title: GADD45-/- -VILI replicate3

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

institute: University of Viginia

description: Gene expression data from lung tissue of control animal

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse320_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) for ABS_Call; Bioconductor GCRMA package for normalization;

growth_protocol: standard conditions (12h light-dark cycle, 25-27ºC, ~40% humidity)

treatment_protocol: VILI (30 ml/kg tidal volume, 65 breath/minute, 4 hours)

tag: Mouse C57BL/6

tag: Mouse, male

tag: Age

value: 8-12 week

value: GADD-/-


title: GADD45-/- - SB replicate2

status: Public on Jul 01 2008

type: RNA

department: Medicine

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Lung

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

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

treatment_protocol: SB

tag: Genotype


title: Androgen ablation, fiber model 10R_AA

city: vancouver

first: Gang

last: Wang

state: BC

address: 675 W10th Ave.

department: Genome Sciences Centre

country: Canada

institute: BC Cancer Agenecy

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneArray Scanner

data_processing: MAS 5.0 data submitted, Genespring 7.2 used to generate RMA data

organism: Homo sapiens

source_name: fiber model, 10R, AA

label_protocol: biotin

extract_protocol: TRIZOL

tag: model

value: fiber model, cell:LNCaP, mouse ID:10R, stage:AA


title: Omentum - 403714

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Clinical T: 4
Clinical N: 1
Clinical M: 1
Clinical Metastatic Sites: Other
Clinical Stage: 4
Clinical Grade: X
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Dukes Stage: D
Primary Site: Rectum
Histology: Metastatic Adenocarcinoma

source_name: Omentum


title: Breast - 421719

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Mammogram: Yes
Number of years in which a mammogram was obtained?: 26-30
Oral contraceptives?: No
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 6-10
Pathological T: 2
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma

source_name: Breast


title: GADD45-/- - SB replicate3


title: GADD45-/- -VILI replicate2


title: Androgen ablation, fiber model 11L_AA

source_name: fiber model, 11L, AA

value: fiber model, cell:LNCaP, mouse ID:11L, stage:AA


title: WT-VILI replicate2

value: Wild type


title: Kidney - 403718

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: Yes
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Renal cell carcinoma

source_name: Kidney


title: Colon - 416799

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 80-89
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Cecum - 421720

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Pathological T: 4
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Mucinous Adenocarcinoma

source_name: Cecum


title: Breast - 383891

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 23
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 6-10
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: WT-VILI replicate3


title: PGF

city: London

first: Tim

last: Forshew

address: 4 Newark Street

department: Centre for Neuroscience

country: United Kingdom

institute: Queen Mary's School of Medicine and Dentistry

description: PGF

hyb_protocol: affymetrix hybridization

scan_protocol: affymetrix scan

data_processing: Affymetrix CEL files were processed using RMA

label: affymetrix labelling

source_name: PGF B-lypmoblastoids, untreated

label_protocol: affymetrix labelling

extract_protocol: QIagen RNeasy plus

tag: Cell

value: PGF, Treatment:None


title: WT-VILI replicate1


title: GADD45-/- - SB replicate1


title: WT-SB replicate1


title: WT-SB replicate3


title: A2lox.mesp1 (day 4 + dox)

city: Saint Louis

first: Coleman

last: Lindsley

state: MO

address: BOX 8118, 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Gene expression data from ES cells differentiated in serum containing medium and Mesp1 induction from days 2-4)

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were normalized and expression values modeled using dChip according to default settings (www.dchip.org).

source_name: A2lox.mesp1 ES cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For differentiation, ES cells were plated in suspension in bacterial petri dishes at 1.5 x 10e4 cells/mL in serum-containing medium (SCM: IMDM with 10% FCS, NEAA, L-glutamine,  NaPyruvate, Pen/Strep, and 2-mercaptoethanol) ), and supplemented where indicated with Dkk1 or doxycycline.

extract_protocol: Total RNA was purified using Rneasy mini kits (Qiagen) per manufacturer's instructions.

treatment_protocol: ES cells were differentiated in low density suspension culture.  Doxycycline (250 ng/mL) was added from days 2-4.

value: Mesp1 transgenic ES cells


title: Gata4 flox/flox ; Nkx2-5 cre/+ rep2

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: The second heart field (SHF) comprises a population of mesodermal progenitor cells that are added to the nascent linear heart to give rise to the majority of the right ventricle, interventricular septum, and outflow tract of mammals and birds. The zinc finger transcription factor GATA4 functions as an integral member of the cardiac transcription factor network in the SHF and its derivatives. In addition to its role in cardiac differentiation, GATA4 is also required for cardiomyocyte replication, although the transcriptional targets of GATA4 required for proliferation have not been previously identified. In the present study, we disrupted Gata4 function exclusively in the SHF and its derivatives. Gata4 SHF knockout mice die by embryonic day 13.5 and exhibit hypoplasia of the right ventricular myocardium and interventricular septum and display profound ventricular septal defects. Loss of Gata4 function in the SHF results in decreased myocyte proliferation in the right ventricle, and we identify numerous cell cycle genes that are dependent on Gata4 by microarray analysis. We show that Gata4 is required for Cyclin D2 expression in the right ventricle and that the Cyclin D2 promoter is bound and activated by GATA4 via three consensus GATA binding sites. These findings establish Cyclin D2 as a direct transcriptional target of GATA4 and support a model in which GATA4 controls cardiomyocyte proliferation by coordinately regulating numerous cell cycle genes.

hyb_protocol: Standard Affymetrix protocol was used.

scan_protocol: Standard Affymetrix protocol was used.

data_processing: Affymetrix PLIER algorithm

label: Biotin

source_name: Pooled mouse heart, E9.5

label_protocol: Total RNA (50 ng) was amplified and converted to cDNA using the Ovation RNA labeling kit (NuGen).

extract_protocol: Total RNA was extracted with TRIzol.

value: Gata4 flox/flox; Nkx2-5 cre/+


title: A2lox.mesp1 (day 3 + DKK1)

description: Gene expression data from ES cells differentiated in serum containing medium supplemented with DKK1 from days 0-4.

treatment_protocol: ES cells were differentiated in low density suspension culture.  Recombinant DKK1 at 150 ng/mL was added from day 0-4.


title: Gata4 flox/+ ; Nkx2-5 cre/+ rep3

value: Gata4 flox/+; Nkx2-5 cre/+


title: A2lox.mesp1 (day 4 + DKK1)


title: Gata4 flox/flox ; Nkx2-5 cre/+ rep4


title: A2lox.mesp1 (day 6 + DKK1)


title: Gata4 flox/flox ; Nkx2-5 cre/+ rep3


title: Gata4 flox/+ ; Nkx2-5 cre/+ rep2


title: GADD45-/- -VILI replicate1


title: A2lox.mesp1 (day 4)

description: Gene expression data from ES cells differentiated in serum containing medium alone.

treatment_protocol: ES cells were differentiated in low density suspension culture.


title: A2lox.mesp1 (day 6)


title: A2lox.mesp1 (day3 + DKK1 + dox)

description: Gene expression data from ES cells differentiated in serum containing medium supplemented with DKK1 from days 0-4 and Mesp1 induction from days 2-4.

treatment_protocol: ES cells were differentiated in low density suspension culture.  Recombinant DKK1 at 150 ng/mL was added from day 0-4 and doxycycline (250 ng/mL) was added from days 2-4.


title: A2lox.mesp1 (day 4 + DKK1 + dox)


title: Gata4 flox/+ ; Nkx2-5 cre/+ rep1


title: Gata4 flox/+ ; Nkx2-5 +/+ rep2

value: Gata4 flox/+; Nkx2-5 +/+


title: A2lox.mesp1 (day 3 + dox)


title: A2lox.mesp1 (day 6 + DKK1 + dox)


title: Gata4 flox/flox ; Nkx2-5 cre/+ rep1


title: Gata4 flox/+ ; Nkx2-5 +/+ rep3


title: Gata4 flox/flox ; Nkx2-5 cre/+ rep5


title: A2lox.mesp1 (day 3)

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.  "

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)."

growth_protocol: For differentiation, ES cells were plated in suspension in bacterial petri dishes at 1.5 x 10e4 cells/mL in serum-containing medium (SCM: IMDM with 10% FCS, NEAA, L-glutamine,  NaPyruvate, Pen/Strep, and 2-mercaptoethanol) ), and supplemented where indicated with Dkk1 or doxycycline."


title: A2lox.mesp1 (day 6 + dox)


title: Gata4 flox/+ ; Nkx2-5 +/+ rep1


title: WT-SB replicate2


title: Wild-type mice rep4

status: Public on Jun 30 2008

city: GRENOBLE

first: Philippe

last: HUBER

address: 17, Rue des martyrs

department: iRTSV

country: France

institute: Inserm-CEA

hyb_protocol: 12,5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450,  protocol EukGE_WS2v5_450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

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: pcdh12-deficient placenta embryonic day 12.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mice were mated and the day on which a vaginal plug was found was designated 0.5.

extract_protocol: Pregnant females were killed by cervical dislocation and conceptuses were dissected in PBS. Total RNA were extracted from E12.5 placentas using RNeasy kit (Qiagen). RNA concentration and integrity were tested with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.).


title: Wild-type mice rep5


title: Wild-type mice rep3


title: Wild-type mice rep2


title: pcdh12-deficient mice rep2

source_name: wild-type placenta embryonic day 12.5


title: pcdh12-deficient mice rep4


title: pcdh12-deficient mice rep5


title: pcdh12-deficient mice rep3


title: Media/Dex/AA/BGP + R568-7-7 days_rep3

status: Public on Jun 28 2008

city: Thousand Oaks

first: Lori

last: Twehues

state: CA

address: One Amgen Ctr

department: Computational Biology

institute: Amgen, Inc

description: Gene expression data from human coronary smooth muscle cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Intensity measurements of the perfect match oligonucleotide reporters were log-transformed, scaled using a nonlinear normalization, and summarized into a single intensity using the arithmetic mean.

