Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

3'GAmES: Systematic refinement of gene termini by mRNA 3' end sequencing

ABSTRACT: Motivation: Alternative cleavage and polyadenylation generates mRNA 3´ isoforms in a cell type- and tissue-specific manner. Due to finite available RNA sequencing data of organisms with vast cell type complexity, currently available gene annotation resources are incomplete, which poses significant challenges to the comprehensive interpretation and quantification of transcriptomes. Results: We developed 3'GAmES, a stand-alone analysis pipeline to identify and annotate novel (cell-type-specific) mRNA 3´ isoforms from 3' mRNA sequencing datasets. When applied to mouse embryonic stem cells or Zebrafish embryos, 3'GAmES expands currently available mRNA 3' annotations by 47% and 57%, respectively; and the resulting annotations significantly improve comprehensive gene-tag counting by cost-effective 3' mRNA sequencing to more accurately mirror whole-transcriptome RNAseq measurements. As a stand-alone analysis tool, 3'GAmES systematically augments cell type-specific transcript annotations and increases the robustness of quantitative gene expression profiling by 3' mRNA sequencing.

ORGANISM(S): Danio rerio

PROVIDER: GSE146738 | GEO | 2020/03/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic signatures of flight muscle, brain and leg tissues during Drosophila pupal development

Project description:Alternative splicing produces multiple, distinct mRNA transcripts from the same gene locus. To explore tissue-type specific gene expression and alternative splicing, we generated mRNA-Seq data from pupal tissues dissected from Drosophila. This allowed us to compare expression between dissected, highly enriched brain and indirect flight muscle (IFM) samples as well as whole legs. Bioinformatic analysis allowed us to characterize tissue-specific differences in gene expression as well as alternative splicing among the three tissues, as well as to identify a multitude of novel splicing events that are not currently contained in the Drosophila annotation. This suggests that tissue or cell-type specific sequencing at multiple timepoints during the fly life cycle will help extend existing annotations, and novel splice junction discovery is an important consideration in mRNA-Seq data analysis.

2022-01-25 | GSE194199 | GEO

Model-based Analysis of 2-Color Arrays (MA2C)

Project description:High-density oligonucleotide tiling-microarrays are currently providing a powerful tool for genome-wide in vivo DNA footprinting assays, yielding unprecedented insights into tissuespecific protein-DNA interactions and chromatin structure. Despite the impressive advances, however, the technology still suffers from numerous complications caused by background noise and probespecific effects. A few computational methods modeling sequencerelated probe effects are now available for Affymetrix tiling arrays, but no counterpart is yet available for two-color arrays. A novel normalization method based on the GC content of probes is developed for two-color tiling-arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. Accompanying the normalization method, a robust algorithm for detecting peak regions is formulated and also shown to perform well compared to other approaches. The tools presented herein have been implemented for NimbleGen tiling arrays as a stand-alone Java program, which can also display various plots of statistical analysis for quality control of experiments. Upon changing the file format, the program also works on Agilent data. Keywords: ChIP-chip

2007-06-26 | GSE7523 | GEO

High-throughput single-molecule long-read RNA sequencing analysis of tissue-specific genes and isoforms in lettuce (Lactuca sativa L.)

Project description:This study utilized the HIT-ISOseq method for high-throughput sequencing of RNA isoforms across multiple lettuce samples, generating millions of long reads per PacBio Sequel II SMRT Cell. Analysis of six tissue types revealed tissue-specific gene expression and RNA isoforms, facilitating updates to the lettuce reference genome annotation with expanded functional annotations.

2024-05-23 | GSE264560 | GEO

A ligation-independent sequencing method reveals tRNA fragments with blocked 3' termini

Project description:Despite the numerous sequencing methods available, the vast diversity in size and chemical modifications of RNA molecules makes the capture of the full spectrum of cellular RNAs a difficult task. By combining quasirandom hexamer priming with a custom template switching strategy, we developed a method to construct sequencing libraries from RNA molecules of any length and with any type of 3’ terminal modification, allowing the sequencing and analysis of virtually all RNA species. Ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to comprehensively characterize changes in small non-coding RNAs and mRNAs simultaneously, with performance comparable to separate dedicated methods. With LIDAR, we comprehensively characterized the coding and non- coding transcriptome of mouse embryonic stem cells, neural progenitor cells, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared to traditional ligation-dependent sequencing methods, and uncovered the presence of tDRs with blocked 3’ ends that had previously escaped detection. Our findings highlight the potential of LIDAR to systematically detect all RNAs in a sample and uncover new RNA species with potential regulatory functions.

