Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of non-conventional small molecule degraders and stabilizers of squalene synthase

ABSTRACT: The dataset was obtained by performing a TMTpro16plex expression proteomics experiment, where HeLa cells were treated with small molecule ligands of squalene synthase (FDFT1). The experiment was successful in re-producing previously obtained Western Blot results in regards to SQS (=FDFT1) levels and aimed at elucidating downstream effects on cholesterol biosynthesis and metabolism. The dataset comprises data for the following samples: DMSO (vehicle), KY02111, PROTAC 18, SQSI and a compound unrelated to this project (TMTpro16plex, processed by Maxquant, each collected in 30 fractions). The experiments were performed in three independent replicates for each compound (R1-R3).

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Luca laraia

PROVIDER: MSV000093137 | MassIVE | Wed Oct 18 01:04:00 BST 2023

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

Identification of non-conventional small molecule degraders and stabilizers of squalene synthase

Project description:The dataset was obtained by performing a TMTpro16plex expression proteomics experiment, where HeLa cells were treated with small molecule ligands of squalene synthase (FDFT1). The experiment was successful in re-producing previously obtained Western Blot results in regards to SQS (=FDFT1) levels and aimed at elucidating downstream effects on cholesterol biosynthesis and metabolism. The dataset comprises data for the following samples: DMSO (vehicle), KY02111, PROTAC 18, SQSI and a compound unrelated to this project (TMTpro16plex, processed by Maxquant, each collected in 30 fractions). The experiments were performed in three independent replicates for each compound (R1-R3).

2023-06-07 | MSV000092115 | MassIVE

Comparison of R1, R2 and R3

Project description:3 samples of R1, R2 and R3 bone marrow monocytes were compared from 3 biological replicates in 3 separate experiments. R1, R2 and R3 were sorted from triplicate experiments from pools of mice

2016-11-24 | GSE90471 | GEO

Functional genomic responses to temperature variation in adult Drosophila mojavensis

2016-03-01 | GSE72169 | GEO

Bean leaves treated with benzothiadiazole (BTH)

Project description:Bean leaves treated with BTH or water. 126 = control R1, 127 = BTH R1, 128 = control R2, 129 = BTH R2, 130 = control R3, 131 = BTH R3

2019-07-31 | MSV000084162 | MassIVE

Mouse brain tissue proteomics-Shui group

Project description:DIA and PRM raw data of mouse brain tissues. R1: Cerebellum, R2: Midbrain, R3: Spinal cord

2019-11-26 | PXD016441 | iProX

Functional genomic responses toÂ temperatureÂ variation in adultÂ Drosophila mojavensis

Project description:Investigation of whole genome transcription expression level changes in Drosophila mojavensis wild-type populations (1 Punta Onah: PO, 2 Organ Pipe National Monument: OPNM, 3 Punta Prieta:PP, and 4 San Quintin: SQ). The experiment was designed to investigate functional genomic responses to temperature variation (15, 25, and 35 Â°C) in adult Drosophila mojavensis wild populations. For each treatment 1-5 replicates were used (R1, R2, R3, R4 & R5). SO and BC represents Sonora deserts and Baja California region respectively. A total of 97 hybridizations were performed in this entire experiment. We used 135K 12-plex NimbleGen arrays. Total RNA was recovered from each sample listed below. The experimental design consisted a total of four populations (Punta Onah:PO; Organ Pipe National Manument:OPNM, Punta Prieta:PP and San Quintin:SQ), two host diets (Agria:AG and Organ pipe:OP) and three temperature treatments (15, 25 and 35 Â°C). Each chip measures the expression level of 14528 transcripts. One to 5 replicates were used for each type (R1, R2, R3, R4 and R5). Fly source details are as follows: Punta Onah 2007:PO07; Organ Pipe National Monument 2008:OPNM08; Punta Prieta 2008:PP08; San Quintin 2008:SQ08.

