Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Destructin-1 related files

ABSTRACT: This is a training data set for destructin-1 protease digestion of a synthetic peptide library for substrate specificity profiling. Data is related to the following publication: O'Donoghue AJ, Knudsen GM, Beekman C, Perry JA, Johnson AD, DeRisi JL, Craik CS, Bennett RJ. "Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome." Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):7478-83. doi: 10.1073/pnas.1507082112. Epub 2015 May 5. Erratum in: Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):E3152. PMCID: PMC4475985.

INSTRUMENT(S): LTQ FT, LTQ Orbitrap XL

ORGANISM(S): Synthetic Construct (ncbitaxon:32630) Pseudogymnoascus (ncbitaxon:78156)

SUBMITTER: Craik, Charles S.

PROVIDER: MSV000079388 | MassIVE | Tue Nov 24 16:02:00 GMT 2015

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

TGFBR2-dependent Alterations of Exosomal Cargo in DNA Mismatch Repair-deficient HCT116 Colorectal Cancer Cells

Project description:DNA mismatch repair-deficient colorectal tumors (CRC) frequently show coding microsatellite frameshift mutations in the MSI tumor driver Transforming Growth Factor Beta Receptor Type 2 (TGFBR2) leading to cellular alteration of MSI tumor cells [Lee, J., Warnken, U., Schnölzer, M., Gebert, J. & Kopitz, J. (2015) Protein Sci. 24, 1686-94; Lee, J., Ballikaya, S., Schonig, K., Ball, C. R., Glimm, H., Kopitz, J. & Gebert, J. (2013) PloS one. 8, e57074]. Whether this receptor expression in MSI tumor cells also impacts the exosomal proteomic cargo of these cells is still unknown.

2017-04-07 | PXD005620 | Pride

Profiling of bulk and ribosome associated mRNA of Arabidopsis roots upon lateral root induction upon TOR activity inhibition with AZD8055 [dataset2]

Project description:We performed targeted purification of polysomal mRNA (TRAP-Seq, Vragović et al, 2015 - http://dx.doi.org/10.1073/pnas.1417947112) using a transgenic line ubiquitously expressing a GFP-tagged RPL18 (Mustroph et al, 2009 - https://doi.org/10.1073/pnas.0906131106) 6h after the synchronous induction of lateral root formation by auxin treatment (IAA) upon inhibition of TOR activity (AZD8055 treatment, AZD). To correct for abundance of mRNA, bulk RNA-Seq was performed on the same samples and used to normalise the reads purified with the ribosomes.

2022-03-23 | GSE199203 | GEO

Variation and genetic control of chromatin architecture in humans (RNAseq)

Project description:This data set comprises population (46 samples) measurements of RNA expression levels for a subset of the 1000 Genomes Project CEPH samples. This data was generated as part of the following study: - Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 2015 Aug 27;162(5):1039-50. doi: 10.1016/j.cell.2015.08.001. Epub 2015 Aug 20. An additional set of 111 samples from the 1000 Genomes Project (GBR and TSI populations) were also assayed using RNA-seq. This data was generated as part of the following study: - Chromatin 3D interactions mediate genetic effects on regulatory networks.

2016-05-27 | E-MTAB-3656 | biostudies-arrayexpress

Variation and genetic control of chromatin architecture in humans (ChIPseq)

Project description:This data set comprises population (47 samples) measurements of transcription factor DNA binding (PU.1 and RPB2) and histone modification (H3K27ac, H3K4me1 and H3k4me3) levels for a subset of the 1000 Genomes Project CEPH samples. This data was generated as part of the following study: - Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 2015 Aug 27;162(5):1039-50. doi: 10.1016/j.cell.2015.08.001. Epub 2015 Aug 20. An additional set of 111 samples from the 1000 Genomes Project (GBR and TSI populations) were also assayed for three histone modifications (H3K27ac, H3K4me1 and H3k4me3). This data was generated as part of the following study: - Chromatin 3D interactions mediate genetic effects on regulatory networks.

