title: Day 5 GFP Negative Batch 1

description:
Cell culture and cell differentiation
Mouse embryonic stem cells (mESCs) were maintained undifferentiated by culturing on a feeder layer of mitomycin C pretreated primary mouse embryonic fibroblasts (PMEFs, Specialty Media, cat.# PMEF-H) at 37oC, 90% humidity and 5% CO2. The cell line used was the mESC D3 (passage #12-18). The basic culture medium was comprised of DMEM (Invitrogen, cat.# 11965-092), heat inactivated (56oC for 30 minutes) fetal bovine serum (Hyclone, cat#. S11550, 15%), Glutamax (Invitrogen, cat.# 35050-065, 1%), non-essential amino acids (Invitrogen, cat.# 11140-050, 1%), sodium pyruvate (Invitrogen, cat.# 11360-070, 1%), ?-mercaptoethanol (Sigma, cat.# M7522, 0.1mM), gentamicin (Cambrex, cat.# 17-518, 25?g/ml) and ESGRO leukemia inhibitory factor (Chemicon, cat.# ESG1106, 1000units/ml). Prior to initiation of differentiation The PMEF feeder layer was subtracted and the mESCs were maintained on a 0.01% gelatin pretreated plate for 24-48 hours. Differentiation through embryoid body (EB) formation was initiated by dissociating the mESCs using trypsin (Invitrogen, cat#. 25300-054, 0.05%) and resuspending them in basic culture medium (without the leukemia inhibitory factor) at a final concentration of 5x104 cells/ml. The hanging droplet (HD) technique was used for EB formation. HDs were plated on the lid of H2O containing tissue culture dishes at a volume of 20?L/droplet (approximately 1000 cells/ droplet). Two days post initiation of differentiation the EBs were transferred in suspension on poly-HEMA (Sigma, cat#. P3932) treated tissue culture dishes. The plates were pretreated with poly-HEMA in order to avoid any cell attachment on the plastic. Basic culture medium was supplemented with ascorbic acid(Takahashi et al., 2003) (Sigma, cat#. A4403, 0.1mg/ml) and it was exchanged with fresh medium every 2 days during differentiation.
Transfection of mouse embryonic stem cells
The mouse Nkx2.5 enhancer fragment #5(Lien et al., 1999) and the hsp68 minimal promoter was excised from the provided vector (XhoI/ NcoI) and inserted in front of the EGFP gene in the Bluescript vector. A vector containing the hygromycin resistance gene (hygromycin phosphotransferase) under the control of the mouse polymerase II promoter was also used in order to select for the transfected mESCs. Prior to transfection the two vectors were linearized. Undifferentiated mESCs were grown to confluency on a layer of primary embryonic fibroblasts and dissociated with trypsin. The cells were combined with the linearized DNA and electroporated (Biorad Gene Pulser Xcell, 240V/ 500?F). The cells were then replated on a fresh layer of PMEFs. Hygromycin B (Invitrogen, cat.# 10687-010, 50?g/ml) was used for 7 days after transfection for selection. Resistant colonies were picked and grown on layers of PMEFs in the presence of antibiotic. Once sufficient cells were present the clones were differentiated in order to check for the correct expression of the GFP in the cardiac areas (spontaneously contracting) of the differentiating cultures. Successful clones were further amplified and used for characterization of the GFP expressing cardiac progenitor cells.
In order to select mESC derived cardiomyocytes for the microarray analysis experiment, a stable transgenic clone of mESCs was made that allowed the expression of the neomycin resistance gene under the control of the alpha myosin heavy chain promoter (U71441) as described by Klug et al., (Klug et al., 1996). The transgenic clone was prepared as described above.
FACS Analysis
For determination of the CPC yield in the differentiating cells, EBs were harvested at the indicated timepoints (between days 6 and 10 of differentiation). Each sample contained approximately 100 hanging droplets on day 0 of differentiation. The EBs were washed in PBS and resuspended in 0.05% trypsin at 4oC (1/2 hour) and 37oC (10 minutes). The percentage of GFP+ cells was determined in a BD FACS Calibur (Cell Quest Pro software). Age matched EBs from untransfected mESCs were used as negative controls. Cells from the same samples were also counted.
FACS sorting
The BD Biosciences FACSAria Cell sorting system was used to sort the GFP+ and GFP- cells between days 5 and 10 of differentiation. EBs were harvested and dissociated as described above. The cells were suspended in sorting medium (96% DMEM without phenol red, 1% fetal bovine serum, 1% Glutamax, 1% non essential amino acids, 1% sodium pyruvate, 25?g/ml gentamicin) and kept at 4oC. The cells were sorted into a fetal bovine serum rich medium (20%) in order to increase their survival. For further culture the cells were resuspended in mESC culture medium at a concentration of 5x105 cells/ml and cultured in suspension for 48 hours. The cells were then transferred on tissue culture plates for another 48 hours. For RNA isolation the cells were spun down and washed in PBS before the RNA isolation procedure.
To assay their proliferation capacity, GFP+ CPCs were FACS sorted on day 5 of differentiation. Cells were reaggregated in suspension (5x105 cells/ ml) in the presence of mouse recombinant Igf1 (Chemicon, Cat.# GF121, 100ng/ml) for 14 days. Cell aggregates were fixed and stained for the colocalization of the antigens: Nkx2-5 and Ki67 or Pcna. The same ICC reagents were used as described above.
GeneChip microarray hybridization
Total RNA for the microarray expression analysis was isolated from FACS sorted cells (GFP+ and GFP-) on days 5, 6, 7, and 8 of differentiation as described above. Two separate differentiation batches were prepared for the sake of data reproducibility. Total RNA was also isolated from terminally differentiated mESC derived genetically selected cardiomyocytes 3 weeks post initiation of differentiation. The GeneChip? two cycle target labeling kit (Affymetrix, cat.# 900494) was used to convert 100ng of total RNA to biotinylated labeled cRNA. This was then hybridized to the Affymetrix murine MOE430 2.0 genome GeneChip? array (Affymetrix, cat.# 900496). Fluorescence was detected using the Affymetrix GS3000 GeneArray scanner and image analysis for each chip was done through the GeneChip? operating system software from Affymetrix (GCOS1.3) using the standard default settings.
Microarray data analysis
To estimate the gene expression signals, data analysis was conducted on the chips? CEL file probe signal values at the Affymetrix probe pair (perfect match (PM) probe and mismatch (MM) probe) level, using the statistical technique RMA (Robust Multiarray Analysis) (Irizarry et al., 2003) with the bioconductor package Affy. The data normalization procedure utilized the quantile normalization method (Bolstad et al., 2003) to reduce the obscuring variation between microarrays, which might be introduced during the processes of sample preparation, manufacture, fluorescence labeling, hybridization and/or scanning.
The Spotfire DecisionSite software package was used for the identification of uniquely upregulated or downregulated (at least 1.5 times increase or decrease in the expression value) probe sets in the CPC population when compared to the rest of the cells in the differentiating EBs. Probe sets that were considered unique for the CPC population were found to be commonly upregulated or downregulated during all four days of analysis. Probe sets that exhibited an increasing or decreasing pattern of expression with at least 1.5 times increase or decrease in the expression values of day 5 CPCs and day 8 CPCs were also reported. Probe sets of the CPC population that exhibited upregulation or downregulation by at least 1.5 times when compared to the mESC derived cardiomyocytes were also reported. The final analysis included probe sets that exhibited a different temporal pattern of expression in the CPC population when compared to the rest of the cells along the four days of differentiation. Specifically in order to identify these probe sets gene expression curve over time was modeled flexibly on a natural cubic spline basis. A q-value for each gene was computed to estimate the false discovery rate (FDR) incurred when calling the gene significant. Differentially expressed genes were obtained by setting a cut-off to the calculated q-values (Storey et al., 2005). The probe level data analysis was implemented with the bioconductor package, Affy under R environment and the time course analysis was performed with the software package EDGE. Finally, only probe sets with gene ontology information associated with them were reported. The Ingenuity Pathways Analysis software package was used to identify canonical pathways that are active in the CPC population (www.ingenuity.com).

scan_protocol: Using Affymetrix? GeneChip Scanner 3000 and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer?s specifications. Global scaling of images to a target intensity of 150.

label: Biotin label.

label_protocol: Two rounds amplification protocol for total RNA following Affymetrix? specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).


title: SKNAS-NmycER, t=144 hrs

status: Public on Aug 24 2007

type: RNA

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: SKNAS-NmycER cells were grown under standard conditions and harvested at diferent timepoints after addition of 4-hydroxytamoxifen. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

hyb_protocol: 10 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol.

data_processing: Expression data (.cel files) were normalized with the MAS5 algorithm (target signal = 100) using GCOS software (Affymetrix).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: SKNAS-NmycER cells

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 μg of total RNA was used for cRNA synthesis and fragmented. Labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: SKNAS-NmycER cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer's protocol.

treatment_protocol: To activate Nmyc-ER in SKNAS-NmycER, 4-hydroxy-tamoxifen was added to the medium to a final concentration of 50 nmol/l.

tag: Cell line from neuroblastoma tumor, stably transfected with NmycER expression vector.


title: IMR32-DKK1 c66, t=72 hrs

description: IMR32-DKK1 cells were grown under standard conditions. Cells were harvested, at 70% confluency, at different time points after adding doxycyclin. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

label: biotin

source_name: IMR32-DKK1 c66

growth_protocol: IMR32-DKK1 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using LiCl/ureum and purified with RNeasy (Qiagen) according to manufacturer's protocol.

treatment_protocol: To induce DKK1 expression in IMR32-DKK1, doxycyclin was added to the medium to a final concentration of 50 ng/ml

tag: Cell line from a neuroblastoma tumor, stably transfected with an inducible DKK1 expression vector


title: SKNAS-NmycER, t=72 hrs


title: SKVCR 2.0 - replicate 2

city: Vancouver

first: T

last: Buys

state: BC

address: 675 W.10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: British Columbia Cancer Research Centre

description:
Keyword = vincristine
Keyword = drug resistant
Keyword = ovarian
Keyword = MAS5

hyb_protocol: Manufacturer's protocols.

