title: CPGSC#34, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S157
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_117
Short description:			24 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#33, chip MOE430A

status: Public on Sep 01 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S157
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_117
Short description:			24 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.2 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul

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

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: V6.5 (P18), Embryonic

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

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

treatment_protocol: Assays to confirm viability:		Stratagene mycoplasma PCR test

tag: Strain:					129SV x C57Bl/6


title: CPGSC#29, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S156
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_116
Short description:			18 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.1 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul


title: CPGSC#31, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S156
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_116
Short description:			18 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.1 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul


title: CPGSC#28, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S155
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_115
Short description:			12 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.2 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul

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


title: CPGSC#26, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S155
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_115
Short description:			12 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			1.14 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 ul


title: CPGSC#30, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S156
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_116
Short description:			18 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			4.4 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul


title: C2C12-puro 1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E102
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102
SCGP Sample ID:				S137
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102#SAMPLE_102
Short description:			C2C12 myoblasts infected with empty virus (puro).
Estimated purity:				100%
RNA concentration:			2.9 ug/ul
Num cells for RNA prep:			>6x10e6

source_name: C2C12, Muscle

growth_protocol:
Growth medium:				DMEM
Media supplements:			10% FCS (heat inactivated), Penicillin/Streptomycin
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			1. Cell line, 2. Puromycin selection
Contaminating cell type:			None

tag: Strain:					C3H

tag: Karyotype:				Normal, diploid

tag: Defining markers:				myoD/myf5


title: C2C12-pax7d 2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E102
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102
SCGP Sample ID:				S310
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102#SAMPLE_199
Short description:			C2C12 myoblasts infected with a retrovirus expressing Pax7d.
Estimated purity:				100%
Num cells for RNA prep:			>6x10e6


title: J1-U2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E95
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95
SCGP Sample ID:				S128
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95#SAMPLE_96
Short description:			Total RNA was extracted from J1 ES cells following 2 days of culture.
Estimated purity:				95%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			8-10x10E6
Sample volume:				20 ul

source_name: J1 ES Cells, embryonic

growth_protocol:
Growth medium:				D-MEM
Media supplements:			10% fetal bovine serum, glutamax, sodium pyruvate, non-essential amino-acids, penicillin, streptomycin, beta-mercaptoethanol, leukemia inhibitory factor
Culture conditions:			On gelatin (0.1%) at 37C, 5% CO2 for 2 days

extract_protocol:
RNA prep method:				RNeasy
Contaminating cell type:			DR4 feeders
Method for estimating purity:		By eye

tag: Strain:					129/Sv

tag: Gender:					Male


title: C2C12-puro 2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E102
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102
SCGP Sample ID:				S137
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102#SAMPLE_102
Short description:			C2C12 myoblasts infected with empty virus (puro).
Estimated purity:				100%
RNA concentration:			2.8 ug/ul
Num cells for RNA prep:			>6x10e6


title: J1-U3, chip MOE430A


title: Myoblast A, chip MG_U74Av2

status: Public on Sep 07 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E59
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59
SCGP Sample ID:				S78
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=59#SAMPLE_59
Short description:			Wild type myoblast A-C: Muscle satellite cells are a self-renewing pool of stem cells that give rise to daughter myogenic precursor cells in adult skeletal muscle.  Published and preliminary data indicated that MyoD and p53 genes are involved in satellite cell differentiation.  We would like to know what downstream genes of both transcription factors are affected in satellite cell-derived myoblasts (MyoD-/-, p53 -/-).
Estimated purity:				> 98%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Growing myoblasts
Sample volume:				10 ul

source_name: Myoblasts, Skeletal muscle

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

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

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

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

tag: Defining markers:				MyoD, Myf5, p53


title: C2C12-pax7d 3, chip MOE430A


title: OGCsort#9 +/-, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S235
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_277
Short description:			Sorted sub-populations of mouse bone marrow.    Triplicates:    OGCsort#1 +/-  OGCsort#7 +/-  OGCsort#9 +/-
Estimated purity:				90%

