title: mMSC CD34- 3, chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S44
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_36
Short description:			CD34- cells isolated from adult bone marrow. Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			1.01 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				14.8 ul
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S44
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_36
Short description:			CD34- cells isolated from adult bone marrow. Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			1.01 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				14.8 ul


title: mMSC CD34- 1, chip MG_U74Av2

status: Public on Dec 09 2005

type: RNA

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.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S44
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_36
Short description:			CD34- cells isolated from adult bone marrow. Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			0.989 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				15.1 ul
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S44
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_36
Short description:			CD34- cells isolated from adult bone marrow. Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			0.989 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				15.1 ul

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow stromal cell clone, Bone marrow

growth_protocol:
Growth medium:				DMEM
Media supplements:			10% fetal bovine serum
Culture conditions:			37C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Single cell colony isolation
Contaminating cell type:			Other bone marrow cells
Method for estimating purity:		FACS analysis with CD34+ marker

tag: Strain:					C57Bl/6

tag: Gender:					Female

tag: Defining markers:				CD34 -, CD117 -, Tie-2 -,FLK-1 -, FLT-1 -, CD44 -


title: 6999B, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. James  Piret (jpiret@chml.ubc.ca; 315-6174 University Boulevard) for analysis.
Stembase Experiment ID:			E177
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177
SCGP Sample ID:				S219
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177#SAMPLE_177
Short description:			RNA samples generated from 3 days growth in serum lot 6999.
Estimated purity:				100%
RNA concentration:			100 ug/ul
Num cells for RNA prep:			3.7x10e6
Sample volume:				10.0 ul

source_name: R1 embryonic stem cell line (Oct-4 GFP), Blastocyst

growth_protocol:
Growth medium:				DMEM, 15% FBS
Media supplements:			LIF, glutamine, non-essential amino acids, penicillin/streptomycin
Culture conditions:			5% CO2, 37C, grown on gelatin

extract_protocol:
RNA prep method:				RNeasy
Contaminating cell type:			None

treatment_protocol: Assays to confirm viability:		Trypan blue exclusion, embryoid body and colony forming assays

tag: Strain:


title: M-O7e SP3, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Mickie Bhatia (mbhatia@robarts.ca; Box 5015; 100 Perth Drive) for analysis.
Stembase Experiment ID:			E37
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37
SCGP Sample ID:				S51
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37#SAMPLE_37
Short description:			Total RNA from M-O7e, a megakaryoblastic cell line, transduced with Smad7 recombinant retroviral vector (MIEV-Smad7).
Estimated purity:				~ 98%
RNA concentration:			3.2 ug/ul
Num cells for RNA prep:			4x10e6 cells
Sample volume:				6.5 ul

organism: Homo sapiens

source_name: M-O7e cell line, Blood

growth_protocol: Growth medium:				IMDM

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Cell sorting
Method for estimating purity:		Reanalysis of sorted population by FACS-Vantage

treatment_protocol: Assays to confirm viability:		7AAD staining

tag: Defining markers:				GFP


title: M-O7e SP2, chip HG-U133A


title: 6473A, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. James  Piret (jpiret@chml.ubc.ca; 315-6174 University Boulevard) for analysis.
Stembase Experiment ID:			E177
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177
SCGP Sample ID:				S220
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177#SAMPLE_178
Short description:			RNA samples generated from 3 days growth in serum lot 6473.
Estimated purity:				100%
RNA concentration:			100 ug/ul
Num cells for RNA prep:			3.6x10e6
Sample volume:				10.0 ul


title: MACS #3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Alain Garnier (Alain.Garnier@gch.ulaval.ca; Pavillon Adrien-Pouliot) for analysis.
Stembase Experiment ID:			E144
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=144
SCGP Sample ID:				S184
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=144#SAMPLE_144
Short description:			Putative muscle derived stem cells from mouse.  Purified with MACS using Sca1 and CD45 beads.  Population is Sca1+/CD45-
Estimated purity:				< 1% CD45+>80% Sca1+
RNA concentration:			65ng/ul
Num cells for RNA prep:			2.04x10E6
Sample volume:				B - 5ul, M - 20ul

source_name: primary culture, Hind limb muscles

growth_protocol:
Growth medium:				F10 Ham
Media supplements:			20% FBS, pen/strep
Culture conditions:			37C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			None
Cell purification method:			MACS
Contaminating cell type:			muscles cells
Method for estimating purity:		FACS

treatment_protocol: Assays to confirm viability:		erythrosin B exclusion

tag: Strain:					C57BL/10J

tag: Karyotype:				BL.C5710J

tag: Defining markers:				Sca1+/CD45-


title: M-O7e SP1, chip HG-U133A


title: PP6 #3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Alain Garnier (Alain.Garnier@gch.ulaval.ca; Pavillon Adrien-Pouliot) for analysis.
Stembase Experiment ID:			E144
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=144
SCGP Sample ID:				S197
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=144#SAMPLE_308
Short description:			Putative muscle derived stem cells purified with preplatings from muscle hind limb muscles.
Analysis requested:			MOE430 Affymetrix chip
RNA concentration:			15ng/ul
Num cells for RNA prep:			6.7x10E6
Sample volume:				B: 5ul  M: 20ul

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			None
Cell purification method:			preplatings
Contaminating cell type:			muscles cells
Method for estimating purity:		none

tag: Defining markers:				none


title: 6999C, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. James  Piret (jpiret@chml.ubc.ca; 315-6174 University Boulevard) for analysis.
Stembase Experiment ID:			E177
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177
SCGP Sample ID:				S219
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177#SAMPLE_177
Short description:			RNA samples generated from 3 days growth in serum lot 6999.
Estimated purity:				100%
RNA concentration:			100 ug/ul
Num cells for RNA prep:			3.0x10e6
Sample volume:				10.0 ul


title: 6999A, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. James  Piret (jpiret@chml.ubc.ca; 315-6174 University Boulevard) for analysis.
Stembase Experiment ID:			E177
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177
SCGP Sample ID:				S219
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177#SAMPLE_177
Short description:			RNA samples generated from 3 days growth in serum lot 6999.
Estimated purity:				100%
RNA concentration:			100 ug/ul
Num cells for RNA prep:			3.1x10e6
Sample volume:				10.0 ul


title: mMSC CD34+ 3, chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S4
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_3
Short description:			CD34+ cells isolated from adult bone marrow.  Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			0.721 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				20.8 ul

