title: MyoD-/-, 1999, 4d, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S351
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_360
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 4 day
Estimated purity:				100%
RNA concentration:			1815.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, 1999, 48hr, chip MG_U74Bv2

status: Public on Mar 01 2008

type: other

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S349
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_358
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 48 hr
Estimated purity:				100%
RNA concentration:			1110.6 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpha2=0.06

label: Biotin

molecule: other

organism: Mus musculus

source_name: Primary Myoblasts, Skeletal Muscle

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

growth_protocol:
Growth medium:				Ham's F10 Nutrient Mixture
Media supplements:			20% FBS, bFGF 250 ng/ml, 4% Penicillin (5x10E3 U/ml)-Streptomycin (5x10E3 ug/ml), 1% L-Glutamine 200 mM
Culture conditions:			37ºC, 5% CO2, 0.01% Collagen coated petri plate; Change with fresh media at day 3rd.

extract_protocol: Cell purification method:			cultured

tag: Strain:					Balb/c MyoD-/-

tag: Gender:					Male

tag: Karyotype:				normal


title: MyoD-/-, P6, 24hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S347
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_356
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 24 hr
Estimated purity:				100%
RNA concentration:			1879.2 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P6, 36hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S348
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_357
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 36 hr
Estimated purity:				100%
RNA concentration:			1298.0 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P6, 48hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S349
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_358
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 48 hr
Estimated purity:				100%
RNA concentration:			1086.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, 1999, 24hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S347
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_356
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 24 hr
Estimated purity:				100%
RNA concentration:			2583.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, 1999, 36hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S348
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_357
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 36 hr
Estimated purity:				100%
RNA concentration:			1709.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, 1999, 12hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S345
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_354
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 12 hr
Estimated purity:				100%
RNA concentration:			2830.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P6, 18hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S346
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_355
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 18 hr
Estimated purity:				100%
RNA concentration:			1960.2 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P10, 12hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S345
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_354
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 12 hr
Estimated purity:				100%
RNA concentration:			2606.6 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P6, 12hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S345
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_354
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 12 hr
Estimated purity:				100%
RNA concentration:			2205.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P10, 36hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S348
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_357
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 36 hr
Estimated purity:				100%
RNA concentration:			1586.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P10, 6hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S344
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_353
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 6 hr
Estimated purity:				100%
RNA concentration:			2606.6 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P10, 24hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S347
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_356
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 24 hr
Estimated purity:				100%
RNA concentration:			2229.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P6, 6hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S344
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_353
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 6 hr
Estimated purity:				100%
RNA concentration:			2205.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P10, 18hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S346
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_355
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 18 hr
Estimated purity:				100%
RNA concentration:			2226.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, 1999, 18hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S346
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_355
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 18 hr
Estimated purity:				100%
RNA concentration:			1419.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD-/-, P10, 0hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S343
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_352
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 0 hr
Estimated purity:				100%
RNA concentration:			1468.0 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD, wt841, 7 days, chip MG_U74Bv2

type: RNA

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S342
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_351
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 7 days
Estimated purity:				100%
RNA concentration:			1142.0 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL

molecule: total RNA

growth_protocol:
Growth medium:				Ham's F10 Nutrient Mixture
Media supplements:			20% FBS,, bFGF 250 ng/ml, 4% Penicillin (5x10E3 U/ml)-Streptomycin (5x10E3 ug/ml), 1% L-Glutamine 200 mM
Culture conditions:			37ºC, 5% CO2, 0.01% Collagen coated petri plate; Change with fresh media at day 3rd.

extract_protocol:
RNA prep method:				RNeasy (Qiagen)
Cell purification method:			cultured
Contaminating cell type:			none

tag: Strain:					Balb/c MyoD wild Type


title: MyoD-/-, P6, 0hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S343
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_352
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 0 hr
Estimated purity:				100%
RNA concentration:			 4327.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD, mb1, 7 days, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S342
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_351
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 7 days
Estimated purity:				100%
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c


title: MyoD-/-, 1999, 0hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S343
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_352
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 0 hr
Estimated purity:				100%
RNA concentration:			3325.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: MyoD, wtp16, 7 days, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S342
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_351
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 7 days
Estimated purity:				100%
RNA concentration:			1637.2 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: MyoD, mb1, 4 days, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S341
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_350
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 4 days
Estimated purity:				100%
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c


title: P+N3AEP, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S379
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_369
Short description:			Seven day old platelet-drived growth factor and neurotrophin-3-generated neurospheres cultured from thr embryonic day 14 basal ganglia (anterior entopeduncular area)
Estimated purity:				Unknown
RNA concentration:			171 ng/u
Sample volume:				~ 50 ul

source_name: PDGF- responsive precursors, E14 anterior entopeduncular area

growth_protocol:
Growth medium:				DMEM:F12 N2
Media supplements:			2% B27
Culture conditions:			PDGF-AA@100 ng/ul, NT-3 @100 ng/ul, 7 days

