title: Female Testosterone-Treated Lacrimal Gland Sample C

description: Young adult female BALB/c mice (n = 30), ovariectomized at age 8 weeks, were purchased from Taconic Laboratories (Germantown, NY) and maintained in constant temperature rooms with fixed light/dark periods of 12 hours.  Animals were allowed to recover from surgery for 10 days, then anesthetized with ketamine and xylazine, and subcutaneous implants of placebo (n = 15; cholesterol, methylcellulose, lactose)- or testosterone (n = 15; 10 mg)-containing pellets were inserted in the subscapular region.  Hormone pellets were obtained from Innovative Research of America (Sarasota, FL) and were designed to maintain male physiologic amounts of testosterone over a two week period.  Following two weeks of hormone exposure, the mice were sacrificed in a CO2 chamber, and the lacrimal, meibomian, and submandibular glands were removed and pooled (5 mice per group) into three groups by treatment (n = 6 groups).  Glands were immediately frozen and stored in liquid nitrogen until RNA isolation.

tag: Series includes pooled (n = 5 mice per biological replicate) samples from lacrimal, meibomian, and submandibular glands of female palcebo- and testosterone-treated BALB/c mice. All mice were ovariectomized at 8 weeks and allowed to recover from surgery for 10 days prior to hormone implanatation. All experiments were run in triplicate (pooled biological replicates) on CodeLink Mouse Uniset I Microarrays.


title: 2hr lit replicate 2

status: Public on Jan 09 2006

type: RNA

city: Columbia

first: Emmanuel

last: Liscum

state: MO

address: Rollin Rd

department: Biological Sciences

country: USA

institute: University of Missouri

description: wild type, blue-light treated Brassica hypocotyl tissue

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 3.0

label: biotin

molecule: total RNA

organism: Brassica oleracea

source_name: hypocotyl

label_protocol: Approximately 20 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 100 3-day-old B. oleracea seedlings that has been stimulated with unidirectional blue-light were trisected into lit flanks, vasculature, and shaded flanks. The shaded flanks were collected and Total RNA was extracted from the tissue  using an RNeasy kit (Qiagen).

tag: wild type, 3 day old seedling


title: 2hr lit replicate 1


title: Dendritic cells_LPS 48h_rep2

status: Public on Jan 10 2006

city: Darlinghurst

first: Charles

middle: Reay

last: Mackay

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute for Medical Research

description: Immature peripheral blood monocyte-derived dendritic cells. Differentiated using IL-4 and GM-CSF and stimulated with LPS for 48 hours.

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

label: PE

organism: Homo sapiens

source_name: Peripheral blood

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

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

treatment_protocol: All cells were cultured in RPMI, 10% heat inactivated fetal calf serum, penicillin/streptomycin. Peripheral blood mononuclear cells (PBMCs) were isolated from human blood via Ficoll gradient centrifugation. Dendritic cells were generated from human PBMCs as previously described (Sallusto et al., J. Exp Med 179:1109-1118, 1994). In brief, CD14+ monocytes were isolated using magnetic sorting (MACS, Miltenyi), and cultured for 5 days at 1X10^6 cells/ml in media containing IL-4 (800 U/ml) and GM-CSF (1500 U/ml). Immature DCs were harvested and resuspended in fresh media containing IL-4 and GM-CSF at 1X10^6 cells/ml/well in 24 well plates,  then stimulated for 48hrs with LPS (100ng/ml) to induce maturation.

tag: Human peripheral blood dendritic cells differentiated from CD14+ peripheral blood monocytes using IL-4 and GM-CSF, then stimulated for 48 hours with LPS to induced maturation


title: 2hr shaded replicate 3

extract_protocol: Approximately 100 3-day-old B. oleracea seedlings that has been stimulated with unidirectional blue-light were trisected into lit flanks, vasculature, and shaded flanks. The lit and shaded flanks were collected and Total RNA was extracted from the tissue  using an RNeasy kit (Qiagen).


title: 2hr bottom replicate 3

description: wild type, gravity treated Brassica hypocotyl tissue

extract_protocol: Approximately 100 3-day-old B. oleracea seedlings that has been gravity stimulated were trisected into top flanks, vasculature, and bottom  flanks. The top and bottom flanks were collected and Total RNA was extracted from the tissue  using an RNeasy kit (Qiagen).


title: Supernatant of infection treated with 3 rounds of SCOTS, replicate 1

type: mixed

city: Montreal

first: Sébastien

middle: P

last: Faucher

state: QUEBEC

address: C.P. 6128 Succ. Centre-Ville

department: Microbiology and Immunology

country: Canada

institute: University of Montreal

description: This sample was used to analyse the expression profiles of Salmonella typhi during infection of human macrophages (THP-1)

hyb_protocol: Samples we hybridized as previously described (Porwolik, S. 2003.Nucleic Acids Res 31:1869-76)

scan_protocol: Slide was scanned with Scan Array Lite (Perkin-Elmer) using Scan Array Express 2.1 software.

data_processing: After backgroud correction and total intensity normalization, ratio to reference were calculated and log base 2 transformed.