2016-03-01 | E-GEOD-72169 | biostudies-arrayexpress

Transcription profiling of ectomycorrhizal fungus Paxillus involutus grown with different sources of nitrogen representing various degrees of complexity

Project description:A microarray analysis to investigate transcriptional responses in the ectomycorrhizal fungus Paxillus involutus, after providing various sources of nitrogen. Five different sources of nitrogen representing various degrees of complexity were provided as patches in peat microcosms for fungal ingrowth: ammonium phosphate (APO), ammonium sulphate (ASU), glutamine (GLN), bovine serum albumin (BSA), and chitin (CHI). After fungal establishment of patches total RNA was isolated and used for global transcriptional analyses using cDNA microarrays. The entire design involved 9 slides (in the range DW2_01--DW2_13), 14 labelled extracts, and 3 biological replicates (R1-R3). The experiment was designed as a loop combining the 5 diffrent samples and including dye-swaps and biological replication. COMMENT: In our analysis of the raw dataset, 3 channels were removed due to poor signal quality: array 12707648b, Cy5 (635nm) channel (GLN R1 sample); array 12707650c, Cy5 (635nm) channel (APO R1 sample); array 12707651b, Cy5 (635nm) channel (APO R1 sample).

2008-06-01 | E-MEXP-1257 | biostudies-arrayexpress

Transcription profiling of rat livers treated with pharmaceutical development compounds

Project description:We used microarrays to analyze gene expression changes in liver after treatment of rats with two compounds from drug development (R1, R2) to identify potential effects related to hepatotoxicity. Experiment Overall Design: Compound R1 or R2, or vehicle control, was given for either 24h or 2 weeks (336h) at different doses.

2009-08-09 | E-GEOD-17388 | biostudies-arrayexpress

Thermal proteome profiling reveals distinct target selectivity for differentially oxidized oxysterols

Project description:The dataset contains mass spectrometric raw data from Thermal Proteomic Profiling experiments aimed to identify the protein targets of three A- and B-ring oxidized sterols (cholestane-3beta,5alfa,6beta-triol (CT), 7keto-cholesterol (7-KC), 4beta-hydroxycholesterol (4beta-HC) ) and a side-chain oxidized sterol (25-hydroxycholesterol (25-HC)). The dataset comprises the raw data for the 4 different oxysterols, measured on both oxysterol (compound) and DMSO (vehicle), each collected in 28 fractions. The experiments were performed in three independent replicates for each oxysterol (R1-R3).

2022-06-16 | MSV000089661 | MassIVE

4C-seq from viewpoint at MYC promoter (VP-MYC1 and VP-MYC2), in wild type (Hap) and variously modified alleles around the locus in human iPS cells.

Project description:We reconstituted arrays of CTCF binding sites (L1, L2, L3, L4, R1, R2 and R3) and devised a synthetic topological insulator with tetO for chromatin-engineering (STITCH). By coupling STITCH with tetR linked to the KRAB domain to induce heterochromatin and disable the insulation, we developed a drug-inducible system to control gene activation by enhancers. We inserted STITCH into five different positions of the remaining allele of the locus: \\"STITCH+30kb\\", \\"STITCH+440kb\\", \\"STITCH+1760kb\\" and \\"STITCH+1790kb\\" have the STITCH insertions away from the MYC promoter for the indicated distances to the telomeric side of the p arm of the chromosome. \\"STITCH-30kb\\", at the 30-kb upstream from the MYC. We also made a deletion clone of the enhancer region, termed del(30-440). We made deletion of each CTCF array, L (delL) and R (delR), inversion of R (invR), deletion of the middle five binding sites from L2 to R2 (del(L2-R2)), and deletion of the six sites but for R3 (del(L1-R2)) in STITCH+30kb. We also obtained deletion and inversion of the whole of STITCH (del(L1-R3) and inv(L1-R3)). We integrated a transgene consisting of tetR-KRAB followed by DNA encoding the 2A peptide and the puromycin resistant gene with piggyBac transposition into the genome in the STITCH+30kb clone (STITCH/KRAB). We performed 4C-seq (Circular chromatin conformation capture assay followed by deep-sequencing) from the MYC promoter as a viewpoint to see how STITCH impacts on the chromatin conformation.

2020-05-01 | E-MTAB-7668 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data