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			none
Cell purification method:			Isolation based on neurosphere formation in response to PDGF-AA +NT-3
Contaminating cell type:			Unknown
Method for estimating purity:		N/A

tag: Strain:					CD-1

tag: Gender:					mixed

tag: Defining markers:				PDGFR-alpha


title: MyoD, wtp16, 3 days, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S340
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_349
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 3 days
Estimated purity:				100%
RNA concentration:			1587.6 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: P+N1AEP, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S379
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_369
Short description:			Seven day old platelet-drived growth factor and neurotrophin-3-generated neurospheres cultured from thr embryonic day 14 basal ganglia (anterior entopeduncular area)
Estimated purity:				Unknown
RNA concentration:			192 ng/ul
Sample volume:				~ 50 ul


title: MyoD, wt841, 4 days, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S341
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_350
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 4 days
Estimated purity:				100%
RNA concentration:			2370.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: MyoD, wt841,  48hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S339
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_348
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 48 hr
Estimated purity:				100%
RNA concentration:			1879.0 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: MyoD, mb1, 3 days, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S340
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_349
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 3 days
Estimated purity:				100%
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c


title: EGF5, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S330
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_368
Short description:			Seven day old epidermal growth factor-generated neurospheres cultured from the embryonic day 14 basal ganglia (medial and lateral ganglionic eminences).
RNA concentration:			100ng/ul
Sample volume:				25-30ul

source_name: EGF-responsive neural stem cell (E14), E14 ge

growth_protocol:
Growth medium:				DMEM:F12 N2
Media supplements:			2% B27
Culture conditions:			PDGF-AA 100ng/ml, 7 days

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			none
Cell purification method:			Isolation based on neurosphere formation in response to EGF


title: MyoD, wt841, 3 days, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S340
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_349
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 3 days
Estimated purity:				100%
RNA concentration:			1467.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: MyoD, mb1,  48hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S339
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_348
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 48 hr
Estimated purity:				100%
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c


title: EGF2, chip MOE430B


title: MyoD-/-, 1999, 6hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E234
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=234
SCGP Sample ID:				S344
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=234#SAMPLE_353
Short description:			Myogenic Primary Myoblast Time Course in vitro Differentiation into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 6 hr
Estimated purity:				100%
RNA concentration:			2830.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6
Sample volume:				27µL


title: EGF4, chip MOE430B


title: MyoD, wtp16, 4 days, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S341
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_350
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 4 days
Estimated purity:				100%
RNA concentration:			1166.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: EGF1, chip MOE430B


title: P+N2AEP, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S379
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_369
Short description:			Seven day old platelet-drived growth factor and neurotrophin-3-generated neurospheres cultured from thr embryonic day 14 basal ganglia (anterior entopeduncular area)
Estimated purity:				Unknown
RNA concentration:			287 ng/u
Sample volume:				~ 50 ul


title: MyoD, wt841, 36hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S338
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_347
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 36 hr
Estimated purity:				100%
RNA concentration:			2726.2 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: EGF3, chip MOE430B


title: EGF6, chip MOE430B


title: MyoD, wtp16,  48hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S339
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_348
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 48 hr
Estimated purity:				100%
RNA concentration:			1724.0 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: PGDF4, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S329
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_367
Short description:			Seven day old platelet-derived growth factor-generated neurospheres cultured from the embryonic day 14 basal ganglia (anterior entopeduncular area).
RNA concentration:			100ng/ul
Sample volume:				25-30ul

source_name: PDGF-responsive precursors, E14 anterior entopeduncular area

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			none
Cell purification method:			Isolation based on neurosphere formation in response to PDGF-AA


title: PGDF5, chip MOE430B


title: MyoD, wtp16, 36hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S338
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_347
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 36 hr
Estimated purity:				100%
RNA concentration:			2482.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: MyoD, mb1, 36hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S338
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_347
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 36 hr
Estimated purity:				100%
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c


title: MyoD, wt841, 24hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S337
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_346
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 24 hr
Estimated purity:				100%
RNA concentration:			1830.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: PGDF6, chip MOE430B


title: MyoD, mb1,  24hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S337
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_346
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 24 hr
Estimated purity:				100%
Num cells for RNA prep:			   More than 2 x 10E+6 Balb/c


title: MyoD, wtp16, 18hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S336
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_345
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 18 hr
Estimated purity:				100%
RNA concentration:			1593.0 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: PGDF3, chip MOE430B


title: PGDF1, chip MOE430B


title: MyoD, wtp16, 24hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S337
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_346
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 24 hr
Estimated purity:				100%
RNA concentration:			1624.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: MyoD, wt841, 12hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S335
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_344
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time course: 12 hr
Estimated purity:				100%
RNA concentration:			2012.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: MyoD, mb1, 18hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S336
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_345
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 18 hr
Estimated purity:				100%
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c


