title: Day 4-1, chip HG-U133B

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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S170
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_130
Short description:			These samples, cord blood derived lineage negative hematopoietic cells, were collected following 4 days of culture.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			1.3x10e6
Sample volume:				3.0 ul


title: M-O7e MP3, chip HG-U133B

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. 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:				S52
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37#SAMPLE_38
Short description:			Total RNA from M-O7e, a megakaryoblastic cell line, transduced with retroviral vector alone (MIEV).
Estimated purity:				~ 98%
RNA concentration:			3.2 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				6.5 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: 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 MP2, chip HG-U133B


title: M-O7e MP1, chip HG-U133B


title: I-6/SSEA- 2, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E208
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=208
SCGP Sample ID:				S265
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=208#SAMPLE_283
Short description:			Human ES cell line I-6 was cultured in standard conditions to maintain an undifferentiated, self renewing phenotype.  The cells were sorted based upon their expression of SSEA4, which is a marker of  the undifferentiated, self renewing phenotype.
Estimated purity:				above 99.5%
RNA concentration:			220ng/ul
Num cells for RNA prep:			1e6 cells/sample
Sample volume:				10ul

source_name: I-6 ES,

growth_protocol:
Growth medium:				KO-DMEM
Media supplements:			KO serum replacement, bFGF
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			sorted by FACS

tag: Gender:					Male

tag: Defining markers:				SSEA-


title: Human retinal sphere RNA-1, 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. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis.
Stembase Experiment ID:			E189
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189
SCGP Sample ID:				S231
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_189
Short description:			RNA isolated from first passage retinal sphere cells.
Estimated purity:				> 90%
RNA concentration:			> 30.0 ng
Num cells for RNA prep:			~160,000
Sample volume:				5.0 ul

source_name: Retinal sphere cells, Ciliary margin of eye

growth_protocol:
Growth medium:				SFM
Media supplements:			FGF, EGF
Culture conditions:			37 C,5% CO2

extract_protocol:
RNA prep method:				TRIzol followed by RNeasy
Cell purification method:			FACS
Method for estimating purity:		FACS

treatment_protocol: Assays to confirm viability:		Sphere assay


title: Osteo d6VD3-3, 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. 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:				S188
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_236
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:			100 ng/ul
Num cells for RNA prep:			3 X 10^6
Sample volume:				12ul - 6ul for BA and 6 ul for exp

organism: Mus musculus

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: Karyotype:				normal

tag: Defining markers:				n/a


title: Osteo d6VD3-2, chip MOE430B


title: M-O7e SP3, chip HG-U133B

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


title: MPB3, 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:			E2
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=2
SCGP Sample ID:				S3
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=2#SAMPLE_2
Short description:			Human mobilized peripheral blood, amplified RNA, biotin labeled, fragmented.
Estimated purity:				~ 100%
RNA concentration:			500 ng/ul
Num cells for RNA prep:			200 000
Sample volume:				30 ul

source_name: Hematopoietic stem cells, Blood

growth_protocol: Growth medium:				None

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			1) Ficoll separation to isolate mononuclear cells 2) Lineage depleted cocktail to enrich progenitors (Lin- population) 3) CD34 and CD38 fluorochromes to enrich hematopoietic stem cells using vantage

tag: Defining markers:				Lin-, CD34+, CD38-


title: Osteo Day 5-3, 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. 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:				S186
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_235
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:			12ul - 6ul for BA and 6 ul for exp
Sample volume:				3 X 10^6


title: MPB1, chip HG-U133A


title: Mouse retinal sphere RNA-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. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis.
Stembase Experiment ID:			E189
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189
SCGP Sample ID:				S232
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_190
Short description:			RNA isolated from first passage retinal sphere cells.
Estimated purity:				> 90%
RNA concentration:			> 0.15ug/ul
Num cells for RNA prep:			~1.7x10e6
Sample volume:				10.0 ul

extract_protocol:
RNA prep method:				Trizol followed by RNeasy
Cell purification method:			FACS
Method for estimating purity:		FACS

treatment_protocol: Assays to confirm viability:		Sphere assy

tag: Strain:					CD1


title: MPB2, chip HG-U133A


title: Osteo Day 5-1, chip MOE430B


title: Osteo Day 4-2, 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. 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:				S185
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_234
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


title: Osteo Day 4-1, chip MOE430B


title: Osteo Day 4-3, chip MOE430B


title: Mouse primary retinal sphere, 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. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis.
Stembase Experiment ID:			E189
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189
SCGP Sample ID:				S240
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_198
Short description:			RNA isolated from primary retinal sphere cells.
Estimated purity:				> 90%
RNA concentration:			> 0.7 ug/ul
Num cells for RNA prep:			~600,000
Sample volume:				5.0 ul


