title: NKcell-IL2stimulated-4 [HG-U133A]


title: NKcell-IL2stimulated-1 [HG-U133A]

status: Public on Jul 13 2010

type: RNA

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

description: Gene expression data from IL2-activated NK cells

hyb_protocol: cRNA was hybridized on GeneChip HGU133A.

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

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: NK cells from PBMC

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

extract_protocol: RNeasy Mini Kit (Qiagen)

tag: tissue

value: peripheral blood

tag: cell type

value: NK cells

tag: treatment agent

tag: time post-treatment


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

description: Gene expression data from resting NK cells


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


title: MemoryTcell-RO-unactivated-1 [HG-U133A]

description: Gene expression data from resting memory T cells

source_name: CD4+ CD45RO+ CD45RA- T cells from PBMC

value: CD4+ CD45RO+ CD45RA- T cells


title: MemoryTcell-RO-activated-2 [HG-U133A]

description: Gene expression data from activated memory T cells


title: MemoryTcell-RO-activated-1 [HG-U133A]


title: MemoryTcell-RO-unactivated-2 [HG-U133A]


title: MemoryTcell-RO-unactivated-3 [HG-U133A]


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


title: CD4Tcell-Th2-restimulated48hour-3 [HG-U133A]

description: Gene expression data from Th2-polarized cells 48 hrs post-restimulation

source_name: CD4+ T cells from PBMC

value: CD4+ T cells

value: 48 hrs


title: CD4Tcell-Th2-restimulated48hour-1 [HG-U133A]


title: MemoryTcell-RO-activated-3 [HG-U133A]


title: CD4Tcell-Th2-restimulated12hour-1 [HG-U133A]

description: Gene expression data from Th2-polarized cells 12 hrs post-restimulation

value: 12 hrs


title: CD4Tcell-Th2-restimulated12hour-3 [HG-U133A]


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


title: CD4Tcell-Th2-restimulated48hour-2 [HG-U133A]


title: CD4Tcell-Th1-restimulated48hour-2 [HG-U133A]

description: Gene expression data from Th1-polarized cells 48 hrs post-restimulation


title: CD4Tcell-Th1-restimulated48hour-3 [HG-U133A]


title: CD4Tcell-N0-3 [HG-U133A]

description: Gene expression data from resting CD4+ T cells

value: control


title: CD4Tcell-Th2-restimulated12hour-2 [HG-U133A]


title: Monocyte-Day1-4 [HG-U133A]

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

source_name: Monocytes from PBMC

value: Monocytes

value: macrophage differentiation medium

value: 1 day


title: CD4Tcell-Th1-restimulated12hour-2 [HG-U133A]

description: Gene expression data from Th1-polarized cells 12 hrs post-restimulation


title: CD4Tcell-Th1-restimulated48hour-1 [HG-U133A]


title: CD4Tcell-N0-1 [HG-U133A]


title: CD4Tcell-Th1-restimulated12hour-1 [HG-U133A]


title: Neutrophil_patient41_time7

status: Public on Sep 09 2010

city: St. Louis

first: J

middle: Perren

last: Cobb

state: MO

address: Campus Box 8109, 660 South Euclid Avenue

institute: Washington University in St. Louis

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

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

scan_protocol: Affymetrix GeneChip using GCOS.

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

source_name: Neutrophil

label_protocol: Affymetrix GeneChip IVT labeling

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

extract_protocol: Modiefied Qiagen Rneasy protocol


title: Monocyte-Day1-6 [HG-U133A]


title: CD8Tcell-N0-1 [HG-U133A]

description: Gene expression data from resting CD8+ T cells

source_name: CD8+ T cells from PBMC

value: CD8+ T cells


title: CD8Tcell-N0-3 [HG-U133A]


title: CD4Tcell-N0-2 [HG-U133A]


title: CD8Tcell-N0-4 [HG-U133A]


title: CD8Tcell-N0-2 [HG-U133A]


title: CAM07

status: Public on Jul 03 2010

city: Minneapolis

first: Robert

last: Hebbel

email: hebbe001@umn.edu, weixx035@umn.edu

state: MN

address: 516 Delaware St SE

department: Medicine

institute: University of Minnesota

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

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: ethnicity

value: Caucasian American

tag: age

tag: sex

value: M

tag: cytogenetics

value: normal

value: blood outgrowth endothelial cell


title: CAF04

value: F


title: CAM05


title: CAF07


title: CAM01


title: CAM06


title: CAF09


title: CAM04


title: CAM08


title: CAF03


title: CAM02


title: CAF05


title: CAF06


title: CAM03


title: CAF08


title: CAF02


title: CAF01


title: AAM11

value: African American


title: AAM12


title: AAM04


title: AAM03


title: AAM10


title: AAM05


title: AAM08


title: AAM02

value: normal; sickle trait


title: AAM07


title: AAM09


title: AAF09


title: AAM06


title: AAF08


title: AAM01


title: AAF06


title: AAF04


title: AAF02


title: Allergic asthmatic_4

status: Public on Jun 24 2010

city: Chicoutimi

first: Catherine

last: Laprise

state: Qc

address: 555 Boul. Université

country: Canada

institute: Université du Québec à Chicoutimi

description: Gene expression data from allergic asthmatic subject, without any stimulation. BAL was done at the same time of the day for each subject and only if he (she) did not experience inflammatory or allergen response.

hyb_protocol: Hybridation was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples

scan_protocol: Scanning was done using a GeneArray Scanner at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples

data_processing: The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix) and the raw image fils obtained (.CEL) were used for statistical analyses. Affy and Limma packages in Bioconductor (www.bioconductor.org) using R2.8.1 were used to perform quality tests, RMA normalization and Smyth's moderated t-test.

source_name: Alveolar macrophages

label_protocol: Probe labelling was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples

growth_protocol: Alveolar macrophages (AM) were purified by adherence (2h) from bronchoalveolar lavage (BAL), giging purity of > 98%

extract_protocol: RNA was extracted using a silica gel-based Rneasy spin column protocol (Qiagen)

value: Alveolar macrophages from broncholaveolar lavage

tag: disease state

value: asthma


title: AAF03


title: AAF01


title: AAF05


title: AAF07


title: Control_5

description: Gene expression data from non allergic non asthmatic subject, without any stimulation. BAL was done at the same time of the day for each subject and only if he (she) did not experience inflammatory or allergen response.


title: Allergic asthmatic_3


title: Control_2


title: Control_4


title: Allergic asthmatic_5


title: Control_3


title: Allergic asthmatic_2


title: Allergic asthmatic_1


title: Control_1


title: PMN 6hr LB 1

status: Public on Jun 01 2010

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

description: LB-treated PMNs

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

scan_protocol: GeneChips were scanned using an Affymetrix scanner.

data_processing: Affymetrix GeneChip Operating Software (GCOS v1.4, http://www.affymetrix.com) was used. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene.

source_name: polymorphnuclear leukocytes, 6hr, treated with latex beads, replicate _1

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

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

treatment_protocol: Human polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors.  PMNs were treated with hospital- and community-associated strains of S. aureus at a bacteria to PMN ratio of 10:1 for 1, 2, 3 or 6 hours at 37C.  Untreated PMNs serve as controls.

value: polymorphnuclear leukocytes

tag: treatment

value: treated with latex beads


title: PMN 6hr LB 2

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with latex beads, replicate _2


title: PMN 6hr 9897 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 9897, replicate _4

value: treated with S. aureus strain 9897


title: PMN 6hr 11490 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 11490, replicate _4

value: treated with S. aureus strain 11490


title: PMN 6hr LB 3

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with latex beads, replicate _3


title: PMN 6hr 9897 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 9897, replicate _3


title: PMN 6hr 10254 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 10254, replicate _3

value: treated with S. aureus strain 10254


title: PMN 6hr 10254 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 10254, replicate _4


title: PMN 6hr 252 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 252, replicate _4

value: treated with S. aureus strain 252


title: PMN 6hr 11490 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 11490, replicate _1


title: PMN 6hr 10254 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 10254, replicate _2


title: PMN 6hr 9897 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 9897, replicate _1


title: PMN 6hr 252 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 252, replicate _1


title: PMN 6hr 252 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 252, replicate _2


title: PMN 6hr Col 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain Col, replicate 1

value: treated with S. aureus strain Col


title: PMN 6hr 10254 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 10254, replicate _1


title: PMN 6hr 9897 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 9897, replicate _2


title: PMN 6hr ctrl 3

description: control PMNs

source_name: polymorphnuclear leukocytes, 6hr, control, replicate 3

value: control


title: PMN 3hr LB 3

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with latex beads, replicate _3


title: PMN 3hr LB 4

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with latex beads, replicate _4


