Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray analysis of murine kidney treated with Amodiaquine and Sulfodoxine-Pyrimethamine

ABSTRACT: Differential gene expression in mice kidney after Amodiaquine and Sulfodoxine-Pyrimethamine anti-malaria treatments were evaluated. Dosages were decided based on standard malaria therapy in human. Mice (Mus musculus) belonging to control and Amodiaquine and Sulfodoxine-Pyrimethamine administered groups (n=4) were sacrificed. The kidneys were snap frozen in liquid nitrogen, and subsequently stored at -80M-BM-:C till further use. Kidney samples were homogenized and total RNA was extracted with TRI reagent. 25 ug of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit. The Cy5 and Cy3 labeled cDNAs were resuspended in Cyscribe Hyb buffer containing 10ug/ml sheared Salmon sperm DNA and 10ug/ml Yeast tRNA. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42M-BM-:C. Fluorescent array images were collected for both Cy3 and Cy5 with Molecular Dynamics III scanner supported with ImageQuant v5.0. Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background-corrected data was LOWESS normalized and log ratios were calculated using Avadis v4. Further, mean log ratios were calculated for duplicate spots. Duplicate experiments were carried out for all the dosages.

ORGANISM(S): Mus musculus

SUBMITTER: Shrawan Mishra

PROVIDER: E-GEOD-19157 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Differential gene expression in mice liver following apigenin administration

Project description:Differential gene expression in mice liver after apigenin administration. Gene expression from control mice were compared with apigenin treated mice at different dose level. To study differential expression primarily at high stringency and in dose dependent manner was to increase the statistical confidence in the detection of important genes and cellular processes with a probable role in the initiation and propagation of toxicity as well as those possibly involved in regeneration during the early phase of tissue response.

2011-04-27 | E-GEOD-12716 | biostudies-arrayexpress

Differential gene expression in mice liver following bulaquine administration

Project description:Global gene expression in livers of bulaquine treated mice was compared with control mice at different time points. Keywords: Time course Mice (Mus musculus) belonging to control and bulaquine-administered groups (n=4) were sacrificed. The livers were snap frozen in liquid nitrogen, and subsequently stored at -80ÂºC till further use. Liver samples were homogenized and total RNA was extracted with TRI reagent. 25 ug of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit. The Cy5 and Cy3 labeled cDNAs were resuspended in Cyscribe Hyb buffer containing 10ug/ml sheared Salmon sperm DNA and 10ug/ml Yeast tRNA. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42ÂºC. Fluorescent array images were collected for both Cy3 and Cy5 with molecular dynamics III scanner supported with ImageQuant v5.0. Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background corrected data was LOWESS normalized and log ratios were calculated using Avadis v4. Replicate experiments were carried out in dye swap manner for each time point.

2010-06-11 | E-GEOD-5980 | biostudies-arrayexpress

Carbon tetrachloride and Acetaminophen hepatotoxicity study

Project description:Differential gene expression in mice liver after carbon tetrachloride and acetaminophen administration. Livers from control mice were compared with drug treated mice livers at different time points. Keywords: Time-course Mice (Mus musculus) belonging to control and carbon tetrachloride and acetaminophen-administered groups (n=4) were sacrificed. The livers were snap frozen in liquid nitrogen, and subsequently stored at -80ÂºC till further use. Liver samples were homogenized and total RNA was extracted with TRI reagent. 25 ug of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit. The Cy5 and Cy3 labeled cDNAs were resuspended in Cyscribe Hyb buffer containing 10ug/ml sheared Salmon sperm DNA and 10ug/ml Yeast tRNA. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42ÂºC. Fluorescent array images were collected for both Cy3 and Cy5 with molecular dynamics III scanner supported with ImageQuant v5.0. Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background corrected data was LOWESS normalized and log ratios were calculated using Avadis v4. Further, mean log ratios were calculated for duplicate spots. Replicate experiments were carried out in dye swap manner for each time point.

