title: CGH_108_BEVA

status: Public on Feb 05 2007

city: Pamplona

first: Jose Angel

middle: Martinez

last: Climent

state: Navarra

address: PIO XII

country: Spain

institute: CIMA/Universidad De Navarra

description: Genome-wide analysis of DNA-copy number changes of BEVA cell line.

data_processing: We used “UCSF SPOT” software (A.N.J. manuscript submitted) to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the September, 2000 freeze of the draft human genome sequence (http://genome.ucsc.edu).  SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content.

source_name: BEVA cell line

tag: Cell line derived from diffuse large B-cell lymphoma with the translocation t(14;18)(q32;q21). Derived from 48-years-old male.

tag: Specimen site

value: bone marrow.

source_name: Reference genomic DNA.

tag: Normal female reference genomic DNA.


title: Ky2: Hippocampus_21PT-Y_rep2

status: Public on Mar 15 2007

type: RNA

city: Lexington

first: Veronique

last: Thibault

state: KY

address: 800 Rose Street

department: Pharmacology

country: USA

institute: University of Kentucky

description: Gene expression data from Young and Aged behaviorally characterized F344 rats

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Rattus Norvegus. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scan.

data_processing: Microarray Data Filtering: Procedures employed were similar to those used previously (Blalock et al., 2003; Blalock et al., 2004). Briefly, the Microarray Analysis Suite 5 (MAS5) algorithm was applied using Affymetrix’ Gene Chip Operating System software (GCOS v1.1). All-probe-set scaling normalization (target intensity 500) was applied, and presence-call and signal intensity values were copied to Excel for further analysis. Annotations were downloaded from the Affymetrix website (July, 2005; augmented by a rat genome database search). For gene symbols represented by > 1 probe set (repeats), the probe set with the smallest test statistic was used. Within group outliers (> 2 SD from the group mean) (Blalock et al., 2004) were treated as missing values.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Behaviorally-characterized Young Unimpaired Hippocampus at Day21 (21PT-Y)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (GCOS manual, 2005, Affymetrix).

growth_protocol: The animals were left undisturbed for a minimum of 1 month in our facility until the beginning of behavioral testing. Rats were housed in pairs in polycarbonate cages (45 x 30 x 18 cm) with corncob bedding and maintained on a 12 h light/dark schedule (lights off at 7:00 P.M.). Food (LabDiet 5001 rodent diet; LabDiet, Brentwood, MO) and water were available ad libitum. Animal health was monitored by a veterinarian; animals showing overt signs of morbidity were removed from the study.

extract_protocol: Immediately after euthanasia, the dorsal half of the left hippocampus was dissected free and frozen. Subsequently, mRNA was extracted, generating ~11micrograms total RNA per hippocampal sample, labeled and hybridized to RAE-230A (Affymetrix) GeneChips according to standard protocols

treatment_protocol: Young and aged rats were separated into home cage (Non-Trained, NT) and behaviorally-characterized groups. Aged animals in the behaviorally-characterized groups were separated into two categories, aged cognitively impaired (AI) and aged cognitively unimpaired (AU) based on their relative performance in the Morris Water Maze task as previously described (Tombaugh et al., 2005)

tag: Strain:F344 Gender:Male Age

value: 4-6 Months old tissue:brain-hippocampus


title: Ky1: Hippocampus_21PT-Y_rep1


title: CGH_108_UPN1

type: genomic

description: Genome-wide analysis OF DNA-copy number changes of UPN1 cell line.

molecule: genomic DNA

organism: Homo sapiens

source_name: UPN1 cell line

tag: Cell line derived from Mantle lymphoma with t(11;14)(q13;32).


title: UtrNeo48hr(3)-5_1

status: Public on Feb 01 2007

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

description: Neo-treated versus control, 48hr timepoint, biological replicate number 3

hyb_protocol: Labeled cDNA populations were precipitated and resuspended in 20ul hybridization buffer (50% formamide, 6x SSPE, 5x Denhart’s, 0.5% SDS. 10% dextran sulfate). Microarray slides were hybridized at 37 degrees C for 12h

scan_protocol: Microarray chips were scanned using a GMS 418 Scanner (Affymetrix, Santa Clara, CA)

data_processing: Microarray images were analyzed with the BioDiscovery Imagene software package to generate raw intensity data.

molecule: polyA RNA

organism: Gallus gallus

source_name: Utricle sensory epithelia

label_protocol: Purified run-off RNAs from each sample were used as templates in an oligo dT12-15 primed cDNA synthesis reaction that included amino-allyl dUTP (Sigma, 0.2mM). The cDNA was then either coupled to Cy3 or Cy5 mono ester dyes (Amersham Pharmacia) and purified as previously described (Hughes et al, 2001)

extract_protocol: Isolation of RNA, cDNA synthesis and amplification were carried out as described in Hawkins et al, 2003 (PMID: 12761041). Following the second round of amplification, cDNA was added to an in vitro transcription kit (Ambion) as per the manufacturers instructions

tag: Isolated sensory epithelia were cultured in the presence of 1mM Neomycin for 24hrs and allowed to recover for 48hr in fresh media without neomycin

tag: time-matched control


title: UtrNeo48hr(2)-5_3

description: Neo-treated versus control, 48hr timepoint, biological replicate number 2


title: UtrNeo48hr(1)-5_2

description: Neo-treated versus control, 48hr timepoint, biological replicate number 1


title: UtrNeo48hr(3)-5_2


title: IgMG FO B cells HEL-stimulated exp2

status: Public on Mar 13 2007

city: Acton

first: Keisuke

last: Horikawa

state: ACT

address: Garran Rd

department: DIG

country: Australia

institute: JCSMR, ANU

description: 2 separate sorts, total 6 mice

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: MAS 5.0, scaled to 150

label: Biotin followed by streptavidin-PE

organism: Mus musculus

source_name: FO B cells

label_protocol: Affymetrix protocol

extract_protocol: Trizol

tag: CD21medCD23hi B cells were sorted from anti-HEL IgMG:RAG2KO:H2KK B10.BR mice 1hr after HEL injection (5 mg/head, ip).


title: UtrNeo48hr(2)-5_1


title: UtrNeo48hr(3)-5_3


title: CGH_108_NAMALWA

description: Genome-wide analysis OF DNA-copy number changes of NAMALWA cell line.

source_name: NAMALWA cell line

tag: Cell line derived from Burkitt lymphoma with t(8;14)(q24;q32).


title: UtrNeo48hr(2)-5_2


title: CVCs, undifferentiated at growing phase

status: Public on Feb 17 2007

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description: Chorionic mesoderm-derived mesenchymal cells

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16 h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Chorionic villi cells

label_protocol: cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates, according to the manufacturer's protocol (One-Cycle Target Labeling and Control Reagent package).

extract_protocol: Total cellular RNA was isolated with the RNeasy (QIAGEN), according to manufacturer's instructions.

tag: Placenta, chorionic mesodermal layer


title: UtrNeo48hr(2)-3_4


title: UtrNeo48hr(2)-5_4


title: UtrNeo48hr(2)-3_2


title: UtrNeo48hr(1)-5_1


title: UtrNeo48hr(3)-3_1


title: UtrNeo48hr(1)-3_3


title: UtrNeo48hr(2)-3_3


title: UtrNeo48hr(3)-3_2


title: CVCs, differentiated at growing phase

description: Differentiated chorionic mesoderm-derived mesenchymal cells

tag: Cardiomyocytes


title: UtrNeo48hr(3)-3_3


title: UtrNeo48hr(1)-3_2


title: UtrNeo24hr(3)-5_1

description: Neo-treated versus control, 24hr timepoint, biological replicate number 3

tag: Isolated sensory epithelia were cultured in the presence of 1mM Neomycin for 24hrs and allowed to recover for 24hr in fresh media without neomycin


title: UtrNeo48hr(1)-3_1


title: UtrNeo24hr(3)-5_3


title: UtrNeo24hr(3)-5_2


title: UtrNeo48hr(2)-3_1


title: UtrNeo24hr(1)-5_2

description: Neo-treated versus control, 24hr timepoint, biological replicate number 1


title: UtrNeo24hr(2)-5_4

description: Neo-treated versus control, 24hr timepoint, biological replicate number 2


title: UtrNeo24hr(2)-5_1


title: UtrNeo24hr(3)-3_3


title: UtrNeo24hr(3)-3_1


title: UtrNeo24hr(1)-5_1


title: UtrNeo24hr(2)-3_1


title: UtrNeo24hr(2)-5_2


title: UtrNeo24hr(2)-3_2


title: UtrNeo24hr(2)-5_3


title: UtrNeo24hr(3)-3_2


title: UtrNeo24hr(1)-3_3


title: UtrNeo24hr(2)-3_3


title: UtrNeo24hr(1)-3_4


title: UtrNeo0hr(3)-5_2

description: Neo-treated versus control, 0hr timepoint, biological replicate number 3

tag: Isolated sensory epithelia were cultured in the presence of 1mM Neomycin for 24hrs and allowed to recover for 0hr in fresh media without neomycin


title: UtrNeo24hr(1)-5_3


title: UtrNeo24hr(2)-3_4


title: UtrNeo0hr(3)-5_1


title: UtrNeo0hr(3)-5_3


title: UtrNeo24hr(1)-3_1


title: UtrNeo0hr(3)-5_5


title: UtrNeo0hr(3)-5_4


title: UtrNeo24hr(1)-3_2


title: UtrNeo0hr(2)-5_5

description: Neo-treated versus control, 0hr timepoint, biological replicate number 2


title: UtrNeo0hr(2)-5_2


title: UtrNeo0hr(1)-5_1

description: Neo-treated versus control, 0hr timepoint, biological replicate number 1


title: UtrNeo0hr(2)-5_4


title: UtrNeo0hr(2)-5_3


title: UtrNeo0hr(2)-5_1


title: UtrNeo0hr(1)-5_2


title: UtrNeo0hr(3)-3_4


title: UtrNeo0hr(3)-3_1


title: UtrNeo0hr(3)-3_2


title: UtrNeo0hr(3)-3_5


title: UtrNeo0hr(3)-3_3


title: UtrNeo0hr(2)-3_5


title: UtrNeo0hr(2)-3_6


title: UtrNeo0hr(2)-3_4


title: UtrNeo0hr(2)-3_3


title: UtrNeo0hr(1)-3_2


title: UtrNeo0hr(2)-3_2


title: UtrNeo0hr(2)-3_1


title: UtrNeo0hr(1)-3_1


title: MM-184_4

status: Public on Jan 01 2007

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data from human multiple myeloma patient MM-184