organism: Salmonella enterica subsp. enterica serovar Typhi

source_name: 3XSCOTS cDNA obtained from infection supernatant

label_protocol: 1.5 µg of cDNA was labeled with Cy5-dCTP (GE Healthcare) by random priming with Klenow (New England Biolabs) as previously described (Porwollik, S. 2001. Mutat Res 483:1-11.).

extract_protocol: TRIzol reagent (Gibco BRL) was used according to the manufacturer instruction. RNA was treated with DNase (Ambion). RNA sample was converted to cDNA in 5 independent reverse-transcription reactions as described previously (Graham, J. 1999. PNAS 96:11554-559). Bacterial transcript were purified from host transcript by using 3 round of the SCOTS procedure (Daigle, F. 2002. Methods Enzymol. 358:108-122).

treatment_protocol: 2E7 THP-1 cells (treated with 1E-7 M phorbol 12-myristate 13-acetate) were infected with Salmonella typhi at a multiplicity of infection of 10:1. At time 0, the supernatant was removed and centrifuge to recover the bacteria. The pellet was lysed with 2 ml of TRIzol (Gibco BRL)

tag: Salmonella typhi infection of THP-1 cells, recovered from the culture medium supernatant

molecule: genomic DNA

source_name: Reference genomic DNA

label_protocol: 1.5 µg of genomic DNA was labeled with Cy3-dCTP (GE Healthcare) by random priming with Klenow (New England Biolabs) as previously described (Porwollik, S. 2001. Mutat Res 483:1-11.).

growth_protocol: Salmonella typhi from overnight culture in LB broth.

extract_protocol: Genomic DNA was extracted by standard phenol-chloroform method (Sambrook, J, Molecular Cloning, 3rd Edition)

tag: Genomic DNA from Salmonella typhi ISP1820


title: 2hr shaded replicate 2


title: Menadione treated 3.00 h sample - summary of normalized experimental data

status: Public on Jan 05 2006

city: Debrecen

first: Istvan

last: Pocsi

address: Egyetem tér 1.

department: Dept.of Microbiology and Biotechnology

country: Hungary

institute: University of Debrecen

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 3 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37969 and GSM37970.

organism: Aspergillus nidulans

source_name: Menadione treated

source_name: Untreated control


title: H2O2 treated 6.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 6 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM38540 and GSM38541.

source_name: H2O2 treated


title: Menadione treated 0.50 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 30 min. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37965 and GSM37966.


title: Menadione treated 9.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 9 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37973 and GSM37974.


title: H2O2 treated 9.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 9 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37963 and GSM37964.


title: 2hr shaded replicate 1


title: Menadione treated 6.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 6 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37971 and GSM37972.


title: H2O2 treated 1.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 1 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37957 and GSM37958.


title: H2O2 treated 3.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 3 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37959 and GSM37960.


title: H2O2 treated 6.00 h sample- 1st print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 6 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM38539.


title: Menadione treated 1.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 1 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37967 and GSM37968.


title: Menadione treated 9.00 h sample- 2nd print of spots - pimary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 9 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37735.


title: Menadione treated 3.00 h sample- 2nd print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 3 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37733.


title: Menadione treated 6.00 h sample- 2nd print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 6 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37734.


title: H2O2 treated 0.50 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 30 min. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37955 and GSM37956.


title: Menadione treated 3.00 h sample- 1st print of spots - primary experimental data.


title: H2O2 treated 6.00 h sample- 2nd print of spots - primary experimental data.


title: Menadione treated 6.00 h sample- 1st print of spots - primary experimental data.


title: Menadione treated 0.50 h sample- 2nd print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 30 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37731.


title: Menadione treated 1.00 h sample- 2nd print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 1 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37732.


title: Menadione treated 0.50 h sample- 1st print of spots - primary experimental data.


title: Menadione treated 9.00 h sample- 1st print of spots - primary experimental data.


title: H2O2 treated 0.25 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 15 min. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37953 and GSM37954.


title: Diamide treated 6.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 6 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37951 and GSM37952.

source_name: Diamide treated


title: H2O2 treated 9.00 h sample- 2nd print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 9 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37730.


title: Diamide treated 3.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 3 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37949 and GSM37950.


title: Diamide treated 1.00 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 1 h. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37942 and GSM37948.


title: Diamide treated 0.25 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 15 min. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37909 and GSM37910.


title: Menadione treated 1.00 h sample- 1st print of spots - primary experimental data.


title: Diamide treated 0.50 h sample - summary of normalized experimental data

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 30 min. Primary unprocessed experimental data are summarized on Platform GPL1756 in files Samples GSM37927 and GSM37928.


title: H2O2 treated 3.00 h sample- 2nd print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 3 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37728.


title: H2O2 treated 1.00 h sample- 1st print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 1 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37726.


title: H2O2 treated 0.25 h sample- 1st print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 15 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37724.


title: Diamide treated 6.00 h sample- 1st print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 6 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37723.


title: H2O2 treated 0.25 h sample- 2nd print of spots - primary experimental data.