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-7-7 days_rep3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (section 2, Eukaryotic Sample and Array Processing, 701024 rev 1, Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Human CSMC (from Clonetics) expanded in D-MEM/15% FBS/1x Na pyruvate/penicillin/streptomycin. Experiments performed on passage 7 cells.

extract_protocol: Total RNA was isolated using QIAgen RNeasy Mini Kit (Valencia, CA)

treatment_protocol: Cells were plated in 6-well dishes at 3,500 cells/cm2, and exposed to differentiation medium alone, differentiation medium + calcitriol (10-8M), differentiation medium + paricalcitol (10-8M), or differentiation medium + R-568 (10-8M) for 4 hours, or 1, 3, or 7 days.

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-7M  Day 7


title: Wild-type mice rep1


title: Media/Dex/AA/BGP + R568-7-4 hours_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-7-4 hours_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-7M  4 hours


title: Adult murine BM, hCD25+ CLP (LIN-B220-CD19-IL7R+FLT3+SCA1lowKITlowhCD25+) #2

status: Public on Jun 29 2008

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

country: Sweden

institute: Lund University

description: Gene expression data from LSKCD34-Flt3- cells FACS sorted from adult BM

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.

data_processing: Expression values were calculated by RMA express using background adjustment and quantile normalization.

source_name: Adult murine BM from 10-15 weeks old mice

label_protocol: Biotinylated cRNA was prepared according to the standard AffymetrixTM; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using AffymetrixTM GeneChipTM Expression 3’amplification kit.

extract_protocol: Cells were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

tag: Wild type C57bl/6


title: Media/Dex/AA/BGP + R568-7-3 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-7-3 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-7M  Day 3


title: pcdh12-deficient mice rep1


title: Media/Dex/AA/BGP + Z-11-10 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-11-10 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-11M  Day 10


title: Adult murine BM, hCD25- CLP (LIN-B220-CD19-IL7R+FLT3+SCA1lowKITlowhCD25-) #2


title: Media/Dex/AA/BGP + Z-11-4 hours_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-11-4 hours_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-11M  4 hours


title: Adult murine BM, pro-B cells (CD19+B220+CD43-IgM-) #2


title: Adult murine BM, pro-B cells (CD19+AA4.1+CD43low) #1


title: Adult murine BM, pro-B cells (CD19+AA4.1+CD43low) #2


title: Adult murine BM, hCD25- CLP (LIN-B220-CD19-IL7R+FLT3+SCA1lowKITlowhCD25+) #1


title: Adult murine BM, pro-B cells (CD19+B220+CD43-IgM-) #1


title: Adult murine BM, hCD25- CLP (LIN-B220-CD19-IL7R+FLT3+SCA1lowKITlowhCD25-) #1


title: Media/Dex/AA/BGP + R568-7-1 day_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-7-1 day_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-7M Day 1


title: Adult murine BM, hCD25- CLP (LIN-B220-CD19-IL7R+FLT3+SCA1lowKITlowhCD25-) #3


title: Adult murine spleen, Mature B cells (CD19+IgM+) #1

source_name: Adult murine spleen from 10-15 weeks old mice


title: Media/Dex/AA/BGP + Z-11-7 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-11-7 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-11M  Day 7


title: Adult murine spleen, Mature B cells (CD19+IgM+) #2


title: Media/Dex/AA/BGP + R568-7-10 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-7-10 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-7M  Day 10


title: Media/Dex/AA/BGP + Z-8-4 hours_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-4 hours_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  4 hours


title: Media/Dex/AA/BGP + Z-11-3 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-11-3 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-11M  Day 3


title: Media/Dex/AA/BGP + Z-8-7 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-7 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  Day 7


title: Media/Dex/AA/BGP + Z-8-1 day_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-1 day_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  Day 1


title: Media/Dex/AA/BGP + Vit D-11-4 hours_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11-4 hours_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M 4 hours


title: Media/Dex/AA-10 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA-10 days_rep3

tag: Media + dexamethasone + absorbic acid Day 10


title: Media/Dex/AA/BGP + Vit D-11-3 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11-3 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 3


title: Media/Dex/AA/BGP + D-8-4 hours_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-4 hours_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M 4 hours


title: Media/Dex/AA/BGP + Vit D-11-7 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11-7 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 7


title: Media/Dex/AA/BGP + D-8-10 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-10 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 10


title: Media/Dex/AA/BGP + D-8-3 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-3 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 3


title: Media/Dex/AA/BGP-7 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-7 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 7


title: Media/Dex/AA/BGP-4 hours_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-4 hours_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate 4 hours


title: Media/Dex/AA-4 hours_rep3

source_name: coronary smooth muscle cells; media/Dex/AA-4 hours_rep3

tag: Media + dexamethasone + absorbic acid 4 hours


title: Media/Dex/AA-3 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA-3 days_rep3

tag: Media + dexamethasone + absorbic acid Day 3


title: Media/Dex/AA/BGP + D-8-1 day_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-1 day_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 1


title: Media/Dex/AA/BGP-1 day_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-1 day_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 1


title: Media/Dex/AA/BGP-10 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-10 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 10


title: Media/Dex/AA/BGP + Z-11-1 day_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-11-1 day_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-11M  Day 1


title: Media/Dex/AA/BGP + R568-8-4 hour_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-8-4 hour_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-8M  4 hours


title: Media/Dex/AA-1 day_rep3

source_name: coronary smooth muscle cells; media/Dex/AA-1 day_rep3

tag: Media + dexamethasone + absorbic acid Day 1


title: Media/Dex/AA/BGP + R568-11-4 hour_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-11-4 hour_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-11M  4 hours


title: Media/Dex/AA/BGP + R568-11-7 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-11-7 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-11M  Day 7


title: Media/Dex/AA/BGP + Vit D-11-1 day_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11-1 day_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 1


title: Media/Dex/AA-7 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA-7 days_rep3

tag: Media + dexamethasone + absorbic acid Day 7


title: Media/Dex/AA/BGP + R568-8-1 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-8-1 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-8M Day 1


title: Media/Dex/AA/BGP + Z-8-3 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-3 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  Day 3


title: Control Time 0-Time 0_rep3

source_name: coronary smooth muscle cells; control Time 0-Time 0_rep3

tag: Time 0 Control


title: Media/Dex/AA/BGP + D-8-7 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-7 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 7


title: Media/Dex/AA/BGP + Vit D-11-10 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11-10 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 10


title: Media/Dex/AA/BGP + R568-11-3 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-11-3 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-11M  Day 3


title: Media/Dex/AA/BGP + R568-8-3 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-8-3 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-8M  Day 3


title: Media/Dex/AA/BGP + R568-11-1 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-11-1 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-11M Day 1


title: Media/Dex/AA/BGP + R568-8-7 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-8-7 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-8M  Day 7


title: Media/Dex/AA/BGP + Z-11-4 hour_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-11-4 hour_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-11M  4 hours


title: Media/Dex/AA/BGP + Z-11-3 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-11-3 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-11M  Day 3


title: Media/Dex/AA/BGP + Z-11-7 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-11-7 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-11M  Day 7


title: Media/Dex/AA/BGP + Z-11-1 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-11-1 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-11M  Day 1


title: Media/Dex/AA/BGP + Z-8-4 hour_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-4 hour_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  4 hours


title: Media/Dex/AA/BGP + Z-8-7 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-7 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  Day 7


title: Media/Dex/AA/BGP + Vit D-11-4 hour_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11-4 hour_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M 4 hours


title: Media/Dex/AA/BGP + Z-8-3 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-3 day_rep2


title: Media/Dex/AA/BGP + Z-8-1 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-1 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  Day 1


title: Media/Dex/AA/BGP + Vit D-11-7 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11-7 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 7


title: Media/Dex/AA/BGP + Vit D-11-1 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11-1 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 1


title: Media/Dex/AA/BGP + D-8-3 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-3 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 3


title: Media/Dex/AA/BGP + D-8-1 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-1 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 1


title: Media/Dex/AA-4 hour_rep2

source_name: coronary smooth muscle cells; media/Dex/AA-4 hour_rep2

tag: Media + dexamethasone + absorbic acid 4 hours


title: Media/Dex/AA/BGP-3 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-3 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 3


title: Media/Dex/AA/BGP + Vit D-11-3 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11-3 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 3


title: Media/Dex/AA/BGP + D-8-4 hour_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-4 hour_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M 4 hours


title: Media alone-7 day_rep2

source_name: coronary smooth muscle cells; media alone-7 day_rep2

tag: Media Day 7


title: Media/Dex/AA/BGP-7 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-7 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 7