scan_protocol: Manufacturer's protocols.

label: Biotin.

source_name: Ovarian tumor cell line - vincristine-resistant derivative

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: RNA was extracted from isolated cells using the RNeasy Mini Kit (Qiagen) and re-dissolved in RNase-free water.

tag: SKVCR 2.0 is a vincristine-resistant derivative of SKOV3 capable of growing in media with 2.0 µg/ml vincristine drug.


title: IMR32-DKK1 c63, t=0

source_name: IMR32-DKK1 c63


title: IMR32-DKK1 c63, t=24 hrs


title: SKOV3 - replicate 2

description:
Keyword = vincristine
Keyword = drug sensitive
Keyword = ovarian

source_name: Ovarian tumor cell line

tag: Ovarian adenocarcinoma cell line SKOV3


title: SKNAS-NmycER, t=0


title: SKVCR 2.0 - replicate 1


title: IMR32-DKK1 c63, t=288 hrs


title: SKOV3 - replicate 1

tag: Ovarian adenocarcinoma cell line SKOV3.


title: Effector CD8 T cells, IL-7Rhi, rep2

status: Public on Aug 23 2007

city: New Haven

first: Susan

last: Kaech

state: CT

address: 300 Cedar St, TAC S641B

country: USA

institute: Yale University

description: Gene expression data from IL-7Rhi effector CD8 T cells

hyb_protocol: cRNA were hybridized to  arrays by Yale University Keck Biotechnology Resource Laboratory using standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 by Yale University Keck Biotechnology Resource Laboratory

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software (GCOS) and arrays were scaled to an average intensity of 500. Data processing was performed by the Yale University Keck Biotechnology Resource Laboratory using standard protocols

organism: Mus musculus

source_name: Effector P14 CD8 T cells, IL-7Rhi, from day 6/7 LCMV infection

label_protocol: Biotinylated cRNA were prepared by Yale University Keck Biotechnology Resource Laboratory using standard Affymetrix protocols.

extract_protocol: Trizol (Invitrogen) extraction of total RNA followed by RNAeasy (Qiagen) cleanup was performed according to the manufacturer's instructions

treatment_protocol: 1x10^4 naïve LCMV-specific P14 transgenic CD8 T cells were transferred into naïve C57Bl/6 mice that were then infected with LCMV. 6-7 days later, P14 cells were sorted based on CD127 expression by FACS

tag: Genotype

tag: Gender

value: female

tag: Tissue

value: Spleen


title: Effector CD8 T cells, IL-7Rlo, rep3

description: Gene expression data from IL-7Rlo effector CD8 T cells

source_name: Effector P14 CD8 T cells, IL-7Rlo, from day 6/7 LCMV infection


title: Lymphatic endothelial cells upon conditioned medium from NSCLC 24 h

city: Pamplona

first: Ana

last: Rouzaut

state: Navarra

address: Pio XII 55

department: Oncology

country: Spain

institute: University of Navarra/CIMA

description: - Normalization: Employing GCOS software, chips were normalized using all probe sets scaling option and target signal at 500.

hyb_protocol: Hybridization: According to the manufacturer's protocol (Affymetrix).

scan_protocol: Scanner: GeneChip Scanner 3000.

data_processing: Microarray suite 5.0, Tiling Array

source_name: Dermal microvascular cells, commercially available

label_protocol: IVT labeling kit from affymetrix

growth_protocol: BEM w/o bFGF and VEGF supplemented with concentrated supernatants from growth media derived from lung adenocarcinoma cells grown under normoxia

extract_protocol: Trizol and mini RNeasy kit (Qiagen)

treatment_protocol: Conditioned medium from lung carcinoma cells growth under 20% oxigen, 24 h

tag: RNA Pooled from 6 different individuals


title: Wild-type CS_12_29_2_WT_2

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: SP-C-rtTA/(tetO)7CMV-Cre/Stat3flx/flx triple-transgenic mice, typeII cell

hyb_protocol: The cRNA was then hybridized to the murine genome MOE430 (consists of ≈ 45000 gene entries) chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings.

data_processing: raw data processed by Affymetrix Microarray Suite 5.0 is provided

label: biotinylate

source_name: SP-C-rtTA/(tetO)7CMV-Cre double transgenic mice

label_protocol: based on Affymetrix protocols

extract_protocol: Alveolar type II cells were isolated from 8 weeks old sex age matched littermate control and Stat3∆/∆ mice using collagenase and differential plating. Type II cells from 3 mice were pooled to obtain one pellet. Two hours after isolation, type II cells were homogenized with TRIzol reagent (Invitrogen, Carlsbad, CA). RNA concentration was measured by spectrophotometer and normalized for cDNA synthesis.

tag: 8 weeks old sex age matched littermates, lung typeII cells


title: Wild-type CS_12_29_1_WT_1


title: Wild-type CS_2_16_WT_3


title: Knockout CS_2_9_KO_1


title: Knockout CS_2_15_KO_2


title: Lymphatic endothelial cells upon hypoxia

growth_protocol: BEM w/o bFGF and VEGF

treatment_protocol: Hipoxia 1% 24 h


title: Knockout CS_MA_5_11_KO_3


title: Lymphatic endothelial in normoxia

treatment_protocol: Normoxia 20 Oxigen % 24 h


title: Effector CD8 T cells, IL-7Rlo, rep2


title: Effector CD8 T cells, IL-7Rlo, rep1


title: Lymphatic endothelial cells upon conditioned medium from NSCLC hypoxia 24 h

growth_protocol: BEM w/o bFGF and VEGF supplemented with concentrated supernatants from growth media derived from lung adenocarcinoma cells grown under hypoxia for 24 h

treatment_protocol: Conditioned medium from lung carcinoma cells growth under 1% oxigen, 24 h


title: Effector CD8 T cells, IL-7Rhi, rep3


title: Effector CD8 T cells, IL-7Rhi, rep1


title: 06-14-05_Miller_U133Plus2_0_A4P4d07EPO

status: Public on Aug 22 2007

city: Bethesda

first: Jeffery

middle: Lynn

last: Miller

state: MD

address: 10 Center Drive

department: Molecular Medicine Branch

institute: NIH/NIDDK

description:
Pool of 3 samples:
22-42 age
M/F
Day 7: proerythroblast

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: MAS 5.0

source_name: CD34+ progenitor cells subjected to EPO and harvested at day 7

label_protocol: standard affymetrix protocol

extract_protocol: cells harvested and homogenate prepared on 10.20.04 -11.10.04. Stored at -80C. RNA prepared between Dec, 2004 - Jan, 2005. Trizol LS and Qiagen Rneasy Mini column clean up

treatment_protocol: EPO (4U/ml)

tag: cell type

value: CD34+ hematopoietic progenitor cells

tag: developmental stage

value: proerythroblast

tag: tissue type

value: primary cells from donated blood


title: 06-14-05_Miller_U133Plus2_0_A5P5d07EPO

description:
Pool of 3 samples:
20-30 age
M/F
Day 7: proerythroblast


title: 06-14-05_Miller_U133Plus2_0_A3P3d07EPO

description:
Pool of 3 samples:
25-45 age
M/F
Day 7: proerythroblast


title: K562_1R-Chl_24hrs_rep2

city: La Jolla

first: C. James

last: Chou

state: CA

address: 10550 N. Torrey Pines Rd. MB-27

department: Molecular Biology

institute: The Scripps Research Institute

description:
[Sample Info]
Chip Type	HG-U133_Plus_2
Chip Lot	4020537
Operator	administrator
Sample Type	human cell line K562
Description
Project	Gottesfeld_Chou
Comments	041407
Solution Type
Solution Lot
[Fluidics]
Protocol	EukGE-WS2v4_450
Wash A1 Recovery Mixes	0
Wash A1 Temperature (C)	25
Number of Wash A1 Cycles	10
Mixes per Wash A1 Cycle	2
Wash B Recovery Mixes	0
Wash B Temperature (C)	50
Number of Wash B Cycles	4
Mixes per Wash B Cycle	15
Stain Temperature (C)	25
First Stain Time (seconds)	600
Wash A2 Recovery Mixes	0
Wash A2 Temperature (C)	25
Number of Wash A2 Cycles	10
Mixes per Wash A2 Cycle	4
Second Stain Time (seconds)	600
Third Stain Time (seconds)	600
Wash A3 Recovery Mixes	0
Wash A3 Temperature (C)	30
Number of Wash A3 Cycles	15
Mixes per Wash A3 Cycle	4
Holding Temperature (C)	25
Station	1
Module	3
Hybridize Date	Sep 07 2006 12:04PM
[Scanner]
Pixel Size	1.56
Filter	570
Scan Temperature
Scan Date	Sep 07 2006 01:30PM
Scanner ID	50206960
Number of Scans	1
Scanner Type	M10

hyb_protocol: Following fargmentation, 15 microg of cRNA were hybridized for 16 hrs on the GeneChip.  GeneChips were washed and stained in the Fluidics Station 450.

scan_protocol: Pixel Size	1.56 Filter	570 Scanner ID	50206960 Number of Scans	1 Scanner Type	GeneChip Scanner 3000 7G

data_processing: MAS5.0 and BRB Arraytools (3.5.0 Beta 2)

label_protocol: Affymetrix labeling reaction (GeneChip Expression 3' Amplification One-Cycle Target Labeling)

growth_protocol: The human CML lymphoblast K562 cell line (obtained from ATCC), which contains the b3a2 Bcr-Abl translocation, was used in this study.  Cells were grown and maintained in RPMI 1640 medium containing 10% FBS, under standard mammalian cell culture conditions as recommended by the ATCC.

extract_protocol: Used and followed Absolutely RNA Miniprep Kit protocols from Stratagene.

treatment_protocol: 250 nM 1R-Chl was added and incubated with cells for 24 hours.