title: Mouse retinal sphere RNA-4, chip MOE430B


title: Osteo Day 5-2, chip MOE430B


title: Osteo d6VD3-1, chip MOE430B


title: M-O7e SP2, chip HG-U133B


title: I-6/SSEA- 1, chip HG-U133A


title: 9887-6 p107 -/-, 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. Ruth Slack (rslack@uottawa.ca; ) for analysis.
Stembase Experiment ID:			E206
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206
SCGP Sample ID:				S272
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206#SAMPLE_261
Short description:			The ganglionic eminence was dissected and neurospheres were cultured from the brain of E13.5 embroys. RNA was isolated from neurospheres cultured from p107-/- embryos and their wildtype littermates. P107 knockout mice have previously been shown to have an increased number of stem cells and enhanced stem cell self renewal. With the microarray experiment we are hoping to discover the genes involved in stem cell number and self renewal along with p107
Analysis requested:			compare against wildtype littermates
Estimated purity:				minimal non-neural contamination
RNA concentration:			2 ug/uL
Num cells for RNA prep:			15 x 10^6
Sample volume:				10 uL

source_name: neurospheres, brain germinal zone

growth_protocol:
Growth medium:				stem cell medium
Media supplements:			bFGF
Culture conditions:			Serum Free Stem Cell Medium, 37C, 5%CO2

extract_protocol:
RNA prep method:				RNeasy, EtOH pptn.
Amplification method:			Replication in growth factor supplement
Cell purification method:			Specialized growth conditions to select cells
Contaminating cell type:			progenitor cells

treatment_protocol: Assays to confirm viability:		Nestin Positive Neurospheres, Cell culture

tag: Strain:					SV129

tag: Defining markers:				Nestin Expression


title: 9447-4 -/-, chip MOE430B


title: PG13 MP3, 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. 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:				S56
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37#SAMPLE_42
Short description:			Total RNA from PG13 transduced with retroviral vector (MIEV) alone.
Estimated purity:				~ 98%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				9.0 ul

source_name: PG13 cell line, Fibroblast


title: suspension, 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. Luc Sabourin (lsab@uottawa.ca; 451 Smyth Road) for analysis.
Stembase Experiment ID:			E26
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=26
SCGP Sample ID:				S28
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=26#SAMPLE_26
Short description:			MEF 3T3 grown in suspension to analyze genes induced by fibronectin stimulation
RNA concentration:			2.5 ug/ul

source_name: MEF 3T3, fibroblast

growth_protocol:
Media supplements:			Serum Free, DMEM
Culture conditions:			Suspension Culture

extract_protocol:
RNA prep method:				RNeasy
Method for estimating purity:		OD and denaturing gel

treatment_protocol: Assays to confirm viability:		exponential growth or substrate adhesion assay

tag: Strain:					C57/Bl6


title: fibronectin, 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. Luc Sabourin (lsab@uottawa.ca; 451 Smyth Road) for analysis.
Stembase Experiment ID:			E26
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=26
SCGP Sample ID:				S29
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=26#SAMPLE_257
Short description:			MEF 3T3 cells plated on fibronectin and allowed to culture for 30 minutes.  This was done to assess the changes of gene expression in the MAPK signalling pathway.
RNA concentration:			2.5 ug/ul

growth_protocol:
Media supplements:			Serum Free, DMEM
Culture conditions:			10 ug/ml Fibronectin


title: C2C12 (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. Lynn Megeney (lmegeney@ohri.ca; 501 Smyth Road, Room 4E102) for analysis.
Stembase Experiment ID:			E1
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=1
SCGP Sample ID:				S2
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=1#SAMPLE_1
Short description:			RNA extracted from C2C12 mouse skeletal muscle cells following 5 days of culture in differentiation medium.
Estimated purity:				100%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			2x10e7
Sample volume:				10.0 ul

source_name: C2C12, Skeletal muscle

growth_protocol:
Growth medium:				DMEM
Media supplements:			2% horse serum, 1X penicillin/streptomycin
Culture conditions:			37C

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Established cell line
Method for estimating purity:		O.D., formaldehyde gel

tag: Strain:					C3H

tag: Defining markers:				Myosin heavy chain, myogenin


title: C2C12 (3), chip MG_U74Av2


title: D4, 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. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E199
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199
SCGP Sample ID:				S256
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199#SAMPLE_207
Short description:			Differentiated mammosphere RNA. Samples labelled D1, D2 and D4 contain RNA extracted from the cells of mouse mammospheres induced to differentiate over a 6-day period.
Analysis requested:			Gene Chip Array: MOE 430A, B
Estimated purity:				50% myoepithelial, 50% luminal
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~ 8.8x10e6
Sample volume:				5.0 ul

source_name: Differentiated mammosphere cells, Mammary gland

growth_protocol:
Growth medium:				High glucose DMEM
Media supplements:			5% fetal bovine serum
Culture conditions:			37C, 5% CO2; On collagen coated dishes

extract_protocol:
RNA prep method:				TRIzol
Cell purification method:			Mammospheres cultures induced to differentiate
Contaminating cell type:			None known
Method for estimating purity:		Use of molecular markers

treatment_protocol: Assays to confirm viability:		Undifferentiated antecedants recapitulate mammary gland development.