title: Media/Dex/AA/BGP + D-8-7 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-7 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 7


title: Media/Dex/AA/BGP-1 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-1 day_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 1


title: Media/Dex/AA-3 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA-3 day_rep2

tag: Media + dexamethasone + absorbic acid Day 3


title: Human Control T-0_rep2

source_name: coronary smooth muscle cells; human Control T-0_rep2

tag: Time 0 Control


title: Media/Dex/AA/BGP-4 hour_rep2

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-4 hour_rep2

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate 4 hours


title: Media/Dex/AA/BGP + R568-11-3 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-11-3 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-11M  Day 3


title: Media/Dex/AA-1 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA-1 day_rep2

tag: Media + dexamethasone + absorbic acid Day 1


title: Media/Dex/AA-7 day_rep2

source_name: coronary smooth muscle cells; media/Dex/AA-7 day_rep2

tag: Media + dexamethasone + absorbic acid Day 7


title: Media alone-1 day_rep2

source_name: coronary smooth muscle cells; media alone-1 day_rep2

tag: Media Day 1


title: Media alone-3 day_rep2

source_name: coronary smooth muscle cells; media alone-3 day_rep2

tag: Media Day 3


title: Media alone-4 hours_rep2

source_name: coronary smooth muscle cells; media alone-4 hours_rep2

tag: Media 4 Hours


title: Media/Dex/AA/BGP + R568-11-4 hours_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-11-4 hours_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-11M  4 hours


title: Media/Dex/AA/BGP + R568-11-7 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-11-7 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-11M  Day 7


title: Media/Dex/AA/BGP + R568-11-1 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-11-1 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-11M Day 1


title: Media/Dex/AA/BGP + R568-8-4 hours_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-8-4 hours_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-8M  4 hours


title: Media/Dex/AA/BGP + R568-8-1 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-8-1 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-8M Day 1


title: Media/Dex/AA/BGP-3 days_rep3

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-3 days_rep3

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 3


title: Media/Dex/AA/BGP + R568-8-3 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-8-3 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-8M  Day 3


title: Media/Dex/AA/BGP + R568-8-7 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + R568-8-7 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + R568 (a calcimimetic) 10e-8M  Day 7


title: Media/Dex/AA/BGP + Z-8-7 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-7 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  Day 7


title: Media/Dex/AA/BGP + Vit D-11 -3 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11 -3 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 3


title: Media/Dex/AA/BGP + Z-8-3 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-3 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  Day 3


title: Media/Dex/AA/ BGP + D-8-7 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/ BGP + D-8-7 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 7


title: fresh LN IKDC

city: Baltimore

first: Franck

last: Housseau

state: MD

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University

description: gene expression data from LN IKDC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip murine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip scanner

data_processing: The data were analyzed with GeneChip operating software version 1.4.

source_name: fresh lymph node IKDC

extract_protocol: TRIZOL and Rneasy total RNA extraction following manufacturer's instructions

treatment_protocol: freshly isolated from organs by cell-sprting

tag: Balb/c mice

tag: 6-8 week old


title: fresh spleen IKDC 1

description: gene expression data from spleen IKDC

source_name: fresh spleen IKDC


title: fresh spleen IKDC 2

description: gene expression data from spleen IKDC


title: Media/Dex/AA/BGP-4 hours_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-4 hours_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate 4 hours


title: fresh spleen NK 2

description: gene expression data from spleen NK

source_name: fresh spleen NK


title: fresh LN CDC

description: gene expression data from LN CDC

source_name: fresh lymph node CDC


title: Media/Dex/AA/BGP + Vit D-11 -4 hours_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11 -4 hours_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M 4 hours


title: Media/Dex/AA/BGP + Vit D-11 -7 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11 -7 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 7


title: fresh spleen CDC 2

description: gene expression data from spleen CDC

source_name: fresh spleen CDC


title: Media/Dex/AA/BGP + Vit D-11 -1 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Vit D-11 -1 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-11M Day 1


title: Media/Dex/AA/BGP + D-8-4 hours_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-4 hours_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M 4 hours


title: fresh spleen NK 1

description: gene expression data from spleen NK


title: fresh LN NK

description: gene expression data from LN NK

source_name: fresh lymph node NK


title: Media/Dex/AA/BGP + D-8-3 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-3 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 3


title: Media/Dex/AA/BGP-7 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-7 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 7


title: Media/Dex/AA/BGP + Z-8-4 hours_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-4 hours_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  4 hours


title: Media/Dex/AA/BGP + D-8-1 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + D-8-1 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Vitamin D 10e-8M Day 1


title: Media/Dex/AA/BGP + Z-8-1 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP + Z-8-1 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate + Zemplar (Paracalcitriol, a Vit D analog) 10e-8M  Day 1


title: fresh spleen CDC 1

description: gene expression data from spleen CDC


title: Media/Dex/AA-3 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA-3 day_rep1

tag: Media + dexamethasone + absorbic acid Day 3


title: Media/Dex/AA/BGP-3 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-3 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 3


title: Media/Dex/AA/BGP-1 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA/BGP-1 day_rep1

tag: Media + dexamethasone + absorbic acid + beta-glycerophosphate Day 1


title: Media/Dex/AA-7 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA-7 day_rep1

tag: Media + dexamethasone + absorbic acid Day 7


title: Media alone-4 hours_rep1

source_name: coronary smooth muscle cells; media alone-4 hours_rep1

tag: Media 4 Hours


title: Media/Dex/AA-4 hours_rep1

source_name: coronary smooth muscle cells; media/Dex/AA-4 hours_rep1

tag: Media + dexamethasone + absorbic acid 4 hours


title: Media/Dex/AA-1 day_rep1

source_name: coronary smooth muscle cells; media/Dex/AA-1 day_rep1

tag: Media + dexamethasone + absorbic acid Day 1


title: Media alone-7 day_rep1

source_name: coronary smooth muscle cells; media alone-7 day_rep1

tag: Media Day 7


title: Neural Stem cells (NSC) sample 3

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

description:
Washing and staining of the arrays was done in an Affymetrix GeneChip Fluidics station 450. The following default Affymetrix washing/staining protocol with antibody amplification was used:
(1) 10 cycles with 6xSSPE/0.01%Tween at 25˚C
(2) 4 cycles with 100 mM MES/ 0.1 M[Na+]/0.01% Tween at 50˚C
(3) 10 min. staining with 10 mg/mL Streptavidin/Phycoerythrin (SAPE, Molecular Probes) and 2 mg/mL acetylated BSA (GIBCO) in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(4) as (1)
(5) 10 min. staining with 3 mg/mL biotinylated anti-strepavidin antibody (goat, Vector Laboratories), 0.1 mg/mL goat IgG (Sigma), 2 mg/mL acetylated BSA in 100 mM MES/ 0.1 M[Na+]/0.05% Tween at 25˚C
(6) as (3)
(7) 15 cycles with 6xSSPE/0.01%Tween at 30˚C

hyb_protocol: Affymetrix arrays were prehybridized with 200 ml MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 mg of labeled cRNA in 200 ml MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scan using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.

source_name: Neural Stem cells (OG2/Rosa26)

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

growth_protocol: Neural stem cells (NSC) were derived from postnatal brain (day 5) of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.. Cells were seeded at a density of 5x104 cells per 6-well plate.

extract_protocol: Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

tag: neural stem cells; strain

value: OG2/Rosa26; Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.


title: Induced pluripotent stem (iPS) cells (Oct4, Sox2, c-Myc, Klf4) sample 1

source_name: iPS cells 4 factors

growth_protocol: Induced pluripotent stem (iPS) cell were grown on irradiated MEF and in ESC medium (DMEM supplemented with 15% FBS, nonessential amino acids, L-glutamine, penicillin/streptomycin, b-mercaptoethanol, and 1,000 U/ml LIF).

treatment_protocol: Neural stem cells (NSC) were derived from postnatal brain (day 5) of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vectors encoding mouse cDNA of Oct4, Sox2, c-Myc, Klf4 (1:1:1:1). Two days after infection, cells were further subcultured on irradiated MEF in ESC medium containing LIF without any further selection. Oct4-GFP–positive colonies were mechanically isolated, and individual cells were dissociated and subsequently replated onto MEF. Colonies were then selected for expansion.

tag: induced pluripotent stem (ips) cells from mouse neural stem cells (nsc). strain


title: Induced pluripotent stem (iPS) cells (Oct4, Klf4) sample 3

source_name: iPS cells 2 factors

treatment_protocol: Neural stem cells (NSC) were derived from postnatal brain (day 5) of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.. Cells were seeded at a density of 5x104 cells per 6-well plate and infected with pMX-based retroviral vectors encoding mouse cDNA of Oct4, Klf4 (1:1). Two days after infection, cells were further subcultured on irradiated MEF in ESC medium containing LIF without any further selection. Oct4-GFP–positive colonies were mechanically isolated, and individual cells were dissociated and subsequently replated onto MEF. Colonies were then selected for expansion.


title: Induced pluripotent stem (iPS) cells (Oct4, Klf4) sample 1

value: Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.