tag: Organism

value: Homo sapiens (human) Morphology:lymphoblast

tag: Source

value: Organ:bone marrow

tag: Disease

value: chronic myelogenous leukemia (CML)

tag: Age

value: 53 years

tag: Cytogenetic Analysis

value: The stemline chromosome number is triploid with the 2S component occurring at 4.2%. Fifteen markers (M1 and M(15)) occurred in nearly all S metaphases. Spontaneous non-specific dicentrics occurred, but rarely. Unstable markers were also rarely seen. The X was disomic, and N9 was nullisomic.


title: K562_1R-Chl_24hrs_rep1

description:
[Sample Info]
Chip Type	HG-U133_Plus_2
Chip Lot	4020537
Operator	administrator
Sample Type	human cell line K562
Description
Project	Gottesfeld_Chou
Comments	041407
Solution Type
Solution Lot
[Fluidics]
Protocol	EukGE-WS2v4_450
Wash A1 Recovery Mixes	0
Wash A1 Temperature (C)	25
Number of Wash A1 Cycles	10
Mixes per Wash A1 Cycle	2
Wash B Recovery Mixes	0
Wash B Temperature (C)	50
Number of Wash B Cycles	4
Mixes per Wash B Cycle	15
Stain Temperature (C)	25
First Stain Time (seconds)	600
Wash A2 Recovery Mixes	0
Wash A2 Temperature (C)	25
Number of Wash A2 Cycles	10
Mixes per Wash A2 Cycle	4
Second Stain Time (seconds)	600
Third Stain Time (seconds)	600
Wash A3 Recovery Mixes	0
Wash A3 Temperature (C)	30
Number of Wash A3 Cycles	15
Mixes per Wash A3 Cycle	4
Holding Temperature (C)	25
Station	1
Module	2
Hybridize Date	Sep 07 2006 12:04PM
[Scanner]
Pixel Size	1.56
Filter	570
Scan Temperature
Scan Date	Sep 07 2006 01:18PM
Scanner ID	50206960
Number of Scans	1
Scanner Type	M10


title: K562_1R-Chl_24hrs_rep3

description:
[Sample Info]
Chip Type	HG-U133_Plus_2
Chip Lot	4020537
Operator	administrator
Sample Type	human cell line K562
Description
Project	Gottesfeld_Chou
Comments	041407
Solution Type
Solution Lot
[Fluidics]
Protocol	EukGE-WS2v4_450
Wash A1 Recovery Mixes	0
Wash A1 Temperature (C)	25
Number of Wash A1 Cycles	10
Mixes per Wash A1 Cycle	2
Wash B Recovery Mixes	0
Wash B Temperature (C)	50
Number of Wash B Cycles	4
Mixes per Wash B Cycle	15
Stain Temperature (C)	25
First Stain Time (seconds)	600
Wash A2 Recovery Mixes	0
Wash A2 Temperature (C)	25
Number of Wash A2 Cycles	10
Mixes per Wash A2 Cycle	4
Second Stain Time (seconds)	600
Third Stain Time (seconds)	600
Wash A3 Recovery Mixes	0
Wash A3 Temperature (C)	30
Number of Wash A3 Cycles	15
Mixes per Wash A3 Cycle	4
Holding Temperature (C)	25
Station	1
Module	4
Hybridize Date	Sep 07 2006 12:04PM
[Scanner]
Pixel Size	1.56
Filter	570
Scan Temperature
Scan Date	Sep 07 2006 01:43PM
Scanner ID	50206960
Number of Scans	1
Scanner Type	M10


title: 06-14-05_Miller_U133Plus2_0_A18P3d14EPO

description:
Pool of 3 samples:
25-45 age
M/F
Day 14: mature erythrocytes

source_name: CD34+ progenitor cells subjected to EPO and harvested at day 14

value: mature erythrocytes


title: 06-14-05_Miller_U133Plus2_0_A17P2d14EPO

description:
Pool of 3 samples:
26-37 age
M/F
Day 14: mature erythrocytes


title: K562_NoTreatmentControl_24hrs_rep1

source_name: K562, NoTreatmentControl, 24hrs, rep1

treatment_protocol: No Treatment


title: 06-14-05_Miller_U133Plus2_0_A16P1d14EPO

description:
Pool of 3 samples:
21-50 age
M/F
Day 14: mature erythrocytes


title: K562_NoTreatmentControl_24hrs_rep2

description:
[Sample Info]
Chip Type	HG-U133_Plus_2
Chip Lot	4020537
Operator	administrator
Sample Type	human cell line K562
Description
Project	Gottesfeld_Chou
Comments	041407
Solution Type
Solution Lot
[Fluidics]
Protocol	EukGE-WS2v4_450
Wash A1 Recovery Mixes	0
Wash A1 Temperature (C)	25
Number of Wash A1 Cycles	10
Mixes per Wash A1 Cycle	2
Wash B Recovery Mixes	0
Wash B Temperature (C)	50
Number of Wash B Cycles	4
Mixes per Wash B Cycle	15
Stain Temperature (C)	25
First Stain Time (seconds)	600
Wash A2 Recovery Mixes	0
Wash A2 Temperature (C)	25
Number of Wash A2 Cycles	10
Mixes per Wash A2 Cycle	4
Second Stain Time (seconds)	600
Third Stain Time (seconds)	600
Wash A3 Recovery Mixes	0
Wash A3 Temperature (C)	30
Number of Wash A3 Cycles	15
Mixes per Wash A3 Cycle	4
Holding Temperature (C)	25
Station	2
Module	4
Hybridize Date	Sep 07 2006 12:04PM
[Scanner]
Pixel Size	1.56
Filter	570
Scan Temperature
Scan Date	Sep 07 2006 12:55PM
Scanner ID	50206960
Number of Scans	1
Scanner Type	M10

source_name: K562, NoTreatmentControl, 24hrs, rep2


title: K562_NoTreatmentControl_24hrs_rep3

description:
[Sample Info]
Chip Type	HG-U133_Plus_2
Chip Lot	4020537
Operator	administrator
Sample Type	human cell line K562
Description
Project	Gottesfeld_Chou
Comments	041407
Solution Type
Solution Lot
[Fluidics]
Protocol	EukGE-WS2v4_450
Wash A1 Recovery Mixes	0
Wash A1 Temperature (C)	25
Number of Wash A1 Cycles	10
Mixes per Wash A1 Cycle	2
Wash B Recovery Mixes	0
Wash B Temperature (C)	50
Number of Wash B Cycles	4
Mixes per Wash B Cycle	15
Stain Temperature (C)	25
First Stain Time (seconds)	600
Wash A2 Recovery Mixes	0
Wash A2 Temperature (C)	25
Number of Wash A2 Cycles	10
Mixes per Wash A2 Cycle	4
Second Stain Time (seconds)	600
Third Stain Time (seconds)	600
Wash A3 Recovery Mixes	0
Wash A3 Temperature (C)	30
Number of Wash A3 Cycles	15
Mixes per Wash A3 Cycle	4
Holding Temperature (C)	25
Station	1
Module	1
Hybridize Date	Sep 07 2006 12:04PM
[Scanner]
Pixel Size	1.56
Filter	570
Scan Temperature
Scan Date	Sep 07 2006 01:07PM
Scanner ID	50206960
Number of Scans	1
Scanner Type	M10

source_name: K562, NoTreatmentControl, 24hrs, rep3


title: 06-14-05_Miller_U133Plus2_0_A20P5d14EPO

description:
Pool of 3 samples:
20-30 age
M/F
Day 14: mature erythrocytes


title: 06-14-05_Miller_U133Plus2_0_A19P4d14EPO

description:
Pool of 3 samples:
22-42 age
M/F
Day 14: mature erythrocytes


title: 06-14-05_Miller_U133Plus2_0_A2P2d07EPO

description:
Pool of 3 samples:
26-37 age
M/F
Day 7: proerythroblast


title: 06-14-05_Miller_U133Plus2_0_A1P1d07EPO

description:
Pool of 3 samples:
21-50 age
M/F
Day 7: proerythroblast


title: 5d DC6

status: Public on Aug 20 2007

city: Debrecen

first: Istvan

last: Szatmari

address: Egyetem tér 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Monocytes (98% CD14+) were obtained from Buffy coats by Ficoll gradient centrifugation and magnetic cell separation using anti-CD14-conjugated microbeads (VarioMACS; Miltenyi Biotec)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: GC-RMA algorithm

source_name: Monocyte derived dendritic cells

label_protocol: cRNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).

growth_protocol: Monocytes were cultured for 5 days with 500 U/ml IL-4 and 800 U/ml GM-CSF. Cytokine treatment was repeated at day 3.

