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ProteomicsProteomic Analysis of RAP (RNA Antisense Purification) isolated RNPs (RiboNucleotide Particles) harboring the novel lncRNA mimi
In neurons, mRNAs and associated RNA-binding proteins assemble into ribonucleoprotein (RNP) granules essential to regulate mRNA trafficking, local translation, and turnover. Dysregulation of RNA-protein condensation can disturb synaptic plasticity. We report that the novel lncRNA mimi is a constitut...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2022-10-12 | PXD034457 | Pride
Elav  drosophila  relative lfq (label free quantification) quantitative proteomics Rap rna protein complex isolation  uv crosslinking  fly brain  neurons  lncrna mimi  fne  rbp9 
ProteomicsMudPIT analyses of the proteins co-purified with RAP01-HA, RAP21-HA, and negative controls from late asexual Plasmodium falciparum parasites
[NOTE: PF3D7_1470600 previously named RAP14 is now named RAP21]. HA-affinity purification - Purified late asexual parasites from parental and HA-tagged PF3D7_0105200 (RAP01-HA) and PF3D7_1470600 (RAP21-HA) lines were suspended in 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 1 % Triton X-100, 1 mM ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Plasmodium Falciparum 3d7 (ncbitaxon:36329) 
2020-12-24 | MSV000086636 | MassIVE
TranscriptomicsIdentification of novel tissue-specific transcription arising from E-cadherin/CDH1 intron2: a novel protein isoform increases gastric cancer cell invasion and angiogenesis.
E-cadherin, a protein encoded by the CDH1 gene is the dominant epithelial cell adhesion molecule playing a crucial role in epithelial tissue polarity and structural integrity. The progression of 90% or more carcinomas is believed to be mediated by disruption of normal E-cadherin expression, subcellu...
ORGANISM(S): Homo sapiens 
2012-08-01 | E-GEOD-32540 | biostudies-arrayexpress
ProteomicsA direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells
Schmidt N, Lareau CA, Keshishian H, Melanson R, Zimmer M, Kirschner L, Ade J, Simone Werner S, Caliskan N, Lander ES, Vogel J, Carr SA, Bodem J, and Munschauer M. 2020. SARS-CoV-2 infections pose a global threat to human health and an unprecedented research challenge. Among the most urgent tasks is ...
ORGANISM(S): Sars-cov-2 Homo Sapiens (ncbitaxon:9606) 
2020-07-13 | MSV000085734 | MassIVE
ProteomicsA KRAS-responsive long non-coding RNA controls microRNA
RNA Antisense Purification and Mass Spectrometry (RAP-MS) was performed to explore the potential RNA binding proteins of lncRNA KIMAT1
ORGANISM(S): Homo sapiens (Human) 
2021-03-01 | PXD024388 | Pride
H1299 Mass spectrometry Non-small cell lung cancer Rna-binding proteins Rna antisense purification Kimat1 
ProteomicsMudPIT analysis of the polysome-associated proteins from Plasmodium falciparum
The Plasmodium falciparum strain 3D7 was cultured in human O+ erythrocytes at 5% haematocrit as previously described (Trager and Jensen, 1976). Cultures were synchronized twice at ring stage with 5% D-sorbitol treatments performed eight hours apart (Lambros and Vanderberg, 1979). Cultures (8% parasi...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Plasmodium Falciparum 3d7 (ncbitaxon:36329) 
2016-03-29 | MSV000079613 | MassIVE
TranscriptomicsThe transcriptome of anthers of rice gamyb mutant expressing various GAMYB homologs was measured at the microspore stage.
To confirm the function of the GAMYB homologs for Selaginella moellendorffii and Physcomitrella patens in rice cells, we examined the expression profile in the anthers of transgenic plants, which OsGAMYB, SmGAMYB, or PpGAMYB2 is expressed under the control of the rice GAMYB promoter in rice gamy mut...
ORGANISM(S): Oryza sativa Japonica Group 
2011-11-07 | E-GEOD-32652 | biostudies-arrayexpress
TranscriptomicsGenome wide binding and transcriptome analysis of human FXR in primary human hepatocytes [HTS]
We report the genome-wide profiling of FXR binding by ChIP-seq from GW4064 or DMSO treated primary human hepatocytes. We reported altered RNA expression profiles in primary human hepatocypes upon GW4064 treatment compared to DMSO control by RNA-seq. We also reported the altered RNA expression profil...
ORGANISM(S): Homo sapiens 
2014-07-24 | E-GEOD-57227 | biostudies-arrayexpress
TranscriptomicsRNA Affinity Purification followed by sequencing (RAP-seq) allows identification of transcriptome-wide RBP binding sites using recombinant RBPs and purified total cellular RNA
RAPseq is a new in vitro method used to study RNA-protein interactions at scale. In RAPseq, a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP-Halo fusion is then incubated with fragmented native total RNA that retains endogenous s...
ORGANISM(S): Homo sapiens 
2023-12-29 | E-MTAB-10834 | biostudies-arrayexpress
TranscriptomicsComparative analysis of transcripts from mia40-4int mutant and wild-type Saccharomyces cerevisiae strains quantified in RNA-seq experiment
The vast majority of the mitochondrial proteome originates from nuclear genes and is transported into the organelle after synthesis in the cytosol. Complex machineries, which maintain the specificity of protein import and sorting exist. Dysfunctions of mitochondrial protein sorting pathways result i...
ORGANISM(S): Saccharomyces cerevisiae 
2015-07-31 | E-MTAB-3588 | biostudies-arrayexpress
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