title: FM95-14 36hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S281
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_290
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1662 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2, DMEM 2.5% horse serum for 36hr


title: FM95-14 4d 0, 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S284
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_293
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1686 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl

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: myoblasts FM95-14 P15, fetal muscle

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2, DMEM 2.5% horse serum for 4d

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

tag: Gender:					Male

tag: Karyotype:				normal male chromosomes


title: RORgamma +/+ thymus vs. RORgamma -/- thymus (ExpID 1667)

status: Public on Apr 01 2006

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: This experiment was performed in order to identify changes in gene expression in thymocytes isolated from RORg-/- mice in comparison to those of wild type mice

data_processing: For each condition, equal amounts of total RNA from thymocytes of three individual wild type or RORg-/- mice were pooled and amplified. Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 1 ug of total RNA, Cy3- or Cy5-labeled cRNA was synthesized according to manufacturer’s protocol.  For each comparison, 750 ng of each Cy3- and Cy5-labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 h in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.  Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Data was obtained with the Agilent Feature Extraction software (v7.1) using defaults for all parameters.

organism: Mus musculus

source_name: RORgamma +/+ thymus (Cy3)

tag: RORgamma +/+ thymus

source_name: RORgamma -/- thymus (Cy5)

tag: RORgamma -/- thymus


title: FM95-14 7d 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S285
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_294
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1206 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2, DMEM 2.5% horse serum for 7d


title: FM95-14 24hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S280
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_289
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1278 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2, DMEM 2.5% horse serum for 24hr


title: FM95-14 36hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S281
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_290
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1583 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: Control(ethanol)-treated sample at 30min, biological rep1

status: Public on Jun 02 2006

city: Chicago

first: Suzanne

middle: Daniela

last: Conzen

state: IL

address: 5841 S. Maryland Ave, SBRI J301, MC 2115

department: Medicine

institute: The University of Chicago

description: Gene expression data from MCF10A-Myc cells treated with ethanol (control) for 30 min.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix human genome HG-U133A genechip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed and normalized Robust Multi-array Average (RMA) algorithm.

label: biotin

source_name: MCF10A-Myc cells treated with ethanol for 30 min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA from each sample was extracted using Qiagen’s RNeasy Kit.

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with vehicle (ethanol) for 30 min.

tag: Genotype

value: unknown

tag: Age


title: FM95-14 48hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S282
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_291
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1821 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2, DMEM 2.5% horse serum for 48hr


title: 10_17_04 BHI 37°C.2 EGDe vs ∆mogR

status: Public on Feb 11 2006

city: Boston

first: Aimee

last: Shen

state: MA

address: Armenise Building, rm 313, 200 Longwood Avenue

department: Microbiology and Molecular Genetics

institute: Harvard University

description: RNA was harvested from 24 hr cultures of EGDe and ∆mogR then competitively hybridized to TIGR microarray

data_processing: Gene Pix Pro 3.0 software

organism: Listeria monocytogenes

source_name: EGDe wild-type

tag: EGDe strain grown 24 hr at 37°C lying flat in 10mL BHI, 10_10_04 RNA sample

source_name: ∆mogR

tag: ∆mogR strain grown 24 hr at 37°C lying flat in 10mL BHI, 10_10_04 RNA sample


title: FM95-14 36hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S281
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_290
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			2402 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 7d 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S285
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_294
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1842 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 18hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S279
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_288
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1460 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2, DMEM 2.5% horse serum for 18hr


title: FM95-14 48hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S282
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_291
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1622 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 12hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S278
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_287
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1280 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2, DMEM 2.5% horse serum for 12hr


title: FM95-14 18hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S279
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_288
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1552 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 6hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S277
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_286
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1162 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2, DMEM 2.5% horse serum for 6hr


title: FM95-14 12hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S278
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_287
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1149 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: FM95-14 12hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S278
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_287
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1264 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: FM95-14 24hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S280
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_289
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			2172 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 6hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S277
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_286
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1740 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: FM95-14 7d 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S285
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_294
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1206 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 18hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S279
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_288
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1104 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 24hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S280
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_289
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1350 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 7d 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S285
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_294
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1368 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 6hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S277
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_286
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1196 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: FM95-14 0hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S276
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_285
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1019 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2


title: FM95-14 0hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S276
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_285
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1089 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 36hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S281
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_290
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1583 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 36hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S281
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_290
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			2402 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 24hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S280
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_289
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1278 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 4d 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S284
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_293
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1686 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 4d 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S284
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_293
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1955 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 4d 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S284
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_293
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1608 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 3d 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S283
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_292
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1614 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl

growth_protocol:
Growth medium:				SKBM-2
Media supplements:			gentamicin + amphotericinB + rhEGF + dexamethasone
Culture conditions:			37ºC, 5% CO2, DMEM 2.5% horse serum for 3d


title: FM95-14 7d 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S285
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_294
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1842 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 36hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S281
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_290
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1662 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 3d 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S283
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_292
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			2233 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 48hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S282
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_291
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1622 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 0hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S276
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_285
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1574 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 3d 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S283
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_292
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1266 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 18hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S279
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_288
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1460 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 6hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S277
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_286
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1162 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: FM95-14 12hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S278
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_287
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1264 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: FM95-14 12hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S278
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_287
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1149 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: FM95-14 24hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S280
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_289
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			2172 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 48hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S282
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_291
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1821 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 24hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S280
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_289
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1350 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 18hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S279
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_288
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1552 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 0hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S276
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_285
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1019 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 48hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S282
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_291
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			3153 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 6hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S277
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_286
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1740 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: FM95-14 6hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S277
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_286
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1196 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: FM95-14 18hr 0, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S279
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_288
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1104 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 0hr 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. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S276
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_285
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1089 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 0hr 0, chip HG-U133A


title: FM95-14 12hr 11, 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:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S278
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_287
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1280 ng/µl
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl.


title: Old Control Day 0 #55 C

status: Public on Aug 18 2003

city: Columbia

first: Scott

last: Pattison

state: MO

institute: University of Missouri

description:
II.	Experiment Description
1)	Experimental Design
·	Authors: J. Scott Pattison, Thomas Ellis Childs, Lillian Folk, Richard Madsen, and Frank W. Booth.
·	Laboratory: Dr. Frank Booth, University of Missouri-Columbia, 1600 E. Rollins St, Columbia, Mo, 65211
·	Contact: boothf@missouri.edu
·	Type of experiment: control young muscle (3-4 months) vs control old muscle (30-31 months).
Experiment 1:
·	Experimental Factors: Age
·	How many hybridizations in the experiment: 45 unique samples were hybridized once per array x 3 arrays each = 135 separate hybridizations in total.
·	Experiment Description: To elucidate the differences in gene expression between young control soleus muscles and old control soleus muscles.
·	Type of experiment: control young muscle (3-4 months) vs control old muscle (30-31 months).
Experiment 2:
·	Experimental Factors: Age and Atrophy
·	How many hybridizations in the experiment: 20 unique samples were hybridized once per array x 3 arrays each = 60 separate hybridizations in total.
·	Experiment Description: To elucidate the differences in gene expression between young and old soleus muscles with and without immobilization.
·	Type of experiment: control young muscle (3-4 months) vs immobilized young muscle (3-4 months) vs. control old muscle (30-31 months) vs. immobilized old muscle (30-31 months).
Experiment 3:
·	Experimental Factors: Age, Atrophy, Recovery (Time)
·	How many hybridizations in the experiment: 95 unique samples were hybridized once per array x 3 arrays each = 285 separate hybridizations in total.
·	Experiment Description: Time course of skeletal muscle recovery following atrophy, comparing young and old responses vs. controls.
·	Type of experiment: control young muscle (3-4 months) vs immobilized young muscle (3-4 months) vs. control old muscle (30-31 months) vs. immobilized old muscle (30-31 months) at each of recovery times 0, 3, 6, 10, and 30 days.
2)	Samples used, Extract preparation, and Labeling
Ø	Biosource properties
·	Organism: Rattus Norvegicus
·	Animal Source: Harlan Labs, NIA colony
·	Sex: male
·	Age: 3-4 months or 30-31 months after birth
·	Organism part: soleus skeletal muscle
·	Cell type: mixed in muscle tissue
·	Strain or line: Fischer x Brown Norway F1 rats
·	Genetic variation: N/A
·	Individual genetic characteristics: N/A
·	Disease state or normal: normal
·	State of muscle: Old Day 0 Control muscle
*The strain of rat used has a propensity for increased longevity over most other strains, due to a failure to develop premature diseases including cancers that shorten the life of other rat strains.

Ø	Biomaterial manipulations
·	Growth conditions: normal
controlled environment
20-22 ºC average temperature
housed in guinea pig cages 2-3/cage
rubber mats covered the bottoms of cages
12/12 hour light/dark cycle
regular rat chow was provided ad libitum
water was available ad libitum
½” x 3” poplar dowel rods doused in apple juice were given for environmental enhancement
·	Treatments: N/A
·	Tissue handling: both soleus muscles from a single rat were excised, weighed, and immediately frozen in liquid N2, the muscles were then stored at –80ºC until RNA isolation.

