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ProteomicsSearching NE-enriched proteomics datasets for splice junction peptides
MudPIT datasets for NaOH-extracted and Salt-and-Detergent (SD)-extracted rat nuclear membranes were obtained from skeletal muscle and liver tissue as described in the following references: Wilkie GS, Korfali N, Swanson SK, Malik P, Srsen V, Batrakou DG, de las Heras J, Zuleger N, Kerr AR, Florens L,...
ORGANISM(S): Rattus Norvegicus (ncbitaxon:10116) 
2018-01-18 | MSV000081951 | MassIVE
ProteomicsComprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome
Localization of lipoproteins endogenously expressed under standard culture conditions was determined using multidimensional protein identification technology (MudPIT) mass spectrometry. B. burgdorferi B31A3 intact spirochetes were subjected to surface proteolysis with proteinase K.
ORGANISM(S): Borrelia Burgdorferi B31 (ncbitaxon:224326) 
2016-12-21 | MSV000080434 | MassIVE
ProteomicsMudPIT analysis of HIV-1 Vpr-asssociated proteins from the permissive CEM.SS human T4-lymphoblastoid cell line
CEM.SS-iH1.Vpr cells expressing a tandem HA-FLAG- epitope-tagged HIV-1 NL4-3 Vpr (hfa-H.Vpr) under control of the Lenti-X Tet-On 3G Inducible Expression System (Clontech), and control CEM.SS cells (3x105 cells/ml, 4 liters), were induced with doxycycline (0.1ug/ml) for 9 hours. Whole cell extracts w...
ORGANISM(S): Hiv-1 Vector Pnl4-3 (ncbitaxon:151458) Homo Sapiens (ncbitaxon:9606) 
2016-03-24 | MSV000079605 | MassIVE
ProteomicsMudPIT analyses of the human proteins biotinylated by proximity to exogenously expressed biotin ligase (BioID)
To identify non-specific biotinylation events, HEK293 cells transfected with a plasmid carrying only the biotin ligase moiety were used as negative controls to BioID experiments. Cells were lysed in the presence of detergents. After purification of biotinylated proteins on streptavidin-conjugated be...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-30 | MSV000080809 | MassIVE
ProteomicsIdentification of the effect of a CRISPR interference knockdown of Borrelia burgdorferi strain B31 BB0838, a outer membrane lipoprotein flippase candidate, on surface lipoprotein secretion using Multidimensional Protein Identification Technology.
To identify the effect of a CRISPR interference knockdown of Borrelia burgdorferi strain B31 BB0838, a outer membrane lipoprotein flippase candidate, on surface lipoprotein secretion using Multidimensional Protein Identification Technology.
ORGANISM(S): Borrelia Burgdorferi B31 (ncbitaxon:224326) 
2022-07-27 | MSV000089990 | MassIVE
ProteomicsMudPIT analyses of the human proteins biotinylated by proximity to biotin ligase (BioID) fused to the C-terminus of activators of the dynein/dynactin motor
To understand how a single motor achieves cargo specificity, we attached a promiscuous biotin ligase (BioID) to 6 distinct activators of the dynein machinery motile activity, including two new activators, ninein and ninein-like. BioID experiments were performed with stable HEK293 cell lines expressi...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-30 | MSV000080808 | MassIVE
ProteomicsMudPIT analyses of the proteins co-purified with the junction-localized tumor suppressors Scribble (Scrib) and Discs Large (Dlg) by immunoprecipitation from fly embryos
Fly embryos (w1118, Dlg-GFP, or Scrib-GFP) were lysed with lysis buffer (25mM Tris-HCl, 150mM EDTA, 1% NP-40, 5% glycerol, 1mM DTT, 1x protease inhibitor). Debris was removed by centrifugation, and extracts were cleared by incubation with Dynabeads (1 hour). Immunocomplexes were formed by incubation...
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) 
MSV000082907 | MassIVE
ProteomicsNovel spliceosomal SF3B component in SAGA functions in transcriptional coactivation
MudPIT analyses of novel spliceosomal SF3B component in SAGA complex Stable Drosophila S2 cell lines expressing SF3B5 (CG11985, NP_652189.1), U2B (SNF; CG4528, NP_511045.1), Ada2b-PB (CG9638, NP_001027151.1), Spt3 (CG3169, NP_650146.1), Spt20 (CG17689, NP_648659.2), ATXN7 (CG9866, NP_722803.1), Ada1...
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) 
2016-03-21 | MSV000079597 | MassIVE
ProteomicsMudPIT analyses of the human proteins biotinylated by proximity to biotin ligase (BioID) fused to the N-terminus of activators of the dynein/dynactin motor
To capture the spatial organization of the dynein/dynactin motor, we attached a promiscuous biotin ligase (BioID) to 6 distinct activators of the dynein machinery motile activity. BioID experiments were performed with stable HEK293 cell lines expressing full length BICD1, BICD2, HOOK1, HOOK3, NIN an...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-30 | MSV000080807 | MassIVE
ProteomicsMudPIT analyses of the human proteins biotinylated by proximity to dynein/dynactin subunits fused to biotin ligase (BioID)
We identified the human dynein proteome by attaching a promiscuous biotin ligase (BioID) to 7 distinct components of the dynein machinery, including a subunit of its essential cofactor dynactin. BioID experiments were performed with stable HEK293 cell lines expressing dynein (IC1, IC2, LIC1, LIC2, R...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080759 | MassIVE
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