title: PGDF2, chip MOE430B


title: MyoD, wt841, 18hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S336
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_345
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time point: 18 hr
Estimated purity:				100%
RNA concentration:			1597.2 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: MZ1468-2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Norman Iscove (iscove@uhnres.utoronto.ca; 610 University Avenue) for analysis.
Stembase Experiment ID:			E217
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=217
SCGP Sample ID:				S300
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=217#SAMPLE_315
Short description:			CD49+cDNA with Scott/EcorI primer on both ends. , Global PCR of stem cells time = 0 after sort., Dulac labeling protocol. , !Sample_description = Estimated purity:				97.03%
RNA concentration:			0.1 ug/ul
Num cells for RNA prep:			~30
Sample volume:				100 ul

source_name: Stem Cells, Bone Marrow CD49+

growth_protocol:
Growth medium:				IBSS+ 7% FBS
Culture conditions:			Time 0 hrs

extract_protocol:
RNA prep method:				Cell Lysis
Amplification method:			PCR
Cell purification method:			Cell Sorting (FC)
Method for estimating purity:		FACS

treatment_protocol: Assays to confirm viability:		Competition R:100

tag: Strain:					B6 LY 5.1 a/a

tag: Defining markers:				Rho- CD3- B220- , CD49b- cKit+ Ly6 A/E+


title: MyoD, wt841, 6hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S334
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_343
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time course: 6 hr
Estimated purity:				100%
RNA concentration:			1212.4 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6   Balb/c
Sample volume:				27µL


title: MyoD, wtp16, 6hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S334
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_343
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time course: 6 hr
Estimated purity:				100%
RNA concentration:			1393.0 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6   Balb/c
Sample volume:				27µL


title: MyoD, mb1, 6hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S334
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_343
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time course: 6 hr
Estimated purity:				100%
Num cells for RNA prep:			More than 2 x 10E+6   Balb/c


title: MZ1468-3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Norman Iscove (iscove@uhnres.utoronto.ca; 610 University Avenue) for analysis.
Stembase Experiment ID:			E217
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=217
SCGP Sample ID:				S299
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=217#SAMPLE_314
Short description:			CD49-cDNA with Scott/EcorI primer on both ends., Global PCR of stem cells time = 0 after sort., Dulac labeling protocol., !Sample_description = Estimated purity:				97.03%
RNA concentration:			0.1 ug/ul
Num cells for RNA prep:			~30
Sample volume:				100 ul

source_name: Stem Cells, Bone Marrow CD49-


title: MyoD, wtp16, 12hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S335
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_344
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time course: 12 hr
Estimated purity:				100%
RNA concentration:			1760.6 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c
Sample volume:				27µL


title: MyoD, wt841, 0hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S333
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_342
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time course: 0 hr
Estimated purity:				100%
RNA concentration:			2297.8 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6   Balb/c
Sample volume:				27µL


title: MZ1484-2, chip MOE430B


title: MZ1484-1, chip MOE430B


title: MZ1468-4, chip MOE430B


title: MZ1468-1, chip MOE430B


title: MyoD, mb1, 12hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S335
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_344
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time course: 12 hr
Estimated purity:				100%
Num cells for RNA prep:			More than 2 x 10E+6 Balb/c


title: P+N2AEP, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S379
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_369
Short description:			Seven day old platelet-drived growth factor and neurotrophin-3-generated neurospheres cultured from thr embryonic day 14 basal ganglia (anterior entopeduncular area)
Estimated purity:				Unknown
RNA concentration:			287 ng/u
Sample volume:				~ 50 ul


title: MyoD, mb1, 0hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S333
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_342
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time course: 0 hr
Estimated purity:				100%
Num cells for RNA prep:			More than 2 x 10E+6   Balb/c


title: P+N1AEP, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S379
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_369
Short description:			Seven day old platelet-drived growth factor and neurotrophin-3-generated neurospheres cultured from thr embryonic day 14 basal ganglia (anterior entopeduncular area)
Estimated purity:				Unknown
RNA concentration:			192 ng/ul
Sample volume:				~ 50 ul


title: R1-D1, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E107
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=107
SCGP Sample ID:				S145
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=107#SAMPLE_107
Short description:			Embryonic stem cells differentiated into embryoid bodies. Their expression pattern will be compared to that of the same cells grown in regular growth conditions. A study of the differential gene expression of these two populations should reveal genes whose expression is necessary for the maintenance of the stem cell phenotype.
RNA concentration:			2 ug/ul
Num cells for RNA prep:			8-10x10e6
Sample volume:				20 ul