tag: Defining markers:				CD34+, CD117-, Tie-2-,FLK-1-, FLT-1-, CD44-


title: PP6 #2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Alain Garnier (Alain.Garnier@gch.ulaval.ca; Pavillon Adrien-Pouliot) for analysis.
Stembase Experiment ID:			E144
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=144
SCGP Sample ID:				S197
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=144#SAMPLE_308
Short description:			Putative muscle derived stem cells purified with preplatings from muscle hind limb muscles.
Analysis requested:			MOE430 Affymetrix chip
RNA concentration:			35ng/ul
Num cells for RNA prep:			6.5x10E6
Sample volume:				B: 5ul  M: 20ul


title: PP6, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis.
Stembase Experiment ID:			E28
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=28
SCGP Sample ID:				S31
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=28#SAMPLE_29
Short description:			PP6: human muscle derived stem cell
RNA concentration:			0.9 ug/ul
Sample volume:				8.0 ul

source_name: Muscle stem cell, Muscle

growth_protocol:
Growth medium:				F10
Media supplements:			10% SVF, 9mM glutamine

extract_protocol:
RNA prep method:				TRIzol
Cell purification method:			After 24 hours of culture, floating cells were collected and plated on new flasks, serial preplates were obtained until pp6.


title: mMSC CD34+ 2, chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S4
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_3
Short description:			CD34+ cells isolated from adult bone marrow.  Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			0.421 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				35.6 ul


title: M1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Kelly McNagny (kelly@brc.ubc.ca; ) for analysis.
Stembase Experiment ID:			E194
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=194
SCGP Sample ID:				S236
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=194#SAMPLE_194
Short description:			Mast cell precursors cultured for 14 to 16 days.
Analysis requested:			Expression analysis, murine genome chip MOE430 set comparison of profiles of mature mast cells, mast cell precursors and stem cells, possibly comparisons with other hematopoletic cells
Estimated purity:				~80%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			1x10e7
Sample volume:				8.0-10.0 ul

source_name: Bone marrow mast cell precursors, Bone marrow (femur and fibula)

growth_protocol:
Growth medium:				RPMI
Media supplements:			Penicillin/streptomycin, FBS 409, sodium pyruvate, glutamine, IL-3
Culture conditions:			37C, 95% CO2 for 14 to 16 days

extract_protocol:
RNA prep method:				TRIzol followed by lithium chloride/ethanol precipitation
Cell purification method:			Growth in IL-3
Contaminating cell type:			Possibly bone marrow stromal cells, monocytes, and macrophages
Method for estimating purity:		Post FACS analysis, morphology

tag: Strain:					C57Bl6

tag: Gender:					M1

value: female; M3 and M5:male

tag: Karyotype:				Wild-type

tag: Defining markers:				c-kit+, CD34+


title: mMSC CD34+ 1, chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S4
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_3
Short description:			CD34+ cells isolated from adult bone marrow.  Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			0.573 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				26.1 ul


title: Osteo16 VD3-3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Derrick Rancourt (rancourt@ucalgary.ca; Room 2221 Health Sciences Centre; 3330 Hospital Drive NW) for analysis.
Stembase Experiment ID:			E202
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202
SCGP Sample ID:				S192
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_238
Short description:			D3 murine embryonic stem cells were allowed to undergo directed differentiation toward the osteoblast lineage by the addition of vitamin D3, B-glycerophosphate, and absorbic acid.  Assessment of the gene expression patterns of differentiated cells at day 4, 5, 6, 8, 16, 25, and 30 and comparison to profiles of mES cells that have undergone non-directed differentiation will allow the elucidation of genes that are important to the early commitment of these cells to the osteoblast lineage.
Analysis requested:			For SCGP, compare gene expression in samples ctrl vs. VD3 treated in Osteo_1  -- Osteo_4
Cell line clone ID:			n/a
Estimated purity:				pure clone
RNA concentration:			100ng/ul
Num cells for RNA prep:			3 X 10^6
Sample volume:				12ul - 6ul for BA and 6 ul for exp

source_name: D3, Blastocyst

growth_protocol:
Growth medium:				DMEM
Media supplements:			Vitamin D3 5 x 10e3 M, B-glycerophosphate, Ascorbic Acid
Culture conditions:			37 C

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			n/a
Cell purification method:			clone
Contaminating cell type:			Undetermined
Method for estimating purity:		n/a

treatment_protocol: Assays to confirm viability:		RT-PCR analysis shows expression of osteocalcin (mature osteoblast marker) peaks at day 30. Cbfa1, a transcription factor implicated in osteoblast differentiation shows expression from days 16-25. Osteocalcin, osteopontin, osteonectin, and bone sia

tag: Strain:					129 SV

tag: Gender:					Male

tag: Karyotype:				normal

tag: Defining markers:				n/a


title: J1 EB 24h 1, chip MOE430B

status: Public on Dec 06 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S252
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_219
Short description:			24 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL

source_name: J1, Fetal cells

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS, non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Culturing
Contaminating cell type:			None
Method for estimating purity:		By eye

treatment_protocol: Assays to confirm viability:		Stratagene mycoplasma PCR test

tag: Strain:					129/Sv


title: J1 EB 24h 3, chip MOE430B


title: J1 EB 24h 2, chip MOE430B


title: J1 EB 18h 2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S251
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_218
Short description:			18 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: Human myoblasts, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques P. Tremblay (jacques-p.tremblay@crchul.ulaval.ca; 2705 boulevard Laurier) for analysis.
Stembase Experiment ID:			E28
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=28
SCGP Sample ID:				S30
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=28#SAMPLE_28
Short description:			Human myoblasts
Estimated purity:				95%
RNA concentration:			3.0 ug/ul
Sample volume:				8.0 ul

source_name: Myoblasts, Muscle

extract_protocol:
RNA prep method:				TRIzol
Cell purification method:			Primary culture of muscle-derived cells
Contaminating cell type:			Fibroblasts
Method for estimating purity:		Immunohistochemistry, FACS