title: PMN 3hr LB 2

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with latex beads, replicate _2


title: PMN 6hr Col 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain Col, replicate 3


title: PMN 6hr ctrl 2

description: control PMNs

source_name: polymorphnuclear leukocytes, 6hr, control, replicate 2


title: PMN 6hr 252 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain 252, replicate _3


title: PMN 6hr ctrl 1

description: control PMNs

source_name: polymorphnuclear leukocytes, 6hr, control, replicate 1


title: PMN 6hr Col 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain Col, replicate 2


title: PMN 6hr ctrl 4

description: control PMNs

source_name: polymorphnuclear leukocytes, 6hr, control, replicate 4


title: PMN 3hr LB 1

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with latex beads, replicate _1


title: PMN 6hr Col 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 6hr, treated with S. aureus strain Col, replicate 4


title: PMN 3hr 9897 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 9897, replicate _3


title: PMN 3hr 9897 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 9897, replicate _2


title: PMN 3hr 11490 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 11490, replicate _2


title: PMN 3hr 11490 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 11490, replicate _1


title: PMN 3hr 10254 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 10254, replicate _3


title: PMN 3hr 11490 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 11490, replicate _3


title: PMN 3hr 9897 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 9897, replicate _1


title: PMN 3hr 10254 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 10254, replicate _1


title: PMN 3hr 252 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 252, replicate _3


title: PMN 3hr 10254 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 10254, replicate _4


title: PMN 3hr 252 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 252, replicate _4


title: PMN 3hr 11490 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 11490, replicate _4


title: PMN 3hr 10254 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 10254, replicate _2


title: PMN 3hr 9897 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 9897, replicate _4


title: PMN 3hr 252 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain 252, replicate _1


title: PMN 3hr ctrl 4

description: control PMNs

source_name: polymorphnuclear leukocytes, 3hr, control, replicate 4


title: PMN 3hr ctrl 3

description: control PMNs

source_name: polymorphnuclear leukocytes, 3hr, control, replicate 3


title: PMN 3hr Col 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain Col, replicate 3


title: PMN 3hr Col 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain Col, replicate 2


title: PMN 2hr LB 3

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with latex beads, replicate _3


title: PMN 3hr Col 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain Col, replicate 1


title: PMN 3hr Col 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 3hr, treated with S. aureus strain Col, replicate 4


title: PMN 2hr LB 1

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with latex beads, replicate _1


title: PMN 2hr LB 4

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with latex beads, replicate _4


title: PMN 3hr ctrl 1

description: control PMNs

source_name: polymorphnuclear leukocytes, 3hr, control, replicate 1


title: PMN 3hr ctrl 2

description: control PMNs

source_name: polymorphnuclear leukocytes, 3hr, control, replicate 2


title: PMN 2hr LB 2

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with latex beads, replicate _2


title: PMN 2hr 9897 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 9897, replicate _2


title: PMN 2hr 9897 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 9897, replicate _4


title: PMN 2hr 9897 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 9897, replicate _3


title: PMN 2hr 252 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 252, replicate _4


title: PMN 2hr 9897 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 9897, replicate _1


title: PMN 2hr 252 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 252, replicate _2


title: PMN 2hr 11490 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 11490, replicate _2


title: PMN 2hr 11490 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 11490, replicate _1


title: PMN 2hr 10254 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 10254, replicate _4


title: PMN 2hr 252 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 252, replicate _3


title: PMN 2hr 252 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 252, replicate _1


title: PMN 2hr 10254 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 10254, replicate _2


title: PMN 2hr 10254 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 10254, replicate _1


title: PMN 2hr ctrl 1

description: control PMNs

source_name: polymorphnuclear leukocytes, 2hr, control, replicate 1


title: PMN 2hr 11490 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 11490, replicate _4


title: PMN 2hr 10254 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 10254, replicate _3


title: PMN 2hr ctrl 4

description: control PMNs

source_name: polymorphnuclear leukocytes, 2hr, control, replicate 4


title: PMN 2hr 11490 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain 11490, replicate _3


title: PMN 2hr ctrl 3

description: control PMNs

source_name: polymorphnuclear leukocytes, 2hr, control, replicate 3


title: PMN 2hr ctrl 2

description: control PMNs

source_name: polymorphnuclear leukocytes, 2hr, control, replicate 2


title: PMN 2hr Col 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain Col, replicate 4


title: PMN 2hr Col 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain Col, replicate 1


title: PMN 1hr LB 4

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with latex beads, replicate _4


title: PMN 2hr Col 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 2hr, treated with S. aureus strain Col, replicate 3


title: PMN 1hr LB 3

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with latex beads, replicate _3


title: PMN 1hr 252 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 252, replicate _4


title: PMN 1hr LB 2

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with latex beads, replicate _2


title: PMN 1hr 9897 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 9897, replicate _2


title: PMN 1hr 252 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 252, replicate _2


title: PMN 1hr 9897 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 9897, replicate _3


title: PMN 1hr 9897 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 9897, replicate _1


title: PMN 1hr 9897 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 9897, replicate _4


title: PMN 1hr 252 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 252, replicate _3


title: PMN 1hr 11490 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 11490, replicate _3


title: PMN 1hr 252 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 252, replicate _1


title: PMN 1hr 11490 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 11490, replicate _1


title: PMN 1hr LB 1

description: LB-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with latex beads, replicate _1


title: PMN 1hr 11490 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 11490, replicate _4


title: PMN 1hr 11490 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 11490, replicate _2


title: PMN 1hr ctrl 1

description: control PMNs

source_name: polymorphnuclear leukocytes, 1hr, control, replicate 1


title: PMN 1hr 10254 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 10254, replicate _1


title: PMN 1hr ctrl 4

description: control PMNs

source_name: polymorphnuclear leukocytes, 1hr, control, replicate 4


title: PMN 1hr ctrl 3

description: control PMNs

source_name: polymorphnuclear leukocytes, 1hr, control, replicate 3


title: PMN 1hr Col 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain Col, replicate 3


title: PMN 1hr 10254 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 10254, replicate _2


title: PMN 1hr 10254 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 10254, replicate _4


title: PMN 1hr Col 1

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain Col, replicate 1


title: PMN 1hr 10254 3

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain 10254, replicate _3


title: PMN 0hr ctrl 3

description: control PMNs

source_name: polymorphnuclear leukocytes, 0hr, control, replicate 3


title: PMN 1hr Col 4

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain Col, replicate 4


title: PMN 0hr ctrl 2

description: control PMNs

source_name: polymorphnuclear leukocytes, 0hr, control, replicate 2


title: PMN 1hr Col 2

description: SA-treated PMNs

source_name: polymorphnuclear leukocytes, 1hr, treated with S. aureus strain Col, replicate 2


title: PMN 0hr ctrl 1

description: control PMNs

source_name: polymorphnuclear leukocytes, 0hr, control, replicate 1


title: PMN 0hr ctrl 4

description: control PMNs

source_name: polymorphnuclear leukocytes, 0hr, control, replicate 4


title: PMN 1hr ctrl 2

description: control PMNs

source_name: polymorphnuclear leukocytes, 1hr, control, replicate 2


title: Cord blood CD4+_act+IFN-alpha_48h_rep1

status: Public on Apr 11 2010

city: Turku

first: Sanna

last: Filén

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology

description: biological replicate 1

hyb_protocol: The biotinylated and fragmented cRNA was hybridized to Affymetrix GeneChip Human Genome U133A arrays overnight (16-18 hours) at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with AutoLoader.

data_processing: The data was analyzed using MAS 5.0. Data was normalized to target intensity 50.

source_name: human cord blood CD4+ T cell, activated and IFN-alpha treated, 48h

label_protocol: Amplification was started from 5 micrograms of total RNA. The cDNA/cRNA synthesis reactions and sample cleanup steps were performed according to Affymetrix´s GeneChip Expression Analysis Technical Manual.

