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Combination of ABT-869 with SAHA on AML with FLT3-ITD

ABSTRACT: For the microarray experiments, MV4-11 and MOLM-14 cells were treated with DMSO control, ABT-869 3 nM, SAHA 6 uM and combination therapy for 24 hours. Cells were then washed in PBS and high-quality total RNA was extracted RNeasy Midi Kit, according to the manufacturer’s instruction (Qiagen, Valencia, USA). RNA quantity, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA, USA). Gene expression profiling was performed using Affymetric U133plus2.0 gene chip (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol.

ORGANISM(S): Homo sapiens

PROVIDER: GSE26114 | GEO | 2011/05/31

SECONDARY ACCESSION(S): PRJNA135197

REPOSITORIES: GEO

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Combination of ABT-869 with SAHA on AML with FLT3-ITD

Project description:For the microarray experiments, MV4-11 and MOLM-14 cells were treated with DMSO control, ABT-869 3 nM, SAHA 6 M and combination therapy for 24 hours. Cells were then washed in PBS and high-quality total RNA was extracted RNeasy Midi Kit, according to the manufacturer’s instruction (Qiagen, Valencia, USA). RNA quantity, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA, USA). Gene expression profiling was performed using Affymetric U133plus2.0 gene chip (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol. MV4-11 and MOLM-14 cells were treated with DMSO control, ABT-869, SAHA or combination therapy for 24 hours.

2011-05-31 | E-GEOD-26114 | biostudies-arrayexpress

SPINK1 promotes Colorectal Cancer progression by down regulating Metallothioneins expression

Project description:Expression profiling was performed using Agilent Whole Human Genome Oligo Microarray (Santa Clara, CA) according to the manufacturer’s protocol. A total of 3 microarray hybridizations were performed using each stable shSPINK1 cell line samples against control shSCRM cells.

2015-07-21 | GSE70761 | GEO

Transcriptome Analysis of Plasmodium CSP stable expressing or control A549 cells

Project description:To investigate the potential effect of overexpression of Plasmodium yoelii cirumsporozoite protein on A549 cells. Control and CSP stable expression A549 cells were constructed by infected with pLenti vector and pLenti-CSP plasmids and cultured with HBSS for 24h. Total RNA from Control and CSP stable expression A549 cells was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (illumina novaseq6000) and 125bp/150bp paired-end reads were generated.

2022-12-31 | GSE189311 | 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

Mice liver and urine LC-MS data

Project description:Mouse livers were analyzed by lipidomics and urine by metabolomics.An Agilent Ultra-Performance Liquid Chromatography/Electrospray Ion Quadrupole Time-of-Flight-Mass Spectrometer (UPLC-ESI-QTOFMS) (Agilent, Santa Clara, CA) was utilized for lipid and other metabolites proofing in this work.

2023-06-07 | PXD041465 | Pride

Transcriptome sequencing Analysis of hLFSCs with and without mechanical stress

Project description:Purpose:The goals of this study are to MS (mechanical stress) how to change the cellular pathway of hLFSCs (human ligament flavum stem cells). Methods: Extract hLFSCs from the ligament flavum of patients.Treat the cells with and without (in control)MS.Total RNA was extracted from cells with Tripure Isolation Reagent.Subsequently, RNA was purified through rRNA depletion and then subjected to cDNA synthesis and RNA amplification. Next, random hexamer primer cDNA libraries were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and sequenced on Illumina Hiseq 4000 sequencing platform (Illumina, San Diego, California, USA) following the manufacturer’s instructions for paired-end 150 bp reads (Lifegenes, Shanghai, China).

2021-10-13 | GSE185614 | GEO

Expression data from mouse flow-sorted Kupffer cells

Project description:RNA was isolated from flow-sorted Kupffer cells under the two different conditions (tacrolimus and control) using RNeasy mini kit (Qiagen). Integrity of DNA and RNA was assessed by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). 500 nanograms of RNA were used for analysis with Affymetrix Mouse Gene 2.0 ST platform

2021-02-03 | GSE166001 | GEO

Genomic profiling of ten prostate cancer cell lines

Project description:Prostate cancer cell lines grow in full serum under standard conditions were profiled on Agilent-014698 Human Genome CGH Microarray 105A. Digestion, labeling, hybridization and data analysis of genomic DNA were performed according to the Agilent Technologies (Santa Clara, CA) protocol version 6.0 for 105 K arrays.

2011-02-01 | GSE26447 | GEO

Microarray analysis of splenic CD11b+Gr-1+ cells

Project description:We extracted RNA of sorted splenic CD11b+Gr-1+ cells and performed microarray analyses. Total RNA was isolated using the manufacturer’s recommended protocol for RNeasy (Qiagen, Valencia, CA). Isolated RNA was quantified, and quality was assessed using an Agilent A 2100 BioAnalyzer with the RNA NanoChip (Agilent, Andover, MA). We used 2μg of total RNA to make single-stranded antisense cDNA with the NuGEN Technologies (San Carlo, CA) Ovation Biotin System in accordance with the manufacturer’s directions. Labeled targets were hybridized to Affymetrix (Santa Clara, CA) MOE430 2.0 GeneChip microarrays for 16h at 45°C. The arrays were washed and scanned according to Affymetrix standard protocols. We used microarrays to detail the global gene expression of CD11b+Gr-1+ cells from the control mice and the clarithromycin-treated mice, and identified distinct classes of up-regulated genes during this process.

2016-05-09 | GSE81241 | GEO

Global gene expression pattern of human brain neuronal (SH-SY5Y) cell lines exposed to sarin (GB).

Project description:Total RNA was isolated from sarin (GB) treated (n = 6 flasks) untreated (control n = 6) neuronal (SH-SY5Y) cell lines using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). (Biological Replicates for each time points). Keywords: Time-course

2009-05-11 | GSE2732 | GEO

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