title: H2O2 treated 0.50 h sample- 2nd print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 30 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37725.


title: Diamide treated 3.00 h sample- 1st print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 3 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37722.


title: H2O2 treated 3.00 h sample- 1st print of spots - primary experimental data.


title: Diamide treated 0.25 h sample- 1st print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 15 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37718.


title: C57BL/6 vs. C57BL/6 Cholesterol

status: Public on Jan 04 2006

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Total RNA was prepared using the RNeasy protocol with on-column DNAse digestion (Qiagen, Hilden, Germany) and confirmed to be intact and free of contaminating DNA using an Agilent 2100 bioanalyzer and a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA). A custom tailored 'in situ' synthesized 60-mer oligonucleotide microarray (Agilent) comprising 8014 murine genes with immunological focus was used for expression profiling. RNA was amplified and labeled using a reverse-transcriptase/T7 polymerase linear amplification labeling kit (Agilent), and 1.5 mg of respective cRNAs labeled either with Cy3 or Cy5 were hybridized for 16 h at 65°C. Slides were used and processed according to the manufacturer's manuals.

data_processing: Features were extracted with an Image Analysis software (Version A.7.5.1, Agilent). Intensities were normalized by local background correction and by rank consistency filtering with a combination of linear and LOWESS normalization. Data analysis was performed with Rosetta Resolver Biosoftware (Build 5.1.0.0.163, Rosetta Biosoftware, Seattle, WA).

organism: Mus musculus

tag: Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany). The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.

source_name: C57BL/6 Cholesterol

tag: Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany) were treated with 2% or 0% cholesterol diet (custom product (Altromin, Lage, Germany). The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.


title: Diamide treated 0.50 h sample- 2nd print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 30 min. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37720.


title: Diamide treated 0.50 h sample- 1st print of spots - primary experimental data.


title: H2O2 treated 1.00 h sample- 2nd print of spots - primary experimental data.


title: Diamide treated 6.00 h sample- 2nd print of spots - primary experimental data.


title: H2O2 treated 0.50 h sample- 1st print of spots - primary experimental data.


title: Diamide treated 3.00 h sample- 2nd print of spots - primary experimental data.


title: Diamide treated 1.00 h sample- 2nd print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 1 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37721.


title: Diamide treated 0.25 h sample-  2nd print of spots - primary experimental data.


title: C2C12 (2), chip MG_U74Cv2

status: Public on Dec 09 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

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

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

label: Biotin

source_name: C2C12, Skeletal muscle

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

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

tag: Strain:					C3H

tag: Defining markers:				Myosin heavy chain, myogenin


title: C2C12 (3), chip MG_U74Cv2


title: HGPS AG10750 cell line, sample 1, B chip (AG10750_1_U133B.txt)

status: Public on Dec 31 2005

city: Boston

first: Sangeeta

last: English

state: MA

address: 300 Longwood Avenue

institute: Children's Hospital

description: Primary fibroblasts were obtained from Coriell Cell Repositories (Coriell Institute for Medical Research, Camden, NJ, USA). The HGPS cell lines AG10750 (M, 9 years), AG11498 (M, 14 years) and AG11513 (F, 8 years) have been shown to be heterozygous for the codon 608 GGC>GGT mutation (Erikkson et al., 2003). The age indicated in parentheses refers to the age of the donor at the time of biopsy. For controls we used primary cell lines derived from age-matched, apparently normal donors: GM00038C (F, 9 years), GM00316B (M, 12 years) and GM08398C (M, 8 years). Total RNA was isolated using the TRIzol reagent (Life Technologies) and further purified on RNeasy mini columns (Qiagen).Five micrograms of total RNA was used in each labeling reaction. Hybridization was done using Affymetrix HG-U133B arrays.

data_processing: Affymetrix HG-U133B arrays were used. Intensity values were quantitated by MAS 5.0 software (Affymetrix). All the chips were scaled to the same target intensity of 500.

source_name: Hutchinson–Gilford progeria syndrome (HGPS) primary fibroblast cell line

tag: Cell Line

value: AG10750, Gender:Male, Age:9 years


title: C2C12 (1), chip MG_U74Cv2


title: HGPS AG10750 cell line, sample 2, A chip (AG10750_2_U133A.txt)

description: Primary fibroblasts were obtained from Coriell Cell Repositories (Coriell Institute for Medical Research, Camden, NJ, USA). The HGPS cell lines AG10750 (M, 9 years), AG11498 (M, 14 years) and AG11513 (F, 8 years) have been shown to be heterozygous for the codon 608 GGC>GGT mutation (Erikkson et al., 2003). The age indicated in parentheses refers to the age of the donor at the time of biopsy. For controls we used primary cell lines derived from age-matched, apparently normal donors: GM00038C (F, 9 years), GM00316B (M, 12 years) and GM08398C (M, 8 years). Total RNA was isolated using the TRIzol reagent (Life Technologies) and further purified on RNeasy mini columns (Qiagen).Five micrograms of total RNA was used in each labeling reaction. Hybridization was done using Affymetrix HG-U133A arrays.

