title: Atopic subject 12, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 09, HDM stimulated CD4 T-cells

status: Public on May 05 2009

type: RNA

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

description: PBMC were from cryopreserved stocks.

hyb_protocol: The samples were hybridized to HuGene ST1.0 microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed in Expression Consol software (Affymetrix) employing the probe logarithmic intensity error algorithm (PLIER, parameters - PM-GCBG background subtraction, quantile normalization, iterPLIER summarization).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBMC-derived HDM-stimulated CD4 T-cells at 24 h

label_protocol: Total RNA was labeled employing the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s instructions (Affymetrix).

growth_protocol: PBMC from cryopreserved stocks were cultured in AIM-V medium for 24 hours.

extract_protocol: At the termination of the cultures, CD4 T-cell were isolated by immunomagnetic separation (DyNAL), and total RNA was extracted by TRIzol (Invitrogen) followed by RNeasy (QIAgen).

treatment_protocol: PBMC were cultured in the presence or absence of HDM extract (CSL).

tag: time point


title: Atopic subject 23, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 13, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.

source_name: PBMC-derived unstimulated CD4 T-cells at 24 h


title: Atopic subject 19, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 21, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 12, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 23, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 14, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 19, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 10, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 21, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 25, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 10, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 20, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 22, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 20, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 17, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 17, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 16, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 14, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 15, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 18, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 11, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 22, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 13, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 18, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 16, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 11, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 07, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 09, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 08, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 06, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 02, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 05, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 03, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 04, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 08, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 06, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 09, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 07, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 01, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 02, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 03, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 01, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: MPO CD4+CD25- (naive) I A unstimulated HG-U133A

status: Public on Apr 20 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: MPO CD4+CD25- (naiv) I A

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: 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 150.

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

growth_protocol: no stimulation

extract_protocol: Rneasy

tag: genetic modification:

tag: tissue

value: Blood


title: THU CD4+ CD25+  II A unstimulated HG-U133A

description: THU CD4+ CD25+  II A


title: Atopic subject 15, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: THU CD4+ CD25- (naive) II A unstimulated HG-U133A

description: THU CD4+ CD25- (naiv) II A


title: MPO CD4+CD25+ I B unstimulated HG-U133A

description: MPO CD4+CD25+ I B

source_name: MPO CD4+CD25+ I B unstimulated HG-U133A


title: CD4-245 (CD25-, CD3) HG-U133A

description: CD4-245 (CD25-, CD3)

growth_protocol: anti CD3 plate bound, 1µg/ml TR66 + 100U/µl IL-2 (rec_human)


title: CD4-Hg CD25+ (anti CD3, CD28) HG-U133A

description: CD4-Hg CD25+ (anti CD3, CD28)

source_name: CD4-Hg CD25+ (anti CD3, CD28) HG-U133A

growth_protocol: anti CD3 plate bound, 1µg/ml, 1µg/µl anti CD28


title: CD4-Hg CD25+ (anti CD3) HG-U133A

description: CD4-Hg CD25+ (anti CD3)

source_name: CD4-Hg CD25+ (anti CD3) HG-U133A


title: HCC4006

status: Public on Apr 15 2009

city: Cologne

first: Thomas

last: Zander

address: Kerpenerstr. 62

institute: University Hospital Cologne

description: gene expression from the human NSCLC cell line HCC4006

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133A. 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: Data were processed with dCHIP 1.3.1

label: Biotin

source_name: human NSCLC cell line HCC4006

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: exponentially growing cells

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

tag: cell line


title: HCC78

description: gene expression from the human NSCLC cell line HCC78

source_name: human NSCLC cell line HCC78


title: HCC2450

description: gene expression from the human NSCLC cell line HCC2450

source_name: human NSCLC cell line HCC2450


title: HCC366

description: gene expression from the human NSCLC cell line HCC366

source_name: human NSCLC cell line HCC366


title: HCC827

description: gene expression from the human NSCLC cell line HCC827

source_name: human NSCLC cell line HCC827


title: CD4-Hg CD25- (anti CD3) HG-U133A

description: CD4-Hg CD25- (anti CD3)

source_name: CD4-Hg CD25- (anti CD3) HG-U133A


title: CD4-245 (CD25+, CD3 u. CD28) HG-U133A

description: CD4-245 (CD25+, CD3 u. CD28)


title: CD4-245 (CD25-, CD3 u. CD28) HG-U133A

description: CD4-245 (CD25-, CD3 u. CD28)


title: HCC2935

description: gene expression from the human NSCLC cell line HCC2935

source_name: human NSCLC cell line HCC2935


title: HCC461

description: gene expression from the human NSCLC cell line HCC461

source_name: human NSCLC cell line HCC461


title: HCC2429

description: gene expression from the human NSCLC cell line HCC2429

source_name: human NSCLC cell line HCC2429


title: HCC95

description: gene expression from the human NSCLC cell line HCC95

source_name: human NSCLC cell line HCC95


title: HCC44

description: gene expression from the human NSCLC cell line HCC44

source_name: human NSCLC cell line HCC44


title: CD4-Hg CD25- (anti CD3, CD28) HG-U133A

description: CD4-Hg CD25- (anti CD3, CD28)

source_name: CD4-Hg CD25- (anti CD3, CD28) HG-U133A


title: HCC515

description: gene expression from the human NSCLC cell line HCC515

source_name: human NSCLC cell line HCC515


title: CD4-245 (CD25+, CD3) HG-U133A

description: CD4-245 (CD25+, CD3)


title: HCC2279

description: gene expression from the human NSCLC cell line HCC2279

source_name: human NSCLC cell line HCC2279


title: HCC193

description: gene expression from the human NSCLC cell line HCC193

source_name: human NSCLC cell line HCC193


title: HCC15

description: gene expression from the human NSCLC cell line HCC15

source_name: human NSCLC cell line HCC15


title: HCC1359

description: gene expression from the human NSCLC cell line HCC1359

source_name: human NSCLC cell line HCC1359


title: HCC1195

description: gene expression from the human NSCLC cell line HCC1195

source_name: human NSCLC cell line HCC1195


title: HCC1833

description: gene expression from the human NSCLC cell line HCC1833

source_name: human NSCLC cell line HCC1833


title: H661

description: gene expression from the human NSCLC cell line H661

source_name: human NSCLC cell line H661


title: H358

description: gene expression from the human NSCLC cell line H358

source_name: human NSCLC cell line H358


title: H460

description: gene expression from the human NSCLC cell line H460

source_name: human NSCLC cell line H460


title: H3255

description: gene expression from the human NSCLC cell line H3255

source_name: human NSCLC cell line H3255


title: H2887

description: gene expression from the human NSCLC cell line H2887

source_name: human NSCLC cell line H2887


title: H820

description: gene expression from the human NSCLC cell line H820

source_name: human NSCLC cell line H820


title: HUVEC infected with Control Vector , biological rep1

status: Public on Apr 17 2009

city: Boston

first: Peter

last: Oettgen

state: MA

address: Harvard Institutes of Medicine, 4 Blackfan Circle

department: Department of Medicine

country: USA

institute: Beth Israel Deaconess Medical Center

description: Gene expression data from HUVEC infected with Control Vector.

hyb_protocol: standard Affymetrix protocole

scan_protocol: GeneChips were scanned using the Affymetrix standrad scanner..

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: cell lines HUVEC (human umbilical vein EC)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: HUVEC


title: HCC1171

description: gene expression from the human NSCLC cell line HCC1171

source_name: human NSCLC cell line HCC1171


title: H2122

description: gene expression from the human NSCLC cell line H2122

source_name: human NSCLC cell line H2122


title: H28

description: gene expression from the human NSCLC cell line H28

source_name: human NSCLC cell line H28


title: H2009

description: gene expression from the human NSCLC cell line H2009

source_name: human NSCLC cell line H2009


title: H1993

description: gene expression from the human NSCLC cell line H1993

source_name: human NSCLC cell line H1993


title: H2126

description: gene expression from the human NSCLC cell line H2126

source_name: human NSCLC cell line H2126


title: H322

description: gene expression from the human NSCLC cell line H322

source_name: human NSCLC cell line H322


title: H23

description: gene expression from the human NSCLC cell line H23

source_name: human NSCLC cell line H23


title: H2052

description: gene expression from the human NSCLC cell line H2052

source_name: human NSCLC cell line H2052


title: H441

description: gene expression from the human NSCLC cell line H441

source_name: human NSCLC cell line H441


title: H1975

description: gene expression from the human NSCLC cell line H1975

source_name: human NSCLC cell line H1975


title: H2882

description: gene expression from the human NSCLC cell line H2882

source_name: human NSCLC cell line H2882


title: H2347

description: gene expression from the human NSCLC cell line H2347

source_name: human NSCLC cell line H2347


title: HUVEC infected with Control Vector,  biological rep2


title: H2087

description: gene expression from the human NSCLC cell line H2087

source_name: human NSCLC cell line H2087


title: H1792

description: gene expression from the human NSCLC cell line H1792

source_name: human NSCLC cell line H1792


title: H1666

description: gene expression from the human NSCLC cell line H1666

source_name: human NSCLC cell line H1666


title: H3122

description: gene expression from the human NSCLC cell line H3122

source_name: human NSCLC cell line H3122


title: H1755

description: gene expression from the human NSCLC cell line H1755

source_name: human NSCLC cell line H1755


title: H1437

description: gene expression from the human NSCLC cell line H1437

source_name: human NSCLC cell line H1437


title: H1648

description: gene expression from the human NSCLC cell line H1648

source_name: human NSCLC cell line H1648


title: H1355

description: gene expression from the human NSCLC cell line H1355

source_name: human NSCLC cell line H1355


title: H1650

description: gene expression from the human NSCLC cell line H1650

source_name: human NSCLC cell line H1650


title: H1395

description: gene expression from the human NSCLC cell line H1395

source_name: human NSCLC cell line H1395


title: H1819

description: gene expression from the human NSCLC cell line H1819

source_name: human NSCLC cell line H1819


title: H1770

description: gene expression from the human NSCLC cell line H1770

source_name: human NSCLC cell line H1770


title: H1299

description: gene expression from the human NSCLC cell line H1299

source_name: human NSCLC cell line H1299


title: Calu3

description: gene expression from the human NSCLC cell line Calu3

source_name: human NSCLC cell line Calu3


title: Calu6

description: gene expression from the human NSCLC cell line Calu6

source_name: human NSCLC cell line Calu6


title: H157

description: gene expression from the human NSCLC cell line H157

source_name: human NSCLC cell line H157


title: Calu1

description: gene expression from the human NSCLC cell line Calu1

source_name: human NSCLC cell line Calu1


title: A549

description: gene expression from the human NSCLC cell line A549

source_name: human NSCLC cell line A549


title: Atopic subject 04, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.

source_name: PBMC-derived unstimulated CD4 T-cells at 24 h


title: Atopic subject 05, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.

