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Prolactin-induced protein (PIP) regulates proliferation of luminal A type breast cancer cells in a hormone-independent manner

ABSTRACT: RNA was extracted from cells using Aurum Total RNA kit from Bio-Rad Laboratories, Inc., Hercules, CA following the manufacturer’s recommendations. Gene expression profiling was performed using the BeadChip HumanHT-12 v4 Expression kit from Illumina®, which contains 47,231 gene-probes (Illumina® Inc., San Diego, CA). The raw signal intensities were imported and analyzed using the GenomeStudio® data software. After background subtraction and normalization, the signal intensity values were exported to the Partek® genomics expression analysis suite using “Partek's Report Plug-in” option in the GenomeStudio® software. Differentially expressed genes in the dox- versus vehicle-treated samples were identified using the “gene expression” workflow in the Partek® software.

ORGANISM(S): Homo sapiens

PROVIDER: GSE41894 | GEO | 2012/10/29

SECONDARY ACCESSION(S): PRJNA178414

REPOSITORIES: GEO

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Prolactin-induced protein (PIP) regulates proliferation of luminal A type breast cancer cells in a hormone-independent manner

Project description:RNA was extracted from cells using Aurum Total RNA kit from Bio-Rad Laboratories, Inc., Hercules, CA following the manufacturerM-bM-^@M-^Ys recommendations. Gene expression profiling was performed using the BeadChip HumanHT-12 v4 Expression kit from IlluminaM-BM-., which contains 47,231 gene-probes (IlluminaM-BM-. Inc., San Diego, CA). The raw signal intensities were imported and analyzed using the GenomeStudioM-BM-. data software. After background subtraction and normalization, the signal intensity values were exported to the PartekM-BM-. genomics expression analysis suite using M-bM-^@M-^\Partek's Report Plug-inM-bM-^@M-^] option in the GenomeStudioM-BM-. software. Differentially expressed genes in the dox- versus vehicle-treated samples were identified using the M-bM-^@M-^\gene expressionM-bM-^@M-^] workflow in the PartekM-BM-. software. T47D cells hoaboring a doxycycline inducible shPIP construct were treated for 24 or 48 hours with 250 ng/mL of doxycycline and their mRNAs analyzed in biological triplicates (a total of 12 samples) using IlluminaM-bM-^@M-^Xs HumanHT-12 v4 BeadChips. The samples for each time point comprised of three samples each for doxycycline or equal volume of water as vehicle control.

2012-10-29 | E-GEOD-41894 | biostudies-arrayexpress

Real-time quantitative PCR analysis of Tomato stress response

Project description:To extract RNA from shoots and roots, 3 weeks old control and treated plants were harvested at 2pm in the greenhouse. Total RNA was extracted using the AccuPrep® Universal RNA extraction kit (Bioneer, Daejeon, Korea) and treated with RNase-free DNase to remove DNA fragments (Qiagen, Hilden, Germany). One microgram of total RNA was used to synthesize cDNA with AccuPower® RT PreMix (Bioneer, Daejeon, Korea). Quantitative real-time RT-PCR was conducted using a T100TM Thermocycler system (Bio-Rad, Hercules, CA, USA). Primer information is given in Table S7. Reactions (10 µL final volume) were prepared using 5 µL of LaboPass™ SYBR Green Q Master Kit (Cosmogenetech, Dajeon, Korea). 0.5 pmol of a primer pair, and 0.5 µL of cDNA template. 4 biological samples and two technical replicates were used for the quantifications. Ubiquitin was used as the reference. gene expression analysis was performed with the 2^−ΔΔCt method using Bio-Rad CFX Maestro software v.4.0 (Bio-Rad). Baseline and threshold levels were set according to the manufacturer’s instructions.

2024-02-04 | GSE248090 | GEO

Modulation of microglia-mediated amyloid-beta clearance with nanoformulated polyphenol through the SIRT1-LDLR pathway

Project description:Light-controlled in situ synthesis of DNA microarrays (Affymetrix GeneChip® Mouse Genome 430 2.0) were performed to determine the altered gene expression. Affymetrix algorithm and multiple analysis comparison software were used for assessing gene expression differences, and mRNAs that increased or decreased in the brains of NP(α-M)-treated mice relative to that in the brains of Blank-NP-treated mice were identified. For the assay, total RNA was extracted using Takara RNAiso Plus Kit (Cat#9109, Takara, DaLian, LiaoNing, CN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions. Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).