title: Embryonic Stem cells sample 2

source_name: Embryonic Stem cells (OG2/Rosa26)

growth_protocol: Embryonic Stem cells (ESC) were grown on irradiated MEF and in ESC medium (DMEM supplemented with 15% FBS, nonessential amino acids, L-glutamine, penicillin/streptomycin, b-mercaptoethanol, and 1,000 U/ml LIF).

treatment_protocol: No treatment

tag: embryonic stem cells; strain


title: Embryonic Stem cells sample 1


title: 3P-RNA at 6h-1

status: Public on Jun 27 2008

city: munich

first: Ramanjaneyulu

last: Allam

address: Schillerstr. 42

department: Medizinische Poliklinik-Innenstadt

institute: Klinikum der Universität München

description: Gene expression data from primary mesangial cells that are stimulated with Non-CpG DNA and 3P-RNA

hyb_protocol: Following fragmentation, we used standard Affymetrix procedures for hybridization

scan_protocol: standard Affymetrix procedures

data_processing: The data were analyzed with RMA Express version 1.0 beta 2

source_name: primary mesangial cells, 3P-RNA at 6h-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Expresssion Analysis Technical Manual  from 6 µg total RNA

growth_protocol: Primary mesangial cells were isolated from kidney and grow them in RPMI 1640 containing 20% FCS, 1% ITS

extract_protocol: RNA was prepared using RNAeasy Mini Kit according manufacturer-suggested protocol

treatment_protocol: primary mesangial cells treated with non CpG DNA and 3P-RNA for 6 hours

tag: Genotype

tag: Age

value: 8-10 week old


title: Non-CpG DNA at 6h-1

source_name: primary mesangial cells, Non-CpG DNA at 6h-1


title: Media alone-3 day_rep1

source_name: coronary smooth muscle cells; media alone-3 day_rep1

tag: Media Day 3


title: 3P-RNA at 6h-3

source_name: primary mesangial cells, 3P-RNA at 6h-3


title: Neural stem cells (NSC) sample 2

treatment_protocol: Neural stem cells (NSC) were derived from postnatal brain (day 5) of Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females.

value: OG2/Rosa26; Oct4-eGFP transgenic OG2 Rosa26 neo/lacZ mice (Do and Schöler, Stem Cells 22, 941-949, 2004) crossed with ICR females


title: Non-CpG DNA at 6h-3

source_name: primary mesangial cells, Non-CpG DNA at 6h-3


title: Media alone-1 day_rep1

source_name: coronary smooth muscle cells; media alone-1 day_rep1

tag: Media Day 1


title: Induced pluripotent stem (iPS) cells (Oct4, Sox2, c-Myc, Klf4) sample 3


title: Control T-0_rep1

source_name: coronary smooth muscle cells; control T-0_rep1

tag: Time 0 Control


title: lipofectamine at 6h-1

source_name: primary mesangial cells, control, lipofectamine at 6h-1


title: lipofectamine at 6h-3

source_name: primary mesangial cells, control, lipofectamine at 6h-3


title: Non-CpG DNA at 6h-2

source_name: primary mesangial cells, Non-CpG DNA at 6h-2


title: lipofectamine at 6h-2

source_name: primary mesangial cells, control, lipofectamine at 6h-2


title: Induced pluripotent stem (iPS) cells (Oct4, Sox2, c-Myc, Klf4) sample 2


title: Induced pluripotent stem (iPS) cells (Oct4, Klf4) sample 2


title: 3P-RNA at 6h-2

source_name: primary mesangial cells, 3P-RNA at 6h-2


title: Embryonic Stem cells sample 3


title: Donor C Untreated VSMCs

city: New Haven

first: Raymond

middle: Emile

last: Eid

state: CT

address: 10 Amistad Street

department: Surgery

institute: Yale University

description: Human Aortic Vascular Smooth Muscle Cells

hyb_protocol: Following fragmentation, cDNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 and expression console (Affymetrix).

data_processing:
GeneSpring GX 7.3 data analysis software (Silicon Genetics, Redwood, CA) with RMA (Robust Multi-Array Average) were used for normalization and fold-change calculations

RMA data was requested from submitter but was not provided

source_name: Untreated VSMCs

label_protocol: Purified RNA was converted to biotinylated cDNA target.

growth_protocol: VSMCs were cultured in M199 media supplemented with 20% FCS, glutamine and Penicillin/Streptomycin.

extract_protocol: Total RNA was extracted and purified from vascular smooth muscle cells using Qiagen RNEasy Micro columns and protocol provided by supplier.

treatment_protocol: VSMCs from the  human aortas were cultured in M199 media supplemented with 20% FCS and used at passage 3. The cells were either not treated or treated with IL-17 at 100 ng/ml for 6 hr.

tag: Control

tag: Donor C


title: Donor B IL-17-treated VSMCs

source_name: IL17-treated VSMCs

tag: IL-17 treated

tag: Donor B


title: Donor A IL-17-treated VSMCs

tag: Donor A


title: Donor A Untreated VSMCs


title: Donor C IL-17-treated VSMCs


title: Normal_2_CD24L(MEC)

city: Houston

first: Mei

last: Zhang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
For tumors: TG1 means transplantation generation 1. H means high, L means low. Therefore, CD29HCD24H means CD29 high, CD24 high; CD29HCD24L means CD29 high, CD24 low; CD29LCD24H means CD29 low, CD24 high; CD29LCD24L means CD29 low, CD24 low.

For normal: MEC means mammary epithelial cell. CD29highCD24positive from normal MEC is shortened to CD29HCD24P(MEC), CD29positiveCD24high from normal is shortened to CD29PCD24H(MEC), and CD24low from normal is shortened to CD24L(MEC).

hyb_protocol: Affymetrix Hybridization

scan_protocol: GeneChip Scanner

data_processing: GCOS-calculated probe set signal intensities

source_name: mammary epithelial cells

label_protocol: mRNA amplification and labeling using a T7 global amplification method (Two-cycle Target Labeling kit; Affymetrix)

extract_protocol: PicoPure RNA isolation kit

tag: Balb/C


title: Normal_2_CD29HCD24P(MEC)


title: Donor B Untreated VSMCs


title: Reference RNA

source_name: Stratagene reference RNA

extract_protocol: Reference RNA purchased from Stratagene

tag: cell lines


title: pkl Mutant Germinating Seeds With Uniconazole Treatment Set 2 of 6

city: West Lafayette

first: Joe

last: Ogas

state: IN

address: 175 S. University St.

department: Biochemistry

institute: Purdue University

description: Relative expression data from germinating seeds of Columbia (wt), the pkl mutant (pkl), Columbia plus uniconazole-P (Uwt) and the pkl-mutant plus uniconazole-P (Upkl). Each experimental condition (wt, pkl, Uwt and Upkl) has six biological replicates for a total of 24 chips.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: MAS 5.0

organism: Arabidopsis thaliana

label_protocol: Affymetrix protocol

growth_protocol: Seeds were germinated in a CU36L5 incubator under 24h illumination.

extract_protocol: Hot Phenol with LiCl precipitation followed by RNeasy clean up (Qiagen).

treatment_protocol: Treated with 10 nM uniconazole and 0.01% methanol (solvent) present in Murashige and Skoog Basal Medium with Gamborg's Vitamins solidified with agar.

tag: Relative expression data from germinating seeds of pkl mutant treated with uniconazole (Upkl) after testa rupture and during endosperm rupture (radicle emergence).


title: T7_CD29HCD24H

source_name: mammary tumor


title: T2_TG1_CD29LCD24H


title: T2_TG1_CD29HCD24L


title: T7_CD29LCD24L


title: Normal_1_CD29PCD24H(MEC)


title: Normal_2_CD29PCD24H(MEC)


title: pkl Mutant Germinating Seeds With Uniconazole Treatment Set 1 of 6


title: T1_TG1_CD29LCD24L


title: T1_TG1_CD29HCD24L


title: T2_TG1_CD29HCD24H

hyb_protocol: Affymetrix hybridization

tag: Balb/c


title: Normal_1_CD29HCD24P(MEC)

source_name: normal mammary epithelial cells


title: pkl Mutant Germinating Seeds With Uniconazole Treatment Set 3 of 6


title: pkl Mutant Germinating Seeds With Uniconazole Treatment Set 5 of 6


title: T2_TG1_CD29LCD24L


title: T1_TG1_CD29HCD24H


title: T1_TG1_CD29LCD24H


title: T7_CD29HCD24L


title: pkl Mutant Germinating Seeds With Uniconazole Treatment Set 4 of 6


title: Wild Type Germinating Seeds With Uniconazole Treatment Set 1 of 6

tag: Relative expression data from germinating seeds of Columbia treated with uniconazole (Uwt) after testa rupture and during endosperm rupture (radicle emergence).


title: T7_CD29LCD24H


title: Wild Type Germinating Seeds With Uniconazole Treatment Set 5 of 6


title: pkl Mutant Germinating Seeds With Uniconazole Treatment Set 6 of 6


title: Wild Type Germinating Seeds With Uniconazole Treatment Set 4 of 6


title: pkl Mutant Germinating Seeds With Solvent Treatment Only Set 6 of 6

treatment_protocol: Treated with 0.01% methanol (solvent) present in Murashige and Skoog Basal Medium with Gamborg's Vitamins solidified with agar.