source_name: PBMC-derived HDM-stimulated CD4 T-cells at 24 h


title: IgM memory B cells, rep 2

status: Public on Dec 31 2008

city: Darlinghurst

first: Stuart

last: Tangye

state: NSW

address: 384 Victoria St

department: Immunology

institute: Garvan Institute of Medical Research

description: Replicate 2 of 2

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 set GeneChips. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method, following which absolute expression or comparison analysis were performed by the software using its statistical expression algorithm. Genes with a fold change of 2 or more, p<0.05, and a present signal of more than 100 were examined.

source_name: sort-purified human splenic IgM memory B cells

label_protocol: Biotinylated cRNA were prepared according to a modified protocol published (Baugh et al, 2001) using an in vitro transcription kit (Enzo Biosciences) that amplifies and labels cRNA from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human splenic tissue (Australian Red Cross) was used as  a source of mature immune cells. Tissue was dissected  and capsule disrupted. Red blood cells were lysed and cells washed in RPMI-10%FCS. MNCs were isolated by collecting the buffy coat after layering on Ficoll-Paque.

extract_protocol: Cells were lysed and RNA extracted using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions, with the inlcusion of the DNase step.

treatment_protocol: Naïve and memory B cell subsets were isolated by cell sorting using antibodies to CD20, CD27 and Ig isotypes. Cells were washed in PBS.

tag: Untreated

tag: Tissue

value: human spleen


title: plasma cells, rep 2

description: Replicate 2 of 2

source_name: sort-purified human splenic plasma B cells


title: switched memory B cells, rep 1

description: Replicate 1 of 2

source_name: sort-purified human splenic IgGAE switched memory B cells


title: IgM memory B cells, rep 1

description: Replicate 1 of 2


title: switched memory B cells, rep 2

description: Replicate 2 of 2


title: plasma cells, rep 1

description: Replicate 1 of 2


title: naïve B cells, rep 1

description: Replicate 1 of 2

source_name: sort-purified human splenic naïve B cells


title: Infected_dendritic_cells_sample_3

status: Public on Oct 21 2008

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Sufficient amount of high quality RNA was isolated and infDC transcriptome was assessed using the HG-U133A Affymetrix microarray.

hyb_protocol: Hybridization and washing was performed following standard procedures for Affymetrix HG-U133A arrays (www.affymetrix.com) on a GeneChip Fluidic station 400, using the EukGe-WS2v4 protocol.

scan_protocol: Scanning was performed twice with filter set at 570 nm on an Agilent gene array scanner (Affymetrix).

data_processing: MAS5.0 (Affymetrix) was used for raw data measurement and quality control. dChip 2006 was used for data normalization, quality control and data analysis.

label: Biotin.

source_name: Dendritic cells infected with L.monocytogenes

label_protocol: Synthesis of biotin labeled cRNA was performed with BioArray HighYield RNA TranscriptLabeling Kit (ENZO) following standard procedures.

growth_protocol: Circulating CD14+ monocytes were positively enriched from PBMC, obtained from buffy coats of healthy donors using CD14 MicroBeads (cell purity > 95%). Immature monocyte-derived dendritic cells (immDC) were generated from the CD14+ monocytes in a serum-free medium (CellGro) supplemented with 2mM glutamine, 500 U/ml IL-4 and 800 U/ml GM-CSF for seven days (cytokines were replenished on day 3 and 5).

extract_protocol: Monocyte-derived DC were harvested 6 hours after infection with L.monocytogenes, lyzed in TRIzol and stored at –80° until further processing. RNA was extracted from cell lyzates with chloroform/isopropanol method, and was clean-uped in silica columns (Qiagen). The quality of the isolated RNA was determined by measuring the A260 / 280 ratio and the integrity of the ribosomal 28s and 18s bands were determined by agarose-gel electrophoresis.

treatment_protocol: After harvesting (day 7 of culture) immature DC were infected with Listeria monocytogenes (L.monocytogenes) at MOI of 10 and consequently incubated for 6 hours.

tag: Inhibitory monocyte-derived human dendritic cells infected with L.monocytogenes.


title: naïve B cells, rep 2

description: Replicate 2 of 2


title: Mature_dendritic_cells_sample_2

description: Sufficient amount of high quality RNA was isolated and matDC transcriptome was assessed using the HG-U133A Affymetrix microarray.

source_name: Mature dendritic cells

extract_protocol: Mature monocyte-derived DC were harvested on day 10, lyzed in TRIzol and stored at –80° until further processing. RNA was extracted from cell lyzates with chloroform/isopropanol method, and was clean-uped in silica columns (Qiagen). The quality of the isolated RNA was determined by measuring the A260 / 280 ratio and the integrity of the ribosomal 28s and 18s bands were determined by agarose-gel electrophoresis.

treatment_protocol: After harvesting (day 7 of culture) immature DC were treated with anti-CD40 mAb and TNFalpha and consequently incubated for three days to obtain mature DC (matDC).

tag: Stimulatory mature monocyte-derived human dendritic cells.


title: Mature_dendritic_cells_PGE2_sample_2

description: Sufficient amount of high quality RNA was isolated and PGE2-DC transcriptome was assessed using the HG-U133A Affymetrix microarray.

source_name: Mature dendritic cells, treated with PGE2

extract_protocol: Mature monocyte-derived PGE2-treated DC were harvested on day 10, lyzed in TRIzol and stored at –80° until further processing. RNA was extracted from cell lyzates with chloroform/isopropanol method, and was clean-uped in silica columns (Qiagen). The quality of the isolated RNA was determined by measuring the A260 / 280 ratio and the integrity of the ribosomal 28s and 18s bands were determined by agarose-gel electrophoresis.

treatment_protocol: After harvesting (day 7 of culture) immature DC were treated with anti-CD40 mAb and TNFalpha with addition of prostaglandin E2 (PGE2) and consequently incubated for three days to obtain mature DC treated with PGE2 (PGE2-DC).

tag: Inhibitory mature monocyte-derived human dendritic cells, treated with PGE2.


title: Mature_dendritic_cells_sample_3


title: Immature_dendritic_cells_sample_2

description: Sufficient amount of high quality RNA was isolated and immDC transcriptome was assessed using the HG-U133A Affymetrix microarray.

source_name: Immature dendritic cells

extract_protocol: Immature monocyte-derived DC were harvested on day 7, lyzed in TRIzol and stored at –80° until further processing. RNA was extracted from cell lyzates with chloroform/isopropanol method, and was clean-uped in silica columns (Qiagen). The quality of the isolated RNA was determined by measuring the A260 / 280 ratio and the integrity of the ribosomal 28s and 18s bands were determined by agarose-gel electrophoresis.

tag: Immature monocyte-derived human dendritic cells.


title: Immature_dendritic_cells_sample_3


title: Infected_dendritic_cells_sample_2


title: Immature_dendritic_cells_sample_1


title: Neutrophils_1

status: Public on Dec 10 2008

city: Modena

first: Francesco

last: Ferrari

address: Via G. Campi 287

department: Department of Biomedical Sciences

country: Italy

institute: University of Modena and Reggio Emilia

description: Normal human neutrophils

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.

data_processing: The data were analyzed using Bioconductor packages and RMA pre-processing procedure

source_name: Normal human neutrophils

label_protocol: RNA samples from cells of different donors were pooled to obtain 5 μg of total cellular RNA that were used for target synthesis according to the standard one-cycle Affymetrix protocol, supplied by the manufacturer (Affymetrix, Santa Clara, CA).

growth_protocol: Human granulocytes were initially collected from cell pellets obtained by Ficoll separation of peripheral blood samples. Erythrocytes contained in cell pellets were removed by means of osmotic lysis. Neutrophils (CD16+ fraction) and Eosinophils (CD16- fraction) were then purified using magnetic microbeads conjugated to mouse monoclonal anti-human CD16 Ab (Miltenyi, Auburn, CA)

extract_protocol: Total cellular RNA was isolated by means of RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer's recommendations.

tag: type

value: primary cells from healthy donors


title: Mature_dendritic_cells_PGE2_sample_3


title: Infected_dendritic_cells_sample_1

growth_protocol: Circulating CD14+ monocytes were positively enriched from PBMC, obtained from buffy coats of healthy donors using CD14 MicroBeads (cell purity > 95%). Monocyte-derived dendritic cells (mo-DC) were generated from the CD14+ monocytes in a serum-free medium (CellGro) supplemented with 2mM glutamine, 500 U/ml IL-4 and 800 U/ml GM-CSF for seven days to generate immature mo-DC (cytokines were replenished on day 3 and 5).


title: Monocytes_1

description: Normal human monocytes

source_name: Normal human monocytes

growth_protocol: Normal human monocytes were selected from the Ficoll separated peripheral blood (PB) mononuclear cells of adult samples by means of magnetic microbeads conjugated with mouse monoclonal (Mo) anti-human CD14 antibody (Ab) (Miltenyi, Auburn, CA)


title: Mature_dendritic_cells_sample_1


title: Eosinophils_1

description: Normal human eosinophils

source_name: Normal human eosinophils


title: Mature_dendritic_cells_PGE2_sample_1


title: iDC_CA_24hr

status: Public on Sep 10 2008

city: Taipei

first: Ning-Sun

last: Yang

state: Taiwan

address: No.128 Sec.2, Academia Rd.

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description: effect of 24-hour treatment of cichoic acid on iDCS

hyb_protocol: Aliquots of 15 micrograms of total cRNA per sample were hybridized to the Affymetrix gene chip HG-U133A following the manufacturer's instructions

data_processing: The cell intensities and detection from the nine hybridized oligonucleotide microarrays were derived by use of the Affymetrix Microarray Suite 5 (MAS 5.0) with default settings.

source_name: iDCs cells, CA treated, at 24hour

label_protocol: seven micrograms of total RNA from each sample was used to synthesize the first-strand cDNA with T7-Oligo (dT) primer and T7 RNA polymerase by in vitro transcription reaction. The biotinylated cRNA products were then cleaned according to the Affymetrix protocol.

growth_protocol: Monocyte-derived dendritic cells were generated from peripheral blood mononuclear cells (PBMCs) isolated from healthy volunteers blood samples as described previously [25]. Briefly, CD14+ monocytes were isolated by passing the PBMCs through a magnetic cell separation system (Miltenyi Biotec, Germany). CD14+ cells at 95% purity were cultured for 7 days in AIM-V medium in the presence of GM-CSF (1000 U/ml) and IL-4 (500 U/ml) to obtain immature dendritic cells (iDCs).

treatment_protocol: Human iDCs (10e5 cells/ml) were incubated with 0.1% DMSO (vehicle control), test plant extract or derived phytochemicals in basal medium in 96-well plates for 24 h in a 5% CO2 incubator.