tag: Strain:					FVB

tag: Gender:					Female

tag: Defining markers:				AlphaSMA-myoepithelial cells, CK18-luminal epithelial cells


title: 9859-11, 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. Ruth Slack (rslack@uottawa.ca; ) for analysis.
Stembase Experiment ID:			E206
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206
SCGP Sample ID:				S271
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206#SAMPLE_260
Short description:			The ganglionic eminence was dissected and neurospheres were cultured from the brain of E13.5 embroys. RNA was isolated from neurospheres cultured from p107-/- embryos and their wildtype littermates. P107 knockout mice have previously been shown to have an increased number of stem cells and enhanced stem cell self renewal. With the microarray experiment we are hoping to discover the genes involved in stem cell number and self renewal along with p107
Analysis requested:			Compare against p107 knockout Littermates
Estimated purity:				minimal non-neural contamination
RNA concentration:			2 ug/uL
Num cells for RNA prep:			15 x 10^6
Sample volume:				10 uL


title: M-O7e SP1, chip HG-U133B


title: 9859-12 p107 -/-, chip MOE430B


title: 9619-3 p107 -/-, chip MOE430B


title: C2C12 (1), chip MG_U74Av2


title: 9887-4, chip MOE430B


title: PG13 MP1, chip MG_U74Av2


title: D2, chip MOE430B


title: M6, 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. 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:				S237
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=194#SAMPLE_278
Short description:			Mature mast cells cultured for 57 to 110 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:			1.0 ug/ul
Num cells for RNA prep:			1x10e7
Sample volume:				8.0-10.0 ul

source_name: Bone marrow mature mast cells, 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 57 to 110 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:					M2 and M4

value: male; M6:female

tag: Karyotype:				Wild-type

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


title: U2, 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. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E199
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199
SCGP Sample ID:				S255
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199#SAMPLE_206
Short description:			Undifferentiated  mouse mammosphere RNA.  Mammospheres are believed to be comprised of stem/progenitor cells.
Estimated purity:				90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~ 1.0x10e7
Sample volume:				5.0 ul

source_name: Mammosphere passage 3, Mammary gland

growth_protocol:
Growth medium:				3:1 DMEM: F12
Media supplements:			B-27 supplement, basic fibroblast growth factor, epidermal growth factor, heparin
Culture conditions:			37C, 5% CO2

extract_protocol:
RNA prep method:				TRIzol
Contaminating cell type:			10% myoepithelial cells
Method for estimating purity:		Analysis of cellular markers

treatment_protocol: Assays to confirm viability:		Transplant into cleared fat pad of mice: mammary gland development recapitulated in recipient.

tag: Defining markers:				Sca-1, Thy-1, Ecadherin


title: 9619-6, chip MOE430B


title: M2, 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. 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:				S237
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=194#SAMPLE_278
Short description:			Mature mast cells cultured for 57 to 110 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


title: U4, chip MOE430B


title: PG13 MP2, chip MG_U74Av2

tag: Defining markers:				GFP


title: M4, 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. 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:				S237
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=194#SAMPLE_278
Short description:			Mature mast cells cultured for 57 to 110 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:				3.0 ul


title: U1, chip MOE430B


title: PG13 SP3, 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. 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:				S55
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37#SAMPLE_41
Short description:			Total RNA from PG13 transduced with Smad7 recombinant retroviral vector (MIEV-Smad7).
Estimated purity:				~ 98%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				9.0 ul


title: M5, 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. 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:			1.5 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

tag: Gender:					M1

value: female; M3 and M5:male


title: M1, 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. 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


title: 3D4, 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. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID:			E30
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID:				S34
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_32
Short description:			Chondroblasts harvested at 3 days.
Estimated purity:				90-95%
Num cells for RNA prep:			6x10e6

source_name: Mesenchymal cells, Limb bud

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Cells were isolated from the subridge region of the developing limb
Contaminating cell type:			Fibroblasts
Method for estimating purity:		Morphology of cultures 3 days post harvest

treatment_protocol: Assays to confirm viability:		Cells were allowed to differentiate <i>in vitro</i> into chondrocytes

tag: Strain:					CD-1

tag: Defining markers:				Sox9, type II collagen


title: 6473A, 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. 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

