Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of Lung MDSC from SKG mice

ABSTRACT: The purpose of this project is to characterize the myeloid derived suppressor cells (MDSCs) in the inflamed lung of interstitial lung disease SKG mice. We compared the gene expression of lung MDSCs with MDSCs from bone marrow or spleen.BD FACSAria III (BD Biosciences) was used to sort CD11b+Gr1+ cells (MDSCs) from BM, spleen and lung of interstitial lung disease model SKG mice. Total RNA was extracted from cultured cells using Maxwell RSC simplyRNA Cells Kit (Promega). Biotinylated cRNA were prepared using GeneChip 3'IVT PLUS Reagent Kit (Thermo Fisher Scientific) according to the standard manufacturer's protocol from 100 ng total RNA. Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450. GeneChips were scanned using the GeneChip Scanner 3000 7G. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Expression Console Software (ThermoFisher Scientific) according to the default analysis settings.

INSTRUMENT(S): GeneSpring, Maxwell RSC simplyRNA Cells Kit (Promega), GeneChip 3'IVT PLUS Reagent Kit (Thermo Fisher Scientific), GeneChip Scanner 3000 7G. Expression Console Software (ThermoFisher Scientific), GeneChip Mouse Genome 430 2.0 Array A-AFFY-45, BD FACSAriaIII (BD Biosciences)

ORGANISM(S): Mus musculus

SUBMITTER: Sho Sendo

PROVIDER: E-MTAB-16508 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of lung alveolar type II epithelial cells from CCSP-rtTA/(teto)7Stat3C bitransgenic mice treated with doxycycline and with spontaneous lung bronchoalveolar adenocarcinoma

Project description:Over-expression of Stat3C in lung alveolar type II epithelial cells of CCSP-rtTA/(teto)7Stat3C bitransgenic mice leads to severe pulmonary inflammation in the lung. As a consequence, spontaneous lung bronchoalveolar adenocarcinoma was observed in bitransgenic mice. Aberrantly expressed genes in the bitransgenic model were identified by Affymetrix GeneChip Microarray. Lungs were isolated from 4 individual mice in each group after 9 months of doxycycline-treatment. To eliminate sample differences generated by individual mice, the lung tissues were combined in each group and homogenized for RNA isolation. The total lung RNAs were purified using the QIAGEN total RNA purification kit as recommended by the manufacturer. The Affymetrix GeneChip assay was performed in duplicate. Briefly, the same amounts (10 ug) of total RNAs from the lungs of doxycycline not treated and treated mice was subject to reverse transcription using oligo dT with T7 promoter sequences attached, followed by second strand cDNA synthesis. Antisense cRNA was then amplified and biotinylated using T7 RNA polymerase, prior to hybridization to the Mouse 430A GeneChip (Affymetrix Inc) using the Affymetrix recommended protocol. Affymetrix MicroArray Suite version 5.0 was used to scan and quantitate the Genechips using default scan settings. Intensity data was collected from each chip, scaled to a target intensity of 1500 and the results were analyzed using GeneSpring 5.0 (Silicon Genetics, Inc.) and JMP4 (SAS Institute, Inc.). Hybridization data were sequentially subject to normalization, transformation, filtering and functional classification. Genes differentially expressed between doxycycline treated and not treated mice were identified by Student t-test at p value < 0.05 and fold change > 2. To evaluate data consistency and reproducibility, coefficiency of variation among replicates were calculated with the maximal cutoff line as 98%.

