title: Chronic hypoxia + 1h reoxygenation

status: Public on Dec 24 2009

city: Brussels

first: Olivier

last: Feron

address: Avenue E. Mounier, 52 - FATH5349

department: IREC

country: Belgium

institute: UCL

description: Gene expression data from HUVEC in chronix hypoxia 3h + reoxygenation 1h

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

scan_protocol: GCOS

data_processing: GeneSpring. The trimmed mean target intensity of each array was arbitrarily set to 1.

label: Biotin

source_name: HUVEC chronic hypoxia + reoxygenation

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

growth_protocol: in vitro HUVEC cells passage 7, in EGM medium (Cambrex)

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

treatment_protocol:
in serum free medium (EBM+gentamycin+hydrocortisone) 2h before hypoxia until collection
chronic hypoxia = 3h ; cyclic hypoxia = 3x1h hypoxia interrupted by 30 minutes reoxygenation
collecting time : at the end of hypoxia or after 1h reoxygenation

tag: endothelial cells

tag: in vitro HUVEC passage 7


title: Vascular Smooth muscle cells, GLUT1 over-expression sample

status: Public on Oct 23 2009

type: RNA

city: Ann Arbor

first: Eileen

middle: Danger

last: Vesely

state: MI

address: 1150 W. Medical Center Drive MSRB I. Room 5518

department: Nephrology

country: USA

institute: University of Michigan

description: Rat vascular Smooth muscle cells, GLUT1 over-expression

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: Ann Arbor quantile-normalized trimmed-mean method

molecule: total RNA

organism: Rattus norvegicus

source_name: A7R5 Vascular Smooth muscle cells, GLUT1 over-expression (ATCC, CRL 1444)

label_protocol: 5 ug of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Total RNA was isolated from each of 2 conditions (control cells in low glucose (5.5mM), and GLUT1 overexpressing cells in low glucose, on three separate days and pooled to obtain one sample for each condition.

treatment_protocol: Scientific Approach:  A7r5 rat embryonic vascular smooth muscle cells (VSMCs) (ATCC, CRL-1444) were infected for 72 hours with adenoviral vectors containing human GLUT1 or empty vector controls at a multiplicity of infection of 10 (MOI of 1 = 100 particles/cell) and grown in low glucose (5.5mM) media.  The human GLUT1 cDNA adenoviral vector and empty vector controls were a gift from Dr Arno Kumagai (University of Michigan).  Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA), followed by extraction with phenol/chloroform until the interface was clear.  Total RNA was further purified using Qiagen RNeasy Mini Kit (Qiagen 74106).  Immunoblot analysis was conducted to confirm GLUT1 overexpression at the time of Total RNA isolation (72 hours post-infection) for each condition.

tag: cell line

value: A7R5 Vascular Smooth muscle cells


title: Chronic hypoxia

description: Gene expression data from HUVEC cells in chronic hypoxia 3h

organism: Homo sapiens

source_name: HUVEC chronic hypoxia


title: Normoxia +1h

description: Gene expression data from HUVEC cells in normoxia 3+1h

source_name: HUVEC normoxia


title: Cyclic hypoxia + 1h reoxygenation

description: Gene expression data from HUVEC cells in cyclic hypoxia 3x1h + reoxygenation 1h

source_name: HUVEC cyclic hypoxia + reoxygenation


title: hMDM_SA_24hr_5

status: Public on Apr 23 2009

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

description: SA-treated hMDMs

hyb_protocol: cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix).  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix scanner.

data_processing: Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene.

label: biotin

source_name: human monocyte-derived macrophages, S. aureus-treated, 24hr, replicate 5

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

extract_protocol: Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Human monocyte-derived macrophages (hMDMs) were separated from fractions of peripheral blood mononuclear cells (PBMCs) obtained from the blood of healthy donors using a lymphocyte separation medium density gradient. Macrophages were treated with the Newman strain of S. aureus at an MOI of 1:50 for 8, 24, and 48 hours at 37C. Untreated macrophages serve as controls.

tag: SA-treated hMDMs


title: hMDM_control_24hr_5

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 24hr, replicate 5

tag: control hMDMs


title: hMDM_SA_48hr_5

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 48hr, replicate 5


title: DGM-00529 [gene_expr]

status: Public on Mar 05 2012

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

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

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

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.

