View Project rosen-illu-mouse-588967

Project Summary
Status:	Public
Publications:	1 Published
Project Detail		Data Detail
Platform:	Illumina	MIAME Areas	Compliance
Species:	Mouse	Array Design Detail	false
Organ/Tissue Type:	striatum	Experiment Detail	true
Organ Region:		Sample Detail	true
Cell Type:	brain tissue	Hybridization Detail	false
Study Type:	time_series_design	Measurement Detail	true
Disease/Condition:	normal
Replicates:	2
Expected Samples:	48

Available Actions

Investigator Contact Detail
Name	Glenn D Rosen
Institution:	Beth Israel Deaconess Medical Center
Street Address:	Department of Neurology
	330 Brookline Ave.,
City, State/Province:	Boston , MA
Zip/Postal Code:	02215
Country:	United States
Work Phone:	617-667-3252
Fax:	617-667-5217
E-mail:	grosen@bidmc.harvard.edu

Proposal Detail

Grant:

NS052397

Status:

Public

Service Type:

Hybrization through Analysis

IACUC:

036-2006

IACUC date:

2007-05-07

Study Relevance:

The striatum is among the most studied structures in the brain, which is not surprising given its importance to cognitive and motor functioning. The ability of the striatum to modulate the execution of movements and various executive functions can be compromised by developmental disturbances. Understanding the genes that modulate the development of this structures would have a strong impact on our understanding of a variety of developmental disorders, including early onset schizophrenia and Tourette’s syndrome. Although neurogenesis in the striatum is well studied, there is surprisingly little known about the processes that regulate the variation in the number of neurons and glia among individuals. Similarly, there is little understanding of the factors that modulate the variation in the volume of this structure. The studies proposed here will provide the foundation for these investigations.

Hypothesis:

We hypothesize that separate and distinct QTLs modulate variation in regional volume as opposed to the number of neurons and glia in the striatum.

Specific Aim:

We aim to o map QTLs that selectively modulate glial and neuronal populations in the striatum. The parent strains of this BXD recombinant inbred (RI) set (C57BL/6J and DBA/2J) have been genotyped, and genome-wide haplotype maps are available in GeneNetwork <www.genenetwork.org> to enhance identification of candidate genes within QTL intervals. Here will will take the first steps toward the creation of a publicly available database of developmental striatal RNA transcript levels in GeneNetwork that will further boost our efforts to select candidate genes.

Experimental Procedure and Design:

We have dissected the striatum from both males and females of parent strains of the BXD RI (C57BL/6J and DBA/2J) at postnatal ages (P)1, P3, P5, P7, P10, and P14. There are, therefore, 24 bio-sources in this experiment (2 strains X 2 sexes X 6 ages). At each age, a minimum of three litters were taken and tissue for RNA extraction was pooled among these three litters. There are two biological replicates for each bio-source for a total of 48 samples. Subjects were sacrificed by decapitation, and their brains quickly removed, bisected mid-sagittally, and placed in RNAlater for 15–20 minutes. This allowed the brain to harden slightly and eased the process of regional identification and dissection. The hemispheres are removed individually from the RNAlater, and the cerebellum, olfactory bulbs, and hippocampus are dissected and stored in RNAlater for the use of collaborators. The septum is dissected away from the medial surface, and the cingulate cortex is teased back to reveal the underlying lateral surface of the striatum. Starting at the ventro-rostral region, the striatum is dissected out en masse. Any ambiguous white or gray matter is removed, and the end result is a well-defined, compact portion of striatum. After the completion of each dissection, the tissue was placed immediately into a fresh vial of RNAlater and stored at -20°C until the RNA is extracted. Dissected tissues were processed to extract total RNA using standard phenol-based protocols. Briefly, tissue was homogenized in Trizol. RNA was extracted with 0.2 ml chloroform/ml Trizol and centrifuged at 12,000g for 15 minutes. The RNA is precipitated from the aqueous phase in 0.5 ml isopropanol/ml and centrifuged for 10 minutes at 12,000g. The supernatant is removed, and the RNA pellet is washed in 75% ethanol, dried, and dissolved in DEPCtreated water.

Quality Control Description:

The quality and purity of RNA is assessed using spectrophotometry and gel electrophoresis. All RNA in this experiment had A260/280 ratios of 1.8 or above. There were technical replicates for each sample undergoing spectrophotometry.

Quality Control Types:

technical_replicate

Replicate Description:

A minimum of three litters were sacrificed at each age, and each litter had 4-9 pups and tissue was segregated by sex. To create a sample, tissue was pooled from each of the litters representing the strain, sex, and age of interest. A separate sample was created from the same litters as a biological replicate.

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
Age	P1, P3, P5, P7, P10, P14	age
Sex	Male, Female	sex
Strain	C57BL/6J, DBA/2J	strain_or_line

Project Samples

Samples associated with this project.