data_processing: Affymetrix HG-U133A arrays were used. Intensity values were quantitated by MAS 5.0 software (Affymetrix). All the chips were scaled to the same target intensity of 500.

source_name: Hutchinson–Gilford progeria syndrome (HGPS) primary fibroblast cell strain

tag: Cell line


title: PG13 MP3, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Mickie Bhatia (mbhatia@robarts.ca; Box 5015; 100 Perth Drive) for analysis.
Stembase Experiment ID:			E37
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37
SCGP Sample ID:				S56
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37#SAMPLE_42
Short description:			Total RNA from PG13 transduced with retroviral vector (MIEV) alone.
Estimated purity:				~ 98%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				9.0 ul

source_name: PG13 cell line, Fibroblast

growth_protocol: Growth medium:				IMDM

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

treatment_protocol: Assays to confirm viability:		7AAD staining

tag: Defining markers:				GFP


title: PG13 MP1, chip MG_U74Cv2


title: 3D4, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID:			E30
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID:				S34
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_32
Short description:			Chondroblasts harvested at 3 days.
Estimated purity:				90-95%
Num cells for RNA prep:			6x10e6

source_name: Mesenchymal cells, Limb bud

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

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

tag: Strain:					CD-1

tag: Defining markers:				Sox9, type II collagen


title: PG13 SP3, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Mickie Bhatia (mbhatia@robarts.ca; Box 5015; 100 Perth Drive) for analysis.
Stembase Experiment ID:			E37
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37
SCGP Sample ID:				S55
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37#SAMPLE_41
Short description:			Total RNA from PG13 transduced with Smad7 recombinant retroviral vector (MIEV-Smad7).
Estimated purity:				~ 98%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				9.0 ul


title: PG13 SP1, chip MG_U74Cv2


title: 1D4, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID:			E30
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID:				S33
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_31
Short description:			Chondroprogenitors harvested at 1 day.
Estimated purity:				90-95%
Num cells for RNA prep:			6x10e6


title: OH4, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID:			E30
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID:				S32
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_30
Short description:			These samples are multipotential mesenchymal cells.
Estimated purity:				90-95%
Num cells for RNA prep:			6x10e6

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


title: C57BL/6 Cholesterol vs. C57BL/6


title: PG13 MP2, chip MG_U74Cv2


title: 1D3, chip MG_U74Cv2


title: 3D3, chip MG_U74Cv2


title: 1D1, chip MG_U74Cv2


title: OH3, chip MG_U74Cv2


title: Untransformed (control 2), chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E17
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=17
SCGP Sample ID:				S19
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=17#SAMPLE_17
Short description:			Untransformed marrow stromal cells from normal C57Bl/6 mice.
Estimated purity:				100%
RNA concentration:			190-274 ug/ul
Num cells for RNA prep:			4-8x10e6
Sample volume:				40 ul

source_name: Primary marrow stromal cells, Bone marrow

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

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

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

tag: Strain:					C57Bl/6

tag: Gender:					Female

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


title: PG13 SP2, chip MG_U74Cv2


title: 3D1, chip MG_U74Cv2


title: OH1, chip MG_U74Cv2


title: GFP_Exe TS (replicate 2), chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S14
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_12
Short description:			GFP-Exe Trophoblast stem cells (WT+GFP transgene)
Estimated purity:				90-95%
RNA concentration:			3.24 ug/ul
Sample volume:				29.0 ul

source_name: TS cell line, Extraembryonic ectoderm

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

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

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

tag: Strain:					ICR

tag: Defining markers:				Eomesodermin, Cdx2, 8MP4


title: RIES, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S13
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_11
Short description:			R1ES: Embryonic stem cells (WT)
Estimated purity:				95-99%
RNA concentration:			3.81 ug/ul
Sample volume:				15.0 ul

source_name: ES cell line, Blastocyst

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

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

tag: Strain:					129/SV

tag: Defining markers:				Oct4


title: Untransformed (control 3), chip MG_U74Cv2


title: Pool 2, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S119
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_89
Short description:			RNA isolated from normal FVB mouse mammary glands.
Estimated purity:				80%
RNA concentration:			2.2 ug/ul
Sample volume:				10.0 ul

source_name: Tissue, Mammary gland

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

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

tag: Strain:					FVB


title: GFP_Exe TS (replicate 3), chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S14
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_12
Short description:			GFP-Exe Trophoblast stem cells (WT+GFP transgene)
Estimated purity:				90-95%
RNA concentration:			3.74 ug/ul
Sample volume:				15.0 ul


title: Pool 3, chip MG_U74Cv2


title: WT2-Expt6, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S65
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_49
Short description:			RNA pool from mammary glands tumours of wild-type PEA3 mice induced by the Her2/Neu transgene.
Estimated purity:				80%
RNA concentration:			2.0 ug/ul
Sample volume:				10.0 ul

