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Microarray analysis of HK-2 cells treated with cisplatin

ABSTRACT: Chemotherapeutic use of cisplatin is limited by its severe side effects. In this study, we demonstrated that cisplatin induces cell death in a proximal tubular cell line by suppressing glycolysis- and tricarboxylic acid (TCA)/mitochondria-related genes. HK-2 cells were cultured to confluence in 100mm dishes. Total RNA was extracted (QIAGEN, Valencia, CA, USA), and the concentration in the samples was measured using a Micro UV-Vis fluorescence spectrophotometer (Malcom, Tokyo, JAPAN). Sample of 10ɥg of Total RNA from HK-2 cells were labeled with biotin (3'IVT Labeling Kit, Affymetrix, USA) and hybridized (GeneAtlas Hybridization, Wash, and Stain Kit for 3' IVT Arrays, Affymetrix). The Microarray platform used was Affymetrix HG U219 Array Strip. The arrays were scanned in a GeneAtlas scanner controlled by GeneAtlas Software (Affymetrix, Sta. Clara, USA). Genes were later filtered according to expression fold change (Affymetrix Expression Console software, Affymetrix)

ORGANISM(S): Homo sapiens

PROVIDER: GSE69644 | GEO | 2015/06/09

SECONDARY ACCESSION(S): PRJNA286081

REPOSITORIES: GEO

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Microarray analysis of HK-2 cells treated with cisplatin

Project description:Chemotherapeutic use of cisplatin is limited by its severe side effects. In this study, we demonstrated that cisplatin induces cell death in a proximal tubular cell line by suppressing glycolysis- and tricarboxylic acid (TCA)/mitochondria-related genes. HK-2 cells were cultured to confluence in 100mm dishes. Total RNA was extracted (QIAGEN, Valencia, CA, USA), and the concentration in the samples was measured using a Micro UV-Vis fluorescence spectrophotometer (Malcom, Tokyo, JAPAN). Sample of 10ɥg of Total RNA from HK-2 cells were labeled with biotin (3'IVT Labeling Kit, Affymetrix, USA) and hybridized (GeneAtlas Hybridization, Wash, and Stain Kit for 3' IVT Arrays, Affymetrix). The Microarray platform used was Affymetrix HG U219 Array Strip. The arrays were scanned in a GeneAtlas scanner controlled by GeneAtlas Software (Affymetrix, Sta. Clara, USA). Genes were later filtered according to expression fold change (Affymetrix Expression Console software, Affymetrix) Using Affymetrix GeneAtlas System, we determined the gene expression profiles of HK-2 cells treated with cisplatin. Two replicates were made for each timepoints (control, 6h and 24h).

2015-06-09 | E-GEOD-69644 | biostudies-arrayexpress

Gene expression comparison between two human cancer cell Lines: Oral squamous cell carcinoma SASL1m and adenoid cystic carcinoma ACC2

Project description:SASL1 is highly metastatic to lymph nodes. ACC2 is not metastatic. We compared gene expression on cultured cells to identify genes associated to metastatic spread patterns. SASL1m cells and ACC2 cells were cultured to confluence in 10 100mm dishes (5 per cell type). Total RNA was extracted (ISOGEN, Nippongene, Japan), purified by centrifugation, pooled and checked for quality (Eukaryote Total RNA Series II, Agilent, Sta Clara, USA) . Two samples of 2ɥg of Total RNA from SASL1m and ACC2 cells were labeled with biotin (3'IVT Labeling Kit, Affymetrix, USA) and hybridized (GeneAtlas Hybridization, Wash, and Stain Kit for 3' IVT Arrays, Affymetrix). The Microarray platform used was Affymetrix HG U219 Array Strip. The arrays were scanned in a GeneAtlas scanner controlled by GeneAtlas Software (Affymetrix, Sta. Clara, USA). No replicates were made. Genes were later filtered according to expression fold change (GeneSpring GX Software, Agilent, Sta Clara USA) and later organized in hypothetical networks (Ingenuity Pathway and Analysis Software, Ingenuity Systems, Redwood, USA). No control or reference samples were included. The expression of genes of interest was confirmed with qrt-PCR in the samples studied and four additional samples from cell cultures (Lightcycler, Roche, Switzerland).

2011-10-24 | E-GEOD-33171 | biostudies-arrayexpress

Expression data from the cerebral cortex of sugarcane top ethanolic extract (STEE)-administered SAMP8 mice, water-administered SAMP8 mice, and water-administered SAMR1 mice.

Project description:STEE regulated a wide range of biological processes in the cerebral cortex of SAMP8 mice. RNA samples were extracted from cerebral cortices with Isogen (Nippon Gene, Toyama, Japan) and were amplified and biotinylated with Affymetrix 3’ IVT PLUS Reagent Kit (Affymetrix, Santa Clara, CA), according to the manufacturer’s instructions. The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and one hundred ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA. Biotinylated cRNA was hybridized onto Affymetrix Mouse Genome 430 PM array strips (Affymetrix) for 16 hrs at 45℃ in the hybridization station. The hybridized arrays were washed, stained, and scanned with GeneAtlas Fluidics and Imaging Station.

