Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human megakaryotic and fibroblast cell lines that have been transduced with either Smad7 recombinant retroviral vector vs control

ABSTRACT: Smad7 is a member of the TGF-B superfamily that plays a signigicant role in fate determination of hematopoietic stem cells. This experiment compares expression between megakaryotic and fibroblast cell lines that have been transduced with either Smad7 recombinant retroviral vector or retroviral vector alone. Experiment Overall Design: this experiment include 4 samples and 30 replicates

ORGANISM(S): Mus musculus

SUBMITTER: OGIC Info Ontario Genomics Innovation Centre (OGIC)

PROVIDER: E-GEOD-3771 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Role of Smad7 in Hematopoietic (M-O7e) and Non-Hematopoietic (PG13) Stem Cells

Project description:Smad7 is a member of the TGF-B superfamily that plays a signigicant role in fate determination of hematopoietic stem cells. This experiment compares expression between megakaryotic and fibroblast cell lines that have been transduced with either Smad7 recombinant retroviral vector or retroviral vector alone. Keywords: other

2005-12-09 | GSE3771 | GEO

Development of an in vitro genotoxicity assay to detect retroviral vector-induced lymphoid insertional mutants [bulk]

Project description:Safety assessment in retroviral vector-mediated gene therapy remains challenging. In clinical trials for different blood and immune disorders, insertional mutagenesis led to myeloid and lymphoid leukemia. We previously developed the In Vitro Immortalization Assay (IVIM) and Surrogate Assay for Genotoxicity Assessment (SAGA) for pre-clinical genotoxicity prediction of integrating vectors. Murine hematopoietic stem and progenitor cells (mHSPC) transduced with mutagenic vectors acquire a proliferation advantage under limiting dilution (IVIM) and activate stem cell- and cancer-related transcriptional programs (SAGA). However, both assays present an intrinsic myeloid bias due to culture conditions. To detect lymphoid mutants, we differentiated mHSPC to mature T cells and analyzed their phenotype, insertion site pattern, and gene expression changes after transduction with retroviral vectors. Mutagenic vectors induced a block in differentiation at an early progenitor stage (double-negative 2) compared to fully differentiated untransduced mock cultures. Arrested samples harbored high-risk insertions close to Lmo2, frequently observed in clinical trials with severe adverse events. Lymphoid insertional mutants displayed a unique gene expression signature identified by the machine learning algorithm of SAGA. The gene expression-based highly sensitive molecular readout will broaden our understanding of vector-induced oncogenicity and help in pre-clinical prediction of retroviral genotoxicity.

2023-09-21 | GSE241155 | GEO

Development of an in vitro genotoxicity assay to detect retroviral vector-induced lymphoid insertional mutants [DN2]

2023-09-21 | GSE241146 | GEO

Epigenetic Suppression of Transgenic T-cell Receptor Expression via Gamma-Retroviral Vector Methylation in Adoptive Cell Transfer Therapy

Project description:Transgenic T-cell receptor (TCR) adoptive cell therapies recognizing tumor antigens are associated with robust initial response rates, but frequent disease relapse. This usually occurs in the setting of poor long-term persistence of cells expressing the transgenic TCR, generated using murine stem cell virus (MSCV) -retroviral vectors. Analysis of clinical transgenic adoptive cell therapy products in vivo revealed that despite strong persistence of the transgenic TCR DNA sequence over time, its expression was profoundly decreased over time at the RNA and protein levels. Patients with the greatest degrees of expression suppression displayed significant increases in DNA methylation over time within the MSCV promoter region, as well as progressive increases in DNA methylation within the entire MSCV vector over time. These increases in vector methylation occurred independently of its integration site within the host genomes. These results have significant implications for the design of future viral-vector gene engineered adoptive cell transfer therapies.

2020-07-06 | GSE153820 | GEO

Vector-transduced neurons transcriptome profiles

Project description:With the goal of specifically dissecting the toxicogenomic signatures of the helper-dependent (HD) human (HAd5) and canine (CAV-2) adenovirus, the VSV-G-pseudotyped SIN HIV-1 (LV) and the Adenoviral-associated vector 2/9 for human neurons (AAV2/9), we transduced a bona fide human neuronal system with HD-HAd5, HD-CAV-2, LV and AAV2/9, we analysed the transcriptional response of more than 47,000 transcripts using gene chips. Chip data showed that HD-CAV-2 and LV vectors both activated the innate arm of the immune response, including Toll-like receptors and hyaluronan circuits. LV vector induced as well an IFN response. Moreover, HD-CAV-2 and LV vectors affected DNA damage pathways - at 5 days in opposite directions - suggesting a differential response of the p53 and ATM pathways to the vector genomes. As a general response to the vectors, human neurons activated pro-survival genes and neuron morphogenesis.