tag: Relative expression data from germinating seeds of pkl mutant (pkl) after testa rupture and during endosperm rupture (radicle emergence).


title: Wild Type Germinating Seeds With Uniconazole Treatment Set 6 of 6


title: pkl Mutant Germinating Seeds With Solvent Treatment Only Set 5 of 6


title: pkl Mutant Germinating Seeds With Solvent Treatment Only Set 4 of 6


title: Wild Type Germinating Seeds With Uniconazole Treatment Set 2 of 6

treatment_protocol: Treated with 10 nM uniconazole in 0.01% methanol (solvent) present in Murashige and Skoog Basal Medium with Gamborg's Vitamins solidified with agar.


title: Wild Type Germinating Seeds With Solvent Treatment Only Set 4 of 6

tag: Relative expression data from germinating seeds of Columbia (wt) after testa rupture and during endosperm rupture (radicle emergence).


title: Wild Type Germinating Seeds With Solvent Treatment Only Set 5 of 6


title: Wild Type Germinating Seeds With Solvent Treatment Only Set 2 of 6


title: pkl Mutant Germinating Seeds With Solvent Treatment Only Set 2 of 6


title: Wild Type Germinating Seeds With Solvent Treatment Only Set 6 of 6


title: pkl Mutant Germinating Seeds With Solvent Treatment Only Set 1 of 6


title: Wild Type Germinating Seeds With Solvent Treatment Only Set 1 of 6


title: Wild Type Germinating Seeds With Solvent Treatment Only Set 3 of 6


title: Affy_Macrophage_28

city: Paris

first: Francois

last: Cambien

state: France

address: 91 Bd de l'Hôpital

department: Cardiovascular Genomics

institute: INSERM

description: All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification.

hyb_protocol: 15 µg of cRNA were hybridized to Affymetrix Human U133 plus 2.0 array for 16 hours at 45°C. Following hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Fluorescent images recorded on a GenChip Scanner 3000 and processed with the GeneChip Operating software (Affymetrix, CA, USA).

data_processing:
Background correction method: Robust Mult-array Average (RMA).
Normalization: quantile
Summarization: for each probe set Median polish method was used to summarized PM intensities into on expression value
Signal intensities were log2-transformed
Detection calls were calculated using the Bioconductor package PANP(Presence-Absence calls with Negative Probesets)

source_name: whole blood, macrophage_28

label_protocol: Double stranded cDNA was amplified and labelled using a biotin-NTP mix in the second IVT reaction. The labelled cRNA was then cleaned up and fragmented.

growth_protocol: The human monocytes CD14+ obtained after MACS separation were cultured at a concentration of 1x 106 cells/ml in pure RPMI 1640 medium in P6 Petri dishes. After 1h of incubation at 37°C, non adherent cells were removed and the medium was replaced with RPMI 1640 Glu+ medium supplemented with 100U/ml penicillin, 100 µg/ml streptomycin and 10 % FCS, together with 10 ng/ml of macrophage colony stimulating-factor (M-CSF, SIGMA). Cells were incubated for 6 days at 37°C/5% CO2 to induce the phagocytic differentiation.

extract_protocol: RNA extraction was done using RNAeasy minikit (Qiagen).

treatment_protocol: Blood was drawn under standardized conditions in EDTA tubes: 40 ml samples were collected immediately after coronary angiography and stored at 4°C. Monocytes isolation was performed within 2 hours after Blood drawing. After density gradient centrifugation and washing, PMBC were mixed with CD14 coated beads (MACS, Miltenyi Biotec). To induce phagocytic differentiation, a fraction of the monocytes was incubated for 6 days with macrophage colony stimulating factor (M-CSF, SIGMA).

tag: Gender

value: male

tag: Tissue

value: whole blood

tag: Cell type

value: macrophage

tag: Patient with symptoms of acute coronary syndrome who had

tag: undergone coronary angiography (who had one stenosis >50 % diagnosed in at least one major coronary artery)


title: pkl Mutant Germinating Seeds With Solvent Treatment Only Set 3 of 6


title: Affy_Monocyte_26

source_name: whole blood, monocyte_26

tag: Age

value: monocyte


title: Affy_Monocyte_28

source_name: whole blood, monocyte_28


title: Affy_Macrophage_16

source_name: whole blood, macrophage_16


title: whole blood_100240

status: Public on Jun 26 2008

city: Sacramento

first: Jeffrey

last: Gregg

institute: University of California, Davis School of Medicine

description: Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hrs at 45C on the Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using wash protocol EukGE-WS2v5.

scan_protocol: Arrays were scanned on a GeneChip® Scanner 3000 7G

data_processing: Raw data values were imported into GENESPRING 7.2 software (Agilent Technologies, Palo Alto, CA) and processed using GC-RMA, followed by normalization. A three-step normalization procedure was applied to raw expression values (Genespring 2004).  First, values less than 0.01 were set to 0.01 (data transformation). Second, per chip normalization was performed by dividing each measurement by the 50.0th percentile of all measurements in that sample. Third, each gene was divided by the median of its measurements in all samples (per gene normalization).

source_name: Whole blood - mental retardation or developmental delay, Male

label_protocol: Biotinylated cRNA were prepared from 3 micrograms of total RNA according to the standard Affymetrix protocol

extract_protocol: Total RNA was extracted from whole blood samples using the PaxGene Blood RNA System according the manufacturer’s specifications.


title: Affy_Macrophage_20

source_name: whole blood, macrophage_20


title: whole blood_100346

tag: mental retardation or developmental delay, Male


title: Affy_Monocyte_21

source_name: whole blood, monocyte_21


title: Affy_Monocyte_16

source_name: whole blood, monocyte_16


title: whole blood_100315

source_name: Whole blood - mental retardation or developmental delay, Female


title: gene expression profiling of cholangiocarcinoma cells overexpressing IL-6

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

description: gene expression profiling of cells stably transfected to overexpress IL-6

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

source_name: gallbladder cancer cell line that is overexpressed with IL-6

label_protocol: standard Affymetrix protocol

growth_protocol: Mz-IL-6 cells were cultured in CMRL 1066 medium containing 10% fetal bovine serum, 1% I-glutamine and 1% antibiotic-antimycotic mix

extract_protocol: RNA isolation kit (Bio-Rad)

treatment_protocol: Mz-IL-6 cells were stably transfected with a pTarget (Promega) plasmid containing the full length IL-6 under the control of a CMV promoter. (Journal of Hepatology 2006;44:1055-1065)

value: Mz-ChA-1 cells overexpressing IL-6


title: whole blood_100265


title: Affy_Monocyte_20

source_name: whole blood, monocyte_20


title: whole blood_101446


title: whole blood_101621


title: gene expression profiling of cholangiocarcinoma cells

description: gene expression profiling of stably transfected cells with the control empty vector

source_name: gallbladder cancer cell line

growth_protocol: Mz-ChA-1 cells were cultured in CMRL 1066 medium containing 10% fetal bovine serum, 1% I-glutamine and 1% antibiotic-antimycotic mix

treatment_protocol: Mz-ChA-1 cells were stably transfected with an empty pTarget (Promega) plasmid

tag: Mz-ChA-1 cells


title: whole blood_100961

tag: mental retardation or developmental delay, Female


title: Affy_Macrophage_26

source_name: whole blood, macrophage_26


title: Affy_Macrophage_21

source_name: whole blood, macrophage_21


title: whole blood_101872


title: whole blood_100801

source_name: Whole blood - General population, Male

tag: General population, Male


title: whole blood_100190

source_name: Whole blood - General population, Female

tag: General population, Female


title: whole blood_100760


title: Wild Type Germinating Seeds With Uniconazole Treatment Set 3 of 6


title: whole blood_101726


title: whole blood_101467


title: whole blood_101794


title: whole blood_101682

source_name: Whole blood - Autism with regression, Male

tag: Autism with regression, Male


title: whole blood_100409


title: whole blood_100251


title: whole blood_102321

source_name: Whole blood - Autism with regression, Female

tag: Autism with regression, Female


title: whole blood_100158


title: whole blood_100374


title: whole blood_100354


title: whole blood_101339


title: whole blood_100716


title: whole blood_101644


title: whole blood_100689


title: whole blood_101669


title: whole blood_101700


title: whole blood_100981


title: whole blood_100278


title: whole blood_101074


title: whole blood_100823


title: whole blood_100476

source_name: Whole blood - Autism no regression, Male

tag: Autism no regression, Male


title: whole blood_100247


title: whole blood_101234


title: whole blood_101025


title: whole blood_101592


title: whole blood_101062


title: whole blood_100812

source_name: Whole blood - Autism no regression, Female

tag: Autism no regression, Female


title: whole blood_101209


title: whole blood_100309


title: whole blood_101060


title: whole blood_100214


title: whole blood_101611


title: whole blood_100603


title: whole blood_101094


title: whole blood_101832


title: whole blood_101369


title: whole blood_100676


title: whole blood_100652


title: whole blood_100537


title: whole blood_100416


title: whole blood_100923


title: whole blood_101291


title: whole blood_101007


title: whole blood_100683


title: whole blood_101584


title: Standard medium supplemented with 9% ethanol (362OH-2)

city: Raleigh

first: Deepa

last: Sambandan

state: NC

address: 100, Derieux

department: Genetics

institute: North Carolina State University

description: Larvae were reared on three different media: standard cornmeal-molasses medium, standard medium supplemented with 9% ethanol and standard medium enriched with tomato paste. After eclosion, we transferred all flies to standard medium at 25°C under a 12:12 hour light/dark cycle prior to characterization of behavioral responses to benzaldehyde and transcription profiling.

