High-throughput mass spectrometry analysis of N-glycans and protein markers after FUT8 knockdown in the syngeneic SW480/SW620 colorectal cancer cell model
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Epithelial Cell, Colon
DISEASE(S): Colon Cancer
SUBMITTER: 
Ruben Lopez-Cortes
LAB HEAD: Rubén López-Cortés
PROVIDER: PXD050012 | Pride | 2024-03-21
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| EGRL161252_HCD_1.raw | Raw | |||
| EGRL161252_HCD_2.raw | Raw | |||
| EGRL161252_HCD_3.raw | Raw | |||
| EGRL161252_HCD_4.raw | Raw | |||
| EGRL161252_HCD_5.raw | Raw |
Items per page: 5 1 - 5 of 23 |
Similar Datasets
Project description:We performed mass-spectrometry analysis of proteins co-purifying with Whi5, a predicted repressor of the MBF transcriptional complex. Whi5 was tagged with GFP at its C-terminal end and expressed from its endogenous promoter at its chromosomal locus. Whi5-GFP was immunoprecipitated from cells growing in MM and after 16 hours in MM-N, and co-purifying proteins were analysed by mass-spectrometry. An untagged wild-type strain was used as a control.
2025-12-20 | PXD057886 | Pride
Project description:Mass spectrometry analysis of proteins co-purifying with Cdc10, a component of the MBF transcriptional complex, was performed both in a wild-type and in a whi5∆ background. Cdc10 was tagged with YFP at its C-terminal end and expressed from its endogenous promoter at its chromosomal locus. Cdc10-YFP was immunoprecipitated from cells cultured in MM-N medium for 16 hours, and co-purifying proteins were analysed by mass spectrometry. An untagged wild-type strain was used as a control.
2025-12-20 | PXD057838 | Pride
Project description:A longstanding limitation of Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) has been the inability to directly measure amide exchange with single amide resolution. Excitation of peptides either during ionization, ion transmission, or collision induced dissociation rapidly induces intermolecular hydrogen migration, leading to a loss of the native-deuterium labeled state of the peptide; a term commonly known as ‘scrambling’. Electron-based fragmentation methods in conjunction with gentle ion transmission settings can minimize scrambling, but often not completely. Scrambling has been shown to vary with ion transmission settings, peptide charge, and size, but the properties that govern the energetic barriers of scrambling within peptides are not well understood. Furthermore, it remains unclear whether scrambling is generally a global process, or if local scrambling networks commonly exist within peptides. Here we examine a panel of peptides using gentle electron transfer dissociation and map the energetic barriers of scrambling to define a relationship between peptide charge density and scrambling propensity. This study suggests that by and large, the scrambling process has a single energetic barrier and involves all exchangeable sites within a peptide. For some peptides the barrier of scrambling is surprisingly close to the barrier of amide bond dissociation.
2025-10-14 | PXD066803 | Pride
Project description:Trichoderma erinaceum secretome The use of lignocellulosic biomass is something that has been encouraged considering the search for sustainable alternatives mainly in the energy sector. However, to use such biomass as feedstock, its degradation is necessary aiming the formation of sugars that could be used in fermentation. For this conversion, enzymatic cocktails with degradative capacity are used, which are normally composed for the of filamentous fungi secretomes. The present work presents the characterization of Trichoderma erinaceum aiming at its use as a producer of lignocellulolytic enzymes. Cultivations were conducted using Mandels-Andreotti media enriched with four different carbon sources (glucose, avicel, pretreated sugarcane straw, or energy cane bagasse) in different time points (72h, 96h, 120h, 144h), and the supernatants were analyzed by mass spectrometry to determine the various patterns of enzyme secretion resulting from the modification of components within the media.
2024-06-05 | PXD051248 | Pride
Project description:HCoV-NL63 is a coronavirus that can cause severe lower respiratory tract infections requiring hospitalization. Of great interest is understanding the HCoV-NL63 coronavirus spike glycoprotein trimer, which is the conformational machine responsible for entry into host cells and the sole target of neutralizing antibodies during infection. We utilized an electron-transfer/higher energy collision dissociation ion fragmentation scheme (Frese, C. K. et al., 2013.) in combination with cryo-electron microscopy to resolve the extensive glycan shield that obstructs the protein surface. These glycans provide a structural framework to understanding the accessibility of the protein to antibodies.
2016-09-27 | PXD004557 | Pride
Project description:The data set contains HDX-MS data files of TEM proteins. HDX-MS data were acquired at 30, 100, 1000, 3000, 9000, and 15000 sec H-D exchange time points.