source_name: , Mammary gland

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


title: Untransformed (control 1), chip MG_U74Cv2


title: mMSC CD34- 3, chip MG_U74Cv2

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

source_name: Bone marrow stromal cell clone, Bone marrow

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

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

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


title: WT1-Expt6, chip MG_U74Cv2


title: mMSC CD34+ 2, chip MG_U74Cv2

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

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


title: mMSC CD34- 1, chip MG_U74Cv2

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


title: mMSC CD34- 2, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S44
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_36
Short description:			CD34- cells isolated from adult bone marrow. Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			1.38 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				10.8 ul
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S44
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_36
Short description:			CD34- cells isolated from adult bone marrow. Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			1.38 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				10.8 ul


title: mMSC CD34+ 1, chip MG_U74Cv2

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


title: C2C12 (3), chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Lynn Megeney (lmegeney@ohri.ca; 501 Smyth Road, Room 4E102) for analysis.
Stembase Experiment ID:			E1
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=1
SCGP Sample ID:				S2
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=1#SAMPLE_1
Short description:			RNA extracted from C2C12 mouse skeletal muscle cells following 5 days of culture in differentiation medium.
Estimated purity:				100%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			2x10e7
Sample volume:				10.0 ul

tag: Strain:					C3H


title: PG13 MP2, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Mickie Bhatia (mbhatia@robarts.ca; Box 5015; 100 Perth Drive) for analysis.
Stembase Experiment ID:			E37
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37
SCGP Sample ID:				S56
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37#SAMPLE_42
Short description:			Total RNA from PG13 transduced with retroviral vector (MIEV) alone.
Estimated purity:				~ 98%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				9.0 ul


title: PG13 MP3, chip MG_U74Bv2


title: C2C12 (1), chip MG_U74Bv2

tag: Defining markers:				Myosin heavy chain, myogenin


title: PG13 MP1, chip MG_U74Bv2


title: mMSC CD34+ 3, chip MG_U74Cv2

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


title: PG13 SP2, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Mickie Bhatia (mbhatia@robarts.ca; Box 5015; 100 Perth Drive) for analysis.
Stembase Experiment ID:			E37
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37
SCGP Sample ID:				S55
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=37#SAMPLE_41
Short description:			Total RNA from PG13 transduced with Smad7 recombinant retroviral vector (MIEV-Smad7).
Estimated purity:				~ 98%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				9.0 ul


title: 3D4, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID:			E30
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID:				S34
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_32
Short description:			Chondroblasts harvested at 3 days.
Estimated purity:				90-95%
Num cells for RNA prep:			6x10e6


title: 3D3, chip MG_U74Bv2


title: PG13 SP3, chip MG_U74Bv2


title: PG13 SP1, chip MG_U74Bv2


title: 3D1, chip MG_U74Bv2


title: 1D4, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID:			E30
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID:				S33
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_31
Short description:			Chondroprogenitors harvested at 1 day.
Estimated purity:				90-95%
Num cells for RNA prep:			6x10e6


title: 1D3, chip MG_U74Bv2


title: H2O2 treated 9.00 h sample- 1st print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 75 mM H2O2 for 9 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37730.


title: 1D1, chip MG_U74Bv2


title: GFP_Exe TS (replicate 1), chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S14
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_12
Short description:			GFP-Exe Trophoblast stem cells (WT+GFP transgene)
Estimated purity:				90-95%
RNA concentration:			3.60 ug/ul
Sample volume:				29 ul


title: Untransformed (control 1), chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E17
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=17
SCGP Sample ID:				S19
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=17#SAMPLE_17
Short description:			Untransformed marrow stromal cells from normal C57Bl/6 mice.
Estimated purity:				100%
RNA concentration:			190-274 ug/ul
Num cells for RNA prep:			4-8x10e6
Sample volume:				40 ul


title: Pool 1, chip MG_U74Cv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S119
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_89
Short description:			RNA isolated from normal FVB mouse mammary glands.
Estimated purity:				80%
RNA concentration:			2.1 ug/ul
Sample volume:				10.0 ul


title: OH3, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. T. Michael Underhill (tunderhi@uwo.ca; 1400 Western Road) for analysis.
Stembase Experiment ID:			E30
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30
SCGP Sample ID:				S32
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=30#SAMPLE_30
Short description:			These samples are multipotential mesenchymal cells.
Estimated purity:				90-95%
Num cells for RNA prep:			6x10e6


title: Untransformed (control 3), chip MG_U74Bv2


title: Untransformed (control 2), chip MG_U74Bv2


title: OH4, chip MG_U74Bv2


title: GFP_Exe TS (replicate 2), chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S14
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_12
Short description:			GFP-Exe Trophoblast stem cells (WT+GFP transgene)
Estimated purity:				90-95%
RNA concentration:			3.24 ug/ul
Sample volume:				29.0 ul


title: OH1, chip MG_U74Bv2


title: GFP_Exe TS (replicate 3), chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S14
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_12
Short description:			GFP-Exe Trophoblast stem cells (WT+GFP transgene)
Estimated purity:				90-95%
RNA concentration:			3.74 ug/ul
Sample volume:				15.0 ul