2008-05-07 | E-MEXP-1137 | biostudies-arrayexpress

Gene expression in lung fibroblasts

Project description:Pulmonary fibrosis is a chronic, progressive, and lethal interstitial lung disease. It is characterized by extracellular matrix deposition, fibroblast proliferation, and accumulation. Fibroblasts from normal or UIP histology were cultured and analyzed. Keywords: Fibroblasts from normal histology lung tissue or UIP histology lung tissue Five samples of primary human lung fibroblasts were obtained from explanted lungs of patients with Usual Interstitial Pneumonia (UIP) at the University of Pittsburgh Medical Center (Pittsburgh, PA, USA) and three samples of primary normal human lung fibroblasts were acquired from normal histololgy lung tissues of organ donors. The experimental protocol was approved by the University of Pittsburgh Institutional Reviews Board (IRB). Total RNA was extracted and used as a template to generate double-stranded cDNA and biotin-labeled cRNA, as recommended by the manufacturer of the arrays. Fragmented cRNA was hybridized to Codelink Uniset I slides. After hybridization, arrays were washed and stained with streptavidin-AlexaFluor 647. The arrays were scanned using a Genepix 4000B microarray scanner. Images were analyzed using Codelink expression II analysis suite, and visually inspected for defects and quality control parameters as recommended by the manufacturer.

2010-06-21 | E-GEOD-10921 | biostudies-arrayexpress

miRNA expression in myeloid-derived suppressor cells (MDSCs) treated with or without whole ?-glucan particles (WGP)

Project description:Murine MDSCs isolated from the spleens of Lewis lung carcinoma mice were treated with or without WGP, and then miRNA array was used to analyze the differentailly expressed miRNAs. Murine MDSCs were isolated from the spleens of Lewis lung carcinoma tumor-bearing mice, and the sorted MDSCs were stimulated with or without 100 µg/ml WGP for 24 h. Then, the total RNA was extracted to perform miRNA array to analyze the differentially expressed miRNAs in MDSCs treated with or without WGP

2015-06-26 | E-GEOD-67578 | biostudies-arrayexpress

Systems biology of interstitial lung diseases

Project description:This SuperSeries is composed of the following subset Series: GSE21369: Gene expression profiles of interstitial lung disease (ILD) patients GSE21394: MicroRNA expression profiles of interstitial lung disease (ILD) patients Refer to individual Series

2011-04-19 | E-GEOD-21411 | biostudies-arrayexpress

Global gene expression across a range of tissues

Project description:The aim of this study is to survey global gene expression across a range of mouse tissues. Biotinylated cRNA was synthesized from total RNA, then fragmented and hybridized to Affymetrix Mouse Genome 430 2.0 GeneChip arrays at the Siteman Cancer Center Gene Chip Core Facility (Washington University, St Louis, Missouri) according to manufacturer's protocols. Image files were generated using MicroArray Suite 5.0 (Affymetrix). Keywords: other

2007-02-23 | GSE1986 | GEO

Gene expression profiles of interstitial lung disease (ILD) patients

Project description:The mechanisms and molecular pathways underlying interstitial lung diseases (ILDs) are poorly understood. Systems biology approaches were used to identify perturbed networks in these disease states to gain a better understanding of the underlying mechanisms of disease. Through profiling genes and miRNAs, we found subsets of genes and miRNAs that distinguish different disease stages, ILDs from controls, and idiopathic pulmonary fibrosis (IPF) from non-specific interstitial pneumonitis (NSIP). Traditional pathway analysis revealed several disease-associated modules involving genes from the TGF-beta, Wnt, focal adhesion and smooth muscle actin pathways that may be involved in advancing fibrosis. A comprehensively integrative approach was used to construct a global gene regulatory network based on the perturbation of key regulatory elements, transcriptional factors and miRNAs. The data also demonstrated that several subnetworks were significantly associated with key molecules involved in the diseases. We present a broad overview of the disease at a molecular level and discuss several possibly key regulatory molecular circuits that could play central roles in facilitating the progression of ILDs. Lung tissue samples from 23 patients with IPF or related disorders were obtained from the Lung Tissue Research Consortium (www.ltrcpublic.org). 11 samples came from patients who had been diagnosed with usual interstitial pneumonia/ idiopathic pulmonary fibrosis (UIP/IPF), 5 samples came from patients with non-specific interstitial pneumonia (NSIP), the remaining from patients with uncharacterized fibrosis and from patients with other ILD variants. B. Biopsies from uninvolved lung tissue from lung cancer patients (5 samples) and from one lung transplant patient were used as controls for comparison with the ILD samples.