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturers instructions.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) and further purified with Rneasy mini kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in dH2O.

treatment_protocol: Cells were cultured on 24-well plates, 2x106 cells/1ml Yssel´s medium, activated via T cell receptor (plate bound antiCD3 500 ng/well, and soluble antiCD28 500 ng/ml, Immunotech, France). Cytokines IL-12 (2.5 ng/ml, R&D Systems), highly purified human leukocyte IFN-alpha (100 U/ml, Red Cross Finland Blood Service) or the combination of IL-12 (2.5 ng/ml) + IL-18 (25 ng/ml, Medical & Biological Laboratories) were added to induce Th1 differentiation. Cells were harvested at 2h, 6h or 48h.

tag: cell source

value: human neonatal umbilical cord blood

value: CD4+ T cell


title: Cord blood CD4+_act+IL-12+IL-18_48h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ T cell, activated and IL-12+IL-18 treated, 48h


title: Unstimulated naïve CD4 cells replicate 2

status: Public on May 29 2010

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression interrogating 54675 transcripts

hyb_protocol: Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix  900432) and cRNA was synthesized,  labeled,  fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix,  Santa Clara,  CA)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: For both Treg and naive CD4 experiments, two sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression in Tregs increased or decreased by twofold or more relative to naive CD4 cells as a common standard was identified and used for further analysis. The data was normalized using the justRMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 2 independent arrays for each cell type and scored P < 0.05 by the t-test.

source_name: Unstimulated naïve CD4 cells sorted from the the PBMC of a healthy human sample, replicate 2

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: Peripheral blood mononuclear cells (PBMCs) were collected using vacutainers with ACD solution B of trisodium citrate and isolated using Ficoll-Hypaque density centrifugation according to the recommended protocol (Amersham Pharmacia, Uppsala, Sweden).

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

treatment_protocol: PBMCs isolated from random healthy blood donors were first labeled with a CD25-PE antibody, and then isolated with goat anti-mouse labeled magnetic beads by magnetic column separation.  Staining of the isolated populations with Foxp3 specific antibody revealed that roughly 50% of the positively selected cells expressed Foxp3, and these cells correlated with the CD25hi population.  The percent purity of CD25 isolated cells varied from 50% to 95%.  The CD25 selected cells could be sorted based on CD25hi expression.  Staining of pre- and post-sorted populations with Foxp3 antibodies showed an increase in purity of TR cells from approximately 60% to over 90% following cell sorting. Sorted cells were able to inhibit the proliferation of autologous CD4 cells in co-culture assays.

value: naïve CD4


title: Cord blood CD4+_act+IFN-alpha_2h

description: biological replicate 1

source_name: human cord blood CD4+ T cell, activated and IFN-alpha treated, 2h


title: Cord blood CD4+_act+IL-12_48h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ T cell, activated and IL-12 treated, 48h


title: Cord blood CD4+_act+IFN-alpha_48h_rep2

description: biological replicate 2


title: Cord blood CD4+_act+IFN-alpha_6h

description: biological replicate 1

source_name: human cord blood CD4+ T cell, activated and IFN-alpha treated, 6h


title: Unstimulated nTreg cells, replicate 2

source_name: Unstimulated Treg cells sorted from the the PBMC of a healthy human sample, replicate 2

value: nTreg


title: Cord blood CD4+_act_48h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ T cell, activated, 48h


title: Cord blood CD4+_act_2h

description: biological replicate 1

source_name: human cord blood CD4+ T cell, activated, 2h


title: Cord blood CD4+_act_6h

description: biological replicate 1

source_name: human cord blood CD4+ T cell, activated, 6h


title: Cord blood CD4+_act+IL-12+IL-18_48h_rep2

description: biological replicate 2


title: Cord blood CD4+_act+IL-12_48h_rep2

description: biological replicate 2


title: Unstimulated nTreg cells, replicate 1

source_name: Unstimulated Treg cells sorted from the the PBMC of a healthy human sample, replicate 1


title: Unstimulated naïve CD4 cells replicate 1

source_name: Unstimulated naïve CD4 cells sorted from the the PBMC of a healthy human sample, replicate 1


title: CXCL4_B

status: Public on Mar 01 2010

city: Eggenfelden

first: Christian

middle: Albert

last: Gleissner

address: Simonsöder Allee 20

department: Cardiology

country: Germany

institute: Rottal-Inn Kliniken KU

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0).

data_processing: Microarray gene expression intensities were normalized to ensure that all chips have the same interquartile ranges (IQR). In addition, they were log-transformed with base 2, which transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.r-project.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering and heat-map analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix web site (www.affymetrix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyze. We eliminated nonexpressed (within 2 SD from zero in all conditions) and housekeeping genes [not significantly regulated with false discovery rate (FDR) <0.05]. We analyzed the regulated genes in two approaches; candidate gene analysis using LPE, HEM, and heat-map analysis, and unbiased analysis of all regulated genes without prior knowledge such using hierarchical clustering analysis.

source_name: primary human monocyte-derived macrophages

label_protocol: Standard Affymetrix protocol.

growth_protocol: With approval from the institutional review board, peripheral blood mononuclear cells were isolated from human peripheral blood using Histopaque (Sigma, St.Louis, MO) followed by negative isolation with magnetic beads (Stem cell, Vancouver, Canada). Monocyte purity was 96.2 ± 0.2 % as assessed by CD14 expression. After red blood cell lysis and several wash steps with 1 mM EDTA, monocytes were essentially free from platelet contamination as demonstrated by virtual absence of CD41 positivity in flow cytometry (data not shown). Monocytes were cultured in macrophage serum-free medium (Gibco, Carlsbard, CA) supplemented with Nutridoma SP (Roche, Indianapolis, IN) and penicillin/streptomycin (Sigma, St. Louis, MO) for six days in the presence of 100 ng/ml rhMCSF (Peprotech, Rocky Hill, NJ) or 1 µM rhCXCL4 (Peprotech). The concentration of 1 µM rhCXCL4 was chosen because this concentration was previously demonstrated to be sufficient to induce macrophage differentiation from monocytes (13). Furthermore, our own preliminary experiments confirmed that after six days, this concentration induced expression of typical macrophage markers like CD11b or CD68 to a similar extent as MCSF (Fig. 1 and data not shown).

extract_protocol: For each condition RNA was isolated from macrophages derived from two donors using columns including a DNAse-step followed by reverse transcription (all reagents from Qiagen, Valencia, CA).

treatment_protocol: Please see growth protocol.

tag: differentiation factor


title: MCSF_A

value: primary human monocyte-derived macrophages

value: MCSF


title: MCSF_B


title: Cord blood CD4+_act_48h_rep2

description: biological replicate 2


title: PMN_mock_60min_rep1

city: St Louis

first: Rekha

last: Meyer

address: 4320 Forest Park Av

institute: Washington University School of Medicine

description: Gene expression data from neutrophils exposed to RPMI media only for 60 minutes; replicate 1.

hyb_protocol: Chips hybridized according to Manufacturer's protocol

data_processing: Data corrected to 1500 Baseline

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: Neutrophils were purified from the whole blood of healthy adult male and female volunteers and used immediately.

extract_protocol: Extraction of total RNA was performed using the Qiagen RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Purified human neutrophils were incubated in a 24 well dish for 60 minutes at 37 degrees C and 5% CO2 with or without bacteria at a multiplicity of infection of 10 bacteria per neutrophil.

tag: gender

value: male

value: neutrophils


title: PMN_UTI89_60min_rep1

description: Gene expresssion data from neutrophils exposed to uropathogenic Escherichia coli strain UTI89 for 60 minutes in RPMI media; replicate 1.


title: PMN_MG1655_60min_rep1

description: Gene expression data from neutrophils exposed to commensal Escherichia coli strain MG1655 for 60 minutes in RPMI media; replicate 1.


title: PMN_MG1655_60min_rep2

description: Gene expression data from neutrophils exposed to commensal Escherichia coli strain MG1655 for 60 minutes in RPMI media; replicate 2.

value: female


title: PMN_mock_60min_rep2

description: Gene expression data from neutrophils exposed to RPMI media only for 60 minutes; replicate 2.


title: PMN_UTI89_60min_rep2

description: Gene expresssion data from neutrophils exposed to uropathogenic Escherichia coli strain UTI89 for 60 minutes in RPMI media; replicate 2.


title: H1299 at T24, biological rep1

status: Public on Feb 27 2010

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University

description: Gene expression data from H1299 24hr after  ionizing irradiation (2 Gy)

hyb_protocol: Following fragmentation, 5.5 ug of  labeled DNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner GCS3000 7G plus.

data_processing: The data were analyzed with Bioconductor in R statistical software.

source_name: H1299 24hr after ionizing irradiation

label_protocol: Fragmented and Labeled DNA Target were prepared according to the standard Affymetrix protocol from 100ng total RNA (Whole Transcript (WT) Sense Target Labeling Assay Technical Manual, 2009, Affymetrix).

growth_protocol: The lung cancer cell lines H460 and  H1299  were maintained as a monolayer in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine at 37°C in humidified 5% CO2 .

extract_protocol: mirVana miRNA Isolation Kit(Ambion) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The exponentially growing cells were irradiated with 2 Gy of γ-radiation using a 4 MV linear accelerator (Clinac 4/100, Varian, Palo Alto, CA). No irradiated cells were used as a negative control. The irradiated and control cells were incubated for various periods of times (0, 2, 4, 8, 12 and 24 hours) before isolating total RNA.

