title: CNT3

description: cell culture extract


title: CNT2

status: Public on Dec 13 2011

type: RNA

city: Memphis

first: Jena

middle: J

last: Steinle

state: TN

address: 930 Madison Ave, Suite 768

department: Ophthalmology

country: USA

institute: University of Tennessee Health Science Center

description: cell culture extract

hyb_protocol: Following fragmentation, 15 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed in Expression Console using Affymetrix default analysis settings for RMA quantile normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: non-treated REC, 24 hr

label_protocol: Biotinylated cDNA were prepared from 200 ng total RNA according to the standard whole transcript labeling protocol for Affymetrix ST arrays (Ambion WT Expression Kit Manual, 2010, Ambion; GeneChip Whole Transcript Sense Target Labeling Kit  Manual, 2007, Affymetrix).

growth_protocol: Human retinal endothelial cells were grown in M131 medium until 90% confluence.

extract_protocol: Extraction of total RNA was performed using RNA Stat-60, according to the manufacturer's instructions. RNA purity was checked by OD260/280 readings, and RNA integrity was checked using Agilent Bioanalyzer capillary electrophoresis profiles.

treatment_protocol: 4 dishes remained untreated. 4 dishes treated with 1mM carboplatin for 24 hours.  All cells collected into Trizol.

tag: cell type

value: retinal endothelial cells

tag: treatment


title: CNT1

description: cell culture extract


title: NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells [Donor3, iRBCs, replicate1]

status: Public on Dec 01 2011

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

description: Gene expression data from RNA extracted from NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells

hyb_protocol: Standard Affymetrix hybridisation protocol for Human Gene Array 1.0 ST.

scan_protocol: Standard Affymetrixscanning protocol for Human Gene Array 1.0 ST with the Affymetrix 3000 7G Scanner system.

data_processing: RMA-16 normalization with Genespring 11 software

source_name: NK cells

label_protocol: Standard Affymetrix labeling protocol for Human Gene Array 1.0 ST.

growth_protocol: P. falciparum laboratory strain 3D7 was maintained in continuous culture as described elsewhere (Trager and Jensen 2005) and frequently tested for mycoplasma contamination by PCR. Parasites were constantly synchronized with 5% sorbitol and mature schizont-infected erythrocytes (iRBCs) were harvested by magnetic cell sorting with LD columns (MACS; Miltenyi Biotec, Berg. Gladbach, Germany). Schizonts` purity (>90%) and red blood cell membrane integrity were observed by giemsa stain.

extract_protocol: Total cellular RNA was isolated from the enriched NK cells with RNeasy Mini Kit (Qiagen) .

treatment_protocol: Venous blood was collected, and immediately processed, from 3 healthy adults with no prior exposure to plasmodium parasites. Samples taken into 9ml ammonium heparine tubes (16I.U. heparin/ml blood; S. Monovette) were diluted 1:1 with RPMI 1640 (Sigma Aldrich) and Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation with Ficoll Paque TM plus (GE Healthcare). Cells were washed twice with FBS 2% in RPMI 1640, resuspended in culture medium (RPMI 1640) containing 5% atologous serum, 1% 100X PenStrep (Invitrogen) and 2mM L-Glutamine (Invitrogen), transferred to 24-wells flat bottomed plates (Nunc) and incubated at 37ºC and 5%CO2. Mononuclear cells from donors 1 and 2 were incubated under 4 different conditions: in culture medium alone (untreated); with a mixture of IL12 and IL18 (Peprotech and MBL; 200ng/106 cells each) as well as with schizont infected erythrocytes (iRBCs) or uninfected erythrocytes (uRBCs) added at a ratio of 3 RBCs for each mononuclear cell. PBMCs from donor 3 were incubated under two different conditions: with iRBCs and with culture medium (untreated).  Co-cultures were kept at 37ºC and 5% CO2 for 24 hours. After the incubation time, NK cells were isolated from each differentially treated PBMCs, checked for purity and submitted to RNA extraction.

tag: donor

value: Donor 3

value: P. falciparum infected red blood cells

tag: replicate


title: NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells [Donor3, iRBCs, replicate2]


title: NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells [Donor2, iRBCs, replicate3]

value: Donor 2


title: NK cells whithin PBMCs that were co-incubated with uninfected red blood cells [Donor2, uRBCs, replicate3]

description: Gene expression data from RNA extracted from NK cells whithin PBMCs that were co-incubated with uninfected red blood cells

value: uninfected red blood cells


title: NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells [Donor3, iRBCs, replicate3]


title: NK cells whithin PBMCs that were co-incubated with a mix of IL12 plus IL18 [Donor2, ILmix, replicate3]

description: Gene expression data from RNA extracted from NK cells whithin PBMCs that were co-incubated with a mix of IL12 plus IL18

value: IL12 plus IL18


title: NK cells whithin PBMCs that were incubated in culture medium only (no stimulus) [Donor2, untreated, replicate2]

description: Gene expression data from RNA extracted from NK cells whithin PBMCs that were incubated in culture medium only (no stimulus)

value: untreated


title: CAF rep2

city: Galveston

first: Celia

last: Chao

state: TX

address: 301 University Boulevard

department: Surgery

institute: Univ TX Medical Branch

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133_Plus_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner G3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: CAF

label_protocol: Biotinylated cRNA were prepared with Enzo's BioArray Synthesis Kit (PN 42406-10) from >7 ug total RNA .

growth_protocol: DMEM, 10% FCS, 1% ITS, 1% nonessential amino acids (Invitrogen), and 1% penicillin-streptomycin

extract_protocol: Total RNA was Extracted with Ambion's RNAqueous (Cat# 1911) according to the manufacturer's instructions.

tag: disease state

value: colon cancer stage II

value: carcinoma associated fibroblast


title: NK cells whithin PBMCs that were incubated in culture medium only (no stimulus) [Donor3, untreated, replicate2]


title: CAF rep1


title: NK cells whithin PBMCs that were incubated in culture medium only (no stimulus) [Donor2, untreated, replicate1]


title: NK cells whithin PBMCs that were incubated in culture medium only (no stimulus) [Donor3, untreated, replicate1]


title: NK cells whithin PBMCs that were co-incubated with a mix of IL12 plus IL18 [Donor2, ILmix, replicate2]


title: NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells [Donor2, iRBCs, replicate2]


title: NK cells whithin PBMCs that were co-incubated with a mix of IL12 plus IL18 [Donor1, ILmix, replicate3]

value: Donor 1


title: NK cells whithin PBMCs that were co-incubated with uninfected red blood cells [Donor1, uRBCs, replicate3]


title: NK cells whithin PBMCs that were co-incubated with uninfected red blood cells [Donor2, uRBCs, replicate2]


title: NK cells whithin PBMCs that were incubated in culture medium only (no stimulus) [Donor1, untreated, replicate3]


title: NK cells whithin PBMCs that were co-incubated with a mix of IL12 plus IL18 [Donor2, ILmix, replicate1]


title: NK cells whithin PBMCs that were co-incubated with uninfected red blood cells [Donor2, uRBCs, replicate1]


title: NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells [Donor1, iRBCs, replicate3]


title: NK cells whithin PBMCs that were incubated in culture medium only (no stimulus) [Donor2, untreated, replicate3]


title: NK cells whithin PBMCs that were incubated in culture medium only (no stimulus) [Donor3, untreated, replicate3]


title: NK cells whithin PBMCs that were incubated in culture medium only (no stimulus) [Donor1, untreated, replicate2]


title: NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells [Donor2, iRBCs, replicate1]


title: NK cells whithin PBMCs that were co-incubated with uninfected red blood cells [Donor1, uRBCs, replicate2]


title: NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells [Donor1, iRBCs, replicate2]


title: NK cells whithin PBMCs that were co-incubated with a mix of IL12 plus IL18 [Donor1, ILmix, replicate2]


title: NK cells whithin PBMCs that were incubated in culture medium only (no stimulus) [Donor1, untreated, replicate1]


title: NK cells whithin PBMCs that were co-incubated with a mix of IL12 plus IL18 [Donor1, ILmix, replicate1]


title: NK cells whithin PBMCs that were co-incubated with uninfected red blood cells [Donor1, uRBCs, replicate1]


title: MAS5_HMVEC control rep6

status: Public on Oct 11 2011

city: Toronto

first: Philip

last: Marsden

state: ON

address: Li Ka Shing Knowledge Institute, St. Michael's Hospital 209 Vicotria St, rm 526

department: Faculty of Medicine

country: Canada

institute: University of Toronto

description: Gene expression data from untreated human microvascular endothelial cells

hyb_protocol: According to the standard protocol of Affymetrix

data_processing: Raw signal intensities were pre-processed using 13 different computational methods.  The base affy package was used to compute MAS5.0, RMA, dChip.PM, and dChip.PM-MM summary expression measures.  GCRMA, PLIER, VSN, mgMOS, mmgMOS, q.FARMS, l.FARMS, and the method of Choe et al, were computed using Bioconductor packages or packages made freely available by the package developers.  PDNN summary expression measures were determined using PerfectMatch v2.3.  All pre-processing methods were used in their default implementations.  Probe sets were then filtered to remove those called 'absent' by the affy package, and then submitted to Cyber-T for statistical analysis.

source_name: primary dermal neonatal microvascular endothelial cells, untreated

growth_protocol: Primary human dermal neonatal microvascular endothelial cells (HMVEC) isolated from a single donor were maintained in EGM-2MV medium (Lonza) and grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total cellular RNA was purified by cesium chloride ultracentrifugation, as described previously (Chirgwin et al, 1979, Biochemistry)

treatment_protocol: Post-confluent cells were treated with 10 fM Shiga toxin-2 (Stx2) for 24 and compared to untreated cells

tag: gender

value: male


title: MAS5_HMVEC - Shiga toxin rep3

description: Gene expression data from human microvascular endothelial cells treated with Shiga toxin

scan_protocol: According to the standard protocol of Affymetrix

source_name: primary dermal neonatal microvascular endothelial cells, 10 fM Shiga toxin, 24 h


title: UKY-29_5

status: Public on Sep 01 2011

city: Lexington

first: Esther

middle: P

last: Black

state: KY

address: 789 S Limestone

department: Pharmaceutical Sciences

institute: University of Kentucky

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) 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: NSCLC cell line

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

growth_protocol: NSCLC cell lines were cultured for 3d in 10% serum-containing RPMI 1640 with no drug treatment.

