Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from human ovarian cancer cells induced by IL-6 and CNTO328

ABSTRACT: The SKOV-3 and Caov-3 ovarian cancer cell lines where seeded onto the 100mm cell culture plate for overnight. The cells were then incubated with IL-6 (30ng/ml) alone for one hour or pre-treated with siltuximab for four hours and then treated with IL-6 for one hour. Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 in the first and most comprehensive whole human genome expression array. This array completes coverage of the whole human Genome with over 47,000 transcripts. The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. GeneSifter was used to analyze the microarray data (http://www.genesifter.net/web/). Fold change in expression between sensitive and resistant cell lines was evaluated using the Mann-Whitney test. A tenfold or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20272 | GEO | 2010/02/11

SECONDARY ACCESSION(S): PRJNA125253

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression data from human ovarian cancer cells induced by IL-6 and CNTO328

Project description:The SKOV-3 and Caov-3 ovarian cancer cell lines where seeded onto the 100mm cell culture plate for overnight. The cells were then incubated with IL-6 (30ng/ml) alone for one hour or pre-treated with siltuximab for four hours and then treated with IL-6 for one hour. Total RNA was collected from these cells using TRIzolÂ® Reagent (GIBCO Grand Island, NY) according to the manufacturerâ??s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 in the first and most comprehensive whole human genome expression array. This array completes coverage of the whole human Genome with over 47,000 transcripts. The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. GeneSifter was used to analyze the microarray data (http://www.genesifter.net/web/). Fold change in expression between sensitive and resistant cell lines was evaluated using the Mann-Whitney test. A tenfold or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set. Evalutate the effect of CNTO328 on IL-6 induced gene expression in ovarian cancer cells

2010-02-24 | E-GEOD-20272 | biostudies-arrayexpress

Expression data from human osteosarcoma cells treated with CDK11 siRNA

Project description:The U-2OS and KHOS osteosarcoma cell lines where seeded onto the 100mm cell culture plate, then treated with CDK11 siRNA (40nM) or nonspecificsiRNA (40nM). Change with regular medium 24 hour later. Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 in the first and most comprehensive whole human genome expression array. This array completes coverage of the whole human Genome with over 47,000 transcripts. The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. GeneSifter and Qlucore were used to analyze the microarray data (http://www.genesifter.net/web/; http://www.qlucore.com). Fold change in expression between CDK11 siRNA treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A tenfold or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

2015-10-07 | GSE73422 | GEO

Expression data from human osteosarcoma cells after transfected miR-206

Project description:The U-2OS and KHOS osteosarcoma cell lines were seeded into the 100mm cell culture plate respectively, then transfected miRSelect pEP-miR-206 or miRSelect pEP-miR-Null into the two cell lines with Lipofectamine LTX and Plus Reagent (Invitrogen) for 48 hours. After that, total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 in the first and most comprehensive whole human genome expression array. This array completes coverage of the whole human Genome with over 47,000 transcripts. The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. Qlucore were used to analyze the microarray data (http://www.qlucore.com). Fold change in expression between miR-206 treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A 1.2 foldchange or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

2016-10-24 | GSE89074 | GEO

Expression data from human osteosarcoma cells after transfected miR-199a-3p

Project description:The U-2OS and KHOS osteosarcoma cell lines were seeded into the 100mm cell culture plate, then transfected miRSelect pEP-miR-199a-3p or miRSelect pEP-miR-Null into the two cell lines with Lipofectamine LTX and Plus Reagent (Invitrogen) for 48 hours. After that, total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Gene Chip U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 is first and most comprehensive whole human genome expression array. This array completes coverage of the whole human Genome with over 47,000 transcripts. The expression level of each mRNA is quantified by measuring its hybridization to these 25-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. The average expression value for each gene across the arrays was used to normalize the mRNA intensities. The CEL files were transformed into intensity information using the RMA normalization of Qlucore 3.2. Qlucore were used to analyze the microarray data (http://www.qlucore.com). Fold change in expression between miR-199a-3p treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A 1.2 foldchange or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

2016-11-01 | GSE89370 | GEO

Differentially expressed mRNA transcripts in the placenta delivered by preterm versus term spontaneous labour

Project description:We hypothesized that preterm spontaneous labor involves aberrant changes in mRNA expression in the placenta. To test this hypothesis, we interrogated the mRNA levels of >50,000 genes and transcript variants using gene expression microarray (Human Genome U133 Plus 2.0 Array, Affymetrix) on 5 placentas collected from preterm spontaneous delivery (<34 weeks of gestation) and another 5 placentas collected from term spontaneous delivery (38-39 weeks). We have identified 229 and 162 genes that were up- or down-regulated, respectively, for more than 3-fold in the preterm placentas compared to the term placentas (Mann-Whitney Rank Sum Test, with multiple testing correction by the Benjamini-Hochberg method, adjusted p-value <= 0.05). Placentas collected from (i) preterm spontaneous delivery (<34 weeks of gestation) and (ii) term spontaneous delivery (38-39 weeks of gestation) were subjected to RNA extraction and hybridization on Affymetrix microarrays. To identify gene expression patterns that are commonly involved in preterm spontaneous labour, we analyzed 5 placentas from each of these 2 groups and tested for any differentially expressed genes by Mann-Whitney Rank Sum Test.