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen) and further purified by using the RNeasy kit (Quiagen).

treatment_protocol: Cells were treated with vehicle (DMSO/ethanol). Ligands or vehicle were added to the cell culture starting from the first day.

tag: tissue

value: freshly isolated human monocyte

tag: gender:male; age

value: 18 yr; weight:73 kg


title: 5d DC5 HS

growth_protocol: Monocytes were cultured for 5 days with 500 U/ml IL-4 and 800 U/ml GM-CSF. Cytokine treatment was repeated at day 3. Cells were cultured in RPMI medium containing 10% human AB serum (HS) instead of FBS.

value: 18 yr; weight:82 kg


title: 5d DC5


title: 5d DC3

value: 41 yr; weight:92 kg


title: 5d DC4 RSG

treatment_protocol: Cells were treated with 2.5 uM rosiglitazone (RSG). Ligands or vehicle were added to the cell culture starting from the first day.

value: 21 yr; weight:110 kg


title: 5d DC2

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen).

value: 47 yr; weight:80 kg


title: 5d DC4 HS


title: 5d DC3 RSG


title: 5d DC2 RSG


title: 5d DC1

tag: gender:female; age

value: 19 yr; weight:65 kg


title: 5d DC6 RSG


title: 24h DC C131Y RSG

description: Monocytes (98% CD14+) were obtained from Buffy coats by Ficoll gradient centrifugation and magnetic cell separation using anti-CD14-conjugated microbeads (VarioMACS; Miltenyi Biotec).

growth_protocol: Monocytes were cultured for 24 hours with 500 U/ml IL-4 and 800 U/ml GM-CSF.

treatment_protocol: Cells were treated with 1 uM rosiglitazone (RSG). Ligands or vehicle were added to the cell culture starting from the first day.

tag: Further information

value: Agostini at al. 2006 Cell Metabolism, 4 303-311


title: 24h DC C114R


title: 5d DC1 RSG


title: 5d DC6 HS


title: 24h DC C114R RSG


title: 5d DC5 RSG


title: 24h DC IR


title: 24h DC IR RSG


title: 5d DC4


title: 24h DC6

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen) and further purified by using the RNeasy kit (Quiagen)

value: 52 yr; weight:75 kg


title: 24h DC5 HS

growth_protocol: Monocytes were cultured for 24 hours with 500 U/ml IL-4 and 800 U/ml GM-CSF. Cells were cultured in RPMI medium containing 10% human AB serum (HS) instead of FBS.

value: 31 yr; weight:95 kg


title: 24h DC C131Y


title: 24h DC6 RSG


title: 24h DC5 RSG


title: 24h DC6 HS


title: 24h DC5


title: 24h DC4 RSG

value: 41 yr; weight:79 kg


title: 24h DC4 HS


title: 24h DC3 RSG

value: 31 yr; weight:89 kg


title: 24h DC4


title: 6h DC4 HS

growth_protocol: Monocytes were cultured for 6 hours with 500 U/ml IL-4 and 800 U/ml GM-CSF. Cells were cultured in RPMI medium containing 10% human AB serum (HS) instead of FBS.


title: 24h DC2 RSG

value: 34 yr; weight:105 kg


title: 24h DC1 RSG

value: 26 yr; weight:71 kg


title: 6h DC3 RSG

growth_protocol: Monocytes were cultured for 6 hours with 500 U/ml IL-4 and 800 U/ml GM-CSF.


title: 6h DC1


title: 6h DC6 RSG

treatment_protocol: Cells were treated with rosiglitazone (RSG). Ligands or vehicle were added to the cell culture starting from the first day.


title: 6h DC5 HS


title: 6h DC3


title: 6h DC5


title: MC6b

growth_protocol: freshly isolated monocytes

treatment_protocol: freshly isolated monocytes


title: 6h DC2


title: 6h DC4


title: 6h DC2 RSG

treatment_protocol: Cells were treated with 1uM rosiglitazone (RSG). Ligands or vehicle were added to the cell culture starting from the first day.


title: 24h DC3


title: 24h DC2


title: 6h DC6


title: 6h DC4 RSG


title: MC5b


title: 24h DC1


title: MC6a


title: MC4b


title: 6h DC1 RSG


title: MC5a


title: MC4a


title: MC3b


title: MC3a


title: 6h DC6 HS

growth_protocol: Monocytes were cultured for 6 hours with 500 U/ml IL-4 and 800 U/ml GM-CSF. Cells were cultured in RPMI medium containing 10% human AB serum (HS) instead of FBS


title: 6h DC5 RSG


title: MC2b


title: MC2a

source_name: monocyte derived dendritic cells


title: MC1a


title: SW480_GFP_with_Dox biological replicate 1

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method

label_protocol: 3-5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was isolated from the harvested cells using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

tag: SW480 colon cancer cell line

tag: doxycyclin treated

value: Y

tag: miRNA34a transfected

value: N


title: SW480_miRNA34a_no_Dox biological replicate 2


title: SW480_GFP_no_Dox biological replicate 2

description: SW480_GFP_no_Dox biological replicate 2


title: protoplast_KIN10_rep2

status: Public on Aug 17 2007

city: Boston

first: Elena

last: Baena-Gonzalez

state: MA

address: Simches Research Building, 185 Cambridge Street, CPZN7250

department: Molecular Biology (MGH) and Department of Genetics (HMS)

institute: Massachusetts General Hospital and Harvard Medical School

description: Hybridization and scanning were performed at the Harvard Medical School-Partners Healthcare Center for Genomic Research (Cambridge, MA).

hyb_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431).  Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371). In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45°C overnight.

scan_protocol: Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station.  Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred to a mirrored storage disk and to a raid 5 server operating on the Partners Healthcare network and backed up nightly via the Partners Healthcare Systems IT backup utility.  All systems are CFR21-11 and HIPPA compliant.

data_processing: Transcript expression values from scanned arrays were imported and examined for quality control using Affymetrix GeneChip® Operating Software (GCOS v. 1.0). Values were subjected to global scaling using a target value of 1500, as suggested by Affymetrix.

label: Biotin-CTP and biotin-UTP

organism: Arabidopsis thaliana

source_name: isolated leaf mesophyll cells (protoplasts) transfected with KIN10 expressing plasmid DNA

label_protocol: Eight micrograms of purified total RNA was labeled for hybridization using an ENZO BioArray HighYield RNA Transcript Labeling Kit (T7) following standard Affymetrix protocols (Affymetrix GeneChip Technical Analysis Manual)

growth_protocol: Plants were grown in soil (Metro Mix-360) under 13h light (80-100 mmol/m2s) /11 h dark conditions at 23ºC and 65% relative humidity.

extract_protocol: Total RNA was extracted using Trizol® (Invitrogen) following the manufacturer's protocol. The RNA was further purified using a Qiagen RNEasy Mini Kit.

treatment_protocol: For protoplast isolation, leaves were harvested 2h after the onset of the light period. Protoplasts (about 3 million) were freshly isolated from the fifth and sixth leaves of 36 randomly picked plants and pooled for two large protoplast-transfection experiments (scaled up 50-fold) as described (Kovtun et al., 2000, PNAS 97, 2940; Hwang and Sheen, 2001, Nature 413, 383; Sheen, 2001, Plant Physiol. 127, 1466). Cells (1.5 x 10-6) were transfected with 1mg of KIN10-expressing plasmid DNA and incubated in 10 ml mannitol buffer in a 150 x 15 mm Petri dish for 6h. Cells were kept at 23ºC under light (80 mmol/m2s) throughout the treatment period.

tag: Arabidopsis thaliana, Columbia-O ecotype, 28 days old plants


title: MC1b


title: SW480_GFP_no_Dox biological replicate 1

description: SW480_GFP_no_Dox biological replicate 1


title: Trib1 #1 Wild-type macrophage LPS

city: Suita

first: Masahiro

last: Yamamoto

state: Osaka

address: 2-2, Yamada-oka

country: Japan

institute: Osaka University

description: Successfully analyzed

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Genechip Mouse Genome array.

scan_protocol: Gene chip scanner 3000 OB

data_processing: MAS5.0 was used

label: Biotinylated RNA

source_name: Trib1 #1 Wild-type macrphages were treated with LPS

label_protocol: Biotinylated cRNA were prepared according to Affymetryx protocol

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

tag: 129/B6 background, 6-10 weeks


title: SW480_GFP_with_Dox biological replicate 2


title: SW480_miRNA34a_with_Dox biological replicate 2


title: SW480_miRNA34a_no_Dox biological replicate 1


title: SW480_miRNA34a_with_Dox biological replicate 1


title: protoplast_controlDNA_rep2

source_name: isolated leaf mesophyll cells (protoplasts) transfected with control DNA

treatment_protocol: For protoplast isolation, leaves were harvested 2h after the onset of the light period. Protoplasts (about 3 million) were freshly isolated from the fifth and sixth leaves of 36 randomly picked plants and pooled for two large protoplast-transfection experiments (scaled up 50-fold) as described (Kovtun et al., 2000, PNAS 97, 2940; Hwang and Sheen, 2001, Nature 413, 383; Sheen, 2001, Plant Physiol. 127, 1466). Cells (1.5 x 10-6) were transfected with 1mg of control plasmid DNA and incubated in 10 ml mannitol buffer in a 150 x 15 mm Petri dish for 6h. Cells were kept at 23ºC under light (80 mmol/m2s) throughout the treatment period.


title: protoplast_hypoxia_rep1

hyb_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed.   Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431).  Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371). In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45°C overnight.

source_name: isolated leaf mesophyll cells (protoplasts)

treatment_protocol: For protoplast isolation, leaves were harvested 2h after the onset of the light period. Protoplasts (about 3 million) were freshly isolated from the fifth and sixth leaves of 36 randomly picked plants and pooled for two large protoplast samples. For hypoxia treatment, cells (1.5 x 10-6) were incubated in 2 ml mannitol buffer in a 15 ml Falcon tube (25 mm depth) for 6h under a light intensity of 80 microEinstein.


title: lymphocytes_HD_M_59y

status: Public on Aug 15 2007

first: Alexandre

last: Kuhn

address: 35 Convent Dr

department: NIA

institute: NIH

description: Affymetrix U133 Human Genome 2.0 Plus arrays

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: lymphocytes (blood)

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufacturer's protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

extract_protocol: TRIzol (Invitrogen) following the manufacturer's protocol, followed by RNeasy column cleanup and ethanol precipitation.