tag: Defining markers:				Desmin, NKH1


title: J1 EB 18h 1, chip MOE430B


title: J1 EB 18h 3, chip MOE430B


title: MACS #2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Alain Garnier (Alain.Garnier@gch.ulaval.ca; Pavillon Adrien-Pouliot) for analysis.
Stembase Experiment ID:			E144
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=144
SCGP Sample ID:				S184
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=144#SAMPLE_144
Short description:			Putative muscle derived stem cells from mouse.  Purified with MACS using Sca1 and CD45 beads.  Population is Sca1+/CD45-
Estimated purity:				< 1% CD45+>80% Sca1+
RNA concentration:			55ng/ul
Num cells for RNA prep:			1.98x10E6
Sample volume:				B - 5ul, M - 20ul

tag: Gender:					Female


title: J1 EB 48h 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S250
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_217
Short description:			48 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: J1 EB 4d 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S246
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_213
Short description:			4 days of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: J1 EB 9d 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S248
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_215
Short description:			9 days of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: J1 EB 48h 1, chip MOE430B


title: J1 EB 48h 2, chip MOE430B


title: J1 EB 9d 1, chip MOE430B


title: J1 EB 14d 1, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S249
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_216
Short description:			14 days of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: J1 EB 7d 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S247
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_214
Short description:			7 days of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: J1 EB 7d 1, chip MOE430B


title: J1 EB 9d 2, chip MOE430B


title: J1 EB 14d 2, chip MOE430B


title: J1 EB 14d 3, chip MOE430B


title: J1 EB 7d 2, chip MOE430B


title: J1 EB 4d 2, chip MOE430B


title: J1 EB 4d 1, chip MOE430B


title: J1 EB 12 hr 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S244
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_211
Short description:			12 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: J1 EB 36 hr 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S245
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_212
Short description:			36 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: J1 EB 6 hr 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S243
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_210
Short description:			6 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: J1 EB 36 hr 2, chip MOE430B


title: J1 EB 36 hr 1, chip MOE430B


title: J1 EB 6 hr 2, chip MOE430B


title: J1 EB 6 hr 1, chip MOE430B


title: J1 EB 12 hr 1, chip MOE430B


title: J1 ES 0 hr 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S242
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_209
Short description:			0 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL


title: J1 EB 24h 3, chip MOE430A


title: 6473C, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. James  Piret (jpiret@chml.ubc.ca; 315-6174 University Boulevard) for analysis.
Stembase Experiment ID:			E177
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177
SCGP Sample ID:				S220
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=177#SAMPLE_178
Short description:			RNA samples generated from 3 days growth in serum lot 6473.
Estimated purity:				100%
RNA concentration:			100 ug/ul
Num cells for RNA prep:			3.5x10e6
Sample volume:				10.0 ul

tag: Strain:


title: J1 EB 24h 2, chip MOE430A


title: J1 EB 48h 1, chip MOE430A


title: J1 EB 24h 1, chip MOE430A


title: J1 EB 9d 2, chip MOE430A


title: J1 EB 18h 2, chip MOE430A


title: J1 EB 9d 1, chip MOE430A


title: J1 EB 18h 1, chip MOE430A


title: J1 EB 18h 3, chip MOE430A


title: J1 EB 48h 2, chip MOE430A


title: J1 EB 9d 3, chip MOE430A


title: J1 ES 0 hr 2, chip MOE430B


title: J1 EB 48h 3, chip MOE430A


title: J1 EB 7d 1, chip MOE430A


title: J1 EB 7d 3, chip MOE430A


title: J1 EB 7d 2, chip MOE430A


title: J1 EB 4d 1, chip MOE430A


title: J1 EB 36 hr 3, chip MOE430A


title: J1 EB 36 hr 2, chip MOE430A


title: J1 EB 4d 2, chip MOE430A


title: J1 EB 12 hr 3, chip MOE430A


title: J1 EB 4d 3, chip MOE430A


title: MaSC2, chip MOE430A

status: Public on Dec 02 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S313
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_341
Short description:			The sample is RNA derived from highly purified mouse mammary stem cells (Masc). These cells were derived from freshly dissociated mouse mammary tissue and were analyzed for cell content by in vivo transplantation arrays. The relevance to the stem cell project is that we have also  isolated a mammary cell highly enriched in progenitor (CFC's). A comparison of the two population would be helpful in identifying stem cell specific genes.
Estimated purity:				1 stem cell in every 50-100 cells
RNA concentration:			531
Num cells for RNA prep:			2000-4000
Sample volume:				~20 ul

source_name: Mouse mammary stem cell, mammary

extract_protocol:
RNA prep method:				Arcturus pico pure
Amplification method:			N/A
Cell purification method:			Negative selection using magnets followed by FACS
Contaminating cell type:			N/A
Method for estimating purity:		FACS and in vitro colony assay

treatment_protocol: Assays to confirm viability:		in vivo transplantation assys

tag: Strain:					FVB

tag: Defining markers:				stromal lineage-, CD49f++, CD24+


title: J1 EB 36 hr 1, chip MOE430A


title: J1 EB 12 hr 1, chip MOE430A


title: MYO3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S312
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_340
Short description:			The sample is RNA derived from  mouse mammary myoepithelial (basal-positioned)cells. These cells are phenotipically similar to mouse mammary stem cells, but are deficient in stem ell contect. Consequentially, these are very useful in identifying stem cell specific genes.
Estimated purity:				~94%
RNA concentration:			301
Num cells for RNA prep:			3000- 24000
Sample volume:				~20 ul

source_name: Basal (Myoepithelial) cells, mammary

extract_protocol:
RNA prep method:				Arcturus pico pure
Amplification method:			N/A
Cell purification method:			Immunomagnetic enrichment and FACS
Contaminating cell type:			N/A
Method for estimating purity:		FACS and in vitro colony assay

treatment_protocol: Assays to confirm viability:		colony assays,in vivo transplantation assays

tag: Defining markers:				stromal lineage-, CD49f+, CD24+


title: J1 EB 12 hr 2, chip MOE430B


title: J1 EB 12 hr 2, chip MOE430A


title: MaSC2, chip MOE430B


title: MYO2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S312
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_340
Short description:			The sample is RNA derived from  mouse mammary myoepithelial (basal-positioned)cells. These cells are phenotipically similar to mouse mammary stem cells, but are deficient in stem ell contect. Consequentially, these are very useful in identifying stem cell specific genes.
Estimated purity:				~94%
RNA concentration:			997
Num cells for RNA prep:			3000- 24000
Sample volume:				~20 ul