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133A arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed..

source_name: Human multiple myeloma patient MM-184

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases

tag: Legend

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

tag: Sex

value: M; Age:63; Stage:III A; MC:nd; BL:nd

tag: TC


title: MM-191_4

description: Gene expression profiling data from human multiple myeloma patient MM-191

source_name: Human multiple myeloma patient MM-191

value: F; Age:79; Stage:II A; MC:Gl; BL:+


title: MM-177_4

description: Gene expression profiling data from human multiple myeloma patient MM-177

source_name: Human multiple myeloma patient MM-177

value: M; Age:73; Stage:III A; MC:Gk; BL:+


title: MM-183_4

description: Gene expression profiling data from human multiple myeloma patient MM-183

source_name: Human multiple myeloma patient MM-183

value: M; Age:78; Stage:II A; MC:Gk; BL:-


title: MM-180_4

description: Gene expression profiling data from human multiple myeloma patient MM-180

source_name: Human multiple myeloma patient MM-180

value: F; Age:65; Stage:I A; MC:Gl; BL:-


title: MM-185_4

description: Gene expression profiling data from human multiple myeloma patient MM-185

source_name: Human multiple myeloma patient MM-185

value: M; Age:59; Stage:III A; MC:nd; BL:nd


title: Hammond_3-13_Control-shoot_Rep3_ATH1

status: Public on Jan 22 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description:
location: Growth Room
Atmosphere: Normal
Humidity: 80 %
Temperature: 22 °C
Lighting: 16 hour day
Medium: 0.8 % (w/v) agar containing 1 % (w/v) sucrose and a 1/10 MS salt  mix
Stratification: imbibed for 3-5 days at 4 °C

hyb_protocol: standard NASC hybridization protocol

scan_protocol: standard NASC scanning protocol

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

organism: Arabidopsis thaliana

label_protocol: standard NASC labeling protocol

extract_protocol: standard NASC extraction protocol

tag: Stock Code

tag: Developmental stage

tag: Tissue

value: shoots


title: MM-173_4

description: Gene expression profiling data from human multiple myeloma patient MM-173

source_name: Human multiple myeloma patient MM-173

value: F; Age:56; Stage:III B; MC:Gl; BL:-


title: MM-179_4

description: Gene expression profiling data from human multiple myeloma patient MM-179

source_name: Human multiple myeloma patient MM-179

value: M; Age:50; Stage:IIIA; MC:Gl; BL:+


title: MM-174_4

description: Gene expression profiling data from human multiple myeloma patient MM-174

source_name: Human multiple myeloma patient MM-174

value: M; Age:85; Stage:II A; MC:Ak; BL:+


title: Hammond_3-3_Caesium-treated-shoot_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: MM-161_4

description: Gene expression profiling data from human multiple myeloma patient MM-161

source_name: Human multiple myeloma patient MM-161

value: F; Age:74; Stage:I A; MC:Gl; BL:-


title: MM-160_4

description: Gene expression profiling data from human multiple myeloma patient MM-160

source_name: Human multiple myeloma patient MM-160

value: F; Age:75; Stage:II A; MC:Gl; BL:+


title: MM-186_4

description: Gene expression profiling data from human multiple myeloma patient MM-186

source_name: Human multiple myeloma patient MM-186

value: F; Age:50; Stage:III A; MC:Gk; BL:+


title: MM-178_4

description: Gene expression profiling data from human multiple myeloma patient MM-178

source_name: Human multiple myeloma patient MM-178

value: F; Age:58; Stage:III A; MC:Gk; BL:+


title: MM-190_4

description: Gene expression profiling data from human multiple myeloma patient MM-190

source_name: Human multiple myeloma patient MM-190

value: M; Age:63; Stage:III A; MC:Gl; BL:-


title: MM-155_4

description: Gene expression profiling data from human multiple myeloma patient MM-155

source_name: Human multiple myeloma patient MM-155

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: F; Age:76; Stage:I A; MC:Gk; BL:-


title: MM-167_4

description: Gene expression profiling data from human multiple myeloma patient MM-167

source_name: Human multiple myeloma patient MM-167

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: M; Age:75; Stage:II A; MC:Gl; BL:+


title: MM-159_4

description: Gene expression profiling data from human multiple myeloma patient MM-159

source_name: Human multiple myeloma patient MM-159

value: M; Age:56; Stage:IIA; MC:k; BL:+


title: MM-151_4

description: Gene expression profiling data from human multiple myeloma patient MM-151

source_name: Human multiple myeloma patient MM-151

value: F; Age:71; Stage:I A; MC:Gl; BL:+


title: MM-158_4

description: Gene expression profiling data from human multiple myeloma patient MM-158

source_name: Human multiple myeloma patient MM-158

value: M; Age:59; Stage:I A; MC:Gl; BL:-


title: MM-149_4

description: Gene expression profiling data from human multiple myeloma patient MM-149

source_name: Human multiple myeloma patient MM-149

value: F; Age:52; Stage:I A; MC:Gl; BL:-


title: MM-152_4

description: Gene expression profiling data from human multiple myeloma patient MM-152

source_name: Human multiple myeloma patient MM-152

value: M; Age:67; Stage:I A; MC:Gk; BL:-


title: MM-143_4

description: Gene expression profiling data from human multiple myeloma patient MM-143

source_name: Human multiple myeloma patient MM-143

value: M; Age:56; Stage:II A; MC:Gk; BL:+


title: MM-153_4

description: Gene expression profiling data from human multiple myeloma patient MM-153

source_name: Human multiple myeloma patient MM-153

value: M; Age:65; Stage:II A; MC:Gk; BL:-


title: MM-150_4

description: Gene expression profiling data from human multiple myeloma patient MM-150

source_name: Human multiple myeloma patient MM-150

value: F; Age:68; Stage:II A; MC:Gl; BL:-


title: MM-146_4

description: Gene expression profiling data from human multiple myeloma patient MM-146

source_name: Human multiple myeloma patient MM-146

value: M; Age:68; Stage:II A; MC:Gl; BL:+


title: MM-154_4

description: Gene expression profiling data from human multiple myeloma patient MM-154

source_name: Human multiple myeloma patient MM-154

value: F; Age:71; Stage:II A; MC:G; BL:-


title: MM-129_4

description: Gene expression profiling data from human multiple myeloma patient MM-129

source_name: Human multiple myeloma patient MM-129

value: M; Age:62; Stage:II A; MC:G; BL:+


title: MM-140_4

description: Gene expression profiling data from human multiple myeloma patient MM-140

source_name: Human multiple myeloma patient MM-140

value: M; Age:62; Stage:III B; MC:nd; BL:nd


title: MM-139_4

description: Gene expression profiling data from human multiple myeloma patient MM-139

source_name: Human multiple myeloma patient MM-139

value: F; Age:57; Stage:II A; MC:Gl; BL:-


title: MM-148_4

description: Gene expression profiling data from human multiple myeloma patient MM-148

source_name: Human multiple myeloma patient MM-148

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: F; Age:55; Stage:I A; MC:Ak; BL:-


title: MM-128_4

description: Gene expression profiling data from human multiple myeloma patient MM-128

source_name: Human multiple myeloma patient MM-128

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: M; Age:54; Stage:II A; MC:k; BL:+


title: MM-123_4

description: Gene expression profiling data from human multiple myeloma patient MM-123

source_name: Human multiple myeloma patient MM-123

value: M; Age:56; Stage:III A; MC:Gk; BL:-


title: MM-138_4

description: Gene expression profiling data from human multiple myeloma patient MM-138

source_name: Human multiple myeloma patient MM-138

value: F; Age:62; Stage:I A; MC:G; BL:nd


title: MM-133_4

description: Gene expression profiling data from human multiple myeloma patient MM-133

source_name: Human multiple myeloma patient MM-133

value: F; Age:64; Stage:II A; MC:Gk; BL:-


title: MM-126_4

description: Gene expression profiling data from human multiple myeloma patient MM-126

source_name: Human multiple myeloma patient MM-126

value: M; Age:62; Stage:II A; MC:Ak; BL:+


title: MM-119_4

description: Gene expression profiling data from human multiple myeloma patient MM-119

source_name: Human multiple myeloma patient MM-119

value: M; Age:50; Stage:II A; MC:l; BL:+


title: MM-121_4

description: Gene expression profiling data from human multiple myeloma patient MM-121

source_name: Human multiple myeloma patient MM-121


title: MM-118_4

description: Gene expression profiling data from human multiple myeloma patient MM-118

source_name: Human multiple myeloma patient MM-118

value: M; Age:62; Stage:III B; MC:k; BL:+


title: MM-113_4

description: Gene expression profiling data from human multiple myeloma patient MM-113