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: department of genetic medicine id

tag: smoking status

value: NS


title: hMDM_SA_8hr_5

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 8hr, replicate 5


title: hMDM_control_48hr_5

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 48hr, replicate 5


source_name: A7R5 Vascular Smooth muscle cells, control sample (ATCC, CRL, 1444)

growth_protocol: Total RNA was isolated from each of 2 conditions (control cells in low glucose (5.5mM), and GLUT1 overexpressing cells in low glucose), on three separate days and pooled to obtain one sample for each condition.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA), followed by extraction with phenol/chloroform until the interface was clear.  Total RNA was further purified using Qiagen RNeasy Mini Kit (Qiagen 74106).  Immunoblot analysis was conducted to confirm GLUT1 overexpression at the time of Total RNA isolation (72 hours post-infection) for each condition.


title: Cyclic hypoxia

description: Gene expression data from HUVEC cells in cyclic hypoxia 3x1h

source_name: HUVEC cyclic hypoxia


title: hMDM_control_48hr_4

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 48hr, replicate 4


title: hMDM_control_8hr_5

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 8hr, replicate 5


title: hMDM_SA_48hr_4

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 48hr, replicate 4


title: Normoxia

description: Gene expression data from HUVEC cells in normoxia 3h


title: hMDM_SA_24hr_4

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 24hr, replicate 4


title: hMDM_SA_8hr_4

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 8hr, replicate 4


title: hMDM_control_8hr_4

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 8hr, replicate 4


title: hMDM_SA_48hr_3

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 48hr, replicate 3


title: hMDM_control_24hr_4

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 24hr, replicate 4


title: hMDM_SA_24hr_3

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 24hr, replicate 3


title: hMDM_control_24hr_3

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 24hr, replicate 3


title: hMDM_control_48hr_3

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 48hr, replicate 3


title: hMDM_control_24hr_2

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 24hr, replicate 2


title: hMDM_SA_8hr_1

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 8hr, replicate 1


title: hMDM_SA_24hr_2

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 24hr, replicate 2


title: hMDM_control_8hr_3

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 8hr, replicate 3


title: hMDM_SA_8hr_3

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 8hr, replicate 3


title: Native A7r5 gene expression (1)

status: Public on Aug 25 2010

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

description: Normoxic A7r5 vascular smooth muscle cells, approximately 50% confluent in 10% serum + DMEM, stably transfected with empty vector.

hyb_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual).

data_processing: Affymetrix CHP and CEL files. Data was normalized using RMA.

source_name: A7r5 vascular smooth muscle cells, native expression complement

extract_protocol: RNA was extracted from freshly cultured A7r5 cells using a Qiagen RNeasy kit.

tag: cell type

value: vascular smooth muscle cells

tag: tranfection

value: empty vector


title: hMDM_SA_8hr_2

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 8hr, replicate 2


title: hMDM_control_8hr_1

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 8hr, replicate 1


title: hMDM_SA_48hr_2

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 48hr, replicate 2


title: Don3_Macrophages+ZymosanA

status: Public on Jan 16 2009

city: Basel

first: Ceylan

last: Eken

address: Hebelstrasse 20

department: Biomedicine Department

country: Switzerland

institute: University Hospital Basel

description: All the steps where done according to Affymetrix protocols.

hyb_protocol: The target is denatured while the Genechips are pre-hybridized during 10 minutes. then the target is loaded onto the Genechips. During 16 hours, the Genechips are rotating in the hybridization oven. Genechips are then washed in Fluidics stations and stained.

scan_protocol: We used Genechip Scanner 3000.

data_processing: GCOS probe analysis algorithm

label: Biotin-streptavidin-PE

source_name: macrophages incubated with zymosanA for 3 hours

label_protocol: We used affymetrix staining protocol with biotynilated cRNA (target), 1st staining with streptavidin-PE (SAPE), 2nd staining with anti-SAPE, 3rd staining with SAPE.