tag: iDCs cells, CA treated, at 24hour


title: iDC_no_0hr_rep2

description: control

source_name: iDCs cells, no treatment at 0hour

tag: iDCs cells, no treatment at 0hour


title: iDC_DMSO_24hr

description: effect of 24-hour treatment of DMSO on iDCS

source_name: iDCs cells, DMSO treated, at 24hour

tag: iDCs cells, DMSO treated, at 24hour


title: iDC_CA_4hr

description: effect of 4 hour treatment of cichoic acid on iDCS

source_name: iDCs cells, CA treated, at 4hour

tag: iDCs cells, CA treated, at 4hour


title: iDC_BF/S+L/Ep-4hr

description: effect of 4-hour treatment of BF/S+L/Ep fraction on iDCS

source_name: iDCs cells, BF/S+L/Ep treated, at 4hour

tag: iDCs cells, BF/S+L/Ep treated, at 4hour


title: iDC_no_0hr_rep1

description: control


title: BL Day 2 siMut12 transfected biological rep2

status: Public on Aug 31 2008

city: Princeton

first: Fei

last: Huang

state: NJ

institute: Bristol-Myers Squibb Co

description: Gene expression data from cultured melanoma cancer cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained using the Affymetrix Fluidics Station 400 according to Affymetrix standard procedures

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 1500.

source_name: cultured human melanoma cancer cell BL

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

extract_protocol: Total RNA isolated from cell culture using RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: NRAS-MUT12 (siMut12) transfected cells from Day 2


title: iDC_DMSO_4hr

description: effect of 4 hour treatment of DMSO on iDCS

source_name: iDCs cells, DMSO treated, at 4hour

tag: iDCs cells, DMSO treated, at 4hour


title: BL Day 2 siSC transfected biological rep3

treatment_protocol: scrambled siRNA (siSC) transfected cells from Day 2


title: BL Day 2 siSC transfected biological rep2


title: iDC_BF/S+L/Ep-24hr

description: effect of 24-hour treatment of BF/S+L/Ep fraction on iDCS

source_name: iDCs cells, BF/S+L/Ep treated, at 24hour


title: iDC_BF/S+L/Ep-12hr

description: effect of 12-hour treatment of BF/S+L/Ep fraction on iDCS

source_name: iDCs cells, BF/S+L/Ep treated, at 12hour


title: BL Day 2 siMut12 transfected biological rep3


title: BL Day 2 siSC transfected biological rep4


title: BL Day 2 siMut10 transfected biological rep2

treatment_protocol: NRAS-MUT10 (siMut10) transfected cells from Day 2


title: BL Day 2 siMut12 transfected biological rep1


title: BL Day 2 siMut10 transfected biological rep4


title: BL Day 1 siSC transfected biological rep3

treatment_protocol: scrambled siRNA (siSC) transfected cells from Day 1


title: BL Day 2 siMut12 transfected biological rep4


title: BL Day 2 siSC transfected biological rep1


title: BL Day 2 siMut10 transfected biological rep3


title: BL Day 1 siSC transfected biological rep2


title: BL Day 1 siSC transfected biological rep4


title: BL Day 1 siMut12 transfected biological rep4

treatment_protocol: NRAS-MUT12 (siMut12) transfected cells from Day 1


title: BL Day 1 siSC transfected biological rep1


title: BL Day 2 siMut10 transfected biological rep1


title: BL Day 1 siMut12 transfected biological rep3


title: BL Day 1 siMut12 transfected biological rep2


title: BL Day 1 siMut12 transfected biological rep1


title: BL Day 1 siMut10 transfected biological rep1

treatment_protocol: NRAS-MUT10 (siMut10) transfected cells from Day 1


title: BL Day 1 siMut10 transfected biological rep4


title: BL Day 1 siMut10 transfected biological rep2


title: BL Day 0 Untransfected biological rep2

treatment_protocol: Untransfected cells from Day 0


title: 224 Day 2 siSC transfected biological rep2

source_name: cultured human melanoma cancer cell 224


title: BL Day 1 siMut10 transfected biological rep3


title: BL Day 0 Untransfected biological rep1


title: 224 Day 2 siSC transfected biological rep1


title: 224 Day 3 siSC transfected biological rep2

treatment_protocol: scrambled siRNA (siSC) transfected cells from Day 3


title: 224 Day 3 siSC transfected biological rep1


title: BL Day 0 Untransfected biological rep3


title: 224 Day 2 siMut10 transfected biological rep2


title: 224 Day 2 siSC transfected biological rep3


title: 224 Day 1 siSC transfected biological rep3


title: 224 Day 3 siSC transfected biological rep3


title: 224 Day 2 siMut10 transfected biological rep3


title: 224 Day 3 siMut10 transfected biological rep2

treatment_protocol: NRAS-MUT10 (siMut10) transfected cells from Day 3


title: 224 Day 2 siMut10 transfected biological rep1


title: 224 Day 1 siSC transfected biological rep2


title: 224 Day 1 siSC transfected biological rep1


title: 224 Day 1 siMut12 transfected biological rep1


title: 224 Day 1 siMut10 transfected biological rep3


title: 224 Day 0 Untransfected biological rep3


title: 224 Day 1 siMut12 transfected biological rep2


title: 224 Day 1 siMut10 transfected biological rep2


title: 224 Day 1 siMut12 transfected biological rep3


title: 224 Day 0 Untransfected biological rep1


title: 224 Day 1 siMut10 transfected biological rep1


title: 224 Day 0 Untransfected biological rep2


title: Cell line 537

status: Public on Aug 30 2008

city: Chicago

first: yuanyuan

last: zha

state: IL

department: Department of Pathology

institute: University of Chicago

description: Gene expression data from Cell line 537

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.Affymetrix GeneChip Scanner 3000.

data_processing: The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix). Subsequent data analysis involved the normalization of array values followed by non-supervised hierarchical clustering, using dChip software.

source_name: Cell line 537

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tumor samples were obtained by core biopsy or excisional biopsy, or were obtained form material resected from patients as part of routine clinical management.  Samples were obtained from patients who signed a written informed consent for tissue procurement clinical trials at the University of Chicago or University of Virginia.

extract_protocol: Total RNA was extracted from tumor samples (80mg each) using the GenElute Mammalian Total RNA Miniprep Kit according to the manufacturer's instructions.

treatment_protocol: Tumor was grossly separated from non-tumor tissue and a portion was quickly frozen in liquid nitrogen for preparation of RNA and for long-term storage.

tag: Cell line 537


title: Cell line 23

description: Gene expression data from Cell line 23

source_name: Cell line 23

tag: Cell line 23


title: Cell line 23B

description: Gene expression data from Cell line 23B

source_name: Cell line 23B

tag: Cell line 23B


title: Cell line 624

description: Gene expression data from Cell line 624

source_name: Cell line 624

tag: Cell line 624


title: CD14 biologic rep1

status: Public on Jul 01 2008

city: Albany

first: Stephen

middle: Henry

last: Wrzesinski

state: NY

address: 317 S. Manning Blvd

department: Medical Oncology

institute: St. Peter's Cancer Care Center

description: Gene Expression Data from CD14 cells from donor 1

hyb_protocol: The RNA was hybridized to the gene chip using the method established by Affymetrix and run on the Affymetrix system (Affymetrix, Santa Clara, CA)

scan_protocol: Affymetrix scanner at the Dartmouth Genomics and Microarray laboratory was used to scan the hybridized gene chips

data_processing: Affymetrix image and data files were directly imported in GeneTraffic Uno Microarray Data Management and Analysis Software Version 3.2, Iobion Informatics LLC, La Jolla, CA.  Data was normalized by transforming with Robust Multichip Analysis (RMA).  Fold change values were generated by comparing BDCA-4 chips to CD14 chips from the same donor.  The dataset was filtered to remove genes without at least one instance of expression change that was greater than or less than an absolute fold change value of  3 across 4 separate gene arrays (one array per four separate BDCA-4 cell isolations).  The resulting genes were analyzed using Significance Analysis of Microarrays (SAM)  to determine reproducibility across replicates as well as identify significant expression changes between cell types.   Using a two-class paired test with a significance cutoff of 0.001%, 1232 genes were identified that were significantly up or down-regulated when compared to CD14 cells.  Subsets of differentially expressed genes were further analyzed using Onto-Express to identify significantly represented ontology groups.

source_name: Autologous CD14 cells isolated from the leukapharesis samples via FACS

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

extract_protocol: Total RNA was extracted via the Quiagen RNAEasy method (Qiagen, Valencia, CA)

treatment_protocol: Cells were magnetically isolated from peripheral blood leukopharesis samples and then sorted by FACS and stored on ice prior to total RNA extraction for gene array studies

tag: unstimulated CD14 cells from same donor


title: BDCA-4 biologic rep3

description: Gene Expression Data from BDCA-4 cells from donor 3

source_name: BDCA-4 cells from peripheral blood leukapharesis samples after MACS and FACS purification

tag: unstimulated plasmacytoid DCs


title: CD14 biologic rep4

description: Gene Expression Data from CD14 cells from donor 4


title: BDCA-4 biologic rep2

description: Gene Expression Data from BDCA-4 cells from donor 2


title: SNU182_04.CEL

status: Public on Jun 24 2008

city: Budapest

first: Balazs

last: Györffy

address: Bókay 53

country: Hungary

institute: Hungarian Academy of Sciences

description: total RNA extracted from different cancer cell lines

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite version 5.0

label: standard Affymetrix procedure

source_name: hepatocellular cancer cell line

label_protocol: standard Affymetrix procedure

extract_protocol: Qiagen Rneasy

tag: cell line


title: CD14 biologic rep2

description: Gene Expression Data from CD14 cells from donor 2


title: SNU475_12.CEL


title: SKMel_13_04.CEL

source_name: melanoma cancer cell line


title: SNU449_03.CEL


title: Cell line 888

description: Gene expression data from Cell line 888

source_name: Cell line 888

tag: Cell line 888


title: Sw13_08.CEL

source_name: prostate cancer cell line


title: SKBR_03.CEL

source_name: breast cancer cell line


title: Periodontitis Neutrophils rep2

status: Public on Aug 20 2008

city: Birmingham

first: Helen

middle: Joan

last: Wright

state: West Midlands

address: St Chads Queensway

department: Oral Biology

country: United Kingdom

institute: University of Birmingham

hyb_protocol: As per manufactures instructions

scan_protocol: As per manufactures instructions

data_processing: MAS 5

source_name: chronic periodontitis patient neutrophils

label_protocol: DNase digested total RNA was used to generate double-stranded cDNA using Super-Script reagents (Life Technologies) and a T7-linked oligo(dT) primer. cRNAs were synthesized using the EnzoBioarray High Yield RNA transcript labeling kit (Affymetrix) and resulting biotinylated labeled cRNA was subsequently fragmented into 35- to 200-bp lengths using Fragmentation buffer (Affymetrix).

extract_protocol: phenol/chloroform extraction (Sigma, Trizol), the aqueous phase was combined with 70% ethanol and added to an RNeasy mini-column (Qiagen). Subsequent purification and DNase treatment were performed as recommended by the manufacturer (Qiagen). RNA was eluted in sterile water

treatment_protocol: Venous blood collected  from the ante-cubital fossa into Vacutainer tubes containing lithium heparin (17 IU/ml). Neutrophils were isolated from venous blood (lithium heparin)  using a discontinuous Percoll gradient (d=1.079:1.098) followed by erythrocyte lysis (0.83% NH4Cl containing 1% KHCO3, 0.04% Na2EDTA.2H2O & 0.25% bovine serum albumen).  Isolated cells were re-suspended in PBS supplemented with glucose (1mM) and cations (1mM MgCl2, 1.5mM CaCl2) at 1x106 cells/ml.  Cell viability, typically >98%, was determined using dye exclusion (trypan blue).