source_name: Human multiple myeloma patient MM-113

value: F; Age:43; Stage:III A; MC:G; BL:+


title: MM-115_4

description: Gene expression profiling data from human multiple myeloma patient MM-115

source_name: Human multiple myeloma patient MM-115

value: F; Age:53; Stage:III A; MC:k; BL:nd


title: MM-116_4

description: Gene expression profiling data from human multiple myeloma patient MM-116

source_name: Human multiple myeloma patient MM-116

value: M; Age:73; Stage:II B; MC:nd; BL:nd


title: MM-114_4

description: Gene expression profiling data from human multiple myeloma patient MM-114

source_name: Human multiple myeloma patient MM-114

value: F; Age:62; Stage:II A; MC:Ak; BL:-


title: MM-117_4

description: Gene expression profiling data from human multiple myeloma patient MM-117

source_name: Human multiple myeloma patient MM-117

value: M; Age:49; Stage:III A; MC:Gl; BL:+


title: MM-111_4

description: Gene expression profiling data from human multiple myeloma patient MM-111

source_name: Human multiple myeloma patient MM-111

value: M; Age:64; Stage:I A; MC:Gl; BL:-


title: MM-109_4

description: Gene expression profiling data from human multiple myeloma patient MM-109

source_name: Human multiple myeloma patient MM-109

value: M; Age:55; Stage:III B; MC:l; BL:+


title: MM-107_4

description: Gene expression profiling data from human multiple myeloma patient MM-107

source_name: Human multiple myeloma patient MM-107

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: F; Age:67; Stage:II A; MC:Ak; BL:-


title: MM-094_4

description: Gene expression profiling data from human multiple myeloma patient MM-094

source_name: Human multiple myeloma patient MM-094

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: M; Age:67; Stage:I A; MC:Al; BL:-


title: MM-089_4

description: Gene expression profiling data from human multiple myeloma patient MM-089

source_name: Human multiple myeloma patient MM-089

value: F; Age:84; Stage:II A; MC:Ak; BL:-


title: MM-092_4

description: Gene expression profiling data from human multiple myeloma patient MM-092

source_name: Human multiple myeloma patient MM-092

value: M; Age:65; Stage:I A; MC:Gl; BL:-


title: MM-100_4

description: Gene expression profiling data from human multiple myeloma patient MM-100

source_name: Human multiple myeloma patient MM-100

value: M; Age:78; Stage:I A; MC:Ak; BL:+


title: MM-104_4

description: Gene expression profiling data from human multiple myeloma patient MM-104

source_name: Human multiple myeloma patient MM-104

value: F; Age:63; Stage:III A; MC:Al; BL:+


title: MM-101_4

description: Gene expression profiling data from human multiple myeloma patient MM-101

source_name: Human multiple myeloma patient MM-101

value: M; Age:63; Stage:II A; MC:l; BL:+


title: MM-087_4

description: Gene expression profiling data from human multiple myeloma patient MM-087

source_name: Human multiple myeloma patient MM-087

value: F; Age:85; Stage:III A; MC:Gl; BL:+


title: MM-078_4

description: Gene expression profiling data from human multiple myeloma patient MM-078

source_name: Human multiple myeloma patient MM-078

value: F; Age:60; Stage:III A; MC:k; BL:+


title: MM-083_4

description: Gene expression profiling data from human multiple myeloma patient MM-083

source_name: Human multiple myeloma patient MM-083

value: M; Age:70; Stage:I A; MC:Gl; BL:-


title: MM-106_4

description: Gene expression profiling data from human multiple myeloma patient MM-106

source_name: Human multiple myeloma patient MM-106

value: M; Age:83; Stage:I A; MC:Gk; BL:+


title: MM-103_4

description: Gene expression profiling data from human multiple myeloma patient MM-103

source_name: Human multiple myeloma patient MM-103

value: M; Age:56; Stage:III A; MC:Ak; BL:+


title: MM-072_4

description: Gene expression profiling data from human multiple myeloma patient MM-072

source_name: Human multiple myeloma patient MM-072

value: F; Age:75; Stage:I A; MC:Al; BL:-


title: MM-081_4

description: Gene expression profiling data from human multiple myeloma patient MM-081

source_name: Human multiple myeloma patient MM-081

value: M; Age:76; Stage:I A; MC:Ak; BL:-


title: MM-067_4

description: Gene expression profiling data from human multiple myeloma patient MM-067

source_name: Human multiple myeloma patient MM-067

value: F; Age:74; Stage:III A; MC:Gk; BL:+


title: MM-068_4

description: Gene expression profiling data from human multiple myeloma patient MM-068

source_name: Human multiple myeloma patient MM-068

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: M; Age:62; Stage:III A; MC:Ak; BL:-


title: MM-063_4

description: Gene expression profiling data from human multiple myeloma patient MM-063

source_name: Human multiple myeloma patient MM-063

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: F; Age:39; Stage:II A; MC:Gk; BL:-


title: MM-082_4

description: Gene expression profiling data from human multiple myeloma patient MM-082

source_name: Human multiple myeloma patient MM-082

value: M; Age:54; Stage:II A; MC:Ak; BL:+


title: MM-131_4

description: Gene expression profiling data from human multiple myeloma patient MM-131

source_name: Human multiple myeloma patient MM-131

value: M; Age:69; Stage:I A; MC:Gk; BL:-


title: MM-074_4

description: Gene expression profiling data from human multiple myeloma patient MM-074

source_name: Human multiple myeloma patient MM-074

value: M; Age:69; Stage:III A; MC:Ak; BL:+


title: MM-079_4

description: Gene expression profiling data from human multiple myeloma patient MM-079

source_name: Human multiple myeloma patient MM-079

value: F; Age:72; Stage:II A; MC:Gk + Gl *; BL:+


title: MM-077_4

description: Gene expression profiling data from human multiple myeloma patient MM-077

source_name: Human multiple myeloma patient MM-077

value: M; Age:62; Stage:II A; MC:Gl; BL:+


title: MM-070_4

description: Gene expression profiling data from human multiple myeloma patient MM-070

source_name: Human multiple myeloma patient MM-070

value: F; Age:82; Stage:III B; MC:Dl; BL:+


title: MM-054_4

description: Gene expression profiling data from human multiple myeloma patient MM-054

source_name: Human multiple myeloma patient MM-054

value: M; Age:59; Stage:I A; MC:Gl; BL:+


title: MM-066_4

description: Gene expression profiling data from human multiple myeloma patient MM-066

source_name: Human multiple myeloma patient MM-066

value: F; Age:78; Stage:III A; MC:Ak; BL:-


title: MM-052_4

description: Gene expression profiling data from human multiple myeloma patient MM-052

source_name: Human multiple myeloma patient MM-052

value: F; Age:39; Stage:I A; MC:Gl + Al; BL:+


title: MM-064_4

description: Gene expression profiling data from human multiple myeloma patient MM-064

source_name: Human multiple myeloma patient MM-064

value: F; Age:45; Stage:II A; MC:Gk; BL:-


title: MM-069_4

description: Gene expression profiling data from human multiple myeloma patient MM-069

source_name: Human multiple myeloma patient MM-069

value: M; Age:66; Stage:II A; MC:Gk; BL:+


title: MM-056_4

description: Gene expression profiling data from human multiple myeloma patient MM-056

source_name: Human multiple myeloma patient MM-056

value: M; Age:72; Stage:I A; MC:Gk; BL:+


title: MM-050_4

description: Gene expression profiling data from human multiple myeloma patient MM-050

source_name: Human multiple myeloma patient MM-050

value: M; Age:71; Stage:I A; MC:Al; BL:-


title: MM-055_4

description: Gene expression profiling data from human multiple myeloma patient MM-055

source_name: Human multiple myeloma patient MM-055

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: F; Age:69; Stage:III A; MC:Gk; BL:-


title: MM-040_4

description: Gene expression profiling data from human multiple myeloma patient MM-040

source_name: Human multiple myeloma patient MM-040

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: F; Age:77; Stage:III B; MC:Gl; BL:+


title: MM-039_4

description: Gene expression profiling data from human multiple myeloma patient MM-039

source_name: Human multiple myeloma patient MM-039

value: M; Age:49; Stage:II A; MC:Gl; BL:+


title: MM-045_4

description: Gene expression profiling data from human multiple myeloma patient MM-045

source_name: Human multiple myeloma patient MM-045

value: M; Age:58; Stage:II A; MC:Gk; BL:+


title: MM-038_4

description: Gene expression profiling data from human multiple myeloma patient MM-038

source_name: Human multiple myeloma patient MM-038

value: F; Age:67; Stage:II A; MC:k; BL:+


title: MM-048_4

description: Gene expression profiling data from human multiple myeloma patient MM-048

source_name: Human multiple myeloma patient MM-048

value: M; Age:53; Stage:I A; MC:Gl; BL:+


title: MM-047_4

description: Gene expression profiling data from human multiple myeloma patient MM-047

source_name: Human multiple myeloma patient MM-047

value: F; Age:47; Stage:III A; MC:Gl; BL:+


title: MM-036_4

description: Gene expression profiling data from human multiple myeloma patient MM-036

source_name: Human multiple myeloma patient MM-036

value: M; Age:66; Stage:II A; MC:Gk; BL:-


title: MM-049_4

description: Gene expression profiling data from human multiple myeloma patient MM-049

source_name: Human multiple myeloma patient MM-049

value: M; Age:63; Stage:III B; MC:k; BL:+


title: MM-034_4

description: Gene expression profiling data from human multiple myeloma patient MM-034

source_name: Human multiple myeloma patient MM-034


title: MM-030_4

description: Gene expression profiling data from human multiple myeloma patient MM-030