extract_protocol: Trizol followed by a cleanup on column (silica based)

tag: Human monocyte derived macrophages culture 7 days with medium supplemented with 10% normal human serum, incubated with zymosanA for 3 hours.


title: Don4_Macrophages+ZymosanA


title: Don3_Macrophages+ZymosanA+PMN-Ectosomes

source_name: macrophages incubated with zymosanA and PMN-Ectosomes for 3 hours

tag: Human monocyte derived macrophages culture 7 days with medium supplemented with 10% normal human serum, incubated with zymosanA and PMN-Ectosomes for 3 hours.


title: Don4_Macrophages+ZymosanA+PMN-Ectosomes


title: Don4_Macrophages alone

source_name: macrophages alone

tag: Human monocyte derived macrophages culture 7 days with medium supplemented with 10% normal human serum.


title: Don4_Macrophages+PMN-Ectosomes

source_name: macrophages incubated with PMN-Ectosomes for 3 hours

tag: Human monocyte derived macrophages culture 7 days with medium supplemented with 10% normal human serum, incubated with PMN-Ectosomes for 3 hours.


title: hMDM_control_24hr_1

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 24hr, replicate 1


title: hMDM_control_48hr_1

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 48hr, replicate 1


title: hMDM_SA_24hr_1

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 24hr, replicate 1


title: hMDM_SA_48hr_1

description: SA-treated hMDMs

source_name: human monocyte-derived macrophages, S. aureus-treated, 48hr, replicate 1


title: Don3_Macrophages+PMN-Ectosomes


title: hMDM_control_8hr_2

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 8hr, replicate 2


title: hMDM_control_48hr_2

description: control hMDMs

source_name: human monocyte-derived macrophages, control, 48hr, replicate 2


title: Don2_Macrophages+ZymosanA+PMN-Ectosomes


title: Don1_Macrophages+ZymosanA

hyb_protocol: The target is denatured while the Genechips are pre-hybridized during 10 minutes. then the target is loaded onto the Genechips. During 16 hours, the Genechips are rotating in the hybridization oven. Genechips are then washed in Fluidics stations and stainined.


title: Don2_Macrophages alone


title: Don2_Macrophages+ZymosanA


title: Don3_Macrophages alone


title: Don1_Macrophages+ZymosanA+PMN-Ectosomes


title: Don2_Macrophages+PMN-Ectosomes


title: P6 Patient None

status: Public on Jun 27 2008

city: Cincinnati

first: Michael

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

description: Macrophages were derived from the peripheral blood of 8 AS patients (median disease duration 13 years [range <1-43 years]) and 9 healthy control subjects over 7 days with the use of granulocyte-macrophage colony-stimulating factor.

hyb_protocol: Affymetrix standard

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

data_processing: Data were imported into GeneSpring 7.3 with RMA preprocessing and normalized to median of all samples.  Normalized data were exported and subjected to Distance Weighted Discrimination (DWD) to account for any batch effects then reimported into Gene Spring and analyzed.

source_name: Macrophages derived from pheripheral blood

label_protocol: Affymetrix standard labeling

growth_protocol: SPeripheral blood samples were diluted with phosphate buffered saline (PBS), then underlaid with Ficoll-Paque Plus (Amersham Biosciences, Piscataway, NJ), and centrifuged under standard conditions to separate mononuclear cells.  PBMCs were removed and plated in nonsupplemented Cellgro RPMI 1640 (Mediatech, Herndon, VA) at 37°C for 2 hours. Following removal of nonadherent cells and media, the attached cells were cultured in R-10 (day 0), which consisted of RPMI 1640 supplemented with 10% fetal bovine serum (Hyclone, Logan, UT), HEPES (Sigma, St. Louis, MO), penicillin/ streptomycin (Gibco), and L-glutamine (Fisher Scientific, Pittsburgh, PA), and which was supplemented with recombinant human granulocyte–macrophage colony-stimulating factor (GM-CSF; 100 units/ml) (PeproTech, Rocky Hill, NJ). Every other day, 75% of the medium was removed and fresh R-10 supplemented with GM-CSF was added.

