title: MCF7_Sangivamycin_Array_2

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

address: Ft. Detrick

department: DTP

institute: NCI Frederick

description: Control dataset for subsequent analysis of drug responses

hyb_protocol: The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in an GeneChip® Scanner 3000

data_processing: Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.

label_protocol: Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).

growth_protocol: RPMI 1640 10% FBS

extract_protocol: RNeasy (Qiagen)

treatment_protocol: Sangivamycin Treated

tag: MCF7 cells treated with 2uM Sangivamycin for 24 hours Array 2


title: U937 cells treated with hyperthermia (0 h)

status: Public on Nov 11 2008

type: RNA

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control). The cells were treated with hyperthermia (42°C for 90 min) and followed by incubation for 0 h at 37°C (no incubation at 37°C). Non-treated cells were served as control.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite 5.0

label: phycoerythrin

molecule: total RNA

organism: Homo sapiens

source_name: Human lymphoma U937 cells

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K. K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: Human lymphoma U937 cells


title: U937 cells treated with hyperthermia (6 h)

description: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control). The cells were treated with hyperthermia (42°C for 90 min) and followed by incubation for 6 h at 37°C. Non-treated cells were served as control.


title: melanoma mice model saliva control 1

city: Los Angeles

first: David

last: Wong

state: CA

address: 73-017 CHS, 10833 Le Conte Ave

department: Dental Research Institute School of Dentistry

country: USA

institute: University of California at Los Angeles

description: Affymetrix protocol

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Dchip

label: biotin

organism: Mus musculus

source_name: melanoma mice model saliva from control mice 1

label_protocol: Affymetrix protocol

extract_protocol: RNeasy Mini kit

treatment_protocol: inject with PBS

tag: C57BL/C mice control, inject with PBS


title: U937 cells treated with hyperthermia (1 h)

description: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control). The cells were treated with hyperthermia (42°C for 90 min) and followed by incubation for 1 h at 37°C. Non-treated cells were served as control.


title: U937 cells treated with hyperthermia (3 h)

description: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control). The cells were treated with hyperthermia (42°C for 90 min) and followed by incubation for 3 h at 37°C. Non-treated cells were served as control.


title: MCF7_Control_Array_2

state: MD

label: Biotin

source_name: MCF7 cells from controls

treatment_protocol: No Treatment

tag: MCF7 Control cells Array 2


title: MCF7_Sangivamycin_Array_1

tag: MCF7 cells treated with 2uM Sangivamycin for 24 hours Array 1


title: MCF7_Doxorubicin_Array_1

source_name: MCF7 cells treated with 2uM Doxorubicin

treatment_protocol: Doxorubicin Treated

tag: MCF7 cells treated with 2uM Doxorubicin for 24 hours Array 1


title: MCF7_Doxorubicin_Array_2

tag: MCF7 cells treated with 2uM Doxorubicin for 24 hours Array 2


title: MCF7_Control_Array_1

tag: MCF7 Control cells Array 1


title: MCF7_ARC_Array_2

source_name: MCF7 cells treated with 2uM ARC

treatment_protocol: ARC NSC 188491 Treated

tag: MCF7 cells treated with 2uM ARC for 24 hours Array 2


title: U937 cells treated with hyperthermia (control)

description: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control).


title: Muscle PCOS control 18

status: Public on Nov 10 2008

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

description: Vastus lateralis muscle

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The R statistical software was applied for data analysis. The RMA method was used for global background correction and constant normalization was used for normalization. Gene expression index calculation was done using model based index calculation (MBEI). Only perfect match probes were included in data analysis. Welch two sample t-test for paired data was used to calculate p-values

source_name: Vastus lateralis muscle

label_protocol: One µg purified total RNA was converted to biotin-labeled aRNA using the MessageAmpTM II-Biotin single round aRNA amplification kit.

extract_protocol: Frozen muscle tissue was homogenized in Trizol with a Polytron Homogenizer and total RNA was purified using TRIzol Reagent including an extra step after phase separation with chloroform. Briefly, 1 volume of phenol-chloroform-isoamylalcohol (25-24-1) was added to the aqueous phase and spun at 10.000 x g for 10 minutes at 4˚C. Then, 1 volume of chloroform was added to the aqueous phase and spun at 12.000 x g for 20 minutes at 4˚C before RNA precipitation.

tag: Vastus lateralis muscle


title: HepG2/C3A cells cultured for 42 h in complete DMEM (+Leu#2)

city: Ithaca

first: Wei

last: Wang

state: NY

address: T2-003 Vet Res Tower

institute: Cornell University

data_processing: 5.0 ExpressionStat

label_protocol: These total RNA samples were labeled according to the standard one-cycle amplification and labeling protocol developed by Affymetrix (Santa Clara, CA).

extract_protocol: Cells cultured as described above were washed twice with ice-cold PBS, and cells were then directly lysed into denaturation solution in the culture dish.  Total RNA was extracted from cells using RNeasy Micro kit (Qiagen

treatment_protocol: HepG2/C3A human hepatocellular carcinoma cells (ATCC CRL-10741) were cultured in a humidified incubator at 37 oC and 5% CO2  in leucine-free Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 1x MEM non-essential amino acid solution, . Cells were plated in complete medium at a density of a 1 x 106 cells per 100 mm diameter culture dish. When the cells reached 50-60% confluence, the medium was replaced with experimental medium, which was either complete medium  or cysteine-devoid medium, and cells were cultured in the experimental medium for 42 h with a medium changes at 18 h and 36 h. Three separate dishes of cells were analyzed by microarray for each of the treatments (i.e., a total of 6RNA samples, 3 for of 2 treatments, were analyzed).

tag: with Leucine (essential amino acid)


title: Muscle PCOS case 231

description: Vastus lateralis muscle


title: Muscle PCOS case 201

description: Vastus lateralis muscle


title: HepG2/C3A cells cultured for 42 h in complete DMEM (+Leu#3)


title: HepG2/C3A cells cultured for 42 h in complete DMEM (+Leu#1)


title: Muscle PCOS control 11

description: Vastus lateralis muscle


title: Muscle PCOS control 15

description: Vastus lateralis muscle


title: Muscle PCOS control 17

description: Vastus lateralis muscle


title: Muscle PCOS control 13

description: Vastus lateralis muscle


title: Muscle PCOS case 41

description: Vastus lateralis muscle


title: HepG2/C3A cells cultured for 42 h in leucine-devoid DMEM (-Leu#1)

tag: without Leucine (essential amino acid)


title: HepG2/C3A cells cultured for 42 h in leucine-devoid DMEM (-Leu#2)

label_protocol: These total RNA samples were labeled according to the standard one-cycle amplification and labeling protocol developed by Affymetrix.


title: Muscle PCOS control 9

description: Vastus lateralis muscle


title: Muscle PCOS control 12

description: Vastus lateralis muscle


title: MCF7_ARC_Array_1

tag: MCF7 cells treated with 2uM ARC for 24 hours Array 1


title: Muscle PCOS control 10

description: Vastus lateralis muscle


title: Muscle PCOS control 6

description: Vastus lateralis muscle


title: Muscle PCOS control 2

description: Vastus lateralis muscle


title: Muscle PCOS case 81

description: Vastus lateralis muscle


title: Muscle PCOS after pioglitazone 82

description: Vastus lateralis muscle


title: Muscle PCOS control 3

description: Vastus lateralis muscle


title: Muscle PCOS control 8

description: Vastus lateralis muscle


title: Muscle PCOS after pioglitazone 272

description: Vastus lateralis muscle


title: Muscle PCOS after pioglitazone 42

description: Vastus lateralis muscle


title: Muscle PCOS after pioglitazone 32

description: Vastus lateralis muscle


title: Muscle PCOS after pioglitazone 202

description: Vastus lateralis muscle


title: Muscle PCOS control 7

description: Vastus lateralis muscle


title: Muscle PCOS after pioglitazone 122

description: Vastus lateralis muscle


title: Muscle PCOS pioglitazone 31

description: Vastus lateralis muscle


title: Muscle PCOS pioglitazone 271

description: Vastus lateralis muscle


title: Muscle PCOS after pioglitazone 102

description: Vastus lateralis muscle


title: Muscle PCOS after pioglitazone 252

description: Vastus lateralis muscle


title: Muscle PCOS pioglitazon 251

description: Vastus lateralis muscle


title: Muscle PCOS after pioglitazone 162

description: Vastus lateralis muscle


title: HepG2/C3A cells cultured for 42 h in leucine-devoid DMEM (-Leu#3)


title: Muscle PCOS after pioglitazone 232

description: Vastus lateralis muscle


title: WT(Ler)_Rc50_replicate1

city: Davis

last: Hu

address: One Shields Ave.

