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ProteomicsHuman VAPome Analysis Reveals MOSPD1 and MOSPD3 as Membrane Contact Site Proteins Interacting with FFAT-Related FFNT Motifs
Membrane contact sites (MCS) are intracellular regions where two organelles come closer to exchange information and material. The majority of the endoplasmic reticulum (ER) MCS are attributed to the ER-localized tether proteins VAPA, VAPB, and MOSPD2. These recruit other proteins to the ER by intera...
ORGANISM(S): Homo sapiens (Human) 
2023-06-29 | PXD043399 | Pride
Emery-dreifuss muscular dystrophy  ffat  ffnt  mospd1  mospd2  mospd3  vapa  vapb  endoplasmic reticulum  membrane contact sites 
ProteomicsPerinuclear Vimentin-RNF26 contacts integrate ER and endosomal responses to ER stress
Compartmentalization of organelles in space and time affects their functional state and enables higher order regulation of essential cellular processes. How organellar residence is maintained in a defined area of the cell remains poorly understood. In this study, we uncover a new role for intermedia...
ORGANISM(S): Homo sapiens (Human) 
2023-09-05 | PXD040760 | Pride
Vimentin Er stress Endosomes Intermediate filaments Rnf26 
UnknownUsing synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing.
Not available
S-EPMC12406214 | biostudies-literature
GenomicsGenome-wide assessment of differential roles for p300 and CBP in transcription regulation
Through ChIP-Seq analysis with the Illumina Whole Genome Analyzer, we identify binding sites for P300 (EP300) and CBP (CREBBP) in Human glioblastoma T98G cells that were cell cycle synchronized before and after stimulation. In our analysis, we focused on the identification of genes differentially bo...
ORGANISM(S): Homo sapiens 
2010-03-30 | E-GEOD-21026 | biostudies-arrayexpress
TranscriptomicsDigital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes
RNA-Seq is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification. We developed a simple strategy for mitigating these complications, allowing truly digital RNA-Seq. Following reverse tra...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2012-01-07 | E-GEOD-34449 | biostudies-arrayexpress
TranscriptomicsQuantitative single-cell RNA-seq
Purpose: We applied cDNA molecule counting using unique molecular identifiers combined with high-throughput sequencing to study the transcriptome of individual mouse embryonic stem cells, with spike-in controls to monitor technical performance. We further examined transcriptional noise in the embryo...
ORGANISM(S): Mus musculus 
2013-12-20 | E-GEOD-46980 | biostudies-arrayexpress
ProteomicsSmall-Molecule Activity-Based Probe for Monitoring Ubiquitin 2 C‑Terminal Hydrolase (UCHL1) Activity in Live Cells and Zebrafish 3 Embryos
Many reagents have emerged to study the function of specific enzymes in vitro. On the other hand, target specific reagents are scarce or need improvement, allowing investigations of the function of individual enzymes in their native cellular context. Here we report the development of a target-select...
ORGANISM(S): Homo sapiens (Human) 
2020-09-18 | PXD021557 | Pride
Orbitrap Human 
UnknownPharmacokinetic and pharmacodynamic properties of calaspargase pegol Escherichia coli L-asparaginase in the treatment of patients with acute lymphoblastic leukemia: results from Children's Oncology Group Study AALL07P4.
Not available
S-EPMC4239306 | biostudies-literature
GenomicsGenome wide binding of ATF4 and CEBPG bZIP transcription factors in MEFs under amino acid deprived (AAD) conditions
The integrated stress response (ISR) controls cellular adaptations to nutrient deprivation, redox imbalances and ER stress. ISR genes are upregulated in stressed cells, primarily by the bZIP transcription factor ATF4 through its recruitment to cis-regulatory C/EBP:ATF response elements (CAREs) toget...
ORGANISM(S): Mus musculus 
2015-11-19 | E-GEOD-75165 | biostudies-arrayexpress
GenomicsPromoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-Seq
Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression. We describe here evidence that promoter-proximal pausing is a general feature of transcription ...
ORGANISM(S): Mus musculus 
2010-04-02 | E-GEOD-20530 | biostudies-arrayexpress
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