source_name: R1, differentiated embryonic stem cells

growth_protocol:
Growth medium:				D-MEM
Media supplements:			10% FBS, glutamax, non-essential amino-acids, penicillin, streptomycin
Culture conditions:			Bacterial Petri dishes at 370C, 5% CO2 for 5 days

extract_protocol: RNA prep method:				RNeasy

tag: Strain:					129/Sv


title: R1-U1, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E107
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=107
SCGP Sample ID:				S146
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=107#SAMPLE_108
Short description:			Embryonic stem cells differentiated into embryoid bodies. Their expression pattern will be compared to that of the same cells grown in regular growth conditions. A study of the differential gene expression of these two populations should reveal genes whose expression is necessary for the maintenance of the stem cell phenotype.
Estimated purity:				95%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			8-10x10e6
Sample volume:				20 ul

source_name: R1,  undifferentiated embryonic stem cells

extract_protocol:
RNA prep method:				RNeasy
Method for estimating purity:		By eye


title: R1-D3, chip MOE430B


title: R1-U2, chip MOE430B


title: R1-D2, chip MOE430B


title: R1-U3, chip MOE430B


title: EGF4, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S330
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_368
Short description:			Seven day old epidermal growth factor-generated neurospheres cultured from the embryonic day 14 basal ganglia (medial and lateral ganglionic eminences).
RNA concentration:			100ng/ul
Sample volume:				25-30ul


title: 24.ko.ctrl.rep8

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

country: USA

institute: UCLA

description: 1541554117_H: array designation within the raw data file linked to the Series record

hyb_protocol: According to Illumina protocol

scan_protocol: Illumina BeadScan Image extraction: BeadStudio version 1.5.1.3, default parameters, no background subtraction

data_processing: Raw data was analyzed using Bioconductor packages (www.bioconductor.org). Data was normalized using quantile normalization. Analysis of differential expression was performed using a linear model fitting (LIMMA package, Smyth 2005).

source_name: Embryonic ATF4 KO cortical neurons, control treated, replicate #8

label_protocol: According to Illumina protocol

extract_protocol:
RNA extraction: Ambion RNAqeuous kit
Quality assessment: Agilent Bioanalyzer

tag: 15.5 dpc ATF4 KO embryonic neurons after control treatment, replicate #8


title: P+N3AEP, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S379
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_369
Short description:			Seven day old platelet-drived growth factor and neurotrophin-3-generated neurospheres cultured from thr embryonic day 14 basal ganglia (anterior entopeduncular area)
Estimated purity:				Unknown
RNA concentration:			171 ng/u
Sample volume:				~ 50 ul


title: EGF6, chip MOE430A


title: 23.wt.hca.rep4

description: 1541554117_G: array designation within the raw data file linked to the Series record

source_name: Embryonic WT cortical neurons, HCA treated, replicate #4

tag: 15.5 dpc ATF4 KO embryonic neurons after oxidative stress induced by the glutamate analog homocysteate (HCA), replicate #4


title: EGF2, chip MOE430A


title: 21.wt.ctrl.rep8

description: 1541554117_E: array designation within the raw data file linked to the Series record

source_name: Embryonic WT cortical neurons, control treated, replicate #8

tag: 15.5 dpc embryonic neurons after control treatment, replicate #8


title: EGF3, chip MOE430A


title: 19.wt.hca.rep3

description: 1541554117_C: array designation within the raw data file linked to the Series record

source_name: Embryonic WT cortical neurons, HCA treated, replicate #3

tag: 15.5 dpc embryonic neurons after oxidative stress induced by the glutamate analog homocysteate (HCA)


title: PGDF6, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E237
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=237
SCGP Sample ID:				S329
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=237#SAMPLE_367
Short description:			Seven day old platelet-derived growth factor-generated neurospheres cultured from the embryonic day 14 basal ganglia (anterior entopeduncular area).
RNA concentration:			100ng/ul
Sample volume:				25-30ul


title: MyoD, wtp16, 0hr, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E233
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=233
SCGP Sample ID:				S333
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=233#SAMPLE_342
Short description:			Time Course in vitro Differentiation of Myogenic Primary Myoblast into Myotubes for Ontario Genome Project 2004-05. , The Differentiation is leaded by removing the Proliferation Medium (Ham's F10 Medium + growth factors) and feeding with Differentiation Medium (DMEM hg + 2.5% Horse serum). , The expected data are: % Viability of cells; Total RNA extraction; BioAnalysis and MicroArray of Undifferentiated and Differentiated cells., Time course: 0 hr
Estimated purity:				100%
RNA concentration:			1170.2 ng/µL
Num cells for RNA prep:			More than 2 x 10E+6   Balb/c
Sample volume:				27µL


title: 20.ko.ctrl.rep7

description: 1541554117_D: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 cortical neurons, control treated, replicate #7