extract_protocol: RNA was extracted using Qiagen Rneasy column preparation

value: non small cell lung cancer cell (NSCLC)

tag: erlotinib sensitivity

value: No


title: MAS5_HMVEC control rep5

label_protocol: According to the standard protocol of Affymetrix


title: MAS5_HMVEC - Shiga toxin rep5


title: MAS5_HMVEC - Shiga toxin rep1


title: PC9

value: Yes


title: MAS5_HMVEC - Shiga toxin rep2


title: MAS5_HMVEC - Shiga toxin rep6


title: PC92-4val


title: Macrophages where c-Myc activation was blocked by using c-Myc chemical inibitors, rep 2

status: Public on Sep 16 2011

city: Rozzano

first: Massimo

last: Locati

state: MILAN

address: Via Manzoni, 113

department: Department of Translational Medicine of the University of Milan Faculty of Medicine, IRCCS Istituto Clinico Humanitas

country: Italy

institute: Istituto Clinico Humanitas

description:
Donor_2 MycI_rep2
R743_N6

hyb_protocol: Following fragmentation, 2.7 ug of cDNA were hybridized for 16 hr at 45C on Human Genome HuGene 1.0 ST . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression dataset was obtained by means of Partek software version 6.3, with RMA method.

source_name: Human macrophages where c-Myc activation was blocked by using c-Myc chemical inibitors

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

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

tag: source tissue

value: normal donor buffy coats

tag: source cell type

value: freshly isolated monocytes

value: macrophages


title: MAS5_HMVEC control rep1


title: Alternative activated macrophages (M2) rep 3

description:
Donor_3 M2_rep3
R743_N8

source_name: Alternative activated macrophages (M2)


title: Alternative activated macrophages (M2) rep 2

description:
Donor_2 M2_rep2
R743_N5


title: UKY29-3


title: MAS5_HMVEC control rep3


title: Resting fully differentiated macrophages (7 days of culture), rep 1

description:
Donor_1 M0_rep1
R743_N1

source_name: Resting fully differentiated human macrophages (7 days of culture)


title: UKY-29_6


title: UKY-29_4


title: Alternative activated macrophages (M2) rep 1

description:
Donor_1 M2_rep1
R743_N2


title: NK cells whithin PBMCs that were co-incubated with P. falciparum infected red blood cells [Donor1, iRBCs, replicate1]


title: Resting fully differentiated macrophages (7 days of culture), rep 3

description:
Donor_3 M0_rep3
R743_N7


title: Macrophages where c-Myc activation was blocked by using c-Myc chemical inibitors, rep 3

description:
Donor_3 MycI_rep3
R743_N9


title: PC-9_10


title: MAS5_HMVEC - Shiga toxin rep4


title: Resting fully differentiated macrophages (7 days of culture), rep 2

description:
Donor_2 M0_rep2
R743_N4


title: PC-9_9


title: PC-9_8


title: MAS5_HMVEC control rep4


title: Macrophages where c-Myc activation was blocked by using c-Myc chemical inibitors, rep 1

description:
Donor_1 MycI_rep1
R743_N3


title: H3255_2


title: H1975-7


title: H32551-Dec


title: H1975G


title: H1975A


title: H1650-8


title: H1650B


title: H1975p20


title: H460A


title: H1650-H


title: H460-3


title: H460-C


title: H460-5


title: H460-D


title: H1650p8


title: A549p6


title: A549p4


title: H1975C


title: H3255_3


title: H3255_1


title: H358


title: H1650A


title: H1975F


title: H460-2


title: H1650C


title: H1975-6


title: A549p5


title: H1975p19


title: H460-B


title: H460-1


title: A549p3


title: A549B


title: A549C


title: A549-3.05


title: A549p2


title: Cervical cancer cell line CaLo_rep1

status: Public on Aug 01 2011

city: Mexico City

first: Jaime

last: Berumen

address: Dr. Balmis #148 Col. Doctores

department: Departamento de Medicina Experimental

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: RMA default expression value derived from Affymetrix Expression Console software

hyb_protocol: Following fragmentation, ssDNA were hybridized for 16 hr at 45C and 60 rpm on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 protocol FS450_0007

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) with GeneChip Scanner 3000

data_processing:
Microarrays were normalized using the RMA algorithm (Robust Multichip Average) in the Affymetrix Expression Console. The analysis was done at Gene Level Default: RMA-Sketch
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

label: Biotin

source_name: Cervical cancer cell line

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cell lines were grown according to standard conditions.

tag: cell line

value: Calo

value: Female


title: Cervical cancer cell line HeLa_rep1

value: Hela


title: Cervical cancer cell line CaSki_rep1

value: Caski


title: Human CD4+ central memory T cells (1)

status: Public on Aug 04 2011

city: Sydney

first: Santi

last: Suryani

state: NSW

address: 384 Victoria Street, Darlinghurst

department: Immunology and Inflammation

country: Australia

institute: Garvan Institute of Medical Research

hyb_protocol: Affymetrix Hu133Plus2 hybridisation protocol was strictly followed

scan_protocol: Affymetrix Hu133Plus2 scanning protocol was strictly followed

data_processing: Data presented are ExpressionStat 5.0  data with no modifications as caculated by GCOS software

source_name: peripheral blood

label_protocol: Affymetrix Hu133Plus2 labelling protocol was strictly followed

growth_protocol: Unstimulated sample

extract_protocol: Trizol was used to extract the total RNA from each sample

treatment_protocol: Unstimulated sample


title: Cervical cancer cell line SiHa_rep1

value: Siha


title: Cervical cancer cell line CaSki_rep2


title: Cervical cancer cell line HeLa_rep2


title: Human CD4+ central memory T cells (2)


title: Cervical cancer cell line CaLo_rep2


title: endo cells, HHV-8 infected, rep3

city: Seattle

first: Lynn

middle: M

last: Amon

state: WA

address: 1100 Fairview, M1-C108

department: Division of Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4).

data_processing: Data were analyzed using aroma.affymetrix. Signal intensity was background corrected using the RMA algorithm and quantile normalized. Gene-level summaries were computed by fitting the data using the RMA probe-level model (RmaPlm).

source_name: TIME cells, HHV-8 infected

growth_protocol: Tert-immortalized dermal microvascular endothelial cells (TIME cells) are described in Venetsanakos et al (2002) and were maintained in EBM-2 bullet kits from Lonza

extract_protocol: TRizol (Invitrogen), DNase treatment and RNeasy Mini Kit (Qiagen).

treatment_protocol: TIME cells were HHV-8 or mock infected in the presence of polybrene for 3 hours and then the innoculum was washed off and the cells were overlayed with complete endothelial cell media. After 48 hours cells were harvested.

value: tert-immoralized microvascular endothelial cells

tag: infection


title: endo cells, HHV-8 infected, rep2

scan_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4).


title: endo cells, mock infected, rep3

source_name: TIME cells, mock infected

label_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4).

value: mock


title: Cervical cancer cell line SiHa_rep2


title: Control5

status: Public on Jun 23 2011

city: STRASBOURG

first: Jean-Nicolas

last: SCHICKEL

address: 15, rue rené descartes

country: France

institute: CNRS UPR9021

description:
Gene expression data from human sorted B cells.
T05
JLP_T05_U133_2.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip human genome U133 plus 2.0 (with probe sets representing 38,572 UniGene clusters) according to the manufacturer’s instructions. After hybridization and washings, arrays were stained with PE-conjugated streptavidin (10 μg/ml) before scanning.

data_processing:
Raw Affymetrix data were analyzed using R (R Development Core Team, 2008; The Comprehensive R Archive Network: http://cran.r-project.org/) and Bioconductor (Bioconductor: http://www.bioconductor.org/) softwares. The quality of the 27 Affymetrix genechips and RNA was assessed using the Bioconductor AffyPLM and simpleaffy packages, with qc, AffyRNAdeg, fitPLM, image, RLE and NUSE functions. For normalization and background correction.  Raw values were pre-processed with RMA or GCRMA (library simpleAffy).
The Sample data table shows genes that are considered as expressed by affy (P) at least in one of the patients and controls, thus, reporting ~65% of the  data rows in the U133 Plus 2.0 Array.

source_name: Human sorted B cells

treatment_protocol: Peripheral blood was drawn into heparin-containing sterile tubes and peripheral blood mononuclear cells were prepared by Ficoll (Amersham) density gradient centrifugation for immediate use. B cells were labeled with a biotin anti-CD19 monoclonal antibody (HIB19 clone, Pharmingen) at 4°C and revealed by phycoerythrin-labelled streptavidin (Biomeda) before immediate B cell sorting with high speed cell sorter (FACS Diva, Beckton-Dickinson).

tag: individual

value: control

tag: tissue

value: blood

value: Sorted B cell


title: Human CD4+ naïve T cells (1)


title: Control10

description:
Gene expression data from human sorted B cells.
T10
JLP_T10_U133_2.CEL


title: Control6

description:
Gene expression data from human sorted B cells.
T06
JLP_T06_U133_2.CEL


title: Control8

description:
Gene expression data from human sorted B cells.
T08
JLP_T08_U133_2.CEL


title: endo cells, mock infected, rep1


title: Control9

description:
Gene expression data from human sorted B cells.
T09
JLP_T09_U133_2.CEL


title: endo cells, mock infected, rep2


title: Human CD4+ effector memory T cells (1)


title: endo cells, HHV-8 infected, rep1


title: Control4

description:
Gene expression data from human sorted B cells.
T04
JLP_T04_U133_2.CEL


title: Human CD4+ effector memory T cells (2)


title: Human CD4+ CXCR5+ T cells (2)


title: Control2

description:
Gene expression data from human sorted B cells.
T02
JLP_T02_U133_2.CEL


title: Human CD4+ naïve T cells (2)


title: Human CD4+ CXCR5+ T cells (1)


title: Control3

description:
Gene expression data from human sorted B cells.
T03
JLP_T03_U133_2_2.CEL


title: Lupus neutrophil, 015

status: Public on Jun 22 2011

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description:
LupusNeutro015
Gene expression data from lupus neutrophils.