tag: cell line


title: H1299 at T24, biological rep2


title: H1299 at T12, biological rep3

description: Gene expression data from H1299 12hr after  ionizing irradiation (2 Gy)

source_name: H1299 12hr after ionizing irradiation


title: H1299 at T12, biological rep2


title: H1299 at T24, biological rep3


title: H1299 at T8, biological rep1

description: Gene expression data from H1299 8hr after  ionizing irradiation (2 Gy)

source_name: H1299 8hr after ionizing irradiation


title: H1299 at T8, biological rep3


title: H1299 at T12, biological rep1


title: H1299 at T0, biological rep6

description: Gene expression data from H1299 before ionizing irradiation

source_name: H1299 non-small lung carcinoma cell line before ionizing irradiation


title: H1299 at T2, biological rep1

description: Gene expression data from H1299 2hr after  ionizing irradiation (2 Gy)

source_name: H1299 2hr after ionizing irradiation


title: H1299 at T4, biological rep2

description: Gene expression data from H1299 4hr after  ionizing irradiation (2 Gy)

source_name: H1299 4hr after ionizing irradiation


title: H1299 at T4, biological rep3


title: H1299 at T2, biological rep2


title: H1299 at T4, biological rep1


title: H1299 at T0, biological rep1


title: H1299 at T0, biological rep4


title: H1299 at T0, biological rep3


title: H1299 at T0, biological rep2


title: H460 at T24, biological rep2

description: Gene expression data from H460 24hr after  ionizing irradiation (2 Gy)

source_name: H460 24hr after ionizing irradiation


title: H1299 at T0, biological rep5


title: H460 at T12, biological rep3

description: Gene expression data from H460 12hr after  ionizing irradiation (2 Gy)

source_name: H460 12hr after ionizing irradiation


title: H460 at T24, biological rep1


title: H460 at T4, biological rep3

description: Gene expression data from H460 4hr after  ionizing irradiation (2 Gy)

source_name: H460 4hr after ionizing irradiation


title: H460 at T12, biological rep2


title: H1299 at T2, biological rep3


title: H460 at T12, biological rep1


title: H460 at T24, biological rep3


title: H460 at T8, biological rep1

description: Gene expression data from H460 8hr after  ionizing irradiation (2 Gy)

source_name: H460 8hr after ionizing irradiation


title: H1299 at T8, biological rep2


title: H460 at T2, biological rep3

description: Gene expression data from H460 2hr after  ionizing irradiation (2 Gy)

source_name: H460 2hr after ionizing irradiation


title: H460 at T8, biological rep3


title: H460 at T2, biological rep2


title: H460 at T4, biological rep1


title: H460 at T0, biological rep6

description: Gene expression data from H460 before ionizing irradiation

source_name: H460 large-cell lung carcinoma cell line before ionizing irradiation


title: H460 at T8, biological rep2


title: H460 at T0, biological rep1


title: H460 at T0, biological rep2


title: H460 at T0, biological rep4


title: H460 at T0, biological rep3


title: H460 at T0, biological rep5


title: H460 at T4, biological rep2


title: H460 at T2, biological rep1


title: Memory B cells_M4-26

status: Public on Feb 01 2010

city: New York

first: Katia

last: Basso

state: NY

address: 1150 St. Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

description: Gene expression data from human memory B cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for at least 16 hr at 45C on GeneChip Human Genome Array U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Memory B cells isolated from tonsil

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's indications.

treatment_protocol: Upon magnetic cell sorting cells were lysated in Trizol Reagent (Invitrogen) and frozen

value: CD27-positive CD10/CD38-negative B-cells purified by magnetic cell separation


title: Memory B cells_M618


title: Naïve B cells_N4117

description: Gene expression data from human naïve B cells

source_name: Naïve B cells isolated from tonsil

value: IgD-positive CD27/CD10/ CD38-negative B-cells purified by magnetic cell separation


title: B086_Treg_Media_24h

status: Public on Dec 31 2009

city: Tel Hashomer

first: Itamar

last: Goldstein

address: Tel Hashomer

country: Israel

institute: Sheba Medical Center and Tel Aviv University

description: Gene-level signal data from Treg untreated for 24hrs.

hyb_protocol: Sample processing was performed according to the Affymetrix WT protocol: http://www.affymetrix.com/support

scan_protocol: GeneChips were scanned using the GENECHIP Scanner 3000 7G and image acquisition was done by the GCOS software.

data_processing: The gene-level log-scale robust multi-array analysis (RMA) sketch algorithm was used for raw data analysis and normalization, performed with Affymetrix Gene-level Signal Expression Console and Partek Genomics Suite 6.2.

source_name: CD25+/hi Treg cultured for 24hrs in control media

label_protocol: cRNA labeling was performed with GeneChip DNA Labeling Reagent, according to the Affymetrix WT protocol.

growth_protocol: Blood samples were obtained from healthy adult blood donors. PBMCs (including lymphocytes) were obtained by density gradient centrifugation on Histopaque 1077. CD4+ T cells were isolated from PBMCs by positive selection with CD4 micro beads (MB) from Miltenyi Biotec, and further purified into CD4+ CD25+/hi and CD25- T cells using a FACSAria cell sorter.

extract_protocol: Total RNA was isolated using the RNeasy mini Kit (Qiagen) performed according to the manufacturer's instructions.

treatment_protocol: Purified T cells were typically plated into 24 well plates (Costar®, Corning Inc.) at 2x10e6 cells/well. For TNF treatment, the various purified T cell populations were incubated for the indicated time with medium supplemented with 50 ng/mL of TNF or control PBS.

value: Freshly isolated circulating T cells

tag: t-cell subtype

value: CD24+ CD25+/hi T-regulatory cells (Treg)

value: untreated

tag: culture time


title: Memory B cells_M512


title: B083_Treg_TNFalfa_2h

description: Gene-level signal data from Treg treated with TNF for 2hrs.

source_name: CD25+/hi Treg cultured for 2 hrs with TNF

value: TNF


title: B087_Treg_TNFalfa_24h

description: Gene-level signal data from Treg treated with TNF for 24hrs.

source_name: CD25+/hi Treg cultured for 24hrs with TNF


title: Naïve B cells_N1 4-21


title: Naïve B cells_N413


title: Naïve B cells_N1 4-7


title: B084_Tcon_Media_24h

description: Gene-level signal data from Tcon untreated for 24hrs.

source_name: CD25- Tcon cultured for 24hrs in control media

value: CD24+ CD25- conventional T cells (Tcon)


title: B081_Tcon_TNFalfa_2h

description: Gene-level signal data from Tcon treated with TNF for 2hrs.

source_name: CD25- Tcon cultured for 2 hrs with TNF


title: Memory B cells_M4-12


title: B082_Treg_Media_2h

description: Gene-level signal data from Treg untreated for 2hrs.

source_name: CD25+/hi Treg cultured for 2 hrs in control media


title: Resting CD8+ T-cells (FACS sorted)

status: Public on Feb 08 2010

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description:
Gene expression data from resting CD8+ T-cells.
CD8-T0

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix Scanning Protocol.

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. Further analysis (e.g., clustering, classification) was carried using BRB-ArrayTools version (3.7.0).

source_name: Normal CD8+ T-cell subset

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 3 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: All the tissues used in the study were fresh frozen and stored below -70 degree C.

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

treatment_protocol: The cryopreserved tissues from pre-treated biopsies obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction.

value: CD8+ T-cell


title: B cell nonsmoking-50B

status: Public on Dec 25 2009

city: Xi'an

first: Feng

last: Pan

state: Shaanxi

address: Xian Ning West Road 28

department: School of life science and technology

country: China

institute: Xi'an Jiaotong University

description: Gene expression data from B cells isolated from healthy US white non-smoking females

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: We use the Affymetrix Microarray Scanner by Hewlett-Packard 2500 and Microarray Suite 5.0 software for chip scanning and raw image generating.

data_processing: Microarray Suite 5.0 (MAS 5.0, Affymetrix, Santa Clara, CA, USA) software was used to generate array raw data in CEL files. A preselecting procedure adopted by our previous study (Xiao et al. 2008) was also used here. We selected a subset of 7,215 probe sets from a total of 22,283 for ~14,500 genes in the HG-133A array. Subsequent data analyses were performed on these selected probe sets. We applied multiple analytic approaches including mas5.0 algorithm (Affymetrix, Santa Clara, CA, USA), RMA (Robust Multiarray Algorithm), GCRMA (the improved GC-content adjusted RMA), and dChip for converting and normalizing our raw probe data to gene expression values.  Genes expressed differentially as determined by consensus using the 4 methods were extracted.