tag: RNA from neutrophils from 4 chronic periodontitis patients pooled


title: MEWO.CEL


title: CD14 biologic rep3

description: Gene Expression Data from CD14 cells from donor 3


title: BDCA-4 biologic rep1

description: Gene Expression Data from BDCA-4 cells from donor 1


title: BDCA-4 biologic rep4

description: Gene Expression Data from BDCA-4 cells from donor 4


title: Healthy Neutrophils rep1

description: RNA from neutrophils of 4 healthy subjects pooled

source_name: neutrophil_healthy subject

tag: cell type

value: unstimulated neutrophil


title: Periodontitis Neutrophils rep1

source_name: chronic Periodontitis patient neutrophils

tag: RNA from 4 chronic periodontitis patients pooled


title: SNU423_11.CEL


title: R193_09.CEL


title: R103_08.CEL


title: HT29_06.CEL

source_name: colon cancer cell line


title: Healthy Neutrophils rep2


title: Skov3_13.CEL

source_name: ovarian cancer cell line


title: SKMel19_12.CEL


title: me-43_19.CEL


title: mda231_06.CEL


title: OVKAR_14.CEL


title: HRT_18_05.CEL


title: Cx2_07.CEL


title: Du145_18.CEL


title: FUOV1_16.CEL


title: Hep_3B_01.CEL


title: colo699_05.CEL

source_name: lung cancer cell line


title: ES2_15.CEL


title: A-375_20.CEL


title: DV90_02.CEL


title: BT20_10.CEL


title: Cervical cancer cell line, MS751

status: Public on Jun 04 2008

city: New York

first: Murty

last: Vundavalli

address: 1130 St Nicholas Ave

department: Pathology

institute: Columbia University Medical Center

description: Cervical cancer cell line

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix

data_processing: GCOS

source_name: Cervical cancer cell line, MS751

label_protocol: Affymettrix protocol

extract_protocol: TRIzol

tag: cervical cancer cell line, MS751


title: Cervical cancer cell line, SiHa

description: cervical cancer cell line, SiHa

source_name: Cervical cancer cell line, SiHa

tag: cervical cancer, SiHa, squamous cell cancer


title: Monocyte infected, biological rep1

status: Public on Jan 05 2008

city: Belmont

first: Katherine

middle: J

last: Martin

address: 61 Carleton Rd

institute: BioArray Consulting

description: Gene expression data from 48 hour DV-infected monocytes.

hyb_protocol: Standard protocol.

scan_protocol: Standard protocol.

data_processing: Signal values were calculated using robust multi-array analysis (RMA) (BioConductor), transformed using inverse nlog, and then imported into GeneSpring (Agilent) for chip normlaization to 50th percentile and gene normalization to the mean of controls (where available) for each cell type independently.

source_name: Monocytes, 48 hour DV infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Blood samples were obtained from healthy volunteers. Monocytes and B cells were negatively selected from heparin-anti-coagulated blood using a rosetting antibody precipitation kit (StemCell) and maintained in RPMI 1640 medium supplemented with 10% FCS and antibiotics. Primary HUVECs were obtained from pooled umbilical cords (two to five donor pools per culture) and maintained in M199 supplemented with 10% FCS, 1 mM glutamine, endothelial cell growth stimulant, porcine intestinal heparin, and antibiotics. HUVEC cultures were split at a ratio of 1:3 or 1:4 for up to two passages.

extract_protocol: Total cellular RNA isolated using RNeasy kit (Qiagen).

treatment_protocol: DV (dengue 2 virus, New Guinea C) was cultured using the C6/36 insect cell line. HUVECs, monocytes and B cells were infected in vitro with DV. Cells were treated with uninfected C6/36 cell supernatant as a negative control (mock infection). Cells were collected for gene expression analysis at 48 h post-infection.

tag: Genotype

value: unknown

tag: Age


title: Cervical cancer cell line, SW756

description: cervical cancer cell line

source_name: Cervical cancer cell line, SW756

tag: Cell line


title: Cervical cancer cell line, HT-3

description: Cervical cancer cell line

scan_protocol: Affymetrix protocl

source_name: Cervical cancer cell line, HT-3

label_protocol: Affymetrix protocol

extract_protocol: TRIzol extraction


title: HUVEC infected, technical rep1

description: Gene expression data from 48 hour DV-infected HUVECs.

source_name: HUVECs, 48 hour DV infection


title: Monocyte control, biological rep2

description: Gene expression data from mock-infected monocytes.

source_name: Monocytes, mock-infected control


title: HUVEC infected, technical rep2


title: B-cells infected

description: Gene expression data from 48 hour DV-infected B-cells.

source_name: B-cells, 48 hour DV infection


title: C8161.CEL

source_name: melanoma cancer cell line


title: Monocyte control, biological rep1


title: Cervical cancer cell line, C-33A

description: Cell line cervical cancer

source_name: Cervical cancer cell line, C-33A


title: Monocyte infected, biological rep2


title: Cervical cancer cell line, HeLa

description: Cell line, HeLa

source_name: Cervical cancer cell line, HeLa

tag: Cervical cancer cell line, HeLa, adenocarcinoma


title: BOEC, at_risk 11

status: Public on Dec 18 2007

city: Minneapolis

middle: P.

last: Hebbel

state: MN

address: MMC 480, 420 Delaware St. SE

department: Medicine

institute: University of Minnesota

description: BOEC (blood outgrowth endothelial cells) from 20 subjects with sickle cell anemia shown to be either at-risk or not-at-risk for ischemic stroke

hyb_protocol: After we prepared biotin-labeled cRNA fragments, samples were turned over immediately to our Microarray Core Facility which used Gene Chip Hybridization Oven 640, Affymetrix FS4000 Fluidics Station for staining with a streptavidin-fluorochrome probe and washing,

scan_protocol: An Affymetrix High Resolution Scanner was used according to the manufacturer's standard manual

data_processing: For raw microarray data, we used the RMA (robust multi-array average) method to summarize expression values from probe pair values; data were background-adjusted, quantile normalized (global scaling across multiple arrays).

source_name: BOEC, at_risk 11

label_protocol: We used the Invitrogen SuperScript Choice system to reverse transcribe and synthesize double-stranded cDNA. For in vitro transcription and biotin-labeling, we synthesized biotin-labeled cRNA using the Enzo Life Sciences BioArray High Yield RNA Transcript Labeling kit. Then fragmentation of cRNA was done by standard protocol, and fragmentation was verified by gel electrophoresis.

growth_protocol: We obtained citrated fresh peripheral blood (50-100 ml) from each donor. For donors outside the Minneapolis metropolitan area, blood was shipped by same-day express delivery in Saf-T-Pak cartons that had been pre-equilibrated to room temperature. Samples were processed immediately upon arrival at the University of Minnesota. Blood buffy coat mononuclear cells were prepared and cultured on rat collagen I, in presence of endothelial cell growth factors, as previous described in detail 15,16. All samples were handled identically

extract_protocol: We prepared BOEC lysates by adding 10 ml trizol (Gibco) to each T75 flask to solubilize the sample. As necessary, trizol lysates were stored in liquid nitrogen. We then isolated total RNA, and cleaned it using an RNeasy kit (Qiagen, CA).

treatment_protocol: BOEC were always harvested at passage 3, which comprised a nominal million-fold expansion since establishing culture and amounted to ~3x107 BOEC. They were always harvested 4 hours after the last change of culture medium, and always when they were at 85-90% confluent.

tag: At Risk

tag: Sex

value: M


title: BOEC, at_risk 10

source_name: BOEC, at_risk 10

value: F


title: Cervical cancer cell line, ME-180

description: Cervical cancer cell line

source_name: Cervical cancer cell line, ME-180

tag: Cervical cancer cell line, ME-180, Human, squamous cell cancer


title: B-cells control

description: Gene expression data from mock-infected B-cells.

source_name: B-cells, mock-infected control


title: Cervical cancer cell line, CaSki

description: Cervical cancer cell line', 'squamous cell carcinoma

source_name: Cervical cancer cell line, CaSki


title: Cervical cancer cell line, C4-I

description: cervical cancer cell line

source_name: Cervical cancer cell line, C4-I

tag: 'cervical cancer cell line C4-I' , 'squamous cell cancer'


title: BOEC, at_risk 9

source_name: BOEC, at_risk 9


title: BOEC, at_risk 5

source_name: BOEC, at_risk 5


title: BOEC, at_risk 6

source_name: BOEC, at_risk 6


title: BOEC, at_risk 2

source_name: BOEC, at_risk 2


title: BOEC, at_risk 8

source_name: BOEC, at_risk 8


title: BOEC, at_risk 4

source_name: BOEC, at_risk 4


title: BOEC, at_risk 12

source_name: BOEC, at_risk 12


title: BOEC, normal 27

description: BOEC (blood outgrowth endothelial cells) from individuals that do not have sickle cell anemia

data_processing: For raw microarray data, we used the RMA (robust multi-array average) method to summarize expression values from probe pair values; data were background-adjusted, quantile normalized (global scaling across multiple arrays). Expression measures were summarized based on log transformed PM (perfect match) values using Median Polish algorithm. Then, we used locally weighted scatterplot smoothing (LOWESS) to do within-array normalization. RMA and LOWESS were performed in Genedata Expressionist Pro3.1® (Basel, Switzerland).

source_name: BOEC, normal 27

value: blood outgrowth endothelial cell

tag: status

value: normal

tag: race

value: Caucasian

tag: age

tag: sex


title: BOEC, not_at_risk 5

source_name: BOEC, not_at_risk 5


title: BOEC, not_at_risk 2

source_name: BOEC, not_at_risk 2


title: BOEC, normal 22

source_name: BOEC, normal 22

value: African American


title: BOEC, normal 20

source_name: BOEC, normal 20


title: BOEC, normal 23

source_name: BOEC, normal 23


title: BOEC, not_at_risk 3

source_name: BOEC, not_at_risk 3


title: BOEC, normal 16

source_name: BOEC, normal 16


title: BOEC, normal 24

source_name: BOEC, normal 24


title: BOEC, normal 21

source_name: BOEC, normal 21


title: BOEC, not_at_risk 4

source_name: BOEC, not_at_risk 4


title: BOEC, normal 25

source_name: BOEC, normal 25


title: BOEC, not_at_risk 1

source_name: BOEC, not_at_risk 1


title: BOEC, normal 26

source_name: BOEC, normal 26


title: BOEC, normal 18

source_name: BOEC, normal 18


title: BOEC, normal 14

source_name: BOEC, normal 14


title: BOEC, normal 12

source_name: BOEC, normal 12


title: BOEC, normal 19

source_name: BOEC, normal 19


title: BOEC, normal 17

source_name: BOEC, normal 17


title: BOEC, normal 6

source_name: BOEC, normal 6


title: BOEC, normal 13

source_name: BOEC, normal 13


title: BOEC, normal 8

source_name: BOEC, normal 8


title: BOEC, normal 15

source_name: BOEC, normal 15


title: BOEC, normal 7

source_name: BOEC, normal 7


title: BOEC, normal 11

source_name: BOEC, normal 11


title: BOEC, at_risk 3

source_name: BOEC, at_risk 3


title: BOEC, normal 4

source_name: BOEC, normal 4


title: BOEC, normal 1

source_name: BOEC, normal 1


title: BOEC, normal 2

source_name: BOEC, normal 2


title: BOEC, normal 5

source_name: BOEC, normal 5


title: BOEC, normal 10

source_name: BOEC, normal 10


title: BOEC, normal 9

source_name: BOEC, normal 9


title: Radiosensitive tumor cell line-IFN-treated-rep1

status: Public on Nov 28 2007

first: Nikolai

middle: N.