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

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

data_processing: The data were analyzed using the GenePattern pipeline: the RMA method and Human Entrez Gene custom CDF annotation version 10 were used for the normalization, and Combat for batch correction.

source_name: Neutrophil from lupus patient

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

extract_protocol: Total RNA was isolated with Tri-pure (Roche), and further purified and concentrated using an Rneasy kit (Qiagen).

value: peripheral blood

value: neutrophils

value: lupus


title: Lupus LDG, 7

description:
LupusLDG7
Gene expression data from lupus LDGs.

source_name: LDG from lupus patient

value: low-density granulocytes


title: Lupus LDG, 006r

description:
LupusLDG006r
Gene expression data from lupus LDGs.


title: Lupus neutrophil, 11

description:
LupusNeutro11
Gene expression data from lupus neutrophils.


title: Lupus LDG, 8

description:
LupusLDG8
Gene expression data from lupus LDGs.


title: Lupus neutrophil, 007

description:
LupusNeutro007
Gene expression data from lupus neutrophils.


title: Healthy control neutrophil, 29

description:
ControlNeutro29
Gene expression data from healthy control neutrophils.

source_name: Control neutrophil from healthy human

value: healthy


title: Healthy control neutrophil, 32

description:
ControlNeutro32
Gene expression data from healthy control neutrophils.


title: Lupus neutrophil, 009

description:
LupusNeutro009
Gene expression data from lupus neutrophils.


title: Lupus neutrophil, 011

description:
LupusNeutro011
Gene expression data from lupus neutrophils.


title: Lupus neutrophil, 21

description:
LupusNeutro21
Gene expression data from lupus neutrophils.


title: Healthy control neutrophil, 31

description:
ControlNeutro31
Gene expression data from healthy control neutrophils.


title: Healthy control neutrophil, 18

description:
ControlNeutro18
Gene expression data from healthy control neutrophils.


title: Lupus LDG, 008r

description:
LupusLDG008r
Gene expression data from lupus LDGs.


title: Healthy control neutrophil, 002

description:
ControlNeutro002
Gene expression data from healthy control neutrophils.


title: Healthy control neutrophil, 005

description:
ControlNeutro005
Gene expression data from healthy control neutrophils.


title: Healthy control neutrophil, 001

description:
ControlNeutro001
Gene expression data from healthy control neutrophils.


title: Lupus neutrophil, 2

description:
LupusNeutro2
Gene expression data from lupus neutrophils.


title: Control1

description:
Gene expression data from human sorted B cells.
T01
JLP_T01_U133_2.CEL


title: Healthy control neutrophil, 004

description:
ControlNeutro004
Gene expression data from healthy control neutrophils.


title: Healthy control neutrophil, 003

description:
ControlNeutro003
Gene expression data from healthy control neutrophils.


title: Lupus neutrophil, 23

description:
LupusNeutro23
Gene expression data from lupus neutrophils.


title: Lupus neutrophil, 013

description:
LupusNeutro013
Gene expression data from lupus neutrophils.


title: Lupus LDG, 014

description:
LupusLDG014
Gene expression data from lupus LDGs.


title: Lupus neutrophil, 9

description:
LupusNeutro9
Gene expression data from lupus neutrophils.


title: Lupus LDG, 010

description:
LupusLDG010
Gene expression data from lupus LDGs.


title: Lupus LDG, 10

description:
LupusLDG10
Gene expression data from lupus LDGs.


title: Lupus LDG, 1

description:
LupusLDG1
Gene expression data from lupus LDGs.


title: Lupus LDG, 12

description:
LupusLDG12
Gene expression data from lupus LDGs.


title: Lupus LDG, 012

description:
LupusLDG012
Gene expression data from lupus LDGs.


title: empty vector + T3 replicate 2

status: Public on May 10 2011

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: HepG2 cells stably transfected with empty vector treated with 100 nM T3 for 6h

hyb_protocol: The purified RNA was provided to the University of California, Davis, Cancer Center Gene Expression Resource for subsequent cDNA probe generation and hybridization to Affymetrix GeneChip Human Gene 1.0 ST microarrays (Affymetrix Incorporated, Santa Clara CA).

data_processing: The raw microarray data was normalized by the Robust Multichip Array (RMA) method using R software.

source_name: HepG2 cells

growth_protocol: HepG2 cells were maintained at 37°C in Dulbecco's Modified Eagle's Medium (DME) supplemented with 10% fetal bovine serum using bicarbonate buffer and a 5% CO2 atmosphere.

extract_protocol: The cells were harvested and the RNA was isolated using an RNeasy kit (Qiagen, Valencia CA).

treatment_protocol: The HepG2 transformant pools expressing ectopic wildtype THRA, THRB, an HCC-TR mutant (αΙ or βN), a RCCC-TR mutant (6α or 15β), or the empty plasmid control were treated with 100 nM T3 or with ethanol carrier alone for 6h in DMEM containing 10% hormone-stripped fetal bovine serum.

value: Hep G2

tag: sample type

value: empty vector

value: with 100 nM T3 for 6h


title: THRB 15b mutant + T3 replicate 2

description: HepG2 cells stably expressing RCCC-THRA mutant 15b treated with 100 nM T3 for 6h

scan_protocol: The purified RNA was provided to the University of California, Davis, Cancer Center Gene Expression Resource for subsequent cDNA probe generation and hybridization to Affymetrix GeneChip Human Gene 1.0 ST microarrays (Affymetrix Incorporated, Santa Clara CA).

tag: genotype

value: RCCC-THRA mutant 15b


title: empty vector + T3 replicate 3

label_protocol: The purified RNA was provided to the University of California, Davis, Cancer Center Gene Expression Resource for subsequent cDNA probe generation and hybridization to Affymetrix GeneChip Human Gene 1.0 ST microarrays (Affymetrix Incorporated, Santa Clara CA).


title: empty vector + T3 replicate 1


title: THRB bN mutant + T3 replicate 1

description: HepG2 cells stably expressing HCC-THRA mutant bN treated with 100 nM T3 for 6h

value: HCC-THRA mutant bN


title: THRB 15b mutant + vehicle replicate 2

description: HepG2 cells stably expressing RCCC-THRA mutant 15b treated with vehicle for 6h.

value: with vehicle for 6h


title: THRB bN mutant + T3 replicate 3


title: empty vector + vehicle replicate 1

description: HepG2 cells stably transfected with empty vector treated with vehicle for 6h.


title: THRA 6a mutant + T3 replicate 1

description: HepG2 cells stably expressing RCCC-THRA mutant 6a treated with 100 nM T3 for 6h.

value: RCCC-THRA mutant 6a

value: with 100 nM T3 for 6h.


title: empty vector + vehicle replicate 3


title: empty vector + vehicle replicate 2


title: THRA 6a mutant + T3 replicate 2


title: THRB 15b mutant + vehicle replicate 1


title: Untreated, replicate 3

status: Public on May 17 2011

city: SSF

first: Weiwei

last: Chen

address: 1st DNA Way

institute: Genentech

hyb_protocol: The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm. Arrays were washed and stained in a Fluidics station.

scan_protocol: The method for array scanning was provided by Affymetrix.  Arrays were scanned on an Affymetrix scanner.

data_processing: Data analysis was performed using the Affymetrix GeneChip Analysis software.

source_name: CCD-18Co, untreated

label_protocol: The method for preparation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.

growth_protocol: Colon fibroblasts were cultured in media plus 0.1% BSA.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit.

treatment_protocol: Colon fibroblasts CCD-18Co were stimulated with SHH (1 ug/ml) for 72 h.

value: colon fibroblasts


title: SHH treated, replicate 3

source_name: CCD-18Co, SHH treated

value: Sonic hedgehog homolog (SHH)


title: THRB bN mutant + vehicle replicate 2

description: HepG2 cells stably expressing HCC-THRA mutant bN treated with vehicle for 6h.


title: THRB bN mutant + vehicle replicate 3


title: THRA 6a mutant + vehicle replicate 3

description: HepG2 cells stably expressing RCCC-THRA mutant 6a treated with vehicle for 6h.


title: THRB 15b mutant + vehicle replicate 3


title: SHH treated, replicate 1


title: THRA 6a mutant + T3 replicate 3


title: Untreated, replicate 2


title: THRA 6a mutant + vehicle replicate 2


title: Untreated, replicate 1


title: THRB bN mutant + vehicle replicate 1


title: SHH treated, replicate 2


title: THRB 15b mutant + T3 replicate 1


title: THRB 15b mutant + T3 replicate 3


title: THRB bN mutant + T3 replicate 2


title: THRA aI mutant + vehicle replicate 3

description: HepG2 cells stably expressing HCC-THRA mutant al treated with vehicle for 6h.

value: HCC-THRA mutant al


title: THRA aI mutant + T3 replicate 3

description: HepG2 cells stably expressing HCC-THRA mutant al treated with 100 nM T3 for 6h


title: THRB wt + vehicle replicate 2

description: HepG2 cells stably expressing wild-type THRB and treated with vehicle for 6h.

value: wild-type THRB and


title: THRB wt + vehicle replicate 1


title: THRA wt + vehicle replicate 1

description: HepG2 cells stably expressing wild-type THRA and treated with vehicle for 6h.

value: wild-type THRA and


title: THRA aI mutant + vehicle replicate 1


title: THRA aI mutant + vehicle replicate 2


title: THRA wt + vehicle replicate 3


title: THRA aI mutant + T3 replicate 1


title: THRA aI mutant + T3 replicate 2


title: THRA 6a mutant + vehicle replicate 1


title: THRA wt + T3 replicate 3

description: HepG2 cells stably expressing wild-type THRA and treated with 100 nM T3 for 6h


title: THRA wt + T3 replicate 1


title: THRB wt + T3 replicate 5

description: HepG2 cells stably expressing wild-type THRB and treated with 100 nM T3 for 6h


title: THRB wt + vehicle replicate 3


title: THRB wt + T3 replicate 3


title: THRA wt + vehicle replicate 2


title: THRB wt + T3 replicate 4


title: COPD7

status: Public on Apr 18 2011

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: alveolar macrophages isolated from bronchoalveolar lavage fluid

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: GeneSpring 7.3 GC-RMA algorithm

source_name: alveolar macrophage

label_protocol: standard Affymetrix protocol

extract_protocol: Qiagen RNeasy Kit according to manufacturer's protocol

value: alveolar macrophage

tag: disease status

value: COPD patient


title: control8

value: control patient


title: control2


title: THRA wt + T3 replicate 2


title: control3


title: COPD4


title: COPD5


title: COPD monocyte

description: Peripheral blood samples were collected from 5 COPD patients and monocytes were isolated using CD14+ magnetic beads.

source_name: peripheral blood monocyte

value: peripheral blood monocyte

tag: pooled rna

value: from 5 patients


title: COPD8

tag: cell type


title: control5


title: control monocyte

description: Peripheral blood samples were collected from 5 healthy control patients and monocytes were isolated using CD14+ magnetic beads.


title: Sum190-CG1 (HuGene-1_0)

status: Public on Apr 12 2011

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: mRNA expression after treatment with 5µM CG-1521 for 48h

hyb_protocol: Standard Affymetrix WT protocol for Gene 1.0 ST arrays

data_processing: Raw CEL files were processed using Affymetrix Expression Console Software using RMA

source_name: SUM190PT 5µM CG-1521

label_protocol: Total RNA was biotin labeled using the NuGEN pico amplification protocol

growth_protocol: SUM190PT cells were grown in Ham's F-12 media supplemented with 5 µg/mL insulin, 1 µg/mL hydrocortisone, 10 mM HEPES, 5mM Ethanolamine, 5µg/mL Transferrin, 10nM Triiodo Thyronine, 50nM Sodium Selenite, 1g/L Bovine Serum Albumin and Antibiotic/Antimycotic at 37° with 5% CO2 and 85% Humidity.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Center for Functional Genomics at State University of New York at Albany (Rensselaer, NY, USA)

treatment_protocol: SUM190PT cells were plated at 1.5 x 10^6 cells per 150 x 25mm dish with 25mL of growth media containing 2%FBS and allowed to adhere for 24h. The media in each plate was then replaced with 25mL fresh media without FBS. After another 24h, each treatment was prepared at 6x concentration, so that 5mL of treatment solution was added to the 25mL growth media.