source_name: circulating B cells in non-smoking woman

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Seventy milliliters of blood were drawn from each recruited female. B cell isolation from 70 ml whole blood was performed using a positive isolation method with Dynabeads® CD19 (Pan B) and DETACHaBEAD® CD19 (Dynal Biotech, Lake Success, NY, USA) following the manufacturer’s protocols. B cell purity was assessed by flow cytometry (BD Biosciences, San Jose, CA USA) with fluorescence labeled antibodies, PE-CD19 and FITC-CD45. The average purity was 96.3% with less than 1% deviation.

tag: menopausal

value: Post

value: B cell

tag: smoking

value: no


title: B cell nonsmoking-57B

value: Pre

tag: cell type


title: B cell nonsmoking-60B


title: Memory B cells_M4-14


title: B cell nonsmoking-80B


title: Naïve B cells_N1 4-23


title: B cell nonsmoking-58B


title: B cell nonsmoking-48B


title: B cell nonsmoking-49B


title: B085_Tcon_TNFalfa_24h

description: Gene-level signal data from Tcon treated with TNF for 24hrs.

source_name: CD25- Tcon cultured for 24hrs with TNF


title: B080_Tcon_Media_2h

description: Gene-level signal data from Tcon untreated for 2hrs.

source_name: CD25- Tcon cultured for 2 hrs in control media


title: B cell nonsmoking-61B


title: B cell nonsmoking-51B


title: B cell nonsmoking-54B


title: B cell nonsmoking-43B


title: B cell nonsmoking-41B


title: B cell nonsmoking-39B


title: B cell nonsmoking-37B


title: B cell nonsmoking-52B


title: B cell nonsmoking-29B


title: B cell nonsmoking-34B


title: B cell nonsmoking-31B


title: B cell nonsmoking-40B


title: B cell nonsmoking-33B


title: B cell nonsmoking-46B


title: B cell nonsmoking-28B


title: B cell nonsmoking-24B


title: B cell nonsmoking-27B


title: B cell nonsmoking-19B


title: B cell nonsmoking-18B


title: B cell nonsmoking-23B


title: B cell nonsmoking-26B


title: B cell nonsmoking-21B


title: B cell nonsmoking-17B


title: B cell nonsmoking-38B


title: B cell nonsmoking-10B


title: B cell nonsmoking-30B


title: B cell nonsmoking-22B


title: B cell nonsmoking-15B


title: B cell nonsmoking-13B


title: B cell nonsmoking-11B


title: B cell nonsmoking-25B


title: B cell smoking-85

description: Gene expression data from B cells isolated from healthy US white smoking females

source_name: circulating B cells in smoking woman

value: yes


title: B cell smoking-88


title: B cell smoking-83


title: B cell smoking-86


title: B cell nonsmoking-01B


title: B cell smoking-73


title: B cell smoking-77


title: B cell smoking-70


title: B cell smoking-78


title: B cell smoking-84


title: B cell smoking-89


title: B cell nonsmoking-03B


title: B cell smoking-72


title: B cell smoking-76


title: B cell smoking-68


title: B cell smoking-87


title: B cell smoking-82


title: B cell smoking-71


title: B cell smoking-75


title: B cell smoking-81


title: B cell smoking-74


title: B cell smoking-66


title: B cell smoking-65


title: B cell smoking-67


title: B cell smoking-69


title: B cell smoking-63


title: B cell smoking-62


title: B cell smoking-64


title: B cell smoking-36


title: B cell smoking-45


title: B cell smoking-47


title: B cell smoking-32


title: B cell smoking-07


title: B cell smoking-53


title: B cell smoking-20


title: B cell smoking-35


title: B cell smoking-42


title: B cell smoking-55


title: B cell smoking-59


title: B cell smoking-44


title: donor 3, H1N1 infected macrophages at 6h

status: Public on Oct 31 2009

city: Hong Kong

first: SMY

last: Lee

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

description: Gene expression data of influenza A H1N1 infected macrophages at 6 h post-infection time

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST 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 with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: macrophages from donor 3 infected with H1N1 at 6h post-infection time

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

growth_protocol: Peripheral-blood leucocytes were separated from buffy coats of healthy donors by Ficoll-Paque density gradient centrifugation and purified by adherence. The cells were allowed to differentaite for 14 days in RPMI 1640 supplemented with 5% heat-inactivated autologous plasma.

extract_protocol: Total RNA was isolated by RNEasy Mini kit (Qiagne) according to the manufacturer's instructions.

treatment_protocol: Differentiated macrophages were infected with H1N1, H5N1 or mock infection at a multiplicity of infection (MOI) of two. Total RNA was extracted from cells after 1, 3, and 6h post-infection

tag: individual

value: donor 3

tag: infection

tag: time point

value: 6h post-infection time

value: monocyte-derived macrophages


title: pbPMN-A1

status: Public on Dec 19 2009

city: Princeton

first: Troels

middle: Torben

last: Marstrand

state: NJ

address: Lewis-Sigler Institute Princeton University

institute: Princeton University

hyb_protocol: Hybridization was according to manufacturer's recommendations

scan_protocol: MicroArray Suite 5

data_processing: Fluorescence signals were normalized using dChip version 1.3, expression values were calculated using the perfect match/mismatch difference model by Li and Wong

source_name: peripheral blood neutrophils

label_protocol: Total RNA was biotinylated according to manufacturer's recommendations

extract_protocol: Total RNA extracted using Trizol according to manufacturer's recommendations

value: peripheral blood neutrophils


title: donor 3, H1N1 infected macrophages at 3h

description: Gene expression data of influenza A H1N1 infected macrophages at 3 h post-infection time

source_name: macrophages from donor 3 infected with H1N1 at 3h post-infection time

value: 3h post-infection time


title: donor 3, mock infected macrophages at 6h

description: Gene expression data of mock infected macrophages at 6 h post-infection time

source_name: macrophages from donor 3 infected with mock at 6h post-infection time

value: mock


title: bmPMN-A2

source_name: bone marrow neutrophils

value: bone marrow neutrophils


title: donor 3, mock infected macrophages at 1h

description: Gene expression data of mock infected macrophages at 1 h post-infection time

source_name: macrophages from donor 3 infected with mock at 1h post-infection time

value: 1h post-infection time


title: pbPMN-A3


title: bmPMN-A3


title: donor 2, H5N1 infected macrophages at 6h

description: Gene expression data of influenza A H5N1 infected macrophages at 6 h post-infection time

source_name: macrophages from donor 2 infected with H5N1 at 6h post-infection time

value: donor 2


title: donor 3, H1N1 infected macrophages at 1h

description: Gene expression data of influenza A H1N1 infected macrophages at 1 h post-infection time

source_name: macrophages from donor 3 infected with H1N1 at 1h post-infection time


title: donor 3, mock infected macrophages at 3h

description: Gene expression data of mock infected macrophages at 3 h post-infection time

source_name: macrophages from donor 3 infected with mock at 3h post-infection time


title: donor 2, H1N1 infected macrophages at 6h

source_name: macrophages from donor 2 infected with H1N1 at 6h post-infection time


title: bmPMN-A1


title: donor 2, H1N1 infected macrophages at 3h

source_name: macrophages from donor 2 infected with H1N1 at 3h post-infection time


title: donor 3, H5N1 infected macrophages at 1h

description: Gene expression data of influenza A H5N1 infected macrophages at 1 h post-infection time

source_name: macrophages from donor 3 infected with H5N1 at 1h post-infection time


title: donor 3, H5N1 infected macrophages at 6h

source_name: macrophages from donor 3 infected with H5N1 at 6h post-infection time


title: donor 2, H5N1 infected macrophages at 3h

description: Gene expression data of influenza A H5N1 infected macrophages at 3 h post-infection time

source_name: macrophages from donor 2 infected with H5N1 at 3h post-infection time


title: donor 2, mock infected macrophages at 3h

source_name: macrophages from donor 2 infected with mock at 3h post-infection time


title: donor 2, mock infected macrophages at 1h

source_name: macrophages from donor 2 infected with mock at 1h post-infection time


title: donor 1, mock infected macrophages at 3h

source_name: macrophages from donor 1 infected with mock at 3h post-infection time

value: donor 1


title: donor 1, H1N1 infected macrophages at 6h

source_name: macrophages from donor 1 infected with H1N1 at 6h post-infection time


title: donor 1, H1N1 infected macrophages at 3h

source_name: macrophages from donor 1 infected with H1N1 at 3h post-infection time


title: donor 2, mock infected macrophages at 6h

source_name: macrophages from donor 2 infected with mock at 6h post-infection time