tag: Sample Group

value: HD patient; Gender:male; Age:59; Tissue:lymphocytes (blood); IT15 CAG repeats:21/45


title: protoplast_controlDNA_rep1

description: Hybridization and scanning were performed at the Brigham and Women’s Hospital Microarray Facility (Boston, MA)


title: lymphocytes_HD_M_55y

value: HD patient; Gender:male; Age:55; Tissue:lymphocytes (blood); IT15 CAG repeats:25/43


title: protoplast_KIN10_rep1


title: lymphocytes_HD_F_44y

value: HD patient; Gender:female; Age:44; Tissue:lymphocytes (blood); IT15 CAG repeats:17/48


title: lymphocytes_HD_F_61y

value: HD patient; Gender:female; Age:61; Tissue:lymphocytes (blood); IT15 CAG repeats:19/44


title: lymphocytes_HD_F_43y_1

value: HD patient; Gender:female; Age:43; Tissue:lymphocytes (blood); IT15 CAG repeats:26/47


title: lymphocytes_HD_M_62y

value: HD patient; Gender:male; Age:62; Tissue:lymphocytes (blood); IT15 CAG repeats:17/47


title: lymphocytes_HD_F_50y

value: HD patient; Gender:female; Age:50; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: lymphocytes_HD_M_51y

value: HD patient; Gender:male; Age:51; Tissue:lymphocytes (blood); IT15 CAG repeats:17/45


title: lymphocytes_HD_F_36y

value: HD patient; Gender:female; Age:36; Tissue:lymphocytes (blood); IT15 CAG repeats:18/51


title: protoplast_control_rep1

treatment_protocol: For protoplast isolation, leaves were harvested 2h after the onset of the light period. Protoplasts (about 3 million) were freshly isolated from the fifth and sixth leaves of 36 randomly picked plants and pooled for two large protoplast samples. Control cells (1.5 x 10-6) were incubated in 10 ml mannitol buffer in a 150 x 15 mm Petri dish (0.6 mm depth) for 6h under a light intensity of 80 microEinstein.


title: lymphocytes_HD_F_56y

value: HD patient; Gender:female; Age:56; Tissue:lymphocytes (blood); IT15 CAG repeats:18/43


title: lymphocytes_HD_F_43y_2

value: HD patient; Gender:female; Age:43; Tissue:lymphocytes (blood); IT15 CAG repeats:15/50


title: lymphocytes_ctl_M_50y

value: control; Gender:male; Age:50; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: lymphocytes_HD_F_41y

value: HD patient; Gender:female; Age:41; Tissue:lymphocytes (blood); IT15 CAG repeats:24/49


title: lymphocytes_ctl_M_38y

value: control; Gender:male; Age:38; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: lymphocytes_ctl_F_30y

value: control; Gender:female; Age:30; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: lymphocytes_ctl_F_39y

value: control; Gender:female; Age:39; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: lymphocytes_ctl_M_42y

value: control; Gender:male; Age:42; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: lymphocytes_ctl_F_51y

value: control; Gender:female; Age:51; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: lymphocytes_ctl_F_68y

value: control; Gender:female; Age:68; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: HMLER sample 3

city: Cambridge

first: Tan

middle: A

last: Ince

address: 9 Cambridge Center

institute: Whitehead Institute

description: BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)

hyb_protocol: Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.

scan_protocol: The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.

data_processing: Affymetrix Microarray Suite 5.0 was used to generate a cell intensity file (*.cel).  Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.

label_protocol: As per Affymetrix instructions

growth_protocol: in vitro cultured in MEGM medium on regular culture plates

extract_protocol:
The standard protocols followed were per Affymetrix’s instructions
(Genechip Expression Analysis Technical Manual
701021 Rev 4). Briefly, total RNA was isolated from cultured cells using
Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s
instructions. The RNA pellet was resuspended in 100 ul
of RNAse free water. The RNeasy Clean-up kit (Qiagen,
Valencia, CA) was utilized per manufacturer’s instructions
resulting in 30 ul total RNA sample. The total RNA concentration
and 260/280 ratio was evaluated on a NanoDrop ND-
1000 UV-Vis Spectrophotomter (NanoDrop Technologies,
Rockland, DE). Only samples with a 260/280 ratio greater
than 1.9 were further processed. An aliquot of 1 ul from each
of the samples was diluted to be within the dynamic range of
the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,
CA), with a target of 100 ng. The Nano Labchip protocol was
followed as per manufacturer’s instructions and was placed
on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for
evaluation. Samples with the highest concentration, only 2
distinct 18 S and 28 S peaks, and no evidence of degradation
were further processed.
To obtain 15 µg of total RNA for first strand cDNA synthesis,
samples were sometimes combined and placed on a spinvacuum
to obtain the necessary concentration (1.66 µg/µl)
and volume (9µl). Six hundred units of SuperScript II reverse
transcriptase were used for the first strand cDNA synthesis
reaction.
The second strand DNA synthesis, the clean-up of
the double-stranded cDNA, the synthesis of the biotin-labeled
cRNA, and the clean-up of the biotin-labeled cRNA were
per Affymetrix instructions. The Genechip Sample Cleanup
module was used for the clean-up steps of the double stranded
cDNA and the biotin-labeled cRNA. Quantification
of the cRNA was evaluated on the NanoDrop. Samples were
used for hybridization only if 20 µg of cRNA were obtained
in an individual sample or by combining samples.

treatment_protocol: transformed by SV40 - largeT/smallT + H-Ras in MEGM medium

tag: Gender

value: female

value: premenopausal

tag: Tissue

value: normal breast


title: HMLER sample 1

source_name: BPE cells (Normal human mammary epithelial cells, hTERT-immortalized)


title: HMLER sample 6

data_processing:
Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
was used to generate a cell intensity file (*.cel).  Probe intensities were
normalized and summarized using GCRMA (with default settings)
with R/Bioconductor.


title: lymphocytes_ctl_F_60y

value: control; Gender:female; Age:60; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: lymphocytes_ctl_M_46y

value: control; Gender:male; Age:46; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: HME sample 4

description: Normal human mammary epithelial cells, hTERT-immortalized

treatment_protocol: immortalized by hTERT in MEGM medium


title: lymphocytes_ctl_M_60y

value: control; Gender:male; Age:60; Tissue:lymphocytes (blood); IT15 CAG repeats:N/A


title: HMLER sample 5


title: HME sample 3

source_name: Normal human mammary epithelial cells, hTERT-immortalized


title: HMLER sample 4


title: HME sample 2


title: HME sample 1


title: BPLER sample 5

growth_protocol: in vitro cultured in WIT medium on Primaria plates

treatment_protocol: transformed by SV40 - largeT/smallT + H-Ras in WIT medium


title: BPLER sample 6


title: BPLER sample 4


title: BPLER sample 3


title: BPLER sample 2


title: BPE sample 5

treatment_protocol: immortalized by hTERT in WIT medium


title: BPE sample 3


title: BPLER sample 1


title: BPE sample 1

description: Normal human mammary epithelial cells

data_processing:
Affymetrix Microarray Suite 5.0. Microarray Suite 5.0
was used to generate a cell intensity file (*.cel).  These were
normalized and summarized using GCRMA (with default settings)
using R/Bioconductor.

source_name: Normal human mammary epithelial cells

treatment_protocol: immortalized by hTERT


title: BPE sample 2


title: BPE sample 4


title: HMLER sample 2


title: folatedeficientAs10ppm3

status: Public on Aug 10 2007

city: Research Triangle Park

first: Gail

middle: M

last: Nelson

state: NC

address: 109 TW Alexander Dr.

institute: U.S. Environmental Protection Agency

description: gene expression data from ODC mouse skin samples

hyb_protocol: Samples were hybridized according to the 2004 Affymetrix Standard Format Protocol

scan_protocol: Mouse 430 2.0 GeneChips were scanned according to 2004 Affymetrix protocol using a Affymetrix High Density GeneChip Scanner 3000

data_processing: Affymetrix GeneChip Operating System (GCOS) software was used for washing, staining, and scanning GeneChips.  GCOS files were generated including quality control metric summaries. GCOS generated .cel files were used to calculate expression summaries in GeneSpring GX 7.3 using RMA normalization.

label: biotin-streptavidin-R-phycoerythrin

source_name: ODC mouse skin samples from a mouse fed folatedeficientAs10ppm

label_protocol: Samples were labeled according to the 2004 Affymetrix One-Cycle IVT Target Labeling protocol

extract_protocol: Total RNA was isolated using the TriReagent procedure (Molecular Research Center, Cincinnati, OH) and the Qiagen Rneasy mini RNA cleanup protocol (Qiagen, Valencia, CA)

treatment_protocol: Mice were fed either a folate deficient purified diet (AIN-76A) with vitamin free casein, corn oil and 1% succinyl sulfathiazole, or the same diet supplemented with 5 mg/kg folic acid (Dyets, Bethlehem, PA; product nos. 117757 and 117758).Mice on both diets were treated with 0, 1, or 10 ppm sodium arsenite in the drinking water for 30 days prior to euthanasia.  Skin samples were harvested from the mid-back, flash frozen in liquid nitrogen, and stored at -80C.

tag: samples were obtained from 6 treatment groups with 4 samples each ( 3 arsenic doses x 2 folate conditions)


title: folatesufficientAs10ppm3

source_name: ODC mouse skin samples from a mouse fed folatesufficientAs10ppm


title: folatedeficientAs10ppm1


title: folatesufficientAs10ppm1


title: folatesufficientAs10ppm2


title: folatedeficientAs10ppm4


title: folatedeficientAs10ppm2


title: folatedeficientAs1ppm1

source_name: ODC mouse skin samples from a mouse fed folatedeficientAs1ppm


title: folatesufficientAs1ppm4

source_name: ODC mouse skin samples from a mouse fed folatesufficientAs1ppm


title: folatedeficientAs1ppm4


title: folatesufficientAs10ppm4


title: folatedeficientAs1ppm2


title: folatedeficientAs1ppm3


title: folatesufficientAs1ppm1


title: folatesufficientAs1ppm2


title: folatesufficientAs1ppm3


title: folatedeficientAs0ppm3

source_name: ODC mouse skin samples from a mouse fed folatedeficientAs0ppm


title: folatedeficientAs0ppm4


title: folatesufficientAs0ppm2

source_name: ODC mouse skin samples from a mouse fed folatesufficientAs0ppm


title: folatesufficientAs0ppm4


title: folatedeficientAs0ppm2


title: 24h -TGF-beta odontoblasts

city: Oulu

first: Virve

last: Pääkkönen

address: Aapistie 3

department: Institute of Dentistry

country: Finland

institute: University of Oulu

hyb_protocol: Experimental procedures for GeneChip (Affymetrix, Santa Clara, CA, USA) were performed according to the Affymetrix GeneChip Expression Analysis Technical Manual.