tag: er

value: mut (Q317X)


title: Sum190-CG2 (HuGene-1_0)

scan_protocol: Standard Affymetrix WT protocol for Gene 1.0 ST arrays


title: Sum190-E1 (HuGene-1_0)

description: mRNA expression after treatment with 10nM 17β-Estradiol for 48h

source_name: SUM190PT 10nM 17β-Estradiol


title: control1


title: Sum190-E+CG3 (HuGene-1_0)

description: mRNA expression after treatment with 10nM 17β-Estradiol and 5µM CG-1521 for 48h

source_name: SUM190PT 10nM 17β-Estradiol-with 5µM CG-1521


title: COPD1


title: Sum190-control1 (HuGene-1_0)

description: mRNA expression after treatment with vehicle (ethanol and DMSO) for 48h

source_name: SUM190PT Vehicle CTRL


title: Sum149-CG3 (HuGene-1_0)

description: mRNA expression after treatment with 7.5µM CG-1521 for 48h

growth_protocol: SUM149PT cells were grown in Ham's F-12 media with 5% fetal bovine serume supplemented with 5 µg/mL insulin, 1 µg/mL hydrocortisone, 10 mM HEPES and Antimycotic/Antibiotic at 37°C with 5%CO2 and 85% humidity.

treatment_protocol: SUM149PT cells were plated at 1.5 x 10^6 cells per 150 x 25mm dish with 25mL of growth media, and allowed to adhere for 48h prior to treatment. The media in each plate was replaced with 25mL fresh media containing the drug treatment.

value: mut (M237I)


title: Sum190-control3 (HuGene-1_0)


title: Sum190-E+CG2 (HuGene-1_0)


title: Sum190-E+CG1 (HuGene-1_0)


title: Sum190-E3 (HuGene-1_0)


title: Sum190-CG3 (HuGene-1_0)


title: Sum149-E+CG2 (HuGene-1_0)

description: mRNA expression after treatment with 10nM 17β-Estradiol and 7.5µM CG-1521 for 48h

source_name: SUM149PT 10nM 17β-Estradiol-with 7.5µM CG-1521


title: Sum149-E+CG3 (HuGene-1_0)


title: Sum149-CG2 (HuGene-1_0)


title: Sum149-E+CG1 (HuGene-1_0)


title: Sum190-control2 (HuGene-1_0)


title: Sum190-E2 (HuGene-1_0)


title: Sum149-E3 (HuGene-1_0)

source_name: SUM149PT 10nM 17β-Estradiol


title: Sum149-E1 (HuGene-1_0)


title: Sum149-control1 (HuGene-1_0)

source_name: SUM149PT Vehicle CTRL


title: Sum149-control2 (HuGene-1_0)


title: Sum149-E2 (HuGene-1_0)


title: Sum149-CG1 (HuGene-1_0)


title: Sum149-control3 (HuGene-1_0)


title: MM3 T-cell

status: Public on Mar 24 2011

city: Stockholm

first: Håkan

last: Mellstedt

department: Oncology & Pathology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: After fragmenting, the labeled cRNA was hybridized to HG-U133 oligonucleotide array chips (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: The arrays were then washed and stained with Streptavidin-Phycoerythrin (SAPE) (Molecular Probes Inc., Eugene, OR, USA) in an Affymetrix fluidics station. The arrays were then scanned in an Affymetrix scanner and the expression values for each probe set were estimated using the Affymetrix Microarray Suite Software (MAS v5.0).

data_processing: The signal values were imported into the GeneSpring 7.0 software tool (Silicon Genetics, Redwood City, CA, USA) to find out genes with significant differential expression. Quantile normalization with regard to 22 448 genes, PM probes and median polishing were utilized.

source_name: T-Cell from Multiple Myeloma

label_protocol: First and second strand cDNA was synthesized from 5 μg high-quality, purified total RNA using a T7-(dT)24 primer and Invitrogen Life Technologies SuperScript Choice system kit (Invitrogen). Biotin-labeled cRNA was then synthesized using ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Diagnostics Inc., Farmingdale, NY) according to the manufacturer’s instruction.

extract_protocol: Total RNA was extracted from freshly purified T cells using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) followed by removal of genomic DNA using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The purity and quality of all extracted RNA samples were confirmed by measuring A260/A280 ratio and separation on agarose gel to ensure RNA integrity prior to microarray analyses

value: Multiple Myeloma

value: Male

tag: age

value: Purified T-cell


title: N3 T-cell

source_name: T-Cell from Healthy donors

value: Healthy


title: N2 T-cell


title: M3 T-cell

source_name: T-Cell from Chronic Lymphatic Leukemia

value: Chronic Lymphocytic Leukemia

value: Female


title: N1 T-cell


title: MM2 T-cell


title: NK_Donor_12

status: Public on Mar 08 2011

city: Little Rock

first: Tarun

middle: Kumar

last: Garg

state: AR

address: 4301 W Markham St

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciences

description:
HD_NK_12
Gene expression data from donor non-expanded NK cells

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.  Scanned images were processed using the GCOS v1.4 software.

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: enriched non-expanded natural killer cells from healthy donor

label_protocol: Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).

growth_protocol:
Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
NK Enrichment Protocol:  NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells.  For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.

extract_protocol: Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).

value: Donor 12

value: natural killer cells

tag: nkc state

value: non-expanded


title: ENK_Donor_18

description:
HD_ENK_18
Gene expression data from donor expanded NK cells

source_name: enriched expanded natural killer cells from healthy donor

value: Donor 18

value: expanded


title: MM1 T-cell

tag: disease state


title: ENK_Donor_19

description:
HD_ENK_19
Gene expression data from donor expanded NK cells

value: Donor 19


title: ENK_Donor_12

description:
HD_ENK_12
Gene expression data from donor expanded NK cells


title: M1 T-cell

tag: gender


title: NK_Donor_19

description:
HD_NK_19
Gene expression data from donor non-expanded NK cells


title: NK_Donor_18

description:
HD_NK_18
Gene expression data from donor non-expanded NK cells


title: NK_Donor_14

description:
HD_NK_14
Gene expression data from donor non-expanded NK cells

value: Donor 14


title: M2 T-cell


title: ENK_Donor_17

description:
HD_ENK_17
Gene expression data from donor expanded NK cells

value: Donor 17


title: ENK_Donor_13

description:
HD_ENK_13
Gene expression data from donor expanded NK cells

value: Donor 13


title: ENK_Donor_16

description:
HD_ENK_16
Gene expression data from donor expanded NK cells

value: Donor 16


title: ENK_Donor_11

description:
HD_ENK_11
Gene expression data from donor expanded NK cells

value: Donor 11


title: ENK_Donor_14

description:
HD_ENK_14
Gene expression data from donor expanded NK cells


title: NK_Donor_13

description:
HD_NK_13
Gene expression data from donor non-expanded NK cells


title: NK_Donor_17

description:
HD_NK_17
Gene expression data from donor non-expanded NK cells


title: Control PB C104

status: Public on Mar 01 2011

city: Prague 2

first: Vojtěch

last: Kulvait

address: U Nemocnice 5

department: Institute of Pathological Physiology

country: Czech Republic

institute: Charles University in Prague - 1st Faculty of Medicine

hyb_protocol: RNA was proceeded according to Affymetrix 3‘ – IVT Express Kit protocol. cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were processed using the Agilent GeneArray Scanner 3000 7G system in the Genomics Facility of the New York University Cancer Institute.

data_processing: Data were summarized using GeneSpring implementation of RMA algorithm and expression data were normalized on median of control samples.

source_name: Control PB C104

label_protocol: RNA was proceeded according to Affymetrix 3‘ – IVT Express Kit protocol. cDNA were prepared using the recommended Affymetrix reagents and kits.

growth_protocol: Peripheral blood from B-CLL patients as well as from healthy donors were firstly separated by Ficoll gradient (GE Healthcare), obtained peripheral mononuclear cells (PBMC). PBMC were shortly incubated in IMDM (Isove’s Modified Dulbecco’s) medium supplemented with 10% fetal calf serum, 1% non essential amino acids, 1% antibiotics. PBMCs from healthy donors were separated by autoMACS Pro Separator and anti FITC microbeads, CD19 human FITC antibody were used.

extract_protocol: Total RNA was extracted by TRIzol Reagent following the manufacturer protocol.   Precipitation by isopropyl alcohol (0.5mL per 1mL TRIzol) was done over night. As carrier of the aqueous phase the Acrylamide was used. The RNA pellets were washed with 75% ethanol (1mL per 1mL TRIzol) and dry pellets were resuspend in 20 uL of RNAse free water.

value: Control

value: peripheral blood


title: NK_Donor_11

description:
HD_NK_11
Gene expression data from donor non-expanded NK cells


title: Control PB C107

source_name: Control PB C107


title: NK_Donor_16

description:
HD_NK_16
Gene expression data from donor non-expanded NK cells


title: Control PB C105

source_name: Control PB C105


title: Control PB C106

source_name: Control PB C106


title: Control PB C103

source_name: Control PB C103


title: healthy CD4 cells - after stimulation - proband39

city: Freiburg

first: Petros

last: Christopoulos

address: Hugstetter Str. 55

department: Medizin I.

institute: Uniklinik Freiburg

description:
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).

source_name: CD4 cells - after stimulation - proband39 - rep1

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.

extract_protocol: Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).

treatment_protocol: For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).

value: peripheral blood CD4 cells

value: healthy

tag: age in years

tag: used in fl/emzl vs healthy comparison (1-yes)

tag: used in cll vs healthy comparison (1-yes)

tag: used in mgus vs healthy comparison (1-yes)


title: Human hepatocellular carcinoma cell line infected with GFP protein (control) 3

status: Public on Feb 17 2011

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: hcc03ctrl 36

hyb_protocol: Followed manufacturer's protocol

scan_protocol: Followed manufacturer's protocol

data_processing: Signal intensities were normalized using RMA algorithm implemented in GenePattern ExpressionFileCreator module (http://www.broadinstitute.org/genepattern).

label_protocol: Followed manufacturer's protocol

growth_protocol: Cells were cultured in DMEM medium with 10% FBS at 5% CO2, 37oC.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen).

treatment_protocol: Recombinant lentivirus were produced by co-transfecting human embryonic kidney 293T cells with miR-517a or empty vector (ViraPower™ Lentiviral Packaging Mix, Invitrogen, Carlsbad, CA) using Lipofectamine 2000. Supernatant containing lentivirus was collected 48h after transfection. Huh-7 cells were transduced with the lentivirus. GFP+ cells were sorted by fluorescence-activated cell sorting (FACS) analysis (Becton Dickinson Instrument, San Jose, CA).

