Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An instructive role for Interleukin-7 receptor α in the development of human B-cell precursor leukemia

ABSTRACT: As part of our effort to elucidate the role of IL7RA aberrations, we transduced normal cord blood cells with lentivirus expressing IL7RA with activated mutation. Additionally in part of the experiments cells were transduced with lentivirus expressing CAS9 and guides targeting the CDKN2A gene. Here we deposit Single Nucleotide Polymorphism (SNP) array data of the leukemic samples that were developed after transplantation of the transduced cells in immunodeficient mice.

ORGANISM(S): Homo sapiens

SUBMITTER: Michal Hameiri-Grossman

PROVIDER: E-MTAB-11258 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of human mesenchymal stem cells transduced with lentivirus reporter gene fluc-mrfp-ttk

Project description:Human mesenchymal stem cells (hMSCs) were transduced using lentivirus containing the the triple fusion reporter gene fluc-mrfp-ttk. Microarray studies of hMSCs after transduction with the triple reporter genes using lentivirus were performed to study the effects of transduction on stem cell properties using an oligonucleotide human microarray. Transduced cells were sorted by FACS. Cells with high and low signals were ftacrtionated, and gene expression profiles were determined. Experiment Overall Design: In this study, 8 samples were experimentally evaluated. 2 samples were used as the control without undergoing any transduction. 2 samples were transduced with the virus containing only the backbone. 2 samples were transduced with the lentivirus containing the triple reporter and has high MGFP (>10^3), while 2 samples <10^3.

2008-06-17 | E-GEOD-9941 | biostudies-arrayexpress

YAP conveys an invasive phenotype to clear cell renal cell carcinoma cell lines via endothelin-2

Project description:To determine the biological mechanisms underlying the oncogenic properties of YAP in ccRCC the human ccRCC cell line MZ1774 was transduced with lentivirus containing a shRNA-cassette targeting YAP-mRNA. Expression profiles of MZ1774 YAP knockdown cells were compared to mock-transduced control cells. Total RNA from MZ1774 cells stably expressing shRNA directed against YAP compared to mock-transduced MZ1174 cells

2014-12-23 | E-GEOD-50053 | biostudies-arrayexpress

SNP array analysis of lung cancer NCI-H1395, diluted to different tumor cell concentrations

Project description:In vitro mix of DNA from patient-matched lung cancer and blood cell lines, representing 30,50,70,100% tumor cell tissue, analyzed on Affymetrix 6.0 arrays. Lung cancer cell line H-1395 and patient-matched blood cell line BL1395 were obtained from ATCC and cultured according to their recommendations. DNA extraction was performed using the DNeasy Tissue Kit (Qiagen, Hilden, Germany). DNA from patient-matched Lung cancer and Blood cell lines NCI-H1395 and NCI-BL1395 were mixed to simulate tumor tissue with 30,50,70,100% cancer cells. The DNA ratio was adjusted to compensate for NCI-H1395 being nearly triploid. DNA was analyzed on Affymetrix SNP6.0 microarrays according to the manufacturer's protocol.

2011-09-08 | E-GEOD-29172 | biostudies-arrayexpress

Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity

Project description:Chromosomal aberrations were studied both in a lung cancer cell line and colorectal cancer tumor samples. Results were verified by SKY karyotypes and by DNA ploidy analysis. The sensitivity of detecting chromosomal aberrations in tumor samples was evaluated by analyzing data from simulated mixtures of the lung cancer cell line H1395 and the normal cell line 1395BL from the same patient. Copy number analysis is presented on 12 colorectal cancer tumor samples and on in silico dilutions of a lung cancer cell line and its patient-matched blood cell line.