Ø	Extract preparation
·	Extraction method: muscle tissue was powdered over liquid N2 then put into TRIzol solution and homogenized with a Polytron homogenizer for 3 bouts of 15 seconds on setting 7.  Total RNA was extracted as per manufacturer instructions.  Total RNA from each sample was used to prepare biotinylated target RNA, with minor modifications from the manufacturers recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).  Briefly, 10 µg of total RNA was used to generate first-strand cDNA by using a T7-oligo(dT24) primer.  Following, second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 100-fold amplification of RNA.  Finally, the biotinylated populations of cRNA were fragmented according to the linked protocol.  A complete description of procedures is available at (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
·	Minor modifications: All incubations were done in a thermocycler instead of a water bath, cDNA was quantified follwing cDNA synthesis, prior to in vitro transcription, using a PicoGreen kit (Molecular Probes). One microgram of cDNA was then in vitro transcribed.
·	Target Preparation: Target cDNA generated from each sample were then processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
·	Quality control: The quality and amount of starting RNA, cDNA, cRNA, and fragmented cRNA were confirmed using agarose gel analyses.
·	Spike controls:  Briefly, spike controls were added to 10 µg fragmented cRNA before prior to hybridization. A complete description of these procedures is available at (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

Ø	Hybridization Procedures
·	Hybridization:  Arrays were pre-hybridized, loaded, and hybridized for 16 hours prior to washing and staining.  A complete description of these procedures is available at (http://www.affymetrix.com/support/technical/manual/expression_manual.affx
·	Washing and Staining: Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner.  A complete description of these procedures is available at (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

Ø	Measurement data and specifications of data processing
·	Scanning:  The scanning protocols are available at (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
·	Raw Image Analysis/Quality Control: After scanning, array images were assessed to confirm scanner alignment.  The corners were examined by eye for proper grid alignment.  Images were also scanned for the absence of bubbles, scratches, and speckling.  If any images with small scratches or speckles that skewed >25% of a given feature, that feature was masked and not quantitated in future analyses.  3'/5' ratios for GAPDH and beta-actin were confirmed to be ~1.0.  From the QC report, spike controls were found to be present on all chips, with BioB, BioC, BioD and CreX being found present in increasing intensity.
·	Scaling/Normalization: All data were scaled to a target intensity of 1500 (using Affymetrix MAS 5.0 array analysis software), scaling factors for all arrays were within acceptable limits, as were background, and mean intensities.  No further normalization was applied.
·	Data Analysis:
·	Experiment 1:
·	Only those probe sets found to be called “present” or “marginal” in > 60% of all samples in an age group were statistically analyzed.  The signal values for all sufficiently detected probe sets were analyzed for significant differences via a Student’s t-test.  A Bonferroni adjustment was applied to all data to control for multiple testing, where a Bonferroni-adjusted p<0.05 (raw p=4.478x10-6) were considered significant.
·	The final list of statistically changing genes can be found at (Supporting Data to be linked to journal web site upon paper acceptance)
·	Experiment 2:
·	Only those probe sets found to be called “present” or “marginal” in > 60% of all samples in an age group were statistically analyzed.  The signal values for all sufficiently detected probe sets were analyzed for significant differences via a 2-way ANOVA.  A Bonferroni adjustment was applied to all data to control for multiple testing, where a Bonferroni-adjusted p<0.05 were considered significant.
·	The final list of statistically changing genes can be found at (Supporting Data to be linked to journal web site upon paper acceptance)
·	 Experiment 3:
·	Only those probe sets found to be called “present” or “marginal”

organism: Rattus norvegicus

source_name: soleus muscle


title: Old Control Day 0 #54 C


title: Old Control Day 0 #55 B


title: Old Control Day 0 #53


title: Old Control Day 0 #52


title: Old Control Day 0 #52 C


title: Old Control Day 0 #54


title: Old Control Day 0 #53 C


title: Old Control Day 0 #51 C


title: Old Control Day 0 #52 B


title: Old Control Day 0 #51 B


title: Old Control Day 0 #53 B

source_name: soleus


title: Old Control Day 0 #55


title: Old Control Day 0 #54 B


title: Wild type voxel A1

status: Public on Mar 29 2002

city: Los Angeles

first: Vanessa

middle: Marie

last: Brown

state: CA

address: 650 Charles E. Young Dr. South, CHS 23-151

department: Department of Molecular & Medical Pharmacology

institute: UCLA

description:
Voxel A1 of mouse brain.
Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain.  In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain.  The mice used in these experiments were C57BL/6J males 10-24 weeks in age.

