis workflow, we find genes upregulated and enriched in NS-DADm myocardium that were consistent with HDAC3 inhibitor treated heart compared with WT Conclusions: Our study represents the first detailed analysis of genes expression in myocardium of HDAC3 enzymatic activity-dead NS-DADm mice

2020-12-15 | GSE163215 | GEO

Next Generation Sequencing Analysis of Wild Type and VAChTNkx2.1-Cre-flox/flox Hippocampal Transcriptomes

Project description:Purpose: The goals of this study are to compare next-generation sequencing-derived hippocampal transcriptome profiling from mice lacking hippocampal Acetycholine release to evaluate the role of the neurotransmitter in hippocampal gene expression.

2017-12-31 | E-MTAB-3897 | biostudies-arrayexpress

Enrichment of Wolbachia Endosymbiont Transcripts from Host Nematode RNA by Cappable-seq

Project description:We report the application of Cappable-seq to selectively enrich prokaryotic endosymbiont transcripts from mixed host-symbiont total RNA.

2017-01-05 | GSE93139 | GEO

Next Generation Sequencing Analysis of Wild Type and SRSF10-/- embryonic day 13.5 heart Transcriptomes

Project description:We generated the SRSF10 -/- mice, and collected their embryonic heart at 13.5 and controls. Then, we extracted RNAs of embryonic heart and performed next generation sequencing. By comparing sequcing data from WT and SRSF10 -/- samples, we profiled the alternative splicing events and gene expression regulated by SRSF10 during mouse heart development process. E13.5 embryonic heart mRNA profiles of wild type (WT) and SRSF10-/- mice were generated by deep sequencing, using Illumina HiSeq2000.

2015-04-01 | E-GEOD-66965 | biostudies-arrayexpress

Expression data from 3T3-MEFs derived from wild-type and SMRT RID mutant mice

Project description:SMRT (silencing mediator of retinoid and thyroid hormone receptors) is recruited by numerous transcription factors to mediate lineage and signal dependent transcriptional repression. We generated a knock-in mutation in the receptor interaction domain (RID) of SMRT (SMRTmRID) that solely disrupts its interaction with nuclear hormone receptors. SMRTmRID-derived 3T3-MEFs display a dramatically increased adipogenic capacity and accelerated differentiation rate. We measured global gene expression in wild-type versus SMRTmRID-derived 3T3-MEFs in the undifferentiated state to examine which pathways were altered. Our results demonstrate that SMRT-RID dependent repression is a key determinant of the adipogenic set point. Keywords: SMRTmRID expression compared to wild-type

2009-01-07 | GSE13143 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data