title: R1ES n+1, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S13
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_11
Short description:			R1ES: Embryonic stem cells (WT)
Estimated purity:				95-99%
RNA concentration:			5.88 ug/ul
Sample volume:				40.0 ul


title: RIES, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S13
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_11
Short description:			R1ES: Embryonic stem cells (WT)
Estimated purity:				95-99%
RNA concentration:			3.81 ug/ul
Sample volume:				15.0 ul


title: R1ES n+2, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Janet Rossant (rossant@mshri.on.ca; 884-600 University Avenue) for analysis.
Stembase Experiment ID:			E11
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11
SCGP Sample ID:				S13
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=11#SAMPLE_11
Short description:			R1ES: Embryonic stem cells (WT)
Estimated purity:				95-99%
RNA concentration:			5.10 ug/ul
Sample volume:				40.0 ul


title: Pool 1, chip MG_U74Bv2


title: C2C12 (2), chip MG_U74Bv2


title: Pool 3, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S119
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_89
Short description:			RNA isolated from normal FVB mouse mammary glands.
Estimated purity:				80%
RNA concentration:			2.2 ug/ul
Sample volume:				10.0 ul


title: Pool 2, chip MG_U74Bv2


title: WT2-Expt6, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S65
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_49
Short description:			RNA pool from mammary glands tumours of wild-type PEA3 mice induced by the Her2/Neu transgene.
Estimated purity:				80%
RNA concentration:			2.0 ug/ul
Sample volume:				10.0 ul


title: Diamide treated 1.00 h sample- 1st print of spots - primary experimental data.

description: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 1.8 mM diamide for 1 h. Processed data after LOESS-type block-by-block normalization are summarized on Platform GPL1752 in file Sample GSM37721.


title: Null2-Expt6, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E6
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6
SCGP Sample ID:				S8
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=6#SAMPLE_6
Short description:			RNA pool from mammary glands tumours of PEA3-null mice induced by the Her2/Neu transgene.
Estimated purity:				80%
RNA concentration:			2.0 ug/ul
Sample volume:				10.0 ul

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


title: WT1-Expt6, chip MG_U74Bv2


title: Null1-Expt6, chip MG_U74Bv2


title: WT3-Expt6, chip MG_U74Bv2


title: mMSC CD34- 3, chip MG_U74Bv2

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


title: mMSC CD34+ 3, chip MG_U74Bv2

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


title: mMSC CD34- 1, chip MG_U74Bv2

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


title: mMSC CD34+ 1, chip MG_U74Bv2

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


title: mMSC CD34+ 2, chip MG_U74Bv2

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


title: mMSC CD34- 2, chip MG_U74Bv2

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S44
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_36
Short description:			CD34- cells isolated from adult bone marrow. Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			1.38 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				10.8 ul
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jacques Galipeau (jgalipea@lab.jgh.mcgill.ca; Sir Mortimer B. Davis-Jewish General Hospital; 3755 Cote Ste-Catherine Road) for analysis.
Stembase Experiment ID:			E3
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3
SCGP Sample ID:				S44
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=3#SAMPLE_36
Short description:			CD34- cells isolated from adult bone marrow. Subsequently, pure colonies were selected and characterized.
Analysis requested:			Compare to control/normal marrow stromal cells previously analyzed for J. Galipeau - Murine genome U74A-C
Estimated purity:				100%
RNA concentration:			1.38 ug/ul
Num cells for RNA prep:			4x10e6
Sample volume:				10.8 ul


title: I-6/SSEA+ 3, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E208
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=208
SCGP Sample ID:				S264
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=208#SAMPLE_282
Short description:			Human ES cell line I-6 was cultured in standard conditions to maintain an undifferentiated, self renewing phenotype.  The cells were sorted based upon their expression of SSEA4, which is a marker of  the undifferentiated, self renewing phenotype.
Estimated purity:				above 99.5%
RNA concentration:			150ng/ul
Num cells for RNA prep:			1e6 cells/sample
Sample volume:				10ul

source_name: I-6 ES,

growth_protocol:
Growth medium:				KO-DMEM
Media supplements:			20% KO serum replacement, bFGF
Culture conditions:			37 C, 5% CO2

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

tag: Gender:					Male

tag: Defining markers:				SSEA+


title: MPB3, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Mickie Bhatia (mbhatia@robarts.ca; Box 5015; 100 Perth Drive) for analysis.
Stembase Experiment ID:			E2
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=2
SCGP Sample ID:				S3
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=2#SAMPLE_2
Short description:			Human mobilized peripheral blood, amplified RNA, biotin labeled, fragmented.
Estimated purity:				~ 100%
RNA concentration:			500 ng/ul
Num cells for RNA prep:			200 000
Sample volume:				30 ul