department: Department of Molecular and Cellular Biology

institute: Univ of California at Davis

description: Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. The SNAP-LITE lighting system (Quantum Devices Inc., Barneveld, WI) was used for red light source. Seedlings were grown for 4 days at 20 degree under 50 umol m-2 s-1  continuous red light (measured by a LI-COR quantum photometer, model LI-189). Seedlings were harvested and immediately frozen in liquid nitrogen under red light.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Affymetrix GCOS

organism: Arabidopsis thaliana

source_name: whole seedling

label_protocol: Affymetrix GeneChip® Expression Analysis kits (One-cycle target labeling and control reagents)

extract_protocol: QIAGEN RNeasy Plant Mini Kit

tag: wild type (Landsberg erecta ecotype); grown under continuous red light (Rc; light intensity = 50 umole m-2 s-1); 4 days (96h) old


title: WT(Ler)_Rc50_replicate2


title: YHB_Rc50_replicate2

tag: Transgenic plant, AtPHYB(genomic)-Y276H/phyAphyB, line #4; grown under continuous red light (Rc; light intensity = 50 umole m-2 s-1); 4 days (96h) old


title: WT(Ler)_Dark_replicate3

description: Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days. Seedlings were harvested and immediately frozen in liquid nitrogen in complete darkness with the aid of Bushnell night vision goggle with a built-in infrared illuminator (model: 26-1020 (1.0 x 20)).

source_name: whole seedlings

label_protocol: Affymetrix

tag: wild type (Landsberg erecta ecotype); dark-grown; 4 days (96h) old


title: WT(Ler)_Rc15_replicate1

description: Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. The SNAP-LITE lighting system (Quantum Devices Inc., Barneveld, WI) was used for red light source. Seedlings were grown for 4 days at 20 degree under 15 umol m-2 s-1 continuous red light (measured by a LI-COR quantum photometer, model LI-189). Seedlings were harvested and immediately frozen in liquid nitrogen under red light.

tag: wild type (Landsberg erecta ecotype); grwon under continuous red light (Rc; light intensity = 15 umole m-2 s-1); 4 days (96h) old


title: YHB_Rc50_replicate1

tag: Transgenic plant, AtPHYB(genomic)-Y276H/phyA-201phyB-5, line #4; grown under continuous red light (Rc; light intensity = 50 umole m-2 s-1); 4 days (96h) old


title: WT(Ler)_Rc15_replicate2

description: Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. The SNAP-LITE lighting system (Quantum Devices Inc., Barneveld, WI) was used for red light source. Seedlings were grown for 4 days at 20 degree under 15 umol m-2 s-1  continuous red light (measured by a LI-COR quantum photometer, model LI-189). Seedlings were harvested and immediately frozen in liquid nitrogen under red light.

tag: wild type (Landsberg erecta ecotype); grown under continuous red light (Rc; light intensity = 15 umole m-2 s-1); 4 days (96h) old


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -10

status: Public on Nov 08 2008

city: Palmerston North

first: Mingshu

last: Cao

address: Tennent Drive

country: New Zealand

institute: HortResearch/AgResearch

hyb_protocol: Standard precedures recomended by Affymetrix

data_processing: RMA background correction and normalization

source_name: ecotype 'Columbia'

label_protocol: according to Affymetrix

extract_protocol: RNA was isolated from 1 g of frozen pooled leaf tissue according to the manufacturer's instructions (PureLinkTM Plant RNA Reagent, Invitrogen) with one RNA clean-up using PureLinkTM Micro-to-Midi Total RNA Purification System (Invitrogen).

tag: Pap1 sample in day 12


title: YHB_Dark_replicate1

tag: Transgenic plant, AtPHYB(genomic)-Y276H/phyA-201phyB-5, line #5;

tag: Dark-grown;

tag: 4 days (96h) old


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -7

scan_protocol: Standard precedures recomended by Affymetrix

tag: Control sample in day 8


title: YHB_Dark_replicate2

tag: transgenic plant, AtPHYB(genomic)-Y276H/phyA-201phyB-5, line #5; dark-grown; 4 days (96h) old


title: phyAphyB_Dark_replicate1

description: Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 micromol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days.

source_name: Whole seedling

label_protocol: Affymetrix GeneChip® Expression Analysis kits

tag: phyA-201phyB-5 mutant in Ler background

tag: Dark-grown

tag: 4 days (96 h) old


title: YHB_Dark_replicate3

tag: Transgenic plant, AtPHYB(genomic)-Y276H/phyA-201phyB-5, line #4; dark-grown; 4 days (96h) old


title: phyAphyB_Dark_replicate3

tag: phyA-201phyB-5 mutant in Ler background; dark-grown; 4 days (96h) old


title: Muscle PCOS pioglitazone 161

description: Vastus lateralis muscle

tag: Vastus lateralis muscle


title: Muscle PCOS pioglitazone 121

description: Vastus lateralis muscle


title: WT(Ler)_Dark_replicate2


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -8

tag: Pap1 sample in day 8


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -9

tag: Control sample in day 12


title: Muscle PCOS pioglitazone 101

description: Vastus lateralis muscle


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -5

tag: Control sample in day 7


title: phyAphyB_Dark_replicate2

tag: phyA-201phyB-5 mutant in Ler backgournd; dark-grown; 4 days (96h) old


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -4

tag: pap1 sample in day2


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -6

tag: Pap1 sample in day 7


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -2

tag: Pap1 sample in day1


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis -3

tag: Control sample in Day2


title: Saos2 TAp73beta-24 h

city: Sapporo

first: Yasushi

last: Sasaki

address: S-1, W-17, Chuo-ku

department: Cancer Research Institute

institute: Sapporo Medical University

description: Saos2 osteosarcoma cells infected with TAp73beta expressing adenovirus for 24 h

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Affymetrix standard protocol, GCOS

source_name: Saos2 osteosarcoma cells

label_protocol: Affymetrix standard protocol

extract_protocol: Trizol


title: Saliva exosomes biological REP-2

status: Public on Nov 07 2008

first: Viswanathan

last: Palanisamy

address: 10833 Le Conte Ave

department: Dental Research Institute

institute: UCLA Dentistry

description: gene expression data from saliva exosomes

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GCRMA packages in bioconductor 2.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: saliva exosomes Batch 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: No growth protocol applied. Human biological fluid saliva collected and analysed for RNA profiling.

extract_protocol: RNA was extracted by Rnaeasy kit (Qiagen) according to manufacture's protocol.

treatment_protocol: No treatment needed. Saliva was collected through normal salivation and centrifuged to obtain microvesicles for RNA extraction

tag: Ultracentrifuged microvesicles from human saliva contains RNA


title: Atg16-hypomorph Paneth cells - replicate 2

city: St. Louis

first: Thaddeus

middle: S.

last: Stappenbeck

state: MO

address: 660 S. Euclid Avenue, Box 8118

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix Standard Protocol

data_processing: Data analyses performed using dChip (May 8, 2008 release)

source_name: Laser-captured murine Paneth cells from Atg16-hypomorph

label_protocol: Labeling with biotin was performed using RiboAmp plus (Item #KIT0511B) from Molecular Devices (MDS Analytical Technologies, Inc).

extract_protocol:
Total RNA extracted from HS LCM caps (Item #LCM0214) using protocol from PicoPure Kit (Item #KIT0204).
Amplification was performed using RiboAmp plus (Item #KIT0511B).
- All kits and items available from Molecular Devices (MDS Analytical Technologies, Inc).