scan_protocol: HP GeneArray Scanner was used.

data_processing: The expression data was analyzed using Affymetrix GeneChip Operating Software version 1.1.1. Signal intensities of all probe sets were scaled to the target value of 500.

source_name: Odontoblasts, tissue cultured for 24h without TGF-beta

label_protocol: Double-stranded DNA was synthesized by means of the Superscript Choice System (Gibco BRL Life Technologies, Rockville, MD, USA) and T7-(dT)24 primer. The DNA was purified using GeneChip Sample Cleanup Module (Qiagen, Valencia, CA, USA). In vitro transcription was performed to produce biotin labeled cRNA using a BioArray HighYield RNA Transcription Labeling Kit (Enzo Diagnostics, Farmingdale, NY, USA) according to the manufacturer’s instructions. Biotinylated cRNA was cleaned with an GeneChip Sample Cleanup Module (Qiagen), fragmented to 35 to 200 nt, and hybridized to Affymetrix HGU133plus 2.0 (odontoblast samples). After being washed, the array was stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR, USA). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA, USA) and second staining with streptavidin-phycoerythrin.

extract_protocol: Total RNA was isolated using Trizol-protocol and further purified by Qiagen RNeasy Mini Kit

treatment_protocol: Fresly extracted human third molars were cut 2-3mm apically from cement-enamel junction and pulp tissues were removed. The crowns were embedded into agarose gel pulp chambers facing upwards, and the pulp chambers were filled with OPTIMEM. Odontoblasts were cultured for 24h without TGF-beta.

tag: Odontoblasts obtained from third molars of young adults and tissue cultured without TGF-beta for 24h.


title: 1h  +TGF-beta odontoblasts

source_name: odontoblasts tissue cultured for 1h with TGF-beta

treatment_protocol: Fresly extracted human third molars were cut 2-3mm apically from cement-enamel junction and pulp tissues were removed. The crowns were embedded into agarose gel pulp chambers facing upwards, and the pulp chambers were filled with OPTIMEM. Odontoblasts were cultured for 1h with TGF-beta.

tag: Odontoblasts obtained from third molars of young patients and tissue cultured for 1h with TGF-beta


title: 24h +TGF-beta odontoblasts

source_name: Odontoblasts, tissue cultured for 24h with TGF-beta

treatment_protocol: Fresly extracted human third molars were cut 2-3mm apically from cement-enamel junction and pulp tissues were removed. The crowns were embedded into agarose gel pulp chambers facing upwards, and the pulp chambers were filled with OPTIMEM. Odontoblasts were cultured for 24h with TGF-beta.

tag: Odontoblasts obtained from third molars of young adults and tissue cultured for 24h with TGF-beta


title: folatesufficientAs0ppm1


title: folatesufficientAs0ppm3


title: 1h -TGF-beta odontoblasts

source_name: Odontoblasts, tissue cultured for 1h without TGF-beta

treatment_protocol: Fresly extracted human third molars were cut 2-3mm apically from cement-enamel junction and pulp tissues were removed. The crowns were embedded into agarose gel pulp chambers facing upwards, and the pulp chambers were filled with OPTIMEM. Odontoblasts were cultured for 1h without TGF-beta.

tag: Odontoblasts obtained from third molars of young patients and tissue cultured for 1h as controls without TGF-beta.


title: folatedeficientAs0ppm1


title: Donor A, post G-CSF

status: Public on Aug 09 2007

city: Tampa

first: Matthew

last: Buzzeo

state: FL

address: 12901 Bruce B. Downs Blvd

institute: University of South Florida College of Medicine

description: Donor A, after G-CSF

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45degC onto HG U133 Plus 2.0 GeneChips. Gene Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3005

data_processing: The data were analyzed with  GeneChip Operating Software Version 1.2, using Affymetrix default analysis settings, a target value of 500 and a normalization value of 1.

source_name: peripheral blood, prior to G-CSF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RBC lysis with ammonium chloride Buffer EL, followed by RNA column purification

tag: no additional information


title: Donor E, post G-CSF

description: Donor E, after G-CSF

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3009


title: Donor C, post G-CSF

description: Donor C, after G-CSF

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3007


title: Donor B, pre G-CSF

description: Donor B, prior to G-CSF

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3001


title: Donor D, pre G-CSF

description: Donor D, prior to G-CSF

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3003


title: Donor A, pre G-CSF

description: Donor A, prior to G-CSF

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000


title: Donor E, pre G-CSF

description: Donor E, prior to G-CSF

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3004


title: Donor D, post G-CSF

description: Donor D, after G-CSF

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3008


title: mgb +/- male, whole E15 embryo (HTM_532)

city: Columbus

first: Kirk

last: McHugh

address: 700 Children's Drive

department: Cell & Developmental Biology

institute: Columbus Children's Hospital

hyb_protocol: For expression profiling, 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.) and 2.2 µg of cDNA was hybridized per microarray. The microarrays utilized were both obtained from Affymetrix (Santa Clara, CA) and included either the Mouse Genome 430 2.0 GeneChip or the Custom GeneChip Chr11/16. After 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA). GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All steps of sample and microarray processing were performed according to manufacturer's recommendations (Affymetrix, Santa Clara, CA).

data_processing: Probe set expression estimates were calculated using WPP algorithm (Auer et al, 2007).

label_protocol: standard Affymetrix protocol

extract_protocol: Whole embryos were harvested from timed pregnant females at embryonic day 15 (E15). Embryonic bladders were micro-dissected, snap frozen in liquid nitrogen, and stored at -80C.  Bladder tissues were homogenized using a Kontes-pellet pestle (Fisher). High quality total cellular RNA was isolated using the Absolutely RNA Miniprep kit according to the manufacture’s protocol (Stratagene, La Jolla, CA). Sample concentration and purity was determined by optical density 260/280 nm ratios using standard procedures. RNA samples were stored at -80C until further use. Total cellular RNA was extracted from whole embryos by homogenizing samples in TRIzol Reagent as outlined by the supplier (Invitrogen, Carlsbad, CA).

tag: mgb +/- male, whole E15 embryo


title: mgb -/- male, whole E15 embryo (HMM_533)

tag: mgb -/- male, whole E15 embryo


title: 90-8_Infect_2

status: Public on Aug 08 2007

first: Bruce

middle: J

last: Aronow

description: Five different human MPNST cell lines, mock treated or infected with G207.

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at  30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.3.
Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.

source_name: MPNST cancer cells infected with G207 and oncolytic HSV.

label_protocol: Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.

extract_protocol:
Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

treatment_protocol: Samples were mock treated or infected with G207.


title: 8814_Mock_2


title: Wip1-/- 4hr

city: Houston

first: Ou

last: Ma

state: TX

address: One Baylor Plaza

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

description: Gene expression data from Wip1-/- mouse MEFs 4hrs after gamma irradiation.

hyb_protocol: Standard Affymetrix hybridization protocol. The exact protocol is not available, but standard procedure can be found at: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: GeneChips were scanned with GeneChip® Scanner 3000 following standard Affymetrix procedure.

data_processing: Data was analyzed with GeneChip® Operating Software, or GCOS (Affymetrix).

source_name: Wip1-/- MEF, 4hr

label_protocol: Standard Affymetrix label protocol from 5ug total RNA. The exact protocol is not available, but standard procedure can be found at: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

extract_protocol: RNA extracted with Qiagen RNeasy Mini Kit, following manufacturer's instructions.

treatment_protocol: gamma-irradiated, harvested 4hrs after

tag: Cell type

value: MEF

tag: Genotype

tag: Treatment

value: gamma irradiation, harvested 4hrs after


title: Donor B, post G-CSF

description: Donor B, after G-CSF

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3006


title: Wild type female, whole E15 embryo (WTF_528)

scan_protocol: standard Affymetrix protocol

tag: wild type female, whole E15 embryo


title: mgb +/- female, whole E15 embryo (HTF_523)

tag: mgb +/- female, whole E15 embryo


title: mgb -/- female, whole E15 embryo (HMF_529)

tag: mgb -/- female, whole E15 embryo


title: Wild type male, whole E15 embryo (WTM_525)

tag: wild type male, whole E15 embryo


title: T265_Infect_1


title: Donor C, pre G-CSF

description: Donor C, prior to G-CSF

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3002


title: T265_Mock_1


title: S462_Infect_1


title: S462_Mock_1


title: B. melitensis 16M replicate 2

city: Davis

first: Renee

last: Tsolis

address: One Shields Avenue

department: Medical Microbiology & Immunology

institute: University of California at Davis

description: Infected with B. melitensis 16M and euthanized 3 days post-infection

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scan

data_processing: dChip 2005

source_name: Spleen

label_protocol: Standard Affymetrix one-cycle labeling protocol

extract_protocol: Trizol

tag: Strain C57BL/6 female


title: Wip1+/+ 4hr

description: Gene expression data from Wip1+/+ mouse MEFs 4hrs after gamma irradiation.

source_name: Wip1+/+ MEF, 4hr

value: gamma irradiated, harvested 4hrs after


title: T265_Mock_3


title: B. melitensis 16M replicate 1

treatment_protocol: Infected with B. melitensis 16M and euthanized 3 days post-infection


title: B. abortus 2308 ADH4.2 replicate 2

description: Infected with B. abortus 2308 ADH4.2 and euthanized 3 days post-infection


title: Wip1+/+ 0hr

description: Gene expression data from Wip1+/+ mouse MEFs prior to gamma irradiation (as control).

source_name: Wip1+/+ MEF, 0hr

treatment_protocol: non-irradiated

value: non-irradiated


title: Wip1-/- 0hr

description: Gene expression data from Wip1-/- mouse MEFs prior to gamma irradiation (as control).