tag: 15.5 dpc ATF4 KO embryonic neurons aftercontrol treatment


title: 22.ko.hca.rep4

description: 1541554117_F: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 KO cortical neurons, HCA treated, replicate #4


title: 17.wt.ctrl.rep7

description: 1541554117_A: array designation within the raw data file linked to the Series record

source_name: Embryonic WT cortical neurons, control treated, replicate #7

tag: 15.5 dpc embryonic neurons after control treatment


title: EGF5, chip MOE430A


title: EGF1, chip MOE430A


title: 18.ko.hca.rep3

description: 1541554117_B: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 KO cortical neurons, HCA treated, replicate #3

tag: 15.5 dpc ATF4 KO embryonic neurons after oxidative stress induced by the glutamate analog homocysteate (HCA)


title: 16.wt.ctrl.rep6

description: 1541554116_H: array designation within the raw data file linked to the Series record

source_name: Embryonic WT cortical neurons, control treated, replicate #6

tag: 15.5 dpc embryonic neurons after control treatment, replicate #6


title: PGDF2, chip MOE430A


title: 14.wt.hca.rep2

description: 1541554116_F: array designation within the raw data file linked to the Series record

source_name: Embryonic WT cortical neurons, HCA treated, replicate #2


title: PGDF3, chip MOE430A


title: PGDF4, chip MOE430A


title: PGDF5, chip MOE430A


title: 15.ko.hca.rep2

description: 1541554116_G: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF KO cortical neurons, HCA treated, replicate #2


title: MZ1468-4, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Norman Iscove (iscove@uhnres.utoronto.ca; 610 University Avenue) for analysis.
Stembase Experiment ID:			E217
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=217
SCGP Sample ID:				S300
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=217#SAMPLE_315
Short description:			CD49+cDNA with Scott/EcorI primer on both ends. , Global PCR of stem cells time = 0 after sort., Dulac labeling protocol. , !Sample_description = Estimated purity:				97.03%
RNA concentration:			0.1 ug/ul
Num cells for RNA prep:			~30
Sample volume:				100 ul


title: 13.ko.ctrl.rep6

description: 1541554116_E: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 KO cortical neurons, control treated, replicate #6

tag: 15.5 dpc ATF4 KO embryonic neurons, control treatment, replicate #6


title: PGDF1, chip MOE430A

source_name: PDGF-responsive precursors, E14 anterior entopeduncular area

tag: Karyotype:				normal


title: MZ1468-2, chip MOE430A

source_name: Stem Cells, Bone Marrow CD49+


title: 10.wt.hca.rep1

description: 1541554116_B: array designation within the raw data file linked to the Series record

source_name: Embryonic WT cortical neurons, HCA treated, replicate #1


title: 11.ko.hca.rep1

description: 1541554116_C: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 KO cortical neurons, HCA treated, replicate #1

tag: 15.5 dpc ATF4 KO embryonic neurons after oxidative stress induced by the glutamate analog homocysteate (HCA), replicate #1


title: 12.wt.ctrl.rep5

description: 1541554116_D: array designation within the raw data file linked to the Series record

source_name: Embryonic WT cortical neurons, control treated, replicate #5

tag: 15.5 dpc embryonic neurons after control treatment, replicate #5


title: 8.ko.ctrl.rep4

description: 1412066061_H: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 KO cortical neurons, control treated, replicate #4

tag: 15.5 dpc embryos


title: MZ1484-2, chip MOE430A


title: 7.ko.ctrl.rep3

description: 1412066061_G: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 KO cortical neurons, control treated, replicate #3


title: R1-U3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E107
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=107
SCGP Sample ID:				S146
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=107#SAMPLE_108
Short description:			Embryonic stem cells differentiated into embryoid bodies. Their expression pattern will be compared to that of the same cells grown in regular growth conditions. A study of the differential gene expression of these two populations should reveal genes whose expression is necessary for the maintenance of the stem cell phenotype.
Estimated purity:				95%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			8-10x10e6
Sample volume:				20 ul

source_name: R1,  undifferentiated embryonic stem cells

tag: Gender:					Male


title: 9.ko.ctrl.rep5

description: 1541554116_A: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 KO cortical neurons, control treated, replicate #5


title: MZ1468-1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Norman Iscove (iscove@uhnres.utoronto.ca; 610 University Avenue) for analysis.
Stembase Experiment ID:			E217
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=217
SCGP Sample ID:				S299
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=217#SAMPLE_314
Short description:			CD49-cDNA with Scott/EcorI primer on both ends., Global PCR of stem cells time = 0 after sort., Dulac labeling protocol., !Sample_description = Estimated purity:				97.03%
RNA concentration:			0.1 ug/ul
Num cells for RNA prep:			~30
Sample volume:				100 ul