extract_protocol: Cells were suspended in TRIzol (Invitrogen, Carlsbad, CA) and processed according to the manufacturer's instructions

treatment_protocol: Cells were stimulated for 24 hours with interferon- (IFN; 100 units/ ml), were left untreated for 24 hours, or were treated for 3 hours with lipopolysaccharide (LPS; 10 ng/ml)

tag: Patient #6, Untreated


title: Don1_Macrophages alone

tag: Human monocyte-derived macrophages culture 7 days with medium supplemented with 10% normal human serum.


title: P5 Patient None

tag: Patient #5, Untreated


title: P7 Patient None

tag: Patient #7, Untreated


title: P7 Patient IFN

tag: Patient #7, IFN treated


title: A7r5 stably transfected with KD mutant BMPR2 (1)

description: Normoxic A7r5 vascular smooth muscle cells, approximately 50% confluent in 10% serum + DMEM, stably transfected with BMPR2 bearing a C994T (kinase domain, KD) mutation.

scan_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual).

source_name: A7r5 vascular SMC stably transfected with KD mutant BMPR2

value: KD mutant BMPR2


title: C9 Control None

tag: Control #9, Untreated


title: P5 Patient IFN

tag: Patient #5, IFN treated


title: P4 Patient IFN

tag: Patient 42, IFN treated


title: P1 Patient IFN

tag: Patient #1, IFN treated


title: P1 Patient None

tag: Patient #1, Untreated


title: P2 Patient None

tag: Patient #2, Untreated


title: Don1_Macrophages+PMN-Ectosomes

tag: Human monocyte derived macrophages culture 7 days with medium supplemented with 10% normal human serum,  incubated with PMN-Ectosomes for 3 hours.


title: C8 Control None

tag: Control #8, Untreated


title: C4 Control None

tag: Control #4, Untreated


title: P4 Patient None

tag: Patient #4, Untreated


title: P2 Patient IFN


title: P6 Patient IFN

tag: Patient #6, IFN treated


title: P3 Patient None

tag: Patient #3, Untreated


title: C3 Control None

tag: Control #3, Untreated


title: C2 Control None

tag: Control #2, Untreated


title: C6 Control None

tag: Control #6, Untreated


title: P8 Patient None

tag: Patient #8, Untreated


title: C7 Control None

tag: Control #7, Untreated


title: C3 Control IFN

tag: Control #3, IFN treated


title: C1 Control None

tag: Control #1, Untreated


title: C9 Control IFN

tag: Control #9, IFN treated


title: C8 Control IFN

tag: Control #8, IFN treated


title: C2 Control IFN

tag: Control #2, IFN treated


title: C5 Control IFN

tag: Control #5, IFN treated


title: C4 Control IFN

tag: Control #4, IFN treated


title: C1 Control IFN

tag: Control #1, IFN treated


title: C7 Control IFN

tag: Control #7, IFN treated


title: C5 Control None

tag: Control #5, Untreated


title: Macrophages IL-4 Dex TGF-beta 24h BC296.3

status: Public on May 15 2008

city: Mannheim

first: Alexei

last: Gratchev

department: Department of Dermatology

country: Germany

institute: Medical Centre Mannheim, University of Heidelberg

description: no additional description

hyb_protocol: Hybridization was performed according to standart Affymetrix protocol

scan_protocol: Scan was performed according to standart Affymetrix protocol

data_processing: MAS 5.0 was used for data processing

label: Labelling was performed according to standart Affymetrix protocol

source_name: Macrophages

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit, treated with DNase and cleaned up with Qiagen RNeasy Mini Kit

tag: Macrophages differentiated in the presence of IL-4 and dexamethasone for 5 days and then stimulated by TGF-beta for 24h


title: Macrophages IL-4 Dex TGF-beta 24h BC287.3

description: no additional description

label_protocol: Labelling was performed according to standart Affymetrix protocol