last: Khodarev

address: 5841 South Maryland Avenue

department: Radiation and Cellular Oncology

institute: The University of Chicago

description: Gene expression data from radiosensitive tumor cell line in vitro, treated by IFNalpha, IFNbeta and IFNgamma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on U133A Human GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner

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 700-800.

source_name: head&neck tumor cell line

growth_protocol: nu61 and SCC61 cell lines were maintained in DMEM/F12 (GIBCO, Carlsbad, CA), supplemented with 20% FBS, 1% hydrocortisone and !% penicillin/streptomicin at 37C, 100% humidity and 5% CO2.IFNs alpha, beta and gamma were from R&D Systems, Minneapolis, MN)

treatment_protocol: cell lines were grown to confluence: cells were transferred in 6-well plates with density 10^6/well and left overnight. Next morning, mixture of IFNa, IFNb and IFNg were added in concentrations of 100, 100 and 5 ng/ml respectively and cells were incubated 5 hours. After this, medium was decanted and cells were processed for RNA extraction.

tag: Squamous cell carcinoma


title: Radioresistant tumor cell line -untreated-rep2

description: Gene expression data from radioresistant tumor cell line in vitro


title: IL-6, Rep5

status: Public on Sep 15 2007

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

description: Interleukin 6 replicate 5

hyb_protocol: Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Data was normalized by dChip 2006 (MBEI)

source_name: Interleukin 6 replicate 5

growth_protocol: Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.

extract_protocol: Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.

treatment_protocol: Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of  manganese superoxide dismutase (MnSOD).

tag: Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells


title: IL-6, Rep1

description: Interleukin 6 replicate 1

source_name: Interleukin 6 replicate 1


title: Radiosensitive tumor cell line -IFN-treated-rep2

description: Gene expression data from radiosensitivet tumor cell line in vitro, treated by IFNalpha, IFNbeta and IFNgamma

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


title: Radiosensitive tumor cell line-untreated-rep1

description: Gene expression data from radiosensitive tumor cell line in vitro


title: Radioresistant tumor cell line-IFN-treated-rep1

description: Gene expression data from radioresistant tumor cell line in vitro, treated by IFNalpha, IFNbeta and IFNgamma


title: BOEC, normal 3

source_name: BOEC, normal 3

tag: cell type


title: Radioresistant tumor cell line -IFN-treated-rep2


title: IL-6, Rep4

description: Interleukin 6 replicate 4

source_name: Interleukin 6 replicate 4


title: IL-6, Rep2

description: Interleukin 6 replicate 2

source_name: Interleukin 6 replicate 2


title: IL-1, Rep4

description: Interleukin 1 replicate 4

source_name: Interleukin 1 replicate 4


title: IL-1, Rep3

description: Interleukin 1 replicate 3

source_name: Interleukin 1 replicate 3


title: Radiosensitive tumor cell line -untreated-rep2


title: Radioresistant tumor cell line-untreated-rep1


title: IL-1, Rep5

description: Interleukin 1 replicate 5

source_name: Interleukin 1 replicate 5


title: IL-6, Rep3

description: Interleukin 6 replicate 3

source_name: Interleukin 6 replicate 3


title: Control, Rep4

description: Control, biological replicate 4

source_name: Control, biological replicate 4


title: Control, Rep2

description: Control, biological replicate 2

source_name: Control, biological replicate 2


title: IL-1, Rep1

description: Interleukin 1 replicate 1

source_name: Interleukin 1 replicate 1


title: Control, Rep5

description: Control, biological replicate 5

source_name: Control, biological replicate 5


title: IL-1, Rep2

description: Interleukin 1 replicate 2

source_name: Interleukin 1 replicate 2


title: Control, Rep3

description: Control, biological replicate 3

source_name: Control, biological replicate 3


title: Control, Rep1

description: Control, biological replicate 1

source_name: Control, biological replicate 1


title: D07 12h TLR2/1L

status: Public on Sep 01 2007

city: Los Angeles

first: Philip

middle: T.

last: Liu

state: CA

address: 611 Charles E Young Dr. East, 522 MBI

department: Department of Medicine, Divison of Dermatology

institute: University of California at Los Angeles

description: Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide.

hyb_protocol: UCLA Microarray Core Facility

scan_protocol: UCLA Microarray Core Facility

data_processing: UCLA Microarray Core Facility

source_name: Total RNA

label_protocol: UCLA Microarray Core Facility

extract_protocol:
Trizol total RNA extraction based on manufacturer's protocol.
RNA cleanup with RNeasy kit based on manufacturer's protocol.

tag: Primary human peripherial monocytes


title: D14 12h TLR2/1L

description: Timecourse of TLR2/1 stimulated human dendritic cells with the Mycobacterium tuberculosis derived 19kDa lipopeptide.

tag: Human dendritic cells derived with GM-CSF and IL-4


title: D09 24h Media


title: D07 0h Media


title: D09 12h TLR2/1L


title: D13 12h Media


title: D15 12h Media


title: D14 12h Media


title: D09 24h TLR2/1L


title: D09 0h Media


title: D09 12h Media


title: D07 12h Media


title: D15 12h TLR2/1L


title: D01 24h Media


title: D01 3h Media


title: D01 6h TLR2/1L


title: D07 6h Media


title: D07 6h TLR2/1L


title: D01 6h Media


title: D12 12h media


title: D13 12h TLR2/1L


title: D12 12h TLR2/1L


title: D01 3h TLR2/1L


title: D03 3h TLR2/1L


title: D10 24h Media


title: D10 0h Media


title: D10 24h TLR2/1L


title: D01 12h Media


title: D01 0h Media


title: D11 24h Media


title: D03 3h Media


title: D01 12h TLR2/1L


title: D04 0h Media


title: D04 3h TLR2/1L


title: D04 3h Media


title: D05 0h Media


title: D05 6h TLR2/1L


title: D06 6h TLR2/1L


title: D05 6h Media


title: D11 0h Media


title: D02 3h Media


title: D02 3h TLR2/1L


title: D06 6h Media


title: D08 12h Media

description: Timecourse of TLR2/1 stimulated human monocytes with the Mycobacterium tuberculosis derived 19kDa lipopeptide


title: Healthy11-CD8

status: Public on Aug 22 2007

first: Gullu

last: Gorgun

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

description: peripheral blood CD8 T cells: Healthy

hyb_protocol: Following fragmentation, cRNA were hybridized for overnight at 45C on Affymetrix hu133A microarray chip.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provided the basis of subsequent analysis.

data_processing: The data were analysed using dCHIP (C Li and W Wong, Proc. Natl. Acad. Sci. Vol. 98, 31-36, 2001a. ).

source_name: peripheral blood CD8 T cells

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

growth_protocol: T cells were isolated from peripheral blood.

treatment_protocol: CD4 or CD8 T cells were isolated using negative selection magnetic labeled antibody mix.

tag: Healthy


title: D08 12h TLR2/1L

source_name: D08 0h Media


title: Healthy5-CD8

description: peripheral blood CD8 T cells: Healthy


title: Healthy10-CD8

description: peripheral blood CD8 T cells: Healthy


title: D02 0h Media


title: Healthy12-CD8

description: peripheral blood CD8 T cells: Healthy


title: Healthy6-CD8

description: peripheral blood CD8 T cells: Healthy


title: Healthy7-CD8

description: peripheral blood CD8 T cells: Healthy


title: Healthy8-CD8

description: peripheral blood CD8 T cells: Healthy


title: Healthy3-CD8

description: peripheral blood CD8 T cells: Healthy


title: D08 0h Media


title: Healthy2-CD8

description: peripheral blood CD8 T cells: Healthy


title: Healthy4-CD8

description: peripheral blood CD8 T cells: Healthy


title: Healthy1-CD8

description: peripheral blood CD8 T cells: Healthy


title: D03 0h Media


title: Healthy9-CD8

description: peripheral blood CD8 T cells: Healthy


title: CLL19-CD8

description: peripheral blood CD8 T cells: CLL

tag: CLL


title: CLL18-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL16-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL17-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL11-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL14-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL15-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL12-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL9-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL7-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL6-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL13-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL10-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL8-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL2-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL5-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL1-CD8

description: peripheral blood CD8 T cells: CLL


title: Healthy11-CD4

description: peripheral blood CD4 T cells: Healthy

source_name: peripheral blood CD4 T cells


title: Healthy12-CD4

description: peripheral blood CD4 T cells: Healthy


title: CLL3-CD8

description: peripheral blood CD8 T cells: CLL


title: CLL4-CD8

description: peripheral blood CD8 T cells: CLL


title: Healthy10-CD4

description: peripheral blood CD4 T cells: Healthy


title: Healthy7-CD4

description: peripheral blood CD4 T cells: Healthy


title: Healthy9-CD4

description: peripheral blood CD4 T cells: Healthy


title: CLL19-CD4

description: peripheral blood CD4 T cells: CLL


title: Healthy4-CD4

description: peripheral blood CD4 T cells: Healthy


title: CLL12-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL24-CD4

description: peripheral blood CD4 T cells: CLL


title: Healthy8-CD4

description: peripheral blood CD4 T cells: Healthy


title: CLL16-CD4

description: peripheral blood CD4 T cells: CLL


title: Healthy6-CD4

description: peripheral blood CD4 T cells: Healthy


title: CLL14-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL13-CD4

description: peripheral blood CD4 T cells: CLL


title: Healthy5-CD4

description: peripheral blood CD4 T cells: Healthy


title: Healthy2-CD4

description: peripheral blood CD4 T cells: Healthy


title: CLL22-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL21-CD4

description: peripheral blood CD4 T cells: CLL


title: Healthy1-CD4

description: peripheral blood CD4 T cells: Healthy


title: CLL23-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL10-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL7-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL20-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL6-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL9-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL15-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL5-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL8-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL4-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL1-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL2-CD4

description: peripheral blood CD4 T cells: CLL


title: CLL3-CD4

description: peripheral blood CD4 T cells: CLL


title: Tcell_0h_rep10

status: Public on May 01 2007

hyb_protocol: Fragmentation of cRNA transcripts and hybridization of the high-density oligonucleotide microarrays (HG-U133A arrays, Affymetrix) were performed according to the manufacturer's GeneChips Expression Analysis Technical Manual (Affymetrix).

scan_protocol: Scanning of the high-density oligonucleotide microarrays (HG-U133A arrays, Affymetrix) were performed according to the manufacturer's GeneChips Expression Analysis Technical Manual (Affymetrix).