source_name: primary, bone marrow

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

tag: Strain:					C57Bl/6

tag: Karyotype:				Diploid

tag: Defining markers:				CD45+  Sca1-


title: OGCsort#5 +/+, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S234
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_276
Short description:			Sorted sub-populations of mouse bone marrow.   Triplicates:  OGCsort#1 +/+  OGCsort#5 +/+  OGCsort#6 +/+
Estimated purity:				90%

tag: Gender:					Female

tag: Defining markers:				CD45+  Sca1+


title: CPGSC#27, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S155
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_115
Short description:			12 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.6 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				27 ul


title: C2C12-puro 3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E102
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102
SCGP Sample ID:				S137
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102#SAMPLE_102
Short description:			C2C12 myoblasts infected with empty virus (puro).
Estimated purity:				100%
RNA concentration:			3.0 ug/ul
Num cells for RNA prep:			>6x10e6


title: J1-D3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E95
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95
SCGP Sample ID:				S127
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95#SAMPLE_95
Short description:			Total RNA was extracted from J1 embryoid bodies following 5 days of culture.
RNA concentration:			2 ug/ul
Num cells for RNA prep:			8-10x10E6
Sample volume:				20 ul

growth_protocol:
Growth medium:				D-MEM
Media supplements:			10% fetal bovine serum, glutamax, non-essential amino-acids, penicillin, streptomycin
Culture conditions:			Bacterial Petri dishes at 37C, 5% CO2 for 5 days

extract_protocol: RNA prep method:				RNeasy


title: J1-D1, chip MOE430A


title: C2C12-pax7d 1, chip MOE430A


title: OGCsort#1 +/-, chip MOE430B


title: OGCsort#8 -/-, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S233
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_191
Short description:			Sorted sub-populations of mouse bone marrow.   Triplicates: OGCsort#4 -/- OGCsort#5 -/- OGCsort#8 -/-
Estimated purity:				90%

tag: Defining markers:				CD45- Sca1-


title: OGCsort#7 +/-, chip MOE430B


title: J1-D2, chip MOE430A


title: OGCsort#4 -/-, chip MOE430B


title: OGCsort#1 +/+, chip MOE430B


title: V6.5 mEB 9d-3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S241
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_202
Short description:			9 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  Time course: 0h, 6h, 12h, 18h, 24h, 36h, 48h, 4 days, 7days, 9 days and 15 days. All samples in triplicate. The cells are differentiating EBs from murine Embryonic Stem Cells, Mouse strain 129 crossed with C67BL/6 isolate V6.5 (P18), obtained from Dr. Josee Coulombe in Dr. M. Rudnicki's lab.
Estimated purity:				100%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 ul


title: OGCsort#5 -/-, chip MOE430B


title: DR4-3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E140
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140
SCGP Sample ID:				S180
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140#SAMPLE_140
Short description:			This sample, investigated in triplicate, is a control for the J1, R1 and V6.5 ES samples.  The DR4 cell type acts as a feeder cell for stem cells and as such is a small contaminant of the embryonic stem cell growth environment.
RNA concentration:			3.0 ug/ul
Num cells for RNA prep:			3x10e6
Sample volume:				> 20 ul

source_name: Embryonic fibroblasts, Embryos (day15)

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

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


title: CPGSE#6, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S147
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_109
Short description:			Mouse bone marrow stained with CD45-APC & Scal-PE, sorted on Moflo for +/+ cells
Analysis requested:			microarray
Estimated purity:				95-98%
RNA concentration:			50ng/ul
Num cells for RNA prep:			9.4 X 10^5
Sample volume:				10ul

source_name: haematopoeitic stem cells, bone marrow

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

tag: Strain:					C57BL/6

tag: Defining markers:				CD45+ScaI+


title: DR4-1, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E140
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140
SCGP Sample ID:				S180
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=140#SAMPLE_140
Short description:			This sample, investigated in triplicate, is a control for the J1, R1 and V6.5 ES samples.  The DR4 cell type acts as a feeder cell for stem cells and as such is a small contaminant of the embryonic stem cell growth environment.
RNA concentration:			2.4 ug/ul
Num cells for RNA prep:			12x10e6
Sample volume:				13 ul