title: MaSC3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S313
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_341
Short description:			The sample is RNA derived from highly purified mouse mammary stem cells (Masc). These cells were derived from freshly dissociated mouse mammary tissue and were analyzed for cell content by in vivo transplantation arrays. The relevance to the stem cell project is that we have also  isolated a mammary cell highly enriched in progenitor (CFC's). A comparison of the two population would be helpful in identifying stem cell specific genes.
Estimated purity:				1 stem cell in every 50-100 cells
RNA concentration:			378
Num cells for RNA prep:			2000-4000
Sample volume:				~20 ul


title: CFC2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S311
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_339
Short description:			The sample is RNA derived from highly purified mouse mammary colony forming cells (CFC). These cells were derived from freshly dissociated mouse mammary tissue and were analyzed for CFC content by in vitro colony arrays. The relevance to the stem cell project is that we have also  purified a mammary cell highly enriched for mammary stem cell. A comparison of mouse mammary progenitor (CFC) and stem cell would be very insightful and useful in identifying stem cell specific genes.
Estimated purity:				1 CFC in every 10 sorted cells
RNA concentration:			259
Num cells for RNA prep:			3000-4000 ( Biological Triplicates)
Sample volume:				~20 ul

source_name: Mammary epithelial colony forming cell, mammary

treatment_protocol: Assays to confirm viability:		In vitro colony assay

tag: Defining markers:				stromal lineage-, CD49f+, CD24++


title: CFC3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S311
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_339
Short description:			The sample is RNA derived from highly purified mouse mammary colony forming cells (CFC). These cells were derived from freshly dissociated mouse mammary tissue and were analyzed for CFC content by in vitro colony arrays. The relevance to the stem cell project is that we have also  purified a mammary cell highly enriched for mammary stem cell. A comparison of mouse mammary progenitor (CFC) and stem cell would be very insightful and useful in identifying stem cell specific genes.
Estimated purity:				1 CFC in every 10 sorted cells
RNA concentration:			146
Num cells for RNA prep:			3000-4000 ( Biological Triplicates)
Sample volume:				~20 ul


title: CFC1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S311
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_339
Short description:			The sample is RNA derived from highly purified mouse mammary colony forming cells (CFC). These cells were derived from freshly dissociated mouse mammary tissue and were analyzed for CFC content by in vitro colony arrays. The relevance to the stem cell project is that we have also  purified a mammary cell highly enriched for mammary stem cell. A comparison of mouse mammary progenitor (CFC) and stem cell would be very insightful and useful in identifying stem cell specific genes.
Estimated purity:				1 CFC in every 10 sorted cells
RNA concentration:			688
Num cells for RNA prep:			3000-4000 ( Biological Triplicates)
Sample volume:				~10 ul


title: MYO1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S312
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_340
Short description:			The sample is RNA derived from  mouse mammary myoepithelial (basal-positioned)cells. These cells are phenotipically similar to mouse mammary stem cells, but are deficient in stem ell contect. Consequentially, these are very useful in identifying stem cell specific genes.
Estimated purity:				~94%
RNA concentration:			823
Num cells for RNA prep:			3000- 24000
Sample volume:				~20 ul


title: MaSC3, chip MOE430B


title: MaSC1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S313
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_341
Short description:			The sample is RNA derived from highly purified mouse mammary stem cells (Masc). These cells were derived from freshly dissociated mouse mammary tissue and were analyzed for cell content by in vivo transplantation arrays. The relevance to the stem cell project is that we have also  isolated a mammary cell highly enriched in progenitor (CFC's). A comparison of the two population would be helpful in identifying stem cell specific genes.
Estimated purity:				1 stem cell in every 50-100 cells
RNA concentration:			534
Num cells for RNA prep:			2000-4000
Sample volume:				~20 ul


title: MaSC1, chip MOE430B


title: MYO3, chip MOE430B


title: MYO2, chip MOE430B


title: CFC1, chip MOE430B


title: MYO1, chip MOE430B


title: 10 T1/2 5, chip MOE430B

status: Public on Oct 07 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E211
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=211
SCGP Sample ID:				S286
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=211#SAMPLE_295
Short description:			10 T1/2 shares a set of genes with stem cells. 10 T1/2 microarray data will be used to subtract these common genes from gene profiles of other stem cell samples. Three best samples to be used for microarray experiment.
Analysis requested:			MOE 430A and B
RNA concentration:			100ng/uL
Sample volume:				5uL

source_name: 10 T1/2, embroyonic fibroblast

growth_protocol:
Growth medium:				DMEM
Media supplements:			10% FBS
Culture conditions:			harvested at 80% confluency

extract_protocol: RNA prep method:				RNeasy


title: K562 transfected with miR-181a versus control transfected K562, 48 hours

status: Public on Nov 18 2005

city: Guangzhou

first: Jueyu

last: Zhou

state: Guangdong

address: Southern Medical University

department: Institute of genetic engineering

country: China

institute: Southern Medical University

description:
Human K562 leukemia cells were cultured in RPMI 1640 medium (Invitrogen, California, USA) supplemented with 10% fetal bovine serum (FBS) (without antibiotics) and maintained at 37 ℃ in 5% CO2.
After transfection experiments, total RNAs from above two group K562 cells were purified using the RNeasy mini kit (Qiagen, Heidelberg, Germany) in accordance with the manufacturer’s protocols. RNA concentration and purity were estimated spectrophotometrically and the quality further assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
Total RNA from control group and transfected group were respectively  reverse transcription,in vitro transcribed and labeled (Cy3 and Cy5) according to the Agilent Low RNA Input Fluorescent Linear Amplification Kit Protocol, green is control group, red is transfected group. The array hybridization, washing, and scanning procedures were performed in our lab according to Agilent 60-mer oligo microarray processing protocol using 0.75 µg samples of labeled, fragmented cRNA on Agilent Human 1A oligo microarray with 22575 probes (Agilent Technologies). Labeled cRNA is incubated with the microarray in a hybridization chamber at 60ºC for 17 hours, 4 rpm/min. The microarray was scanned using Agilent 2565BA DNA microarray scanner (Agilent Technologies). Data collection was performed by Agilent DNA microarray scanner. Using the Agilent Feature Extraction Software(v.7.5), spots were identified, measured for fluorescence intensity, local background, and arraywide parameters used to normalize the signals. Outliers and saturated spots were rejected according to 1.42xIQR, and local backgroud subtracted from the signals. Signals were then normalized to remove dye bias and arraywide drift in flourescence.
The following two tests are performed to determined the significance of a feature: (1) Log ratio P-value of the red over green processed signals was calculated using two-sided t-test with P<0.01 considered significant, and (2) a boolean flag of 1 indicated that the feature BGSubSignal is well above background and passes the IsPosAndSignif test.