source_name: Hematopoietic stem cells, Blood

growth_protocol: Growth medium:				None

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

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


title: I-6/SSEA+ 1, chip HG-U133B


title: I-6/SSEA+ 2, chip HG-U133B


title: I-6/SSEA- 2, chip HG-U133B

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

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

tag: Defining markers:				SSEA-


title: MPB1, chip HG-U133B


title: I-6/SSEA- 1, chip HG-U133B


title: MPB2, chip HG-U133B


title: JEACFU-F-III, chip RAE230A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jane Aubin (jane.aubin@utoronto.ca; 6230 Medical Building; 1 King's College Circle) for analysis.
Stembase Experiment ID:			E179
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179
SCGP Sample ID:				S223
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179#SAMPLE_181
Short description:			RNA was isolated from colonies expressing neither the osteocalcin nor the adipsin markers.
Num cells for RNA prep:			100-300 (single colonies)
Sample volume:				17 ul (first strand cDNA)

organism: Rattus norvegicus

source_name: Primary culture; single cell colonies, Calvaria

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

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

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

tag: Strain:					Wistar

tag: Gender:					Both male and female fetuses

tag: Karyotype:				Diploid

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


title: JEACFU-Bi-II, chip RAE230A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jane Aubin (jane.aubin@utoronto.ca; 6230 Medical Building; 1 King's College Circle) for analysis.
Stembase Experiment ID:			E179
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179
SCGP Sample ID:				S222
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179#SAMPLE_180
Short description:			RNA was isolated from colonies expressing both the osteocalcin and the adipsin markers.
Num cells for RNA prep:			100-300 (single colonies)
Sample volume:				17 ul (first strand cDNA)


title: Null1-Expt6, chip MG_U74Cv2


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

source_name: Retinal sphere cells, Ciliary margin of eye

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

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

treatment_protocol: Assays to confirm viability:		Sphere assay


title: Lin+-1, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S173
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_133
Short description:			These cord blood derived lineage positive hematopoietic cells were collected following 4 days of culture from cord blood derived, lineage negative, hematopoietic cells.
Estimated purity:				>99%
RNA concentration:			Low
Num cells for RNA prep:			2.0x10e5

source_name: Hematopoietic, Cord blood

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

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

tag: Defining markers:				Lin+


title: JEACFU-Bi-III, chip RAE230A


title: JEACFU-F-II, chip RAE230A


title: Human primary retinal sphere, 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. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis.
Stembase Experiment ID:			E189
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189
SCGP Sample ID:				S238
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_196
Short description:			RNA isolated from primary retinal sphere cells.
Estimated purity:				> 90%
Num cells for RNA prep:			~600,000
Sample volume:				5.0 ul

source_name: Primary retinal sphere cells, Ciliary margin of eye


title: JEACFU-F-I, chip RAE230A


title: JEACFU-Bi-I, chip RAE230A


title: JEACFU-O-III, chip RAE230A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Jane Aubin (jane.aubin@utoronto.ca; 6230 Medical Building; 1 King's College Circle) for analysis.
Stembase Experiment ID:			E179
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179
SCGP Sample ID:				S221
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=179#SAMPLE_179
Short description:			RNA was isolated from colonies expressing the osteocalcin marker.
Num cells for RNA prep:			100-300 (single colonies)
Sample volume:				17 ul (first strand cDNA)


title: I-6/SSEA- 3, chip HG-U133B


title: JEACFU-O-II, chip RAE230A


title: FM-3, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S172
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_132
Short description:			Cord blood derived, lineage negative, hematopoietic cells were cultured for 4 days and then subjected to a fresh medium exchange.  The cells were then allowed to incubate for 24 hours prior to RNA extraction.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			9.2x10e5
Sample volume:				3.0 ul

extract_protocol: RNA prep method:				TRIzol

tag: Defining markers:				Lin-


title: I-6/SSEA- 3, chip HG-U133A


title: FM-2, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S172
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_132
Short description:			Cord blood derived, lineage negative, hematopoietic cells were cultured for 4 days and then subjected to a fresh medium exchange.  The cells were then allowed to incubate for 24 hours prior to RNA extraction.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			1.0x10e6
Sample volume:				3.0 ul


title: FM-1, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S172
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_132
Short description:			Cord blood derived, lineage negative, hematopoietic cells were cultured for 4 days and then subjected to a fresh medium exchange.  The cells were then allowed to incubate for 24 hours prior to RNA extraction.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			2.1x10e6
Sample volume:				3.0 ul


title: JEACFU-O-I, chip RAE230A


title: Osteo30 VD3-2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Derrick Rancourt (rancourt@ucalgary.ca; Room 2221 Health Sciences Centre; 3330 Hospital Drive NW) for analysis.
Stembase Experiment ID:			E202
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202
SCGP Sample ID:				S196
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_240
Short description:			D3 murine embryonic stem cells were allowed to undergo directed differentiation toward the osteoblast lineage by the addition of vitamin D3, B-glycerophosphate, and absorbic acid.  Assessment of the gene expression patterns of differentiated cells at day 4, 5, 6, 8, 16, 25, and 30 and comparison to profiles of mES cells that have undergone non-directed differentiation will allow the elucidation of genes that are important to the early commitment of these cells to the osteoblast lineage.
Analysis requested:			For SCGP, compare gene expression in samples ctrl vs. VD3 treated in Osteo_1  -- Osteo_4
Cell line clone ID:			n/a
Estimated purity:				pure clone
RNA concentration:			100 ng/ul
Num cells for RNA prep:			3 x 10^6
Sample volume:				12ul - 6ul for BA and 6 ul for exp