tag: Mus Musculus (Strain

value: mixed C57BL/6 - 129ola)

tag: Pooled from mixed sex

tag: 6 weeks old

tag: Laser-captured Paneth cells


title: Wildtype Paneth cells - replicate 1

source_name: Laser-captured murine Paneth cells from wildtype

tag: Wildtype


title: WT(Ler)_Dark_replicate1

tag: wild type (Landsberg erecta ecotype)

tag: Dark-grown

tag: 4 days (96h) old


title: Saos2 p53-24 h

description: Saos2 osteosarcoma cells infected with p53 expressing adenovirus for 24 h


title: chondrocyte Slc39a13 knockout-rep3

city: Yokohama

first: Toshiyuki

last: Fukada

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN

description: Primary chobdrocytes were isolated and cultured as described previously (Lefebvre V., et al. Matrix Biol. 14, 329-335, 1994).

hyb_protocol: Twenty micro gram of labeled sample was used. Hybridization was performed at 45C for 16hr with continuous rotation.

scan_protocol: Washing and streptavidin-phycoerythrin staining was done using a GeneChip Fluidics Station (Affymetrix), then scanning was performed using a GeneChip scanner 3000 (Affymetrix) as the default setting.

data_processing: CHP file was directly submitted to GEO. MAS 5.0 algorithm

source_name: knockout mouse primary chondrocyte

label_protocol: Labeling was performed using One-cycle target labeling kit (Affymetrix) as manufacture's indication.

extract_protocol: Total RNA was extracted with Sepasol-RNA I (Nacalai Tesque). Qulity of total RNA was checked using a bioanalyzer (Agilent).

tag: Strain:129/C57B6, tissue:bone, Slc39a13 knock out


title: Saos2 GFP-24 h

description: Saos2 osteosarcoma cells infected with control adenovirus for 24 h


title: Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis

tag: Controls samples in day1


title: Saliva exosomes biological REP-3

source_name: saliva exosomes Batch 3


title: chondrocyte Slc39a13 knockout-rep2


title: STOX1 overexpression in choriocarcinoma cells

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

institute: INSERM

description: 45 % of the genes were detectable at a sufficient fluorescence level

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: MAS 5.0

source_name: Choriocarcinoma cells from cell line overexpressing STOX1

label_protocol: Standard Affymetrix

growth_protocol: Classical cell culture in the presence of gentamycin

extract_protocol: Trizol extraction

treatment_protocol: Modified by permanent transfection with STOX1

tag: JEG-3 cells from Erwin-Turner tumour


title: chondrocyte wild type-rep3

source_name: wild type mouse primary chondrocyte

tag: Strain:129/C57B6, tissue:bone


title: Wildtype Paneth cells - replicate 2

tag: Wildtype mice


title: chondrocyte Slc39a13 knockout-rep1


title: chondrocyte wild type-rep2


title: Saliva exosomes biological REP-1

source_name: saliva exosomes Batch 1


title: Atg16-hypomorph Paneth cells - replicate 1


title: chondrocyte wild type-rep1


title: Control transfection in choriocarcinoma cells

source_name: Choriocarcinoma cells from mock-transfected cell line

treatment_protocol: Permanently mock-transfected by empty pCMX vector


title: p53 KO LSKs

city: New York

first: Agnes

last: Viale

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: p53 Regulates Hematopoietic Stem Cell Quiescence

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: according to manufacturer

data_processing: GCOS/MAS 5.0 with overall intensity targetted to 500.

label: biotin dnTP

source_name: p53 KO LSKs

label_protocol: Affymetrix one cycle kit

extract_protocol: RNeasy

tag: Lin-Sca-1+c-kit+ cells from C57B6 background

tag: Steady state


title: Saliva exosomes biological REP-4

source_name: saliva exosomes Batch 4


title: WT LSKs

source_name: WT LSKs


title: osteoblast wild type

description: For primary osteoblasts, calvaria from newborn mice were dissected aseptically and digested sequentially in isolation buffer (25mM HEPES pH 7.5,10mM NaHCO3, 100mM NaCl, 3mM K2HPO4, 1mM CaCl2, 30mM KCl, 1mg/ml BSA, 5mg/ml D-glucose) containing 0.75 mg/ml collagenase and 0.2% dispase. Fractions 3–5 were cultured in -MEM containing 10% fetal calf serum (FCS).

source_name: wild type mouse primary osteoblast


title: osteoblast Slc39a13 knockout

source_name: knockout mouse primary osteoblast


title: P53 KO/MEF KO (DKO) LSKs

source_name: P53 KO/MEF KO (DKO) LSKs


title: WT 2

status: Public on Nov 06 2008

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

description: Age: 2 days

data_processing: RMA, Bioconductor standard implementation

source_name: Liver

extract_protocol: Trizol Reagent

tag: Genotype

value: WT


title: KO 3

description: Age: 2 days


title: KO 2

description: Age: 2 days


title: KO 1

description: Age: 2 days


title: WT 3

description: Age: 2 days


title: WT 4

description: Age: 2 days


title: KO 4

description: Age: 2 days


title: WT 1

description: Age: 2 days


title: normal cochlea rep6

status: Public on Nov 01 2008

city: Boston

first: Joe

middle: Claud

last: Adams

state: MA

address: 243 Charles St.

department: Otolaryngology

institute: Massachusetts Eye & Ear Infirmary

hyb_protocol: For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2.  Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process.  The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.  Quantification of the samples is carried out on a Bio-Tek UV Plate Reader.    Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of material is the nominal amount used on the GeneChip® arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.

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

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

source_name: NORMAL COCHLEA

label_protocol: Processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process.  The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.

extract_protocol: Total RNA was extracted from cochlear soft tissue using Invitrogen's   TRIZOL protocol and purified using Qiagen's RNEasy Mini kit in   accordance with their standard procedure.

treatment_protocol: Mice were given a fatal dose of urethane (300 mg/kg, i.p.) and exsanguinated by cardiac perfusion with sterile saline to remove blood cells from the tissue. Cochleas were collected in RNAlater and the other bony shell of the cochlea was removed with jeweler’s forceps. All soft tissue (spiral ligament, organ of Corti, and modiolus) was collected in RNAlater.

tag: CBA/CaJ, male, 9 weeks, cochlea


title: 400mMsorbitolTSCJian6h rap 1

status: Public on Nov 04 2008

city: Detroit

first: wenbo

last: xu

state: MI

address: 3127 Scott Hall ,540 East Canfield

institute: wayne state university

description: Gene expression data from Mouse embryos  treated  with 400mMsorbitol for 6h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Murine Genome 430.2  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymatrix gene chip scanner 3000.

data_processing: All cel files were read and normalized by D-Chip software, normalized data were analysed by GeneSpring software

source_name: mouse embryos

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: Mouse placental trophoblast stem cells were cultured in standard media supplemented with conditioned media from mouse embryonic fibroblasts and 10ng/ml fibroblast growth factor (FGF)4 and heparin. The latter two are known to keep trophoblast stem cells in a undifferentiated pluripotent state.

extract_protocol: Total RNA was isolated from cells 2-3 times for each time point. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mouse trophoblast stem cells were cultured in the same media in the ‘growth protocol’ except 400mM sorbitol was added to cause hyperosmolar stress. Cells were harvested for analysis by microarray at 5 time points from 0-24hr of stress.


title: 400mMsorbitolTSCJian0h rap 2

description: Gene expression data from Mouse embryos  treated  with 400mMsorbitol for 0h


title: 400mMsorbitolTSCJian2h rap 1

description: Gene expression data from Mouse embryos  treated  with 400mMsorbitol for 2h


title: normal cochlea rep8


title: normal cochlea rep7


title: 400mMsorbitolTSCJian0.5h rap 2

description: Gene expression data from Mouse embryos  treated  with 400mMsorbitol for 0.5h


title: normal cochlea rep3


title: 400mMsorbitolTSCJian0.5h rap 3

tag: embryos  treated  with 400mMsorbitol for 0.5h


title: 400mMsorbitolTSCJian2h rap 2

tag: embryos  treated  with 400mMsorbitol for 2h


title: normal cochlea rep2


title: 400mMsorbitolTSCJian6h rap 2

tag: embryos  treated  with 400mMsorbitol for 6h


title: normal cochlea rep4


title: 400mMsorbitolTSCJian24h rap 2

description: Gene expression data from Mouse embryos  treated  with 400mMsorbitol for 24h


title: 400mMsorbitolTSCJian0.5h rap 1


title: 400mMsorbitolTSCJian0h rap 1

tag: embryos  treated  with 400mMsorbitol for 0h


title: normal cochlea rep1


title: 400mMsorbitolTSCJian24h rap 1

tag: embryos  treated  with 400mMsorbitol for 24h


title: normal cochlea rep5


title: C57BL-6-heatshock-10h-rep1

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

description: All methodolgy for this datasetis was described in the manuscript of "Differential gene expression in the testes of different murine strains under normal and hyperthermic conditions"

hyb_protocol: Standard hybridization protocol using 15ug cRNA wash/stain protocol EukGe-2v5-450

scan_protocol: Affymetrix GeneChip® Operating Software (GCOS) automates the control of GeneChip® Fluidics Stations and Scanners. In addition, GCOS acquires data, manages sample and experimental information, and performs gene expression data analysis.