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: 6999B, 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. 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


title: PG13 SP1, chip MG_U74Av2


title: 3D3, chip MG_U74Av2


title: 6473B, 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. 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:			3.1x10e6
Sample volume:				10.0 ul


title: PG13 SP2, chip MG_U74Av2


title: PP6 #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. 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

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:			preplatings
Contaminating cell type:			muscles cells
Method for estimating purity:		none

treatment_protocol: Assays to confirm viability:		erythrosin B exclusion

tag: Strain:					C57BL/10J

tag: Karyotype:				BL.C5710J

tag: Defining markers:				none


title: 6473C, 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. 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


title: 1D4, 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. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID:			E30
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID:				S33
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_31
Short description:			Chondroprogenitors harvested at 1 day.
Estimated purity:				90-95%
Num cells for RNA prep:			6x10e6


title: JEACFU-F-II, chip RAE230B

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. Jane Aubin (jane.aubin@utoronto.ca; 6230 Medical Building; 1 King's College Circle) for analysis.
Stembase Experiment ID:			E179
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179
SCGP Sample ID:				S223
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179#SAMPLE_181
Short description:			RNA was isolated from colonies expressing neither the osteocalcin nor the adipsin markers.
Num cells for RNA prep:			100-300 (single colonies)
Sample volume:				17 ul (first strand cDNA)

organism: Rattus norvegicus

source_name: Primary culture; single cell colonies, Calvaria

growth_protocol:
Growth medium:				a-MEM
Media supplements:			Ascorbic Acid, BGP, Dex, fetal bovine serum
Culture conditions:			37C, 5% CO2, for 4 weeks

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			Affymetrix small sample target labelling (V. I)
Cell purification method:			Single cell sorting by flow cytometry

treatment_protocol: Assays to confirm viability:		Colony type was categorized by osteoblast and adipocyte specific gene expression

tag: Strain:					Wistar

tag: Gender:					Both male and female fetuses

tag: Karyotype:				Diploid

tag: Defining markers:				Gene expression of osteocalcin, adipcin, L32


title: PP6 #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. 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

tag: Gender:					Female


title: JEACFU-F-III, chip RAE230B


title: MACS #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. 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

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

tag: Defining markers:				Sca1+/CD45-


title: M3, chip MOE430B

tag: Strain:					C57Bl6

tag: Karyotype:				Wild-type


title: JEACFU-F-I, chip RAE230B


title: MACS #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. 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


title: 1D3, chip MG_U74Av2


title: 6999C, 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. 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: 3D1, chip MG_U74Av2


title: 6999A, 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. 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: JEACFU-Bi-III, chip RAE230B

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. Jane Aubin (jane.aubin@utoronto.ca; 6230 Medical Building; 1 King's College Circle) for analysis.
Stembase Experiment ID:			E179
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179
SCGP Sample ID:				S222
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179#SAMPLE_180
Short description:			RNA was isolated from colonies expressing both the osteocalcin and the adipsin markers.
Num cells for RNA prep:			100-300 (single colonies)
Sample volume:				17 ul (first strand cDNA)


title: 1D1, chip MG_U74Av2


title: OH4, 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. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID:			E30
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID:				S32
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_30
Short description:			These samples are multipotential mesenchymal cells.
Estimated purity:				90-95%
Num cells for RNA prep:			6x10e6

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Morphology of cultures 3 days post harvest
Contaminating cell type:			Fibroblasts
Method for estimating purity:		Cells were isolated from the subridge region of the developing limb


title: JEACFU-Bi-I, chip RAE230B


title: JEACFU-Bi-II, chip RAE230B


title: JEACFU-O-II, chip RAE230B

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. Jane Aubin (jane.aubin@utoronto.ca; 6230 Medical Building; 1 King's College Circle) for analysis.
Stembase Experiment ID:			E179
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179
SCGP Sample ID:				S221
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179#SAMPLE_179
Short description:			RNA was isolated from colonies expressing the osteocalcin marker.
Num cells for RNA prep:			100-300 (single colonies)
Sample volume:				17 ul (first strand cDNA)


title: Osteo30 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:				S196
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_240
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:			100 ng/ul
Num cells for RNA prep:			3 x 10^6
Sample volume:				12ul - 6ul for BA and 6 ul for exp

tag: Strain:					129 SV

tag: Gender:					Male

tag: Karyotype:				normal

tag: Defining markers:				n/a


title: JEACFU-O-III, chip RAE230B


title: OH3, chip MG_U74Av2

tag: Strain:					CD-1

tag: Defining markers:				Sox9, type II collagen


title: JEACFU-O-I, chip RAE230B


title: R1 gelatin, 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. Luc Sabourin (lsab@uottawa.ca; 451 Smyth Road) for analysis.
Stembase Experiment ID:			E22
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=22
SCGP Sample ID:				S26
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=22#SAMPLE_232
Short description:			R1 ES cells grown in standard conditions for undifferentiated proliferation.
RNA concentration:			2.5 ug/ul