data_processing: CEL raw data files were normalized using R

source_name: T cells resting, 0h

label_protocol: In all, 5ug of total RNA was used to generate doublestranded cDNA with a T7-(dT)24-oligonucleotide primer (Sigma-ARK, Steinheim, Germany) performed with the Superscriptt double stranded cDNA-synthese Kit (Invitrogen Life Technologies). After purification with the Sample Cleanup Module (Affymetrix, Santa Clara, USA), cDNA served as a template to prepare biotinylated cRNA via in vitro transcription, using the BioArrayt HighYieldt RNA Transcript Labeling Kit (Enzo Biochem, Farmingdale, USA). The labeled cRNA transcripts were purified using the Sample Cleanup Module (Affymetrix).

extract_protocol: CD4+ T cells were isolated from blood samples by using RosetteSep CD4+ enrichment kit (StemCell Technologies, Meylan, France); purity: > 90% as determined by flow cytometry.  RNA was isolated with Trizol(r) method according to the manufacturer's protocol. The RNA was purified with the RNeasy MiniElute Cleanup Kit (Qiagen, Hilden, Germany)

tag: T cells resting, 0h


title: Tcell_8h_rep3

source_name: T cells resting, 8h

tag: T cells resting, 8h


title: Tcell_0h_rep6


title: Tcell_0h_rep1


title: Tcell_2h_rep3

source_name: T cells resting, 2h

tag: T cells resting, 2h


title: Tcell_8h_rep1

data_processing: CEL raw data files were normalized using R.


title: Tcell_0h_rep9


title: Tcell_0h_rep4


title: Tcell_0h_rep3


title: Tcell_0h_rep2


title: Tcell_2h_rep1


title: Tcell_8h_rep2


title: KM12 hg133a21

status: Public on Mar 26 2007

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

description:
Background Avg = 40.39
Background Max = 42.4
Background Min = 38.6
Background Stdev = 0.80
Central- Avg = 804
Central- Count = 9
Corner+ Avg = 19
Corner+ Count = 32
Corner- Avg = 914
Corner- Count = 32
Noise Avg = 1.51
Noise Max = 1.7
Noise Min = 1.3
Noise Stdev = 0.06
RawQ = 1.61
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon

scan_protocol: Affymetrix CEL analysis (Percentile); Protocol Type = feature_extraction; Parameter CellMargin = 2; Parameter OutlierHigh = 1.500; Parameter OutlierLow = 1.004; Parameter Percentile = 75; Software: Affymetrix MicroArraySuite, type: feature_extraction_software; Protocol Type = image_acquisition; Software: Affymetrix MicroArraySuite, type: image_acquisition_software; Hardware: ;

data_processing: ExpressionStat; Protocol Type = bioassay_data_transformation; Parameter Alpha1 = 0.05; Parameter Alpha2 = 0.065; Parameter BG = 4; Parameter Epsilon = 0.5; Parameter Gamma1H = 0.0045; Parameter Gamma1L = 0.0045; Parameter Gamma2H = 0.006; Parameter Gamma2L = 0.006; Parameter HZ = 4; Parameter NF = 1.000000000000; Parameter Perturbation = 1.1; Parameter SF = 1.000000000000; Parameter SmoothFactorBG = 100; Parameter Tau = 0.015; Parameter VZ = 4; Software: Affymetrix GeneChip Operating Software, type: bioassay_data_transformation_software;

source_name: adenocarcinoma

label_protocol: Affymetrix Labeling Protocol; The exact protocol is not available. But Standard Operating Proceadure can be found at          http://www.affymetrix.com/support/technical/manual/expression_manual.affx         or         http://www.affymetrix.com/Auth/support/downloads/manuals/expression_ever_manual.zip         Manual number: 701025 Revision 6, page 2.1.3; Protocol Type = labeling;

growth_protocol: NCI60Adherent; RNA harvesting protocol for adherent cells           Media used:         RPMI 1640 500 ml          FBS 25 ml -use the DTP serum if possible, from Bio Whittaker, not heat         inactivated          200 mM Glutamine 5 ml           1 flask = ~15 x 106 cells yields ~ 100 ugr RNA. Grow 10 flasks.                    Cells: start from growing cells from Frederick (not frozen). Started before at         passage #8-12. Do not use past passage 20.                    Growth schedule prior to harvest: Grow cells to         ~80 confluencey. Trypsinize cells with 5 ml try-EDTA per T162, 15 min., 370C. Pipet up and         down several times w 10 ml pipet to get good dispersment of cells. Count cells. Pass cells         to as many flasks as there are cells for. When passing cells, combine flasks into a single         pool. Pass 1x106 cells into each T162 w 30 ml media.  Repeat growth cycle until 10 flasks         are available.   Refeed Refeed cells the day prior to harvest without harvesting).  Draw off         media (wo cells). Add back media, 30 ml per T162. Add back to T-162âs. 37 deg C, ON  Harvest         Target confluency 80%  # of flasks = 10   Draw off media from 1st flask. Lyse cells in 15         ml lysis buffer (w 10 ul fresh BME per ml). Scrape cells. Draw off media from 2nd flask.         Pipet lysis buffer from flask 1 into flask 2. Repeat lysis with up to 4 T162âs. Pipet into         50 ml tube.  Repeat w next set of 4 flasks.  When done, vortex 10 sec.. Draw lysate thru a         20 guage needle 12xâs. Freeze at ö800C.  Purify using Quiagen Midi Kit.  Use a maximun of         100 x 106 cells per column. More will not bind to the column.                           Company Info         ------------           Quiagen Midi Kit Cat # 75144  RLT Buffer (lysis buffer) Cat. # 79216 $60-list, $51- discounted 1-800-362-7737                    Fetal Bovine Serum 500 ml, list $261- Cat #14-502F Lot # 9S083F Cambrex (old Bio Whittaker) 1-800-638-8174                   1x PBS pH 7.3-7.5 Bio Whittaker cat #17-516F $5.30 per 500 ml bottle (1-11)                    250 ml conical tubes Corning cat #25350-250                    RPMI-1640 wo L-glutamine cat # 12-167F  $13.25 per 500 ml bottle (for 1-11 bottles) Cambrex (old Bio Whittaker) Walkersville, Md. 21793 301-898-7025 1-800-638-8174                  Trypsin (0.05%)-EDTA (0.1%) In phosphate buffered saline without calcium and magnesium. cat # 118-087-061 $4.20 per 100 ml bottle Quality Biological, Inc. 301-840-9331                    L-glutamine 200 mM, 100x Gibco-BRL cat # 25030-149 20 ml 1-800-828-6686                    162 cm2 flask cat # 3150                    Costar Tissue Culture Cell Scrapper, 25 cm Sarstedt Cat. # 83.1830                    Cells are received from Nick Scudiero,  E-mail: SCUDIERO@dtpax2.ncifcrf.gov          Also trypsin, FBS and glutamine have been coming from there as well.; Protocol Type = grow;

extract_protocol: NCI60 Extraction Protocol; Harvest         Target confluency  80%            # of flasks = 10                  Draw off media from 1st flask.         Lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml).         Scrape cells.         Draw off media from 2nd flask.         Pipet lysis buffer from flask 1 into flask 2.         Repeat lysis with up to 4 T162’s.         Pipet into 50 ml tube.                  Repeat w next set of 4 flasks.                  When done, vortex 10 sec..         Draw lysate thru a 20 guage needle 12x’s.         Freeze at –800C.                  Purify using Quiagen Midi Kit.          Use a maximun of 100 x 106 cells per column. More will not bind to the column.         ; Protocol Type = nucleic_acid_extraction;

value: adenocarcinoma


title: Tcell_0h_rep7


title: PC-3 hg133a21

description:
Background Avg = 54.83
Background Max = 61.9
Background Min = 49.5
Background Stdev = 3.02
Central- Avg = 1084
Central- Count = 9
Corner+ Avg = 22
Corner+ Count = 32
Corner- Avg = 1027
Corner- Count = 32
Noise Avg = 2.32
Noise Max = 2.8
Noise Min = 1.9
Noise Stdev = 0.14
RawQ = 2.35
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: prostate

source_name: prostate adenocarcinoma

value: prostate adenocarcinoma

value: male


title: SF-268 hg133a21

description:
Background Avg = 59.19
Background Max = 62.0
Background Min = 56.5
Background Stdev = 1.12
Central- Avg = 889
Central- Count = 9
Corner+ Avg = 20
Corner+ Count = 32
Corner- Avg = 806
Corner- Count = 32
Noise Avg = 2.55
Noise Max = 3.1
Noise Min = 2.3
Noise Stdev = 0.15
RawQ = 2.50
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

source_name: glioblastoma undifferntiated

value: glioblastoma undifferntiated

value: glioblastoma undifferentiated

value: female


title: CLL20-CD8

description: peripheral blood CD8 T cells: CLL


title: Tcell_0h_rep8


title: LOXIMVI hg133a21

description:
Background Avg = 61.60
Background Max = 64.4
Background Min = 59.3
Background Stdev = 0.75
Central- Avg = 1429
Central- Count = 9
Corner+ Avg = 44
Corner+ Count = 32
Corner- Avg = 1438
Corner- Count = 32
Noise Avg = 3.19
Noise Max = 3.9
Noise Min = 2.7
Noise Stdev = 0.24
RawQ = 2.27
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: amelanotic melanoma

value: amelanotic melanoma

value: malignant amelanotic melanoma


title: CLL11-CD4

description: peripheral blood CD4 T cells: CLL


title: NCI-ADR-RES hg133a21

description:
Background Avg = 39.21
Background Max = 41.0
Background Min = 37.8
Background Stdev = 0.67
Central- Avg = 1350
Central- Count = 9
Corner+ Avg = 24
Corner+ Count = 32
Corner- Avg = 1380
Corner- Count = 32
Noise Avg = 1.42
Noise Max = 1.6
Noise Min = 1.3
Noise Stdev = 0.06
RawQ = 1.83
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary


title: Tcell_0h_rep5


title: BT-549 hg133a21

description:
Background Avg = 36.61
Background Max = 38.7
Background Min = 33.1
Background Stdev = 1.05
Central- Avg = 1463
Central- Count = 9
Corner+ Avg = 23
Corner+ Count = 32
Corner- Avg = 1594
Corner- Count = 32
Noise Avg = 1.79
Noise Max = 2.0
Noise Min = 1.6
Noise Stdev = 0.08
RawQ = 1.85
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: breast

source_name: papillary infiltrating ductal carcinoma

value: papillary infiltrating ductal carcinoma

value: invasive papillary breast carcinoma


title: CAKI-1 hg133a21

description:
Background Avg = 36.96
Background Max = 39.2
Background Min = 35.5
Background Stdev = 0.71
Central- Avg = 989
Central- Count = 9
Corner+ Avg = 21
Corner+ Count = 32
Corner- Avg = 925
Corner- Count = 32
Noise Avg = 1.33
Noise Max = 1.6
Noise Min = 1.2
Noise Stdev = 0.05
RawQ = 1.66
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