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Name	Description	Bio-Source	Extracts
RNA1	D2-P1 Male Sample 1	D2 - P1 Male	1
RNA2	D2-P1 Male Sample 2	D2 - P1 Male	1
RNA3	B6-P7 Female Sample 1	B6 - P7 Female	1
RNA4	B6-P7 Female Sample 2	B6 - P7 Female	1
RNA5	B6-P1 Male Sample 1	B6 - P1 Male	1
RNA6	B6-P1 Male Sample 2	B6 - P1 Male	1
RNA7	B6-P3 Male Sample 1	B6 - P3 Male	1
RNA8	B6-P3 Male Sample 2	B6 - P3 Male	1
RNA9	B6-P5 Male Sample 1	B6 - P5 Male	1
RNA10	B6-P5 Male Sample 2	B6 - P5 Male	1
RNA11	B6-P7 Male Sample 1	B6 - P7 Male	1
RNA12	B6-P7 Male Sample 2	B6 - P7 Male	1
RNA13	B6-P10 Male Sample 1	B6 - P10 Male	1
RNA14	B6-P10 Male Sample 2	B6 - P10 Male	1
RNA15	B6-P1 Female Sample 1	B6 - P1 Female	1
RNA16	B6-P1 Female Sample 2	B6 - P1 Female	1
RNA17	B6-P3 Female Sample 1	B6 - P3 Female	1
RNA18	B6-P3 Female Sample 2	B6 - P3 Female	1
RNA19	B6-P5 Female Sample 1	B6 - P5 Female	1
RNA20	B6-P5 Female Sample 2	B6 - P5 Female	1
RNA21	B6-P10 Female Sample 1	B6 - P10 Female	1
RNA22	B6-P10 Female Sample 2	B6 - P10 Female	1
RNA23	B6-P14 Male Sample 1	B6 - P14 Male	1
RNA24	B6-P14 Male Sample 2	B6 - P14 Male	1
RNA25	B6-P14 Female Sample 1	B6 - P14 Female	1
RNA26	B6-P14 Female Sample 2	B6 - P14 Female	1
RNA27	D2-P1 Female Sample 1	D2 - P1 Female	1
RNA28	D2-P1 Female Sample 2	D2 - P1 Female	1
RNA29	D2-P5 Female Sample 1	D2 - P5 Female	1
RNA30	D2-P5 Female Sample 2	D2 - P5 Female	1
RNA31	D2-P7 Female Sample 1	D2- P7 Female	1
RNA32	D2-P7 Female Sample 2	D2- P7 Female	1
RNA33	D2-P10 Female Sample 1	D2 - P10 Female	1
RNA34	D2-P10 Female Sample 2	D2 - P10 Female	1
RNA35	D2-P14 Female Sample 1	D2- P14 Female	1
RNA36	D2-P14 Female Sample 2	D2- P14 Female	1
RNA37	D2-P5 Male Sample 1	D2 - P5 Male	1
RNA38	D2-P5 Male Sample 2	D2 - P5 Male	1
RNA39	D2-P7 Male Sample 1	D2- P7 Male	1
RNA40	D2-P7 Male Sample 2	D2- P7 Male	1
RNA41	D2-P3 Male Sample 1	D2 - P3 Male	1
RNA42	D2-P3 Male Sample 2	D2 - P3 Male	1
RNA43	D2-P3 Female Sample 1	D2 - P3 Female	1
RNA44	D2-P3 Female Sample 2	D2 - P3 Female	1
RNA45	D2-P10 Male Sample 1	D2 - P10 Male	1
RNA46	D2-P10 Male Sample 2	D2 - P10 Male	1
RNA47	D2-P14 Male Sample 1	D2- P14 Male	1
RNA48	D2-P14 Male Sample 2	D2- P14 Male	1

Project Hybridizations

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Name	Labeled Extract	Hybridization Protocol
Hybridization48	RNA46_le1	Illumina
Hybridization49	RNA31_le1	Illumina
Hybridization50	RNA26_le1	Illumina
Hybridization51	RNA29_le1	Illumina
Hybridization52	RNA39_le1	Illumina
Hybridization53	RNA4_le1	Illumina
Hybridization54	RNA17_le1	Illumina
Hybridization55	RNA7_le1	Illumina
Hybridization56	RNA32_le1	Illumina
Hybridization57	RNA36_le1	Illumina
Hybridization58	RNA8_le1	Illumina
Hybridization59	RNA5_le1	Illumina
Hybridization60	RNA43_le1	Illumina
Hybridization61	RNA23_le1	Illumina
Hybridization62	RNA11_le1	Illumina
Hybridization63	RNA12_le1	Illumina
Hybridization64	RNA35_le1	Illumina
Hybridization65	RNA16_le1	Illumina
Hybridization66	RNA48_le1	Illumina
Hybridization67	RNA24_le1	Illumina
Hybridization68	RNA9_le1	Illumina
Hybridization69	RNA33_le1	Illumina
Hybridization70	RNA6_le1	Illumina
Hybridization71	RNA1_le1	Illumina
Hybridization72	RNA15_le1	Illumina
Hybridization73	RNA20_le1	Illumina
Hybridization74	RNA44_le1	Illumina
Hybridization75	RNA21_le1	Illumina
Hybridization76	RNA19_le1	Illumina
Hybridization77	RNA42_le1	Illumina
Hybridization78	RNA45_le1	Illumina
Hybridization79	RNA10_le1	Illumina
Hybridization80	RNA27_le1	Illumina
Hybridization81	RNA34_le1	Illumina
Hybridization82	RNA38_le1	Illumina
Hybridization83	RNA25_le1	Illumina
Hybridization84	RNA28_le1	Illumina
Hybridization85	RNA30_le1	Illumina
Hybridization86	RNA40_le1	Illumina
Hybridization87	RNA37_le1	Illumina
Hybridization88	RNA47_le1	Illumina
Hybridization89	RNA3_le1	Illumina
Hybridization90	RNA22_le1	Illumina
Hybridization91	RNA18_le1	Illumina
Hybridization92	RNA41_le1	Illumina
Hybridization93	RNA13_le1	Illumina
Hybridization94	RNA2_le1	Illumina
Hybridization95	RNA14_le1	Illumina

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