title: Macrophages IL-4 - TGF 24h BC351.2

description: no additional description

tag: Macrophages differentiated in the presence of IL-4 for 5 days and then stimulated by TGF-beta for 24h


title: Macrophages IL-4 Dex TGF-beta 24h BC286.2

description: no additional description


title: Macrophages IL-4 Dex TGF-beta 24h BC284.2

description: no additional description


title: Macrophages IL-4 - TGF 24h BC348.1

description: no additional description


title: Macrophages IL-4 Dex TGF-beta 3h BC284.1

description: no additional description

tag: Macrophages differentiated in the presence of IL-4 and dexamethasone for 5 days and then stimulated by TGF-beta for 3h


title: Macrophages IL-4 Dex TGF-beta 3h BC286.2

description: no additional description


title: Macrophages IL-4 - TGF 24h BC348.3

description: no additional description


title: Macrophages IL-4 Dex - control BC296.3

description: no additional description

tag: Macrophages differentiated in the presence of IL-4 and dexamethasone for 5 days


title: Macrophages IL-4 Dex TGF-beta 24h BC284.1

description: no additional description


title: Macrophages IL-4 - TGF 24h BC349.4

description: no additional description


title: Macrophages IL-4 - TGF 24h BC350.3

description: no additional description


title: Macrophages IL-4 Dex TGF-beta 3h BC287.3

description: no additional description


title: P3 Patient IFN

tag: Patient #3, IFN treated


title: Macrophages IL-4 Dex TGF-beta 3h BC284.2

description: no additional description


title: Macrophages IL-4 Dex TGF-beta 3h BC296.3

description: no additional description


title: Macrophages IL-4 Dex - control BC287.3

description: no additional description


title: Macrophages IL-4 Dex - control BC284.2

description: no additional description

tag: Macrophages differentiated in the presence of IL-4 adn dexamethasone for 5 days


title: Macrophages IL-4 Dex - control BC286.2

description: no additional description


title: Baseline macrophages from subject with atherosclerosis, pair P.

status: Public on Dec 14 2007

city: Göteborg

first: Daniel

last: Hägg

address: Vita Stråket 15

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: Göteborg University

description: Gene expression profile

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

source_name: Monocyte-derived macrophages

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol


title: Foam cells from subject with atherosclerosis, pair O.

description: Gene expression profile


title: Macrophages IL-4 Dex - control BC284.1

description: no additional description


title: Macrophages IL-4 - control BC348.3

description: no additional description

tag: Macrophages differentiated in the presence of IL-4 for 5 days


title: Macrophages IL-4 - control BC350.3

description: no additional description


title: Foam cells from subject without atherosclerosis, pair P.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair P.

description: Gene expression profile


title: Macrophages IL-4 - control BC349.4

description: no additional description


title: Foam cells from subject with atherosclerosis, pair P.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair O.

description: Gene expression profile


title: Macrophages IL-4 - control BC351.2

description: no additional description


title: Macrophages IL-4 - control BC348.1

description: no additional description


title: Foam cells from subject without atherosclerosis, pair M.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair M.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair L.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair L.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair N.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair O.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair N.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair O.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair N.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair L.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair N.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair M.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair M.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair L.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair K.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair K.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair J.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair K.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair F.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair F.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair J.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair I.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair J.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair H.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair K.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair I.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair F.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair H.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair H.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair H.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair I.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair E.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair I.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair E.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair D.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair D.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair C.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair C.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair D.

description: Gene expression profile


title: Baseline macrophages from subject without atherosclerosis, pair F.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair C.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair D.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair E.

description: Gene expression profile


title: C6 Control IFN

tag: Control #6, IFN treated


title: Foam cells from subject with atherosclerosis, pair J.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair B.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair B.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair C.

description: Gene expression profile


title: Foam cells from subject with atherosclerosis, pair A.

description: Gene expression profile


title: Foam cells from subject without atherosclerosis, pair B.

description: Gene expression profile


title: Baseline macrophages from subject with atherosclerosis, pair A.