title: donor 1, H5N1 infected macrophages at 1h

source_name: macrophages from donor 1 infected with H5N1 at 1h post-infection time


title: donor 1, H5N1 infected macrophages at 3h

source_name: macrophages from donor 1 infected with H5N1 at 3h post-infection time


title: donor 2, H1N1 infected macrophages at 1h

source_name: macrophages from donor 2 infected with H1N1 at 1h post-infection time


title: donor 2, H5N1 infected macrophages at 1h

source_name: macrophages from donor 2 infected with H5N1 at 1h post-infection time


title: donor 1, mock infected macrophages at 6h

source_name: macrophages from donor 1 infected with mock at 6h post-infection time


title: donor 3, H5N1 infected macrophages at 3h

source_name: macrophages from donor 3 infected with H5N1 at 3h post-infection time


title: donor 1, H1N1 infected macrophages at 1h

source_name: macrophages from donor 1 infected with H1N1 at 1h post-infection time


title: Control T cells at T4, biological replicate 2

status: Public on Sep 02 2009

city: Salamanca

first: José

middle: Antonio

last: Pérez Simón

state: Salamanca

address: Paseo de San Vicente, s/n

department: Hematology Service

country: Spain

institute: University Hospital

description: Gene expression data from induced T cells, control replicate 2, after 4 days

hyb_protocol: Following fragmentation with NuGEN protocol (catalog number 4200-12), 5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using an Affymetrix Genechip Scanner 7g Plus

data_processing: The data were analyzed with Affymetrix Expression Console 1.1 using default analysis settings and iterPLIER by quantiles as normalization method and PM-GCBG as background correction method.

source_name: primary human T cells

label_protocol: Biotinylated cRNA were prepared according to the standard NuGEN protocols from 50 ng total RNA (Catalog numbers 3300-12, 2000-12, 4200-12).

growth_protocol: antiCD3 plus antiCD28 treated T cells

extract_protocol: TRizol (Invitrogen, Carlsbard, CA, USA) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 5-azacytidine during 2 to 4 days

value: untreated

value: T cell

tag: time

value: 4 days


title: donor 1, mock infected macrophages at 1h

source_name: macrophages from donor 1 infected with mock at 1h post-infection time


title: Treated T cells at T2, biological replicate 3

description: Gene expression data from induced T cells, treated replicate 3, after 2 days

value: 5-azaC treated

value: 2 days


title: Treated T cells at T4, biological replicate 3

description: Gene expression data from induced T cells, treated replicate 3, after 4 days


title: Treated T cells at T2, biological replicate 2

description: Gene expression data from induced T cells, treated replicate 2, after 2 days


title: Control T cells at T4, biological replicate 3

description: Gene expression data from induced T cells, control replicate 3, after 4 days


title: Control T cells at T2, biological replicate 2

description: Gene expression data from induced T cells, control replicate 2, after 2 days


title: Control T cells at T2, biological replicate 3

description: Gene expression data from induced T cells, control replicate 3, after 2 days


title: Treated T cells at T4, biological replicate 2

description: Gene expression data from induced T cells, treated replicate 2, after 4 days


title: Treated T cells at T4, biological replicate 1

description: Gene expression data from induced T cells, treated replicate 1, after 4 days


title: LEC control, rep4

status: Public on Sep 30 2009

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

country: United Kingdom

institute: UCL

description: Biological replicate 4 of 6.

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf

data_processing: Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm  ('RMA') .

source_name: lymphatic endothelial cells

label_protocol: 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)

growth_protocol: Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV-infected LEC and BEC were grown under the same conditions. All cells were mycoplasma free.

extract_protocol: TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).

treatment_protocol: Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.

value: lymphatic endothelial cell


title: donor 1, H5N1 infected macrophages at 6h

source_name: macrophages from donor 1 infected with H5N1 at 6h post-infection time


title: LEC control, rep3

description: Biological replicate 3 of 6.


title: LEC control, rep5

description: Biological replicate 5 of 6.


title: Control T cells at T0, biological replicate 3

description: Gene expression data from induced T cells, control replicate 3, start

value: 0 day


title: LEC non-target-siRNA, rep3

description: Biological replicate 3 of 3.

data_processing: Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA') .

source_name: lymphatic endothelial cells, control siRNA

growth_protocol: Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. Transfected LEC were grown under the same conditions. All cells were mycoplasma free.

treatment_protocol: Lymphatic endothelial cells (LECs) were plated in six well plates (5x10^4cells/well) overnight. The cells were transfected with siRNA against MAF or non-targeting control siRNA (Dharmacon). Two days after transfection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.

value: lymphatic endothelial cells

tag: vector

value: non-targeted-siRNA


title: LEC control, rep6

description: Biological replicate 6 of 6.


title: Control T cells at T0, biological replicate 2

description: Gene expression data from induced T cells, control replicate 2, start


title: Control T cells at T4, biological replicate 1

description: Gene expression data from induced T cells, control replicate 1, after 4 days


title: LEC control, rep1

description: Biological replicate 1 of 6.


title: LEC control, rep2

description: Biological replicate 2 of 6.


title: MM_1

status: Public on Aug 31 2009

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data of endothelial cells from Multiple Myeloma patient MM_1

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133A arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization and log2-transformed.

source_name: Human bone marrow endothelial cells from Multiple Myeloma patient MM

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

growth_protocol: Freshly-isolated ECs were cultured in complete medium RPMI-1640 medium supplemented with 10% heat-inactivated FCS and 1% glutamine to allow cell spreading and growth.

extract_protocol: Total RNA was extracted from frozen ECs with TRIzol reagent (Invitrogen, Carlsbad, CA), purified with the RNeasy total RNA Isolation Kit (Qiagen, Valencia, CA).

treatment_protocol: Centrifugation on Ficoll gradient of heparinized BM-aspirates was followed by polystyrene flask adherence to isolate stromal cells from plasma cells in suspension. Adherent stromal elements were first immunodepleted of macrophages and residual plasma cells with CD14 and CD38 monoclonal antibody (mAb)-coated flasks (mAbs were from Immunotech, Coulter, Marseilles, France), and then incubated with magnetic microbeads coated with Ulex europaeus-1 lectin. The purity and viability of EC cultures grown at least one passage (more than 97% viable cells) were assessed by fluorescence-activated cell sorting (FACS, FACS Canto II, Becton Dickinson, San Jose, CA) with double positivity for factor VIII-related antigen (FVIII-RA, a highly specific EC marker) and CD105 (or endoglyn) as well as for CD14 and CD38 negativity. Analysis of mRNA transcripts for FVIII-RA, CD38, CD105 and IgH VDJ region was also performed by RT-PCR, and EC viability was assessed by trypan blue viable staining.

tag: Legend

value: Durie-Salmon Staging System in Multiple Myeloma (Durie BG, Salmon SE Cancer, 1975); immunoglobulin (Ig) protein monoclonal component

tag: Sex

value: M; stage IIIA; IgG


title: MM_3

description: Gene expression profiling data of endothelial cells from Multiple Myeloma patient MM_3

value: M; stage IIIA; IgA


title: MM_4

description: Gene expression profiling data of endothelial cells from Multiple Myeloma patient MM_4

value: F; stage IIIA; IgG


title: MM_2

description: Gene expression profiling data of endothelial cells from Multiple Myeloma patient MM_2


title: MGUS_5

description: Gene expression profiling data of endothelial cells from Monoclonal Gammopathy of Undetermined Significance patient MGUS_5

source_name: Human bone marrow endothelial cells from Monoclonal Gammopathy of Undetermined Significance patient MGUS

value: Immunoglobulin (Ig) protein monoclonal component

value: F; IgA


title: MM_9

description: Gene expression profiling data of endothelial cells from Multiple Myeloma patient MM_9

value: F; stage IIIA; IgA


title: MGUS_2

description: Gene expression profiling data of endothelial cells from Monoclonal Gammopathy of Undetermined Significance patient MGUS_2

value: M; IgG


title: HUVEC_8

description: Gene expression profiling data of Umbilical Vein Endothelial Cells HUVEC_8

source_name: Human Umbilical Vein Endothelial Cells HUVEC

growth_protocol: HUVEC cells were cultured in EGM-2MV media (Clonetics Biowhittaker).