title: V6.5 mEB 9d-2, chip MOE430B

tag: Strain:					129SV x C57Bl/6


title: CPGSC#43, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S181
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_141
Short description:			4 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.2 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: CPGSE#4, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S147
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_109
Short description:			Mouse bone marrow stained with CD45-APC & Scal-PE, sorted on Moflo for +/+ cells
Analysis requested:			microarray
Estimated purity:				95-98%
RNA concentration:			50ng/ul
Num cells for RNA prep:			6.9 X 10^5
Sample volume:				10ul


title: CPGSC#47, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S175
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_135
Short description:			14 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			1.6 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: V6.5 mEB 9d-1, chip MOE430B


title: CPGSC#40, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S159
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_119
Short description:			48 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.95 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#42, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S181
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_141
Short description:			4 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.8 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: CPGSC#49, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S175
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_135
Short description:			14 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: CPGSC#48, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S175
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_135
Short description:			14 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			1.5 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: CPGSC#44, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S174
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_134
Short description:			7 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				90 ul


title: CPGSC#45, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S174
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_134
Short description:			7 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.1 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: CPGSC#46, chip MOE430B


title: CPGSC#41, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S181
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_141
Short description:			4 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: J1-U1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E95
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95
SCGP Sample ID:				S128
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95#SAMPLE_96
Short description:			Total RNA was extracted from J1 ES cells following 2 days of culture.
Estimated purity:				95%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			8-10x10E6
Sample volume:				20 ul


title: CPGSC#38, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S159
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_119
Short description:			48 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			4.1 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#36, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S158
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_118
Short description:			36 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.9 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: DR4-2, chip MOE430B


title: CPGSC#34, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S157
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_117
Short description:			24 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#39, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S159
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_119
Short description:			48 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.2 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#32, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S157
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_117
Short description:			24 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#37, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S158
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_118
Short description:			36 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			4.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#30, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S156
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_116
Short description:			18 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			4.4 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul


title: CPGSC#28, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S155
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_115
Short description:			12 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.2 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul


title: CPGSC#27, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S155
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_115
Short description:			12 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.6 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				27 ul


title: CPGSC#35, chip MOE430B


title: CPGSC#31, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S156
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_116
Short description:			18 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.1 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul


title: CPGSC#33, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S157
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_117
Short description:			24 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.2 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				60 ul


title: CPGSC#26, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S155
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_115
Short description:			12 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			1.14 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 ul


title: CPGSC#25, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S154
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_114
Short description:			6 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			1.45 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 ul


title: CPGSC#29, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S156
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_116
Short description:			18 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.1 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul


title: CPGSC#21, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S153
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_113
Short description:			0 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.9 ug/ul
Num cells for RNA prep:			2X10e6
Sample volume:				30 ul

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


title: CPGSC#24, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S154
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_114
Short description:			6 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.5 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 ul


title: CPGSC#23, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S154
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_114
Short description:			6 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.3 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				30 ul


title: C2C12-puro 2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E102
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102
SCGP Sample ID:				S137
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102#SAMPLE_102
Short description:			C2C12 myoblasts infected with empty virus (puro).
Estimated purity:				100%
RNA concentration:			2.8 ug/ul
Num cells for RNA prep:			>6x10e6

tag: Strain:					C3H


title: C2C12-puro 1, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E102
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102
SCGP Sample ID:				S137
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102#SAMPLE_102
Short description:			C2C12 myoblasts infected with empty virus (puro).
Estimated purity:				100%
RNA concentration:			2.9 ug/ul
Num cells for RNA prep:			>6x10e6

tag: Karyotype:				Normal, diploid


title: CPGSC#22, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S153
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_113
Short description:			0 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.7 ug/ul
Num cells for RNA prep:			2X10e6
Sample volume:				30 ul


title: J1-U3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E95
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95
SCGP Sample ID:				S128
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95#SAMPLE_96
Short description:			Total RNA was extracted from J1 ES cells following 2 days of culture.
Estimated purity:				95%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			8-10x10E6
Sample volume:				20 ul


title: C2C12-puro 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E102
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102
SCGP Sample ID:				S137
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=102#SAMPLE_102
Short description:			C2C12 myoblasts infected with empty virus (puro).
Estimated purity:				100%
RNA concentration:			3.0 ug/ul
Num cells for RNA prep:			>6x10e6