description: Gene expression profile


title: cells stimulated with lipoprotein prep 3, biological rep1

status: Public on Sep 19 2007

city: COPENHAGEN

first: Silvio

last: Zaina

address: Blegdamsvej 9

department: Clinical Biochemistry

country: Denmark

institute: Rigshospitalet

description: Gene expression data

hyb_protocol: Standard Affymetrix protocol EukGE-WS2v5_450

scan_protocol: Arrays were scanned using an Affymetrix GeneChip® Scanner 3000

data_processing: dChip (build April 15, 2005) was used for normalization and modeling using the PM-only model, Control rep1 as baseline array

source_name: Human THP-1 macrophages, stimulated with lipoprotein prep3

label_protocol: Biotinylated cRNA prepared as standard Affymetrix protocol

growth_protocol: Standard THP-1 cell media

extract_protocol: By Rneasy system (Qiagen) according to manufacturer's instructions.

treatment_protocol: Standard media was replaced with serum-free media containing 2% BSA, lipoproteins (in PBS) or the equivalent volume of PBS (controls) were added, incubaton was carried out for 24h, cells were then washed twice in PBS, scraped and stored at -80deg

tag: Monocyte cell line, can be differentiated to macrophage, ATCC no. TIB-202


title: cells stimulated with lipoprotein prep 2, biological rep3

description: Gene expression data

source_name: Human THP-1 macrophages, stimulated with lipoprotein prep2


title: cells stimulated with lipoprotein prep 2, biological rep2

description: Gene expression data


title: cells stimulated with lipoprotein prep 3, biological rep2

description: Gene expression data


title: cells stimulated with lipoprotein prep 1, biological rep2

description: Gene expression data

source_name: Human THP-1 macrophages, stimulated with lipoprotein prep1


title: control (unstimulated) cells, biological rep2

description: Gene expression data

source_name: Human THP-1 macrophages, unstimulated


title: Baseline macrophages from subject without atherosclerosis, pair B.

description: Gene expression profile


title: control (unstimulated) cells, biological rep3

description: Gene expression data


title: cells stimulated with lipoprotein prep 1, biological rep3

description: Gene expression data


title: humanMDM_Healthy_LPS

status: Public on Aug 01 2007

city: Munich

first: Thomas

last: Hofer

address: Max-Lebsche-Platz 31

department: Comprehensive Pneumology Center

institute: Helmholtz Zentrum Munich

description: see Affymetrix standard protocol

hyb_protocol: see Affymetrix standard protocol

scan_protocol: see Affymetrix standard protocol

data_processing: Data were normalized, and transcript-specific gene expression levels were calculated, using gcrma (Wu et al., J. Comput. Biol., 12, 882-93, 2005; Wu et al., Nat. Biotechnol. 22, 656-8,, 2004) or rma (Bolstad et al., Bioinformatics, 19, 185-93, 2003; Irizarry et al., Nucleic Acids Res., 31, e15, 2003) as implemented in R (R Development Core Team, R foundation for statistical computing, Vienna, 2007) and Bioconductor (Gentleman et al., Genome Biology, 5, R80, 2004). Differentially expressed genes were identified using the permutation-based method of Tusher et al. (Proc. Natl. Acad. Sci. USA, 98, 5116-21, 2001) (sam) as implemented in the "samr" R package, using the median false discovery rate over 100 data permutations as a measure for statistical significance.

label: see Affymetrix standard protocol

label_protocol: see Affymetrix standard protocol

extract_protocol: phenol-chloroform extraction of total RNA

tag: monocyte-derived macrophages of 13 male healthy subjects


title: Baseline macrophages from subject without atherosclerosis, pair A.

description: Gene expression profile


title: humanMDM_Healthy_Particles

description: see Affymetrix standard protocol


title: humanMDM_Healthy_untreated

description: see Affymetrix standard protocol

data_processing: Data were normalized, and transcript-specific gecdne expression levels were calculated, using gcrma (Wu et al., J. Comput. Biol., 12, 882-93, 2005; Wu et al., Nat. Biotechnol. 22, 656-8,, 2004) or rma (Bolstad et al., Bioinformatics, 19, 185-93, 2003; Irizarry et al., Nucleic Acids Res., 31, e15, 2003) as implemented in R (R Development Core Team, R foundation for statistical computing, Vienna, 2007) and Bioconductor (Gentleman et al., Genome Biology, 5, R80, 2004). Differentially expressed genes were identified using the permutation-based method of Tusher et al. (Proc. Natl. Acad. Sci. USA, 98, 5116-21, 2001) (sam) as implemented in the "samr" R package, using the median false discovery rate over 100 data permutations as a measure for statistical significance.