2011-03-24 | E-GEOD-21369 | biostudies-arrayexpress

MicroRNA expression data from lung tissue of Idiopathic Pulmonary Fibrosis

Project description:Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and usually lethal lung disease characterized by unknown causes and few treatment options We used microarray to determine the expression of miRNA and 17 miRNAs were differentially expressed in IPF lungs, including 10 upregulated and 7 downregulated miRNAs. Lung tissue was obtained from 4 IPF patients with histological evidence of usual interstitial pneumonia at the time of surgical lung biopsy or lung transplantation. The diagnosis of IPF was derived according to the standards accepted by the American Thoracic Society/European Respiratory Society. Histological normal lung tissues used as controls was obtained from 3 patients with primary spontaneous pneumothorax at the time of thoracoscopy with stapling of any air leak.The miRNA expression profile was determined by Affymetrix microarray, and transcriptome with Affymetrix array

2015-12-04 | E-GEOD-75647 | biostudies-arrayexpress

control-ethanol liver RNA

Project description:cRNAs were hybridized with HumU133A oligo arrays (Affymetrix, Santa Clara, CA) which contain 22,283 probe sets. Preliminary studies indicated that Affymetrix Human GeneChips detected more than 60% of pig liver transcripts. All Affymetrix data were filtered for those genes with fluorescent intensity value of less than 100. Genes whose expressions in livers from the folate deficient and ethanol fed groups were either increased or decreased by 2-fold or more (p<0.05) compared to those in livers from the control group were considered significantly changed. GeneChip cRNA probes used in GeneChip expressions were obtained by following a protocol from the manufacturer. First strand cDNA was synthesized by reverse transcription of 8 μg total RNA with superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) and T7-oligo (dT) 24 primer (Genset Oligos, Boulder, CO), followed by second strand cDNA synthesis. Biotin-labeled cRNA probes were generated by reverse transcription of double stranded cDNA using BioArray High yield RNA transcript labeling kit (ENZO Life Sciences, Inc., Farmingdale, NY). The cRNA probes were purified from unincorporated nucleotides by RNeasy mini column (QIAGEN, Valencia, CA), fragmented and hybridized overnight at 680 C to the Human GeneChip array (HG U133A, Affymetrix). Keywords: parallel sample

2004-12-22 | GSE2099 | GEO

Transcriptional profile of mouse lung during the fibrotic phase of the response to bleomycin

Project description:Wildtype mice were given saline or bleomycin by oropharyngeal instillation. After 14 days, during the fibrotic phase of the response, lungs were dissected and total RNA was extracted and used for gene expression profiling. The aim was to identify those genes regulated during the development of fibrosis in this animal model of bleomycin-induced lung fibrosis. Wildtype male C57Bl/6J mice (8-10 weeks old) were used in the study, with three mice per group. Bleomycin (1mg/kg body weight in 50μl of saline) or saline was administered by oropharyngeal installation as described previously by Lakatos et al, Exp Cell Res, 2006, under light halothane-induced anaesthesia. After 14 days, lungs were removed, blotted dry and the trachea and major airways were excised before the separated lobes were snap frozen in liquid nitrogen. Lungs were then pulverized under liquid nitrogen, and the resulting lung powder was used for total RNA extraction using Trizol. Following DNase-treatment, clean-up, cDNA synthesis and cRNA synthesis, samples were hybridized to Affymetrix MOE430A genechips using standard protocols. The data were analyzed using RMA with quantiles normalization.

2009-07-07 | E-GEOD-16846 | biostudies-arrayexpress

Expression data from 45-month-old Slovak children with high PCBs exposure

Project description:Exposure to polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of different diseases and disorders are not fully understood. The knowledge of global gene expression will help us to develop early disease or disorder biomarkers for PCB-induced health effects. We used microarrays to detail the global gene expression profile underlying the effects of high PCB exposure to Slovak 45-month-old children leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes. Extraction of total RNA was performed by using Qiagen PAXgene Blood RNA Kit IVD according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Arrays (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

2011-08-31 | E-GEOD-22868 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data