tag: infection

value: GFP protein (control)


title: healthy CD4 cells - after stimulation - proband33

source_name: CD4 cells - after stimulation - proband33 - rep1


title: healthy CD4 cells - after stimulation - proband35

source_name: CD4 cells - after stimulation - proband35 - rep1


title: healthy CD4 cells - after stimulation - proband31

source_name: CD4 cells - after stimulation - proband31 - rep1


title: Human hepatocellular carcinoma cell line infected with MIR517A and GFP protein 1

value: MIR517A and GFP protein


title: Human hepatocellular carcinoma cell line infected with MIR517A and GFP protein 2


title: Human hepatocellular carcinoma cell line infected with GFP protein (control) 1


title: healthy CD4 cells - after stimulation - proband29

source_name: CD4 cells - after stimulation - proband29 - rep1


title: healthy CD4 cells - after stimulation - proband40

source_name: CD4 cells - after stimulation - proband40 - rep1


title: healthy CD4 cells - after stimulation - proband27

source_name: CD4 cells - after stimulation - proband27 - rep1


title: Human hepatocellular carcinoma cell line infected with MIR517A and GFP protein 3


title: healthy CD4 cells - after stimulation - proband28

source_name: CD4 cells - after stimulation - proband28 - rep1


title: healthy CD4 cells - after stimulation - proband46

source_name: CD4 cells - after stimulation - proband46 - rep1


title: healthy CD4 cells - after stimulation - proband44

source_name: CD4 cells - after stimulation - proband44 - rep1


title: healthy CD4 cells - after stimulation - proband36

source_name: CD4 cells - after stimulation - proband36 - rep1


title: healthy CD4 cells - after stimulation - proband38

source_name: CD4 cells - after stimulation - proband38 - rep1


title: healthy CD4 cells - after stimulation - proband4

source_name: CD4 cells - after stimulation - proband4 - rep1


title: healthy CD4 cells - after stimulation - proband34

source_name: CD4 cells - after stimulation - proband34 - rep1


title: Human hepatocellular carcinoma cell line infected with GFP protein (control) 2


title: healthy CD4 cells - after stimulation - proband32

source_name: CD4 cells - after stimulation - proband32 - rep1


title: gd cell activation+7day,donor 4

status: Public on Feb 15 2011

city: Toulouse

first: Jean Jacques

last: FOURNIE

address: 2 av Hubert Curien

department: oncology

institute: INSERM

description: Gene expression data from purified TCRVgamma9 positive cells

hyb_protocol: Labeled complementary RNA (cRNA) from these samples was then fragmented and hybridized to Affymetrix GeneChip arrays HG-U133 plus 2.0.

scan_protocol: The chips were then washed, scanned on the Affymetrix Fluidics Station 400 and analyzed with GeneChip Operating Software.

source_name: human blood sample, freshly isolated and purified, 7 days after in vitro activation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-3 µg total RNA from human cells, amplified and labeled following the one-Cycle Target Labeling protocol (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Cells were cultured in complete RPMI 1640 medium containing 2 mM L-glutamine, 100 µg/ml streptomycin, 100 IU/ml penicillin and 1 mM sodium-pyruvate supplemented with 10% fetal calf serum and recombinant human IL-2 (100 IU/ml) added every three days.

treatment_protocol: Cells were activated by adding BrHPP (500 nM) ad day 0.

value: peripheral blood lymphocytes isolated and activated in vitro for 7 days

value: TCRVgamma9+ gamma delta T cells

tag: treatment

tag: time

value: 7 d

tag: individual

value: donor 4


title: gd cell activation+7day,donor 3

tag: sample type

value: donor 3


title: gd cell activation+6h,donor 3

source_name: human blood sample, freshly isolated and purified, 6 hours after in vitro activation

value: peripheral blood lymphocytes isolated and activated in vitro for 6 hrs

value: 6 h


title: gd cell control time 0,donor 4

source_name: human blood sample, freshly isolated and purified

value: peripheral blood lymphocytes isolated prior to activation

value: control


title: gd cell activation+6h,donor 2

value: donor 2


title: gd cell activation+7day,donor 2


title: gd cell activation+6h,donor 4


title: gd cell control time 0,donor 3


title: gd cell control time 0,donor 2


title: gd cell activation+7day,donor 1

value: donor 1


title: gd cell control time 0,donor 1


title: gd cell activation+6h,donor 1


title: F348_WBS

status: Public on Jan 31 2011

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

hyb_protocol: Twelve micrograms of biotinylated cRNA from each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays, according to standard procedures. Washing and staining was performed using the EuGE-WS2v5 protocol.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G and hybridization quality control were assessed using RACE (Psarros et al., 2005), a web service based on Bioconductor “affy” and “affyPLM” packages (Gautier et al., 2004).

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: F348, WBS, skin fibroblasts

label_protocol: Target preparations were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the DNA array facility of the University of Lausanne (Switzerland). 3 ug of each pool was used to perform the chiparray experiment according to the Affymetrix Gene Expression procedure.

extract_protocol: Total RNA was prepared using TRIzol (Invitrogen) and purified on Qiagen RNeasy Mini columns (Qiagen), according to manufacturers' instructions.

tag: cell line

value: F348, WBS, skin fibroblasts

tag: microdeletion

value: female

tag: age at biopsy

value: 3 years


title: F055_WBS

source_name: F055, WBS, skin fibroblasts

value: F055, WBS, skin fibroblasts

value: 4 years


title: F223_WBS

source_name: F223, WBS, skin fibroblasts

value: F223, WBS, skin fibroblasts


title: 5290_CNTL

source_name: 5290, control, skin fibroblasts

value: 5290, control, skin fibroblasts

value: 7 years


title: 9118_CNTL

source_name: 9118, control, skin fibroblasts

value: 9118, control, skin fibroblasts

value: 5 years


title: no GvHD d150

status: Public on Dec 31 2010

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description:
no GvHD d150
MHH0891

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: RMA summarization using GeneSpring GX11 (Agilent Technology)

source_name: blood from allogeneic stem cell transplantation (SCT) patient

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

extract_protocol: RNAeasy, Qiagen

value: no GvHD

tag: cell type

value: CD4+CD25highCD127low/- Tregs

value: 150 days


title: 5850_CNTL

source_name: 5850, control, skin fibroblasts

value: 5850, control, skin fibroblasts


title: D890_WBS

source_name: D890, WBS, skin fibroblasts

value: D890, WBS, skin fibroblasts


title: 5042_CNTL

source_name: 5042, control, skin fibroblasts

value: 5042, control, skin fibroblasts

value: 8 years


title: 9837_CNTL

source_name: 9837, control, skin fibroblasts

value: 9837, control, skin fibroblasts


title: HFF-RH+TNF6hr-1

status: Public on Jan 10 2011

city: Cambridge

first: Emily

middle: E

last: Rosowski

state: MA

address: 77 Massachusetts Ave, 68-258d

department: Biology

institute: MIT

hyb_protocol: Following fragmentation, 4 ug of cDNA from uninfected samples or 5 ug of cDNA from infected samples were hybridized on GeneChip Human Genome U133A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 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. The trimmed mean target intensity of each array was arbitrarily set to 500.  Data was then normalized, setting all data to have a minimum value of 50.  Probes called absent or M were also set to have a value of 50.

source_name: HFF + RH, 18hr + TNF-alpha, 6hr

label_protocol: Labeled cDNA were prepared with the NuGEN Applause system from 50-100ng total RNA.

growth_protocol: Human foreskin fibroblasts (HFFs) were grown in T25 flasks (BD Biosciences) at 37C, 5% CO2 to confluency.  Parasite strains were maintained in vitro by serial passage on monolayers of HFFs.

treatment_protocol: Parasite strains were syringe lysed, washed at least once with PBS, and added to HFF monolayers for 18-24 hours.  Some samples were also stimulated with human TNF for 6 hours.

tag: tissue

value: Human foreskin fibroblast (HFF)

tag: age


title: GvHD d150

description:
GvHD d150
MHH0897

tag: disease state

value: GvHD


title: chronic GvHD

description:
chronic GvHD
MHH0899

value: chronic GvHD


title: 8495_CNTL

source_name: 8495, control, skin fibroblasts

value: 8495, control, skin fibroblasts

tag: gender

value: female


title: H652_WBS

source_name: H652, WBS, skin fibroblasts

value: H652, WBS, skin fibroblasts


title: acute GvHD

description:
acute GvHD
MHH0893wdh

value: acute GvHD


title: 10590_WBS

source_name: 10590, WBS, skin fibroblasts

value: 10590, WBS, skin fibroblasts

value: 3 years


title: 6089_CNTL

source_name: 6089, control, skin fibroblasts

value: 6089, control, skin fibroblasts

value: 4 years


title: 10358_WBS

source_name: 10358, WBS, skin fibroblasts

value: 10358, WBS, skin fibroblasts

value: 7 years


title: 4319_WBS

source_name: 4319, WBS, skin fibroblasts

value: 4319, WBS, skin fibroblasts


title: mDC normoxia 2

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

institute: Istiuto Giannina Gaslini

description: Human peripheral blood mononuclear cells (PBMC) were isolated from venous blood of voluntary healthy donors. All cultures were maintained in RPMI 1640 medium supplemented with 10% FBS heat inactivated, 50μg/ml gentamycin. Monocytes were purified by negative selection. To generate normoxic mDC the monocytes were incubated in six-well culture plates for 4 days under normoxic conditions.

hyb_protocol: Fragmented cRNA was used for hybridization to Affymetrix HG-U133 plus 2.0 arrays according to the Affymetrix’s instructions.

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

data_processing: Expression values were quantified and array quality control was performed with the statistical algorithms implemented in Affymetrix Microarray Suite 5.0.

source_name: Monocyte derived dendritic cells under normoxic conditions

label_protocol: The RNA was reverse-transcribed into cDNA and biotin labeled according to the Affymetrix’s instructions.

extract_protocol: Total RNA was independently isolated from DCs derived from the Mn of three different donors using RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

value: Monocyte derived dendritic cells

tag: treatment group

value: normoxic conditions

tag: disease status

value: healthy donor


title: 1104_CNTL

source_name: 1104, control, skin fibroblasts

value: 1104, control, skin fibroblasts


title: mDC hypoxia 1

description: Human peripheral blood mononuclear cells (PBMC) were isolated from venous blood of voluntary healthy donors. All cultures were maintained in RPMI 1640 medium supplemented with 10% FBS heat inactivated, 50μg/ml gentamycin. Monocytes were purified by negative selection. To generate hypoxic mDC the monocytes were incubated in six-well culture plates for 4 days under hypoxic conditions.

source_name: Monocyte derived dendritic cells cultured under hypoxic condition

value: hypoxic condition


title: 2433_CNTL

source_name: 2433, control, skin fibroblasts

value: 2433, control, skin fibroblasts

value: 5 years


title: mDC normoxia 1

source_name: Monocyte derived dendritic cells cultured under normoxic condition

value: normoxic condition


title: GvHD d90

description:
GvHD d90
MHH0895

source_name: blood from allogeneic stem cell transplantation (SCT) patient

value: GvHD

value: CD4+CD25highCD127low/- Tregs

value: 90 days


title: mDC normoxia 3


title: no GvHD d90

description:
no GvHD d90
MHH0889

value: no GvHD


title: mDC hypoxia 2


title: mDC hypoxia 3


title: WM262-sh302

status: Public on Dec 01 2010

city: New York

first: Dana

last: Pe'er

address: 1212 Amsterdam Ave.