source_name: Stem Cells, Bone Marrow CD49-

tag: Strain:					B6 LY 5.1 a/a


title: R1-U2, chip MOE430A


title: MZ1484-1, chip MOE430A

tag: Defining markers:				Rho- CD3- B220- , CD49b- cKit+ Ly6 A/E+


title: 5.ko.ctrl.rep1

description: 1412066061_E: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 KO cortical neurons, control treated, replicate #1

tag: cortical neurons from 15.5 dpc ATF4 KO embryos, control treated, replicate #1


title: 6.ko.ctrl.rep2

description: 1412066061_F: array designation within the raw data file linked to the Series record

source_name: Embryonic ATF4 KO cortical neurons, control treated, replicate #2

tag: cortical neurons from 15.5 dpc ATF4 KO embryos, control treated, replicate #2


title: R1-D3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E107
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=107
SCGP Sample ID:				S145
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=107#SAMPLE_107
Short description:			Embryonic stem cells differentiated into embryoid bodies. Their expression pattern will be compared to that of the same cells grown in regular growth conditions. A study of the differential gene expression of these two populations should reveal genes whose expression is necessary for the maintenance of the stem cell phenotype.
RNA concentration:			2 ug/ul
Num cells for RNA prep:			8-10x10e6
Sample volume:				20 ul

source_name: R1, differentiated embryonic stem cells

tag: Strain:					129/Sv


title: R1-U1, chip MOE430A

source_name: R1, undifferentiated embryonic stem cells


title: MZ1468-3, chip MOE430A


title: 4.wt.ctrl.rep4

description: 1412066061_D: array designation within the raw data file linked to the Series record

source_name: Embryonic cortical neurons, control treated, replicate #4

tag: cortical neurons from 15.5 dpc WT embryos, control treated, replicate #4


title: 3.wt.ctrl.rep3

description: 1412066061_C: array designation within the raw data file linked to the Series record

source_name: Embryonic cortical neurons, control treated, replicate #3

tag: cortical neurons from 15.5 dpc WT embryos, control treated, replicate #3


title: R1-D1, chip MOE430A


title: 2.wt.ctrl.rep2

description: 1412066061_B: array designation within the raw data file linked to the Series record

source_name: Embryonic WT cortical neurons, control treated, replicate #2

tag: cortical neurons from 15.5 dpc WT embryos, control treated, replicate #2


title: 1.wt.ctrl.rep1

description: 1412066061_A: array designation within the raw data file linked to the Series record

source_name: Embryonic cortical neurons, control treated, replicate #1

tag: cortical neurons from 15.5 dpc embryos, control treated, replicate 1


title: 3dpa con 3 (adult and larval fin study)

status: Public on Feb 29 2008

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description: The caudal fin of zebrafish larvae at 2day post fertilization were amputated, follwed by exposure with TCDD or vehicle. Regenerating fin tissue was collected at 2 and 3 days post amputation for mRNA abundance analysis.

hyb_protocol: Hybridization was conducted as stipulated by Affymetrix GeneChip Expression Analysis Technical Manual (701021 Rev. 5).

scan_protocol: Affymetrix fluidics station 400 was used to wash the arrays. Arrays were scanned with an Affymetrix scanner 3000.

data_processing: Data was GC-RMA preprocessed and each gene was normalized to the median using Gene Spring 7.1 software.

label: Labeling and probe processing was conducted under manufactures recommendations.

organism: Danio rerio

source_name: 3 day post amputation fin; Vehicle Exposed; replicate 3

label_protocol: A total of 100ng of RNA from the larval fin tissue (+/-TCDD) at 2 and 3 dpa were used to generate biotinylated complementary RNA (cRNA) using the Two-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Caudal fins from two day old embryos (AB strain, Eugene, OR) were amputated and the animals were exposed to either DMSO (vehicle control) or 0.5ng/mL TCDD (>99% pure, Chemsyn, Lenexa, KS) in the water for 1 hr. After several rinses in TCDD free water, the larvae were reared until 2 and 3 days post amputation (dpa) when their regenerating fin tissue was amputated and collected for RNA analysis. RNA was extracted from the fin tissue using the RNAqueous Micro kit (Ambion, Austin, TX). Three groups at each time point and treatment, each comprised of 150 larval fins, were pooled to make an individual replicate. The quality and quantity of RNA was analyzed by UV absorbance. The abundance of ribosomal RNA and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).

tag: AB strain larval zebrafish - regenerating caudal fin


title: 2dpa con 3 (adult and larval fin study)

source_name: 2 day post amputation fin; Vehicle Exposed; replicate 3

extract_protocol: Caudal fins from two day old embryos (AB strain, Eugene, OR) were amputated and the animals were exposed to either DMSO (vehicle control) or 0.5ng/mL TCDD (>99% pure, Chemsyn, Lenexa, KS) in the water for 1 hr (Figure 1). After several rinses in TCDD free water, the larvae were reared until 2 and 3 days post amputation (dpa) when their regenerating fin tissue was amputated and collected for RNA analysis. RNA was extracted from the fin tissue using the RNAqueous Micro kit (Ambion, Austin, TX). Three groups at each time point and treatment, each comprised of 150 larval fins, were pooled to make an individual replicate. The quality and quantity of RNA was analyzed by UV absorbance. The abundance of ribosomal RNA and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).