2018-09-14 | GSE119904 | GEO

Response of yeast to tomatidine treatment

Project description:Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the fungistatic saponin tomatidine. Overnight batch cultures of strain S288C were diluted to an optical density at 600nm of 0.1. After 1 hour of growth at 30°C, the compounds were added and the cultures were incubated for an additional 5 hours prior to harvesting. Control cultures were treated with the solvent dimethylformamide (DMF). Tomatidine treated cultures were grown in the presence of tomatidine (dissolved in DMF) at concentations of 7.5 uM and 15 uM. Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen. Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA). Microarray hybridisation was performed using the Affymetrix GeneChip® Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001). Data were analyzed using Affymetrix® Microarray Suite version 5.0 software Keywords: dose response

2004-11-06 | GSE1927 | GEO

Response of yeast to saponin treatment

Project description:Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the saponins tomatidine, tomatine and the sterol biosynthesis inhibitory compound fenpropimorph Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen. Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA). Microarray hybridisation was performed using the Affymetrix GeneChip® Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001). Data were analyzed using the RMA algorithm using Expressionist Pro (GeneData Inc., Switzerland). Keywords: response to abiotic stress

2006-07-28 | GSE4669 | GEO

Transcription profiling of Oryza sativa subtypes Cultivar Nagina-22 (N22) and IR64 subtypes under normal and drougth conditions.

Project description:High quality RNA was extracted from the whole seedlings (Combined root and leaf samples) using TRI Reagent (Ambion, Inc. USA) and pooled from 12 independent stressed and non-stressed plant samples separately, and treated with DNase-I (QIAGEN GmbH, Germany). Subsequently, RNA cleanup was carried out using RNeasy Plant Mini Kit (QIAGEN GmbH, Germany) and 5 ug of total RNA from each sample in triplicates were reverse-transcribed to double stranded cDNA using the GeneChipï¾® One-Cycle cDNA Synthesis Kit. The biotin-labelled cRNA was made using the GeneChipï¾® IVT Labelling Kit (Affymetrix, CA, USA). Twenty microgram of cRNA samples was fragmented and out of which which 7.5 ug cRNA were hybridized for 16 hours at 45C to the Affymetrix GeneChipï¾® Rice Genome Array (Santa Clara, CA, USA). After washing and staining with R-phycoerythrin streptavidin in a Fluidics Station, using the Genechipï¾® Fluidics Station 450, the arrays were scanned by the Genechipï¾® 3000 Scanner. The chip images were scanned and extracted using default settings and the CEL files were produced with the Affymetrix GeneChip Operating Software (GCOS 1.2). The resulting .CEL files were imported into the GeneSpring GX 10 (Agilent Technologies Inc, Santa Clara CA) and normalized with the PLIER16 algorithm. The resulting expression values were log2-transformed. Average log signal intensity values of three technical replicates for each sample were used for advance analysis.

2010-10-09 | E-MEXP-2401 | biostudies-arrayexpress

Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors (Illumina)

Project description:Gene expression profiling of 17 fresh frozen chondrosarcoma biopsies using the Human-6 v2 Expression BeadChip (Illumina Inc., San Diego, CA, USA). DNA copy number analyses was also performed in these tumors. Keywords: chondrosarcoma, gene expression profiling, Illumina Samples displaying a tumor content of >70%, as determined from haematoxylin and eosin-stained frozen sections, were analyzed using the Homo sapiens-6 v2 Expression BeadChips (Illumina Inc., San Diego, CA, USA), containing more than 48,000 transcript probes. In samples demonstrating a lower amount of tumor versus normal tissue, macrodissection of tumor material was performed. For each hybridization, 200 ng of total RNA were processed according to the Illumina® TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX, USA), to produce double-stranded cDNA and subsequently to generate biotin-labelled cRNA. Following the manufacturer’s specifications (Illumina), 1.5 µg of the biotin labeled cRNA were hybridized onto the Homo sapiens-6 v2 Expression BeadChips overnight, and subsequently detected with streptavidin-Cy3 using an Illumina® BeadArray Reader. Image analysis was performed using the Illumina® BeadStudio Application Software.

2009-04-01 | E-GEOD-12475 | biostudies-arrayexpress

Expression profile of Normal Breast Tissue in Brazilian women

Project description:Control samples used to performed gene expression comparison with breast cancer tissues. mRNA samples from normal breast tissue were amplified, labeled, and hybridized to the Affymetrix GeneChip Human Exon 1.0 ST array. After normalization and analysis of the microarray data using Partek® software (http://www.partek.com).

2021-11-03 | GSE180835 | GEO

Lymph node gene expression profiling in hyperlipidemic mice

Project description:Total RNA in mesenteric LNs from chow- or high fat diet-fed Ldlr–/– mice were isolated using an RNeasy mini kit (Qiagen) with on-column DNaseI digestion. The DNA array was conducted using a Mouse Oligo chip 24k (TORAY Industries Inc.) and a 3D-Gene® Scanner (TORAY Industries Inc.) by Kamakura Techno-Science, Inc. (TORAY Industries Inc.).

2021-02-21 | GSE167142 | GEO

The prevalence of human cytomegalovirus in colorectal cancer and viral gene expression profiles

Project description:Five HCMV (+) CRC tissues detected by PCR were selected for RNA-seq. GEPs were pre-processed by Cutadapter and FastQC to remove jointed reads and low-quality reads. Tophat (v.2.0.0) was used to compare the sequences with Homo sapiens and HCMV genomes. The GEPs of HCMV was determined by Integrated Genomics Viewer (IGV) and Partek® Genomics Suite™ (version 6.5 beta, Partek Inc., St. Louis, MO, USA).

2021-04-30 | GSE173609 | GEO

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