source_name: R1 ES, Inner Cell Mass

growth_protocol:
Growth medium:				DMEM gelatin
Media supplements:			LIF, beta-mercaptoethanol

extract_protocol: RNA prep method:				RNeasy

treatment_protocol: Assays to confirm viability:		Exponential growth or substrate adhesion assay

tag: Strain:


title: OH1, chip MG_U74Av2


title: Osteo30 VD3-2, chip MOE430A


title: NSC, 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. Luc Sabourin (lsab@uottawa.ca; 451 Smyth Road) for analysis.
Stembase Experiment ID:			E22
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=22
SCGP Sample ID:				S25
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=22#SAMPLE_23
Short description:			Samples isolated from E13.5 telencephalon neurospheres.
RNA concentration:			2.5 ug/ul

source_name: , E13.5 telencephalon

growth_protocol:
Growth medium:				DMEM0 F12
Media supplements:			FGF2

extract_protocol:
RNA prep method:				RNeasy
Contaminating cell type:			Astrocytes, glia, oligodendrocytes

tag: Defining markers:				98% Nestin+


title: Osteo25 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:				S194
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_239
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:			100 ng/ul
Num cells for RNA prep:			3 x 10^6
Sample volume:				12ul - 6ul for BA and 6 ul for exp

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


title: R1 suspension, 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. Luc Sabourin (lsab@uottawa.ca; 451 Smyth Road) for analysis.
Stembase Experiment ID:			E22
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=22
SCGP Sample ID:				S24
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=22#SAMPLE_22
Short description:			Samples from R1 ES cells grown as unattached embryoid bodies for 48 hours in the presence of LIF.
RNA concentration:			2.5 ug/ul

growth_protocol:
Growth medium:				DMEM
Media supplements:			LIF, beta-mercaptoethanol


title: Osteo30 VD3-1, chip MOE430A


title: Osteo25 VD3-2, chip MOE430A


title: R1 aggregation, chip MG_U74Av2


title: Osteo16 VD3-2, 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. 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


title: Osteo d8VD3-3, 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:				S190
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_237
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:			100 ng/ul
Num cells for RNA prep:			3 x 10^6
Sample volume:				12ul - 6ul for BA and 6 ul for exp


title: Osteo16 VD3-1, chip MOE430A


title: Osteo25 VD3-1, chip MOE430A


title: Untransformed (control 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:			E17
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=17
SCGP Sample ID:				S19
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=17#SAMPLE_17
Short description:			Untransformed marrow stromal cells from normal C57Bl/6 mice.
Estimated purity:				100%
RNA concentration:			190-274 ug/ul
Num cells for RNA prep:			4-8x10e6
Sample volume:				40 ul

source_name: Primary marrow stromal cells, Bone marrow

growth_protocol:
Growth medium:				DMEM
Media supplements:			10% fetal bovine serum, 50 U/ml penicillin, 50 ug/ml streptomycin

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Mixed population of 100% marrow stromal cells arising after more than two months in culture and 10-15 passages
Method for estimating purity:		Cell culture and flow cytometry analysis

treatment_protocol: Assays to confirm viability:		RNA samples run on gel

tag: Strain:					C57Bl/6

tag: Defining markers:				CD31-, CD34 low/-, CD45-


title: Osteo d8VD3-1, chip MOE430A

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


title: Osteo d6VD3-3, 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:				S188
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_236
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:			100 ng/ul
Num cells for RNA prep:			3 X 10^6
Sample volume:				12ul - 6ul for BA and 6 ul for exp


title: Osteo d8VD3-2, chip MOE430A


title: Osteo d6VD3-1, chip MOE430A


title: Untransformed (control 1), chip MG_U74Av2


title: Osteo d6VD3-2, chip MOE430A


title: Untransformed (control 2), chip MG_U74Av2


title: Osteo Day 5-1, 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. 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:				S186
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_235
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:			12ul - 6ul for BA and 6 ul for exp
Sample volume:				3 X 10^6


title: Osteo Day 5-2, chip MOE430A


title: GFP_Exe TS (replicate 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. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S14
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_12
Short description:			GFP-Exe Trophoblast stem cells (WT+GFP transgene)
Estimated purity:				90-95%
RNA concentration:			3.74 ug/ul
Sample volume:				15.0 ul

source_name: TS cell line, Extraembryonic ectoderm

growth_protocol:
Growth medium:				RPMI 1640, tissue culture plastic
Media supplements:			+20% Cansera FBS, FGf4 (25 ng/ml) therapin, NaPyruvate, nonessential aa, L-glutamine, B-mercaptoethanol, !Sample_extract_protocol = RNA prep method:				RNeasy

