Sort   by:  
 Page size 
ProteomicsImprovements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics data sets
We have performed a Proteogenomics meta-analysis of data sets deposited in ProteomeXchange: PXD000265, PXD000313, PXD000923, PXD001030, PXD001058, PXD002291, PXD002739, PXD002740 and PXD003156 and using 29 RNA-Seq data sets on rice (Oryza sativa). We created a search database comprising translated r...
ORGANISM(S): Oryza sativa (Rice) 
2018-10-30 | PXD008960 | Pride
Rice Proteogenomics Proteomics Rna-seq Big data analysis 
TranscriptomicsYM500: An integrative small RNA sequencing (smRNA-seq) database for microRNA research
MicroRNAs (miRNAs) are small RNAs of ~22 nucleotides in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next generation sequencing applications, have reshaped the miRNA resea...
ORGANISM(S): Homo sapiens 
2012-12-03 | E-GEOD-39841 | biostudies-arrayexpress
TranscriptomicsDe Novo Transcriptomic Analysis of Hydrogen Production in the Green Alga Chlamydomonas moewusii through RNA-Seq
Background: Microalgae can make a significant contribution towards meeting global renewable energy needs in both lipid-based liquid biofuel and hydrogen biofuel. The development of energy-related products and chemicals from algae could be accelerated with improvements in systems biology tools, and r...
ORGANISM(S): Chlamydomonas moewusii 
2013-09-04 | E-GEOD-46225 | biostudies-arrayexpress
TranscriptomicsRNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM® genes for hereditary disorders of hearing and balance
Purpose: To identify orthologous genes in Xenopus that are implicated in deafness and vestibular disorders in humans and to compare RNA-Seq and microarray to determine the advantages of each technology for Xenopus transcriptomic analysis. Methods: Inner ear RNA from X. laevis stages 56-58 was isolat...
ORGANISM(S): Xenopus laevis 
2016-02-28 | E-GEOD-69701 | biostudies-arrayexpress
ProteomicsCooper Salvia columbariae chia seeds, roots, hypocotyls, and cotyledons
Cooper sought to increase the sensitivity of peptide detection and broaden the range of tissues covered through his analysis of chia proteomes. Targeted tissues were ungerminated seeds and the roots, hypocotyls, and cotyledons of five-day-old seedlings. As in Husselmann 2017, TCEP was employed for...
ORGANISM(S): Salvia Columbariae (ncbitaxon:95165) 
2021-02-15 | MSV000086863 | MassIVE
ProteomicsKlein / Husselmann chia under salt and caffeic acid stress
Husselmann 2017: Following gel and TOF/TOF investigation of chia salinity stress by Achmat Williams [http://hdl.handle.net/11394/5650], Husselmann and Klein designed an LC-MS/MS experiment for five replicates in each of five cohorts: caffeic acid stress, salt stress, both stresses, and controls for ...
ORGANISM(S): Salvia Hispanica (ncbitaxon:49212) 
2021-02-12 | MSV000086861 | MassIVE
ProteomicsSearching NE-enriched proteomics datasets for splice junction peptides
MudPIT datasets for NaOH-extracted and Salt-and-Detergent (SD)-extracted rat nuclear membranes were obtained from skeletal muscle and liver tissue as described in the following references: Wilkie GS, Korfali N, Swanson SK, Malik P, Srsen V, Batrakou DG, de las Heras J, Zuleger N, Kerr AR, Florens L,...
ORGANISM(S): Rattus Norvegicus (ncbitaxon:10116) 
2018-01-18 | MSV000081951 | MassIVE
TranscriptomicsTransposon-based construction of strand-specific RNA-seq libraries
We have developed two methods for efficiently consructing RNA-seq libraries using transposition. Each method constructs high quality RNA-seq libraries when compared to standard approaches. One of the methods (Directional Tn-RNA-seq) maintains strand-of-origin information and exhibits strand specifi...
ORGANISM(S): Homo sapiens 
2011-10-10 | E-GEOD-32307 | biostudies-arrayexpress
TranscriptomicsA rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages
The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat tran...
ORGANISM(S): Rattus norvegicus 
2014-02-14 | E-GEOD-53960 | biostudies-arrayexpress
ProteomicsEMpire: Deep isoform level integration of the transcriptome, translatome, and proteome
In this study, we make used of mRNA-seq and its ability to reliably quantify isoforms, integrating this data with ribosome profiling and LC-MS/MS, to assign ribosome footprints and peptides at the isoform level. We leverage the principle that most cell types, and even tissues, predominantly express...
ORGANISM(S): Homo sapiens (Human) 
2018-08-21 | PXD008693 | Pride
Proteomics Mrna-seq Protien isoforms Lc-ms/ms 
Sort   by:  
 Page size