2011-09-08 | E-GEOD-26302 | biostudies-arrayexpress

Affymetrix SNP array data for ovarian cancer cells OVCAR-3 and FU-OV-1

Project description:A subset of ovarian cancer are characterized by 19q12 amplification. To perform funtional studies of this amplicon the profile has been determined by SNP analysis. Affymetrix SNP arrays were performed according to the manufacturer's directions on genomic DNA extracted from ovarian cancer cell lines OVCAR-3 and FU-OV-1

2010-12-24 | E-GEOD-26301 | biostudies-arrayexpress

Expression analysis of ZBP-89 deficient human primary erythroid progenitors

Project description:The molecular mechanisms underlying erythroid-specific gene regulation remain incompletely understood. Closely spaced binding sites for GATA, NF-E2/maf and CACCC interacting transcription factors play functionally important roles in globin and other erythroid-specific gene expression. We and others recently identified the CACCC-binding transcription factor ZBP-89 as a novel GATA-1 and NF-E2/mafK interacting partner. Here, we examined the role of ZBP-89 in human globin gene regulation and erythroid maturation using a primary CD34+ cell ex vivo differentiation system. We show that ZBP-89 protein levels rise dramatically during human erythroid differentiation, and that ZBP-89 occupies key cis-regulatory elements within the globin and other erythroid gene loci. ZBP-89 binding correlates strongly with RNA Pol II occupancy, active histone marks, and high-level gene expression. ZBP-89 physically associates with the histone acetyltransferases (HATs) p300 and Gcn5/Trrap, and occupies common sites with Gcn5 within the human globin loci. Lentiviral shRNA knockdown of ZBP-89 results in reduced Gcn5 occupancy, decreased acetylated histone 3 levels, lower globin and erythroid-specific gene expression, and impaired erythroid maturation. Addition of the HDAC inhibitor valproic acid partially reverses the reduced globin gene expression. These findings reveal an activating role for ZBP-89 in human globin gene regulation and erythroid differentiation. Keywords: Human primary erythroid progenitors Expression data of human erythroid progenitors transduced with lentivirus expressing short hairpins against ZBP-89 and control empty vector

2011-08-01 | E-GEOD-31092 | biostudies-arrayexpress

An instructive role for IL7RA in the development of human B-cell precursor leukemia

Project description:10X single cell analysis of human leukemia, pre-leukemia and normal control. The leukemia was developed in xenograft mice that was serialy transplanted with cells from primary mouse that was transplanted with normal cord blood after transduction with virues encoding hyper activated mutant IL7RA. The preleukemic cells are from the primary engrafted mouse and the control is the same cord blood that was transduced with backbone virus expressing GFP.

2021-11-23 | GSE151126 | GEO

Single-nucleotide polymorphism array analysis reveals distinct chromosomal aberrations in breast cancer tumors according to the circulating tumor cells status

Project description:Recent technological advances have made it possible to detect circulating breast cancer cells as precursors of distant metastasis and as prognosis marker in nonmetastatic breast cancer patients. Association of circulating tumor cells (CTCs) with molecular alteration in the primary tumor is not widely explored. We reported differential profile of altered genome, copy number alteration and copy-neutral loss of heterogeneity in 14 primary tumors when comparing patients with CTCs+ versus CTCs- using single-nucleotide polymorphism array. The most prevalent copy number alteration in CTCs+ patients was at 8q and particularly at the cytoband 8q24 (MYC loci). As the role of MYC in the process of tumor cell invasion and migration is controversial, we further validated in a larger series of patients whether altered MYC (amplification or gained) in primary tumors was correlated with the presence of CTCs in peripheral blood (as a surrogate of micrometastais).Â No correlation between MYC alteration and presence of CTCs was observed, providing clinical support to the recent data that MYC suppresses cancer metastasis or at least suggesting that MYC alteration could be contributory but insufficient for the generation of CTCs. This molecular association needs to be further characterized in preclinical model and especially clinically. We analyzed CN and LOH of CTC+ and CTC-

2014-11-19 | E-GEOD-43149 | biostudies-arrayexpress

5658af53-befe-4737-9775-ec5f542df8a0 - samples

Project description:3 control iPSC lines differentiated into iPSC-derived motor neurons transduced with either EGFP or NOVA1 lentivirus.

| EGAD00001008423 | EGA

A dominant-negative isoform of IKAROS expands primitive normal human hematopoietic cells

Project description:Human cord blood CD34+ cells transduced with control of IK6 lentivirus were transplanted into NSG mice. Control and IK6 transduced CD34+38- progeny were acquired 10 weeks later by FACS

2014-09-14 | GSE60957 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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