source_name: Human multiple myeloma patient MM-030

value: M; Age:69; Stage:III A; MC:Gl; BL:-


title: MM-032_4

description: Gene expression profiling data from human multiple myeloma patient MM-032

source_name: Human multiple myeloma patient MM-032

value: M; Age:56; Stage:III B; MC:Gl; BL:-


title: MM-026_4

description: Gene expression profiling data from human multiple myeloma patient MM-026

source_name: Human multiple myeloma patient MM-026

value: F; Age:73; Stage:III B; MC:k; BL:+


title: MM-042_4

description: Gene expression profiling data from human multiple myeloma patient MM-042

source_name: Human multiple myeloma patient MM-042

value: M; Age:54; Stage:III A; MC:Al; BL:+


title: MM-035_4

description: Gene expression profiling data from human multiple myeloma patient MM-035

source_name: Human multiple myeloma patient MM-035

value: M; Age:74; Stage:I A; MC:Gk; BL:-


title: MM-037_4

description: Gene expression profiling data from human multiple myeloma patient MM-037

source_name: Human multiple myeloma patient MM-037

value: F; Age:51; Stage:II A; MC:Gk+Ak; BL:+


title: MM-031_4

description: Gene expression profiling data from human multiple myeloma patient MM-031

source_name: Human multiple myeloma patient MM-031

value: Age = age at diagnosis; Stage = stage at diagnosis; MC = monoclonal component; BL = bone lesions

value: M; Age:53; Stage:III A; MC:Ak; BL:+


title: MM-014_4

description: Gene expression profiling data from human multiple myeloma patient MM-014

source_name: Human multiple myeloma patient MM-014

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); +11 = chromosome 11 trisomy; +19 = chromosome 19 trisomy; HD = hyperdiploidy status; del(13) = chromosome 13 deletion; +1q = chromosome 1q gain.

value: F; Age:59; Stage:II A; MC:Gk; BL:+


title: MM-043_4

description: Gene expression profiling data from human multiple myeloma patient MM-043

source_name: Human multiple myeloma patient MM-043

value: F; Age:73; Stage:I A; MC:Gk + Gl; BL:+


title: MM-025_4

description: Gene expression profiling data from human multiple myeloma patient MM-025

source_name: Human multiple myeloma patient MM-025

value: F; Age:64; Stage:I A; MC:Gl; BL:-


title: MM-027_4

description: Gene expression profiling data from human multiple myeloma patient MM-027

source_name: Human multiple myeloma patient MM-027

value: M; Age:61; Stage:I A; MC:Gk; BL:-


title: MM-033_4

description: Gene expression profiling data from human multiple myeloma patient MM-033

source_name: Human multiple myeloma patient MM-033

value: F; Age:66; Stage:I A; MC:Gl; BL:-


title: FR4

status: Public on Dec 28 2006

description: Gene expression profiling data from human myeloma cell line FR4

source_name: Human multiple myeloma cell line (HMCL) FR4

growth_protocol: Iscove's modified Dulbecco’s medium supplemented with 10% FCS

tag: HMCL derived from multiple myeloma primary tumor.


title: MM-019_4

description: Gene expression profiling data from human multiple myeloma patient MM-019

source_name: Human multiple myeloma patient MM-019

value: M; Age:65; Stage:II A; MC:Gl; BL:+


title: MM-016_4

description: Gene expression profiling data from human multiple myeloma patient MM-016

source_name: Human multiple myeloma patient MM-016

value: M; Age:66; Stage:III B; MC:Gk; BL:+


title: MM-004_4

description: Gene expression profiling data from human multiple myeloma patient MM-004

source_name: Human multiple myeloma patient MM-004

value: F; Age:54; Stage:I A; MC:Gk; BL:-


title: AMO-1

description: Gene expression profiling data from human myeloma cell line AMO-1

source_name: Human multiple myeloma cell line (HMCL) AMO-1


title: MM-021_4

description: Gene expression profiling data from human multiple myeloma patient MM-021

source_name: Human multiple myeloma patient MM-021

value: M; Age:67; Stage:II A; MC:Gk; BL:-


title: MM-015_4

description: Gene expression profiling data from human multiple myeloma patient MM-015

source_name: Human multiple myeloma patient MM-015

value: M; Age:70; Stage:II A; MC:Gk; BL:+


title: KMS20

description: Gene expression profiling data from human myeloma cell line KMS20

source_name: Human multiple myeloma cell line (HMCL) KMS20


title: CMA-01

description: Gene expression profiling data from human myeloma cell line CMA-01

source_name: Human multiple myeloma cell line (HMCL) CMA-01

growth_protocol: Iscove's modified Dulbecco’s medium supplemented with 10% FCS and 20 U/mL recombinant human IL-6 (R&D System, Minneapolis, MN, USA)

tag: HMCL derived from multiple myeloma primary tumor. CMA-01 shows t(11;14) translocation


title: NCU-MM1

description: Gene expression profiling data from human myeloma cell line NCU-MM1

source_name: Human multiple myeloma cell line (HMCL) NCU-MM1


title: KMM1

description: Gene expression profiling data from human myeloma cell line KMM1

source_name: Human multiple myeloma cell line (HMCL) KMM1

tag: HMCL derived from multiple myeloma primary tumor. KMM1 shows t(6;14) translocation


title: U266

description: Gene expression profiling data from human myeloma cell line U266

source_name: Human multiple myeloma cell line (HMCL) U266

tag: HMCL derived from multiple myeloma primary tumor. U266 shows t(11;14) translocation


title: KMS12

description: Gene expression profiling data from human myeloma cell line KMS12

source_name: Human multiple myeloma cell line (HMCL) KMS12

tag: HMCL derived from multiple myeloma primary tumor. KMS12 shows t(11;14) translocation


title: KMS27

description: Gene expression profiling data from human myeloma cell line KMS27

source_name: Human multiple myeloma cell line (HMCL) KMS27

tag: HMCL derived from multiple myeloma primary tumor. KMS27 shows t(11;14) translocation


title: CMA-03

description: Gene expression profiling data from human myeloma cell line CMA-03

source_name: Human multiple myeloma cell line (HMCL) CMA-03

tag: HMCL derived from multiple myeloma primary tumor. CMA-03 shows t(20;unknown) translocation


title: KM4

description: Gene expression profiling data from human myeloma cell line KM4

source_name: Human multiple myeloma cell line (HMCL) KM4

tag: HMCL derived from multiple myeloma primary tumor. KM4 shows t(14;16) translocation


title: CMA-02

description: Gene expression profiling data from human myeloma cell line CMA-02

source_name: Human multiple myeloma cell line (HMCL) CMA-02

tag: HMCL derived from multiple myeloma primary tumor. CMA-02 shows t(14;16) translocation


title: KMS26

description: Gene expression profiling data from human myeloma cell line KMS26

source_name: Human multiple myeloma cell line (HMCL) KMS26

tag: HMCL derived from multiple myeloma primary tumor. KMS26 shows t(4;14) and t(16;unknown) translocations


title: RPMI8226

description: Gene expression profiling data from human myeloma cell line RPMI8226

source_name: Human multiple myeloma cell line (HMCL) RPMI8226

tag: HMCL derived from multiple myeloma primary tumor. RPMI-8226 shows t(16;unknown) translocation


title: OPM2

description: Gene expression profiling data from human myeloma cell line OPM2

source_name: Human multiple myeloma cell line (HMCL) OPM2

tag: HMCL derived from multiple myeloma primary tumor. OPM2 shows t(4;14) and t(20;unknown) translocations


title: LP1

description: Gene expression profiling data from human myeloma cell line LP1

source_name: Human multiple myeloma cell line (HMCL) LP1

tag: HMCL derived from multiple myeloma primary tumor. LP1 shows t(4;14) translocation


title: JJN3

description: Gene expression profiling data from human myeloma cell line JJN3

source_name: Human multiple myeloma cell line (HMCL) JJN3

tag: HMCL derived from multiple myeloma primary tumor. JJN3 shows t(14;16) translocation


title: SKMM1

description: Gene expression profiling data from human myeloma cell line SKMM1

source_name: Human multiple myeloma cell line (HMCL) SKMM1

tag: HMCL derived from multiple myeloma primary tumor. SKMM1 shows t(14;20) translocation


title: KMS11

description: Gene expression profiling data from human myeloma cell line KMS11

source_name: Human multiple myeloma cell line (HMCL) KMS11

tag: HMCL derived from multiple myeloma primary tumor. KMS11 shows t(4;14) and t(14;16) translocations


title: KMS18

description: Gene expression profiling data from human myeloma cell line KMS18

source_name: Human multiple myeloma cell line (HMCL) KMS18

tag: HMCL derived from multiple myeloma primary tumor. KMS18 shows t(4;14) translocation


title: NCI-H929

description: Gene expression profiling data from human myeloma cell line NCI-H929

source_name: Human multiple myeloma cell line (HMCL) NCI-H929

tag: HMCL derived from multiple myeloma primary tumor. NCI-H929 shows t(4;14) translocation


title: KMS28

description: Gene expression profiling data from human myeloma cell line KMS28

source_name: Human multiple myeloma cell line (HMCL) KMS28

tag: HMCL derived from multiple myeloma primary tumor. KMS28 shows t(4;14) translocation


title: KMS34

description: Gene expression profiling data from human myeloma cell line KMS34

source_name: Human multiple myeloma cell line (HMCL) KMS34

tag: HMCL derived from multiple myeloma primary tumor. KMS34 shows t(4;14) translocation


title: BrdU incorporated regions in HU

status: Public on Sep 02 2006

city: Montpellier

first: Armelle

last: Lengronne

address: 141 rue de la Cardonille

department: Institut de Genetique Humaine

country: France

institute: CNRS

description: BrdU distribution on chromosome VI in wild type cells arrested in HU at 25°C

hyb_protocol: Hybridization, blocking and washing were carried out as previously described (Katou et al., 2003, Nature) (Lengronne et al., 2004, Nature). Samples were  hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix).