data_processing: Data collection was performed with Agilent Feature Extraction software

source_name: Mock transfected K562 cells, 48 hours

tag: Mock transfected K562 cells were treated with Oligofectamine(tranfection reagent but no miR-181a RNA duplex) and totle RNA was extracted from these cells at 48-hour post transfection

source_name: miR-181a transfected K562 cells, 48 hours

tag: Total RNA was extracted from miR-181a transfected K562 cells at 48-hour post transfection


title: 10 T1/2 4, chip MOE430B


title: 10 T1/2 5, chip MOE430A


title: 10 T1/2 1, chip MOE430B


title: Lin-(3), chip MOE430B

status: Public on Sep 15 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E207
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207
SCGP Sample ID:				S293
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207#SAMPLE_281
Short description:			Lineage depleted cells of murine bone marrow are enriched for hematopoietic progenitors. They are a good source of enriched cells for the isolation of hematopoietic multipotent and further downstream lineage committed progenitors once labeled with murine hematopoietic stem cell markers, Sca-1 and cKit and sorted into four differently labeled populations. Gene expression profile of lineage depleted cells will be used to compare with that of the four sorted populations.
Estimated purity:				20-24 fold purification
RNA concentration:			6.4-150.8 ng/ul
Num cells for RNA prep:			5-10 x 10^5
Sample volume:				3 ul

source_name: Hematopoietic cells, Bone marrow

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			SpinSep murine hematopoietic progenitor enrichment kit
Method for estimating purity:		Colony forming cell (CFC) and cobblestone area forming cell (CAFC) assays

treatment_protocol: Assays to confirm viability:		Trypan Blue dye exclusion to estimate the viability

tag: Strain:					C57BL/6


title: Myospheres 2, chip MOE430B

status: Public on Oct 06 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E209
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=209
SCGP Sample ID:				S274
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=209#SAMPLE_284
Short description:			Cells were isolated from muscle (hind leg) of Balb/c mouse (male). Then cells were enriched at FACS by using Sca1 antigen. Cells were grown 4 days in NSC medium, passaged and RNA isolated. Cells were at passage 1.
Analysis requested:			Murinr chip MOE 430 A, B
RNA concentration:			small sample
Num cells for RNA prep:			from 2E+06 cells (FACS enrichment)
Sample volume:				5uL

source_name: myospheres, muscle (hind leg)

growth_protocol:
Growth medium:				neurocult
Media supplements:			bf6f, LIF, B27, EGF
Culture conditions:			37C +CO2

extract_protocol:
RNA prep method:				RNEasy
Cell purification method:			Enriched with Sca1 antigen

tag: Strain:					Balb/c


title: Lin-(2), chip MOE430B


title: Myospheres 2, chip MOE430A


title: Myospheres 1, chip MOE430A


title: Total 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E207
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207
SCGP Sample ID:				S292
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207#SAMPLE_280
Short description:			Murine bone marrow is a major source of hematopoietic stem cells. Single cell suspension extracted from the bone marrow is depleted of cells expressing lineage markers and stained for Sca-1 and cKit antigens, two of the markers defined to be expressed on most murine hematopoietic stem cells. Four way sorting for these antigens isolates 4 differently labeled populations, one of which is supposed to be enriched for hematopoietic multipotent progenitors and some for more downstream lineage committed progenitors. Gene expression profile of total population of bone marrow cells will be used to compare with that of the four sorted poulations.
RNA concentration:			130-390 ng/ul
Num cells for RNA prep:			1-5 x 10^6
Sample volume:				3 ul

treatment_protocol: Assays to confirm viability:		Trypan Blue dye exclusion to check the viability


title: 10 T1/2 4, chip MOE430A


title: Myospheres 3, chip MOE430A


title: Total 1, chip MOE430B


title: Myospheres 1, chip MOE430B


title: Total 2, chip MOE430B


title: Myospheres 3, chip MOE430B


title: Lin-(1), chip MOE430B


title: 10 T1/2 1, chip MOE430A


title: Lin-Sca-1+cKit-, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E207
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207
SCGP Sample ID:				S291
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207#SAMPLE_279
Short description:			The gene expression profile of this population will be compared with that of the other three sorted populations of murine bone marrow cells.
Estimated purity:				98%
RNA concentration:			10 ng/ul
Num cells for RNA prep:			~160,000
Sample volume:				3 ul

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Flow cytometry sorting
Method for estimating purity:		Flow cytometry analysis

treatment_protocol: Assays to confirm viability:		Colony forming cell (CFC) and cobblestone area forming cell (CAFC) assays and trypan blue dye exclusion to estimate the viability

tag: Defining markers:				Sca-1 and cKit


title: Lin-Sca-1-cKit+ 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E207
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207
SCGP Sample ID:				S295
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207#SAMPLE_263
Short description:			This population of hematopoietic cells is believed to be enriched for more downstream hematopoietic progenitors. The gene expression profile is going to be compared to that of the more primitive progenitors which may indicate the genes that are upregulated or downregulated during the differentiation process.
Estimated purity:				> 90%
RNA concentration:			11-315 ng/ul
Num cells for RNA prep:			5 -6 x 10^5
Sample volume:				3 ul

treatment_protocol: Assays to confirm viability:		Colony forming cell (CFC) and cobblestone area forming cell (CAFC) assays as well as trypan blue dye exclusion to estimate the viability


title: Lin-Sca-1-cKit- 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E207
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207
SCGP Sample ID:				S296
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207#SAMPLE_264
Short description:			It is suggested that this population of bone marrow cells is more enriched for downstream hematopoietic progenitors specifically towards the lymphoid lineage. The gene expression profile of this population is going to be compared with that of the more primitive hematopoietic progenitors in an attempt to indicate the upregulated and downregulated genes during the hematopoietic differentiation process.
Estimated purity:				> 90%
RNA concentration:			12-226 ng/ul
Num cells for RNA prep:			5 -6 x 10^5
Sample volume:				3 ul