2009-10-31 | E-GEOD-18809 | biostudies-arrayexpress

Differentially expressed mRNA transcripts in the placenta delivered by preterm versus term spontaneous labour

2009-10-31 | GSE18809 | GEO

Validation of a subset of copy number variants from GSE24424 by aCGH

Project description:This dataset was used to validate CNV predictions from GSE24424. We designed a custom CGH array to interrogate a total of 4,420 individual CNVs and their flanks predicted in 17 individuals. On the basis of a test that compares signals of probes located within to those mapping outside of CNVs (two-tailed P<0.05, Mann-Whitney U test), we could confirm about 77% of the tested predictions and thus establish a set of 3,383 validated CNVs. The vast majority of confirmed CNVs (3,299 of 3,383 or 97.5%) show a consistent direction of change between the initial array (GSE24424) and the custom array, suggesting a false-confirmation rate of approximately 5%.

2010-12-31 | GSE24640 | GEO

Comparative proteomics analysis of decidua tissues in early recurrent pregnancy loss

Project description:The project aimed to determine proteomics changes in decidua from patients suffering from unexplained early recurrent pregnancy loss (RPL) compared to women undergoing elective abortions. Comparative proteomics analysis by label-free data-independent LC-MS/MS was performed on fresh frozen decidua tissues from 19 RPL patients and 10 controls. Samples from EPL patients were preselected to include only patients with 2 or more recurrent pregnancy losses (RPL), no previous live birth, gestational week from 6-10 weeks and excluded fetal chromosomal abnormalities. Control samples were from women without history of previous miscarriage, ectopic pregnancy or preterm delivery, with at least one live born child, at 6-10 gestational weeks and without fetal chromosomal abnormalities. Patients and controls had no significant differences regarding age (Median age RPL = 30; Median age Controls = 34; Mann–Whitney U-test p = 0.082). The mean gestational weak (GW) was 7.9±1.0 weeks in the RPL group and 8.3±1.2 weeks in the control group, without statistically significant difference between groups (Median GW RPL = 8; Median GW Controls = 8; Mann–Whitney U-test p = 0.361).

2024-06-12 | PXD048340 | Pride

Comparative proteomics analysis of chorionic villi in recurrent pregnancy loss

Project description:The project aimed to determine proteomics changes in chorionic villi from patients suffering from unexplained early recurrent pregnancy loss (RPL) compared to women undergoing elective abortions. Comparative proteomics analysis by label-free data-independent LC-MS/MS was performed on fresh frozen chorionic villi from 13 RPL patients and 10 controls. Samples from EPL patients were preselected to include only patients with 2 or more recurrent pregnancy losses (RPL), no previous live birth, gestational week from 6-10 weeks and excluded fetal chromosomal abnormalities. Control samples were from women without history of previous miscarriage, ectopic pregnancy or preterm delivery, with at least one live born child, at 6-10 gestational weeks and without fetal chromosomal abnormalities. Patients and controls were between 24-44 years with no significant differences among groups regarding age (Median age RPL = 29; Median age Controls = 34; Mann–Whitney U-test p = 0.078). The mean gestational weak (GW) was 7.9±0.8 weeks in the RPL group and 8.3±1.2 weeks in the control group, without statistically significant difference between groups (Median GW RPL = 8; Median GW Controls = 8; Mann–Whitney U-test p = 0.484).

2024-08-27 | PXD048344 | Pride

Transcription profiling of Brugia Wolbachia elimination

Project description:Female worms (Brugia malayi) were collected from infected jirds treated with 2.5 mg/ml tetracycline in drinking water for 7, 14, or 21 days to eliminate the worm's endosymbiont, Wolbachia.<br>Control age matched female worms were recovered from infected jirds given normal water for drinking.<br>The Filarial Nematode Oligonucleotide Array (version 2) was used in hybridization analyses on cDNA generated from extracted total RNA.<br>Each microarray was hybridized with a mixture of control and experimental cDNA differentially labeled with Cy3 and Cy5 in a flip-dye experiment.<br>Gridding and analysis of images were performed using ScanArray v3.0, each spot defined pixel-by-pixel using a modified Mann-Whitney test, and the resulting values processed with Gene-Spring 7.1 software.

2009-05-22 | E-MEXP-2185 | 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