department: Biological Sciences

institute: Columbia University

hyb_protocol: The fragmented cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to GeneChip Human Gene 1.0 ST Array chips overnight at 45°C (performed by the Dana Farber Cancer Institute Microarray Core). A fluidics instrument was used by the core to perform washes to remove cDNA that had not hybridized to its complementary oligonucleotide probe. The bound cDNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were subsequently added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: A confocal laser scanner was used for excitation and measurement of cDNAs bound to complementary oligonucleotides by the Dana Farber Cancer Institute Microarray Core.

data_processing:
Arrays were normalized using RMA with Affymetrix Expression Console v. 1.1, mean intensity level of all arrays was set to the original mean of intensity means. We merged probe sets for genes if these agreed and removed inconsistent genes. Analysis was done using MatLab. inconsistent genes.
Control arrays of the same cell line were averaged, and test arrays were compared ot control. Data in the matrix file attached is the fold change observed after knock down relative to shGFP controls.  Ratio data is available on the Series record as a supplementary file.

label_protocol: Fragmented single-stranded cDNA was end-labeled with a biotinylated nucleotide-analog by the Dana Farber Cancer Institute Microarray Core.

growth_protocol: Melanoma short-term cultures (STCs) derived from metastatic foci (Lin et al., 2008b) were cultured in RPMI medium (MediaTech) supplemented with 10% fetal bovine serum (Gemini). A375 melanoma cell line and 293T virus packaging cells were cultured in DMEM medium (MediaTech) with 10% fetal bovine serum. All cells were maintained in 100 units/mL penicillin, 100 μg/ml streptomycin at 37°C under 5% CO2.

extract_protocol: Total RNA was harvested using the RNeasy Mini Kit (Qiagen)

treatment_protocol: To perform knockdown experiments, target cells (1.2x106 - 3x106) were plated the day before infection to obtain 30-40% confluence at the time of infection. Cells were then incubated with virus at the dilution established by growth curves the virus-containing media was removed and fresh media was added. The next day, puromycin was added to select for infected cells (WM1960 and WM1385 at 2 μg/ml; WM1346, WM1976, WM1930, WM262 and A375 at 1 μg/ml).

tag: hairpin

tag: gene


title: WM1960-sh1490


title: WM1960-shGFP3

value: shGFP

value: Control


title: WM262-shGFP2


title: WM1960-shGFP2


title: Adult Naïve CD4+ T cells 2

status: Public on Dec 17 2010

city: San Francisco

first: Jeff

middle: E.

last: Mold

state: CA

address: UCSF Box 1234, SFGH Bldg 3

department: Division of Experimental Medicine

institute: University of California San Francisco

description: Gene Expression

hyb_protocol: Arrays were hybridized using Affymetrix GeneChip Fluidics Station 450 according to manufacturer's protocol

scan_protocol: Arrays were scanned with an Affymetrix Model 3000 scanner

data_processing: Data were analyzed using the Bioconductor package affyPLM. Preprocessing followed the following procedures: (1) background correction; (2) normalization using the quantile method; (3) summarization of probe set values using the RMA (Robust Multi-Array Average) method.

source_name: Sort Purified Adult CD3+CD4+CD45RA+CCR7+CD27+ Naïve T cells

label_protocol: RNA was converted to cDNA and amplified (NuGEN WT-Ovation kit) and then fragmented (WT-Ovation kit) and labeled with biotin (FL-Ovation cDNA biotin module, NuGEN)

growth_protocol: Cells were isolated from fetal mesenteric lymph nodes (mechanical dispersion) and adult peripheral blood (Ficoll-Hypaque)

extract_protocol: Immediately after sorting cell pellets were lysed in RNA lysis buffer (Stratagene) and RNA was obtained using the Absolutely RNA microprep kit (Stratagene) in accordance with manufacturer’s protocol

treatment_protocol: After isolation total cells were cultured overnight (12 hours) in low-serum media (RPMI with 2% FBS) to attempt to normalize differences associated with tissue of origin (blood vs lymph node)

value: Sort Purified T cells

tag: phenotype


title: WM1960-shGFP4


title: WM1960-sh865


title: Adult Naïve CD4+ T cells 3

description: Gene Expression


title: WM1960-sh477


title: WM1930-sh865


title: WM1960-sh302


title: WM262-shGFP1


title: WM1976-sh302


title: Adult Naïve CD4+ T cells 1

description: Gene Expression


title: WM1385-sh477


title: WM1385-shGFP2


title: WM1930-sh477


title: WM262-sh1490


title: WM1960-shGFP1


title: WM1930-shGFP1


title: WM1976-shGFP


title: WM1930-shGFP2


title: WM1976-sh1490


title: WM1385-sh865


title: Adult CD4+CD25+ Treg 1

description: Gene Expression

source_name: Sort Purified Adult CD3+CD4+CD25bright Treg cells


title: Adult CD4+CD25+ Treg 3

description: Gene Expression


title: WM1385-shGFP1


title: WM1346-shGFP2


title: A375-shGFP1


title: WM1346-sh1490


title: A375-sh865


title: WM1346-sh302


title: Adult CD4+CD25+ Treg 2

description: Gene Expression


title: WM1346-shGFP1


title: 2 IL-4 macrophage+Rosigl. rep 2, 6h

status: Public on Nov 18 2010

city: Boston

first: Attila

last: Szanto

address: 185 Cambridge St.

institute: Massachusetts General Hospital

description: Gene expression data from macrophages treated with interleukin-4 and Rosiglitazone for 6h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Human Genome U133 Plus 2 Affymetrix Array according to Affymetric standardized protocol.

scan_protocol: Microarray were scanned canned according to Affymetric standardized protocol.

data_processing: The data were generated with GCOS, and cel files were analyzed in GeneSpring 7.3 using GC-RMA.

source_name: Macrophages treated with interleukin-4 and Rosiglitazone for 6h

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: Isolated monocytes were cultured in RPMI+10% FCS supplemented with glutamine, penicillin and streptomycin.

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

treatment_protocol: Cell were treated after plating into 6-well cell culture plates with 100 ug/ml IL-4. Simultaneously, vehicle (DMSO:ethanol) or 1 uM Rosiglitazone was added.

tag: donor

value: macrophage

tag: activation

tag: treatment

value: Rosiglitazone


title: 2 IL-4 macrophage rep 1, 6h

description: Gene expression data from macrophages treated with interleukin-4 and vehicle for 6h

source_name: Macrophages treated with interleukin-4 and vehicle for 6h

tag: time


title: 3 Control macrophage+Rosigl., 72h

description: Gene expression data from macrophages treated with Rosiglitazone for 72h

source_name: Macrophages treated with Rosiglitazone for 72h

treatment_protocol: Cell were treated after plating into 6-well cell culture plates with the indicated cytokines (100 ug/ml IL-4, or 100 ug/ml IFNg+50 ug/ml TNF. Simultaneously, vehicle (DMSO:ethanol) or 1 uM Rosiglitazone was added.


title: 2 IL-4 macrophage+Rosigl. rep 1, 6h


title: 3 IL-4 macrophage+Rosigl., 72h

description: Gene expression data from macrophages treated with interleukin-4 and Rosiglitazone for 72h

source_name: Macrophages treated with interleukin-4 and Rosiglitazone for 72h


title: 3 IFNg+TNF macrophage+Rosigl., 72h

description: Gene expression data from macrophages treated with IFNg+TNF and Rosiglitazone for 72h

source_name: Macrophages treated with IFNg+TNF and Rosiglitazone for 72h

value: IFNg+TNF


title: 1 IL-4 macrophage+Rosigl. rep 2, 6h


title: 2 IL-4 macrophage rep 2, 6h


title: 2 IFNg+TNF macrophage+Rosigl., 24h

description: Gene expression data from macrophages treated with IFNg+TNF and Rosiglitazone for 24h

source_name: Macrophages treated with IFNg+TNF and Rosiglitazone for 24h


title: 3 IL-4 macrophage+Rosigl., 12h

description: Gene expression data from macrophages treated with interleukin-4 and Rosiglitazone for 12h

source_name: Macrophages treated with interleukin-4 and Rosiglitazone for 12h


title: 2 IFNg+TNF macrophage, 24h

description: Gene expression data from macrophages treated with IFNg+TNF and vehicle for 24h

source_name: Macrophages treated with IFNg+TNF and vehicle for 24h


title: 3 Control macrophage+Rosigl., 12h

description: Gene expression data from macrophages treated with Rosiglitazone for 12h

source_name: Macrophages treated with Rosiglitazone for 12h


title: 3 IL-4 macrophage, 72h

description: Gene expression data from macrophages treated with interleukin-4 and vehicle for 72h

source_name: Macrophages treated with interleukin-4 and vehicle for 72h


title: A375-shGFP2

tag: cell line


title: 1 IL-4 macrophage rep 1, 6h


title: 3 Control macrophage, 12h

description: Gene expression data from macrophages treated with vehicle for 12h

source_name: Macrophages treated with vehicle for 12h


title: 3 Control macrophage, 72h

description: Gene expression data from macrophages treated with vehicle for 72h

source_name: Macrophages treated with vehicle for 72h


title: 3 IL-4 macrophage, 12h

description: Gene expression data from macrophages treated with interleukin-4 and vehicle for 12h

source_name: Macrophages treated with interleukin-4 and vehicle for 12h


title: 3 IFNg+TNF macrophage, 12h

description: Gene expression data from macrophages treated with IFNg+TNF and vehicle for 12h

source_name: Macrophages treated with IFNg+TNF and vehicle for 12h


title: 1 IL-4 macrophage+Rosigl. rep 1, 6h


title: 3 IFNg+TNF macrophage+Rosigl., 12h

description: Gene expression data from macrophages treated with IFNg+TNF and Rosiglitazone for 12h

source_name: Macrophages treated with IFNg+TNF and Rosiglitazone for 12h


title: 3 IFNg+TNF macrophage, 72h

description: Gene expression data from macrophages treated with IFNg+TNF and vehicle for 72h

source_name: Macrophages treated with IFNg+TNF and vehicle for 72h


title: 2 IL-4 macrophage, 24h

description: Gene expression data from macrophages treated with interleukin-4 and vehicle for 24h

source_name: Macrophages treated with interleukin-4 and vehicle for 24h


title: 2 Control macrophage+Rosigl., 24h

description: Gene expression data from macrophages treated with Rosiglitazone for 24h

source_name: Macrophages treated with Rosiglitazone for 24h


title: 2 IL-4 macrophage+Rosigl., 24h

description: Gene expression data from macrophages treated with interleukin-4 and Rosiglitazone for 24h

source_name: Macrophages treated with interleukin-4 and Rosiglitazone for 24h


title: 2 IFNg+TNF macrophage+Rosigl., 12h


title: 2 IL-4 macrophage+Rosigl., 12h


title: 1 IFNg+TNF macrophage,12h


title: 2 Control macrophage+Rosigl., 12h


title: 1 IL-4 macrophage+Rosigl., 4h

description: Gene expression data from macrophages treated with interleukin-4 and Rosiglitazone for 4h

