Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

9369b624-2feb-4efe-baef-1a33c2730233 - samples

ABSTRACT: Targeted sequencing (t-NGS) of frozen advanced cancers tissue was established with three panels covering 395 to 560 candidate cancer genes. Sequencing was done using the 2x150-bp paired-end technology on the Illumina MiSeq and NextSeq500 platforms. The DNA libraries of all coding exons were done with the HaloPlex Target Enrichment System (Agilent, Santa Clara, CA, USA).

PROVIDER: EGAD00001006289 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

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

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

Novel dynamic network analysis approach characterizes progressive and complex effects of weight gain and obesity on breast cancer signaling

Project description:ER-positive tumor data was derived by RNA-sequencing of formalin-fixed paraffin-embedded specimens (FFPE) collected from 44 women diagnosed with ER+ and progesterone receptor-positive but HER2 negative (ER+/PR+/HER2-) breast cancer at the Karmanos Cancer Institute. According to a pathologist review, all tumor specimens were invasive cancer with 70% or greater cancer cell content. Patients had not received neoadjuvant cancer therapy, nor were they treated for diabetes with systemic drugs (e.g., metformin) before surgical resec- tion. Following manufacturer instructions, the Recoverall Nucleic Acid Isolation Kit for FFPE Tissue (Ambion, Austin, TX) was used to isolate RNA. Quantitation and fragmentation analysis were performed using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 and RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA). A Qubit fluorometric assay (Thermo Fisher Scientific) was used to quantitate and equalize dsDNA prepared using the Truseq RNA Access library preparation kit (Illu- mina, San Diego, CA). Libraries were randomized, indexed, multiplexed, and paired end sequenced (200 cycles total) on an Illumina Nextseq500. Bioinformatic quality control was done using the FastQC software (v0.11.4), adapter and low-quality reads were removed using Trimmomatic v0.36. FPKM normalization and aligning were done using TopHat v2.1.1.

2022-12-31 | GSE189757 | GEO

Immune-mediated Inflammation May Contribute to the Pathogenesis of Cardiovascular Disease in Mucopolysaccharidosis Type I

Project description:Comparisons of canine arterial gene expression between control and untreated MPS animals were conducted with a canine-specific microarray covering 43,803 probes (Agilent G2519F 4x44k, Santa Clara, CA), for a total of four comparison groups: MPS ascending aorta vs. control ascending aorta, MPS descending aorta vs. control descending aorta, MPS carotid artery vs. control carotid artery, and finally pooled MPS artery (ascending aorta, descending aorta, carotid artery) vs. pooled control artery. Each comparison used four pairs of MPS vs corresponding age- and gender- matched animals to produce four biologic replicates.

2016-03-05 | GSE78889 | GEO

Maternal Stress and Genomic Variation

Project description:Custom Affymetrix SNP used to assay 24 mothers for desired variants. Data processed using the Affymetrix SNP Genotyping Console (Version 4.2, Affymetrix Inc., Santa Clara, CA, USA).

2017-11-30 | GSE107512 | GEO

Expression data from Col-0 and hcr1 roots

Project description:Transcript profiling analysis of Hydraulic conductivity of Root 1 (HCR1) mutant compared to wild type (Col-0) using ARABIDOPSIS GENE1.1ST ARRAY STRIP (901793, Affymetrix, Santa Clara, USA).

2017-02-19 | GSE78087 | GEO

ena-DATASET-IPC-22-08-2018-12:18:11:645-116 - samples

Project description:Targeted next-generation-sequencing of 494 cancer-associated genes was done in a series of 14 frozen pairs of matched primary breast cancers and brain metastases (28 samples). DNA libraries of all coding exons were prepared using the Haloplex Target Enrichment System. Sequencing was done using the 2*150bp paired-end technology on the Illumina NextSeq500 platform.

| EGAD00001004309 | EGA

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 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.

2011-05-31 | GSE26114 | GEO

Nep1 Treatment

Project description:In order to study the Nep1 responsive genes in Arabidopsis, experiments were performed with the Affymetrix GeneChip Arabidopsis ATH1 Genome Array (Santa Clara, CA; Cat # 900385). Keywords: Arabidopsis, Nep1, Affymetrix GenChip

2006-04-11 | GSE4638 | GEO

Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (MeDIP)

Project description:The analysis of DNA methylation profiles was performed by methylated DNA immunoprecipitation (MeDIP) using anti-5-methylcytidine antibody (Eurogentec, Seraing, Belgium) followed by the Human 244K Agilent CpG island microarray (Agilent, Santa Clara, CA)

2012-03-31 | GSE35312 | GEO

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