tag: Defining markers:				myoD/myf5


title: J1-U1, chip MOE430B

tag: Strain:					129/Sv


title: J1-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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E95
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95
SCGP Sample ID:				S127
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=95#SAMPLE_95
Short description:			Total RNA was extracted from J1 embryoid bodies following 5 days of culture.
RNA concentration:			2 ug/ul
Num cells for RNA prep:			8-10x10E6
Sample volume:				20 ul

tag: Gender:					Male


title: J1-D2, chip MOE430B


title: J1-D3, chip MOE430B


title: J1-U2, chip MOE430B


title: CPGSC#19, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E112
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=112
SCGP Sample ID:				S151
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=112#SAMPLE_112
Short description:			CPGS#17, 18 & 19 Skeletal muscle cells (myoblasts - human fetal cells from 17 week old embryo)
Cell line clone ID:			Lot#2F0241
Estimated purity:				100%
RNA concentration:			3.9 ug/ul
Num cells for RNA prep:			3.5X10^6
Sample volume:				15ul

organism: Homo sapiens

source_name: SkMC Myoblast, embryonic

growth_protocol:
Growth medium:				SkGM - Skeletal, Muscle Cell Medium
Media supplements:			Fetal Bovine serum, hEGF, Desamethasome, insulin, gentamycin
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				Qiagen RNeasy
Cell purification method:			Cultured
Contaminating cell type:			none
Method for estimating purity:		Cell line obtained from Claire Palmer (Dr. M. Rudnicki's lab)

treatment_protocol: Assays to confirm viability:		Stratagene mycoplasma PCR test kit - neg


title: CPGSC#20, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S153
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_113
Short description:			0 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.8 ug/ul
Num cells for RNA prep:			2X10e6
Sample volume:				30 ul


title: CPGSC#17, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E112
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=112
SCGP Sample ID:				S151
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=112#SAMPLE_112
Short description:			CPGS#17, 18 & 19 Skeletal muscle cells (myoblasts - human fetal cells from 17 week old embryo)
Cell line clone ID:			Lot#2F0241
Estimated purity:				100%
RNA concentration:			3.1 ug/ul
Num cells for RNA prep:			3.5X10^6
Sample volume:				15ul


title: CPGSC#18, 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E112
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=112
SCGP Sample ID:				S151
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=112#SAMPLE_112
Short description:			CPGS#17, 18 & 19 Skeletal muscle cells (myoblasts - human fetal cells from 17 week old embryo)
Cell line clone ID:			Lot#2F0241
Estimated purity:				100%
RNA concentration:			3.2 ug/ul
Num cells for RNA prep:			3.5X10^6
Sample volume:				15ul


title: CPGSC#17, chip HG-U133B


title: CPGSC#18, chip HG-U133A


title: R1 EB 14d 2, chip MOE430B

status: Public on Jul 22 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S217
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_175
Short description:			14 days of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL

source_name: R1, Fetal cells

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

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

tag: Strain:					129/Sv x 129/Sv-CP


title: R1 EB 14d 3, chip MOE430B


title: CPGSC#19, chip HG-U133B


title: R1 EB 14d 1, chip MOE430B


title: R1 EB 9d 2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S216
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_174
Short description:			9 days of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 9d 3, chip MOE430B


title: R1 EB 7d 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S215
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_173
Short description:			7 days of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 4d 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S213
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_172
Short description:			4 days of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 9d 1, chip MOE430B


title: R1 EB 4d 2, chip MOE430B


title: R1 EB 4d 1, chip MOE430B


title: R1 EB 7d 1, chip MOE430B


title: R1 EB 7d 2, chip MOE430B


title: R1 EB 48h 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S212
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_171
Short description:			48 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 48h 1, chip MOE430B


title: R1 EB 36h 2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S211
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_170
Short description:			36 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 48h 2, chip MOE430B


title: R1 EB 24h 2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S210
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_169
Short description:			24 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 24h 3, chip MOE430B