scan_protocol: Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

data_processing: Data were processed following the protocol provided by Affymetrix (GCOS ver 1.4)

organism: Saccharomyces cerevisiae

source_name: Chromatin Immunoprecipitated DNA

tag: Strain containing CTF18-HA6 tagged


title: Retinoblastoma  VUMC_RB004_b31_s69

status: Public on Aug 30 2006

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: all protocols available via the VUMC MACF website

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.0 (BlueGnome, Cambridge, UK). Spots were excluded when the Confidence value was less than 0.15. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their average value.

source_name: retina

tag: retinoblastoma

source_name: reference DNA

tag: Pooled DNA from the blood of 10 normal individuals


title: Retinoblastoma  VUMC_RB001_b31_s67


title: Carcinoma  VUMC_B2081_b36_s47

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 2.0 (BlueGnome, Cambridge, UK). Log2ratio’s were normalized to their average value.

source_name: breast

tag: carcinoma


title: MCF7_DamID_CBX3V5T4Dam(Cy3)-T4Dam(Cy5)_H265-27

status: Public on Oct 17 2006

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

hyb_protocol: Please see www.nki.nl/nkidep/vansteensel for detailed protocols.

scan_protocol: Arrays were scanned using a Agilent Technologies Scanner, Model: G2505B and ChipScan software. Image analyses were done using Imagene 6.0 software (BioDiscvovery)

data_processing: Data was normalized using R-package limma 2.0.8. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized within arrays (method=“loess”). Column ‘VALUE’ contains the normalized log2 ratios (CBX-Dam/Dam).

growth_protocol: MCF7 cells were maintained in DMEM medium supplemented with 10% FCS and antibiotics.

extract_protocol: For detailed protocols go to www.nki.nl/nkidep/vansteensel.

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this experiment, MCF7 cells were transiently transfected with T4Dam or T4Dam-fusion protein expressing constructs. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays. For detailed protocols, please go to www.nki.nl/nkidep/vansteensel.

tag: MCF7 human breast carcinoma cells expressing T4Dam protein.

tag: MCF7 human breast carcinoma cells expressing CBX3-V5-T4Dam fusion protein.


title: MDA-MB-231 cells expressing vector control, P1

status: Public on Nov 21 2006

city: Ann Arbor

first: Bae Keun

last: Park

state: MI

address: 1011 N University Ave

department: BMS/Prosthodontics

institute: University of Michigan

description: For gene expression data, signal intensity was calculated using the one-step Turkey's Biweight Estimate.

hyb_protocol: After following of fragmentation, 10 mg of biotin labeled RNAs was hybridized with a human U133A gene chip at 45°C for 16 hour. Labeled bacterial RNAs were spiked into the hybridization mix for an internal standard and normalization. Chips were washed and stained with Streptavidin R-phycoerythrin (Molecular Probes).

scan_protocol: The arrayes were scanned with the GeneArray scanner (Affymetrix).

data_processing: Affymetrix Microarray Suite (MAS, version 5.0) was used for data analysis.

label: Biotin

source_name: Human breast cancer cell line MDA-MB-231

label_protocol: cDNAs transcribed from RNAs were used in an in vitro transcription reaction in the presence of biotin-modified ribonucleotides to generate single stranded RNAs according to the Affymetrix (Santa Clara, CA) protocol.

extract_protocol: Trizol reagent extraction of total RNAs followed by the manufacturer's protocol. Total RNAs were cleaned with an RNeasy kit (Qiagen) to eliminate contaminated genomic DNA.

treatment_protocol: MDA-MB-231 cells were transduced with retroviruses in the presence of 4 mg/ml (Sigma). 48 hour later, cells were selected with G-418 (800 mg/ml) for 10 days. The surviving cells were pooled, and cells expressing the proteins of interests were confirmed by Western blot analysis.

tag: Bone metastasis of MDA-MB-231 cells was compared with two different retroviral infections of control empty vector and Flag-SR-IkBa


title: Carcinoma  VUMC_B2134R_b36_s44


title: Carcinoma  VUMC_C004_b31_s73

source_name: colon


title: MCF7_DamID_CBX1V5T4Dam(Cy3)-T4Dam(Cy5)_H208-28

data_processing: Data was normalized using R-packages limma 2.0.8. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized within arrays (method=“loess”). Column ‘VALUE’ contains the normalized log2 ratios (CBX1-Dam/Dam).

label_protocol: For detailed protocols go to www.nki.nl/nkidep/vansteensel.

tag: MCF7 human breast carcinoma cells expressing CBX1-V5-T4Dam fusion protein.


title: Carcinoma  VUMC_C012_b31_s72


title: Retinoblastoma  VUMC_RB002_b31_s70


title: Carcinoma  VUMC_B2097_b36_s18


title: Diffuse large B-cell lymphoma  VUMC_L97_b31_s76

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Log2ratio’s of spots that were not excluded after quality flagging were normalized to their mode value.

source_name: lymph node

tag: Diffuse large B-cell lymphoma


title: MDA-MB-231 cells expressing SR-IkBa, P2


title: Retinoblastoma  VUMC_RB005_b31_s71


title: Carcinoma  VUMC_B2091_b36_s15


title: Carcinoma  VUMC_B2098_b36_s19


title: MEF_DamID_EcoDamV5CBX1(Cy5)-EcoDam(Cy3)_MO55-69

data_processing: Data was normalized using R-packages limma 2.0.8 and vsn 1.6.3. DamID data were normalized between different arrays (method=“vsn”). Column ‘VALUE’ contains the normalized log2 ratios (EcoDamV5CBX1/EcoDam).

source_name: MEFs

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this experiment, MEFs cells were infected with lentiviral construct expressing Dam or Dam-fusion protein. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays.
For detailed protocols please go to www.nki.nl/nkidep/vansteensel.

tag: MEFs mouse INK4a-/- embryonal fibroblasts expressing EcoDam-V5-CBX1 fusion protein.

tag: MEFs mouse INK4a-/- embryonal fibroblasts expressing EcoDam protein.


title: Carcinoma  VUMC_B2176_b39_s22


title: Diffuse large B-cell lymphoma  VUMC_L96_b31_s75


title: Diffuse large B-cell lymphoma  VUMC_L98_b31_s77


status: Public on Oct 04 2006

city: Tsurumi, Yokohama

first: Masaki

last: Hikida

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: RCAI

institute: RIKEN

description: Total RNA was prepared from SV40 transformed FDC-like cell line FL-Y

data_processing: raw data

label_protocol: One-Cycle Target Labeling Kit


title: Adenoma  VUMC_C001_b31_s74

tag: adenoma


title: Carcinoma  VUMC_B2079rpt_b41_s31


title: MCF7_DamID_EcoDam(Cy3)-EcoDam(Cy5)_cbx_HO44-43_SeriesD

description: this is a control experiment where we hybridized amplified methylated DNA from cells expressing Dam protein.

data_processing: Data was normalized using R-packages limma 2.0.8 and vsn 1.6.3. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized between different arrays (method=vsn). Column ‘VALUE’ contains the normalized log2 ratios (Dam/Dam) for each individual array.

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this control experiment, MCF7 cells were transfected with Dam protein expressing constructs.  Cells were selected with G418 for stable integration of the constructs. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays.
For detailed protocols please go to www.nki.nl/nkidep/vansteensel.

tag: MCF7 human breast carcinoma cells expressing EcoDam protein.


title: Carcinoma  VUMC_B2157_b36_s53


title: Carcinoma  VUMC_B2086_b36_s13


title: MCF7_DamID_CBX1V5EcoDam(Cy5)-EcoDam(Cy3)_HO44-38_SeriesB

data_processing: Data was normalized using R-packages limma 2.0.8 and vsn 1.6.3. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized between different arrays (method=“vsn”).

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this experiment, MCF7 cells were transfected with Dam or Dam-fusion protein expressing constructs.  Cells were selected with G418 for stable integration of the constructs. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays.
For detailed protocols please go to www.nki.nl/nkidep/vansteensel.

tag: MCF7 human breast carcinoma cells expressing CBX1-V5-EcoDam fusion protein.


title: Carcinoma  VUMC_B2083_b36_s11


title: Carcinoma  VUMC_B2095_b36_s17


title: Carcinoma  VUMC_B2100_b36_s48


title: Activated SV40 transformed FDC-like cell line FL-Y

description: Total RNA was prepared from anti-LTbeta receptor activated FDC-like cell line FL-Y


title: Breast tumor cell line  VUMC_MCF7_b13_s31

tag: breast tumor cell line


title: Carcinoma  VUMC_B2087_b36_s14


title: Retinoblastoma  VUMC_RB003_b31_s68


title: Carcinoma  VUMC_B2080rpt_b41_s32


title: Carcinoma  VUMC_B2094_b36_s16


title: Carcinoma  VUMC_B2159_b36_s54


title: Carcinoma  VUMC_B2084_b36_s12


title: Carcinoma  VUMC_B2160_b36_s55


title: Carcinoma  VUMC_B2099_b36_s20


title: Breast tumor cell line  VUMC_ZR-75-1_b39_s66

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.2 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their average value.