title: Lin-Sca-1-cKit- 2, chip MOE430B


title: Total 3, chip MOE430A


title: Lin-(2), chip MOE430A


title: Lin-(3), chip MOE430A


title: Lin-Sca-1-cKit- 1, chip MOE430B


title: Lin-Sca-1-cKit+ 2, chip MOE430B


title: 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E207
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207
SCGP Sample ID:				S294
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207#SAMPLE_262
Short description:			This population of murine bone marrow cells is believed to be highly enriched for hematopoietic progenitor and stem cell activity. Analysis of the gene expression profile for this population might lead to identification of unique markers that are exclusively expressed by the hematopoietic stem cells.
Estimated purity:				> 90%
RNA concentration:			10 ng/ul
Num cells for RNA prep:			7.6-29 x 10^4
Sample volume:				3 ul

treatment_protocol: Assays to confirm viability:		Colony forming cell (CFC) and cobblestone area forming cell (CAFC) assays as well as Trypan Blue dye exclusion to estimate the viability


title: Lin-(1), chip MOE430A


title: Lin-Sca-1-cKit+ 1, chip MOE430B


title: Total 2, chip MOE430A


title: 2, chip MOE430B


title: Total 1, chip MOE430A


title: 1, chip MOE430B


title: Lin-Sca-1-cKit+ 3, chip MOE430A


title: Lin-Sca-1-cKit+ 1, chip MOE430A


title: Lin-Sca-1-cKit- 3, chip MOE430A


title: 2, chip MOE430A


title: Lin-Sca-1-cKit- 2, chip MOE430A


title: Lin-Sca-1-cKit+ 2, chip MOE430A


title: Lin-Sca-1+cKit-, chip MOE430A


title: CFC2, chip MOE430B


title: 2C5/7-myogenin(2), chip MG_U74Av2

status: Public on Sep 07 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E223
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=223
SCGP Sample ID:				S364
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=223#SAMPLE_330
Short description:			myogenin+ 2C5/7 dblKO:  Gene expression changes induced by MyoD or Myf5 were examined in a double-knockout fibroblast cell line lacking endogenous functional myoD or myf5 genes.  Use of this cell line precluded the possibility of auto- or cross-activation of endogenous myoD or myf5.  Myogenin or hrGFP were expressed in parallel samples as controls.  Following infection with retrovirus - expressing the relevant myogenic regulatory factor (MRF) from the viral LTR promoter and hrGFP through an IRES element in the same mRNA transcript - GFP+ cells were sorted by FACS and harvested for total RNA.
Estimated purity:				GFP+~75-85%
RNA concentration:			>= 2.0ug/ul
Sample volume:				> 10ul

source_name: embryonic fibroblast-derived cell line, embryonic

growth_protocol:
Growth medium:				DMEM
Media supplements:			10% FCS; penicillin/streptomycin
Culture conditions:			adherent; tissue culture plastic

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			FACS, using GFP fluorescence (non-clonal), !Sample_extract_protocol = Contaminating cell type:			none
Method for estimating purity:		FACS, !Sample_description = This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  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.

tag: Strain:					myoD-/-; myf5-/-

tag: Karyotype:				Normal, diploid

tag: Defining markers:				myogenin expression; hrGFP expression  myoD-/-; myf5-/-; neomycin-resistant;


title: MyoD (5), chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E223
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=223
SCGP Sample ID:				S361
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=223#SAMPLE_327
Short description:			MyoD+ 2C5/7 dblKO:   Gene expression changes induced by MyoD or Myf5 were examined in a double-knockout fibroblast cell line lacking endogenous functional myoD or myf5 genes.  Use of this cell line precluded the possibility of auto- or cross-activation of endogenous myoD or myf5.  Myogenin or hrGFP were expressed in parallel samples as controls.  Following infection with retrovirus - expressing the relevant myogenic regulatory factor (MRF) from the viral LTR promoter and hrGFP through an IRES element in the same mRNA transcript - GFP+ cells were sorted by FACS and harvested for total RNA.
Estimated purity:				GFP+~75-85%
RNA concentration:			>= 2.0ug/ul
Sample volume:				> 10ul

tag: Defining markers:				MyoD expression; hrGFP expression  myoD-/-; myf5-/-; neomycin-resistant;


title: 1, chip MOE430A

tag: Gender:					Male


title: hrGFP (3), chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E223
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=223
SCGP Sample ID:				S363
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=223#SAMPLE_329
Short description:			hrGFP+ 2C5/7 dblKO:  Gene expression changes induced by MyoD or Myf5 were examined in a double-knockout fibroblast cell line lacking endogenous functional myoD or myf5 genes.  Use of this cell line precluded the possibility of auto- or cross-activation of endogenous myoD or myf5.  Myogenin or hrGFP were expressed in parallel samples as controls.  Following infection with retrovirus - expressing the relevant myogenic regulatory factor (MRF) from the viral LTR promoter and hrGFP through an IRES element in the same mRNA transcript - GFP+ cells were sorted by FACS and harvested for total RNA.
Estimated purity:				GFP+~75-85%
RNA concentration:			>= 2.0ug/ul
Sample volume:				> 10ul

tag: Defining markers:				hrGFP expression; hrGFP expression  myoD-/-; myf5-/-; neomycin-resistant;


title: hrGFP (4), chip MG_U74Av2


title: 2C5/7-myogenin(3), chip MG_U74Av2


title: hrGFP (5), chip MG_U74Av2


title: Myf5 (4), chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E223
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=223
SCGP Sample ID:				S362
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=223#SAMPLE_328
Short description:			Myf5+ 2C5/7 dblKO:  Gene expression changes induced by MyoD or Myf5 were examined in a double-knockout fibroblast cell line lacking endogenous functional myoD or myf5 genes.  Use of this cell line precluded the possibility of auto- or cross-activation of endogenous myoD or myf5.  Myogenin or hrGFP were expressed in parallel samples as controls.  Following infection with retrovirus - expressing the relevant myogenic regulatory factor (MRF) from the viral LTR promoter and hrGFP through an IRES element in the same mRNA transcript - GFP+ cells were sorted by FACS and harvested for total RNA.
Estimated purity:				GFP+~75-85%
RNA concentration:			>= 2.0ug/ul
Sample volume:				> 10ul

tag: Defining markers:				Myf5 expression; hrGFP expression  myoD-/-; myf5-/-; neomycin-resistant;