source_name: Wip1-/- MEF, 0hr

value: non-irradiated (control)


title: B. abortus 2308 ADH4.2 replicate 1

treatment_protocol: Infected with B. abortus 2308 ADH4.2 and euthanized 3 days post-infection


title: B. abortus 2308 BA41 replicate 2

description: Infected with B. abortus 2308 BA41 and euthanized 3 days post-infection


title: T265_Infect_2


title: S462_Infect_3


title: 90-8_Mock_1


title: S462_Mock_3


title: B. abortus 2308 replicate 2

description: Infected with B. abortus 2308 and euthanized 3 days post-infection


title: B. abortus BA41 replicate 1

treatment_protocol: Infected with B. abortus 2308 BA41 and euthanized 3 days post-infection


title: 26T_Mock_2


title: Control replicate 1

description: Infected with PBS and euthanized 3 days post-infection


title: 26T_Infect_2


title: 26T_Mock_1


title: S462_Infect_2


title: B. abortus 2308 replicate 1

treatment_protocol: Infected with B. abortus 2308 and euthanized 3 days post-infection


title: Control replicate 2

treatment_protocol: Infected with PBS and euthanized 3 days post-infection


title: S462_Mock_2


title: ApoE-/+, offspring hypercholesterolemic ApoE-/- mother, wt father LUMC_HKG_MOUSE_430_2-4

city: Leiden

first: Anja

last: Schiel

address: Einthovenweg 20

department: Human Clinical Genetics

institute: Leiden University Medical Center

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: MAS5, GCOS

source_name: carotic artery

label_protocol:
2 cycle
AmbionMessageAmpIIaRNAAmplification kit, oligodT
AmbionMessageAmpII-Biotin Enhanced

extract_protocol: RNAqueous-Micro

treatment_protocol: Disection, immediate storage in liquid nitrogen

tag: genotype/variation (offspring)

value: ApoE-/+

tag: cross


title: 8814_Mock_1


title: 26T_Infect_1


title: T265_Mock_2


title: ApoE-/+, offspring normocholesterolemic wt mother, Apo-/- father LUMC_HKG_MOUSE_430_2

description: ApoE-/+, offspring normocholesterolemic wt mother, ApoE-/- father


title: ApoE-/+, offspring normocholesterolemic wt mother, ApoE-/- father LUMC_HKG_MOUSE_430_2-2


title: ApoE-/+, offspring hypercholesterolemic ApoE-/- mother, wt father LUMC_HKG_MOUSE_430_2-5


title: ApoE-/+, offspring hypercholesterolemic ApoE-/- mother, wt father LUMC_HKG_MOUSE_430_2-6


title: 90-8_Mock_2


title: ApoE-/+, offspring hypercholesterolemic ApoE-/- mother, wt father LUMC_HKG_MOUSE_430_2-7


title: ApoE-/+, offspring normocholesterolemic wt mother, ApoE-/- father LUMC_HKG_MOUSE_430_2-3


title: NK_timepoint8hours

status: Public on Aug 07 2007

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description: The isolation of RNA, hybridization and image processing was performed strictly according to the protocol set up by Affymetrix (Affymetrix Inc, CA).  Briefly, extracted RNA  (at least 2.6g used for each time point) was assessed by the Bio-analyzer 2100 (Agilent  Inc, CA), and single round amplification protocol (one-cycle target labeling kit, Affymetrix Inc) was utilized for RNA amplification. Antisense biotin-labeled cRNA (10g), generated by in vitro transcription were hybridized and biotinylated probes hybridized to the array were detected using pycoerythrin labeled streptavidin. All arrays were scanned using the Gene-chip scanner 3000 (Affymetrix Inc, CA).

data_processing: The Affymetrix GeneChip® Operating Software (GCOS) was utilized for management, sharing, and analysis of data generated.

label: Biotin-pycoerythrin

source_name: Natural killer cells

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA.

tag: Primary NK cells were isolated from healthy donors and peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature.  Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 8 hours at 37ºC and 5% CO2, before harvest and storage in Trizol at -80°C till RNA isolation.


title: Lymphoid control

description: The isolation of RNA, hybridization and image processing was performed strictly according to the protocol set up by Affymetrix (Affymetrix Inc, CA).  Briefly, extracted RNA  (at least 2.6g used for each time point) was assessed by the Bio-analyzer 2100 (Agilent  Inc, CA), and single round amplification protocol (one-cycle target labeling kit, Affymetrix Inc) was utilized for RNA amplification. Antisense biotin-labeled cRNA (10g), generated by in vitro transcription were hybridized and biotinylated probes hybridized to the array were detected using pycoerythrin labeled streptavidin. All arrays were scanned using the Gene-chip scanner 3000 (Affymetrix Inc, CA). The Affymetrix GeneChip® Operating Software (GCOS) was utilized for management, sharing, and analysis of data generated

label: Biotin-phycoerythin

source_name: Lymphoid tissues

tag: lymphoid RNA reference standard, consisting of RNA from tonsil, thymus, spleen, and cell lines derived from malignant pre-B cells, plasma cells and NK cells

tag: ref:

tag: Dybkaer K, Zhou G, Iqbal J, Kelly D, Xiao L, Sherman S, d'Amore F, Chan WC

value: Suitability of stratagene reference RNA for analysis of lymphoid tissues. BioTechniques 2004, 37(3):470-472, 474.


title: NK_time2hours

tag: Primary NK cells were isolated from  healthy donors and  peripheral blood mononuclear cells (PBMCs)  were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature.  Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 2 hours at 37ºC and 5% CO2, before harvest and storage in Trizol at -80°C till RNA isolation.


title: Native odontoblast

scan_protocol: HP GeneArray Scanner was used

source_name: Pooled native odontoblasts

label_protocol: Experimental procedures for GeneChip (Affymetrix, Santa Clara, CA, USA) were performed according to the Affymetrix GeneChip Expression Analysis Technical Manual. In essence, using 10 µg of total RNA as template double-stranded DNA was synthesized by means of the Superscript Choice System (Gibco BRL Life Technologies, Rockville, MD, USA) and T7-(dT)24 primer. The DNA was purified using GeneChip Sample Cleanup Module (Qiagen, Valencia, CA, USA). In vitro transcription was performed to produce biotin labeled cRNA using a BioArray HighYield RNA Transcription Labeling Kit (Enzo Diagnostics, Farmingdale, NY, USA) according to the manufacturer’s instructions. Biotinylated cRNA was cleaned with an GeneChip Sample Cleanup Module (Qiagen), fragmented to 35 to 200 nt, and and hybridized to the array After being washed, the array was stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR, USA). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA, USA) and second staining with streptavidin-phycoerythrin,

extract_protocol: Trizol-protocol

tag: Native odontoblasts extracted from third molars of young adults.


title: 90-8_Infect_1

institute: Cincinnati Children's Hospital Medical Center


title: Resting_CD8Tcells

data_processing: The Affymetrix GeneChip® Operating Software (GCOS) was utilized for management, sharing, and analysis of data generated

source_name: CD8 positive T cells

tag: Primary T cells were isolated from healthy donorsPrimary NK cells


title: CAD_T2

status: Public on Aug 04 2007

first: Jiangwen

last: Zhang

address: 7 Divinity Ave

department: FAS Center for Systems Biology

institute: Harvard University

description: CAD transfected with RIPmiR-124a-2 plasmid, expressing miR-124a-2, biological rep2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were were normalized by robust multi-chip analysis (RMA) (Bioconductor release 1.9) using PM-only models.

source_name: mouse neuroblastoma cell CAD

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: CAD cell line (Qi et al., 1997) was propagated in DMEM supplemented with 10% fetal bovine serum (FBS) or Fetaclone III and 1% penicillin/streptomycin.

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

treatment_protocol: CAD cell line (Qi et al., 1997) was propagated in DMEM supplemented with 10% fetal bovine serum (FBS) or Fetaclone III and 1% penicillin/streptomycin, transfected RIPmiR-124a-2 plasmid, expressing miR-124a-2.

tag: cultured mouse neuroblastoma cell CAD


title: NK_timepoint24hours

tag: Primary NK cells were isolated from healthy donors and peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature.  Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 24 hours at 37ºC and 5% CO2, before harvest and storage in Trizol at -80°C till RNA isolation.


title: Resting_NK

source_name: Natural Killer cells

tag: Natural Killer cells isolated from peripheral blood of healthy individuals


title: CAD_C1

description: CAD transfected with control empty plasmid, RI vector, biological rep1

treatment_protocol: CAD cell line (Qi et al., 1997) was propagated in DMEM supplemented with 10% fetal bovine serum (FBS) or Fetaclone III and 1% penicillin/streptomycin, transfected empty plasmids, RI vector


title: CAD_T1

description: CAD transfected with RIPmiR-124a-2 plasmid, expressing miR-124a-2, biological rep1


title: 8814_Infect_1


title: CAD_T3

description: CAD transfected with RIPmiR-124a-2 plasmid, expressing miR-124a-2, biological rep3


title: Biopsy of a colorectal adenoma from patient #32

status: Public on Aug 03 2007

city: Zurich

first: Giancarlo

last: Marra

address: Winterthurerstrasse 190

department: Molecular Cancer Research

country: Switzerland

institute: University of Zurich

description: Gene expression data from colorectal adenoma.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HG-133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: standard Affymetrix procedures

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Human colorectal adenoma

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

extract_protocol: For each polyp, three biopsies of normal mucosa were collected from the same colon segment (> 2 cm from the site of the polyp). Immediately after removal, a small sample of epithelial tissue (5-15 mg) was cut from the tip of each polyp, leaving the underlying muscularis mucosae intact. Total RNA was extracted (RNeasy Mini kit, Qiagen) from homogenized tissue samples (5- to 15-mg), and its integrity was verified by capillary gel electrophoresis (Bio Analyzer, Agilent Technologies).