data_processing: For each microarray, probe set signal values were initially normalized by scaling to a target intensity of 125.

source_name: Murine testes of C57BL/6 10hr after heatshock at 43C for 15min

label_protocol: GeneChip Expression 3' - Amplification one-cycle cDNA synthesis kit (lpn-900431)

tag: Gene expression profile of testes from two mouse strains, AKR/N, C57BL/6, including controls and different time points after heat treatment at 43C for 15 min


title: AKR_N-heatshock-24h-rep2

source_name: Murine testes of AKR/N 24hr after heatshock at 43C for 15min


title: AKR_N-heatshock-Control-rep1

source_name: Murine testes of AKR/N control (no heat treatment)


title: AKR_N-heatshock-8h-rep1

source_name: Murine testes of AKR/N 8hr after heatshock at 43C for 15min


title: AKR_N-heatshock-24h-rep1


title: C57BL-6-heatshock-12h-rep2

source_name: Murine testes of C57BL/6 12hr after heatshock at 43C for 15min


title: C57BL-6-heatshock-10h-rep2


title: AKR_N-heatshock-12h-rep2

source_name: Murine testes of AKR/N 12hr after heatshock at 43C for 15min


title: C57BL-6-heatshock-Control-rep1

source_name: Murine testes of C57BL/6 control (no heat treatment)


title: AKR_N-heatshock-10h-rep1

source_name: Murine testes of AKR/N 10hr after heatshock at 43C for 15min


title: AKR_N-heatshock-10h-rep2


title: C57BL-6-heatshock-24h-rep2

source_name: Murine testes of C57BL/6 24hr after heatshock at 43C for 15min


title: C57BL-6-heatshock-24h-rep1


title: C57BL-6-heatshock-8h-rep1

source_name: Murine testes of C57BL/6 8hr after heatshock at 43C for 15min


title: C57BL-6-heatshock-Control-rep2


title: C57BL-6-heatshock-12h-rep1


title: AKR_N-heatshock-Control-rep2


title: AKR_N-heatshock-8h-rep2


title: mtestis_C57BL-6_rep1

description: All methodolgy for this dataset was described in the manuscript of "Differential gene expression in the testes of different murine strains under normal and hyperthermic conditions"

source_name: Murine testes of C57BL/6 strain replicates 1

tag: Gene expression profile of testes from three mouse strains, AKR/N, C57BL/6,MRL/MpJ+/+ (all mice used were 8 weeks old)


title: mtestis_MRL-MPJ_rep2

source_name: Murine testes of MRL/MpJ+/+ strain replicates 2


title: mtestis_AKR-N_rep2

source_name: Murine testes of AKR/N strain replicates 2


title: mtestis_C57BL-6_rep2

source_name: Murine testes of C57BL/6 strain replicates 2


title: HRV-infected, normal S9 (U133 Plus 2.0 Array)

city: Madison

first: Yury

middle: A

last: Bochkov

state: WI

address: 600 Highland Ave, K4/945 CSC

department: Pediatrics

institute: University Of Wisconsin-Madison

description: Gene expression data from HRV-infected PBE cells from normal (control) individual

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human Genome U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Fluorescent signal intensities were extracted from scanned images using Affymetrix default analysis settings of the GCOS version 1.4 software. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. HG U133 Plus 2.0 GeneChip quality control parameters for all samples were within recommended range. Log2-transformed expression values across all the chips were extracted using the Robust Multichip Average (RMA) method.  Processing with RMA involved background correction, probe level quantile normalization across all the 22 chips and expression summarization.

source_name: HRV-infected PBE cells, normal S9

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).

growth_protocol: Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen-coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen-coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).

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

treatment_protocol: One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.

tag: Human primary bronchial epithelial cells from normal (control) individuals, cultured in monolayers, passage 3

tag: 16 hours p.i.


title: C57BL-6-heatshock-8h-rep2


title: AKR_N-heatshock-12h-rep1


title: mtestis_MRL-MPJ_rep1

source_name: Murine testes of MRL/MpJ+/+ strain replicates 1


title: HRV-infected, normal S13 (U133 Plus 2.0 Array)

source_name: HRV-infected PBE cells, normal S13


title: HRV-infected, normal S14 (U133 Plus 2.0 Array)

source_name: HRV-infected PBE cells, normal S14


title: liver-AHRKO-TCDD-rep1

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: mouse liver, AHR knockout, 1000 ug/kg TCDD treated, 19 hours

hyb_protocol: Manufacturer's protocol

scan_protocol: Manufacturer's protocol

data_processing: Array data were loaded into the R statistical package (version 2.0.0) using the affy package (version 1.5.8; http://www.bioconductor.org) (Gautier et al., 2004) of the BioConductor open-source project (Gentleman et al., 2004). Data were investigated for spatial and distributional homogeneity, then preprocessed with a sequence-specific version of the RMA algorithm (Irizarry et al., 2003) termed GCRMA, as implemented in BioConductor (version 1.1.3).

source_name: liver-AHRKO-TCDD

label_protocol: Manufacturer's protocol

growth_protocol: Male Ahr–/– mice (10 weeks old) in a C57BL/6J background were obtained from The Jackson Laboratory (Bar Harbor, ME). Wild-type (Ahr+/+) male C57BL/6J mice (15 weeks old) were bred at the National Public Health Institute (Kuopio, Finland) from stock originally obtained from The Jackson Laboratory.

extract_protocol: Liver was harvested 19 h after treatment, sliced, snap-frozen, and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (QIAGEN, Valencia, CA) according to the manufacturer's instructions. DNase (QIAGEN) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry, and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Mice were given a single dose of 1000 µg/kg TCDD or corn oil vehicle by gavage. TCDD initially was dissolved in ether and added to corn oil; the ether subsequently was evaporated off. TCDD was purchased from the UFA-Oil Institute (Ufa, Russia) and was >99% pure as determined by gas chromatography-mass spectrometry.


title: liver-AHRKO-TCDD-rep2


title: mock-infected, normal S15 (U133 Plus 2.0 Array)

description: Gene expression data from mock-infected PBE cells from normal (control) individual

source_name: mock-infected PBE cells, normal S15


title: liver-AHRKO-cornoil-rep3

description: mouse liver, AHR knockout, cornoil treated, 19 hours

source_name: liver-AHRKO-cornoil


title: 12WT, replicate 1

city: Granada

first: Antonio

last: Suarez

state: Granada

address: Pharmacy Faculty, Campus Cartuja s/n

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Granada

description: Affymetrix Technical Manual

hyb_protocol: Affymetrix Technical Manual

scan_protocol: Affymetrix Technical Manual

data_processing: Normalized with Bioconductor

source_name: Intestine from wild type mice

label_protocol: Affymetrix Technical Manual

extract_protocol: Trizol reagent

tag: Wild type mice (C57B6/J)

tag: Tissue

value: full-thickness colon

tag: Age

value: 12 weeks

tag: Grown under conventional conditions


title: HRV-infected, normal S7 (U133 Plus 2.0 Array)

source_name: HRV-infected PBE cells, normal S7


title: HRV-infected, normal S15 (U133 Plus 2.0 Array)

source_name: HRV-infected PBE cells, normal S15


title: mock-infected, normal S7 (U133 Plus 2.0 Array)

source_name: mock-infected PBE cells, normal S7


title: mock-infected, normal S13 (U133 Plus 2.0 Array)

source_name: mock-infected PBE cells, normal S13


title: mock-infected, normal S14 (U133 Plus 2.0 Array)