title: control (unstimulated) cells, biological rep1

description: Gene expression data


title: cells stimulated with lipoprotein prep 3, biological rep3

description: Gene expression data


title: humanMDM_COPD_untreated

description: see Affymetrix standard protocol

tag: monocyte-derived macrophages of 13 male COPD patients


title: Alternative or M2 activated macrophages, biological rep3 HG-U133A

status: Public on Jul 10 2006

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

country: United Kingdom

institute: University of Surrey

description: Monocytes

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 series. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RNA using Bioconductor's R.

source_name: Blood

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

growth_protocol: RPMI 1640 20%FCS 100 ng/ml M-CSF

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

treatment_protocol: mature macrophages supplemented with 20 ng/ml IL-4

tag: ALternative or M2 activated macrophages, biological rep3


title: classical or M1 activated macrophages, biological rep3 HG-U133A

description: Monocytes

treatment_protocol: mature macrophages supplemented with 20 ng/ml IFN-g+ 100 ng/ml LPS


title: cells stimulated with lipoprotein prep 2, biological rep1

description: Gene expression data


title: classical or M1 activated macrophages, biological rep1 HG-U133A

description: Monocytes

growth_protocol: mature macrophages supplemented with 20 ng/ml IFN-g+ 100 ng/ml LPS


title: Macrophage at 7 days, biological rep3 HG-U133A

description: Monocytes

treatment_protocol: monocytes stimulated for 7 days with 100 ng/ml M-CSF

tag: Macrophage at 7 days, biological rep3


title: humanMDM_COPD_LPS

description: see Affymetrix standard protocol


title: Alternative or M2 activated macrophages, biological rep1 HG-U133A

description: Monocytes

tag: ALternative or M2 activated macrophages, biological rep1


title: classical or M1 activated macrophages, biological rep2 HG-U133A

description: Monocytes


title: Alternative or M2 activated macrophages, biological rep2 HG-U133A

description: Monocytes

tag: ALternative or M2 activated macrophages, biological rep2


title: Monocyte at 3 days, biological rep3 HG-U133A

description: Monocytes

treatment_protocol: monocytes stimulated for 3 days with 100 ng/ml M-CSF

tag: Monocyte at 3 days, biological rep3


title: humanMDM_COPD_Particles

description: see Affymetrix standard protocol


title: Monocyteat 3 days, biological rep2 HG-U133A

description: Monocytes

tag: Monocyteat 3 days, biological rep2


title: Monocyte at T0, biological rep3 HG-U133A

description: Monocytes

growth_protocol: Cells were cultured in Petriperm dishes tomimic circulating conditions

treatment_protocol: freshly isolated monocytes

tag: Monocyte at T0, biological rep3


title: Monocyte at 3 days, biological rep1 HG-U133A

description: Monocytes

tag: Monocyte at 3 days, biological rep1


title: Macrophage at 7 days, biological rep2 HG-U133A

description: Monocytes

tag: Macrophage at 7 days, biological rep2


title: Monocyte at T0, biological rep2 HG-U133A

description: Monocytes

tag: Monocyte at T0, biological rep2


title: Baseline macrophages from subject without atherosclerosis, pair E.

description: Gene expression profile


title: Macrophage at 7 days, biological rep1 HG-U133A

description: Monocytes

tag: Macrophage at 7 days, biological rep1


title: Foam cells from subject without atherosclerosis, pair A.

description: Gene expression profile


title: cells stimulated with lipoprotein prep 1, biological rep1

description: Gene expression data


title: Monocyte at T0, biological rep1 HG-U133A

description: Monocytes

tag: Monocyte at T0, biological rep1