source_name: clear cell carcinoma

value: clear cell carcinoma

value: carcinoma


title: OVCAR-8 hg133a21

description:
Background Avg = 47.09
Background Max = 49.5
Background Min = 44.6
Background Stdev = 1.14
Central- Avg = 1056
Central- Count = 9
Corner+ Avg = 29
Corner+ Count = 32
Corner- Avg = 1002
Corner- Count = 32
Noise Avg = 2.02
Noise Max = 2.4
Noise Min = 1.7
Noise Stdev = 0.10
RawQ = 2.15
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary

source_name: carcinoma

value: carcinoma-undifferentiated


title: HCT-15 hg133a21

description:
Background Avg = 49.32
Background Max = 52.2
Background Min = 47.4
Background Stdev = 0.84
Central- Avg = 1104
Central- Count = 9
Corner+ Avg = 46
Corner+ Count = 32
Corner- Avg = 1207
Corner- Count = 32
Noise Avg = 2.41
Noise Max = 2.9
Noise Min = 2.1
Noise Stdev = 0.14
RawQ = 1.99
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon

value: unknown


title: UO-31 hg133a21

description:
Background Avg = 46.48
Background Max = 48.6
Background Min = 44.9
Background Stdev = 0.90
Central- Avg = 807
Central- Count = 9
Corner+ Avg = 46
Corner+ Count = 32
Corner- Avg = 877
Corner- Count = 32
Noise Avg = 2.32
Noise Max = 2.8
Noise Min = 2.0
Noise Stdev = 0.12
RawQ = 2.02
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

source_name: renal cell carcinoma

value: renal cell carcinoma

value: renal cell carcinoma-very poorly differentiated


title: HCC-2998 hg133a21

description:
Background Avg = 71.78
Background Max = 77.1
Background Min = 67.9
Background Stdev = 1.51
Central- Avg = 1194
Central- Count = 9
Corner+ Avg = 78
Corner+ Count = 32
Corner- Avg = 1254
Corner- Count = 32
Noise Avg = 4.40
Noise Max = 5.6
Noise Min = 3.8
Noise Stdev = 0.26
RawQ = 2.84
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon


title: U251 hg133a21

description:
Background Avg = 65.44
Background Max = 78.5
Background Min = 57.5
Background Stdev = 4.45
Central- Avg = 1299
Central- Count = 9
Corner+ Avg = 39
Corner+ Count = 32
Corner- Avg = 1325
Corner- Count = 32
Noise Avg = 3.05
Noise Max = 4.3
Noise Min = 2.3
Noise Stdev = 0.33
RawQ = 2.52
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

source_name: glioblastoma undifferentiated


title: MDA-MB-231/ATCC hg133a21

description:
Background Avg = 56.17
Background Max = 62.8
Background Min = 50.4
Background Stdev = 2.70
Central- Avg = 4268
Central- Count = 9
Corner+ Avg = 58
Corner+ Count = 32
Corner- Avg = 4337
Corner- Count = 32
Noise Avg = 3.36
Noise Max = 4.4
Noise Min = 2.6
Noise Stdev = 0.33
RawQ = 2.67
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: breast

source_name: breast epithelial adenocarcinoma

value: breast epithelial adenocarcinoma


title: A498 hg133a21

description:
Background Avg = 43.36
Background Max = 44.4
Background Min = 42.0
Background Stdev = 0.41
Central- Avg = 1151
Central- Count = 9
Corner+ Avg = 23
Corner+ Count = 32
Corner- Avg = 1137
Corner- Count = 32
Noise Avg = 1.66
Noise Max = 1.9
Noise Min = 1.5
Noise Stdev = 0.06
RawQ = 1.66
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

value: adenocarcinoma


title: NCI-H522 hg133a21

description:
Background Avg = 55.68
Background Max = 58.3
Background Min = 52.7
Background Stdev = 1.12
Central- Avg = 1229
Central- Count = 9
Corner+ Avg = 35
Corner+ Count = 32
Corner- Avg = 1262
Corner- Count = 32
Noise Avg = 3.06
Noise Max = 3.8
Noise Min = 2.7
Noise Stdev = 0.17
RawQ = 2.60
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung


title: MALME-3M hg133a21

description:
Background Avg = 61.37
Background Max = 63.4
Background Min = 59.9
Background Stdev = 0.71
Central- Avg = 1288
Central- Count = 9
Corner+ Avg = 43
Corner+ Count = 32
Corner- Avg = 1220
Corner- Count = 32
Noise Avg = 3.00
Noise Max = 3.6
Noise Min = 2.7
Noise Stdev = 0.15
RawQ = 2.64
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: malignant melanoma

value: malignant melanoma


title: SK-MEL-5 hg133a21

description:
Background Avg = 59.01
Background Max = 62.0
Background Min = 56.1
Background Stdev = 1.01
Central- Avg = 1212
Central- Count = 9
Corner+ Avg = 44
Corner+ Count = 32
Corner- Avg = 1378
Corner- Count = 32
Noise Avg = 2.46
Noise Max = 3.1
Noise Min = 2.0
Noise Stdev = 0.18
RawQ = 2.15
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: melanoma

value: melanoma

value: melanoma-premelanotic


title: NCI-H226 hg133a21

description:
Background Avg = 65.09
Background Max = 68.4
Background Min = 62.3
Background Stdev = 0.99
Central- Avg = 1553
Central- Count = 9
Corner+ Avg = 48
Corner+ Count = 32
Corner- Avg = 1833
Corner- Count = 32
Noise Avg = 2.97
Noise Max = 3.7
Noise Min = 2.5
Noise Stdev = 0.17
RawQ = 2.46
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: squamous cell carcinoma

value: squamous cell carcinoma

value: male


title: SF-295 hg133a21

description:
Background Avg = 97.22
Background Max = 105.0
Background Min = 92.6
Background Stdev = 2.11
Central- Avg = 1332
Central- Count = 9
Corner+ Avg = 109
Corner+ Count = 32
Corner- Avg = 1680
Corner- Count = 32
Noise Avg = 5.32
Noise Max = 6.2
Noise Min = 4.7
Noise Stdev = 0.27
RawQ = 4.09
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

value: glioblastoma undifferentiated

value: female


title: SK-MEL-28 hg133a21

description:
Background Avg = 67.79
Background Max = 69.9
Background Min = 65.3
Background Stdev = 0.77
Central- Avg = 859
Central- Count = 9
Corner+ Avg = 33
Corner+ Count = 32
Corner- Avg = 781
Corner- Count = 32
Noise Avg = 3.12
Noise Max = 3.7
Noise Min = 2.9
Noise Stdev = 0.16
RawQ = 2.38
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin


title: MDA-MB-435 hg133a21

description:
Background Avg = 40.73
Background Max = 43.9
Background Min = 37.9
Background Stdev = 1.02
Central- Avg = 1429
Central- Count = 9
Corner+ Avg = 40
Corner+ Count = 32
Corner- Avg = 1735
Corner- Count = 32
Noise Avg = 1.64
Noise Max = 2.0
Noise Min = 1.4
Noise Stdev = 0.09
RawQ = 1.62
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: ductal breast carcinoma

value: ductal breast carcinoma

value: ductal breast carcinoma; metastatic site:pleural effusion; In a recent study using cDNA microarrays, the parent line (MD A-MB-435) of MDA-MB-435S clustered with cell lines of melanoma origin. Ross DT et al. Nature Genetics 24:227-235, 2000 )


title: Healthy3-CD4

description: peripheral blood CD4 T cells: Healthy

source_name: peripheral blood CD4 T cells


title: OVCAR-4 hg133a21

description:
Background Avg = 47.82
Background Max = 50.4
Background Min = 46.1
Background Stdev = 0.86
Central- Avg = 1053
Central- Count = 9
Corner+ Avg = 28
Corner+ Count = 32
Corner- Avg = 1087
Corner- Count = 32
Noise Avg = 2.21
Noise Max = 2.7
Noise Min = 1.9
Noise Stdev = 0.15
RawQ = 2.01
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary


title: Tcell_2h_rep2


title: SW-620 hg133a21

description:
Background Avg = 49.86
Background Max = 54.7
Background Min = 45.4
Background Stdev = 2.10
Central- Avg = 748
Central- Count = 9
Corner+ Avg = 20
Corner+ Count = 32
Corner- Avg = 802
Corner- Count = 32
Noise Avg = 2.09
Noise Max = 2.6
Noise Min = 1.8
Noise Stdev = 0.12
RawQ = 2.13
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon


title: OVCAR-5 hg133a21

description:
Background Avg = 65.49
Background Max = 68.5
Background Min = 61.4
Background Stdev = 1.33
Central- Avg = 1648
Central- Count = 9
Corner+ Avg = 33
Corner+ Count = 32
Corner- Avg = 1288
Corner- Count = 32
Noise Avg = 2.69
Noise Max = 3.1
Noise Min = 2.3
Noise Stdev = 0.16
RawQ = 2.40
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary

value: adenocarcinoma-wd


title: COLO205 hg133a21

description:
Background Avg = 63.33
Background Max = 66.9
Background Min = 60.9
Background Stdev = 1.01
Central- Avg = 1316
Central- Count = 9
Corner+ Avg = 55
Corner+ Count = 32
Corner- Avg = 1539
Corner- Count = 32
Noise Avg = 3.17
Noise Max = 4.0
Noise Min = 2.7
Noise Stdev = 0.22
RawQ = 2.49
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon


title: M14 hg133a21

description:
Background Avg = 40.12
Background Max = 42.7
Background Min = 38.6
Background Stdev = 0.86
Central- Avg = 1492
Central- Count = 9
Corner+ Avg = 23
Corner+ Count = 32
Corner- Avg = 1456
Corner- Count = 32
Noise Avg = 1.49
Noise Max = 1.7
Noise Min = 1.3
Noise Stdev = 0.06
RawQ = 1.90
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: melanoma-melanotic

value: melanoma-melanotic


title: T47D hg133a21

description:
Background Avg = 44.20
Background Max = 48.5
Background Min = 42.2
Background Stdev = 1.05
Central- Avg = 1481
Central- Count = 9
Corner+ Avg = 35
Corner+ Count = 32
Corner- Avg = 1649
Corner- Count = 32
Noise Avg = 1.70
Noise Max = 1.9
Noise Min = 1.5
Noise Stdev = 0.07
RawQ = 1.96
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: breast

source_name: breast epithelial carcinoma

value: breast epithelial carcinoma

value: infiltrating ductal carcinoma


title: UACC-257 hg133a21

description:
Background Avg = 80.99
Background Max = 87.3
Background Min = 76.5
Background Stdev = 2.01
Central- Avg = 1467
Central- Count = 9
Corner+ Avg = 86
Corner+ Count = 32
Corner- Avg = 1720
Corner- Count = 32
Noise Avg = 3.99
Noise Max = 4.9
Noise Min = 3.3
Noise Stdev = 0.30
RawQ = 2.86
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

