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Expression data from human osteosarcoma cells treated with CDK11 siRNA

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE73422 | GEO | 2015/10/07

SECONDARY ACCESSION(S): PRJNA297856

REPOSITORIES: GEO

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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

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 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.

2010-02-11 | GSE20272 | GEO

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

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

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

2010-12-31 | E-GEOD-24640 | biostudies-arrayexpress

Mesp1Cre;Hira-/fl and Mesp1Cre;Hira+/fl in heart at E11.5 and E12.5

Project description:Purpose: The goals of this study are to compare transcriptome profiling (RNA-seq) resulting from a Mesp1Cre driven ablation of Hira in the heart at E11.5 and E12.5. Methods: RNA extraction was done in triplicate from Mesp1Cre;Hira-/fl and Mesp1Cre;Hira+/fl embryonic hearts at E11.5 and E12.5 using the QIAGEN RNeasy mini kit. RNAseq was processed by the ICH genomics facility, reads were aligned and normalised using BOWTIE and DEseq R package. Strand NGS 2.5 software was used to re-analyse the aligned files (.bam). By applying the Mann Whitney unpaired test, Benjamini Hochberg False discovery rate (FDR) and filtering the genes using adjusted p-value ≤ 0.05 and absolute fold change ≥ 1.5, 95 % of the results were identical to the DEseq package used by the UCL Genomics facility. Results: We identified 360 coding transcripts changed in the mutant hearts (Mann Whitney unpaired test, Benjamini Hochberg FDR, p ≤ 0.05, FC ≥ 1.5) with no trend towards up- or down-regulation of global transcription (48.8% down vs 51.2% up) at E12.5. Conclusions: This work analyses the role of HIRA in mouse cardiac development. It was found that Tnni2 is the most upregulated gene in the absence of Hira. qRT-PCR validation of 25 targets. Little (<5%) or no variation of fold change between RNAseq and qRT-PCR data were observed.

2016-08-12 | GSE79937 | GEO

Placentas delivered by term spontaneous labour compared to those delivered by elective term Cesarean section

Project description:Differentially expressed mRNA transcripts in the placenta delivered by term spontaneous labour compared to those delivered by elective term cesarean section. We hypothesized that the labour process involves 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 term spontaneous delivery and another 5 placentas collected from elective term cesarean delivery. To minimize the effect of gestational age on gene expression, these two groups of placentas were matched for their gestational ages at delivery. We have identified 134 and 128 genes that were up- or down-regulated, respectively, for more than 3-fold in the term (spontaneous) labour placentas compared to the term (elective) cesarean placentas (Mann-Whitney Rank Sum Test, p-value <= 0.05 after Benjamini and Hochberg adjustment for multiple testing).

2009-11-02 | GSE18850 | GEO

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