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ProteomicsThe matrisome: in silico definition and in vivo characterization of tumor extracellular matrix
Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO. Mol Cell Proteomics 2012, 11: M111.014647. doi:10.1074/mcp.M111.014647. PMCID:PMC3322572. Tranche_hash:onoKvMCC9umP0dW2GlZSGN/DVfz6tqoyRvsA16h351RjGJZiqjk0wWGYQB9+zPpRj+ASAgKsd779N0Td4250FCPJ6jUAAAAAAABFoQ==
2013-11-20 | MSV000078494 | MassIVE
TranscriptomicsRNA-seq from tibialis muscles from rats aged 15 months (adult) and 27 months (old)
To gain new insights into molecular changes in skeletal muscle aging and disease with a special focus on differential alternative splicing and senescence, we performed RNA-seq on tibialis muscles from 15 months old (adult, a) and 27 months old (old, o) rats. Whole (w) muscle samples were prepared fo...
ORGANISM(S): Rattus norvegicus 
2021-06-26 | E-MTAB-10582 | biostudies-arrayexpress
TranscriptomicsRNA-seq from gastrocnemius muscles from rats aged 6, 12, 18, 21, 24 and 27 months
To gain new insights into molecular changes in skeletal muscle aging and disease with a special focus on differential alternative splicing and senescence, we performed RNA-seq on rat gastrocnemius muscles of animals aged 6, 12, 18, 21, 24 and 27 months, using a rat sarcopenia model we had previously...
ORGANISM(S): Rattus norvegicus 
2021-06-26 | E-MTAB-10583 | biostudies-arrayexpress
ProteomicsIntegrative proteogenomics for differential expression and splicing variation in a DM1 mouse model
Here, we performed a large-scale coordinated transcriptomic and proteomic analysis to characterize a DM1 mouse model (HSALR) in comparison to wild-type. Our integrative proteogenomics approach comprised gene- and splicing-level assessments for mRNA and protein. It recapitulated many known instances ...
ORGANISM(S): Mus musculus (Mouse) 
2024-01-26 | PXD025589 | Pride
Mouse model Proteogenomics Transcriptomics Alternative splicing Proteomics Myotonic dystrophy type 1 (dm1) 
TranscriptomicsGlobal effects of the CSR-1 RNA interference pathway on transcriptional landscape
Argonaute proteins and their small RNA co-factors short interfering RNAs (siRNAs) are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) antisense to germline trans...
ORGANISM(S): Caenorhabditis elegans 
2014-02-28 | E-GEOD-49946 | biostudies-arrayexpress
TranscriptomicsZFP-1(AF10)/DOT-1 Complex Opposes H2B Ubiquitination to Reduce Pol II Transcription
Inhibition of transcriptional elongation plays an important role in gene regulation in metazoans, including C. elegans, which lacks Negative Elongation Factor homologs. Here we combine genomic and biochemical approaches to dissect a novel role of C. elegans AF10 homolog, ZFP-1, in transcriptional c...
ORGANISM(S): Caenorhabditis elegans 
2013-07-05 | E-GEOD-47132 | biostudies-arrayexpress
TranscriptomicsHighly Aneuploid Zebrafish Malignant Peripheral Nerve Sheath Tumors have Genetic Alterations Similar to Human Cancers
Aneuploidy is a hallmark of human cancers, but most mouse cancer models lack the extensive aneuploidy seen in many human tumors. The zebrafish is becoming an increasingly popular model for studying cancer. Here we report that malignant peripheral nerve sheath tumors (MPNSTs) that arise in zebrafish ...
ORGANISM(S): Danio rerio 
2010-09-08 | E-GEOD-23666 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of C. elegans L1-L2 stage nematodes wild type and four mutants (alg-1, zfp-1, rde-4, lin-35)
Expession data from L1-L2 stage nematodes (C. elegans), wild type and four mutants (alg-1, zfp-1, rde-4, lin-35). In C. elegans, a vast number of endogenous short RNAs corresponding to thousands of genes have been discovered recently. This finding suggests that these short interfering RNAs may contr...
ORGANISM(S): Caenorhabditis elegans 
2009-01-13 | E-GEOD-13258 | biostudies-arrayexpress
GenomicsNkx2-1 Represses a Latent Gastric Differentiation Program in Lung Adenocarcinoma
Tissue-specific differentiation programs become dysregulated during cancer evolution. The transcription factor Nkx2-1 is a master regulator of pulmonary differentiation that is downregulated in poorly differentiated lung adenocarcinoma. Here we use conditional murine genetics to study the fate of l...
ORGANISM(S): Mus musculus 
2013-04-09 | E-GEOD-43252 | biostudies-arrayexpress
TranscriptomicsSuppression of Lung Adenocarcinoma Progression by Nkx2-1
Despite the high prevalence and poor outcome of patients with metastatic lung cancer, the mechanisms of tumour progression and metastasis remain largely uncharacterized. We modelled human lung adenocarcinoma, which frequently harbours activating point mutations in KRAS1 and inactivation of the p53-p...
ORGANISM(S): Mus musculus 
2011-01-27 | E-GEOD-26874 | biostudies-arrayexpress
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