source_name: mock-infected PBE cells, normal S14


title: liver-AHRKO-TCDD-rep3


title: liver-AHRKO-cornoil-rep1


title: 12WT, replicate 3

description: Affymetrix Technical Manual


title: 12WT, replicate 2

description: Affymetrix Technical Manual


title: HRV-infected, normal S8 (U133 Plus 2.0 Array)

source_name: HRV-infected PBE cells, normal S8


title: mock-infected, normal S9 (U133 Plus 2.0 Array)

source_name: mock-infected PBE cells, normal S9


title: 12SPF, replicate 1

description: Affymetrix Technical Manual

source_name: Intestine from IL10-/- knockout mice

tag: IL10-/- knockout mice (C57B6/J)

tag: Grown under Specific Pathogen Free (SPF) conditions


title: mtestis_AKR-N_rep1

source_name: Murine testes of AKR/N strain replicates 1


title: HRV-infected, asthmatic S18 (U133 Plus 2.0 Array)

description: Gene expression data from HRV-infected PBE cells from asthmatic individual

source_name: HRV-infected PBE cells, asthmatic S18

tag: Human primary bronchial epithelial cells from patients with mild asthma, cultured in monolayers, passage 3


title: 12CC, replicate 3

description: Affymetrix Technical Manual


title: 12SPF, replicate 3

description: Affymetrix Technical Manual


title: mock-infected, normal S8 (U133 Plus 2.0 Array)

source_name: mock-infected PBE cells, normal S8


title: HRV-infected, asthmatic S16 (U133 Plus 2.0 Array)

source_name: HRV-infected PBE cells, asthmatic S16


title: liver-AHRKO-cornoil-rep2


title: 12CC, replicate 1

description: Affymetrix Technical Manual


title: 9WT, replicate 3

description: Affymetrix Technical Manual

value: 9 weeks


title: HRV-infected, asthmatic S17 (U133 Plus 2.0 Array)

source_name: HRV-infected PBE cells, asthmatic S17


title: 9WT, replicate 1

description: Affymetrix Technical Manual


title: HRV-infected, asthmatic S12 (U133 Plus 2.0 Array)

source_name: HRV-infected PBE cells, asthmatic S12


title: mock-infected, asthmatic S18 (U133 Plus 2.0 Array)

description: Gene expression data from mock-infected PBE cells from asthmatic individual

source_name: mock-infected PBE cells, asthmatic S18


title: HRV-infected, asthmatic S10 (U133 Plus 2.0 Array)

source_name: HRV-infected PBE cells, asthmatic S10


title: 12SPF, replicate 2

description: Affymetrix Technical Manual


title: mock-infected, asthmatic S17 (U133 Plus 2.0 Array)

source_name: mock-infected PBE cells, asthmatic S17


title: 9WT, replicate 2

description: Affymetrix Technical Manual

source_name: Intestine from wild type mice


title: 12CC, replicate 2

description: Affymetrix Technical Manual


title: Dark-grown WT control (vector#4)

data_processing: Arrays were normalized in the GeneChip Operation Software (GCOS)

source_name: vector transgenic line #4, dark-grown 7-day-old seedlings

label_protocol:
ds cDNA synthesis: SuperScript Choice System from Invitrogen
ds cDNA cleanup: GeneChip Sample Cleanup Module from Affymetrix
cRNA synthesis: Bioarray High-Yield RNA Transcript Labeling Kit from Enzo Biochem. UTP and CTP is biotinylated
cRNA cleanup: GeneChip Sample Cleanup Module from Affymetrix

extract_protocol: Qiagen RNeasy Plant Mini Prep Kit

tag: Transgenic line

value: pRR2222 vector #4, T2 generation.

tag: Growth conditions

value: Seeds were sowed on 1x MS media with 50µg/mL of Hygromycin, stratified at 4oC in darkness for 2 days; germination was induced by exposure to light for 2 hours; seedlings were grown vertically at 22oC for 7 days in the dark before harvesting seedling materials for RNA extraction. Only the Hygromycin-resistant seedlings were harvested.


title: 9SPF, replicate 2

description: Affymetrix Technical Manual


title: mock-infected, asthmatic S16 (U133 Plus 2.0 Array)

source_name: mock-infected PBE cells, asthmatic S16


title: 35S-MIF1 line#127, dark grown

source_name: MIF1-OE transgenic line #127, dark-grown 7-day-old seedlings

tag: Ecotype

value: Columbia

value: MIF1OE#127, T2 generation.


title: 35S-MIF1 line #124, dark grown, replicate2

source_name: MIF1-OE transgenic line #124, dark-grown 7-day-old seedlings

value: MIF1OE#124, T2 generation.


title: Dark-grown WT control (vector#1)

source_name: vector transgenic line #1, dark-grown 7-day-old seedlings

value: pRR2222 vector line#1, T2 generation.


title: 9SPF, replicate 3

description: Affymetrix Technical Manual


title: mock-infected, asthmatic S10 (U133 Plus 2.0 Array)

source_name: mock-infected PBE cells, asthmatic S10


title: mock-infected, asthmatic S12 (U133 Plus 2.0 Array)

source_name: mock-infected PBE cells, asthmatic S12


title: 9CC, replicate 2

description: Affymetrix Technical Manual

source_name: Intestine from IL10-/- knockout mice


title: 9CC, replicate 3

description: Affymetrix Technical Manual


title: 9SPF, replicate 1

description: Affymetrix Technical Manual


title: 35S-MIF1 line#127, light grown

source_name: MIF1-OE transgenic line #127, light-grown 7-day-old seedlings

tag: Growth condition

value: Seeds were sowed on 1x MS media with 50µg/mL of Hygromycin, stratified at 4oC in darkness for 2 days, and then grown vertically at 22oC for 7 days before harvesting seedling materials for RNA extraction. The light intensity was 70~120 µmol m-2 s-1 and the photoperiod was 16h light/8h dark. Only the Hygromycin-resistant seedlings were harvested.


title: 35S-MIF1 line #124, dark grown, replicate1


title: Light-grown WT control (vector#7)

source_name: vector transgenic line #7, light-grown 7-day-old seedlings

value: pRRR2222 vector #7, T2 generation.


title: 35S-MIF1 line #124, light grown, replicate2

source_name: MIF1-OE transgenic line #124, light-grown 7-day-old seedlings


title: Light-grown WT control (vector#4)

source_name: vector transgenic line #4, light-grown 7-day-old seedlings

value: pRRR2222 vector #4, T2 generation.


title: 7WT, replicate 3

description: Affymetrix Technical Manual

value: 7 weeks


title: Light-grown WT control (vector#1)

source_name: vector transgenic line #1, light-grown 7-day-old seedlings

value: pRRR2222 vector #1, T2 generation.


title: 7WT, replicate 2

description: Affymetrix Technical Manual


title: PrSC, FOXF2 siRNA, array B

city: Rotterdam

first: Leonie

last: van der Heul

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus MC

description: Gene expression of PrSC cells treated with FOXF2 siRNA.

hyb_protocol: Hybridization to Affymetrix Human U133plus2.0 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, and washing were performed as described by Affymetrix (Affymetrix, Santa Clara, CA, USA) and performed by Erasmus MC Center for Biomics.

scan_protocol: Scanning procedures were performed as described by Affymetrix (Affymetrix, Santa Clara, CA, USA) and performed by Erasmus MC Center for Biomics.

data_processing: Data was processed using Affymetrix GCOS software (MAS5.0 algorithm).

source_name: Human primary prostate stromal cells, siRNA directed against FOXF2

label_protocol: 5ug of total RNA was used to prepare antisense biotinylated RNA according to manufacturer's one-cycle instructions (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Incubation with siRNA directed against FOXF2, 72h, special PRSC medium without serum.

extract_protocol: RNA was isolated from the prostate stromal cells by lysing the cells (PCU, Kinematica GmbH, Luzern, Switzerland) in RNAbee reagent (Tel-test Inc, Friendswood, USA). Chloroform was added and centrifuged at 12,000 g. The water phase was extracted and precipitated with isopropanol. The RNA was washed with 75 % ethanol and dissolved in RNAse free water.

tag: Primary prostate stromal cells in which FOXF2 is knocked down.


