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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
TranscriptomicsCAGE-seq of human colon cancer cell line (HCT116) upon TBX3 overexpression
The Wnt/β-catenin signaling pathway plays crucial roles in nearly all parts of embryonic development and adult stem cell homeostasis. Its aberrant activation has been linked to many diseases such as developmental irregularities and various severe forms of cancer, with colorectal cancer (CRC) as a pr...
ORGANISM(S): Homo sapiens 
2024-01-01 | E-MTAB-13647 | biostudies-arrayexpress
TranscriptomicsTranscriptomic study (RNAseq) of Brachypodium distachyon ecotypes Bd21 and Bd2-3 under submergence stress
Purpose: The goal of this study is to compare the transcriptomes expressed during submergence stress of two Brachypodium distachyon ecotypes with contrasting survival under this stress. Bd21 is a submergence sensitive ecotype with EC50 of 2.5 days and Bd2-3 is a tolerant ecotype with EC50 of 4 days....
ORGANISM(S): Brachypodium distachyon 
2016-01-04 | E-GEOD-74222 | biostudies-arrayexpress
TranscriptomicsEstablishment of photosynthesis through chloroplast development is controlled by two distinct regulatory phases
A pluripotent inducible cell line was generated from Arabidopsis to address the limitations of traditional in planta dicot systems and to develop a well-controlled experimental setup where the individual regulatory check points of chloroplast development could be defined. Following light exposure, t...
ORGANISM(S): Arabidopsis thaliana 
2018-05-12 | E-MTAB-5777 | biostudies-arrayexpress
TranscriptomicsCooperative binding of DNA sequence non-specific HMGbox Factor Ubf and TBP-TAF complex SL1 determines RNA Polymerase I promoter recognition in vivo and its dysfunction underlies the Ubf-E210K neuroregression syndrome
Transcription of the >200 rRNA genes (rDNA) by RNA Polymerase I (RPI) determines as much as 35% of total nuclear RNA synthesis and is a major determinant of cell growth implicated in a range of hypertrophic and developmental disorders. Activation of the rDNA involves the formation of an extended nuc...
ORGANISM(S): Mus musculus 
2021-08-31 | E-MTAB-10433 | biostudies-arrayexpress
TranscriptomicsPRPF8 CLIP seq for iPSC, kidney organoid, retinal organoid, and retinal epithelium derived from c.6926A>C RPE with Retinitis Pigmentosa patients and CRISPR/Cas9 corrected
Retinitis Pigmentosa is a group of inherited eye disorders characterized by progressive degeneration of photoreceptor cells in the retina, leading to vision loss and eventual blindness. One of the known genetic mutations associated with RP is the c.6926A>C mutation in the RPE (retinal pigment epithe...
ORGANISM(S): Homo sapiens 
2024-03-13 | E-MTAB-13171 | biostudies-arrayexpress
MetabolomicsTowards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor-like kinase
Soil-borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our pr...
2021-08-11 | MTBLS2597 | MetaboLights
TranscriptomicsRNA-seq of human adipose-derived mesenchymal stem cells cultured in hypoxia against normoxia controls, and human tympanic membrane keratinocytes
Human adipose-derived mesenchymal stem cells were cultured either in hypoxia (Hx; <0.1% oxygen) or standard culture conditions (normoxia, Nx) over 48 hours in serum-free medium. Human tympanic membrane keratinocytes were cultured in standard culture conditions over 48 hours in serum-free medium.
ORGANISM(S): Homo sapiens 
2022-03-31 | E-MTAB-9979 | biostudies-arrayexpress
TranscriptomicsRNA Sequencing Quantitative Analysis of cell lines derived from tumours from two mouse models of human osteosarcoma that recapitulate clinically distinct human osteosarcoma subtypes.
Purpose: Osteosarcoma (OS) is the most common primary bone malignancy. OS consists of several subtypes including fibroblastic, osteoblastic and chondroblastic OS. We have developed genetically engineered mouse models of human OS that recapitulate two distinct subtypes, fibroblastic (Osx-CreLox p53-/...
ORGANISM(S): Mus musculus 
2015-07-06 | E-GEOD-58916 | biostudies-arrayexpress
GenomicsChIP-seq for NF-YA and Pbx4 on whole zebrafish embryos at 3.5hpf
NF-YA and Pbx4 ChIP-seq on pooled whole zebrafish embryos at 3.5 hours post fertilisation (hpf)
ORGANISM(S): Danio rerio 
2020-04-28 | E-MTAB-8137 | biostudies-arrayexpress
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