title: Breast tumor cell line  VUMC_HCT116_b41_s33


title: Breast tumor cell line  VUMC_T47D_b41_s6


title: Breast tumor cell line  VUMC_MDA-MB-361_b41_s15


title: Breast tumor cell line  VUMC_ZR-75-30_b41_s61


title: Breast tumor cell line  VUMC_VP267_b39_s54


title: Breast tumor cell line  VUMC_SKBR3_b36_s49


title: Breast tumor cell line  VUMC_MDA-MB-157_b41_s9


title: Breast tumor cell line  VUMC_SUM44_b39_s2


title: Breast tumor cell line  VUMC_MDA-MB-453_b41_s11


title: Breast tumor cell line  VUMC_MDA-MB-175_b41_s12


title: Breast tumor cell line  VUMC_VP229_b39_s44


title: Breast tumor cell line  VUMC_SUM52_b39_s79


title: Breast tumor cell line  VUMC_MDA-MB-134_b41_s10


title: Breast tumor cell line  VUMC_SUM149_b41_s16


title: Breast tumor cell line  VUMC_UACC812_b41_s54


title: Breast tumor cell line  VUMC_MT3_b36_s7


title: Breast tumor cell line  VUMC_MDA-MB-436_b41_s8


title: Breast tumor cell line  VUMC_CAL51_b41_s14


title: Drosophila SL2_C2 versus C3_ replicate 3

status: Public on Aug 18 2006

city: Boston

first: Meghana

middle: M

last: Kulkarni

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: First, the total RNA is reverse transcribed using the included deoxynucleotide triphosphate mix and special Cy3/Cy5 RTdT primers. Thus, total RNA from the D1- and C1- treated samples were reverse transcribed using complementary Cy3 and Cy5 RTdT primers. Similarly total RNA from C2- and C3- treated samples were reverse transcribed using complementary Cy3/Cy5 RTdT primers (see Table 1 above). Then, the complementary cDNAs were mixed (D1 and C1; C2 and C3) and hybridized to the cDNA array. Cy3/Cy5 Fluorescent 3DNA reagents are then hybridized to the microarray in a second hybridization step. The Cy3 and Cy5 fluorescent 3DNA reagents will hybridize to the cDNA because they include a ï'capture sequenceï' that is complementary to a sequence on the 5ï' end of the Cy3/Cy5 RT primer respectively. Each competitive hybridization was independently performed in triplicate including a color-flip to preclude dye bias.

scan_protocol: Post hybridization the microarrays were scanned using PMT-adjusted Axonï's GenePix 4000B microarray scanner. GenePix Pro 5.0 was used for raw intensity value calculations.

data_processing: GenePix Results files (.GPR) were used as input for MIDAS V2.19 software (Saeed et al. 2003) to normalize the raw cDNA microarray signals by LOWESS method. We used t-test followed by the false discovery rate (FDR) adjustment to detect differentially expressed genes. The FDR adjusted p-value cutoff was 0.01. We calculated the base 2 log of the fold-changes. The clustering was performed by a hierarchical clustering algorithm with the centroid-linkage method.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster SL2 culture cells, SL2 cells treated with double-stranded RNA (dsRNA)

label_protocol: 25 microgms of total RNA from Drosophila SL2 cells treated with C2 dsRNAs targeting the PP2A-B' gene were reverse transcribed and labeled using Superscript RT II (Invitrogen) and Genisphere's 3DNA Array 350 labeling kit.

growth_protocol: Drosophila Schneider SL2 cells were cultured in Schneiderï's medium (GibcoBRL) supplemented with 10% fetal bovine serum (JRH Bioscience) and Penicillin-Streptomycin (GibcoBRL) at 25 degree C, unless noted otherwise. 4x106 SL2 cells were seeded in each well of a 6-well cell culture dish (Falcon) in 1ml of serum-free media and treated with 15 microgms of dsRNA at room temperature for 45 min. After 45 min, 2 ml of serum-supplemented Schneiderï's medium was added and cells were further incubated for 72 hr. For expression profiling experiments three independent treatments were setup for each dsRNA.

extract_protocol: Total RNA was isolated by Trizol according to the manufacturerï's specifications (GibcoBRL), purified with RNeasy columns (Qiagen) and quality was assessed using the Agilent Bioanalyzer according to manufacturerï's specifications (Agilent)

treatment_protocol: SL2 cells treated with C2 dsRNA targeting all splice forms of the PP2A-B' gene

tag: Drosophila melanogaster SL2 culture cells, SL2 cells embryonically derived

label_protocol: 25 microgms of total RNA from Drosophila SL2 cells treated with C3 dsRNAs targeting the PP2A-B' gene were reverse transcribed and labeled using Superscript RT II (Invitrogen) and Genisphere's 3DNA Array 350 labeling kit.

growth_protocol: Drosophila Schneider SL2 cells were cultured in Schneiderï's medium (GibcoBRL) supplemented with 10% fetal bovine serum (JRH Bioscience) and Penicillin-Streptomycin (GibcoBRL) at 25 degree C, unless noted otherwise. 4x106 SL2 cells were seeded in each well of a 6-well cell culture dish (Falcon) in 1ml of serum-free media and treated with 15 microgmsof dsRNA at room temperature for 45 min. After 45 min, 2 ml of serum-supplemented Schneiderï's medium was added and cells were further incubated for 72 hr. For expression profiling experiments three independent treatments were setup for each dsRNA.

extract_protocol: Total RNA was isolated by Trizol according to the manufacturer's specifications (GibcoBRL), purified with RNeasy columns (Qiagen) and quality was assessed using the Agilent Bioanalyzer according to manufacturer's specifications (Agilent)

treatment_protocol: SL2 cells treated with C3 dsRNA targeting all splice forms of the PP2A-B' gene


title: Breast tumor cell line  VUMC_VP185_b41_s17


title: wt_ethylene_2_polyA

status: Public on Aug 08 2006

city: La Jolla

first: Joseph

middle: R.

last: Ecker

state: CA

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

description: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturer's instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.

hyb_protocol: ATH1 Array  was hybridized for 16 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: ATH1 Array were scanned on Affymetrix scanner

data_processing: The following procedure was used to process and analyze tiling microarray data for RNA expression. CEL files of the each two biological replicate (total 4 CEL files) within genotype comparison (e.g., comparison between wt and ein2 of poly-A RNA profiling) were subject to quantile normalization.

source_name: seedling

extract_protocol: total RNA was isolated from mature leaves using RNAeasy kit following instructions from the manufacturer (QIAGEN)

treatment_protocol: Ethylene

tag: Strain;wild type colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition


title: wt_ethylene_1_polyA


title: ein2_air_2_polyA

data_processing: The following procedure was used to process and analyze microarray data for RNA expression. CEL files of the each two biological replicate within genotype comparison (e.g., comparison between wt and ein2 of poly-A RNA profiling) were subject to quantile normalization.

treatment_protocol: untreated

tag: Strain;ein2 colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition


title: wt_air_2_polyA


title: ein5_ethylene_2_polyA

treatment_protocol: ethylene


title: ein5_ethylene_1_polyA


title: ein5_air_1_polyA


title: 3000132345_adultworm_female_45_left

status: Public on Aug 24 2006

city: Campos dos Goytacazes

first: Thiago

middle: Motta

last: Venancio

state: RJ

address: Av Alberto Lamego 2000

country: Brazil

institute: UENF

description: Raw intensity values were extracted from images with ArrayVision. An individual spot background was extracted for each spot using the following software settings: Background: Mean; Enable background subtraction; corners between spots; mode: individual.

data_processing: Spot signals below individual spot background are marked ‘null’ in the VALUE column. The last line of each of 12 subarrays contained a set of Lucidea Universal scorecard controls (GE Healthcare), which include 2 negative controls per set, totalizing 48 negative control spots per slide that were used as a cutoff value for filtering out low intensity spot signals. Low intensity data points below the average plus 2 standard deviations of the negative control signal were filtered out and are marked ‘null’ in the VALUE column. Positive and negative external controls were excluded and are marked ‘null’ in the VALUE column. Data intensity from each array was normalized by a factor proportional to the total intensity of the slide, excluding positive and negative external controls.

organism: Schistosoma mansoni

source_name: adult worm, female, sample 45

label_protocol: Fluorescently labeled cDNA targets were generated using Superscript-plus indirect cDNA labeling system (Invitrogen), according to the manufacturer instructions.

extract_protocol: Extractions of mRNA were performed with MAC magnetic beads isolation kits (Miltenyi Biotec) using approximately 300 mg of worm tissue.

treatment_protocol: Worms were conserved in RNAlater (Ambion) according to the manufacturer instructions. Materials from 3 perfusions performed at different dates were pooled, and male and female parasites were separated manually.

tag: Gender

value: male Gender:female

tag: Tissue

value: whole worm

tag: Life cycle stage

value: adult worms obtained from portal perfusion of hamsters 7 to 8 weeks after infection.


title: ein2_ethylene_2_polyA


title: ein2_ethylene_1_polyA


title: rice leaf superSAGE Array

status: Public on Jul 28 2006

city: Ueda

first: Hideo

last: Matsumura

state: Nagano

address: Tokita 3-15-1

department: Gene Research Center

institute: Shinshu University

description: Total RNA was converted to double-stranded cDNA using SuperScript II Double-Stranded cDNA synthesis kit (Invitrogen) and an oligo-dT primer containing the T7 RNA polymerase promoter.   In vitro transcription (IVT) was used to produce biotin-labeled cRNA from cDNA using MEGAscript T7 kit (Ambion).  Briefly, 1 µg double-stranded cDNA was incubated with 7.5 mM ATP and GTP, 5.6 mM UTP and CTP, 1.9 mM bio-11-CTP and bio-16 UTP (Enzo) and 1x T7 enzyme mix in 1x transcription buffer for 5 h at 37degC. Before hybridization, cRNA was fragmented to an average size of 50 to 200 bp by incubation in 100 mM potassium acetate, 30 mM magnesium acetate, and 40mM tris-acetate for 35 min at 94degC. Fragmentation was monitored by a Bioanalyzer (Agilent).

