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TranscriptomicsTranscription profiling of Xenopus tropicalis tadpole tail tissue regeneration following removal
In this experiment, we show transcription profiling of the Xenopus tropicalis tadpole tail tissue regeneration following removal. The tail tissues include its spinal cord, notochord, muscle, and dorsal aorta. We characterized the early, intermediate, and late stages of Xenopus tropicalis tail regene...
ORGANISM(S): Xenopus tropicalis 
2010-10-01 | E-MEXP-2420 | biostudies-arrayexpress
TranscriptomicsThe rcf1-1 mutation affects global gene expression in Arabidopsis thaliana with or without cold stress.
Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of cold-responsive genes and used the Affymetrix whole-genome arrays to define downstream targets of this important protein. We used the microarra...
ORGANISM(S): Arabidopsis thaliana 
2013-02-25 | E-GEOD-39090 | biostudies-arrayexpress
TranscriptomicsGenome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under cold stress as determined by tiling array analysis.
Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regula...
ORGANISM(S): Arabidopsis thaliana 
2013-02-25 | E-GEOD-41378 | biostudies-arrayexpress
TranscriptomicsAn PWI- and RRM Motif-Containing Protein Is Critical for Pre-mRNA Splicing and ABA Responses in Arabidopsis
We used RNA-seq platform to determine role of a splicing factor RBM25 in regulation of gene expression and pre-mRNA splicing. We found that a loss-of-function allele of RBM25, rbm25-1, causes up- and down-regulation of a large number of genes. We further found that the rbm25-1 mutation results in d...
ORGANISM(S): Arabidopsis thaliana 
2015-10-28 | E-GEOD-66737 | biostudies-arrayexpress
ProteomicsProteogenomic analysis of rice hypoxic germination
Post-transcriptional mechanisms, including alternative splicing (AS) and alternative translation initiation (ATI), have been used to explain the protein diversity involved in plant developmental processes and stress responses. Rice germination under hypoxia conditions is a classical model system for...
ORGANISM(S): Oryza sativa (Rice) 
2019-11-12 | PXD010923 | Pride
Oryza sativa Proteogenomics Splicing factor Alternative splicing Hypoxia Seed germination Translation initiation 
ProteomicsSWATH-MS quantitative analysis of proteins in the rice inferior and superior spikelets during grain filling
Modern rice cultivars have large panicle, however, yield potential of these cultivars is often not fully achieved due to the poor grain-filling of their late-flowering inferior spikelets (IS). Our earlier work suggests broad transcriptional reprogramming during grain filling and shows a difference i...
ORGANISM(S): Oryza sativa (Rice) 
2017-07-03 | PXD005401 | Pride
Proteomics Swath-ms analysis Grain filling Rice. Post-transcriptional regulation 
TranscriptomicsGenome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under normal growth conditions as determined by tiling array analysis.
Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regula...
ORGANISM(S): Arabidopsis thaliana 
2013-02-25 | E-GEOD-41377 | biostudies-arrayexpress
Genomicsena-DATASET-MDACC-20-08-2014-16:58:44:853-680 - samples
This is the targeted capture deep sequencing (TCS) data for validation of the mutations discovered in the WES step. There are 58 bam files of TCS data including 48 tumor samples and 10 peripheral blood WBC samples.
EGAD00001000985 | EGA
Genomicsena-DATASET-MDACC-20-08-2014-16:52:57:923-677 - samples
This is the Whole Exome Sequencing (WES) data from 59 samples from 11 patients with lung adenocarcinomas including 48 tumor samples and 11 peripheral white blood cell samples
EGAD00001000984 | EGA
GenomicsIntra-tumor heterogeneity of localized lung adenocarcinomas defined by multi-region sequencing
Background: Intra-tumor heterogeneity (ITH) may have profound impacts on biopsy strategy, characterization of actionable targets, treatment planning, and drug resistance. ITH of lung cancers has not been well studied. Methods: We performed multi-region whole exome sequencing (average sequencing de...
EGAS00001000930 | EGA
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