title: R1 EB 24h 1, chip MOE430B


title: R1 EB 36h 3, chip MOE430B


title: R1 EB 18h 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S209
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_168
Short description:			18 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL


title: R1 EB 18h 2, chip MOE430B


title: R1 EB 12h 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S208
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_167
Short description:			12 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 uL


title: R1 EB 36h 1, chip MOE430B


title: R1 EB 12h 2, chip MOE430B


title: R1 EB 18h 1, chip MOE430B


title: R1 EB 6h 2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S207
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_166
Short description:			6 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15 uL


title: R1 EB 6h 1, chip MOE430B


title: R1 EB 6h 3, chip MOE430B


title: R1 ES 0h 3, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E165
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165
SCGP Sample ID:				S206
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=165#SAMPLE_165
Short description:			0 hours of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.  The cells are differentiating embryoid bodies from murine embryonic stem cells.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				15.0 uL

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Culturing
Contaminating cell type:			None


title: Dermis #3, chip MOE430A

status: Public on Mar 03 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E158
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=158
SCGP Sample ID:				S200
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=158#SAMPLE_160
Estimated purity:				unknown
RNA concentration:			100ng/ul
Sample volume:				5

source_name: Spheres, Dermis

tag: Strain:					Balb/C

tag: Karyotype:				normal, diploid

tag: Defining markers:				unknown


title: OGCsort#6 +/+, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E191
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191
SCGP Sample ID:				S234
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=191#SAMPLE_276
Short description:			Sorted sub-populations of mouse bone marrow.   Triplicates:  OGCsort#1 +/+  OGCsort#5 +/+  OGCsort#6 +/+
Estimated purity:				90%

tag: Strain:					C57Bl/6

tag: Karyotype:				Diploid


title: NSC #3, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E158
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=158
SCGP Sample ID:				S198
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=158#SAMPLE_158
Estimated purity:				unknown
RNA concentration:			100 ng/ul
Sample volume:				5

source_name: Spheres, Brain(embryonic[E14] stratia)

tag: Strain:					CD1


title: NSC #2, chip MOE430A


title: FAT #1, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E158
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=158
SCGP Sample ID:				S199
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=158#SAMPLE_159
Estimated purity:				unknown
RNA concentration:			100ng/ul
Sample volume:				5

source_name: Spheres, Adipose tissue


title: Dermis #2, chip MOE430A


title: NSC #1, chip MOE430A


title: FAT #3, chip MOE430A


title: Dermis #3, chip MOE430B


title: Dermis #1, chip MOE430A


title: R1 ES 0h 2, chip MOE430B


title: R1 ES 0h 1, chip MOE430B


title: FAT #2, chip MOE430B


title: NSC #1, chip MOE430B


title: Dermis #2, chip MOE430B


title: R1 EB 12h 1, chip MOE430B


title: NSC #2, chip MOE430B


title: FAT #2, chip MOE430A


title: NSC #3, chip MOE430B


title: FAT #1, chip MOE430B


title: Dermis #1, chip MOE430B


title: FAT #3, chip MOE430B


title: RTG_9R40 (16k1.2 array)

status: Public on Jan 25 2006

city: Rehovot

first: Naama

last: Barkai

address: P.O box 26

country: Israel

institute: Weizmann Institute

description: S. cerevisiae cells, Transfered at 9 hours of sporulation to YPA and harvested 40 minutes after the transfer

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using ScanArray 4000 scanner (Packard BioScience) and image intensity data were extracted and analyzed with QuantArray analysis software.

data_processing: For each array, bad spots were omitted from the analysis. For each spot, the Quantarray program outputs the level of signal intensity and background fluorescence. As a first step, we re-defined the spot intensity by subtracting the spot-specific background. For each channel (Cy3 or Cy5) we then calculated the value of background signal, defined by the mean (intensity-background) of the controlled spots printed with 3x SSC buffer. All intensity values below this background level were reset to this background level. The data for each spot was then transformed into a log2-ratios. The data was normalized by subtracting from each log2ratio the median. Values of duplicates were averaged.