title: Myf5 (5), chip MG_U74Av2


title: MyoD (3), chip MG_U74Av2


title: MyoD (4), chip MG_U74Av2


title: P53 -/- B, chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E59
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59
SCGP Sample ID:				S80
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59#SAMPLE_61
Short description:			p53 -/- A-C: Muscle satellite cells are a self-renewing pool of stem cells that give rise to daughter myogenic precursor cells in adult skeletal muscle.  Published and preliminary data indicated that MyoD and p53 genes are involved in satellite cell differentiation.  We would like to know what downstream genes of both transcription factors are affected in satellite cell-derived myoblasts (MyoD-/-, p53 -/-).
Estimated purity:				> 98%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Growing myoblasts
Sample volume:				10 ul

source_name: Myoblasts, Skeletal muscle

growth_protocol:
Growth medium:				HAM F/O
Media supplements:			20% FCS, 4ng/ml bFGF
Culture conditions:			Collagen-coated plates

extract_protocol:
RNA prep method:				Trizol x2
Cell purification method:			Preplating method and serial passage
Method for estimating purity:		Myf5, c-met expressions

treatment_protocol: Assays to confirm viability:		Immunohistochemistry with muscle specific antibodies

tag: Strain:					Balb/c, MyoD -/-, p53 -/-

tag: Defining markers:				Myf5, MyoD


title: P53 -/- C, chip MG_U74Av2


title: Myo D -/-  C, chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E59
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59
SCGP Sample ID:				S79
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59#SAMPLE_60
Short description:			MyoD -/- A-C: Muscle satellite cells are a self-renewing pool of stem cells that give rise to daughter myogenic precursor cells in adult skeletal muscle.  Published and preliminary data indicated that MyoD and p53 genes are involved in satellite cell differentiation.  We would like to know what downstream genes of both transcription factors are affected in satellite cell-derived myoblasts (MyoD-/-, p53 -/-).
Estimated purity:				> 98%
RNA concentration:			2.5 ug/ul
Sample volume:				10 ul

extract_protocol:
RNA prep method:				Trizol
Cell purification method:			Preplating method and serial passage
Method for estimating purity:		Myf5, c-met expressions

tag: Defining markers:				Myf5, p53


title: Myo D -/-  B, chip MG_U74Av2


title: Myo D -/-  A, chip MG_U74Av2


title: P53 -/- A, chip MG_U74Av2


title: Myoblast C, chip MG_U74Av2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E59
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59
SCGP Sample ID:				S78
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59#SAMPLE_59
Short description:			Wild type myoblast A-C: Muscle satellite cells are a self-renewing pool of stem cells that give rise to daughter myogenic precursor cells in adult skeletal muscle.  Published and preliminary data indicated that MyoD and p53 genes are involved in satellite cell differentiation.  We would like to know what downstream genes of both transcription factors are affected in satellite cell-derived myoblasts (MyoD-/-, p53 -/-).
Estimated purity:				> 98%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Growing myoblasts
Sample volume:				10 ul

growth_protocol:
Growth medium:				HAM F/O
Media supplements:			20% fetal calf serum, 4ng/ml bFGF
Culture conditions:			Collagen-coated plates

extract_protocol:
RNA prep method:				TriZol
Cell purification method:			Preplating method and serial passage
Method for estimating purity:		Desmin, Myf5, MyoD expressions

tag: Defining markers:				MyoD, Myf5, p53


title: Myoblast B, chip MG_U74Av2


title: 3, chip MOE430A


title: 2C5/7-myogenin(6), chip MG_U74Av2


title: Myf5 (3), chip MG_U74Av2


title: CFC3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Connie Eaves (ceaves@bccrc.ca; ) for analysis.
Stembase Experiment ID:			E232
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232
SCGP Sample ID:				S311
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=232#SAMPLE_339
Short description:			The sample is RNA derived from highly purified mouse mammary colony forming cells (CFC). These cells were derived from freshly dissociated mouse mammary tissue and were analyzed for CFC content by in vitro colony arrays. The relevance to the stem cell project is that we have also  purified a mammary cell highly enriched for mammary stem cell. A comparison of mouse mammary progenitor (CFC) and stem cell would be very insightful and useful in identifying stem cell specific genes.
Estimated purity:				1 CFC in every 10 sorted cells
RNA concentration:			146
Num cells for RNA prep:			3000-4000 ( Biological Triplicates)
Sample volume:				~20 ul

tag: Strain:					FVB

tag: Gender:					Female

tag: Defining markers:				stromal lineage-, CD49f+, CD24++


title: Myo D -/-  A, chip MG_U74Bv2


title: P53 -/- B, chip MG_U74Cv2


title: Myo D -/-  C, chip MG_U74Bv2


title: P53 -/- C, chip MG_U74Cv2


title: Myoblast C, chip MG_U74Bv2


title: P53 -/- A, chip MG_U74Bv2


title: Myo D -/-  B, chip MG_U74Bv2


title: P53 -/- A, chip MG_U74Cv2


title: Myoblast B, chip MG_U74Bv2


title: Myoblast A, chip MG_U74Bv2


title: Myo D -/-  C, chip MG_U74Cv2


title: Myo D -/-  A, chip MG_U74Cv2


title: Myo D -/-  B, chip MG_U74Cv2


title: Myoblast C, chip MG_U74Cv2


title: Myotube (D3), chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E103
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=103
SCGP Sample ID:				S49
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=103#SAMPLE_274
Short description:			Myotube (D1-D3)

source_name: Myoblast, Muscle

growth_protocol: Culture conditions:			Cultured in the presence of 2.5% horse serum.