hyb_protocol: Following fragmentation, 10 mkg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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 500.

label: Biotinylated cRNA

organism: Drosophila melanogaster

source_name: whole body

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.

growth_protocol: under standard conditions 25C, 12:12 light/dark cycle

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

treatment_protocol: Larvae were reared in Ethanol medium prior to RNA extraction


title: Standard medium supplemented with 9% ethanol (158 OH 1)


title: Standard medium supplemented with 9% ethanol (304 OH 1)


title: Standard medium enriched with tomato paste (362 TOM 1)

treatment_protocol: Larvae were reared in TOM medium prior to RNA extraction


title: Standard medium enriched with tomato paste (380TOM-4)


title: Standard medium supplemented with 9% ethanol (304 OH 2)


title: Standard medium supplemented with 9% ethanol (8590H-2)


title: Standard medium enriched with tomato paste (859 TOM 1)


title: Standard medium supplemented with 9% ethanol (362OH-1)


title: Standard medium enriched with tomato paste (362TOM-3)


title: Standard medium enriched with tomato paste (380TOM-3)


title: Standard medium enriched with tomato paste (786TOM-3)


title: Standard medium enriched with tomato paste (786 TOM 2)


title: Standard medium supplemented with 9% ethanol (786 OH 2)


title: Standard medium enriched with tomato paste (379TOM-3)


title: Standard medium supplemented with 9% ethanol (379 OH 1)


title: Standard medium supplemented with 9% ethanol (379 OH 2)


title: Standard medium supplemented with 9% ethanol (380 OH 2)


title: Standard medium supplemented with 9% ethanol (158 OH 2)


title: Standard medium enriched with tomato paste (774TOM-3)


title: Standard medium enriched with tomato paste (859TOM-4)


title: Standard medium supplemented with 9% ethanol (774 OH 1)


title: Standard medium enriched with tomato paste (304TOM-4)


title: Standard medium enriched with tomato paste (304TOM-3)


title: Standard medium supplemented with 9% ethanol (380 OH 1)


title: Standard medium enriched with tomato paste (158TOM-3)


title: Standard medium supplemented with 9% ethanol (774 OH 2)


title: Standard medium enriched with tomato paste (158 TOM 2)


title: Standard medium enriched with tomato paste (379 TOM 1)


title: Standard medium enriched with tomato paste (774TOM-4)


title: Standard medium supplemented with 9% ethanol (786 OH 1)


title: Standard cornmeal-molasses medium (859 STD 2)

treatment_protocol: Larvae were reared in STD medium prior to RNA extraction


title: Standard medium supplemented with 9% ethanol (8590H-3)


title: Standard cornmeal-molasses medium (786 STD 2)


title: Standard cornmeal-molasses medium (859 STD 1)


title: Standard cornmeal-molasses medium (362 STD 1)


title: Standard cornmeal-molasses medium (774 STD 2)


title: Standard cornmeal-molasses medium (304 STD 1)

source_name: whole body 3-5 day


title: Standard cornmeal-molasses medium (362 STD 2)


title: Standard cornmeal-molasses medium (379 STD 2)


title: Standard cornmeal-molasses medium (158 STD 2)


title: Standard cornmeal-molasses medium (774 STD 1)


title: Standard cornmeal-molasses medium (380 STD 1)


title: Standard cornmeal-molasses medium (786 STD 1)


title: Naive_Furin_Wild-type_1

city: Bethesda

first: Lai

last: Wei

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

description: Purified naive (CD4+ CD62L+ CD44-) T cells from 10-11 weeks old T cell specific Furin knockout (CD4-cre fur flox/flox) and littermate wild type (fur flox/flox) control mice were profiled for gene expression using Affymetrix MOE 430 2.0 microarray platform.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip MOE430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

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

treatment_protocol: Fresh isolated. Sorted for CD4+ CD62L+ CD44- T cells

tag: mouse T cells

value: 10-11 weeks


title: Standard cornmeal-molasses medium (304 STD 2)


title: Naive_Furin_Knockout_1


title: Standard cornmeal-molasses medium (158 STD 1)

tag: STD, raleigh inbred line 1 replicate 1


title: Naive_Furin_Knockout_2


title: Naive_Furin_Wild-type_2


title: Standard cornmeal-molasses medium (379 STD 1)


title: Tolerant PBMC_TOL_25

status: Public on Jun 25 2008

city: Barcelona

first: Alberto

last: Sanchez-Fueyo

address: Villarroel 170

department: Liver Transplantation Unit

country: Spain

institute: Hospital Clinic Barcelona / IDIBAPS

description: see M.Martinez-LLordella et al. Am J Transplant

hyb_protocol: Standrad Affymetrix protocol

scan_protocol: Standrad Affymetrix protocol

label: streptavidin-PE

source_name: Peripheral blood mononuclear cells

label_protocol: Standrad Affymetrix protocol

extract_protocol: Tryzol extraction

treatment_protocol: Ficoll isolation from peripheral blood

tag: Peripheral blood mononuclear cells obtained from tolerant liver transplant recipient, virus hepatitis C negative


title: Non-tolerant PBMCs_NoTOL_15

description: see  M.Martinez-LLordella et al.  Am J Transplant

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

label_protocol: Standard Affymetrix protocol

treatment_protocol: Ficoll PBMC isolation from peripheral blood

tag: Peripheral blood mononuclear cells obtained from a non-tolerant liver transplant recipient under tacrolimus treatment, no hepatitis C virus infection


title: Tolerant PBMC_TOL_28

tag: Peripheral blood mononuclear cells obtained from a tolerant liver transplant recipient, hepatitis C virus negative


title: Tolerant PBMC_TOL_27

tag: Peripheral blood mononuclear cells obtaiend from a tolerant liver transplant recipient, virus hepatitis C negative


title: Standard cornmeal-molasses medium (380 STD 2)

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.


title: Non-tolerant PBMCs_NoTOL_VHC_19

tag: Peripheral blood mononuclear cells obtained from non-tolerant liver transplant recipient, with hepatitis C infection and under treatment with cyclosporine A.


title: Non-tolerant PBMCs_NoTOL_VHC_20

tag: Peripheral blood mononuclear cells obtained from non-tolerant liver transplant recipient with hepatitis C infection and under treatment with tacrolimus.


title: Tolerant PBMC_TOL_VHC_26

tag: Peripheral blood mononuclear cells obtained from a tolerant liver transplant recipient with hepatitis C virus infection


title: Non-tolerant PBMCs_NoTOL_VHC_10

description: see M.Martinez-Llordella et al. Am J Transplant

tag: Peripheral blood mononuclear cells from a non-tolerant human liver transplant recipient with hepatitis C virus infection and under treatment with cyclosporine A.


title: Tolerant PBMC_TOL_17

tag: Peripheral blood mononuclear cells obtained from a tolerant liver transplant recipient, virus hepatitis C negative


title: Tolerant PBMC_TOL_18


title: Non-tolerant PBMCs_NoTOL_VHC_21

tag: Peripheral blood mononuclear cells obtained from non-tolerant liver transplant recipient with hepatitis C infection and under treatment with cyclosporine A.


title: Non-tolerant PBMCs_NoTOL_16

tag: Peripheral blood mononuclear cells obtained from non-tolerant liver transplant recipient, hepatitis C virus negative, under treatment with tacrolimus.


title: Proficiency_Site11_34

status: Public on Jun 24 2008

city: Pleasanton

first: Rachel

last: Li

address: 4300 Hacienda Dr.

institute: Roche

description: Performed by Operator 3 from Site11 at Proficiency stage

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 as recommended by the manufacturer.

data_processing: Data pre-processing included the summarization to generate probe set level signals for each microarray experiment and was performed using DQN algorithm.

label_protocol:
For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24  T7 primer(Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA).
The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol:
The eight samples that were analysed during the training course were represented by MCF-7 (breast adenocarcinoma) and HepG2 (liver carcinoma) cell line total RNA (Ambion, Austin, TX, USA) with 1.0 µg to 8.0 µg input of total RNA (for labeling described below), and four leukaemia patient sample lysates prepared from mononuclear cells obtained after Ficoll density purification.
The total RNA from the patient lysates was extracted at each centre as part of the training program, making these samples a test of the entire microarray process workflow post sample acquisition (RNeasy kit, Qiagen, Hilden, Germany).