2019-03-14 | E-MTAB-3657 | biostudies-arrayexpress

Gene expression analysis of root tissue from rice grown on arsenite-spiked sediments

Project description:The experiment intended to identify biomarker genes for arsenite exposure in rice roots. These biomarker genes were tested as alternative endpoints in an sediment-contact test with rice (Brinke et al. Environ Sci Pollut R 22.16 (2015): 12664-12675)

2017-10-01 | E-MTAB-5430 | biostudies-arrayexpress

Identifying crossover locations in Arabidopsis thaliana wild type Col x CLC, msh2 Col x CLC and msh2 Col x Ler F2 populations using genotyping by sequencing.

Project description:Genomic DNA from 189 wild type Col x CLC, 191 msh2 Col x CLC or 187 msh2 Col x Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Serra et al 2018 PNAS). Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline (Rowan et al., 2015 G3).

2020-09-02 | E-MTAB-8252 | biostudies-arrayexpress

Interactions of CDK19 with MED12 and cyclin-C assessed by chemical cross-linking mass spectrometry

Project description:Chemical cross-linking coupled to mass spectrometry was used to study binary and ternary complexes involving cyclin-dependent kinase 19 (CDK19), cyclin-C, and an N-terminal fragment of subunit 12 of the Mediator complex (MED12 1-100). Cross-linking was performed using disuccinimidyl suberate (DSS). These results were generated in the context of the study published as Klatt et al., A precisely positioned MED12 activation helix stimulates CDK8 kinase activity, Proc. Natl. Acad. Sci. USA 2020 (DOI: 10.1073/pnas.1917635117) with the associated data set PXD015394, but were not included in the article.

2020-05-18 | PXD019251 | Pride

Transcription profiling by array of A818-1 pancreatic cancer cells was grown either in 2D or 3D culture

Project description:The pancreatic cancer cell line A818-1 was grown either in 2D monolayers or in 3-dimensional “hollow spheres” as described in Lehnert et al. (1999), Ann N Y Acad Sci 880:83-93. Total RNA was extracted and analyzed from 3 independent experiments.

2015-02-27 | E-MTAB-3372 | biostudies-arrayexpress

GM-CSF-transduced proliferating myeloid cells represent cell cycle related gene signature

Project description:We previously established a method to generate myeloid lineage cells with proliferation capacity from induced pluripotent stem cells (iPSCs) (Zhang R. Cancer Immunol Res. 3: 668, 2015). In this study, we generated the GM-CSF-producing cells by genetic engineering of mouse iPSC-derived proliferation myeloid cells (iPSC-pMCs). Gene expression profiles revealed GM-CSF-transduced iPSC-pMCs (GM-pMCs) generated from C57BL/6 mice and 129Sv mice shared 180 up-regulated genes and 236 down-regulated genes compared with their corresponding iPSC-pMCs. Gene ontology analysis showed that the up-regulated gene signature shared by C57BL/6 GM-pMCs and 129Sv GM-pMCs was enriched for transcripts associate with cell cycle, cell cycle process, mitotic cell cycle and regulation of mitotic cell cycle.

2020-08-31 | GSE136993 | GEO

A spatiotemporal molecular atlas of mouse spinal cord injury identifies a distinct astrocyte subpopulation and therapeutic potential of IGFBP2

Project description:Spinal cord injury (SCI) triggers a cascade of intricate molecular and cellular changes that determine the outcome. In this study, we resolve the spatiotemporal organization of the injured mouse spinal cord and quantitatively assess in situ cell-cell communication following SCI. By analyzing existing single-cell RNA-sequencing datasets alongside our spatial data, we delineate a subpopulation of Igfbp2-expressing astrocytes that migrate from the white matter (WM) to grey matter (GM) and become reactive upon SCI, termed as Astro-GMii. Further, Igfbp2 upregulation promotes astrocyte migration, proliferation and reactivity, and the secreted IGFBP2 protein fosters neurite outgrowth. Finally, we show that IGFBP2 significantly reduces neuronal loss and remarkably improves the functional recovery in a mouse model of SCI in vivo. Together, this study not only provides a comprehensive molecular atlas of SCI but also exemplifies how the rich resource can be applied to endow cells and genes with functional insight and therapeutic potential.

2024-06-19 | GSE256397 | GEO