Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data

ABSTRACT: Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data

PROVIDER: PRJNA667257 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data

Project description:The accuracy of methods for assembling transcripts from short-read RNA sequencing data is limited by the lack of long-range information. Here we introduce Ladder-seq, an approach that separates transcripts according to their lengths prior to sequencing and uses the additional information to improve the quantification and assembly of transcripts. Using simulated data, we demonstrate that a kallisto algorithm extended to process Ladder-seq data quantifies transcripts of complex genes with substantially higher accuracy than conventional kallisto. For reference-based assembly, a modified StringTie2 algorithm reconstructs a single transcript with 30.8% higher precision than its conventional counterpart and is >30% more sensitive for complex genes. For de novo assembly, a modified Trinity algorithm correctly assembles 78% more transcripts than conventional Trinity, while improving precision by 78%. In experimental data, Ladder-seq reveals 40% more genes harboring isoform switches compared with conventional RNA-seq and unveils widespread changes in isoform usage upon m6A depletion by Mettl14 knock-out.

2021-10-11 | GSE158985 | GEO

Within-host diversity improves phylogenetic reconstruction of SARS-CoV-2 outbreaks

Project description:Within-host diversity improves phylogenetic reconstruction of SARS-CoV-2 outbreaks

| PRJEB53224 | ENA

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data.

Project description:Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances. We apply the method to natural and simulated microbial communities, and correctly recover community structure from known and previously unreported rRNA gene sequences. An implementation of the method is freely available at https://github.com/csmiller/EMIRGE.

| S-EPMC3219967 | biostudies-literature

Frequency of delayed gastric emtpying depending on the alimentaty reconstruction (Billroth-II vs. Roux-en-Y) following pancreatoduodenectomy

Project description:Interventions: Group 1: Data collection from our pancreatic resection database (whipple procedure with Billroth-II reconstruction). Data collected: Age, BMI, diagnosis, risk factors, intraoperative characteristics, delayed gastric emptying, surgical complications, length of stay. Group 2: Data collection from our pancreatic resection database (whipple procedure with Roux-en-Y reconstruction). Data collected: Age, BMI, diagnosis, risk factors, intraoperative characteristics, delayed gastric emptying, surgical complications, length of stay. Primary outcome(s): Frequency and severity of delayed gastric emptying according to the International Study Group of Pancreatic Surgery (ISGPS) definition during the hospital stay and readmission. Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: other

| 2432935 | ecrin-mdr-crc

Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities.

Project description:Premise of the Study:DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants. Methods:To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants. Results:Performance tests on simulated data suggest that Kraken and Centrifuge outperform MegaBLAST. Kraken tends to be the most conservative approach with high precision, whereas Centrifuge has higher sensitivity. Reanalysis of 13,000 years of ancient sedimentary DNA from North America characterizes potential post-glacial vegetation succession. Discussion:Classification method choice has an impact on performance and any downstream interpretation of results. The reanalysis of ancient DNA from glacial lake sediments yielded vegetation histories that varied depending on method, potentially changing paleoecological conclusions drawn from molecular evidence.

| S-EPMC5895191 | biostudies-literature

Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads.

Project description:MOTIVATION: A reconstruction of full-length transcripts observed by next-generation sequencer or tiling arrays is an essential technique to know all phenomena of transcriptomes. Several techniques of the reconstruction have been developed. However, problems of high-level noises and biases still remain and interrupt the reconstruction. A method is required that is robust against noise and bias and correctly reconstructs transcripts regardless of equipment used. RESULTS: We propose a completely new statistical method that reconstructs full-length transcripts and can be applied on both next-generation sequencers and tiling arrays. The method called ARTADE2 analyzes 'positional correlation', meaning correlations of expression values for every combination on genomic positions of multiple transcriptional data. ARTADE2 then reconstructs full-length transcripts using a logistic model based on the positional correlation and the Markov model. ARTADE2 elucidated 17 591 full-length transcripts from 55 transcriptome datasets and showed notable performance compared with other recent prediction methods. Moreover, 1489 novel transcripts were discovered. We experimentally tested 16 novel transcripts, among which 14 were confirmed by reverse transcription-polymerase chain reaction and sequence mapping. The method also showed notable performance for reconstructing of mRNA observed by a next-generation sequencer. Moreover, the positional correlation and factor analysis embedded in ARTADE2 successfully detected regions at which alternative isoforms may exist, and thus are expected to be applied for discovering transcript biomarkers for a wide range of disciplines including preemptive medicine. AVAILABILITY: http://matome.base.riken.jp CONTACT: toyoda@base.riken.jp SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

| S-EPMC3315713 | biostudies-literature

Proteome validation for novel full-length genes in the giant panda

Project description:we applied RNA-seq to detect novel expressed transcripts in 12 tissues of giant pandas, using a transcriptome reconstruction strategy combining reference-based and de novo methods. Then we used mass spectrometry method to identify proteomes of five selected tissues, aiming at validating these novel full-length genes we identified.

2015-12-23 | PXD002917 | Pride

Full-length transcriptome reconstruction reveals large diversity of RNA isoforms and open reading frames in rat hippocampus

Project description:Full-length transcriptome reconstruction reveals large diversity of RNA isoforms and open reading frames in rat hippocampus

| PRJNA526538 | ENA

Impact of short photoperiod length on smoltification (RNAseq)

Project description:Impact of short photoperiod length on smoltification (RNAseq)

| PRJEB45301 | ENA

The amniotic fluid proteome improves prediction of imminent delivery relative to quantitative cervical length: a cross-sectional study in women with a short cervix

Project description:For women identified as at risk for preterm birth attributable to a sonographic short cervix, the determination of imminent delivery is crucial for patient management. The current study aimed to identify amniotic fluid proteins that could predict imminent delivery in asymptomatic patients with a short cervix. An aptamer-based multiplex platform was used to profile 1,310 AF proteins, and the significance of protein dysregulation was determined by moderated t-tests between women who destined to deliver within two weeks of amnicentesis. The area under the receiver operating characteristic curve was calculated to determine whether protein abundance in combination with cervical length improved the prediction of imminent delivery after amnicentesis as compared to cervical length alone.

2022-09-26 | GSE186135 | 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