tag: HUVEC cells from Clonetics Biowhittaker (Walkersville, MD)


title: MGUS_1

description: Gene expression profiling data of endothelial cells from Monoclonal Gammopathy of Undetermined Significance patient MGUS_1


title: MGUS_4

description: Gene expression profiling data of endothelial cells from Monoclonal Gammopathy of Undetermined Significance patient MGUS_4

value: F; IgG


title: HUVEC_1

description: Gene expression profiling data of Umbilical Vein Endothelial Cells HUVEC_1


title: MGUS_3

description: Gene expression profiling data of endothelial cells from Monoclonal Gammopathy of Undetermined Significance patient MGUS_3

value: M; IgA


title: HUVEC_2

description: Gene expression profiling data of Umbilical Vein Endothelial Cells HUVEC_2


title: HUVEC_4

description: Gene expression profiling data of Umbilical Vein Endothelial Cells HUVEC_4


title: Immune Response of Immature Dendritic Cells after Infection with Human Cytomegalovirus Strain TB40E TB treated sample 2

status: Public on Aug 01 2009

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

description: RMA normalized data not provided by submitter

hyb_protocol: Standard Affymetrix Hybridisation protocol

scan_protocol: Standard Affymetrix Scanning protocol

data_processing: RMA normalisation, ArrayAssist Data analysis with t-test

source_name: Dendritic Cells

label_protocol: Standard Affymetrix Labeling protocol

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from 50-ml Buffy Coat blood (Blutspendedienst Tübingen / Frankfurt, Germany) by Ficoll-Hypaque density gradient centrifugation.
CD14+ cells were isolated from PBMCs by magnetic-associated cell sorting (MACS) using paramagnetic microbeads conjugated to monoclonal anti-human CD14 antibodies (Miltenyi, Bergisch Gladbach, Germany). Monocytes were seeded into six-well plates (2,5 x 106 cells / 3 ml / well) in RPMI-1640 (+ GlutaMAX) medium containing 10% fetal calf serum (FCS) and 100 mg/ml gentamicin sulfate (Refobacin® 80 mg, Merck, Darmstadt, Germany), supplemented with 100 ng/ml recombinant human granulocyte-macrophage colony-stimulating factor (GM-CSF; Leukomax, Novartis, Basel, Switzerland) and 20 ng/ml Interleukin-4 (IL-4; R&D Systems, Wiesbaden, Germany). Cultures were fed with fresh medium and cytokines every other day. DC differentiation was monitored by light microscopy and purity of DC culture was analyzed after 7 days by flow cytometry (FACSCalibur, Becton Dickinson, Heidelberg, Germany).
At least 95% of the DC population stained was positive for CD1a, CD40, CD80 and CD86 and was negative for CD14 and CD83.
Standard qiagen Isolation protocol

treatment_protocol:
Human foreskin fibroblasts (HFF) were isolated from foreskins of male neonates by trypsin treatment and were used for experiments between passages 10 and 25. Alternatively, MRC-5 fibroblasts were purchased from Sigma-Aldrich, Taufkirchen, Germany.
Fibroblasts were cultured in MEM containing glutamine (2.4 mmol/l), gentamicin (100 g/ml), and fetal calf serum (5 %). For high-titer virus preparations, fibroblasts were infected at a low multiplicity of infection (MOI) with TB40E. Six days after infection, 100 ml cell-free supernatant was concentrated by ultracentrifugation at 80,000 × g for 70 min, and pelleted virus particles were resuspended in appropriate volumes of RPMI.
1 x 106 DCs were incubated with the virus preparation at 37 °C (MOI=50) in complete RPMI medium supplemented with IL-4 and GM-CSF. After 2h, cells were washed once with Hanks and resolved in fresh medium. For mock-infection, cells were exposed to fresh medium as an appropriate control for cell-free virus concentrates.
TB40E-infected or mock-infected DCs were collected after 24 h to assess the efficiency of infection. Cells were washed in PBS / 2% fetal calf serum (FCS) / 2mmol EDTA, cytocentrifuged for 5 min at 550 rpm and fixed on glass slides with acetone for 10 min. HCMV immediate early (IE) antigen expression was detected by indirect immunofluorescence staining. Slides were incubated with monoclonal antibody directed against the non-structural proteins IE72 and IE86 (pUL122/123, Biosoft, Paris, France) at the appropriate dilution for 90 min at 37°C, then were incubated with Cy3-conjugated Fab´2 goat anti-mouse IgG (Jackson ImmunoResearch Laboratories, West Grove, USA) for 45 min at 37°C. Nuclei were counterstained with DAPI. The slides were washed in PBS for 5 min after each incubation step. The percentage of infected cells was determined by immunofluorescence microscopy. As previously reported by Grigoleit et al., 2002, IE antigen was detected in 35% – 75% of the DCs infected with TB40E.

value: Human Cytomegalovirus Strain TB40E TB

value: Dendritic Cells


title: HUVEC_3

description: Gene expression profiling data of Umbilical Vein Endothelial Cells HUVEC_3


title: CD8+ T-cells_healty control_donor1

status: Public on Jul 29 2009

city: Milan

first: Alessandro

last: Aiuti

address: via olgettina 58

institute: San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)

description: Gene expression data from CD8+ T-cells isolated from healty control

hyb_protocol: Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).

source_name: CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C1

label_protocol: The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.

growth_protocol: Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.

extract_protocol: RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.

treatment_protocol: Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.

tag: tissue

value: peripheral blood

value: CD8+ T-cells

tag: treatment type

value: normal donor


title: Immune Response of Immature Dendritic Cells after Infection with Human Cytomegalovirus Strain TB40E mock sample 1

data_processing: RMA normalisation, ArrayAssist DAtaanalysis with t-test

value: Human Cytomegalovirus Strain TB40E mock


title: Immune Response of Immature Dendritic Cells after Infection with Human Cytomegalovirus Strain TB40E TB treated sample 3


title: CD4+ T-cells_healty control_donor1

description: Gene expression data from CD4+ T-cells isolated from healty control

source_name: CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C1

value: CD4+ T-cells


title: CD4+ T-cells_healty control_donor4

source_name: CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C4


title: Immune Response of Immature Dendritic Cells after Infection with Human Cytomegalovirus Strain TB40E mock sample 3


title: Normal_Germinal_B_4

status: Public on Jul 31 2009

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

institute: University of Southern California

hyb_protocol: followed affymetrix protocol

scan_protocol: followed affymetrix protocol

data_processing: log transformed RMA normalized

source_name: normal B cells

label_protocol: followed affymetrix protocol

extract_protocol: as recommended by affymetrix

treatment_protocol: cell population was isolated by FACS

value: isolated from normal human lymph nodes

value: normal germinal center B cells


title: Normal_Germinal_B_2


title: CD8+ T-cells_healty control_donor4

source_name: CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C4


title: CD4+ T-cells_healty control_donor2

source_name: CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C2


title: Immune Response of Immature Dendritic Cells after Infection with Human Cytomegalovirus Strain TB40E TB treated sample 1


title: CD8+ T-cells_healty control_donor3

source_name: CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C3


title: CD8+ T-cells_healty control_donor2

source_name: CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C2


title: CD4+ T-cells_healty control_donor3

source_name: CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C3


title: Normal_Germinal_B_1


title: Normal_Germinal_B_3


title: ZR-75-1

status: Public on Jul 13 2009

city: Rotterdam

first: Antoinette

last: Hollestelle

address: Dr. Molenwaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

description: Gene expression of ZR-75-1.

scan_protocol: Standard Affymetrix protocol.

data_processing: Intensity values for all genes were scaled using the global normalization factor as specified by GCOS 1.1.

source_name: breast cancer cell line

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Cell lines were grown to optimal cell density in RPMI 1640 supplemented with 10% FBS at 37C. Medium was changed 24h prior to RNA isolation.

extract_protocol: Cells were washed with PBS at 37C prior to isolation. Total RNA was isolated using the Rneasy kit from Qiagen. Lysis of the cells was performed in the culture flask directly after washing with PBS. Total RNA was DNAseI-treated for 1 hour at 37C. RNA QC using Agilent Technologies 2100 Bioanalyzer.

value: breast cancer

tag: morphology

value: non-spindle


title: SUM185PE

description: Gene expression of SUM185PE.

tag: cell line


title: UACC893

description: Gene expression of UACC893.


title: T47D

description: Gene expression of T47D.


title: SUM229PE

description: Gene expression of SUM229PE.

value: spindle


title: SUM1315MO2

description: Gene expression of SUM1315MO2.


title: ZR-75-30

description: Gene expression of ZR-75-30.


title: Immune Response of Immature Dendritic Cells after Infection with Human Cytomegalovirus Strain TB40E mock sample 2


title: UACC812

description: Gene expression of UACC812.


title: SUM159PT

description: Gene expression of SUM159PT.


title: SUM44PE

description: Gene expression of SUM44PE.


title: SUM102PT

description: Gene expression of SUM102PT.


title: MPE600

description: Gene expression of MPE600.


title: OCUB-F

description: Gene expression of OCUB-F.

value: OCUB-F


title: SK-BR-5

description: Gene expression of SK-BR-5.