organism: Saccharomyces cerevisiae

label_protocol: The cDNA of sporulation derived samples and reference (YPA growing cells) was synthesized from total RNA and labeled with Cy3 and Cy5, respectively by the indirect amino-allyl method. The RNA (20 µg) was annealed with 4 µg oligo dT12-18, and reverse-transcribed into cDNA with M-MLV Reverse Transcriptase RNase H Minus (Promega) for 2h at 45°C in the presence of 2.5mM MgCl2,  0.5 mM of dATP, dCTP and dGTP, 0.1mM dTTP, 0.4mM amino-allyl dUTP. Additional 400U M-MLV Reverse Transcriptase RNase H Minus was added and incubated for another 2 hours. After hydrolysis of RNA in 0.2 M NaOH (30min, 65oC), Tris was removed from the reaction with a Microcon-30 concentrator.

growth_protocol: wild type SK1 cells (NKY1551) grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in YPA. Each YPA culture was monitored immediately after the transfer, after 20 and 40 minutes.

tag: Strain

value: SK1 wild type (NKY1551), diploid

source_name: S. cerevisiae grown in YPA at 30oC

extract_protocol: 5x10^8 cells were collected, pelleted and immediately frozen. Total RNA was obtained using RNeasy Midi Kit (Qiagen); same RNA was used as reference for the whole series


title: RTG_5R20 (6.4kv2 array)

description: S. cerevisiae cells, Transfered at 5 hours of sporulation to YPD and harvested 20 minutes after the transfer

data_processing: : For each array, bad spots were omitted from the analysis. For each spot, the Quantarray program outputs the level of signal intensity and background fluorescence. As a first step, we re-defined the spot intensity by subtracting the spot-specific background. For each channel (Cy3 or Cy5) we then calculated the value of background signal, defined by the mean (intensity-background) of the controlled spots printed with 3x SSC buffer. All intensity values below this background level were reset to this background level. The data for each spot was then transformed into a log2-ratios. The data was normalized by subtracting from each log2ratio the median. Values of duplicates were averaged.

growth_protocol: Cells were grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours, diluted into YPA (1% yeast extract, 2% bactopeptone 1% Potassium Acetate) and grown overnight. Part of that culture was used as reference for all hybridizations preformed in this study. The cells were then washed twice with sterile water and resuspended in SPM media (0.3% Potassium Acetate and 0.02% Rafinose) to initiate the sporulation process. At different stages of the sporulation process (2, 3, 4, 5, 6, 7, 8, 9 and 10 hours) RNA was extracted for microarray hybridizations. At each hour, part of the culture was centrifuged and resuspended in YPD. Each YPD culture was monitored immediately after the transfer, after 20 and 40 minutes.

extract_protocol: 5x10^8 cells were collected, pelleted and immediately frozen. Total RNA was obtained using RNeasy Midi Kit (Qiagen)


title: TaY-type1

status: Public on Jan 11 2006

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

country: Japan

institute: Tokyo Medical University

description:
Keywords = T cell line
Keywords = inflammatory response array

hyb_protocol: Hybridization was carried out automatically using GeneTAC Hybstation (Genomic Solutions, AnnArbor, MI, US) according to the supplier’s instruction. The conditions of hybridization were 55oC for 2 hrs, 50oC for 2 hrs, and 46oC for 2 hrs, then 42oC for 12 hrs.

scan_protocol: The hybridized signals were scanned by GenePix 4000B Microarray Scanner (Axon Instruments, Union City, CA, USA) as raw data.

data_processing: The scanned data were normalized, verified, and analyzed using the Genomic Profiler software (Mitsui Industrial Knowledge Inc., Tokyo, Japan). First, the value was adjusted by subtraction of background fluorescence of an equivalent area. Analysis was done by taking the median signal of the probe value for each transcript set, and the 75% rank for the total hybridization was calculated. Microarray data obtained from three independent experiments were then verified in a single file. The normalized log data of fluorescence ratio (Cy5 to Cy3), which was quantified for each gene to reflect the relative abundance of gene in each experimental sample compared with reference sample, were deposited to GEO.

molecule: polyA RNA

source_name: TaY (T cell leukemia cell line)

label_protocol: 1 microgramof mRNA were reverse transcribed into cDNA and labeled by cyanine 5 (Cy5)-conjugated deoxyuracil triphosphate (dUTP) (Amersham Biosciences, Piscataway, NJ, USA) using a LabelStar Array kit (Qiagen), according to the supplier’s instruction.

growth_protocol: Cells were maintained in RPMI1640 with 10% heat-inactivated FBS and 20 U/ml of IL-2.