2025-12-11 | PXD069558 | Pride
Project description:Expression profiling of stem cell lines derived from the early embryo representing the trophoblast, primitive endoderm, early epiblast (inner cell mass E3.5) and late post-implantation epiblast (E5.5). Cells were grown without feeders and harvested. Comparisons were made to provide evidence of unique gene expression between the cell lines. Specifically, pre-implantation (ICM, epiblast and primitive endoderm, and trophoblast), as well as pre-implantation and post-implantation epiblasts.
2012-05-21 | E-GEOD-34799 | biostudies-arrayexpress
Project description:Cornea transcriptomic analysis in a mouse model of slowly progressing aniridia-associated keratopathy (AAK) the heterozygous 129S1.Cg-Pax6Sey/Mmmh strain on the 129S1/SvImJ background (MMRRC stock #050624-MU)(4, 5). The Pax6 mutation of this model is a spontaneous point mutation in exon 8 of the Pax6 gene (G to T substitution), leading to a premature stop codon. Mice were treated with 10 μM duloxetine eyedrops (samples named Het-Dul) or vehicle (Samples named Het-Veh) twice daily, for 90 days. The experimental design also included non-mutant, WT mouse eyes that were either administered with the same regimen of duloxetine (samples named Wt-Dul) or untouched (Samples names Wt-Ctrl).
2026-01-30 | E-MTAB-16492 | biostudies-arrayexpress
Project description:Airway epithelial cells from 3 different breeds of chicken infected with Newcastle Disease virus were sequenced and compared to cells from uninfected control birds. The 3 breeds were an indigenous breed, commercial Rhode Island Reds and a hybrid breed (Kenbro).
2015-01-19 | E-MTAB-3068 | biostudies-arrayexpress
Project description:A critical transcription factor required for mammalian male sex determination is SRY (sex determining region on the Y chromosome). The expression of SRY in precursor Sertoli cells is one of the initial events in testis development. The current study was designed to determine the impact of environmentally induced epigenetic transgenerational inheritance on SRY during gonadal sex determination in the male. The agricultural fungicide vinclozolin and vehicle control (DMSO) exposed gestating females (F0 generation) during gonadal sex determination promoted the transgenerational inheritance of differential DNA methylation in sperm of the F3 generation (great grand-offspring). The fetal gonads in F3 generation males were used to identify potential alterations in SRY binding sites in the developing Sertoli cells. Chromatin immunoprecipitation with an SRY antibody followed by genome-wide promoter tiling array (ChIP-Chip) was used to identify alterations in SRY binding. A total of 81 adjacent oligonucleotide sites and 173 single oligo SRY binding sites were identified to be altered transgenerationally in the Sertoli cell vinclozolin lineage F3 generation males. Observations demonstrate the majority of the previously identified normal SRY binding sites were not altered and the altered SRY binding sites were novel and new additional sites. The chromosomal locations, gene associations and potentially modified cellular pathways were investigated. In summary, environmentally induces epigenetic transgenerational inheritance of germline epimutations appears to alter the cellular differentiation and development of the precursor Sertoli cell SRY binding during gonadal sex determination that influence the developmental origins of adult onset testis disease. The experimental design involved the intraperitoneal exposure of gestating female rats to vinclozolin or a vehicle control (dimethyl sulfoxide, DMSO) transiently from embryonic days E8-E14. Sister littermates were divided into control and vinclozolin treatment groups and mated to similar males to minimize the genetic variation between the control and vinclozolin lineages. Sufficient females were used so no inbreeding (sibling or cousin) occurred in any generation. The F1 generation was bred within the lineage to generate the F2 generation and these F2 generation bred to generate the F3 generation. The only exposure was the F0 generation female. The F3 generation control and vinclozolin lineage embryonic day 13 (E13) embryos were collected and the gonads micro-dissected and then sexed with an SRY PCR protocol. The male gonads were pooled from a minimum of three different litters and the pools used to collect DNA. Three different experiments were performed to collect 3 control and vinclozolin E13 F3 generation testis pools, each with different animals (n=25 gonads/pool). The chromatin DNA (not denatured) from each pool was fragmented and used in an SRY chromatin immunoprecipitation (ChIP) procedure for each pool separately. The control and vinclozolin SRY ChIP DNA were paired for a competitive hybridization on a genome-wide promoter tiling array (ChIP-Chip) assay. The hybridization data obtained was used to identify the SRY binding sites that were different in the F3 generation vinclozolin versus control lineage in E13 testis.
2015-08-28 | E-GEOD-72469 | biostudies-arrayexpress