2013-05-22 | GSE47130 | GEO

Expression data from C2C12 myoblasts transduced with PRDM16 or vector

Project description:PRDM16 is a 140 kDa transcriptional coregulatory protein. PRDM16 has been shown to function as a bi-directional switch in brown fat cell fate by stimulating the development of brown fat cells from myf-5 positive myoblastic precursors. We used microarrays to detail the global programme of gene expression underlying the myoblasts-brown fat conversion induced by PRDM16. undifferentiated C2C12 myoblasts were stably expressed with retroviral PRDM16 or vector control. Total RNAs were isolated by Trizol, and subjected to Affymetrix microarrays.

2010-03-03 | E-GEOD-15895 | biostudies-arrayexpress

Expression data from retroviral vector-infected immortalized mouse embryonic fibroblasts (MEFs)

Project description:Cultured cancer cells exhibit substantial phenotypic heterogeneity when measured in a variety of ways such as sensitivity to drugs or the capacity to grow under various conditions. Among these, the ability to exhibit anchorage-independent cell growth (colony forming capacity in semisolid media) has been considered to be fundamental in cancer biology because it has been connected with tumor cell aggressiveness in vivo such as tumorigenic and metastatic potentials, and also utilized as a marker for in vitro transformation. Although multiple genetic factors for anchorage-independence have been identified, the molecular basis for this capacity is still largely unknown. To investigate the molecular mechanisms underlying anchorage-independent cell growth, we have used genome-wide DNA microarray studies to develop an expression signature associated with this phenotype. Using this signature, we identify a program of activated mitochondrial biogenesis associated with the phenotype of anchorage-independent growth and importantly, we demonstrate that this phenotype predicts potential for metastasis in primary breast and lung tumors. Keywords: c-Myc or v-Src retroviral vector-infected immortalized mouse embryonic fibroblasts.

2009-04-10 | GSE15161 | GEO

Transcription profiling of p8 knock-out mice cells immortalized with rasV12/E1A and infected with an empty or a p8-overexpressing retroviral vector

Project description:MEF from p8 knock-out mice were immortalized with rasV12/E1A and infected with an empty or a p8-overexpressing retroviral vector as described. Total RNA was isolated and gene expression profile was studied.

2006-03-07 | E-MEXP-577 | biostudies-arrayexpress

Murine iTreg cells: Control (MIEG3) vs. YY1-expression vector transduced

Project description:Transcriptional profiling of mouse induced Treg (iTreg) cells comparing control (MIEG3) vector-transduced iTreg cells with iTreg cells transduced with YY1-overexpression vector. Tranduced cells were sorted by GFP expression. Goal was to determine the effects of YY1 on global iTreg gene expression.

2015-11-17 | GSE75052 | GEO

MicroRNA expression profile in human foreskin keratinocytes (HFKs) transduced with retroviral vectors carrying E6 and E7 genes of either HPV6 or HPV16 and with the LXSN empty vector

Project description:Cervical cancer is a leading cause of cancer-related death in women worldwide. Nearly all cases of cervical cancer are attributed to infection with human papillomavirus (HPV), mainly high-risk type HPV16 and HPV18. Two viral genes, E6 and E7, play an important role in viral life cycle, since they delay keratinocyte differentiation and stimulate cell cycle progression, allowing the virus to exploit host DNA replication machinery to replicate its genome. Some of the oncogenic properties of E6 and E7 are mediated by host microRNAs (miRNAs) involved in the control of cell proliferation, senescence, and apoptosis. In order to identify genome-wide changes in miRNA expression profile, miRNA microarray analysis was performed on HFKs transduced with retroviral vectors carrying E6 and E7 genes of either HPV6 or HPV16 and with the LXSN empty vector. This dataset was used to identify and to further investigate the role of miR-146a-5p in cervical cancer.

2018-01-16 | E-MTAB-6360 | biostudies-arrayexpress

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