View Project lorin-affy-mouse-501743

Project Summary
Status:	Public
Publications:	1 Published
Project Detail		Data Detail
Platform:	Affymetrix	MIAME Areas	Compliance
Species:	Mouse	Array Design Detail	false
Organ/Tissue Type:	nervous system	Experiment Detail	true
Organ Region:		Sample Detail	false
Cell Type:	neuronally differertiated embryonic stem cells	Hybridization Detail	false
Study Type:	time_series_design	Measurement Detail	false
Disease/Condition:	Transgenic huntington disease
Replicates:	3
Expected Samples:	12

Available Actions

Investigator Contact Detail
Name	Dr. Matt T Lorincz
Institution:	University Of Michigan
Street Address:	109 Zina Pitcher Pl
	5019 BSRB
City, State/Province:	Ann Arbor , MI
Zip/Postal Code:	48109-2200
Country:	United States
Work Phone:	734 615-8234
Fax:
E-mail:	lorincz@umich.edu

Proposal Detail

Grant:

NS045180

Status:

Public

Service Type:

Start to Finish Profiling

IACUC:

A3114-01

IACUC date:

2002-10-02

Study Relevance:

Huntington’s disease (HD) is a devastating neurodegenerative disease, with out effective treatment. Despite significant advances, our understanding of how an expanded CAG repeat in the amino terminus of the large ubiquitously expressed HD gene product remains incomplete. Augmented adult neurogenesis in response to acute and chronic injury, including Huntington’s disease, has been demonstrated, but its role development, disease, and recovery is largely unknown, as are the factors controlling it. The HD gene product, huntingtin (htt) is know to interact with a number of transcription factors which subsequently influence gene expression. Understanding the factors involved in controlling neurogenesis in response to disease would bridge a significant knowledge gap and have tremendous therapeutic potential.

Hypothesis:

Our hypothesis is that expanded CAG repeats in the Huntington’s disease gene facilitates neurogenesis by altering transcription of genes critical in neurogenesis.

Specific Aim:

We propose to identify transcripts responsible for CAG repeat facilitated neurogenesis.

Experimental Procedure and Design:

We have developed a model in which mouse embryonic stem cells (ESC) with expanded CAG repeats have facilitated neurogenesis. In this model more ESC with expanded CAG repeats transition to neuronal precursors and then develop into mature neurons more rapidly than control ESC. We propose to compare the gene expression profiles between ESC with expanded CAG repeats and control ESCs on days 4 and 6 of neuronal differentiation. Initial studies indicate that key transcriptional differences are occurring at these time points. Control ECS and a an ESC line with150 CAG repeats will be differentiated in triplicate, and RNA isolated form each replicate. It is anticipated that comparison of gene expression between the control and CAG repeat lines at each time point will identify transcripts involved in CAG repeat facilitated neurogenesis. Observed differences at day 4 may be more relevant to the transition from ESC to neuronal precursor whereas differences at day 6 may be more relevant to the neuronal precursor to neuron transition.

Quality Control Description:

Triplicate biological replicate for each cell line at each time point which will be treated identically.

Quality Control Types:

biological_replicate

Replicate Description:

Triplicate biological replicate for each cell line at each time point.

Replicate Types:

biological_replicate

Experimental Factors:

Conditions that are tested in the experiment. At least one is required. Experimental factors are the independent variables in the experiment.

Factor Name	Description	Factor Category
Cell line	HM1 is a control embryonic stem cell ...	cell_line
duration of neuronal differentiation	Control (HM1) and expanded CAG repeat...	developmental_stage

Project Samples

Samples associated with this project.

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Name	Description	Bio-Source	Extracts
HM1 day 4 replicate 1	HM1 embryonic stem cells fo...	HM1	1
HM1 day4 replicate 2	HM1 embryonic stem cells fo...	HM1	1
HM1 day4 replicate 3	HM1 embryonic stem cells fo...	HM1	1
CAG 150 day 4 replicate 1	CAG 150 embryonic stem cell...	CAG 150 embryonic stem cells	1
CAG 150 day 4 replicate 2	CAG 150 embryonic stem cell...	CAG 150 embryonic stem cells	1
CAG 150 Day 4 replicate 3	CAG 150 embryonic stem cell...	CAG 150 embryonic stem cells	1
CAG 150 day 6 replicate 1	CAG 150 embryonic stem cell...	CAG 150 embryonic stem cells	1
CAG 150 day 6 replicate 2	CAG 150 embryonic stem cell...	CAG 150 embryonic stem cells	1
CAG 150 day 6 replicate 3	CAG 150 embryonic stem cell...	CAG 150 embryonic stem cells	1
HM1 day 6 replicate 1	HM1 embryonic stem cells fo...	HM1	1
HM1 day 6 replicate 2	HM1 embryonic stem cells fo...	HM1	1
HM1 day 6 replicate 3	HM1 embryonic stem cells fo...	HM1	1

Project Hybridizations

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Name	Array	Labeled Extract
Mouse Genome 430 2.0 Array_1_hyb	Mouse Genome 430 2.0 Array_1	HM1 day 4 replicate 1_le1
Mouse Genome 430 2.0 Array_2_hyb	Mouse Genome 430 2.0 Array_2	HM1 day 4 replicate 2_le1
Mouse Genome 430 2.0 Array_3_hyb	Mouse Genome 430 2.0 Array_3	HM1 day 4 replicate 3_le1
Mouse Genome 430 2.0 Array_4_hyb	Mouse Genome 430 2.0 Array_4	CAG150 day 4 replicate 1_le1
Mouse Genome 430 2.0 Array_5_hyb	Mouse Genome 430 2.0 Array_5	CAG 150 day 4 replicate 2_le1
Mouse Genome 430 2.0 Array_6_hyb	Mouse Genome 430 2.0 Array_6	CAG 150 day 4 replicate 3_le1
Mouse Genome 430 2.0 Array_7_hyb	Mouse Genome 430 2.0 Array_7	CAG 150 day 6 replicate 1_le1
Mouse Genome 430 2.0 Array_8_hyb	Mouse Genome 430 2.0 Array_8	CAG 150 day 6 replicate 2_le1
Mouse Genome 430 2.0 Array_9_hyb	Mouse Genome 430 2.0 Array_9	CAG 150 day 6 replicate 3_le1
Mouse Genome 430 2.0 Array_10_hyb	Mouse Genome 430 2.0 Array_10	HM1 day 6 replicate 1_le1
Mouse Genome 430 2.0 Array_11_hyb	Mouse Genome 430 2.0 Array_11	HM1 day 6 replicate 2_le1
Mouse Genome 430 2.0 Array_12_hyb	Mouse Genome 430 2.0 Array_12	HM1 day 6 replicate 3_le1

Project Reference Files

File Name	Size
Lorincz.DTT	1.39 Gb
chp.TXT	4.20 Mb

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