source_name: normal whole brain

source_name: wild type voxel A1


title: Wild type voxel A2

description:
Voxel A2 of mouse brain.
Voxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene expression patterns in the brain.  In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain.  The mice used in these experiments were C57BL/6J males 10-24 weeks in age.

source_name: wild type voxel A2


title: SHFD206

status: Public on Jun 08 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52958.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42°C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70°C for 10 minutes, and was neutralized by adding 15 ul of 0.1 N HCl.  Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore).  After 20 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified.  For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100°C for 3 minutes, incubated at 37°C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher).  The slides were incubated at 65°C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry.  Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.65; Parameter Scan Time = 11:46:50; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19609; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.98; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.65; Parameter Scan Time = 11:46:50; Parameter PMT Volts = 610; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19013; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi

organism:
Pan troglodytes
Homo sapiens

source_name: aURNA


title: SHFD207

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52957.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42°C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70°C for 10 minutes, and was neutralized by adding 15 ul of 0.1 N HCl.  Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore).  After 20 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified.  For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100°C for 3 minutes, incubated at 37°C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher).  The slides were incubated at 65°C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry.  Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.41; Parameter Scan Time = 11:36:44; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19600; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.99; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.41; Parameter Scan Time = 11:36:44; Parameter PMT Volts = 610; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 19004; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi


title: SHFD231

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52953.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42°C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70°C for 10 minutes, and was neutralized by adding 15 ul of 0.1 N HCl.  Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore).  After 20 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified.  For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100°C for 3 minutes, incubated at 37°C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher).  The slides were incubated at 65°C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry.  Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.13; Parameter Scan Time = 10:35:41; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 19471; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.98; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.13; Parameter Scan Time = 10:35:41; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 18875; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi

source_name: CHRISTA


title: SHFD232

description:
Simple annotation: Normal tissue, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-06/52954.gif; format: GIF
Sample_label_ch1 = Cy3
Sample_label_ch2 = Cy5
For the second batch, we amplified the nine RNA samples by using the MessageAmp aRNA Amplification Kit (Ambion) according to manufacturer's specifications. Briefly, for each sample, dye-labeled cDNA probes were made during reverse transcription in a reaction volume of 30 ul containing 2 ug mRNA(or amplified RNA)/ 4 ug oligo (dT) primer / 0.5 uM each dATP, dCTP, dGTP / 0.2 uM dTTP / 0.1 uM Cy3/5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ) / 0.01 M DTT / 400 units Superscript II reverse transcriptase (Life Technologies). We labeled the reference sample with Cy3-dUTP; thus in this study the Cy5/Cy3 ratio is taken as the measure of transcript levels in individual test samples. After incubation at 42°C for 2-3 hours, the RNA was degraded by adding 15 ul of 0.1 N NaOH at 70°C for 10 minutes, and was neutralized by adding 15 ul of 0.1 N HCl.  Equal amounts of the Cy3 and Cy5 probes were combined and concentrated by using a Microcon YM-100 column (Millipore).  After 20 ug Cot1 human DNA (Gibco-BRL), 20 ug PolyA RNA (Sigma, #P9403) and 20 ug tRNA (Gibco-BRL, #15401-011) were added, the probes were purified.  For final probe preparation, 6 ul of 20x SSC (BioWhittaker, MD) and 1 ul of 10% SDS were added. The probes were denatured at 100°C for 3 minutes, incubated at 37°C for 30 minutes, and placed on the array under a 24 mm x 60 mm glass cover slip (Fisher).  The slides were incubated at 65°C for 16 hours in a hybridization chamber (GeneMachine, San Carlos, California). Slides were washed in graded SSC with 0.1% SDS: 2x for 2 to 5 minutes, 1x for 2 minutes, and 0.1x for 2 minutes, and spun dry.  Fluorescent array images were collected for Cy3 and Cy5 channels by using a GenePix 4000B scanner (Axon Instruments, Foster City, CA) at a resolution of 5 mm per pixel.
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.49; Parameter Scan Time = 10:44:26; Parameter PMT Volts = 520; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 19480; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.98; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.49; Parameter Scan Time = 10:44:26; Parameter PMT Volts = 620; Parameter Scan Date = 2004-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 18883; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86227]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Vida,,Shokoohi