extract_protocol:
Cell purification method:			None
Contaminating cell type:			differentiated TS cells may be present
Method for estimating purity:		Visual inspection

treatment_protocol: Assays to confirm viability:		None, grown in normal stem cell conditions

tag: Strain:					ICR

tag: Defining markers:				Eomesodermin, Cdx2, 8MP4


title: Osteo Day 4-2, 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. 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:				S185
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_234
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


title: GFP_Exe TS (replicate 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. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S14
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_12
Short description:			GFP-Exe Trophoblast stem cells (WT+GFP transgene)
Estimated purity:				90-95%
RNA concentration:			3.24 ug/ul
Sample volume:				29.0 ul


title: R1ES n+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. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S13
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_11
Short description:			R1ES: Embryonic stem cells (WT)
Estimated purity:				95-99%
RNA concentration:			5.88 ug/ul
Sample volume:				40.0 ul

source_name: ES cell line, Blastocyst

growth_protocol:
Growth medium:				0.1% gelatin
Media supplements:			high glucose, +15% HyClone FBS, Lif, NaPyruvate, nonessential aa, L-glutamine, B-mercaptoethanol, !Sample_extract_protocol = RNA prep method:				RNeasy

extract_protocol:
Cell purification method:			None
Contaminating cell type:			differentiated ES cells may be present
Method for estimating purity:		Visual inspection

tag: Strain:					129/SV

tag: Defining markers:				Oct4


title: Osteo Day 5-3, chip MOE430A


title: Osteo Day 4-1, chip MOE430A


title: Mouse primary retinal sphere, 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. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis.
Stembase Experiment ID:			E189
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189
SCGP Sample ID:				S240
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_198
Short description:			RNA isolated from primary retinal sphere cells.
Estimated purity:				> 90%
RNA concentration:			> 0.7 ug/ul
Num cells for RNA prep:			~600,000
Sample volume:				5.0 ul

source_name: Retinal sphere cells, Ciliary margin of eye

growth_protocol:
Growth medium:				SFM
Media supplements:			FGF, EGF
Culture conditions:			37 C,5% CO2

extract_protocol:
RNA prep method:				Trizol followed by RNeasy
Cell purification method:			FACS
Method for estimating purity:		FACS

tag: Strain:					CD1


title: Mouse retinal sphere RNA-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. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis.
Stembase Experiment ID:			E189
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189
SCGP Sample ID:				S232
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_190
Short description:			RNA isolated from first passage retinal sphere cells.
Estimated purity:				> 90%
RNA concentration:			> 0.15ug/ul
Num cells for RNA prep:			~1.7x10e6
Sample volume:				10.0 ul


title: 9447-4 -/-, 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. Ruth Slack (rslack@uottawa.ca; ) for analysis.
Stembase Experiment ID:			E206
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206
SCGP Sample ID:				S272
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206#SAMPLE_261
Short description:			The ganglionic eminence was dissected and neurospheres were cultured from the brain of E13.5 embroys. RNA was isolated from neurospheres cultured from p107-/- embryos and their wildtype littermates. P107 knockout mice have previously been shown to have an increased number of stem cells and enhanced stem cell self renewal. With the microarray experiment we are hoping to discover the genes involved in stem cell number and self renewal along with p107
Analysis requested:			compare against wildtype littermates
Estimated purity:				minimal non-neural contamination
RNA concentration:			2 ug/uL
Num cells for RNA prep:			15 x 10^6
Sample volume:				10 uL

source_name: neurospheres, brain germinal zone

growth_protocol:
Growth medium:				stem cell medium
Media supplements:			bFGF
Culture conditions:			Serum Free Stem Cell Medium, 37C, 5%CO2

extract_protocol:
RNA prep method:				RNeasy, EtOH pptn.
Amplification method:			Replication in growth factor supplement
Cell purification method:			Specialized growth conditions to select cells
Contaminating cell type:			progenitor cells

tag: Strain:					SV129

tag: Defining markers:				Nestin Expression


title: Mouse retinal sphere RNA-3, chip MOE430A


title: Lin+-1, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S173
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_133
Short description:			These cord blood derived lineage positive hematopoietic cells were collected following 4 days of culture from cord blood derived, lineage negative, hematopoietic cells.
Estimated purity:				>99%
RNA concentration:			Low
Num cells for RNA prep:			2.0x10e5

source_name: Hematopoietic, Cord blood

growth_protocol:
Growth medium:				Stem span
Media supplements:			Thrombopoetin, Flt-3 ligand, stem cell factor
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				TRIzol
Cell purification method:			FACS
Contaminating cell type:			Lineage negative cells
Method for estimating purity:		Flow cytometry