2023-06-06 | GSE233343 | GEO

Hypoxia and Intrinsic Transcriptomic Subtyping of Soft Tissue Sarcoma

Project description:The heterogeneity and multiple histological categories of soft tissue sarcoma (STS) underlie a need for better classification schemes to improve their management. As none are currently available, we aimed to derive hypoxia and intrinsic molecular subtype mRNA abundance signatures for localized soft tissue sarcoma. RNA sequencing was used to identify genes induced by hypoxia in seven STS cell lines.

2017-11-17 | E-MTAB-6087 | biostudies-arrayexpress

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing

Project description:Alternative pre-mRNA splicing has long been proposed to greatly contribute to proteome complexity. However, the extent to which mature mRNA isoforms are successfully translated into protein remains controversial. Here, we used high-throughput RNA sequencing and mass spectrometry (MS)-based proteomics to better evaluate the translation of alternatively spliced mRNAs. To increase proteome coverage and improve protein quantitation, we optimized cell fractionation and sample processing steps at both the protein and peptide level. Furthermore, we generated a custom spectral library trained on analysis of RNA-Seq data with MAJIQ, an algorithm optimized to detect differential and unannotated junction usage for a given splice site. Using this custom library to match against tandem mass spectra acquired by data independent acquisition (DIA), we improved identification of splicing-derived proteoforms by ~30% as compared to use of the SwissProt database alone. Moreover, our increased depth and detection of proteins allowed us to track changes in the transcriptome and proteome induced by T cell stimulation, as well as fluctuations in protein sub-cellular localization. In sum, our data here confirms that use of generic databases in proteomic studies under-estimates the number of spliced mRNA isoforms that are translated into protein and provides a workflow that improves isoform detection in large-scale proteomic experiments.

2019-10-14 | PXD012556 | Pride

eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [APA-Seq]

Project description:Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized cell types. However, the molecular mechanisms underlying this translational burst and the involvement of initiation factors remains largely unknown. Here, we investigate the roles of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP and alternative polyadenylation (APA)-Seq, we show eIF3 crosslinks to many neurologically relevant mRNAs in NPCs. Our data reveal eIF3 predominantly interacts with 3’ untranslated region (3’-UTR) termini of multiple mRNA isoforms, adjacent to the poly(A) tail. High eIF3 crosslinking at 3’-UTR termini of mRNAs correlates with high translational activity, as determined by ribosome profiling. We identify the transcriptional regulator inhibitor of DNA binding 2 (ID2) mRNA as a case in which active translation levels and eIF3 crosslinking are dramatically increased upon early NPC differentiation. Furthermore, we find that eIF3 engagement at 3’-UTR ends is dependent on polyadenylation. The results presented here show that eIF3 engages with 3’-UTR termini in highly translated mRNAs, supporting a role of mRNA circularization in the mechanisms governing mRNA translation in NPCs.

2023-12-08 | GSE246786 | GEO

eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [Quick-irCLIP]

2023-12-08 | GSE246727 | GEO

Gene expression profile at single cell level of peripheral blood mononuclear cells (PBMCs) from 17 healthy donor

Project description:Quantifying aging rate is important for evaluating age-associated decline and mortality. Here we generate a similar dataset for a reference 17-sample aging cohort to compute a single cell level aging clock. The cell type annotations are available in https://doi.org/10.6084/m9.figshare.23789844.v1.

2023-06-29 | GSE213516 | GEO

Identification of the molecular basis of anti-cancer effect of Huaier.

Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None. Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes. For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..

| 2612481 | ecrin-mdr-crc

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