title: PrSC, control siRNA, array A

description: Gene expression of PrSC cells treated with negative control siRNA.

source_name: Human primary prostate stromal cells, negative control siRNA

growth_protocol: Incubation with negative control siRNA, 72h, special PRSC medium without serum.

tag: Control primary prostate stromal cells.


title: PrSC, control siRNA, array B


title: 7SPF, replicate 3

description: Affymetrix Technical Manual

tag: Grown in Specific Pathogen Free (SPF) conditions


title: PrSC, FOXF2 siRNA, array C


title: 7SPF, replicate 2

description: Affymetrix Technical Manual


title: PrSC, FOXF2 siRNA, array A


title: Dark-grown WT control (vector#7)

source_name: vector transgenic line #7, dark-grown 7-day-old seedlings


title: 7WT, replicate 1

description: Affymetrix Technical Manual

source_name: Intestine from wild type mice


title: PrSC, control siRNA, array C


title: 9CC, replicate 1

description: Affymetrix Technical Manual


title: 7SPF, replicate 1

description: Affymetrix Technical Manual


title: 7CC, replicate 1

description: Affymetrix Technical Manual

tag: Grown in conventional conditions


title: 7CC, replicate 3

description: Affymetrix Technical Manual


title: 35S-MIF1 line #124, light grown, replicate1


title: Xenograft treated with BEV 26-1004 avastin 34b

city: Singapore

first: Kun

last: Yu

department: Cellular & Molecular Research

country: Singapore

institute: National Cancer Centre

description: Gene expression data  for xenograft treated with BEV

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: Xenografts of Hepatocellular Carcinoma

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

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

value: liver


title: Xenograft treated with RAPA 26-1004 rapa 31a

description: Gene expression data  for xenograft treated with RAPA


title: Xenograft treated with RAPA 26-1004 rapa 32a


title: Xenograft control 26-1004c1 control

description: Gene expression data  for xenograft control


title: 7CC, replicate 2

description: Affymetrix Technical Manual


title: Xenograft treated with RAPA/BEV 26-1004 av+rapa 41b

description: Gene expression data  for xenograft treated with RAPA/BEV


title: Xenograft control 26-1004b1 control


title: Xenograft treated with BEV 26-1004 avastin 35b


title: Xenograft treated with BEV 26-1004 avastin 33b


title: Xenograft treated with RAPA/BEV 26-1004 av+rapa 39a


title: Xenograft control 26-1004a1 control


title: ependimoma

city: Valencia

first: Manolo

last: Mata

address: Avda. Blasco Ibanez, 17

department: UCIM

institute: university of valencia

hyb_protocol: 16 hours at 42ºC and processed in FS450 (protocol eukgene_ws_2v5)

scan_protocol: Gene Chip 3000G

data_processing: GCOS. TGT of 500

source_name: brain tumor

label_protocol: biotin

extract_protocol: total RNA extraction using mirVANA isolation kit (Ambion)

tag: non metastatic


title: Xenograft treated with RAPA 26-1004 rapa 29b


title: Xenograft treated with RAPA 5-1318-3 rapa 15b


title: Xenograft control 5-1318-3c1 control


title: Xenograft treated with RAPA 5-1318-3 rapa 17b


title: Xenograft treated with RAPA 5-1318-3 rapa 16b


title: Xenograft control 5-1318-3b1 control


title: Xenograft treated with BEV 5-1318-3 avastin 20a


title: Xenograft treated with RAPA/BEV 5-1318-3 av+rapa 25a


title: Xenograft treated with RAPA/BEV 5-1318-3 av+rapa 24a


title: Xenograft treated with BEV 5-1318-3 avastin 19b


title: Xenograft control 2-1318b1 control


title: Xenograft treated with RAPA 2-1318 rapa 3b


title: Xenograft treated with RAPA/BEV 26-1004 av+rapa 37b


title: Xenograft treated with RAPA 2-1318 rapa 1b


title: Xenograft treated with RAPA 2-1318 rapa 4a


title: Xenograft control 2-1318a2 control


title: Xenograft treated with BEV 5-1318-3 avastin 21a


title: Primary 30-1004(30.08.01)

description: Gene expression data  for primary

source_name: PrimaryHepatocellular Carcinoma


title: Primary 26-1004 cirr primary (b)

description: Gene expression data  for primary


title: Xenograft treated with RAPA/BEV 2-1318 av+rapa 9a


title: Xenograft control 2-1318c1 control


title: Xenograft control 5-1318-3a2 control


title: Xenograft treated with RAPA/BEV 5-1318-3 av+rapa 23a


title: Xenograft treated with BEV 2-1318 avastin 7a


title: Xenograft treated with RAPA/BEV 2-1318 av+rapa 10a


title: Primary 5-1318(13.08.01)

description: Gene expression data  for primary


title: Primary 5-1318-3(13.08.01)

description: Gene expression data  for primary


title: Primary 26-1004(26.10.04)

description: Gene expression data  for primary


title: Xenograft 30-1004-xeno

description: Gene expression data  for xenograft


title: Primary 2006(20.06.01)

description: Gene expression data  for primary


title: Primary 2-1318(13.08.01)

description: Gene expression data  for primary


title: Xenograft treated with BEV 2-1318 avastin 5a


title: Xenograft treated with RAPA/BEV 2-1318 av+rapa 11a


title: Xenograft 2006-xeno

description: Gene expression data  for xenograft


title: Xenograft 26-1004 cirr xeno (b)

description: Gene expression data  for xenograft


title: Xenograft 5-1318

description: Gene expression data  for xenograft


title: Xenograft 26-1004-xeno

description: Gene expression data  for xenograft


title: metastasic

tag: metastatic


title: PBMCs_LB_before exercise_16

status: Public on Oct 31 2008

city: Irvine

first: Shlomit

last: Radom-Aizik

address: 101 Academy

institute: University of California, Irvine

hyb_protocol: 10 µg of  fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix U133+2 arrays.

scan_protocol: The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip® Scanner 3000.

data_processing: The results were quantified and analyzed using GCOS 1.4 software (Affymetrix, Inc.) using default values (Scaling Target Signal Intensity=500; Normalization, All probe sets; Parameters, all set at default values). The microarray data was analyzed using ArrayAssistÒ version 4.0.3 (STRATAGENEÒ ) using GC-RMA.

source_name: Late Boys PBMCs before exercise

label_protocol: 4 μg total RNA was used as a template for double‑stranded cDNA synthesis. Single-stranded then double-stranded cDNA was synthesized from the poly A spike-in controls, and mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA), and a T-7-oligo(dT) primer (Integrated DNA Technologies Inc.,Coralville,IA) that contains a T7 RNA polymerase promoter site added to it’s 3' end. A portion of the resulting double-stranded cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Affymetrix GeneChip® IVT Labeling Kit.

extract_protocol: PBMCs were isolated using OptiPrepÒ Density Gradient Medium (SIGMA).  Total RNA was extracted using TRIzol®  reagent and purified using the RNeasy Midi columns method (Qiagen, Valencia, CA).

tag: PBMCs, healthy male, age 18

tag: before-exercise


title: Xenograft 5-1318-3

description: Gene expression data  for xenograft

tag: Tissue


title: Xenograft 2-1318-xeno

description: Gene expression data  for xenograft


title: PBMCs_LB_before exercise_20

tag: PBMCs, healthy male, age 27


title: Cell line HK-Hep1(b)

description: Gene expression data  for cell line

source_name: cell line


title: PBMCs_LB_before exercise_19

tag: PBMCs, healthy male, age 15


title: PBMCs_LB_before exercise_15

tag: PBMCs, healthy male, age 17


title: PBMCs_LB_after exercise_20

source_name: Late Boys PBMCs after 30 min bout of exercise

tag: after-exercise


title: PBMCs_LB_before exercise_18

tag: PBMCs, healthy male, age 16


title: PBMCs_LB_after exercise_19


title: PBMCs_LB_after exercise_16


title: PBMCs_LB_after exercise_17


title: PBMCs_LB_after exercise_15


title: Cell line PLC-PRL(b)

description: Gene expression data  for cell line


title: Cell line Hep3B(a)