source_name: D3, Blastocyst

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

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

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

tag: Strain:					129 SV

tag: Karyotype:				normal

tag: Defining markers:				n/a


title: Osteo30 VD3-3, chip MOE430B


title: CM-3, chip HG-U133B

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


title: Osteo30 VD3-1, chip MOE430B


title: CM-2, chip HG-U133B

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


title: CM-1, chip HG-U133B

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


title: Osteo16 VD3-3, chip MOE430B

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


title: Osteo25 VD3-2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Derrick Rancourt (rancourt@ucalgary.ca; Room 2221 Health Sciences Centre; 3330 Hospital Drive NW) for analysis.
Stembase Experiment ID:			E202
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202
SCGP Sample ID:				S194
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_239
Short description:			D3 murine embryonic stem cells were allowed to undergo directed differentiation toward the osteoblast lineage by the addition of vitamin D3, B-glycerophosphate, and absorbic acid.  Assessment of the gene expression patterns of differentiated cells at day 4, 5, 6, 8, 16, 25, and 30 and comparison to profiles of mES cells that have undergone non-directed differentiation will allow the elucidation of genes that are important to the early commitment of these cells to the osteoblast lineage.
Analysis requested:			For SCGP, compare gene expression in samples ctrl vs. VD3 treated in Osteo_1  -- Osteo_4
Cell line clone ID:			n/a
Estimated purity:				pure clone
RNA concentration:			100 ng/ul
Num cells for RNA prep:			3 x 10^6
Sample volume:				12ul - 6ul for BA and 6 ul for exp


title: I-6/SSEA+ 2, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E208
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=208
SCGP Sample ID:				S264
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=208#SAMPLE_282
Short description:			Human ES cell line I-6 was cultured in standard conditions to maintain an undifferentiated, self renewing phenotype.  The cells were sorted based upon their expression of SSEA4, which is a marker of  the undifferentiated, self renewing phenotype.
Estimated purity:				above 99.5%
RNA concentration:			150ng/ul
Num cells for RNA prep:			1e6 cells/sample
Sample volume:				10ul


title: Day 4-2, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S170
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_130
Short description:			These samples, cord blood derived lineage negative hematopoietic cells, were collected following 4 days of culture.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			3.7x10e5
Sample volume:				3.0 ul


title: Osteo25 VD3-3, chip MOE430B


title: I-6/SSEA+ 3, chip HG-U133A


title: Human retinal sphere RNA-2, chip HG-U133B


title: Day 4-3, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Peter Zandstra (peter.zandstra@utoronto.ca; 170 College Street) for analysis.
Stembase Experiment ID:			E130
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130
SCGP Sample ID:				S170
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=130#SAMPLE_130
Short description:			These samples, cord blood derived lineage negative hematopoietic cells, were collected following 4 days of culture.
RNA concentration:			50 ng/ul
Num cells for RNA prep:			4.2x10e5
Sample volume:				3.0 ul


title: Osteo d8VD3-2, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Derrick Rancourt (rancourt@ucalgary.ca; Room 2221 Health Sciences Centre; 3330 Hospital Drive NW) for analysis.
Stembase Experiment ID:			E202
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202
SCGP Sample ID:				S190
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=202#SAMPLE_237
Short description:			D3 murine embryonic stem cells were allowed to undergo directed differentiation toward the osteoblast lineage by the addition of vitamin D3, B-glycerophosphate, and absorbic acid.  Assessment of the gene expression patterns of differentiated cells at day 4, 5, 6, 8, 16, 25, and 30 and comparison to profiles of mES cells that have undergone non-directed differentiation will allow the elucidation of genes that are important to the early commitment of these cells to the osteoblast lineage.
Analysis requested:			For SCGP, compare gene expression in samples ctrl vs. VD3 treated in Osteo_1  -- Osteo_4
Cell line clone ID:			n/a
Estimated purity:				pure clone
RNA concentration:			100 ng/ul
Num cells for RNA prep:			3 x 10^6
Sample volume:				12ul - 6ul for BA and 6 ul for exp


title: Osteo d8VD3-3, chip MOE430B


title: Osteo25 VD3-1, chip MOE430B


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


title: Osteo d8VD3-1, chip MOE430B


title: Osteo16 VD3-2, chip MOE430B


title: Osteo16 VD3-1, chip MOE430B


title: Human primary retinal sphere, chip HG-U133A


title: Human retinal sphere RNA-2, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Rod McInnes (mcinnes@sickkids.on.ca; 555 University Ave, Elm Wing 11-101) for analysis.
Stembase Experiment ID:			E189
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189
SCGP Sample ID:				S231
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=189#SAMPLE_189
Short description:			RNA isolated from first passage retinal sphere cells.
Estimated purity:				> 90%
RNA concentration:			> 30.0 ng
Num cells for RNA prep:			~160,000
Sample volume:				5.0 ul