tag: Defining markers:				Lin+


title: Osteo Day 4-3, chip MOE430A

tag: Strain:					129 SV

tag: Gender:					Male


title: D1, 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. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E199
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199
SCGP Sample ID:				S256
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199#SAMPLE_207
Short description:			Differentiated mammosphere RNA. Samples labelled D1, D2 and D4 contain RNA extracted from the cells of mouse mammospheres induced to differentiate over a 6-day period.
Analysis requested:			Gene Chip Array: MOE 430A, B
Estimated purity:				50% myoepithelial, 50% luminal
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~ 8.8x10e6
Sample volume:				5.0 ul

source_name: Differentiated mammosphere cells, Mammary gland

growth_protocol:
Growth medium:				High glucose DMEM
Media supplements:			5% fetal bovine serum
Culture conditions:			37C, 5% CO2; On collagen coated dishes

extract_protocol:
RNA prep method:				TRIzol
Cell purification method:			Mammospheres cultures induced to differentiate
Contaminating cell type:			None known
Method for estimating purity:		Use of molecular markers

tag: Strain:					FVB

tag: Gender:					Female

tag: Defining markers:				AlphaSMA-myoepithelial cells, CK18-luminal epithelial cells


title: FM-3, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S172
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_132
Short description:			Cord blood derived, lineage negative, hematopoietic cells were cultured for 4 days and then subjected to a fresh medium exchange.  The cells were then allowed to incubate for 24 hours prior to RNA extraction.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			9.2x10e5
Sample volume:				3.0 ul

extract_protocol: RNA prep method:				TRIzol

tag: Defining markers:				Lin-


title: 9887-6 p107 -/-, chip MOE430A


title: GFP_Exe TS (replicate 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. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S14
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_12
Short description:			GFP-Exe Trophoblast stem cells (WT+GFP transgene)
Estimated purity:				90-95%
RNA concentration:			3.60 ug/ul
Sample volume:				29 ul


title: RIES, 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. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S13
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_11
Short description:			R1ES: Embryonic stem cells (WT)
Estimated purity:				95-99%
RNA concentration:			3.81 ug/ul
Sample volume:				15.0 ul


title: FM-2, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S172
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_132
Short description:			Cord blood derived, lineage negative, hematopoietic cells were cultured for 4 days and then subjected to a fresh medium exchange.  The cells were then allowed to incubate for 24 hours prior to RNA extraction.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			1.0x10e6
Sample volume:				3.0 ul


title: 9859-12 p107 -/-, chip MOE430A


title: Pool 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. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S119
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_89
Short description:			RNA isolated from normal FVB mouse mammary glands.
Estimated purity:				80%
RNA concentration:			2.2 ug/ul
Sample volume:				10.0 ul

source_name: Tissue, Mammary gland

extract_protocol:
RNA prep method:				CsCl and Qiagen purification
Cell purification method:			FACS for sca-1+
Method for estimating purity:		PCR for sca-1 transcripts

treatment_protocol: Assays to confirm viability:		PCR and immunocytochemistry for sca-1


title: FM-1, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S172
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_132
Short description:			Cord blood derived, lineage negative, hematopoietic cells were cultured for 4 days and then subjected to a fresh medium exchange.  The cells were then allowed to incubate for 24 hours prior to RNA extraction.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			2.1x10e6
Sample volume:				3.0 ul


title: 9619-3 p107 -/-, chip MOE430A


title: 9887-4, 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. Ruth Slack (rslack@uottawa.ca; ) for analysis.
Stembase Experiment ID:			E206
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206
SCGP Sample ID:				S271
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=206#SAMPLE_260
Short description:			The ganglionic eminence was dissected and neurospheres were cultured from the brain of E13.5 embroys. RNA was isolated from neurospheres cultured from p107-/- embryos and their wildtype littermates. P107 knockout mice have previously been shown to have an increased number of stem cells and enhanced stem cell self renewal. With the microarray experiment we are hoping to discover the genes involved in stem cell number and self renewal along with p107
Analysis requested:			Compare against p107 knockout Littermates
Estimated purity:				minimal non-neural contamination
RNA concentration:			2 ug/uL
Num cells for RNA prep:			15 x 10^6
Sample volume:				10 uL


title: Pool 2, chip MG_U74Av2


title: CM-3, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S171
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_131
Short description:			Cord blood derived, lineage negative, hematopoietic cells were cultured for 4 days and then subjected to a mock medium exchange.  This included centrifugation of the cells and re-suspension in the same medium.  The cells were then allowed to incubate for 24 hours prior to RNA extraction.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			1.0x10e6
Sample volume:				3.0 ul


title: Pool 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. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S119
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_89
Short description:			RNA isolated from normal FVB mouse mammary glands.
Estimated purity:				80%
RNA concentration:			2.1 ug/ul
Sample volume:				10.0 ul