2020-09-14 | GSE151727 | GEO

Gene expression after 24h Urolithin A incubation in LNCaP cells

Project description:The identification of new agents that may modulate the progression of cancer cell growth is of great interest. In this regard, dietary agents can be utilized to identify molecular targets to be used as part of a chemopreventive strategy. Walnuts contain several bioactive compounds, including pedunculagin, a polyphenol metabolized by microbiota to form urolithins, namely urolithin A (UA). We performed a genomic analysis to study the effect of UA on androgen-dependent LNCaP prostate adenocarcinoma cells. Cells were incubated with 40µM UA for 24 hours, then, RNA was extracted. RNA samples were processed in the automated Biomek FX System (Beckman Coulter), where aRNA was produced, and labeled with Biotin, purified , fragmented and hybridized onto HG U219-24 Array, using the GeneChip HT 3’IVT Express Kit . Afterwards, the GeneTitan® Multi-Channel (MC) Instrument (Affymetrix) was used to hybridize, wash , stain , and scan the arrays. Microarray results were analyzed using the GeneSpring GX v13.0 software.

2016-07-27 | GSE65527 | GEO

HCaRG-9 vs NEO-1

Project description:HEK293 cells were transfected with control plasmid (pcDNAI/Neo;Invitrogen) or with the plasmid encoding HCaRG. Stable transfectants were synchronized and grown in the presence of 10% FBS for 48 h. Total RNAs were purified with the mini RNeasy kit (Qiagen). Chips HG-U133A: - Labeling protocol: Enzo BioArray HighYield RNA Transcript Labeling Kit. - Hybridization: According to the manufacturer's protocol (Affymetrix). - Scanner: GeneArray 2500. - Normalization: Employing GCOS software, chips were normalized using all probe sets scaling option and target signal at 500. Chips HG-U133 Plus 2.0: - Labeling protocol: GeneChip IVT Labeling Kit. - Hybridization: According to the manufacturer's protocol (Affymetrix). - Scanner: GeneChip Scanner 3000. - Normalization: Employing GCOS software, chips were normalized using all probe sets scaling option and target signal at 500. Keywords: parallel sample

2005-10-19 | GSE2555 | GEO

Genomic alterations in MM - CEL

Project description:RNA from the same tumor sample (n=98) was also processed using the 3' IVT kit (Affymetrix) and hybridized to U133 Plus 2.0 arrays (Affymetrix).

| EGAD00010001577 | EGA

Gene expression after 24h Urolithin A incubation in LNCaP cells

Project description:The identification of new agents that may modulate the progression of cancer cell growth is of great interest. In this regard, dietary agents can be utilized to identify molecular targets to be used as part of a chemopreventive strategy. Walnuts contain several bioactive compounds, including pedunculagin, a polyphenol metabolized by microbiota to form urolithins, namely urolithin A (UA). We performed a genomic analysis to study the effect of UA on androgen-dependent LNCaP prostate adenocarcinoma cells. Cells were incubated with 40ÂµM UA for 24 hours, then, RNA was extracted. RNA samples were processed in the automated Biomek FX System (Beckman Coulter), where aRNA was produced, and labeled with Biotin, purified , fragmented and hybridized onto HG U219-24 Array, using the GeneChip HT 3âIVT Express Kit . Afterwards, the GeneTitanÂ® Multi-Channel (MC) Instrument (Affymetrix) was used to hybridize, wash , stain , and scan the arrays. Microarray results were analyzed using the GeneSpring GX v13.0 software. LNCaP cells were plated in 35mm wells, the following day they were treated with 40ÂµM urolithin A (UA) for 24 hours, after incubation Total RNA was extracted using Qiagen RNAeasy minikit. The Affymetrix Human Genome U219 array plate was used, which measures gene expression of more than 36 000 transcripts and variants per sample, which represent more than 20 000 genes.

2016-07-27 | E-GEOD-65527 | biostudies-arrayexpress

Homo sapiens

Project description:FFPE samples profiled on HG-U219 array with Affymetrix's SensationPlusTM FFPE Amplification and 3'IVT Labeling kit

| PRJNA360631 | ENA

Yeast genomic expression patterns in response to zymolyase treatment

Project description:The evaluation of zymolyase treatment using yeast gene expression comparison analysis. The yeast BY4743 strain was used for this study. Yeast cells were treated with Zymolyase (final conc. 300 U/ml), and incubated at 37 degree for ten minutes. Digestion process was not provided for control sample. Total RNA was isolated with commercial kit (FastRNA Pro Red kit, Q-Biogene), and amplified RNA (aRNA) was synthesized with 3'IVT Express kit (Affymetrix). All samples were hybridized with Gene Chip (Yeast Genome 2.0 Array, Affymetrix), then each array chip was scanned by GeneChip Sanner 3000 (Affymetrix).

2013-03-21 | GSE36955 | GEO

Yeast genomic expression patterns in response to type B trichothecenes

Project description:The evaluation of mycotoxicity of type B trichothecenes using a yeast gene expression comparison analysis. The yeast BY4743 derivative PDR5 mutant was used for this study. The yeast cells were treated with trichothecene mycotoxins, and incubated at 25 degree for two hours, respectively. Total RNA was isolated with commercial kit (FastRNA Pro Red kit, Q-Biogene), and amplified RNA (aRNA) was synthesized with 3'IVT Express kit (Affymetrix). All samples were hybridized with Gene Chip (Yeast Genome 2.0 Array, Affymetrix), then each array chip was scanned by GeneChip Sanner 3000 (Affymetrix).

2012-09-12 | GSE36954 | GEO

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