value: unknown


title: SK-OV-3 hg133a21

description:
Background Avg = 40.81
Background Max = 43.0
Background Min = 39.8
Background Stdev = 0.57
Central- Avg = 1384
Central- Count = 9
Corner+ Avg = 31
Corner+ Count = 32
Corner- Avg = 1236
Corner- Count = 32
Noise Avg = 1.40
Noise Max = 1.6
Noise Min = 1.3
Noise Stdev = 0.05
RawQ = 1.68
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary

source_name: adenocarcinoma


title: HCT-116 hg133a21

description:
Background Avg = 60.76
Background Max = 63.4
Background Min = 58.1
Background Stdev = 0.92
Central- Avg = 1527
Central- Count = 9
Corner+ Avg = 35
Corner+ Count = 32
Corner- Avg = 1578
Corner- Count = 32
Noise Avg = 2.75
Noise Max = 3.1
Noise Min = 2.2
Noise Stdev = 0.13
RawQ = 2.35
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon

source_name: carcinoma very poorly differentiated

value: carcinoma very poorly differentiated

value: carcinoma


title: DU-145 hg133a21

description:
Background Avg = 49.84
Background Max = 53.5
Background Min = 47.6
Background Stdev = 1.00
Central- Avg = 1339
Central- Count = 9
Corner+ Avg = 26
Corner+ Count = 32
Corner- Avg = 1341
Corner- Count = 32
Noise Avg = 2.03
Noise Max = 2.2
Noise Min = 1.8
Noise Stdev = 0.07
RawQ = 2.19
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: prostate


title: SN12C hg133a21

description:
Background Avg = 47.02
Background Max = 49.7
Background Min = 44.6
Background Stdev = 0.88
Central- Avg = 1207
Central- Count = 9
Corner+ Avg = 32
Corner+ Count = 32
Corner- Avg = 1294
Corner- Count = 32
Noise Avg = 2.19
Noise Max = 2.6
Noise Min = 1.9
Noise Stdev = 0.12
RawQ = 1.88
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

value: renal cell carcinoma

value: renal cell carcinoma-poorly differentiated


title: RXF-393 hg133a21

description:
Background Avg = 57.92
Background Max = 60.6
Background Min = 55.2
Background Stdev = 1.06
Central- Avg = 1031
Central- Count = 9
Corner+ Avg = 23
Corner+ Count = 32
Corner- Avg = 820
Corner- Count = 32
Noise Avg = 2.23
Noise Max = 2.6
Noise Min = 1.9
Noise Stdev = 0.13
RawQ = 2.16
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

source_name: hypernephroma

value: hypernephroma

value: hypernephroma-poorly differentiated


title: EKVX hg133a21

description:
Background Avg = 42.92
Background Max = 46.3
Background Min = 40.1
Background Stdev = 1.27
Central- Avg = 935
Central- Count = 9
Corner+ Avg = 28
Corner+ Count = 32
Corner- Avg = 1109
Corner- Count = 32
Noise Avg = 2.03
Noise Max = 2.4
Noise Min = 1.8
Noise Stdev = 0.10
RawQ = 1.93
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

value: adenocarcinoma


title: NCI-H322M hg133a21

description:
Background Avg = 70.97
Background Max = 73.2
Background Min = 66.9
Background Stdev = 1.25
Central- Avg = 1918
Central- Count = 9
Corner+ Avg = 44
Corner+ Count = 32
Corner- Avg = 1546
Corner- Count = 32
Noise Avg = 2.97
Noise Max = 3.5
Noise Min = 2.5
Noise Stdev = 0.16
RawQ = 2.52
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: small cell bronchioalveolar carcinoma

value: small cell bronchioalveolar carcinoma

value: male


title: 786-0 hg133a21

description:
Background Avg = 31.94
Background Max = 34.0
Background Min = 29.2
Background Stdev = 0.82
Central- Avg = 777
Central- Count = 9
Corner+ Avg = 15
Corner+ Count = 32
Corner- Avg = 788
Corner- Count = 32
Noise Avg = 1.31
Noise Max = 1.5
Noise Min = 1.1
Noise Stdev = 0.05
RawQ = 1.53
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney


title: SF-539 hg133a21

description:
Background Avg = 64.64
Background Max = 69.4
Background Min = 60.9
Background Stdev = 1.66
Central- Avg = 1436
Central- Count = 9
Corner+ Avg = 37
Corner+ Count = 32
Corner- Avg = 1473
Corner- Count = 32
Noise Avg = 3.14
Noise Max = 3.7
Noise Min = 2.7
Noise Stdev = 0.19
RawQ = 2.75
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

source_name: glial neoplasm

value: glial neoplasm

value: female


title: HOP-62 hg133a21

description:
Background Avg = 55.65
Background Max = 60.3
Background Min = 52.7
Background Stdev = 1.55
Central- Avg = 1515
Central- Count = 9
Corner+ Avg = 29
Corner+ Count = 32
Corner- Avg = 1835
Corner- Count = 32
Noise Avg = 2.44
Noise Max = 2.9
Noise Min = 2.1
Noise Stdev = 0.10
RawQ = 2.66
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: adenocarcinoma-undifferentiated

value: adenocarcinoma-undifferentiated


title: IGROV1 hg133a31

description:
Background Avg = 36.47
Background Max = 37.5
Background Min = 34.9
Background Stdev = 0.62
Central- Avg = 2129
Central- Count = 9
Corner+ Avg = 27
Corner+ Count = 32
Corner- Avg = 2353
Corner- Count = 32
Noise Avg = 1.43
Noise Max = 1.6
Noise Min = 1.2
Noise Stdev = 0.06
RawQ = 1.59
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary

source_name: cystoadenocarcinoma

value: cystoadenocarcinoma


title: SNB-19 hg133a21

description:
Background Avg = 63.67
Background Max = 70.1
Background Min = 59.5
Background Stdev = 1.59
Central- Avg = 996
Central- Count = 9
Corner+ Avg = 42
Corner+ Count = 32
Corner- Avg = 1034
Corner- Count = 32
Noise Avg = 3.42
Noise Max = 4.2
Noise Min = 2.9
Noise Stdev = 0.20
RawQ = 2.61
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

value: glioblastoma undifferentiated


title: MDA-N hg133a21

description:
Background Avg = 43.00
Background Max = 47.5
Background Min = 38.7
Background Stdev = 1.85
Central- Avg = 2001
Central- Count = 9
Corner+ Avg = 26
Corner+ Count = 32
Corner- Avg = 1927
Corner- Count = 32
Noise Avg = 1.64
Noise Max = 1.9
Noise Min = 1.5
Noise Stdev = 0.09
RawQ = 1.80
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: MDA-N was derived from MDA-MB435 by transfection with a plasmid designed to express erbB2. MDA-N and MDA-MB435 are very similar under non selective conditions.


title: IGROV1 hg133a21

description:
Background Avg = 44.11
Background Max = 46.4
Background Min = 42.6
Background Stdev = 0.63
Central- Avg = 2929
Central- Count = 9
Corner+ Avg = 51
Corner+ Count = 32
Corner- Avg = 2672
Corner- Count = 32
Noise Avg = 1.95
Noise Max = 2.3
Noise Min = 1.7
Noise Stdev = 0.10
RawQ = 1.78
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary


title: OVCAR-3 hg133a21

description:
Background Avg = 50.09
Background Max = 53.4
Background Min = 48.1
Background Stdev = 0.99
Central- Avg = 1110
Central- Count = 9
Corner+ Avg = 41
Corner+ Count = 32
Corner- Avg = 1098
Corner- Count = 32
Noise Avg = 2.52
Noise Max = 3.0
Noise Min = 2.1
Noise Stdev = 0.16
RawQ = 2.12
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary


title: MCF7 hg133a31

description:
Background Avg = 55.81
Background Max = 58.5
Background Min = 53.3
Background Stdev = 0.83
Central- Avg = 3273
Central- Count = 9
Corner+ Avg = 63
Corner+ Count = 32
Corner- Avg = 3876
Corner- Count = 32
Noise Avg = 2.63
Noise Max = 3.1
Noise Min = 2.3
Noise Stdev = 0.13
RawQ = 2.25
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: breast

value: breast epithelial adenocarcinoma


title: ACHN hg133a21

description:
Background Avg = 45.52
Background Max = 47.7
Background Min = 43.7
Background Stdev = 0.87
Central- Avg = 800
Central- Count = 9
Corner+ Avg = 20
Corner+ Count = 32
Corner- Avg = 884
Corner- Count = 32
Noise Avg = 1.85
Noise Max = 2.1
Noise Min = 1.6
Noise Stdev = 0.10
RawQ = 2.11
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

source_name: renal cell carcinoma

value: renal cell carcinoma-poor or moderately differentiated


title: SK-MEL-2 hg133a21

description:
Background Avg = 51.70
Background Max = 56.0
Background Min = 49.6
Background Stdev = 1.06
Central- Avg = 872
Central- Count = 9
Corner+ Avg = 22
Corner+ Count = 32
Corner- Avg = 925
Corner- Count = 32
Noise Avg = 1.92
Noise Max = 2.2
Noise Min = 1.7
Noise Stdev = 0.07
RawQ = 1.98
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

value: melanoma


title: HT29 hg133a21

description:
Background Avg = 62.96
Background Max = 66.3
Background Min = 60.5
Background Stdev = 0.97
Central- Avg = 1063
Central- Count = 9
Corner+ Avg = 48
Corner+ Count = 32
Corner- Avg = 1362
Corner- Count = 32
Noise Avg = 2.72
Noise Max = 3.3
Noise Min = 2.2
Noise Stdev = 0.18
RawQ = 2.35
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon


title: HS578T hg133a21

description:
Background Avg = 57.74
Background Max = 79.3
Background Min = 47.6
Background Stdev = 6.73
Central- Avg = 3356
Central- Count = 9
Corner+ Avg = 46
Corner+ Count = 32
Corner- Avg = 3591
Corner- Count = 32
Noise Avg = 3.02
Noise Max = 3.9
Noise Min = 2.4
Noise Stdev = 0.32
RawQ = 2.49
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: breast

source_name: breast epithelial carcinosarcoma

value: breast epithelial carcinosarcoma

value: carcinosarcoma


title: NCI-H460 hg133a21

description:
Background Avg = 50.95
Background Max = 53.1
Background Min = 48.6
Background Stdev = 0.64
Central- Avg = 2613
Central- Count = 9
Corner+ Avg = 39
Corner+ Count = 32
Corner- Avg = 2475
Corner- Count = 32
Noise Avg = 2.31
Noise Max = 2.8
Noise Min = 2.0
Noise Stdev = 0.12
RawQ = 2.23
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: large cell carcinoma-undifferentiated

value: unknown

value: large cell carcinoma-undifferentiated

value: carcinoma


title: TK-10 hg133a21

description:
Background Avg = 51.54
Background Max = 59.5
Background Min = 44.6
Background Stdev = 2.79
Central- Avg = 1530
Central- Count = 9
Corner+ Avg = 39
Corner+ Count = 32
Corner- Avg = 1808
Corner- Count = 32
Noise Avg = 2.90
Noise Max = 4.3
Noise Min = 2.3
Noise Stdev = 0.34
RawQ = 2.28
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

source_name: renal spindle cell carcinoma

value: renal spindle cell carcinoma