tag: Tissue

value: adenoma

tag: Location

value: sigmoid colon

tag: Size

tag: Patient ID

value: PN

tag: CEL Filename

value: 190106_PN_po (vi_po_42).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: CAD_C3

description: CAD transfected with control empty plasmid, RI vector, biological rep3


title: Biopsy of a colorectal adenoma from patient #29

value: MA

value: 021005_MA_po (vi_po_38).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: CAD_C2

description: CAD transfected with control empty plasmid, RI vector, biological rep2


title: Biopsy of a colorectal adenoma from patient #26

value: ascending colon

value: RC

value: 120705_RC_po (vi_po_33).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #27

value: TMA

value: 120705_TMA_po (vi_po_34).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #30

value: MM

value: 021005_MM_po (vi_po_39).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #28

value: rectum

value: NM

value: 120705_NM_po (vi_po_35).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #31

value: NF

value: 190106_NF_po (vi_po_41).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #16

value: adenoma

value: sigmoid colon

value: MP

value: 220205_MP_po (vi_po_19).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #21

value: SMA

value: 080605_SMA_po (vi_po_27).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #24

value: BA

value: 210605_BA_po (vi_po_30).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #17

value: LG

value: 220205_LG_po (vi_po_20).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #23

value: GN

value: 210605_GN_po (vi_po_29).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #25

value: PF

value: 210605_PF_po (vi_po_32).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #13

value: rectum

value: PR

value: 040205_PR_po (vi_po_16).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #19

value: adenoma

value: LS

value: 080605_LS_2_po (vi_po_24).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #15

value: sigmoid colon

value: MP

value: 040205_MP_po (vi_po_18).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #22

value: descending colon

value: MR

value: 080605_MR_po (vi_po_28).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #20

value: PL

value: 080605_PL_po (vi_po_26).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #18

value: BG

value: 230305_BG_po (vi_po_22).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #10

value: ME

value: 101204_ME_po (vi_po_12).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #12

value: ascending colon

value: RA

value: 040205_RA_po (vi_po_15).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #1

value: adenoma

value: GL

value: 131004_GL_po.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #9

value: rectum

value: MA

value: 101204_MA_po (vi_po_11).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #14

value: SD

value: 040205_SD_po (vi_po_17).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #11

value: descending colon

value: PC

value: 220205_PC_2_po_II (vi_po_13_II).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #2

value: sigmoid colon

value: PR

value: 131004_PR_po.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #4

value: 151004_GL_2_po.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #7

value: transversum

value: CD

value: 230305_CD_po_II (vi_po_9_II).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #3

value: adenoma

value: 151004_PC_po.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #6

value: FP

value: 121104_FP_2_po.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #8

value: rectum

value: 280105_CD_2_po_II (vi_po_10_II).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of a colorectal adenoma from patient #5

value: 230305_FP_po_II (vi_po_7_II).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #29

description: Gene expression data from colonic normal mucosa.

source_name: Human colonic normal mucosa

value: normal

value: MA

value: 021005_MA_nm (vi_nm_38).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #32

value: sigmoid colon

value: PN

value: 190106_PN_nm (vi_nm_42).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #31

value: ascending colon

value: NF

value: 190106_NF_nm (vi_nm_41).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #24

value: BA

value: 210605_BA_nm (vi_nm_30).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #25

value: PF

value: 210605_PF_nm (vi_nm_32).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #18

value: descending colon

value: BG

value: 230305_BG_nm_ (vi_nm_22).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #20

value: PL

value: 080605_PL_nm (vi_nm_26).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #21

value: normal

value: SMA

value: 080605_SMA_nm (vi_nm_27).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #27

value: sigmoid colon

value: TMA

value: 120705_TMA_nm (vi_nm_34).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #30

value: MM

value: 021005_MM_nm (vi_nm_39).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #17

value: rectum

value: LG

value: 220205_LG_nm (vi_nm_20).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #28

value: NM

value: 120705_NM_nm (vi_nm_35).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #19

value: LS

value: 080605_LS_2_nm (vi_nm_24).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #22

value: descending colon

value: MR

value: 080605_MR_nm (vi_nm_28).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #15

value: normal

value: MP

value: 040205_MP_nm (vi_nm_18).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #11

value: PC

value: 230305_PC_2_nm_II (vi_nm_13_II).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #14

value: ascending colon

value: SD

value: 040205_SD_nm (vi_nm_17).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #16

value: sigmoid colon

value: 220205_MP_nm (vi_nm_19).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #6

value: FP

value: 121104_FP_2_nm.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #8

value: rectum

value: CD

value: 031204_CD_2_nm (vi_nm_10).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #4

value: GL

value: 151004_GL_2_nm.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #7

value: normal

value: transversum

value: 031204_CD_nm (vi_nm_9).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #23

value: GN

value: 210605_GN_nm (vi_nm_29).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #13

value: PR

value: 040205_PR_nm (vi_nm_16).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #5

value: 121104_FP_nm.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #26

value: ascending colon

value: RC

value: 120705_RC_nm (vi_nm_33).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #12

value: RA

value: 040205_RA_nm (vi_nm_15).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #10

value: rectum

value: ME

value: 101204_ME_nm (vi_nm_12).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #9

value: MA

value: 101204_MA_nm (vi_nm_11).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: UET-13TR-EWS/ERG 24hr

city: Okura

first: Yoshitaka

last: Miyagawa

address: Setagaya-ku

institute: National Research Institute for Child Health and Development

description: Gene expression data from UET-13TR-EWS/ERG cells incubated in the absence of tetracycline for 24 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GCS3000.

data_processing: The arrays were analyzed using GeneChip Operating Software 1.2 (GCOS 1.2) (Affymetrix).  Background subtraction and normalization were performed by GeneSpring GX 7.3 software (Agilent Technologies, Inc., Santa Clara, CA).

source_name: UET-13TR-EWS/ERG 24hr

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

growth_protocol: UET-13 transfectants (UET-13TR-EWS/FLI1 and UET-13TR-EWS/ERG ) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% Tet System Approved Fetal Bovine Serum (T-FBS)(Takara, Shiga, Japan) at 37°C under a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from cells using RNeasy kit (QIAGEN, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: UET-13 transfectants were treated with or without 3 μg/ml of tetracycline for the indicated periods.

tag: UET-13TR-EWS/ERG cells were cultured in the absence of tetracycline for 24 hours


title: Biopsy of the normal mucosa of the colon from patient #1

value: normal

value: descending colon

value: GL

value: 131004_GL_nm.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: Biopsy of the normal mucosa of the colon from patient #2

value: sigmoid colon

value: PR

value: 230305_PR_nm_II (vi_nm_3_II).CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: UET-13TR-EWS/ERG 48hr tet+

description: Gene expression data from UET-13TR-EWS/ERG cells incubated in the presence of tetracycline for 48 hours

source_name: UET-13TR-EWS/ERG 48hr tet+

tag: UET-13TR-EWS/ERG cells were cultured in the presence of tetracycline for 48 hours


title: Biopsy of the normal mucosa of the colon from patient #3

value: PC

value: 151004_PC_nm.CEL, where "nm" is for normal mucosa (colorectal) and "po" is for polyp (colorectal)"


title: UET-13TR-EWS/ERG 24hr tet+

description: Gene expression data from UET-13TR-EWS/ERG cells incubated in the presence of tetracycline for 24 hours

source_name: UET-13TR-EWS/ERG 24hr tet+

tag: UET-13TR-EWS/ERG cells were cultured in the presence of tetracycline for 24 hours


title: UET-13TR-EWS/ERG72hr tet+

description: Gene expression data from UET-13TR-EWS/ERG cells incubated in the presence of tetracycline for 72 hours

source_name: UET-13TR-EWS/ERG72hr tet+

tag: UET-13TR-EWS/ERG cells were cultured in the presence of tetracycline for 72 hours


title: UET-13TR-EWS/FLI1 48hr tet+

description: Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the presence of tetracycline for 48 hours

source_name: UET-13TR-EWS/FLI1 48hr tet+

tag: UET-13TR-EWS/FLI1 cells were cultured in the presence of tetracycline for 48 hours


title: UET-13TR-EWS/ERG 48hr

description: Gene expression data from UET-13TR-EWS/ERG cells incubated in the absence of tetracycline for 48 hours

source_name: UET-13TR-EWS/ERG 48hr

tag: UET-13TR-EWS/ERG cells were cultured in the absence of tetracycline for 48 hours


title: UET-13TR-EWS/ERG 72hr

description: Gene expression data from UET-13TR-EWS/ERG cells incubated in the absence of tetracycline for 72 hours

source_name: UET-13TR-EWS/ERG 72hr

tag: UET-13TR-EWS/ERG cells were cultured in the absence of tetracycline for 72 hours


title: UET-13TR-EWS/FLI1 24hr

description: Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the absence of tetracycline for 24 hours

source_name: UET-13TR-EWS/FLI1 24hr

tag: UET-13TR-EWS/FLI1 cells were cultured in the absence of tetracycline for 24 hours


title: UET-13TR-EWS/FLI1 72hr tet+

description: Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the presence of tetracycline for 72 hours

source_name: UET-13TR-EWS/FLI1 72hr tet+

tag: UET-13TR-EWS/FLI1 cells were cultured in the presence of tetracycline for 72 hours


title: UET-13TR-EWS/FLI1 48hr

description: Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the absence of tetracycline for 48 hours

source_name: UET-13TR-EWS/FLI1 48hr

tag: UET-13TR-EWS/FLI1 cells were cultured in the absence of tetracycline for 48 hours


title: UET-13TR-EWS/FLI1 72hr

description: Gene expression data from UET-13TR-EWS/FLI1 cells incubated in the absence of tetracycline for 72 hours

source_name: UET-13TR-EWS/FLI1 72hr

tag: UET-13TR-EWS/FLI1 cells were cultured in the absence of tetracycline for 72 hours


title: Tg34

city: Chicago

first: Yugang

last: Wang

state: IL

address: 5841 S. Maryland

department: Pathology

institute: University of Chicago

description: Gene expression data from wt B6 mice liver HFD 2 weeks.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array.

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) 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: LIGHT Tg, HFD 2wks

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 and Qiagen Column.

treatment_protocol: Mice were feed high-fat diet(TD88137) for 2 weeks

tag: Lck LIGHT Tg

tag: Age

value: 4-8 wks


title: Tg35


title: WT78

source_name: B6, HFD 2wks

tag: B6 wild type