Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

1f674c6a-01cb-4241-aced-1f6e2aaf0f65 - samples

ABSTRACT: Bone marrow mononuclear cells from patients diagnosed with B cell precursor acute lymphoblastic leukemia were obtained at three sequential time points: first diagnosis, remission after chemotherapy and relapse. Genomic DNA was isolated and targeted gene panel sequencing was performed using a customized biotinylated RNA oligo pool (SureSelect, Agilent, Santa Clara, California) to hybridize the target regions comprising 362 kbp on a HiSeq2000. Target regions were selected to validate mutations previously identified in these samples using whole exome sequencing.

PROVIDER: EGAD00001004977 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Untargeted serum metabolomics of ulcerative colitis patients vs healthy subjects using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry

Project description:Metabolic profiling of serum samples were performed on an Agilent 1290 infinity system (Agilent technologies, Santa-Clara, California, USA) coupled to an AB SCIEX Triple TOF 6600 System (AB SCIEX, Framingham, MA, USA) with an electrospray ion (ESI) source in both positive and negative ion modes. There were 30 differential metabolites under positive ion mode and 23 differential metabolites under negative ion mode, respectively.

2024-09-27 | MTBLS7438 | MetaboLights

miRNA expression profiling in mouse embryonic stem cell conditioned media

Project description:To identify novel putative factors that the anti-senescence effects of mouse embryonic stem cell conditioned media (E-CM) against celllular senescence, we conduvted a miRNA array analysis on E-CM and the mouse embryonic fibroblast (MEF)-CM The miRNA array was performed using the affymetrix GeneChip® miRNA 3.0 Array (Affymetrix, Santa Clara, California, United States).

2018-08-08 | GSE118208 | GEO

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

Juvenile Rheumatoid Arthritis Profiles In PBMC and SFMC

Project description:Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA). 57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course. Keywords = juvenile rheumatoid arthritis (JRA) Keywords = peripheral blood mononuclear cells (PBMC) Keywords = synovial fluid mononuclear cells (SFMC) Keywords: other

2004-08-11 | GSE1402 | GEO

MIR-204 target genes

Project description:The aim of this study is to discover genes regulated by miR-204. Differential gene expression in HEK-293 cells transfected with miR-204-mimic compared to HEK-293 cells transfected with control oligo (HEK-293 control) was analyzed using the Agilent Human Whole Genome 4x44K gene expression array (Agilent Technologies, Santa Clara, CA).

2012-03-31 | GSE28400 | GEO

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

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

Genomic rearrangements in C3 glomerulopathies

Project description:Copy number variations and genomic rearrangements in the CFH-CFHRs region were assessed with a custom-designed high-density 8x15k oligonucleotide CGH arrays spanning the RCA gene cluster region in human chromosome 1q32 (median resolution of 110 bp) (AMADID 040193, Agilent Technologies, Santa Clara, CA). A healthy male donor sample, fully genotyped for that region, was used as hybridization control. Microarray data were extracted and visualized using the Feature Extraction Software v10.7 and Genomic Workbench Standard Edition 7.0 (Agilent Corp, Santa Clara, CA). Copy number altered regions were detected using ADM-2 (set as 5) statistic provided by DNA Analytics, with a minimum number of 5 consecutive probes. Genomic build hg19 was used for the experiment.

2013-05-28 | GSE45585 | GEO

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

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