tag: Strain:


title: Grow (G3), chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E103
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=103
SCGP Sample ID:				S48
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=103#SAMPLE_103
Short description:			Myoblast (1-2) G(1-2)


title: Myoblast A, chip MG_U74Cv2


title: Myotube (D1), chip HG-U133A


title: Myotube (D2), chip HG-U133A


title: Myoblast (2) G2, chip HG-U133A


title: OGCsort#7 +/-, chip MOE430A

status: Public on Sep 01 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S235
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_277
Short description:			Sorted sub-populations of mouse bone marrow.    Triplicates:    OGCsort#1 +/-  OGCsort#7 +/-  OGCsort#9 +/-
Estimated purity:				90%

source_name: primary, bone marrow

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Cell sorting
Method for estimating purity:		Flow cytometer

tag: Strain:					C57Bl/6

tag: Karyotype:				Diploid

tag: Defining markers:				CD45+  Sca1-


title: OGCsort#9 +/-, chip MOE430A


title: OGCsort#6 +/+, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S234
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_276
Short description:			Sorted sub-populations of mouse bone marrow.   Triplicates:  OGCsort#1 +/+  OGCsort#5 +/+  OGCsort#6 +/+
Estimated purity:				90%

tag: Defining markers:				CD45+  Sca1+


title: OGCsort#1 +/-, chip MOE430A


title: OGCsort#8 -/-, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S233
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_191
Short description:			Sorted sub-populations of mouse bone marrow.   Triplicates: OGCsort#4 -/- OGCsort#5 -/- OGCsort#8 -/-
Estimated purity:				90%

tag: Defining markers:				CD45- Sca1-


title: Myoblast (1) G1, chip HG-U133A


title: OGCsort#5 +/+, chip MOE430A


title: OGCsort#1 +/+, chip MOE430A


title: CPGSE#6, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S147
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_109
Short description:			Mouse bone marrow stained with CD45-APC & Scal-PE, sorted on Moflo for +/+ cells
Analysis requested:			microarray
Estimated purity:				95-98%
RNA concentration:			50ng/ul
Num cells for RNA prep:			9.4 X 10^5
Sample volume:				10ul

source_name: haematopoeitic stem cells, bone marrow

extract_protocol:
RNA prep method:				Qiagen
Cell purification method:			Moflo cell sorter
Method for estimating purity:		cell sorter reading

tag: Strain:					C57BL/6

tag: Defining markers:				CD45+ScaI+


title: OGCsort#5 -/-, chip MOE430A


title: OGCsort#4 -/-, chip MOE430A


title: DR4-3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E140
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140
SCGP Sample ID:				S180
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140#SAMPLE_140
Short description:			This sample, investigated in triplicate, is a control for the J1, R1 and V6.5 ES samples.  The DR4 cell type acts as a feeder cell for stem cells and as such is a small contaminant of the embryonic stem cell growth environment.
RNA concentration:			3.0 ug/ul
Num cells for RNA prep:			3x10e6
Sample volume:				> 20 ul

source_name: Embryonic fibroblasts, Embryos (day15)

growth_protocol:
Growth medium:				D-MEM
Media supplements:			15% Hyclone FBS (heat inactivated), Glutamax, sodium pyruvate, non-essential amino acids, Penicillin/Streptomycin, beta-mercaptoethanol, LIF
Culture conditions:			Gelatin (0.1%), 37 C, 5% CO2

tag: Strain:					129/SV x OlaHsd x Balb/C x C57BL/6


title: CPGSC#42, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S181
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_141
Short description:			4 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.8 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul

source_name: V6.5 (P18), Embryonic

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, beta-mercaptoethanol
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Cultured
Contaminating cell type:			none

tag: Strain:					129SV x C57Bl/6


title: DR4-1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E140
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140
SCGP Sample ID:				S180
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140#SAMPLE_140
Short description:			This sample, investigated in triplicate, is a control for the J1, R1 and V6.5 ES samples.  The DR4 cell type acts as a feeder cell for stem cells and as such is a small contaminant of the embryonic stem cell growth environment.
RNA concentration:			2.4 ug/ul
Num cells for RNA prep:			12x10e6
Sample volume:				13 ul


title: V6.5 mEB 9d-2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S241
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_202
Short description:			9 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  Time course: 0h, 6h, 12h, 18h, 24h, 36h, 48h, 4 days, 7days, 9 days and 15 days. All samples in triplicate. The cells are differentiating EBs from murine Embryonic Stem Cells, Mouse strain 129 crossed with C67BL/6 isolate V6.5 (P18), obtained from Dr. Josee Coulombe in Dr. M. Rudnicki's lab.
Estimated purity:				100%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 ul


title: CPGSC#41, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S181
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_141
Short description:			4 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: CPGSC#43, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S181
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_141
Short description:			4 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.2 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: DR4-2, chip MOE430A


title: V6.5 mEB 9d-3, chip MOE430A


title: CPGSC#46, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S174
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_134
Short description:			7 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.1 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: V6.5 mEB 9d-1, chip MOE430A


title: Lin-Sca-1-cKit- 1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E207
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207
SCGP Sample ID:				S296
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=207#SAMPLE_264
Short description:			It is suggested that this population of bone marrow cells is more enriched for downstream hematopoietic progenitors specifically towards the lymphoid lineage. The gene expression profile of this population is going to be compared with that of the more primitive hematopoietic progenitors in an attempt to indicate the upregulated and downregulated genes during the hematopoietic differentiation process.
Estimated purity:				> 90%
RNA concentration:			12-226 ng/ul
Num cells for RNA prep:			5 -6 x 10^5
Sample volume:				3 ul

tag: Gender:					Male

tag: Defining markers:				Sca-1 and cKit


title: CPGSE#4, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S147
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_109
Short description:			Mouse bone marrow stained with CD45-APC & Scal-PE, sorted on Moflo for +/+ cells
Analysis requested:			microarray
Estimated purity:				95-98%
RNA concentration:			50ng/ul
Num cells for RNA prep:			6.9 X 10^5
Sample volume:				10ul


title: CPGSC#44, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S174
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_134
Short description:			7 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				90 ul


title: Myoblast B, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E59
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59
SCGP Sample ID:				S78
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59#SAMPLE_59
Short description:			Wild type myoblast A-C: Muscle satellite cells are a self-renewing pool of stem cells that give rise to daughter myogenic precursor cells in adult skeletal muscle.  Published and preliminary data indicated that MyoD and p53 genes are involved in satellite cell differentiation.  We would like to know what downstream genes of both transcription factors are affected in satellite cell-derived myoblasts (MyoD-/-, p53 -/-).
Estimated purity:				> 98%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Growing myoblasts
Sample volume:				10 ul

tag: Strain:					Balb/c, MyoD -/-, p53 -/-


title: CPGSC#45, chip MOE430A


title: CPGSC#39, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S159
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_119
Short description:			48 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.2 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#36, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S158
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_118
Short description:			36 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.9 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#37, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S158
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_118
Short description:			36 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			4.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#40, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S159
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_119
Short description:			48 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.95 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#32, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S157
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_117
Short description:			24 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#35, chip MOE430A


title: CPGSC#38, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). 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:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S159
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_119
Short description:			48 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			4.1 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul