Sort   by:  
 Page size 
ProteomicsEnhanced interactome capture (eRIC) of steady-state and arsenite stressed HuH7 cell cytoplasmic and nuclear fractions
HuH7 cells were grown under steady-state conditions or exposed 100 µM Na-arsenite for 1h. Subsequently, the cells were irradiated or not with 253 nm UV light (150 mJ/cm^2), processed to nuclear and cytoplasmic fractions, and subjected to eRIC for determining the nuclear and cytoplasmic RNA-binding ...
ORGANISM(S): Homo sapiens (Human) 
2020-04-06 | PXD016735 | Pride
Human Cell culture Arsenite 
ProteomicsDe-novo synthesized targets of NMD and ER stress
Nonsense-mediated mRNA decay (NMD) has originally been described as a surveillance mechanism to inhibit the expression of mRNAs with truncated open reading frames (ORFs) and to contribute to the fidelity of gene expression. It is now recognized that NMD also controls the expression of physiological ...
ORGANISM(S): Homo sapiens (Human) 
2016-02-22 | PXD002648 | Pride
Upr Aha Nmd Dtt Click chemistry Upf1 Pulsed silac 
ProteomicsIdentification of HLA class I-presented peptides in MSI CRC model cell line HCT-116
HCT-116 cells were treated either with 5 µM of the NMD inhibitor 5-azacytidine (PMID: 25319547) or DMSO (negative solvent control) for 24 h to examine differences in HLA class I-mediated peptide presentation. Moreover, data were used for the identification of tumor-specific neoepitopes originating f...
ORGANISM(S): Homo sapiens (Human) 
2021-04-14 | PXD021755 | Pride
Hla Microsatellite instability Immunopeptidomics Colorectal cancer 
ProteomicsEnhanced RNA interactome capture (eRIC) of human malignant bone tumor cells and normal bone/mesenchymal cells
Patient-derived bone tumor (osteosarcoma and giant cell tumor of bone) cells, and the normal mesenchymal stem cells and osteoblasts were cultured and subjected to UV crosslinking (UV) at 254 nm or without crosslinking (noUV) as negative controls. Subsequently, RNA-binding proteins (RBPs) were identi...
ORGANISM(S): Homo sapiens (Human) 
2024-02-28 | PXD038185 | Pride
Eric Human Osteosarcoma 
TranscriptomicsArray-CGH screening of pediatric T-lymphoblastic leukemias (n=73)
DNA copy-number profiling of 73 T-ALLs Keywords: Genetic modification Comparison of tumor DNA (tumor) versus control DNA (pool of lymphocyte DNA from 10 healthy donors). Whole-genome screening for DNA copy-number aberrations using array-based comparative genomic hybridization (aCGH). Tumor DNA label...
ORGANISM(S): Homo sapiens 
2007-08-25 | E-GEOD-8738 | biostudies-arrayexpress
TranscriptomicsGRHL1 acts as a tumor suppressor in neuroblastoma and is negatively regulated by MYCN and HDAC3
Neuroblastoma is an embryonic solid tumor of neural crest origin and accounts for 11% of all cancer-related deaths in children. Novel therapeutic strategies are therefore urgently required. MYCN oncogene amplification, which occurs in 20% of neuroblastomas, is a hallmark of high risk. Here we aimed ...
ORGANISM(S): Homo sapiens 
2014-05-22 | E-GEOD-47407 | biostudies-arrayexpress
TranscriptomicssiRNA profiling of human HeLa cells response to UPF1 depletion
Nonsense-mediated mRNA decay (NMD) is a molecular pathway of mRNA surveillance that ensures rapid degradation of mRNAs containing premature translation termination codons (PTCs) in eukaryotes. Originally, NMD was thought of as a quality control pathway that targets non-functional mRNAs arising from ...
ORGANISM(S): Homo sapiens 
2008-06-15 | E-GEOD-7009 | biostudies-arrayexpress
TranscriptomicsTranscription profiling time series of human bone marrow samples stored at room temperature for up to 48 hours after aspiration
Impact of pre-analytical handling on Bone Marrow (BM) mRNA Gene Expression: We have investigated the impact of RNA extraction protocols and time delays (24 and 48h) between sample aspiration and RNA extraction on RNA quality and gene expression profiles. Intact RNA can be extracted from BM samples s...
ORGANISM(S): Homo sapiens 
2007-07-28 | E-GEOD-1347 | biostudies-arrayexpress
TranscriptomicsModified iCLIP sequencing of HEK293 cells with antibody PTBP1
For modified iCLIP experiment, 4SU was used for crosslinking as described in published protocol (citation is bellow) and the RNase conditions were optimised to ensure efficient RNase I-dependent fragmentation. In detail, HEK293T cells were grown on 10 cm 2 dishes, incubated for 8 h with 100 M 4SU an...
ORGANISM(S): Homo sapiens 
2016-11-24 | E-MTAB-5027 | biostudies-arrayexpress
TranscriptomicsPTBP1 - Modified iCLIP
This experiments was performed in HeLa cells according to the iCLIP protocol with the following modifications: no antiRNase was used and the concentration of RNase I was 0.5 U/ml. In iCLIP4, the dephosphorylation step was omitted from the standard protocol. The rest of the protocol was identical to...
ORGANISM(S): Homo sapiens 
2016-11-24 | E-MTAB-5026 | biostudies-arrayexpress
Sort   by:  
 Page size