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TAP-GluN1, PSD95-TAP, WT (control) BNP-LC-MS/MS proteomics

ABSTRACT: TAP-GluN1 (840 kDa and 1.5 MDa), PSD95-TAP (1.5 MDa) and WT (control; 1.5 MDa) native complexes from Grin1^TAP/TAP, Dlg4^TAP/TAP, and WT mouse forebrain (cortex and hippocampus), respectively. Purified samples were seperated by blue native PAGE. Bands were excised, digested with trypsin. Peptides were identified by LC-MS/MS.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain

SUBMITTER: Rene Frank

LAB HEAD: Seth Grant

PROVIDER: PXD000011 | Pride | 2016-04-20

REPOSITORIES: Pride

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			Action	DRS
	95-TAP_1500_P4a.raw	Raw
	95-TAP_1500_P4b_1.raw	Raw
	95-TAP_1500_P4b_2.raw	Raw
	95-TAP_1500_P4b_3.raw	Raw
	95-TAP_1500_P4c_1.raw	Raw

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Publications

NMDA receptors are selectively partitioned into complexes and supercomplexes during synapse maturation.

Frank René A W RA Komiyama Noboru H NH Ryan Tomás J TJ Zhu Fei F O'Dell Thomas J TJ Grant Seth G N SG

Nature communications 20160427

How neuronal proteomes self-organize is poorly understood because of their inherent molecular and cellular complexity. Here, focusing on mammalian synapses we use blue-native PAGE and 'gene-tagging' of GluN1 to report the first biochemical purification of endogenous NMDA receptors (NMDARs) directly from adult mouse brain. We show that NMDARs partition between two discrete populations of receptor complexes and ∼1.5 MDa supercomplexes. We tested the assembly mechanism with six mouse mutants, which ...[more]

PMID: 27117477

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2021-09-09 | PXD022396 | Pride

Development of GRO-cap (GRO-seq followed by 5'-cap enrichment) to map transcription start sites in C. elegans

Project description:Dosage Compensation is required to correct for uneven gene dose between the sexes. We utilized global run-on sequencing (GRO-seq) to examine how Caenorhabditis elegans dosage compensation reduces transcription of X-linked genes. To facilitate these experiments, we required accurate 5M-bM-^@M-^Y-ends of genes that have been missing due to a co-transcriptional trans-splicing event common in nematodes. We developed a modified GRO-seq protocol to identify TSSs that are supported by transcription, and determined that TSSs lie more than 1 kb upstream of the previously annotated TSS for nearly one-quarter of all genes. We then investigated the changes that occur in transcriptionally engaged RNA Polymerase when dosage compensation is disrupted, and find that dosage compensation controls recruitment of RNA Polymerase to X-linked genes. GRO-cap reactions were performed with TAP, and without TAP as a control.

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Comparison of the nucleotide-resolution, genome-wide, 5'-end maps of the transcriptomes of Escherichia coli K12 strain BW25113 and Streptomyces coelicolor A3(2) strain M145

Project description:The differential RNA-seq data contained within this entry is complemented by global RNA-seq. S. coelicolor and E. coli reference strains were grown in batch culture with shaking. The E. coli sample was extracted during mid-exponential growth, while the S. coelicolor sample was extracted at the start of pigmented antibiotic production. Each of the two samples was incubated with or without TAP (tobacco acid pyrophosphatase) before library construction. Thus, 4 libraries were analysed. TAP treatment allows the cloning and sequencing of 5' ends that were originally triphosphorylated.

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Identification of proteins associated with the human mitochondrial degradosome

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Nucleotide-resolution, genome-wide, 5'-end maps of the transcriptome of Propionibacterium acnes (cultured with and without potassium downshift)

Project description:The differential RNA-seq data contained within this entry is complemented by global RNA-seq and microarray data, which is also deposited in GEO. Duplicate cultures of Propionibacterium acnes strain KPA171202 were grown exponentially in batch culture under anaerobic growth. Samples were taken following subculture with and without potassium downshift (i.e. removal from medium). This produced 4 samples; 2 replicates x 2 conditions. Aliquots of each of the 4 samples were then incubated with or without incubation TAP (tobacco acid pyrophosphatase) before library construction. Thus, 8 libraries were analysed. TAP treatment allows the cloning and sequencing of 5' ends that were originally triphosphorylated.

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Proteins associated wth Trypanosoma brucei HNRNPF/H

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