title: 2dpa con 1 (adult and larval fin study)

source_name: 2 day post amputation larval regenerating fin; Vehicle Exposed; replicate 1

tag: AB strain larval zebrafish - regenerating caudal fin.


title: 5 dpa con c (adult and larval fin study)

description: Adult male zebrafish were i.p. injected with 50 ng/g TCDD or vehicle and caudal fins were amputated. Regenerating fin tissue was collected at 1, 3 and 5 days post amputation for mRNA abundance analysis.

source_name: Adult Male Zebrafish Caudal Fin 5 Day Post Amputaion, Vehicle Exposed Replicate C

label_protocol: 2.5 µg of total RNA was used to generate biotinylated complementary RNA (cRNA) for each treatment group using the One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA). RNA was reverse transcribed using a T7-(dT)24 primer and Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA).

growth_protocol: Fish were matained at 27oC until under standard conditions.

extract_protocol: Amputated tissue was stored in RNAlater (Qiagen, Valencia, CA) and frozen at -80oC. RNAlater was removed from the samples and total RNA was purified with TRI reagent (Molecular Research Laboratories, Cincinnati, OH) according to the manufacturer’s instructions. Total RNA was DNase treated with RQ1 DNase (Promega, Madison, WI) according to the manufacture’s protocol and RNA quantity and quality was determined by UV absorbance. Ribosomal RNA abundance and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Adult male zebrafish (Danio rerio) (AB strain, Eugene, OR) were anesthetized with tricaine methanesulfonate (MS-222) and their caudal fins were amputated at the bifurcation of the fin rays. Fish were then injected with phosphatidylcholine liposomes (vehicle control) alone or liposomes incorporated with TCDD (>99% pure, Chemsyn, Lenexa, KS) resulting in a final dose of 50 ng TCDD/g fish. At the indicated dpa, fish were euthanized with an over dose of MS-222. Regenerated fin tissue was then isolated by amputation within two ray segments anterior to the original amputation plane. Amputated tissue was then stored in RNAlater (Qiagen, Valencia, CA) and frozen at -80oC until RNA was isolated from the tissue. Tissues from 10 fish were combined to comprise a single experimental group (replicate). Three groups of tissue were obtained from vehicle control or TCDD exposed fish at 1, 3, and 5 dpa.

tag: Adult Male Zebrafish AB Strain Caudal Fin 5 Day Post Amputaion, Vehicle Exposed


title: Unamputated adult caudal fin 2

description: The caudal fin of adult zebrafish were amputated. Unamputated fin tissue as well as regenerating fin tissue was collected at 1,  2 and 3 days post amputation for mRNA abundance analysis.

source_name: Adult male AB Zebrafish unamputated caudal fin, Replicate 2

treatment_protocol: Adult male zebrafish (Danio rerio) (AB strain, Eugene, OR) were anesthetized with tricaine methanesulfonate (MS-222) and their caudal fins were amputated at the bifurcation of the fin rays. For unamputated control, RNA was isolated from the non regenerating caudal fin. At the indicated dpa, fish were euthanized with an over dose of MS-222. Regenerated fin tissue was then isolated by amputation within two ray segments anterior to the original amputation plane. Amputated tissue was then stored in RNAlater (Qiagen, Valencia, CA) and frozen at -80oC until RNA was isolated from the tissue. Tissues from 10 fish were combined to comprise a single experimental group (replicate). Three groups of tissue were obtained from at 1, 3, and 5 dpa.

tag: Adult male AB Zebrafish unamputated caudal fin.


title: 5 dpa con b (adult and larval fin study)

source_name: Adult Male Zebrafish Caudal Fin 5 Day Post Amputaion, Vehicle Exposed Replicate B


title: 3 dpa con c (adult and larval fin study)

source_name: Adult Male Zebrafish Caudal Fin 3 Day Post Amputaion, Vehicle Exposed Replicate C

tag: Adult Male Zebrafish AB Strain Caudal Fin 3 Day Post Amputaion, Vehicle Exposed


title: 2dpf unamputated caudal fin; replicate 1

description: The caudal fin of zebrafish larvae at 2day post fertilization was amputated. Regenerating fin tissue was collected at 2dpf, 1,  2 and 3 days post amputation for mRNA abundance analysis.