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 72.00403; Lot# = 125PO54621A


title: Proficiency_Site11_32

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 83.15535; Lot# = 105PO55509A


title: Proficiency_Site11_36

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 72.28049; Lot# = 125PO54621A


title: Tolerant PBMC_TOL_14

description: see M. Martinez-Llordella et al. Am J Transplant

treatment_protocol: PBMC Ficoll isolation from peripheral blood

tag: Peripheral blood mononuclear cells obtained from a tolerant liver transplant recipient (no immunosuppressive drugs)


title: Proficiency_Site11_31

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 72.25887; Lot# = 105PO55509A


title: Proficiency_Site11_30

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 81.22496; Lot# = 105PO55509A


title: Proficiency_Site11_33

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 46.88182; Lot# = 125PO54621A


title: Proficiency_Site11_35

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 75.60905; Lot# = 125PO54621A


title: Proficiency_Site11_20

description: Performed by Operator 1 from Site11 at Proficiency stage

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 72.66; Lot# = 125PO54621A


title: Proficiency_Site11_23

description: Performed by Operator 2 from Site11 at Proficiency stage

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 108.05; Lot# = 105PO55509A


title: Proficiency_Site11_24

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 69.81; Lot# = 105PO55509A


title: Proficiency_Site11_29

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 69.76291; Lot# = 105PO55509A


title: Proficiency_Site11_22

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 77.25; Lot# = 105PO55509A


title: Proficiency_Site11_19

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 68.37; Lot# = 125PO54621A


title: Proficiency_Site11_26

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 66.53; Lot# = 125PO54621A


title: Proficiency_Site11_27

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 61.25; Lot# = 125PO54621A


title: Proficiency_Site11_21

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 45.94; Lot# = 105PO55509A


title: Proficiency_Site11_15

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 73.9; Lot# = 105PO55509A


title: Proficiency_Site11_18

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 58.76; Lot# = 125PO54621A


title: Proficiency_Site11_17

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 33; Lot# = 125PO54621A


title: Proficiency_Site11_28

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 73.27; Lot# = 125PO54621A


title: Tolerant PBMC_TOL_VHC_2

tag: Peripheral blood mononuclear cells obtained from tolerant liver transplant recipient with hepatitis C virus infection.


title: Proficiency_Site11_16

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 48.75; Lot# = 105PO55509A


title: Non-tolerant PBMCs_NoTOL_VHC_9

tag: Peripheral blood mononuclear cells obtained from non-tolerant liver transplant recipient with hepatitis C infection, under treatment with tacrolimus.


title: Tolerant PBMC_TOL_VHC_7

tag: Peripheral blood mononuclear cells from tolerant liver transplant recipient with hepatitis C virus infection


title: Proficiency_Site11_13

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 43.53; Lot# = 105PO55509A


title: Proficiency_Site11_25

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 55.85; Lot# = 125PO54621A


title: Proficiency_Site11_14

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 69.82; Lot# = 105PO55509A


title: Training_Site11_08

description: Performed by Operator 2 from Site11 at Training stage

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 77.54588; Lot# = 035PO41658D


title: Non-tolerant PBMCs_NoTOL_VHC_1

tag: Peripheral blood obtained from non-tolerant liver transplant recipient with hepatitis C virus infection


title: Training_Site11_07

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 36.38669; Lot# = 035PO41658D


title: Training_Site11_04

description: Performed by Operator 1 from Site11 at Training stage

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 60.07922; Lot# = 035PO41658D


title: Training_Site11_02

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 74.97908; Lot# = 124PO44836A


title: Proficiency_Site1_13

description: Performed by Operator 1 from Site1 at Proficiency stage

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 14.05; Lot# = 124PO44836A


title: Proficiency_Site1_19

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 46.56; Lot# = 035PO41658D


title: Proficiency_Site1_17

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 16.66; Lot# = 035PO41658D


title: Proficiency_Site1_14

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 21.76; Lot# = 124PO44836A


title: Proficiency_Site1_20

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 51.23; Lot# = 035PO41658D


title: Training_Site1_08

description: Performed by Operator 1 from Site1 at Training stage

source_name: AML with t(8;21)

tag: acute myeloid leukemia [AML w/ translocation t(8;21) or FAB M2] patient lysates of mononuclear cells


title: Training_Site1_05

source_name: CML in blast crisis

tag: chronic myeloid leukemia [CML] patient lysates of mononuclear cells


title: Training_Site1_04

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 37.56; Lot# = 035PO41658D


title: Training_Site1_06

source_name: CLL

tag: chronic lymphocytic leukemia [CLL] patient lysates of mononuclear cells


title: Training_Site11_05

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 47.75099; Lot# = 124PO44836A


title: Training_Site1_07


title: Training_Site11_03

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 41.74569; Lot# = 035PO41658D


title: Training_Site1_02

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 24.84; Lot# = 124PO44836A


title: Proficiency_Site1_18

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 30.6; Lot# = 035PO41658D


title: Training_Site11_01

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 43.23011; Lot# = 124PO44836A


title: Training_Site1_03

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 11.46; Lot# = 035PO41658D


title: Proficiency_Site10_23

description: Performed by Operator 1 from Site10 at Proficiency stage

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 64.7; Lot# = 065PO36893A


title: Training_Site1_01

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 10.08; Lot# = 124PO44836A


title: Training_Site11_06

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 60.83983; Lot# = 124PO44836A


title: Proficiency_Site1_16

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 47.5; Lot# = 124PO44836A


title: Proficiency_Site10_22

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 38.06; Lot# = 065PO36893A


title: Proficiency_Site10_18

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 53.62; Lot# = 075PO52329B


title: Proficiency_Site10_20

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 65.5; Lot# = 065PO36893A


title: Proficiency_Site10_19

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 58.5; Lot# = 075PO52329B


title: Proficiency_Site10_17

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 47.9; Lot# = 075PO52329B


title: Proficiency_Site1_15

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 48.64; Lot# = 124PO44836A


title: Proficiency_Site10_21


title: Proficiency_Site10_16

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 52.5; Lot# = 075PO52329B


title: Training_Site10_15

description: Performed by Operator 1 from Site10 at Training stage

tag: acute myeloid leukemia [AML w/ translocation t(8;21) or FAB M2] patient lysates of mononuclear cells

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 57.75; Lot# =  ---


title: Training_Site10_03

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 16.9; Lot# = 065PO36893A


title: Proficiency_Site6_20

description: Performed by Operator 1 from Site6 at Proficiency stage

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 69.75; Lot# = 035PO41658D


title: Proficiency_Site6_18

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 68.54; Lot# = 035PO41658D


title: Training_Site10_02

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 61.1; Lot# = 075PO52329B


title: Training_Site10_04

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 67.45; Lot# = 065PO36893A


title: Training_Site10_01

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 9.4; Lot# = 075PO52329B


title: Training_Site10_07

tag: chronic lymphocytic leukemia [CLL] patient lysates of mononuclear cells


title: Proficiency_Site6_14

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 41.46; Lot# = 055PO30555B


title: Training_Site6_07

description: Performed by Operator 1 from Site6 at Training stage


title: Proficiency_Site6_17

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 37.3; Lot# = 035PO41658D


title: Proficiency_Site6_15

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 71.14; Lot# = 055PO30555B


title: Proficiency_Site6_16

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 78.77; Lot# = 055PO30555B


title: Training_Site10_08


title: Proficiency_Site10_06

tag: chronic myeloid leukemia [CML] patient lysates of mononuclear cells


title: Proficiency_Site6_13

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 22.4; Lot# = 055PO30555B


title: Training_Site6_03

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 9.23404; Lot# = 035PO41658D


title: Training_Site6_06


title: Proficiency_Site6_19

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 69.82; Lot# = 035PO41658D


title: Proficiency_Site5_20

description: Performed by Operator 1 from Site5 at Proficiency stage

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 67.896; Lot# = 035PO41658D


title: Training_Site6_08

tag: acute myeloid leukemia [AML w/ translocation t(8;21) or FAB M2] patient lysates of mononuclear cells


title: Proficiency_Site5_19

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 132.59; Lot# = 035PO41658D


title: Training_Site6_01

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 10.80333; Lot# = 055PO30555B


title: Training_Site6_04

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 18.9313; Lot# = 035PO41658D


title: Training_Site6_05


title: Training_Site6_02

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 16.79483; Lot# = 055PO30555B


title: Proficiency_Site5_17

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 48.99; Lot# = 035PO41658D


title: Proficiency_Site5_18

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 76.383; Lot# = 035PO41658D


title: Training_Site5_08

description: Performed by Operator 1 from Site5 at Training stage


title: Proficiency_Site5_15

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 76.935; Lot# = 055PO30555B


title: Proficiency_Site5_14

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 46.851; Lot# = 055PO30555B


title: Training_Site5_06

tag: chronic lymphocytic leukemia [CLL] patient lysates of mononuclear cells


title: Training_Site5_03

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 28.29; Lot# = 035PO41658D


title: Proficiency_Site5_16

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 85.721; Lot# = 055PO30555B


title: Proficiency_Site5_13

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 35.811; Lot# = 055PO30555B


title: Training_Site5_05

tag: chronic myeloid leukemia [CML] patient lysates of mononuclear cells


title: Proficiency_Site8_21

description: Performed by Operator 1 from Site8 at Proficiency stage

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 25.2; Lot# = 035PO41658D


title: Training_Site5_07

tag: acute myeloid leukemia [AML w/ translocation t(8;21) or FAB M2] patient lysates of mononuclear cells


title: Training_Site5_02

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 73.991; Lot# = 055PO30555B


title: Training_Site5_04

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 59.478; Lot# = 035PO41658D


title: Training_Site5_01

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 20.44355; Lot# = 055PO30555B