description: Gene expression data  for cell line


title: PBMCs_LB_before exercise_17


title: PBMCs_LB_before exercise_13

tag: PBMCs, healthy male, age 19


title: PBMCs_LB_before exercise_14


title: Cell line HepG2(b)

description: Gene expression data  for cell line


title: PBMCs_LB_before exercise_12


title: PBMCs_LB_after exercise_18


title: PBMCs_LB_after exercise_14


title: PBMCs_LB_after exercise_13


title: PBMCs_LB_before exercise_11


title: PBMCs_LB_after exercise_12


title: PBMCs_LB_after exercise_11


title: PBMCs_EB_before exercise_08

source_name: Early Boys PBMCs before exercise

tag: PBMCs, healthy male, age 12


title: PBMCs_EB_after exercise_09

source_name: Early Boys PBMCs after 30 min bout of exercise

tag: PBMCs, healthy male, age 11


title: PBMCs_EB_after exercise_08


title: PBMCs_EB_before exercise_10

tag: PBMCs, healthy male, age 9


title: PBMCs_EB_before exercise_07


title: PBMCs_EB_after exercise_10


title: PBMCs_EB_before exercise_04


title: PBMCs_EB_after exercise_07


title: PBMCs_EB_after exercise_02


title: PBMCs_EB_before exercise_05


title: PBMCs_EB_after exercise_01

tag: PBMCs, healthy male, age 8


title: PBMCs_EB_before exercise_03

tag: PBMCs, healthy male, age 10


title: PBMCs_EB_before exercise_06


title: PBMCs_EB_after exercise_06


title: PBMCs_EB_after exercise_04


title: PBMCs_EB_before exercise_02


title: PBMCs_EB_before exercise_09


title: PBMCs_EB_before exercise_01


title: PBMCs_EB_after exercise_03


title: PBMCs_EB_after exercise_05


title: NIH3T3_replicate_2

first: Junying

last: Yuan

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

description: RNA analyses were performed at the microarray core facility at the Harvard Medical School and Partners Healthcare Center for Genetics and Genomics.

hyb_protocol: As per Affymetrix instructions.

scan_protocol: As per Affymetrix instructions.

source_name: NIH3T3 cell line

label_protocol: As per Affymetrix instructions.

extract_protocol: Trizol (Invitrogen) and RNeasy columns (Qiagen). The quantity, purity and integrity of RNA were evaluated by UV spectrophotometry and RNA-nano Bioanalyzer (Agilent).

tag: Unstimulated.

tag: Sensitive to apoptosis.

tag: Available from ATCC.


title: Ascites Treg_biological_rep2

first: Yu

last: Zhao

address: 660 S. Euclid

institute: Washington University

hyb_protocol: Chips hybridized according to Manufacturer's protocol

data_processing: MAS5 signal

source_name: IP-tumor Ascites Treg

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

extract_protocol:
Cell isolation: Naïve Treg cells were purified from the resting spleens of FoxP3-GFP knock-in mice made in the 129/SvJ strain. Ascites Treg cells were tumor-associated FoxP3-GFP+ cells sorted from the tumor ascites of 129/SvJ mice IP-injected with 1 x 10e6 RMAS cells 5 days earlier; Spleen-T Treg cells were purified from the spleens of the same tumor-bearing mice.
RNA extracted with Trizol

tag: Genotype

value: Foxp3-GFP KI, Ascites Treg cells were tumor-associated FoxP3-GFP+ cells sorted from the tumor ascites of 129/SvJ mice IP-injected with 1 x 106 RMAS cells 5 days earlier;


title: L929_replicate_2

source_name: L929 cell line

tag: Sensitive to necrosis.


title: Naïve Treg_biological_rep3

source_name: Naive CD4+Foxp3+ Treg cells

tag: strain

tag: tissue

value: spleen

tag: cell type

value: Naive CD4+Foxp3+ Treg cells


title: Ascites Treg_biological_rep3


title: Naïve Treg_biological_rep1


title: Protected, d5

city: Houston.

first: Jason

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

description: Protected, d5

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: dChip used to normalize and model all chips in this series

label: biotin and phycoerythrin

source_name: Laser-capture microdissected islets from NOD.Scid injected at d0 with BDC2.5 transgenic, diabetogenic T cells and also injected twice with anti-Ifng antibodies

label_protocol: Affymetrix-recommended cRNA synthesis with biotinylated nucleotides followed by fragmentation

growth_protocol: mice were sacrificed 5 days after transfer of CD4+ BDC2.5 diabetogenic T cells and following two injections of anti-Ifng antibody (at day -1 and day 2 relative to T cell transfer)

extract_protocol: Islets were captured from frozen sections that had been fixed in methanol, briefly eosin-stained in ethanol and immediately dehydrated without exposure to aqueous solution at any time. Agilent PicoPure column with DNAse treatment was used to extract RNA from captured laser-capture caps.

treatment_protocol: Captured RNA was extracted using Agilent PicoPure columns, pooled and ~30 ng was amplified using one round of Arcturus RiboAmp HS kit amplification followed by the RNA Amplification and Labeling Kit from Enzo Life Sciences

tag: pooled from 5 NOD.Scid mice protected from developing diabetes by Ifng antibody injection


title: Protected, d8

description: Protected, d8

growth_protocol: mice were sacrificed 8 days after transfer of CD4+ BDC2.5 diabetogenic T cells and following two injections of anti-Ifng antibody (at day -1 and day 2 relative to T cell transfer)


title: Ascites Treg_biological_rep1


title: NIH3T3_replicate_1


title: Foxa2-mutant-1-E7.5  (MOE 430 2.0)

first: Owen

middle: James

last: Tamplin

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

description: E7.5 POOLED EMBRYOS: n=53; Stages between mid-streak and headfold according to Downs & Davies

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Affymetrix MAS5.0, target normalized to 1000

source_name: E7.5 EMBRYO EPIBLAST ONLY

label_protocol: AFFYMETRIX GeneChip® T7-Oligo(dT) Promoter Primer Kit

extract_protocol: TRIZOL REAGENT

treatment_protocol: EXTRA-EMBRYONIC REGION OF EMBRYO REMOVED PRIOR TO EXTRACTION

tag: STRAIN

value: ICR

tag: GENDER

value: MIXED


title: MALT_036

status: Public on Oct 30 2008

first: Wee

middle: Joo

last: Chng

address: 5 Lower Kent Ridge Road

department: Haematology-Oncology

institute: National University Cancer Institute, Singapore

description: Gene expression data from fresh frozen biopsy at diagnosis

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Pulmonary MALT

tag: MALT1 Tx

tag: Sex

value: Male


title: Diabetogenic, d4

description: Diabetogenic, d4

source_name: Laser-capture microdissected islets from NOD.Scid injected at d0 with BDC2.5 transgenic, diabetogenic T cells

growth_protocol: mice were sacrificed 4 days after transfer of CD4+ BDC2.5 diabetogenic T cells

tag: pooled from 5 NOD.Scid mice after diabetogenic stimulus


title: L929_replicate_1


title: Diabetogenic, d3

description: Diabetogenic, d3

hyb_protocol: standard Affymetrix

scan_protocol: standard Affymetrix

growth_protocol: mice were sacrificed 3 days after transfer of CD4+ BDC2.5 diabetogenic T cells

tag: pooled from 5 NOD.Scid mice induced to develop diabetes by transfer of diabetogenic T cells


title: Foxa2-mutant-2-E7.5  (MOE 430 2.0)

description: E7.5 POOLED EMBRYOS: n=48; Stages between mid-streak and headfold according to Downs & Davies


title: Wild type 2 E7.5  (MOE 430 2.0)

description: E7.5 POOLED EMBRYOS: n=50; Stages between mid-streak and headfold according to Downs & Davies


title: NZW/LacJ Liver No treatment 10w

city: Jupiter

first: Mathew

middle: T

last: Pletcher

state: FL

address: 5353 Parkside Dr

institute: Scripps Florida

hyb_protocol: 20 μg biotin-labeled cRNA was fragmented and hybridized to Affymetrix Mouse 430 2.0 microarray overnight in the Affy 640 hybridization oven with a speed of 60 rpm for 16 hr. Microarrays were washed and stained using the Affymetrix Fluidics Station FS400.