source_name: 2days post fertilization caudal fin; replicate 1

label_protocol: A total of 100ng of RNA from the larval fin tissue  at 2dpf, and 1, 2 and 3 dpa were used to generate biotinylated complementary RNA (cRNA) using the Two-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Caudal fins from two day old embryos (AB strain, Eugene, OR) were amputated. The caudal fin at 2dpf were used as the unamputaed control and the larvae were reared until 1, 2 and 3 days post amputation (dpa) when their regenerating fin tissue was amputated and collected for RNA analysis. RNA was extracted from the fin tissue using the RNAqueous Micro kit (Ambion, Austin, TX). Three groups at each time point, each comprised of 150 larval fins, were pooled to make an individual replicate. The quality and quantity of RNA was analyzed by UV absorbance. The abundance of ribosomal RNA and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).


title: 3dpa con 1 (adult and larval fin study)

source_name: 3 day post amputation fin; Vehicle Exposed; replicate 1


title: 2dpf unamputated caudal fin; replicate 2


title: Unamputated adult caudal fin 3

source_name: Adult male AB Zebrafish unamputated caudal fin, Replicate 3


title: 3dpa con 2 (adult and larval fin study)

source_name: 3 day post amputation fin; Vehicle Exposed; replicate 2


title: 1dpa con 3

source_name: 1 day post amputation larval regenerating fin; replicate 1


title: 3 dpa con a (adult and larval fin study)

source_name: Adult Male Zebrafish Caudal Fin 3 Day Post Amputaion, Vehicle Exposed Replicate A


title: 5 dpa con a (adult and larval fin study)

source_name: Adult Male Zebrafish Caudal Fin 5 Day Post Amputaion, Vehicle Exposed Replicate A


title: 2dpa con 2 (adult and larval fin study)

source_name: 2 day post amputation fin; Vehicle Exposed; replicate 2


title: 1dpa con 1


title: 3 dpa con b (adult and larval fin study)

source_name: Adult Male Zebrafish Caudal Fin 3 Day Post Amputaion, Vehicle Exposed Replicate B


title: R1-D2, chip MOE430A

source_name: R1, differentiated embryonic stem cells


title: 2dpf unamputated caudal fin; replicate 3


title: Unamputated adult caudal fin 1

source_name: Adult male AB Zebrafish unamputated  caudal fin, Replicate 1

tag: Adult male AB Zebrafish unamputated  caudal fin.


title: 3dpa tcdd 3

source_name: 3 day post amputation fin; TCDD Exposed; replicate 3


title: 1dpa con 2

source_name: 1 day post amputation larval regenerating fin;  replicate 1


title: 1 dpa con d (adult and larval fin study)

source_name: Adult male AB Zebrafish 1 day post amputation caudal fin, Vehicle Dosed Replicate d

extract_protocol: Amputated tissue was stored in RNAlater (Qiagen, Valencia, CA) and frozen at -80oC.  RNAlater was removed from the samples and total RNA was purified with TRI reagent (Molecular Research Laboratories, Cincinnati, OH) according to the manufacturer’s instructions. Total RNA was DNase treated with RQ1 DNase (Promega, Madison, WI) according to the manufacture’s protocol and RNA quantity and quality was determined by UV absorbance. Ribosomal RNA abundance and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).


title: 1 dpa con e (adult and larval fin study)

source_name: Adult Male Zebrafish Caudal Fin 1 Day Post Amputaion, Vehicle Exposed Replicate E

tag: Adult Male Zebrafish AB Strain Caudal Fin 1 Day Post Amputaion, Vehicle Exposed


title: 1 dpa con b (adult and larval fin study)

source_name: 1 day post amputation fin; Vehicle Exposed; replicate b

tag: Adult male AB strain zebrafish regenerating caudal fin.


title: 3dpa tcdd 2

source_name: 3 day post amputation fin; TCDD Exposed; replicate 2


title: 3dpa tcdd 1

source_name: 3 day post amputation fin; TCDD Exposed; replicate 1


title: 2dpa tcdd 2

source_name: 2 day post amputation fin; TCDD Exposed; replicate 2


title: 2dpa tcdd 1

source_name: 2 day post amputation fin; TCDD Exposed; replicate 1


title: 2dpa tcdd 3

source_name: 2 day post amputation fin; TCDD Exposed; replicate 3


title: 3dpa con 2

source_name: 3 day post amputation fin; Vehicle Exposed; replicate 2


title: 2dpa con 1

source_name: 2 day post amputation larval regenerating fin; Vehicle Exposed; replicate 1


title: 2dpa con 2


title: 2dpa con 3

source_name: 2 day post amputation fin; Vehicle Exposed; replicate 3


title: 3dpa con 1

source_name: 3 day post amputation fin; Vehicle Exposed; replicate 1


title: 3dpa con 3

source_name: 3 day post amputation fin; Vehicle Exposed; replicate 3