source_name: Macrophages treated with interleukin-4 and Rosiglitazone for 4h


title: 2 Control macrophage, 24h

description: Gene expression data from macrophages treated with vehicle for 24h

source_name: Macrophages treated with vehicle for 24h


title: 1 IL-4 macrophage+Rosigl., 12h


title: 1 IFNg+TNF macrophage+Rosigl., 12h


title: 2 Control macrophage, 12h


title: 2 Monocyte

description: Gene expression data from freshly isolated monocytes

source_name: Freshly isolated monocytes

value: monocyte


title: 1 IFNg+TNF macrophage+Rosigl., 4h

description: Gene expression data from macrophages treated with IFNg+TNF and Rosiglitazone for 4h

source_name: Macrophages treated with IFNg+TNF and Rosiglitazone for 4h


title: 2 IL-4 macrophage, 12h


title: 1 IL-4 macrophage, 4h

description: Gene expression data from macrophages treated with interleukin-4 and vehicle for 4h

source_name: Macrophages treated with interleukin-4 and vehicle for 4h


title: 1 Control macrophage, 4h

description: Gene expression data from macrophages treated with vehicle for 4h

source_name: Macrophages treated with vehicle for 4h


title: 1 Control macrophage+Rosigl., 12h

description: Gene expression data from macrophages treated with Rosiglitazone for 12h

source_name: Macrophages treated with Rosiglitazone for 12h


title: 1 IFNg+TNF macrophage, 4h

description: Gene expression data from macrophages treated with IFNg+TNF and vehicle for 4h

source_name: Macrophages treated with IFNg+TNF and vehicle for 4h


title: 1 IL-4 macrophage, 12h


title: 2 IFNg+TNF macrophage, 12h


title: 1 Control macrophage, 12h

description: Gene expression data from macrophages treated with vehicle for 12h

source_name: Macrophages treated with vehicle for 12h


title: 1 Monocyte


title: blood CD1c+ DC #2

status: Public on Oct 27 2010

city: DEBRECEN

first: LAJOS

last: SZELES

address: Egyetem tér

institute: UNIVERSITY OF DEBRECEN

description: N

hyb_protocol: 10 ug of fragmented biotinylated cRNA was hybridized for 16 hr at 45C on GeneChip HG133_plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: CHP file were generated by Affymetrix Expression Console, using RMA algorithm

source_name: CD1c+ Dendritic cell isolated from human blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using 3` IVT Expression kit (Affymetrix).

growth_protocol: monocyte derived DC: CD14+ monocyte were cultured in the presence of IL4 and GMCSF, other DC subtypes were not treated

extract_protocol: RNeasy mini kit was used to extract total RNA (according to the manufacturer's instructions).

value: blood

value: CD1c+ dendritic cell


title: Langerhans cell #3

source_name: Langerhans cell isolated from skin

value: skin

value: Langerhans cell


title: blood CD1c+ DC #1

description: M


title: dermal DC #3

description: EU_Dermal DC #3

source_name: dermal Dendritic cell

value: dendritic cell


title: blood CD1c+ DC #3

description: O


title: Langerhans cell #2


title: Monocyte-derived Dc #2

source_name: in vitro differentiated Monocyte-derived Dendritic cell

value: blood (buffy coat)

value: Monocyte-derived dendritic cell


title: human macrophages treated with P. gingivalis, biological rep2

status: Public on Oct 23 2010

first: Han

last: Hu

address: 44 Cummington St

department: Bioinformatics

institute: Boston University

description: Gene expression data from human macrophages treated with P. gingivalis for 2 hours.

hyb_protocol: Hybridization was conducted according to the Affymetrix GeneChip Manual. Twenty micrograms of in vitro transcription material were used on each GeneChip Human Genome U133 Plus 2.0 array, which contains 54674 gene probe sets.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing: Data were processed using R/Bioconductor software. The raw data were read from CEL files into the object of class AffyBatch. We compared the expression of genes in macrophages under three conditions: live P. gingivalis-stimulated versus control, LPS-stimulated versus control, and FimA-stimulated versus control. For each condition, background correction and quantile normalization were adjusted by Robust Multichip Average (RMA) in the Affy package, followed by non-specific filtering to eliminate the uninformative probe sets whose inconsistent phenotypes appeared in the three replicated arrays. The calculation of fold change and adjusted p-value (false discovery rate, FDR) under different conditions was implemented by the limma package.

source_name: human macrophages, 2hr treatment with P. gingivalis 381

label_protocol: GeneChip Expression Amplification Reagents kit-30 reactions (P/N 900449).

growth_protocol: Human PBMC were derived by Ficoll-Hypaque density gradient centrifugation from buffy coats of different healthy blood donors obtained from the Interstate Blood Bank (Memphis, TN). CD14-positive monocytes were enriched from PBMC to >95% purity by immunomagnetic elimination of T cells, NK cells, B cells, dendritic cells, and basophils using the Monocyte Isolation Kit II. Purity of monocytes was determined by flow-cytometric analysis of FITC-conjugated anti-CD14 and PE-conjugated anti-biotin. Purified human monocytes were plated at a density of 2 x 10^6 cells/ml in DMEM with 20% FBS, 10% human serum AB, and 50 µg/ml gentamicin in 6-well or 10-cm diameter tissue culture plates for 5 days at 37°C in a humidified atmosphere containing 5% CO2. On days 5 and 7, half of the medium were removed and replaced with medium lacking FBS. Media on the cultured macrophages were replaced with fresh DMEM containing 1% human serum on day 9, 1 hour before experiments were begun.

extract_protocol: Two hours after infection with P. gingivalis, or treatment with P. gingivalis LPS, FimA, or saline (control), human macrophages were washed three times with ice cold PBS, and total RNA was extracted using an RNeasy Mini Kit according to the manufacturer’s instructions.

treatment_protocol: Macrophages were infected with live P. gingivalis. In additional cultures, purified LPS or FimA from P. gingivalis were added to the cell culture medium. Cells were incubated at 37°C in an atmosphere containing 5% CO2. Cells and supernatants were harvested at indicated times after incubation with live P. gingivalis or its components.

value: macrophages

value: live P. gingivalis 381

tag: treatment time

value: 2 hours

tag: day


title: human macrophages treated with PG-fimbriae, biological rep1

description: Gene expression data from human macrophages treated with PG-fimbriae for 2 hours.

source_name: human macrophages, 2hr treatment with P. gingivalis-fimbriae

tag: cell type

value: P. gingivalis fimbriae


title: human macrophages treated with PG-LPS, biological rep3

description: Gene expression data from human macrophages treated with PG-LPS for 2 hours.

source_name: human macrophages, 2hr treatment with P. gingivalis-LPS

tag: tissue

value: P. gingivalis lipopolysaccharide (LPS)


title: dermal DC #1

description: EU_Dermal DC #1


title: human macrophages treated with P. gingivalis, biological rep1


title: 1 IL-4 macrophage rep 2, 6h

description: Gene expression data from macrophages treated with interleukin-4 and vehicle for 6h

source_name: Macrophages treated with interleukin-4 and vehicle for 6h

value: Control


title: human macrophages treated with PG-fimbriae, biological rep2


title: human macrophages treated with saline, biological rep1

description: Gene expression data from human macrophages treated with saline (control) for 2 hours.

source_name: human macrophages, 2hr treatment with saline

value: saline


title: Monocyte-derived Dc #1


title: 1 Control macrophage+Rosigl., 4h

description: Gene expression data from macrophages treated with Rosiglitazone for 4h

source_name: Macrophages treated with Rosiglitazone for 4h

value: macrophage

value: Rosiglitazone


title: A375-sh477

data_processing:
Arrays were normalized using RMA with Affymetrix Expression Console v. 1.1, mean intensity level of all arrays was set to the original mean of intensity means. We merged probe sets for genes if these agreed and removed inconsistent genes. Analysis was done using MatLab.
Control arrays of the same cell line were averaged, and test arrays were compared ot control. Data in the matrix file attached is the fold change observed after knock down relative to shGFP controls.  Ratio data is available on the Series record as a supplementary file.


title: human macrophages treated with saline, biological rep3


title: human macrophages treated with PG-LPS, biological rep1


title: 01-M

status: Public on Sep 09 2010

first: Dan

last: Littman

address: 540 1st ave

institute: NYU Medical Center

description: Donor 1

hyb_protocol: According to Affymetrix protocols

scan_protocol: According to Affymetrix protocols

data_processing: Data was analyzed using R version 2.6.0 (r43408) and Bioconductor packages "simpleaffy" (version 2.14.05) and "hgu133plus2" (version 2.0.1) with the MAS 5.0 algorithm.

source_name: Monocyte-derived dendritic cells

label_protocol: According to Affymetrix protocols

growth_protocol: Human CD14+ monocytes were isolated from buffy coats of adult peripheral blood using a Ficoll gradient and two sequential purifications with anti-CD14 magnetic beads (Miltenyi). Purified monocytes were cultured in the presence of GM-CSF and IL-4 for 4 days in RPMI media containing 10% fetal bovine serum and antibiotics.

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

treatment_protocol: 100,000 MDDC were plated in 96 well U bottom plate in the presence of 5 micrograms/ml of polybrene. MDDC were infected with HIVGFP(G) and SIVVLP(G) supernatants that were generated by transient transfection of 293T cells. Celles were harvested 48 hours after infection.

value: Monocyte-derived dendritic cells

tag: virus


title: human macrophages treated with PG-fimbriae, biological rep3

value: blood


title: human macrophages treated with P. gingivalis, biological rep3


title: human macrophages treated with saline, biological rep2


title: 02-M

description: Donor 2


title: human macrophages treated with PG-LPS, biological rep2


title: Neutrophil_patient51_time9

city: St. Louis

first: J

middle: Perren

last: Cobb

state: MO

address: Campus Box 8109, 660 South Euclid Avenue

institute: Washington University in St. Louis

description: Gene expression data (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

hyb_protocol: GeneCip IVT hyb. Affymetrix EukGE-WSv5 wash and stain protocol

scan_protocol: Affymetrix GeneChip using GCOS.

data_processing: The data were analyzed with RMA using default analysis settings and log2 scaling.

source_name: Neutrophil

label_protocol: Affymetrix GeneChip IVT labeling

growth_protocol: Samples from each patient were enriched using a previously described (monocyte or Neutrophil) enrichment protocol or Buffy coat protocol.

extract_protocol: Modiefied Qiagen Rneasy protocol


title: Neutrophil_patient50_time11


title: Neutrophil_patient45_time9


title: Neutrophil_patient41_time1


title: Neutrophil_patient45_time3


title: Neutrophil_patient51_time3


title: dermal DC #2

description: EU_Dermal DC #2


title: Neutrophil_patient51_time1


title: Neutrophil_patient50_time7


title: Neutrophil_patient41_time9


title: Neutrophil_patient50_time5


title: Neutrophil_patient45_time7


title: Neutrophil_patient41_time11


title: Neutrophil_patient51_time7


title: Neutrophil_patient45_time5


title: Neutrophil_patient50_time9


title: Neutrophil_patient51_time5


title: CD57negNK cell, donor 56, biological rep3

status: Public on Aug 18 2010

first: Sandra

middle: Laurence

last: Lopez-Verges

address: 513 Parnassus Ave, Room HSE 1001G

department: Microbiology and Immunology

description:
Gene expression data from CD57neg CD3negCD56dimCD16+ NK cells sorted from PBMC
Don56 CD57negNK

hyb_protocol: GeneChip Whole Transcript Sense Target  Labeling Assay Manual was used according to the manufacturer's instructions. cRNA was hybridized on Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GCS3000.

