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ProteomicsMHC-I peptidome analysis of human foreskin fibroblasts
Ribosome profiling (Ribo-seq) recently revealed the expression of thousands of short open reading frames (sORFs) in eukaryotic cells. They encode for a class of instable peptides, which evade experimental validation by whole-proteome mass spectrometry. Here, we show that computational elimination of...
ORGANISM(S): Homo sapiens (Human) 
2018-04-05 | PXD007203 | Pride
Human Hff Peptidome Mhc-i 
ProteomicsLC-MSMS of HSV-1 infected HFFs
Herpes simplex virus 1 (HSV-1) is the causative agent of the common cold sores and life-threatening disease. Here, we characterize the full complement of viral gene expression during lytic infection using an integrative Omics approach. This revealed hundreds of novel viral gene products arising from...
ORGANISM(S): Homo sapiens (Human) Human herpesvirus 1 (strain 17) (HHV-1) (Human herpes simplex virus 1) 
2020-05-22 | PXD013010 | Pride
Hsv-1 Hff Silac Lc-msms 
TranscriptomicsGenome-wide miRNA-expression analysis after p53 activation in colorectal cancer cells
In order to comprehensively identify miRNA-expression changes after p53-activation a miRNA-Seq analysis was conducted after activation of a conditional p53 allele in SW480 cells. SW480/pRTR-p53-VSV cells were subjected to miRNA-Seq analysis after 16 hours doxycycline-treatment. Kompetenzzentrum für ...
ORGANISM(S): Homo sapiens 
2015-07-21 | E-GEOD-67181 | biostudies-arrayexpress
TranscriptomicsWide-spread disruption of transcription termination in HSV-1 infection: Next generation sequencing of total and newly transcribed (4sU-RNA) RNA
Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Newly transcribed RNA was labelled by adding 500µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. N...
ORGANISM(S): Homo sapiens 
2015-05-26 | E-GEOD-59717 | biostudies-arrayexpress
TranscriptomicsWide-spread disruption of transcription termination in HSV-1 infection: Next-generation sequencing of translational activityd by ribosome profiling
Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at various times during infection with minor modification to the protocol described in Stern-Ginossar N et al., Science...
ORGANISM(S): Homo sapiens 
2015-05-26 | E-GEOD-60040 | biostudies-arrayexpress
Otherp53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses.
Data from ProteomeXchange, PXD ID: PXD001976. File: ELITE-RSLC001392.mzml. Published as part of . From the Abstract: {{i}} We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino a...
ORGANISM(S): Homo_sapiens_viruses, Human 
GPM32320017018 | GPMDB
Resource Reanalysis 
TranscriptomicsTranscriptome analysis of Bacillus subtilis salt stress adaptation
Whole-genome microarray technology and state-of-the-art proteomic techniques were applied to provide a global and time-resolved picture of the physiological response of B. subtilis cells exposed to a severe and sudden osmotic up-shift. This combined experimental approach provided quantitative data f...
ORGANISM(S): Bacillus subtilis 
2010-05-19 | E-GEOD-18345 | biostudies-arrayexpress
Proteomics,Multiomicsp53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses
We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino acids in cell culture, pSILAC) in combination with mRNA and non-coding RNA expression analyses by next generation sequencing ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-05-24 | MSV000079767 | MassIVE
ProteomicsThe HLA-Ligand-Atlas. A resource of natural HLA ligands presented on benign tissues
The human leukocyte antigen (HLA) complex regulates the adaptive immune response by showcasing the intracellular and extracellular protein content to the immune system. T cells recognize these HLA-presented peptides as self or foreign and can elicit an immune response. In this work, we describe the...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-10-31 | MSV000096271 | MassIVE
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