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GenomicsA functional map of DNA-associated proteolysis
We established an assay to localize DNA-associated proteins that are slated for degradation by the ubiquitin-proteasome system. The genome-wide map we describe here ties proteolysis to active enhancer elements and to transcription start sites of specific gene families. ChIP-sequencing of ubiquitin a...
ORGANISM(S): Mus musculus 
2013-12-01 | E-GEOD-33821 | biostudies-arrayexpress
TranscriptomicsBulk RNAseq of mouse gastruloids developed with homemade N2B27 and commercial NDiff227
Procedure: three independent experiments were done to generate three 96-well plates of E14-Tg2A gastruloids made with either homemade or commercial N2B27. 48 gastruloids per sample were used for RNA extraction using the Qiagen RNeasy Micro Kit. Library preparation and sequencing were done by the CRG...
ORGANISM(S): Mus musculus 
2025-04-01 | E-MTAB-14893 | biostudies-arrayexpress
ProteomicsThermal proteome profiling of cell cycle
We combined quantitative mass spectrometry with thermal profiling to systematically analyze the thermal stability and solubility of proteins during the eukaryotic cell cycle on a proteome-wide scale.
ORGANISM(S): Homo sapiens (Human) 
2018-05-02 | PXD008646 | Pride
Complexes Disordered proteins Cell cycle Thermal stability 
ProteomicsThermal proteome profiling in Escherichia coli
We adapted thermal proteome profiling (TPP) to study the thermostability of Escherichia coli proteins in vivo. We monitored the E. coli meltome and proteome at different growth phases, in a tolC knock-out mutant and after drug treatment.
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2018-07-09 | PXD009495 | Pride
Target engagement Escherichia coli Drugs Growth phase Meltome Thermal proteome profiling 
ProteomicsThermal proteome profiling of anti-HEV compound
We performed thermal proteome profiling (TPP) to identify targets of a new anti hepatitis E virus compound.
ORGANISM(S): Homo sapiens (Human) Hepatitis E virus type 1 
2021-01-04 | PXD014485 | Pride
Target engagement Drugs Thermal proteome profiling 
ProteomicsThermal proteome profiling of darobactin in Escherichia coli
We performed two dimensional thermal proteome profiling (2D-TPP) of darobactin to study its impact in Escherichia coli.
ORGANISM(S): Escherichia coli 
2019-10-29 | PXD013319 | Pride
Target engagement Darobactin Escherichia coli Drugs Thermal proteome profiling 
ProteomicsThermal proteome profiling in of CA-074me
We performed thermal proteome profiling (TPP) to study changes to protein thermal stability and abundance of CA-074me (cathepsin inhibitor) in RAW264.7 macrophages after Salmonella typhimurium infection.
ORGANISM(S): Mus musculus (Mouse) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) 
2020-02-07 | PXD016086 | Pride
Target engagement Cathepsin inhibitor Salmonella Thermal proteome profiling 
ProteomicsThermal proteome profiling of Escherichia coli mutants
We performed two dimensional thermal proteome profiling (2D-TPP) in Escherichia coli mutants to measure changes in abundance and thermal stability.
ORGANISM(S): Escherichia coli 
2020-09-11 | PXD016589 | Pride
Escherichia coli Genetic perturbation Mutants Thermal proteome profiling 
ProteomicsThermal proteome profiling of nlpI mutants in Escherichia coli
We performed two dimensional thermal proteome profiling (2D-TPP) of nlpI mutants to study its function in Escherichia coli.
ORGANISM(S): Escherichia coli 
2020-02-25 | PXD016819 | Pride
Escherichia coli Knock-out Thermal proteome profiling 
ProteomicsThermal proteome profiling of temporal dynamics of infection of SARS-CoV-2
We performed two dimensional thermal proteome profiling (2D-TPP) to profile the infection dynamics of SARS-CoV-2 infection in Caco-2 cells.
ORGANISM(S): Homo sapiens (Human) 
2020-11-23 | PXD022115 | Pride
Virus Sars-cov-2 Infection Coronavirus Thermal proteome profiling 
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