data_processing: The protocol used for data processing was GCOS 1.4. Raw intensities from the array CEL files will be analyzed using Affymetrix Power Tools (APT, version 1.10.1) to generate a RMA (robust multi-array average; Irizarry et al 2003) expression intensities on a log2 scale for each probe set and calculate various quality metrics. The probe intensities will be background corrected, quantile-normalized, and summarized for each probe set using a robust fit of linear models.

source_name: CD57neg CD3negCD56dimCD16+ NK cells sorted from peripheral blood mononuclear cells (PBMC) from healthy donor 56

label_protocol: Samples were prepared using  NuGEN WT -Ovation Pico RNA Amplification System,  NuGEN WT-Ovation Exon Module, and NuGEN Encore Biotin Module.

extract_protocol:
Collection protocol: PBMC were obtained from leukocyte reduction Pall filters (Blood Centers of the Pacific) after density gradient centrifugation over Ficoll-Paque (GE Healthcare). CD57+CD3negCD56dimCD16+ and CD57negCD3negCD56dimCD16+ NK cells from three healthy adult donors were sorted.
Extraction protocol: Total RNA was extracted according to the manufacturer's instructions using RNAqueous-Micro kit, Ambion.

treatment_protocol: CD57+CD3negCD56dimCD16+ and CD57negCD3negCD56dimCD16+ NK cells from PBMC from three healthy adult donors were sorted into Lysis Solution (100 ml per 10,000 cells) (RNAqueous-Micro kit, Ambion).

tag: donor age

value: between 20-60 years old

value: NK cell

tag: cd57 status (of nk cell)


title: Neutrophil_patient41_time3


title: Neutrophil_patient45_time1


title: CD57negNK cell, donor 54, biological rep1

description:
Gene expression data from CD57neg CD3negCD56dimCD16+ NK cells sorted from PBMC
Don54 CD57negNK

source_name: CD57neg CD3negCD56dimCD16+ NK cells sorted from peripheral blood mononuclear cells (PBMC) from healthy donor 54


title: Neutrophil-Resting-4 [HG-U133A]

status: Public on Jul 13 2010

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

institute: Genentech, Inc.

description: Gene expression data from resting neutrophils from peripheral blood

hyb_protocol: cRNA was hybridized on GeneChip HGU133A.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Neutrophils from PBMC

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

extract_protocol: RNeasy Mini Kit (Qiagen)

value: peripheral blood

value: Neutrophils

tag: treatment agent

tag: time post-treatment


title: CD57+NK cell, donor 54, biological rep1

description:
Gene expression data from CD57+ CD3negCD56dimCD16+ NK cells sorted from PBMC
Don54 CD57+NK

source_name: CD57+ CD3negCD56dimCD16+ NK cells sorted from peripheral blood mononuclear cells (PBMC) from healthy donor 54


title: Neutrophil_patient50_time3


title: Neutrophil-Resting-2 [HG-U133A]


title: CD57negNK cell, donor 55, biological rep2

description:
Gene expression data from CD57neg CD3negCD56dimCD16+ NK cells sorted from PBMC
Don55 CD57negNK

source_name: CD57neg CD3negCD56dimCD16+ NK cells sorted from peripheral blood mononuclear cells (PBMC) from healthy donor 55


title: CD57+NK cell, donor 56, biological rep3

description:
Gene expression data from CD57+ CD3negCD56dimCD16+ NK cells sorted from PBMC
Don56 CD57+NK

source_name: CD57+ CD3negCD56dimCD16+ NK cells sorted from peripheral blood mononuclear cells (PBMC) from healthy donor 56


title: CD57+NK cell, donor 55, biological rep2

description:
Gene expression data from CD57+ CD3negCD56dimCD16+ NK cells sorted from PBMC
Don55 CD57+NK

source_name: CD57+ CD3negCD56dimCD16+ NK cells sorted from peripheral blood mononuclear cells (PBMC) from healthy donor 55


title: DendriticCell-LPSstimulated-4 [HG-U133A]

description: Gene expression data from dendritic cells from peripheral blood 24 hrs following LPS activation

source_name: CD14+ cells from PBMC

value: CD14+ cells

value: LPS

value: 24 hrs


title: Neutrophil-Resting-3 [HG-U133A]


title: DendriticCell-LPSstimulated-1 [HG-U133A]


title: DendriticCell-LPSstimulated-2 [HG-U133A]


title: Neutrophil-Resting-5 [HG-U133A]


title: DendriticCell-LPSstimulated-3 [HG-U133A]


title: DendriticCell-Control-3 [HG-U133A]

description: Gene expression data from resting dendritic cells from peripheral blood

value: control


title: DendriticCell-LPSstimulated-5 [HG-U133A]


title: DendriticCell-Control-6 [HG-U133A]


title: DendriticCell-Control-5 [HG-U133A]


title: DendriticCell-LPSstimulated-6 [HG-U133A]


title: DendriticCell-Control-4 [HG-U133A]


title: Monocyte-Day7-12 [HG-U133A]

description: Gene expression data from monocytes after 7 days in vitro macrophage differentiation

source_name: Monocytes from PBMC

value: Monocytes

value: macrophage differentiation medium

value: 7 day


title: Neutrophil-Resting-1 [HG-U133A]


title: Monocyte-derived Dc #3

source_name: in vitro differentiated Monocyte-derived Dendritic cell

value: blood (buffy coat)

value: Monocyte-derived dendritic cell


title: DendriticCell-Control-1 [HG-U133A]


title: Monocyte-Day7-7 [HG-U133A]


title: DendriticCell-Control-2 [HG-U133A]


title: Langerhans cell #1

source_name: Langerhans cell isolated from skin

value: skin

value: Langerhans cell


title: Monocyte-Day7-8 [HG-U133A]


title: Monocyte-Day7-9 [HG-U133A]


title: Monocyte-Day7-10 [HG-U133A]


title: Monocyte-Day1-12 [HG-U133A]

description: Gene expression data from monocytes after 1 day in vitro macrophage differentiation

value: 1 day


title: Monocyte-Day7-6 [HG-U133A]


title: Monocyte-Day7-1 [HG-U133A]


title: Monocyte-Day1-11 [HG-U133A]


title: Monocyte-Day7-5 [HG-U133A]


title: Monocyte-Day7-2 [HG-U133A]


title: Monocyte-Day1-10 [HG-U133A]


title: Monocyte-Day1-9 [HG-U133A]


title: Monocyte-Day1-8 [HG-U133A]


title: Monocyte-Day1-5 [HG-U133A]


title: Monocyte-Day0-3 [HG-U133A]

description: Gene expression data from freshly isolated monocytes

value: 0 day


title: Monocyte-Day1-3 [HG-U133A]


title: Monocyte-Day1-7 [HG-U133A]


title: Monocyte-Day0-1 [HG-U133A]


title: Monocyte-Day7-3 [HG-U133A]


title: Monocyte-Day7-11 [HG-U133A]


title: Monocyte-Day0-6 [HG-U133A]


title: Monocyte-Day0-2 [HG-U133A]


title: Monocyte-Day0-10 [HG-U133A]


title: Monocyte-Day0-8 [HG-U133A]


title: Monocyte-Day1-2 [HG-U133A]


title: Monocyte-Day0-9 [HG-U133A]


title: PlasmaCell-FromBoneMarrow-4 [HG-U133A]

description: Gene expression data from resting bone marrow plasma cells

source_name: Plasma cells from bone marrow

value: bone marrow

value: Plasma cells


title: Monocyte-Day0-5 [HG-U133A]

value: peripheral blood


title: Monocyte-Day0-12 [HG-U133A]


title: PlasmaCell-FromBoneMarrow-3 [HG-U133A]


title: PlasmaCell-FromBoneMarrow-1 [HG-U133A]


title: Monocyte-Day0-7 [HG-U133A]


title: Monocyte-Day1-1 [HG-U133A]


title: PlasmaCell-FromBoneMarrow-2 [HG-U133A]


title: PlasmaCell-FromPBMC-3 [HG-U133A]

description: Gene expression data from resting peripheral blood plasma cells

source_name: Plasma cells from PBMC


title: PlasmaCell-FromPBMC-2 [HG-U133A]


title: Bcell-Memory_IgG_IgA-3 [HG-U133A]

description: Gene expression data from IgG/IgA memory B cells

source_name: B cells from PBMC

value: IgG/IgA memory B cells


title: Bcell-Memory_IgM-4 [HG-U133A]

description: Gene expression data from IgM memory B cells

value: IgM memory B cells


title: Bcell-Memory_IgM-3 [HG-U133A]


title: Bcell-Memory_IgM-2 [HG-U133A]


title: Monocyte-Day0-4 [HG-U133A]


title: Bcell-Memory_IgG_IgA-4 [HG-U133A]


title: Monocyte-Day0-11 [HG-U133A]


title: PlasmaCell-FromPBMC-1 [HG-U133A]


title: Bcell-Memory_IgG_IgA-2 [HG-U133A]


title: Bcell-naïve-6 [HG-U133A]

description: Gene expression data from naïve B cells

value: B cells


title: Bcell-naïve-5 [HG-U133A]

description: Gene expression data from naïve B cells


title: Bcell-Memory_IgG_IgA-1 [HG-U133A]


title: Bcell-naïve-7 [HG-U133A]

description: Gene expression data from naïve B cells


title: NKcell-IL15stimulated-6 [HG-U133A]

description: Gene expression data from IL15-activated NK cells

source_name: NK cells from PBMC

value: NK cells


title: Bcell-naïve-4 [HG-U133A]

description: Gene expression data from naïve B cells


title: Bcell-Memory_IgM-1 [HG-U133A]


title: NKcell-IL15stimulated-4 [HG-U133A]


title: Bcell-naïve-3 [HG-U133A]

description: Gene expression data from naïve B cells


title: NKcell-IL15stimulated-5 [HG-U133A]


title: Bcell-naïve-2 [HG-U133A]

description: Gene expression data from naïve B cells


title: NKcell-IL15stimulated-1 [HG-U133A]


title: NKcell-IL15stimulated-3 [HG-U133A]


title: NKcell-IL2stimulated-3 [HG-U133A]

description: Gene expression data from IL2-activated NK cells


title: NKcell-IL15stimulated-2 [HG-U133A]


title: Bcell-naïve-1 [HG-U133A]

description: Gene expression data from naïve B cells


title: NKcell-IL2stimulated-5 [HG-U133A]


title: NKcell-IL2stimulated-2 [HG-U133A]