title: Proficiency_Site8_20

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 69.4; Lot# = 055PO30555B


title: Proficiency_Site8_24

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 73; Lot# = 035PO41658D


title: Proficiency_Site8_23

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 66.2; Lot# = 035PO41658D


title: Proficiency_Site8_19

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 63.3; Lot# = 055PO30555B


title: Proficiency_Site8_22

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 57; Lot# = 035PO41658D


title: Training_Site8_09

description: Performed by Operator 1 from Site8 at Training stage

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 6.7; Lot# = 055PO30555B


title: Proficiency_Site8_17

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 20.7; Lot# = 055PO30555B


title: Training_Site8_12

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 49.5; Lot# = 035PO41658D


title: Training_Site8_13


title: Training_Site8_16


title: Training_Site8_11

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 8.2; Lot# = 035PO41658D


title: Training_Site8_15


title: Training_Site8_14

tag: chronic lymphocytic leukemia [CLL] patient lysates of mononuclear cells


title: Proficiency_Site7_19

description: Performed by Operator 1 from Site7 at Proficiency stage

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 71; Lot# = 035PO41658D


title: Proficiency_Site8_18

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 39.5; Lot# = 055PO30555B


title: Proficiency_Site7_16

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 60.9; Lot# = 055PO30555B


title: Proficiency_Site7_15_2

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 73.5; Lot# = 055PO30555B


title: Training_Site8_10

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 43.6; Lot# = 055PO30555B


title: Proficiency_Site7_20

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 49.3; Lot# = 035PO41658D


title: Proficiency_Site7_17

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 27.8; Lot# = 035PO41658D


title: Proficiency_Site7_13

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 32; Lot# = 055PO30555B


title: Training_Site7_05

description: Performed by Operator 1 from Site7 at Training stage

tag: chronic myeloid leukemia [CML] patient lysates of mononuclear cells


title: Proficiency_Site7_18

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 69.5; Lot# = 035PO41658D


title: Training_Site7_04

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 38.39; Lot# = 035PO41658D


title: Proficiency_Site2_20

description: Performed by Operator 1 from Site2 at Proficiency stage

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 52.63; Lot# = 035PO41658D


title: Training_Site7_07

tag: acute myeloid leukemia [AML w/ translocation t(8;21) or FAB M2] patient lysates of mononuclear cells


title: Training_Site7_06


title: Proficiency_Site7_14

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 55.54; Lot# = 055PO30555B


title: Training_Site7_03

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 8; Lot# = 035PO41658D


title: Training_Site7_02

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 21.4; Lot# = 055PO30555B


title: Proficiency_Site2_19

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 42.66; Lot# = 035PO41658D


title: Training_Site7_08


title: Proficiency_Site2_17

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 17.87; Lot# = 035PO41658D


title: Training_Site7_01

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 8; Lot# = 055PO30555B


title: Proficiency_Site2_18

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 48.82; Lot# = 035PO41658D


title: Training_Site2_03

description: Performed by Operator 1 from Site2 at Training stage

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 9.97694; Lot# = 035PO41658D


title: Training_Site2_02

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 41.70452; Lot# = 124PO44836A


title: Training_Site2_05


title: Proficiency_Site9_34

description: Performed by Operator 2 from Site9 at Proficiency stage

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 38.62; Lot# = 075PO52329B


title: Training_Site2_06

tag: chronic lymphocytic leukemia [CLL] patient lysates of mononuclear cells


title: Training_Site2_08


title: Proficiency_Site2_16

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 65.09; Lot# = 124PO44836A


title: Proficiency_Site9_36

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 43.51; Lot# = 075PO52329B


title: Proficiency_Site2_15

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 58.88; Lot# = 124PO44836A


title: Training_Site2_04

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 49.16112; Lot# = 035PO41658D


title: Training_Site2_07

tag: acute myeloid leukemia [AML w/ translocation t(8;21) or FAB M2] patient lysates of mononuclear cells


title: Proficiency_Site2_13

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 17.02; Lot# = 124PO44836A


title: Training_Site2_01

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 11.94436; Lot# = 124PO44836A


title: Training_Site9_20

description: Performed by Operator 1 from Site9 at Training stage


title: Proficiency_Site9_30

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 72.5; Lot# = 035PO41658D


title: Proficiency_Site9_23

description: Performed by Operator 1 from Site9 at Proficiency stage

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 62.98; Lot# = 035PO41658D


title: Proficiency_Site2_14

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 32.98; Lot# = 124PO44836A


title: Proficiency_Site9_29

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 34.7; Lot# = 035PO41658D


title: Proficiency_Site9_27

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 62.5; Lot# = 075PO52329B


title: Proficiency_Site9_26

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 55.6; Lot# = 075PO52329B


title: Proficiency_Site9_33

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 27.25; Lot# = 075PO52329B


title: Proficiency_Site9_35

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 63.11; Lot# = 075PO52329B


title: Proficiency_Site9_28

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 79.5; Lot# = 075PO52329B


title: Proficiency_Site9_31

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 68.6; Lot# = 035PO41658D


title: Proficiency_Site9_22

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 78.315; Lot# = 035PO41658D


title: Proficiency_Site9_25

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 36.4; Lot# = 075PO52329B


title: Proficiency_Site9_32

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 52.8; Lot# = 035PO41658D


title: Training_Site9_18

tag: chronic lymphocytic leukemia [CLL] patient lysates of mononuclear cells


title: Training_Site9_12

description: Performed by Operator 2 from Site9 at Training stage

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 37.3; Lot# = 035PO41658D


title: Training_Site9_10

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 28.13; Lot# = 075PO52329B


title: Training_Site9_17

tag: chronic myeloid leukemia [CML] patient lysates of mononuclear cells


title: Training_Site9_11

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 11.05; Lot# = 035PO41658D


title: Proficiency_Site9_24

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 66.85; Lot# = 035PO41658D


title: Proficiency_Site9_21

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 28.814; Lot# = 035PO41658D


title: Proficiency_Site3_18

description: Performed by Operator 1 from Site3 at Proficiency stage

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 55.68; Lot# = 035PO41658D


title: Proficiency_Site3_16

tag: MCF-7 (breast adenocarcinoma) cell line

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 66.47; Lot# = 124PO44836A


title: Proficiency_Site3_14

tag: input total RNA (ug) = 3ug; cRNA yield (ug) = 64.79; Lot# = 124PO44836A


title: Proficiency_Site3_20

tag: input total RNA (ug) = 8ug; cRNA yield (ug) = 58.93; Lot# = 035PO41658D


title: Proficiency_Site3_17

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 53.75; Lot# = 035PO41658D


title: Proficiency_Site3_13

tag: input total RNA (ug) = 1.5ug; cRNA yield (ug) = 34.54; Lot# = 124PO44836A


title: Proficiency_Site3_19

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 60.34; Lot# = 035PO41658D


title: Training_Site9_01

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 11.3; Lot# = 075PO52329B


title: Training_Site9_09

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 8.56; Lot# = 075PO52329B


title: Training_Site9_03

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 22.1; Lot# = 035PO41658D


title: Training_Site9_04

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 56.2; Lot# = 035PO41658D


title: Training_Site9_02

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 39.1; Lot# = 075PO52329B


title: Training_Site3_08

description: Performed by Operator 1 from Site3 at Training stage

tag: acute myeloid leukemia [AML w/ translocation t(8;21) or FAB M2] patient lysates of mononuclear cells


title: Training_Site3_07


title: Proficiency_Site3_15

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 59.72; Lot# = 124PO44836A


title: Training_Site3_06

tag: chronic lymphocytic leukemia [CLL] patient lysates of mononuclear cells


title: Non-tumor cerebellar tissue control 6

city: Boston

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

institute: Boston Children's Hospital

description: Non-tumor cerebellar tissue from Ptc1+/- mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Trizol extraction of total RNA followed by additional purification using RNeasy (Qiagen) performed according to the manufacturer's instructions.

tag: submitter:DR,  date:2006/12/18,  run#:55


title: Non-tumor cerebellar tissue control 5

description: Non-tumor cerebellar tissue from Mxi1-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:33


title: Ptc1+/- cerebellar tumor, biological replicate 2

description: Cerebellar tumor from Ptc1+/- mice

source_name: Cerebellar tumor from Ptc1+/- mice

tag: Cerebellar tumor from Ptc1+/- mice

tag: submitter:KL,  date:2007/09/05,  run#:34


title: Non-tumor cerebellar tissue control 1

description: Non-tumor cerebellar tissue from Olig2-tva-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:25


title: Ptc1+/- cerebellar tumor, biological replicate 1

description: Cerebellar tumor from Ptc1+/- mice

tag: submitter:DR,  date:2006/12/18,  run#:56


title: Non-tumor cerebellar tissue control 4

source_name: Non-tumor cerebellar tissue from Mxi1-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:35


title: Training_Site3_03

tag: HepG2 (liver carcinoma) cell line

tag: input total RNA (ug) = 1ug; cRNA yield (ug) = 17.2; Lot# = 035PO41658D


title: Training_Site3_04

tag: input total RNA (ug) = 5ug; cRNA yield (ug) = 80.14; Lot# = 035PO41658D


title: Non-tumor cerebellar tissue control 3

description: Non-tumor cerebellar tissue from hGFAP-cre:SmoM2 mice

tag: submitter:DR,  date:2006/10/13,  run#:28