title: SK-BR-7

description: Gene expression of SK-BR-7.


title: MDA-MB-415

description: Gene expression of MDA-MB-415.


title: MDA-MB-330

description: Gene expression of MDA-MB-330.


title: MDA-MB-468

description: Gene expression of MDA-MB-468.


title: MDA-MB-435s

description: Gene expression of MDA-MB-435s.


title: SUM52PE

description: Gene expression of SUM52PE.


title: MDA-MB-361

description: Gene expression of MDA-MB-361.


title: SUM149PT

description: Gene expression of SUM149PT.


title: Hs578T

description: Gene expression of Hs578T.


title: MDA-MB-157

description: Gene expression of MDA-MB-157.


title: MDA-MB-175VII

description: Gene expression of MDA-MB-175VII.


title: MDA-MB-134VI

description: Gene expression of MDA-MB-134VI.


title: MDA-MB-231

description: Gene expression of MDA-MB-231.


title: DU4475

description: Gene expression of DU4475.


title: HCC1937

description: Gene expression of HCC1937.


title: MCF7

description: Gene expression of MCF7.


title: SK-BR-3

description: Gene expression of SK-BR-3.


title: MDA-MB-453

description: Gene expression of MDA-MB-453.


title: EVSA-T

description: Gene expression of EVSA-T.

value: EVSA-T


title: BT474

description: Gene expression of BT474.


title: BT20

description: Gene expression of BT20.


title: BT549

description: Gene expression of BT549.


title: CAMA-1

description: Gene expression of CAMA-1.


title: BT483

description: Gene expression of BT483.


title: LEC non-target-siRNA, rep2

description: Biological replicate 2 of 3.

value: lymphatic endothelial cells

value: non-targeted-siRNA


title: tumor-reactive CD8+ T cell clone p26

status: Public on Jun 15 2009

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: tumor-reactive CD8+ T cell clone p26

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: Data has been normalized using dChip software

source_name: peripheral blood, tumor-reactive CD8+ T cell clone p26

label_protocol: 50 to 100 nanograms of total RNA was used to generate double-stranded cDNA with a T7(dT)24-oligonucleotide primer performed with the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA, USA) followed by a second IVT reaction to amplify the cDNA. After purification with the Sample Cleanup Module (Affymetrix), cDNA served as a template to prepare biotinylated cRNA via IVT, using the IVT Labeling Kit (Affymetrix). The labeled cRNA transcripts were purified using the Sample Cleanup Module.

extract_protocol: 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: tumor-reactive CD8+ T cell clone


title: pDC CD2- (032504)

status: Public on May 21 2009

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: CD2 negative plasmacytoid dendritic cell subset

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

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

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

extract_protocol: RNeasy Mini extraction of 50,000 cells

value: CD2- plasmacytoid dendritic cell


source_name: peripheral blood, non-tumor-reactive CD8+ T cell clone p10

tag: non-tumor-reactive CD8+ T cell clone


source_name: peripheral blood, non-tumor-reactive CD8+ T cell clone p19


title: P_CD8_10

status: Public on May 20 2009

first: Rifca

last: Le Dieu

address: 3rd Floor, John Vane Science Building, Charterhouse Square

department: Institute of Cancer

institute: Queen Mary University of London

description: PS10 CD8

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridised for 16 hours at 45C on Affymetrix U133Plus2 GeneChips. Chips were then washed and stained with SAPE in an Affymetrix GeneChip 450 Fluidics Station.

scan_protocol: GeneChips were scanned using the Ayymetrix GeneChip 3000 scanner

data_processing: Data was normalised using RMA

label: Biotin

source_name: CD8 T cells, Positive Selection

label_protocol: Affymetrix Expression GeneChip Protocol one-cycle procedure. Between 2 and 5micrograms of RNA was used as starting material.

extract_protocol: RNA was extracted using Trizol.

tag: age

tag: gender

value: Male


title: tumor-reactive CD8+ T cell clone p40

description: tumor-reactive CD8+ T cell clone p40

source_name: peripheral blood, tumor-reactive CD8+ T cell clone p40


title: pDC CD2- (022704)

tag: cell type


title: pDC CD2+ (022704)

description: CD2 positive plasmacytoid dendritic cell subset

value: CD2+ plasmacytoid dendritic cell


title: Resting CD45RA+ FoxP3low CD4+ Tregs (Fr.I)

city: Kyoto

first: Makoto

last: Miyara

address: 53 Shogoin Kawahara-cho,

department: Institute for Medical Sciences

country: Japan

institute: Kyoto University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

source_name: PBMC

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA extracted from FACS-sorted T cells was reverse transcribed according to the manufacturer’s instructions (RNeasy Micro kit, Qiagen)

tag: surface marker

value: T reg


title: pDC CD2+ (032504)


title: N_CD8_1

description: NS1 CD8

source_name: CD8 T cells, Negative Selection


title: N_CD4_5

description: NS5 CD4

source_name: CD4 T cells, Negative Selection


title: N_CD8_3

description: NS3 CD8


title: CD25-/+ CD45RA- FoxP3- CD4+ T cells (Fr. IV, V)

value: CD127high CD25-/+ CD45RA-

value: T cell


title: Activated CD45RA- FoxP3high CD4+ Tregs (Fr. II)


title: P_CD8_9

description: PS9 CD8

value: Female


title: CD25- CD45RA+ FoxP3- CD4+ T cells (Fr. VI)

value: CD127high CD25- CD45RA+


title: N_CD8_2

description: NS2 CD8


title: N_CD4_4

description: NS4 CD4


title: CD45RA- FoxP3low CD4+ T cells (Fr. III)


title: P_CD8_7

description: PS7 CD8


title: P_CD8_8

description: PS8 CD8


title: P_CD4_6

description: PS6 CD4

source_name: CD4 T cells, Positive Selection


title: N_CD8_5

description: NS5 CD8


title: P_CD8_11

description: PS11 CD8


title: P_CD4_7

description: PS7 CD4


title: N_CD8_4

description: NS4 CD8


title: P_CD4_8

description: PS8 CD4


title: N_CD4_2

description: NS2 CD4


title: N_CD4_1

description: NS1 CD4


title: Healthy_CD4_7

description: Healthy7 CD4

data_processing: Data were analysed with MicroArray Suite 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: CD4 T cells

extract_protocol: T cells were isolated by immunomagnetic selection. RNA was then extracted using Trizol.

value: female

value: Not applicable


title: Healthy_CD4_9

description: Healthy9 CD4

value: male


title: Healthy_CD8_10

description: Healthy10 CD8

source_name: CD8 T cells


title: Healthy_CD4_6

description: Healthy6 CD4


title: Healthy_CD8_2

description: Healthy2 CD8


title: Healthy_CD8_9

description: Healthy9 CD8


title: Healthy_CD4_2

description: Healthy2 CD4


title: Healthy_CD4_8

description: Healthy8 CD4


title: Healthy_CD8_7

description: Healthy7 CD8


title: Nonatopic subject 13, resting CD4 T-cells

status: Public on May 05 2009

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).

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

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).


title: Nonatopic subject 14, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 11, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 10, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Healthy_CD4_5

description: Healthy5 CD4


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

description: PBMC were from cryopreserved stocks.

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


title: Healthy_CD8_1

description: Healthy1 CD8


title: Healthy_CD8_3

description: Healthy3 CD8


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

description: PBMC were from cryopreserved stocks.


title: Healthy_CD4_4

description: Healthy4 CD4


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

description: PBMC were from cryopreserved stocks.


title: Healthy_CD8_8

description: Healthy8 CD8


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

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 15, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


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

description: PBMC were from cryopreserved stocks.


title: Healthy_CD8_6

description: Healthy6 CD8


title: Healthy_CD4_1

description: Healthy1 CD4


title: Healthy_CD8_4

description: Healthy4 CD8


title: Healthy_CD8_11

description: Healthy11 CD8


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

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 12, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 09, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


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

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 03, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 07, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


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

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 05, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


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

description: PBMC were from cryopreserved stocks.


title: Atopic subject 30, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 30, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 28, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 08, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 29, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 06, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 01, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


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

description: PBMC were from cryopreserved stocks.


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

description: PBMC were from cryopreserved stocks.


title: Atopic subject 26, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 27, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


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

description: PBMC were from cryopreserved stocks.


title: Atopic subject 29, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 26, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 04, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


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

description: PBMC were from cryopreserved stocks.


title: Nonatopic subject 02, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 27, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 25, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 28, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 24, HDM stimulated CD4 T-cells

description: PBMC were from cryopreserved stocks.


title: Atopic subject 24, resting CD4 T-cells

description: PBMC were from cryopreserved stocks.


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

description: PBMC were from cryopreserved stocks.