data_processing: RMA algorithum

organism: Oryza sativa

source_name: rice leaf

tag: Rice (c.v. Kakehashi) mature green leaf


title: rice suspension cultured cell1

source_name: suspension cultured cell

tag: Rice (c.v. Kakehashi) suspension cultured cells


title: wt_air_1_polyA


title: ein5_air_2_polyA


title: ein2_air_1_polyA

description: Cold-treated seeds in MS plates were placed in chambers at 24oC in the dark with hydrocarbon-free airflow for three days, after which some of the chambers were connected to ethylene gas at 10 ppm while the others remained on air treatment. Four hours later the seedlings of each plate were quickly collected and frozen in liquid nitrogen.  Total RNA was prepared from both air-treated and ethylene-treated etiolated seedlings of Arabidopsis Col-0, ein2-5 and ein5-1 using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Biotinylated target RNA was prepared from 16 ?g of total RNA using the procedure described by the manufacturer (Affymetrix, Santa Clara, CA). Briefly, a primer encoding a T7 RNA polymerase promoter fused to (dT)24 (Genset Oligos, La Jolla, CA) was used to prime double-stranded cDNA synthesis using the SuperScript Choice System (Life Technologies). The resulting cDNA was transcribed in vitro using the BioArray High-Yield RNA Tran-script Labeling Kit (Enzo Biochem, New York, NY) in the presence of biotinylated UTP and CTP to produce biotinylated target complementary RNA (cRNA). The labeled target cRNA was purified, fragmented, and hybridized to Arabidopsis microoarrays (Affymetrix whole genome tiling, and ATH1 gene expression arrays) according to protocols provided by the manufacturer in a hybridization oven model 640 (Affymetrix, Santa Clara, CA). The arrays were washed and stained with streptavidin-phycoerythrin using a GeneChip Fluidics Station model 400 and then scanned with a Gene Array Scanner (Hewlett-Packard, Palo Alto, CA). Scanned images were processed and quantified using GeneChip Suite 3.2. Genespring software (Silicon Genetics, Redwood City, CA) was used to manage and filter the array data. Each measurement was divided by the 50.0th percentile of all measurements in that sample.  The percentile was calculated with all normalized measurements above 10.  For samples where the bottom tenth percentile was less than the negative of the 50.0th percentile, it was used as a background, and subtracted from all the other genes first. Experiments were carried out in duplicate and hybridized to two sets of expression chips.  Expression values were analyzed using GeneSpring™ software version 4.2 (Silicon  Genetics, Redwood, California).

growth_protocol: Strain;ein2 colmbia, Tissue; seedling, Age; 3days, Growth; on agar plate under continuous dark condition in hydrocarbon-free air


title: Lung cancer_Paitent_340

status: Public on Jun 07 2006

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Preparation of cDNA probes: Total RNA of the specimens was extracted using Trizol (GIBCO-BRL; Gaithersburg, MD) and four micrograms of total RNAs was amplified using an Ambion amplification kit (Ambion, TX, USA) and labeled with digoxigenin during reverse transcription. The labeling reactions were performed during reverse transcription in the presence of 6 mM random primers; 0.5 mM each dATP, dCTP, and dGTP; 40 mM dTTP; 40 mM Dig-16-dUTP (Roche Molecular Biochemicals; Mannheim, Germany); 1X reaction buffer; 10 mM DTT; 0.5 unit/ml Ribonuclease inhibitor (GIBCO-BRL; Gaithersburg, MD); and 200 units of MMLV reverse transcriptase (GIBCO-BRL; Gaithersburg, MD) in a 50-ml solution. The reaction mixture was incubated at room temperature for 10 minutes, then transferred to 42oC for 90 minutes, and was stopped by heating the reaction mixture to 99oC for 5 minutes. The RNA was degraded by adding of 5.5 ml of 3 M NaOH followed by a 30-min incubation at 50oC. The labeled samples were neutralized by the addition of 5.5 ml of 3 M acetic acid, and then precipitated by adding 50 ml of 7.5 M ammonium acetate, 20 mg of linear polyacrylamide as a carrier, 375 ml of absolute alcohol, and water, to make a total of 525 ml. The solution was mixed evenly and stood at -80oC for 30 min, then was centrifuged at 14,000 rpm for 20 min to precipitate a single stranded DNA probe. The pellet was washed with 1 ml of 70% of ethanol and dried by speed vacuum, then dissolved in 5 ml of de-ionized water. Microarray hybridization and Colorimetric detection: The membrane carrying the double-stranded cDNA targets was pre-hybridized in 3 ml of hybridization buffer (5XSSC, 0.1% N-lauroylsarcosine, 0.1% SDS, 1% blocking reagent made by Roche Molecular Biochemicals, and 50 mg/ml salmon sperm DNA) at 68¢XC for 1 hour before hybridization was carried out. cDNA probes were resuspended in 15 ml hybridization buffer containing 200 mg/ml d(A)10 and  400 mg/ml human COT-1 DNA (GIBCO-BRL; Gaithersburg, MD) to prevent non-specific binding, and were hybridized to the cDNA fragments on the membrane by a Southern hybridization procedure. The 15 ml reaction mixture was sealed with the microarray membrane in a hybridization assembly (SureSeal, Hybaid, Middlesex, UK) at 68¢XC for 12 hours. The membrane was then washed with 2XSSC containing 0.1% SDS for 5 min at room temperature followed by three washes with 0.1XSSC containing 0.1% SDS at 65oC for 15 min each. After hybridization, the membrane was blocked by 1 ml of 1% blocking reagent (Roche Molecular Biochemicals; Mannheim, Germany) containing 2% dextran sulphate at room temperature for 1 hour, and then was rinsed with 1 X TBS buffer solution (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.3% BSA). To detect the spots on the membrane in a single-color mode, AP-conjugated anti-Dig (GIBCO-BRL; Gaithersburg, MD) was employed. The membrane was incubated with a 3-ml mixture containing 1000 X diluted AP-conjugated anti-Dig, 4% polyethylene glycol 8000 (Sigma, St. Louis, MO), and 0.3% BSA in 1 X TBS buffer for 2 hours. The membrane was then washed with 1 X TBS buffer three times, for 10 min each. The chromogen was generated by treating the membrane with AP substrate in 1 X substrate buffer (pH=9.5) for 1 hour at 37oC. The color development reactions were stopped by AP stop solution. To measure the expression levels of the genes, the microarray was scanned using a flatbed scanner (PowerLook 3000, UMAX, Taipei, Taiwan). The images captured by a scanner were converted from true color to a gray scale, and digitized by analysis software GenePix 5.0 (Axon, Union City, CA).

hyb_protocol: The details of target preparation, hybridization, color development, image analysis, and spot quantification have been described in our previous studies (Chen JJW. etc. J Clin Oncol 23: 953-964, 2005; Chen JJW. etc. Cancer Res. 61: 5223-5230, 2001).

data_processing: The averaged intensity for each gene (there were two copies on a metachip for each gene) was used for the subsequent analyses. To reduce the variation arising from experimental results derived from different microarrays, the intensity values of the spots from each microarray were rescaled using a quantile normalization method. To reduce background noise, any background intensity lower than 3,000 was assigned the value of 3,000. After background correction, each intensity value was converted to the logarithm to the base 2. We used the coefficient of variation (CV) threshold of 3% to select most variable genes; if the CV for a gene was less than 3%, the gene was excluded from analysis. Finally, for prediction of metastasis and survival, the intensity of gene expression was transformed to an ordinal level using the quantile, i.e. if the intensity of gene expression was < or =25th, > 25 and< or =50th, > 50th and < or =75th percentile, or > 75th, it was coded as 1, 2, 3, or 4, respectively.

label: digoxigenin

source_name: Frozen lung cancer

growth_protocol: Non

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Non

tag: Age

value: Male

tag: Cell type

value: Squamous cell carcinoma

tag: Cancer stage

value: III

tag: Survival time (month)

tag: Metastasis time (month)


title: Lung cancer_Paitent_346

scan_protocol: The details of target preparation, hybridization, color development, image analysis, and spot quantification have been described in our previous studies (Chen JJW. etc. J Clin Oncol 23: 953-964, 2005; Chen JJW. etc. Cancer Res. 61: 5223-5230, 2001).

value: Female

value: Mixed ( Small / large cell carcinoma)

value: II


title: Lung cancer_Paitent_347

label_protocol: The details of target preparation, hybridization, color development, image analysis, and spot quantification have been described in our previous studies (Chen JJW. etc. J Clin Oncol 23: 953-964, 2005; Chen JJW. etc. Cancer Res. 61: 5223-5230, 2001).