2010-06-11 | E-GEOD-4874 | biostudies-arrayexpress

Identification of microRNAs involved in acute rejection and spontaneous tolerance in murine hepatic allografts

Project description:Graft acceptance without the need for immunosuppressive drugs is the ultimate goal of transplantation therapy. In murine liver transplantation, allografts are accepted across major histocompatibility antigen complex barriers without the use of immunosuppressive drugs and constitute a suitable model for research on immunological rejection and tolerance. MicroRNA (miRNA) has been known to be involved in the immunological responses. In order to identify mRNAs in spontaneous liver allograft tolerance, miRNA expression in hepatic allografts was examined using this transplantation model. According to the graft pathological score and function, miR-146a, 15b, 223, 23a, 27a, 34a and 451 were upregulated compared with the expression observed in the syngeneic grafts. In contrast, miR-101a, 101b and 148a were downregulated. Our results demonstrated the alteration of miRNAs in the allografts and may indicate the role of miRNAs in the induction of tolerance after transplantation. Furthermore, our data suggest that monitoring the graft expression of novel miRNAs may allow clinicians to differentiate between rejection and tolerance. A better understanding of the tolerance inducing mechanism observed in murine hepatic allografts may provide a therapeutic strategy for attenuating allograft rejection. B10.BR mice were used as donors and B10.D2 mice were used as recipients. Liver allo-transplantation surgery on the mice was performed in this combination. Three mice from each group were sacrificed, and the liver grafts were removed on days 5, 8, 14 and 100 after transplantation. Total RNA, including miRNA was isolated. 100ng of total RNA was labeled by Cy3 and used as probe for hybridization to the microarray.

2014-10-21 | E-GEOD-52164 | biostudies-arrayexpress

Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation

Project description:This SuperSeries is composed of the following subset Series: GSE24877: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs NA16) GSE24878: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs COLONY) GSE24879: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs. Tumor) Refer to individual Series

2010-11-14 | E-GEOD-24893 | biostudies-arrayexpress

Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs NA16)

Project description:Cell substrate adhesion plays an important role in cellular transformation of rat fibroblast cell lines, however a few viable non-adherent fibroblast cells when placed in suspension for a time period of 16 h (NA16) showed varied phenotypic characteristics like colony and tumor formation In order to understand the molecular events associated with adhesion independent cell survival ability of NA16, whole genome profiling was performed using Affymetrix Rat 230_2 GeneChips Keywords: Expression profiling of a adhesion deprived transformed cell line F111 fibroblast cell lines were grown in adhesion (A16) and suspension (NA16) conditions for 16h. These suspension cells (NA16) were plated on soft agar for colony formation and also injected in nude mice subcutaneously for tumor formation. A16 samples were considered as the control ones. Total RNA isolated from the samples (A16, NA16, Colony and Tumor) was subjected for expression analysis using Affymetrix Rat 230.2 GeneChip System. The experiment was repeated biologically and technically twice.

2010-11-14 | E-GEOD-24877 | biostudies-arrayexpress

Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs COLONY)

2010-11-14 | E-GEOD-24878 | biostudies-arrayexpress

Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs. Tumor)

2010-11-14 | E-GEOD-24879 | biostudies-arrayexpress

ER stress impairs the insulin signaling pathway through mitochondrial damage in SH-SY5Y human neuroblastoma cells

Project description:This SuperSeries is composed of the following subset Series: GSE24497: ER stress impairs the insulin signaling pathway through mitochondrial damage in SH-SY5Y human neuroblastoma cells (part 1) GSE24499: ER stress impairs the insulin signaling pathway through mitochondrial damage in SH-SY5Y human neuroblastoma cells (part 2) Refer to individual Series

2010-10-07 | E-GEOD-24500 | biostudies-arrayexpress

Systemic transcriptome alternation under mtDNA depletion in 143B TK- osteosarcoma cells

Project description:The mitochondrial protein repertoire varies depending on cellular states, tissue type, species, and disease state. However, little is known about how this repertoire changes under different cellular or disease states. To gain a better understanding of dynamic mitochondrial proteomic changes, we compared alterations of mitochondrial proteome with transcriptome under mitochondrial DNA depletion. Total RNA obtained from 143B TK- osteosarcoma ?+ cells or 143B TK- osteosarcoma ?° cells

2010-07-17 | E-GEOD-22970 | 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