Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Laser Capture Microdissection of Normal Kidney Biopsy Glomeruli and Tubulointerstitium Characterized by LC-MS/MS

ABSTRACT: The Kidney Precision Medicine Project (KPMP) is funded by the NIDDK for "the purpose of understanding and finding new ways to treat chronic kidney disease and acute kidney injury. " To accomplish this goal, the KPMP chose several technologies to successfully deliver their goals. One of the technologies chosen was using a combination of laser capture microdissection (LCM) in combination with LC -MS /MS to characterize quantitative protein changes in the diseased kidney. The data presented here is from the initial pilot study using normal kidney biopsies for proof of principal. Samples analyzed were either LCM collected glomeruli or tubulointerstitium. Protein was retrieved from the LCM collected tissue, proteins were trypsinized and samples run on the fusion orbitrap.

INSTRUMENT(S): Orbitrap Eclipse

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

SUBMITTER: Samir Parikh

PROVIDER: MSV000089251 | MassIVE | Wed Apr 13 09:05:00 BST 2022

SECONDARY ACCESSION(S): PXD033207

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

PROTEOMIC ANALYSIS OF THE UMBILICAL CORD IN FETAL GROWTH RESTRICTION AND PREECLAMPSIA

Project description:Fetal growth restriction (FGR) is associated with adverse perinatal outcomes. Pre-eclampsia (PreE) increases the associated perinatal morbidity and mortality. The structure of the umbilical cord in the setting of FGR and PreE has yet to be determined. This study aimed to examine changes in the umbilical cord (UC) composition in pregnancies complicated by FGR and FGR with PreE. UC from gestational age-matched pregnancies with isolated FGR (n = 5), FGR with PreE (n = 5) and controls (n = 5) were collected, and a portion of the UC was processed for histologic and proteomic analysis. Manual segmentation analysis was performed to measure cross-section areas of umbilical cord regions. Wharton's Jelly samples were analyzed on a tims-TOF Pro. Spectral count and ion abundance data were analyzed simultaneously, creating an intersection dataset from a combination of multiple mass spectrometry search and inference engines. UCs from FGR and FGR with PreE had lower cross-sectional area and Wharton's Jelly area compared with control (p &#61 ;0.03). When comparing isolated FGR to control, 28 proteins were significantly different in abundance analysis and 34 in spectral count analysis (p-value < 0.05). Differential expression analysis between PreE with FGR vs controls, demonstrated 48 proteins were significantly different in abundance and 5 in spectral count (p-value < 0.05). The majority of proteomic changes occur in proteins associated with extracellular matrix, cellular process, inflammatory, and angiogenesis pathways.

2021-03-15 | MSV000087051 | MassIVE

Cold-Induced Adaptations to the Proteome of Mouse Subcutaneous White Adipose Tissue (scWAT) Reveal Proteins Relevant for Tissue Remodeling and Plasticity

Project description:White adipose tissue (WAT) is one of the most dynamic and plastic organs or tissues in the body, capable of expanding its mass in response to positive energy balance (either by proliferation of adipocytes - hyperphasia, or by increasing adipoycyte size - hypertrophy), developing inducible brown adipocytes through a process termed "browning", and changing its mitochondrial mass in response to stimuli such as cold exposure. Most notably, cold stimulation and release of norepinephrine from sympathetic nerve terminals is able to drive lipolysis in WAT (and thus smaller lipid droplet size and adipocyte size), as well as promote sympathetic nerve branching and increased neurite density, as well as development of pockets of browning around these neurite-dense regions of tissue. While several RNA-sequencing (including newer single cell RNAseq studies) have been done in WAT across situations of positive energy balance (such as high fat diet, obesity) or negative energy balance (such as cold stimulation of energy expenditure), very little work has been done to investigate changes to the adipose proteome while the tissue is actively remodeling. Here, we have carried out proteomics analysis on inguinal subcutaneous (sc)WAT of C57BL/6 mice after 24 or 72hrs of cold stimulation, a period during which UCP1 is actively turned on during the browning process. Through these data, we have found that numerous protein pathways changed by cold stimulation relate to tissue remodeling and plasticity, including changes to mitochondrial dynamics, tissue immune cells, and peripheral nerves.

2021-05-25 | MSV000087516 | MassIVE

Clostridium acetobutylicum ATCC 824 time course with Agilent Arrays

Project description:Using our newly designed C. acetobutylicum arrays we analyzed the mRNA changes during a time course experiment (up to 66 h) paying special attention on the study of the late timepoints. Keywords: time course Samples were taken from a Bioflow II reactor at 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 54, 58, and 66 hrs after bioreactor inoculation. Two slides per timepoint were hybridized on a dye swap configuration. The control mRNA was generated by combining samples taken at 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 54, 58, and 66 hrs after bioreactor inoculation. For timepoints 6, 8, 14, 32, 38, 66 our internal quality control check suggested a larger than normal variation of the intensities in the control channel and a third slide was hybridized. The discarded slides are GSM141189, GSM141203, GSM141222, GSM141229 and GSM141242.

2010-05-25 | E-GEOD-6094 | biostudies-arrayexpress

Differential gene expression of Arabidopsis in response to fumonisin B1 and exogenous ATP treatments

Project description:To identify genes underpinning the antagonistic effects of extracellular ATP on programmed cell death induced by fumonisin B1 (FB1), we conducted a kinetic DNA microarray experiment using samples harvested in the critical time window when exogenous ATP is known to suppress cell death. Arabidopsis cell suspension cultures were treated with FB1 at time = 0 h and exogenous ATP added at time = 40 h. Differential gene expression analysis using microarrays was performed on samples harvested at 41, 42, 44, and 48 h.

2019-12-31 | E-MTAB-3685 | biostudies-arrayexpress

Gene expression profiles of E15.5 cortical collecting duct and anlage of loop of Henle isolated from developing kidney using LCM. (GUDMAP Series ID: 18)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in laser capture microdissected components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. Keywords: Comparison of kidney components.

2007-07-04 | GSE8360 | GEO

Gene expression profiles of components isolated from developing kidney at E15.5 using LCM. (GUDMAP Series ID: 12)

2006-12-23 | GSE6589 | GEO

Gene expression profiles of components isolated from developing kidney at E11.5, E12.5 & E15.5 using LCM. (GUDMAP Series ID: 10)

2006-11-18 | GSE6290 | GEO

Co-hybridization of Adenovirus type 40 and 41

Project description:Co-hybridization of Adenovirus type 40 and 41 to test probe specificity for closely related viral targets. ATCC strains of Adenovirus type 40 and 41 were hybridized to the array as a control run and a proof of concept. Degree of cross hybridization between polio nucleic acid and non-adenovirus 40 and 41 probes was evaluated. Specificity of the probe design was determined between closely related members of the same virus family. Keywords: control study: target detection and specificity

2008-02-28 | GSE10569 | GEO

Gene expression profiles of components isolated from developing kidney at E11.5, E12.5 & E15.5 using LCM. (GUDMAP Series ID: 10)

2006-11-18 | E-GEOD-6290 | biostudies-arrayexpress

Co-hybridization of Adenovirus type 40 and 41

2010-05-26 | E-GEOD-10569 | biostudies-arrayexpress