value: Adenocarcinoma

value: I


title: Lung cancer_Paitent_332


title: Lung cancer_Paitent_355


title: Lung cancer_Paitent_334


title: Lung cancer_Paitent_327


title: Lung cancer_Paitent_75


title: Lung cancer_Paitent_350


title: Lung cancer_Paitent_363


title: Lung cancer_Paitent_365


title: Lung cancer_Paitent_329


title: Lung cancer_Paitent_343


title: Lung cancer_Paitent_351


title: Lung cancer_Paitent_326


title: Lung cancer_Paitent_319


title: Lung cancer_Paitent_320


title: Lung cancer_Paitent_325


title: Breast tumor cell line  VUMC_MDA-MB-415_b41_s13

tag: Pooled DNA from the blood of 10 normal individuals


title: Lung cancer_Paitent_313


title: Lung cancer_Paitent_312


title: Lung cancer_Paitent_317


title: Lung cancer_Paitent_314


title: Lung cancer_Paitent_309


title: Lung cancer_Paitent_311


title: Lung cancer_Paitent_308


title: Lung cancer_Paitent_307


title: Lung cancer_Paitent_321


title: Lung cancer_Paitent_306


title: Lung cancer_Paitent_298


title: Lung cancer_Paitent_292


title: Lung cancer_Paitent_295


title: Lung cancer_Paitent_304


title: Lung cancer_Paitent_289


title: Lung cancer_Paitent_287


title: Lung cancer_Paitent_297


title: Lung cancer_Paitent_315


title: Lung cancer_Paitent_303


title: Lung cancer_Paitent_299


title: Lung cancer_Paitent_300


title: Lung cancer_Paitent_301


title: Lung cancer_Paitent_283


title: Lung cancer_Paitent_286


title: Lung cancer_Paitent_278


title: Lung cancer_Paitent_296


title: Lung cancer_Paitent_277


title: Lung cancer_Paitent_280


title: Lung cancer_Paitent_271


title: Lung cancer_Paitent_273


title: Lung cancer_Paitent_272


title: Lung cancer_Paitent_274


title: Lung cancer_Paitent_270


title: Lung cancer_Paitent_266


title: Lung cancer_Paitent_267


title: Lung cancer_Paitent_261


title: Lung cancer_Paitent_264


title: Lung cancer_Paitent_263


title: Lung cancer_Paitent_237


title: Lung cancer_Paitent_244


title: Lung cancer_Paitent_238


title: Lung cancer_Paitent_246


title: Lung cancer_Paitent_250


title: Lung cancer_Paitent_247


title: Lung cancer_Paitent_259


title: Lung cancer_Paitent_253


title: Lung cancer_Paitent_245


title: Lung cancer_Paitent_256


title: Lung cancer_Paitent_252


title: Lung cancer_Paitent_243


title: Lung cancer_Paitent_226


title: Lung cancer_Paitent_239


title: Lung cancer_Paitent_242


title: Lung cancer_Paitent_232

value: Bronchioloalveolar carcinoma


title: Lung cancer_Paitent_248


title: Lung cancer_Paitent_223


title: Lung cancer_Paitent_224


title: Lung cancer_Paitent_227


title: Lung cancer_Paitent_214


title: Lung cancer_Paitent_217


title: Lung cancer_Paitent_222


title: Lung cancer_Paitent_215


title: Lung cancer_Paitent_219


title: Lung cancer_Paitent_207


title: Lung cancer_Paitent_211


title: Lung cancer_Paitent_208


title: Lung cancer_Paitent_198


title: Lung cancer_Paitent_199

value: Large cell carcinoma


title: Lung cancer_Paitent_195


title: Lung cancer_Paitent_194


title: Lung cancer_Paitent_203


title: Lung cancer_Paitent_202


title: Lung cancer_Paitent_201


title: Lung cancer_Paitent_206


title: Lung cancer_Paitent_200


title: Lung cancer_Paitent_204


title: Lung cancer_Paitent_186


title: Lung cancer_Paitent_192


title: Lung cancer_Paitent_213


title: Lung cancer_Paitent_216


title: Lung cancer_Paitent_193


title: Lung cancer_Paitent_184


title: Lung cancer_Paitent_185


title: Lung cancer_Paitent_210


title: Lung cancer_Paitent_190


title: Lung cancer_Paitent_183


title: Lung cancer_Paitent_182


title: Lung cancer_Paitent_181


title: Lung cancer_Paitent_151


title: Lung cancer_Paitent_174


title: Lung cancer_Paitent_175


title: Lung cancer_Paitent_144


title: Lung cancer_Paitent_165


title: Lung cancer_Paitent_128


title: Lung cancer_Paitent_169


title: Lung cancer_Paitent_170


title: Lung cancer_Paitent_160


title: Lung cancer_Paitent_102


title: Lung cancer_Paitent_115


title: Lung cancer_Paitent_116


title: Lung cancer_Paitent_110


title: Lung cancer_Paitent_177


title: Lung cancer_Paitent_101


title: Lung cancer_Paitent_179


title: Lung cancer_Paitent_109


title: Lung cancer_Paitent_100


title: Lung cancer_Paitent_113


title: Control(ethanol)-treated sample at 24hr, biological rep3

status: Public on Jun 02 2006

city: Chicago

first: Suzanne

middle: Daniela

last: Conzen

state: IL

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

department: Medicine

institute: The University of Chicago

description: Gene expression data from MCF10A-Myc cells treated with ethanol for 24 hr.

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

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

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

source_name: MCF10A-Myc cells treated with ethanol for 24hr

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

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

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with ethanol for 24 hr.

tag: Genotype

value: unknown


title: Dex-treated sample at 24hr, biological rep2

description: Gene expression data from MCF10A-Myc cells treated with dex for 24 hr.

source_name: MCF10A-Myc cells treated with dexamethasone for 24hr

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with dexamethasone for 24 hr.


title: Control(ethanol)-treated sample at 30min, biological rep3

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

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

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


title: Dex-treated sample at 2hr, biological rep3

description: Gene expression data from MCF10A-Myc cells treated with Dex for 2 hr.

source_name: MCF10A-Myc cells treated with dexamethasone for 2hr

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with dexamethasone for 2 hr.


title: Dex-treated sample at 24hr, biological rep3

description: Gene expression data from MCF10A-Myc cells treated with Dex for 24 hr.


title: Dex-treated sample at 30min, biological rep3

description: Gene expression data from MCF10A-Myc cells treated with Dex for 30 min.

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

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


title: Control(ethanol)-treated sample at 2hr, biological rep3

description: Gene expression data from MCF10A-Myc cells treated with ethanol for 2 hr.

source_name: MCF10A-Myc cells treated with ethanol for 2hr

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with ethanol for 2 hr.


title: Dex-treated sample at 4hr, biological rep2

description: Gene expression data from MCF10A-Myc cells treated with dex for 4 hr.

source_name: MCF10A-Myc cells treated with dexamethasone for 4hr

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with dexamethasone for 4 hr.


title: Control(ethanol)-treated sample at 4hr, biological rep3

description: Gene expression data from MCF10A-Myc cells treated with ethanol for 4 hr.

source_name: MCF10A-Myc cells treated with ethanol for 4hr

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with ethanol for 4 hr.


title: Control(ethanol)-treated sample at 24hr, biological rep2


title: Control(ethanol)-treated sample at 2hr, biological rep2


title: Control(ethanol)-treated sample at 30min, biological rep2

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


title: Dex-treated sample at 4hr, biological rep3

description: Gene expression data from MCF10A-Myc cells treated with Dex for 4 hr.


title: Dex-treated sample at 2hr, biological rep2

description: Gene expression data from MCF10A-Myc cells treated with dex for 2 hr.


title: Control(ethanol)-treated sample at 4hr, biological rep1

description: Gene expression data from MCF10A-Myc cells treated with ethanol for 4hr

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with ethanol for 4hr.


title: Dex-treated sample at 30min, biological rep2

description: Gene expression data from embryos in slow phase of cellularisation.

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


title: Dex-treated sample at 2hr, biological rep1

description: Gene expression data from MCF10A-Myc cells treated with dexamethasone for 2hr.

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with dexamethasone for 2hr.


title: Control(ethanol)-treated sample at 2hr, biological rep1

description: Gene expression data from MCF10A-Myc cells treated with ethanol for 2hr.


title: Dex-treated sample at 24hr, biological rep1

description: Gene expression data from MCF10A-Myc cells treated with dexamethasone for 24hr

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with dexamethasone (Dex) for 24hr.


title: Dex-treated sample at 4hr, biological rep1

description: Gene expression data from MCF10A-Myc cells treated with dexamethasone for 4hr

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with dexamethasone for 4hr.


title: Dex-treated sample at 30min, biological rep1

description: Gene expression data from MCF10A-Myc cells treated with dexamethasone for 30 min.


title: Control(ethanol)-treated sample at 4hr, biological rep2


title: Control(ethanol)-treated sample at 24hr, biological rep1

description: Gene expression data from MCF10A-Myc cells treated with ethanol for 24hr

treatment_protocol: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with ethanol for 24hr.


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

status: Public on Apr 01 2006

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

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

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

source_name: RORgamma -/- thymus (Cy3)

tag: RORgamma -/- thymus

source_name: RORgamma +/+ thymus (Cy5)

tag: RORgamma +/+ thymus


title: FM95-14 3d 0, chip HG-U133B

status: Public on Dec 09 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S283
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_292
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			2233 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl

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

source_name: myoblasts FM95-14 P15, fetal muscle

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

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

tag: Gender:					Male

tag: Karyotype:				normal male chromosomes


title: FM95-14 7d 1, chip HG-U133B

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

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


title: FM95-14 3d 1, chip HG-U133B

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


title: FM95-14 4d 1, chip HG-U133B

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

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


title: FM95-14 48hr 1, chip HG-U133B

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

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


title: FM95-14 3d 11, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S283
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_292
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1266 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl


title: FM95-14 4d 11, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E210
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210
SCGP Sample ID:				S284
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=210#SAMPLE_293
Short description:			Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.  Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum.  Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days.
Analysis requested:			HGU133A,B
Estimated purity:				100%
RNA concentration:			1955 ng/ul
Num cells for RNA prep:			6 x 10E+6
Sample volume:				27µl