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ProteomicsncRNA DUBR RAP-MS in HCT116 cells
Non-coding RNAs (ncRNAs) are finely tuned cellular regulators important for human cell growth and cancer progression. DUBR (also known as linc00883) is a nuclear ncRNA first discovered in mice for its role in regulating myoblast differentiation through interactions with chromatin and DNA methyltrans...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD057811 | Pride
Dubr Hct116 Ncrna Rap-ms 
MetabolomicsFSCN1 as a new druggable target in adrenocortical carcinoma

Adrenocortical carcinoma (ACC) is a rare endocrine malignancy with a high risk of relapse and metastatisation. The actin-bundling protein fascin (FSCN1) is overexpressed in aggressive ACC and represents a reliable prognostic indicator. FSCN1 has been shown to synergize with the Rho/Rac GEF VAV2 i...

2023-03-20 | MTBLS6402 | MetaboLights
GenomicsXist exploits three-dimensional chromosome architecture to spread across the X-chromosome
Many large noncoding RNAs (lncRNAs) regulate chromatin, but the mechanisms by which they localize to genomic targets remain unexplored. Here we investigate the localization mechanisms of Xist during X-chromosome inactivation (XCI), a paradigm of lncRNA-mediated chromatin regulation. During the maint...
ORGANISM(S): Mus musculus 
2013-05-30 | E-GEOD-46918 | biostudies-arrayexpress
GenomicsXist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing
Xist orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the 3-dimensional structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here w...
ORGANISM(S): Mus musculus 
2016-07-24 | E-GEOD-80510 | biostudies-arrayexpress
GenomicsRNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites
We developed a general method based on RNA Antisense Purification (RAP) to identify the intermolecular RNA-RNA interactions of a target RNA (RAP-RNA). RAP-RNA identifies endogenous RNA-RNA complexes through in vivo crosslinking, RNA capture with antisense oligonucleotides, and high-throughput RNA se...
ORGANISM(S): Mus musculus 
2014-09-01 | E-GEOD-55914 | biostudies-arrayexpress
MetabolomicsJiayi Huatu Decoction mitigates intestinal fibrosis via a gut microbiota–metabolite axis

Ulcerative colitis (UC)-associated intestinal fibrosis represents a serious and currently untreatable complication, highlighting an urgent need for novel therapeutic strategies. This study investigates the therapeutic potential of Jiayi Huatu Decoction (JHD), a traditional Chinese herbal formula ...

2026-02-09 | MTBLS13875 | MetaboLights
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
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 
MetabolomicsBile acid is a significant host factor shaping the gut microbiome of diet induced obese mice (untargeted metabolome profile assay)

BACKGROUND: Intestinal bacteria are known to regulate the bile acid (BA) homeostasis via intestinal biotransformation of BAs and stimulating the expression of fibroblast growth factor 19 through intestinal nuclear farnesoid X receptor (FXR). On the other hand, BAs directly regula...

2017-11-23 | MTBLS545 | MetaboLights
MetabolomicsBile acid is a significant host factor shaping the gut microbiome of diet induced obese mice (targeted bile acid analysis assay)

BACKGROUND: Intestinal bacteria are known to regulate the bile acid (BA) homeostasis via intestinal biotransformation of BAs and stimulating the expression of fibroblast growth factor 19 through intestinal nuclear farnesoid X receptor (FXR). On the other hand, BAs directly regula...

2017-11-23 | MTBLS547 | MetaboLights
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