title: CM-2, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S171
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_131
Short description:			Cord blood derived, lineage negative, hematopoietic cells were cultured for 4 days and then subjected to a mock medium exchange.  This included centrifugation of the cells and re-suspension in the same medium.  The cells were then allowed to incubate for 24 hours prior to RNA extraction.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			7.8x10e5
Sample volume:				3.0 ul


title: 9859-11, chip MOE430A


title: U4, 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. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E199
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199
SCGP Sample ID:				S255
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=199#SAMPLE_206
Short description:			Undifferentiated  mouse mammosphere RNA.  Mammospheres are believed to be comprised of stem/progenitor cells.
Estimated purity:				90%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~ 1.0x10e7
Sample volume:				5.0 ul

source_name: Mammosphere passage 3, Mammary gland

extract_protocol:
RNA prep method:				TRIzol
Contaminating cell type:			10% myoepithelial cells
Method for estimating purity:		Analysis of cellular markers

tag: Defining markers:				Sca-1, Thy-1, Ecadherin


title: D2, chip MOE430A


title: U2, chip MOE430A


title: D1, chip MOE430A


title: 9619-6, chip MOE430A


title: WT3-Expt6, 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. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S65
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_49
Short description:			RNA pool from mammary glands tumours of wild-type PEA3 mice induced by the Her2/Neu transgene.
Estimated purity:				80%
RNA concentration:			2.0 ug/ul
Sample volume:				10.0 ul

source_name: , Mammary gland

extract_protocol:
RNA prep method:				CsCl and Qiagen purification
Cell purification method:			FACS for Sca-1 +ve
Method for estimating purity:		PCR for sca-1 transcripts


title: WT1-Expt6, chip MG_U74Av2


title: WT2-Expt6, chip MG_U74Av2


title: Day 4-3, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S170
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_130
Short description:			These samples, cord blood derived lineage negative hematopoietic cells, were collected following 4 days of culture.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			4.2x10e5
Sample volume:				3.0 ul


title: Day 4-2, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S170
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_130
Short description:			These samples, cord blood derived lineage negative hematopoietic cells, were collected following 4 days of culture.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			3.7x10e5
Sample volume:				3.0 ul


title: D4, chip MOE430A


title: Null2-Expt6, 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. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S8
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_6
Short description:			RNA pool from mammary glands tumours of PEA3-null mice induced by the Her2/Neu transgene.
Estimated purity:				80%
RNA concentration:			2.0 ug/ul
Sample volume:				10.0 ul

extract_protocol:
RNA prep method:				CsCl and Qiagen purification
Cell purification method:			FACS for sca-1 +ve
Method for estimating purity:		PCR for sca-1 transcripts


title: M2, 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:				S237
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=194#SAMPLE_278
Short description:			Mature mast cells cultured for 57 to 110 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 mature mast cells, 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 57 to 110 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:					M2 and M4

tag: Karyotype:				Wild-type

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


title: CM-1, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S171
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_131
Short description:			Cord blood derived, lineage negative, hematopoietic cells were cultured for 4 days and then subjected to a mock medium exchange.  This included centrifugation of the cells and re-suspension in the same medium.  The cells were then allowed to incubate for 24 hours prior to RNA extraction.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			1.8x10e6
Sample volume:				3.0 ul


title: U1, chip MOE430A

growth_protocol:
Growth medium:				3:1 DMEM: F12
Media supplements:			B-27 supplement, basic fibroblast growth factor, epidermal growth factor, heparin
Culture conditions:			37C, 5% CO2


title: Day 4-1, 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. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S170
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_130
Short description:			These samples, cord blood derived lineage negative hematopoietic cells, were collected following 4 days of culture.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			1.3x10e6
Sample volume:				3.0 ul


title: M4, 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:				S237
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=194#SAMPLE_278
Short description:			Mature mast cells cultured for 57 to 110 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:				3.0 ul


title: M5, 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:			1.5 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

tag: Gender:					M1


title: M6, 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:				S237
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=194#SAMPLE_278
Short description:			Mature mast cells cultured for 57 to 110 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:			1.0 ug/ul
Num cells for RNA prep:			1x10e7
Sample volume:				8.0-10.0 ul


title: M3, chip MOE430A


title: M-O7e MP3, 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:				S52
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37#SAMPLE_38
Short description:			Total RNA from M-O7e, a megakaryoblastic cell line, transduced with retroviral vector alone (MIEV).
Estimated purity:				~ 98%
RNA concentration:			3.2 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				6.5 ul

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

tag: Defining markers:				GFP


title: M-O7e MP1, chip HG-U133A


title: M-O7e MP2, chip HG-U133A


title: Null1-Expt6, chip MG_U74Av2


title: 6473B, 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:			3.1x10e6
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

tag: Strain:


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:				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:			1.38 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				10.8 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:			1.38 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				10.8 ul

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