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit (Qiagen, Germantown, MD, USA). For microarray analysis, mRNA was purified using an Oligotex™-dT30<Super> mRNA Purification Kit (Takara, Shiga, Japan).

tag: EBV negative, HTLV-1 positive

source_name: normal human lymphocytes

label_protocol: a LabelStar Array kit (Qiagen)

tag: Normal human lymphocyte mRNA was purchased from Ambion (Austin, TX, USA)


title: Cord blood-derived mast cells_control_rep2

status: Public on Jan 10 2006

city: Darlinghurst

first: Charles

middle: Reay

last: Mackay

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute for Medical Research

description: ~95% pure population of human cord blood-derived mast cells differentiated using IL-10, IL-6 and stem cell factor, unstimulated

hyb_protocol: Fifteen micrograms of cRNA was fragmented by heating at 94°C for 35 min in fragmentation buffer (40mM Tris-acetate (pH 8.1), 125mM KOAc, 30mM MgOAc). Hybridization cocktails were then made by adding fragmented cRNA, control cRNAs, grid alignment oligonucleotides and blocking reagents. These mixtures were hybridized for 16 hours to individual U133A and B genechips (Affymetrix, Santa Clara, CA) at 45 °C. Washing and staining of the hybridized arrays were performed using an Affymetrix Fluidics Station.

label: PE

source_name: Cord blood

label_protocol: cRNA was transcribed from cDNA and biotinylated using the BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Farmingdale, NY).

extract_protocol: Trizol was used for total RNA extraction. cRNA was prepared according to methods for small RNA samples (Baugh et al, Nucleic acids research 29:E29, 2001). 500-1000 ng of RNA was reverse transcribed to cDNA using a poly(T) primer containing a T7-(dT)24 (Geneworks, Australia).

treatment_protocol: Mast cells were derived from cord blood using an established method (Ochi et al., J. Exp Med. 190: 267-280, 1999). Briefly, mononuclear leukocytes were isolated using a Ficoll Paque (Pharmacia Biotech AB, Uppsala, Sweden) density gradient. Cells were then seeded at 2 x 10^6 cells/ml of complete media supplemented with 100 ng/ml stem cell factor (SCF) (a gift from Amgen), 10 ng/ml interleukin (IL)-10 (BD), and 5 ng/ml IL-6 (BD). Mast cell cultures were passaged and transferred to new flasks weekly at a concentration of 10^6 cells/ml of media containing SCF/IL-10/IL-6 (described above). Mast cell maturity was assessed by metachromatic staining with 1%Toluidine blue (Sigma) in 0.5M HCl which specifically stains mast cell granules. Mast cells were used after 7-10 weeks of culture when cells were up to 95% pure and mature as determined by Toluidine Blue staining.

tag: Human cord blood-derived mast cells differentiated over 7-10 weeks using IL-10, IL-6 and stem cell factor, unstimulated


title: B cells_unstimulated_rep1

description: Human CD19+, peripheral blood B cells, unstimulated, cells were >96% pure.

source_name: Peripheral blood

extract_protocol:
Trizol was used for total RNA extraction.
Trizol was used for total RNA extraction. cRNA was prepared according to methods for small RNA samples (Baugh et al, Nucleic acids research 29:E29, 2001). 500-1000 ng of RNA was reverse transcribed to cDNA using a poly(T) primer containing a T7-(dT)24 (Geneworks, Australia).

treatment_protocol: Blood was collected in EDTA tubes. Peripheral blood mononuclear cells (PBMC) were isolated from healthy volunteers by centrifugation over Ficoll Paque (Amersham Biosciences, Uppsala, Sweden) and washed. CD19+ B cells cells were sorted from PBMC using a FACSVantage SE DiVa® (BD Biosciences, San Jose, CA). Doublets and aggregated cells were excluded to minimise contaminating cells.