scan_protocol: GeneChip arrays were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: The probe set intensities were quantified using the GeneChip Operating Software (GCOS) and analyzed with GCRMA normalization using Array Assist Software (Stratagene, Cedar Creek, TX). All hybridized chips met standard quality control criteria, and mean fluorescence values of each array were scaled to a mean intensity of 500.

source_name: NZW/LacJ Liver

label_protocol: Double-stranded cDNA was prepared from 1 μg of total RNA using the Affymetrix cDNA synthesis kit and then in vitro transcribed using an IVT labeling kit (Affymetrix),  with the cRNA product purified using a GeneChip Sample Cleanup Module (Affymetrix).

extract_protocol: Trizol, Qiagen RNeasy. Liver tissue was lysed using the Qiagen TissueLyser (Qiagen). Total RNA was isolated from each homogenate using the standard Trizol protocol and then further purified with the RNeasy kit (Qiagen). Samples were quantified using the NanoDrop ND-1000.

tag: Male NZW/LacJ 10 week old liver


title: Diabetogenic, d8

description: Diabetogenic, d8

growth_protocol: mice were sacrificed 8 days after transfer of CD4+ BDC2.5 diabetogenic T cells


title: Wild type 1 E7.5 (MOE 430 2.0)


title: FVB/NJ Liver No treatment 10w

source_name: FVB/NJ Liver

tag: Male FVB/NJ 10 week old liver


title: Protected, d4

description: Protected, d4

growth_protocol: mice were sacrificed 4 days after transfer of CD4+ BDC2.5 diabetogenic T cells and following two injections of anti-Ifng antibody (at day -1 and day 2 relative to T cell transfer)


title: Protected, d3

description: Protected, d3

growth_protocol: mice were sacrificed 3 days after transfer of CD4+ BDC2.5 diabetogenic T cells and following two injections of anti-Ifng antibody (at day -1 and day 2 relative to T cell transfer)


title: RIIIS/J Liver No treatment 10w

source_name: RIIIS/J Liver

tag: Male RIIIS/J 10 week old liver


title: C57BL/6J Liver No treatment 10w

source_name: C57BL/6J Liver

tag: Male C57Bl/6J 10 week old liver


title: BALB/CByJ Liver No treatment 10w

source_name: BALB/CByJ Liver

tag: Male BALB/CByJ 10 week old liver


title: MALT_033


title: Naïve Treg_biological_rep2

city: St. Louis


title: Untreated NOD.Scid (d0)

description: Untreated NOD.Scid (d0)

source_name: Laser-capture microdissected islets from untreated NOD.Scid mice

growth_protocol: These mice were untreated.

treatment_protocol: Captured RNA was extracted using Agilent PicoPure columns, pooled and ~30 ng was amplified using one round of Arcturus RiboAmp HS kit amplification followed by the RNA Amplification and Labeling Kit from Enzo Life Science

tag: Pooled from 5 untreated, adult NOD.Scid mice


title: MALT_026


title: MALT_031

value: female


title: MALT_032


title: MALT_025


title: MALT_030


title: MALT_023


title: MALT_034


title: MALT_022


title: MALT_029


title: MALT_016


title: MALT_019


title: MALT_018


title: MALT_021


title: MALT_014


title: MALT_020


title: MALT_015


title: MALT_028


title: MALT_024


title: MALT_027


title: MALT_006


title: MALT_017


title: MALT_007


title: MALT_013


title: MALT_008


title: MALT_012


title: MALT_011


title: MALT_010


title: MALT_005


title: MALT_004


title: MALT_003


title: MALT_002


title: MALT_009


title: MALT_001


title: Direct draw, Tempus tube, replicate Y (Blood_direct_ABI_Y)

city: Baltimore

first: Zhong

last: Gao

address: Ross 844 720 Rutland Avenue

institute: Johns Hopkins University

description: direct draw, Tempus tube, replicate Y

hyb_protocol: Hybridization on Affymetrix HG-U133 2.0 plus array according to manufacturer's instructions.

data_processing: The data normalizaion was performed using Bioconductor package THREESTEP(background.method="MASIM", noemalize.method="scaling", summary.method="tukey.biweight").

source_name: Peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol. cRNA target amplificationwas performed using the Affymetrix In-vitro Transcription (IVT) Kit followed by a Globin Reduction step.

extract_protocol: RNA was extracted at the ITN Central Nucleic Acid Isolation Core facility, Pittsburgh, PA according to the ITN modified method for Tempus. Whole blood samples collected into Tempus vacuette were extracted using ABI Prism 6100 Nucleic Acid PrepStation and using Tempus extraction reagents. The PAXgene whole blood sample were processed using the PAXgene Blood RNA Kit based on the Qiagen method for column purification of nucleic acid.

treatment_protocol: Whole blood from 5 healthy individuals was drawn directly in PAXgene or Tempus tubes. The same 5 healthy control samples were also drawn in Li Heparin tubes with no PHA stimulation


title: Direct draw, Tempus tube, replicate U (Blood_direct_ABI_U)

description: direct draw, Tempus tube, replicate U


title: Heparin, Tempus tube, replicate Y (Blood_Heparin_ABI_Y)

description: Heparin, Tempus tube, replicate Y


title: Heparin, Tempus tube, replicate U (Blood_Heparin_ABI_U)

description: Heparin, Tempus tube, replicate U


title: Direct draw, PAXgene tube, replicate Y (Blood_direct_PAX_Y)

description: direct draw, PAXgene tube, replicate Y


title: Heparin, PAXgene tube, replicate U (Blood_Heparin_PAX_U)

description: Heparin, PAXgene tube, replicate U


title: Direct draw, PAXgene tube, replicate U (Blood_direct_PAX_U)

description: direct draw, PAXgene tube, replicate U


title: Direct draw, Tempus tube, replicate T (Blood_direct_ABI_T)

description: direct draw, Tempus tube, replicate T


title: Heparin, PAXgene tube, replicate T (Blood_Heparin_PAX_T)

description: Heparin, PAXgene tube, replicate T


title: Heparin, Tempus tube, replicate S (Blood_Heparin_ABI_S)

description: Heparin, Tempus tube, replicate S


title: Heparin, Tempus tube, replicate T (Blood_Heparin_ABI_T)

description: Heparin, Tempus tube, replicate T


title: Direct draw, Tempus tube, replicate S (Blood_direct_ABI_S)

description: direct draw, Tempus tube, replicate S


title: Heparin, Tempus tube, replicate R (Blood_Heparin_ABI_R)

description: Heparin, Tempus tube, replicate R


title: Direct draw, PAXgene tube, replicate T (Blood_direct_PAX_T)

description: direct draw, PAXgene tube, replicate T


title: Heparin, PAXgene tube, replicate R (Blood_Heparin_PAX_R)

description: Heparin, PAXgene tube, replicate R


title: Direct draw, Tempus tube, replicate R (Blood_direct_ABI_R)

description: direct draw, Tempus tube, replicate R


title: PHA stimulated, PAXgene, replicate Y (Blood_PHA25_PAX_Y)

description: PHA stimulated, PAXgene RNA extraction method, replicate Y

treatment_protocol: Whole blood from 7 healthy individuals was collected using Li Heparin tubes, and was incubated for 3 hours at room temperature with or without addition of 25 ug/mL of PHA. After incubation, samples were subsequently transferred to either Tempus or PAXgene tubes.


title: PHA stimulated, Tempus, replicate Y (Blood_PHA25_ABI_Y)

description: PHA stimulated, Tempus RNA extraction method, replicate Y


title: Direct draw, PAXgene tube, replicate R (Blood_direct_PAX_R)

description: direct draw, PAXgene tube, replicate R


title: Heparin, PAXgene tube, replicate S (Blood_Heparin_PAX_S)

description: Heparin, PAXgene tube, replicate S


title: Direct draw, PAXgene tube, replicate S (Blood_direct_PAX_S)

description: direct draw, PAXgene tube, replicate S


title: PHA unstimulated, PAXgene, replicate Y (Blood_PHA0_PAX_Y)

description: PHA unstimulated, PAXgene RNA extraction method, replicate Y


title: PHA stimulated, PAXgene, replicate U (Blood_PHA25_PAX_U)

description: PHA stimulated, PAXgene RNA extraction method, replicate U


title: Heparin, PAXgene tube, replicate Y (Blood_Heparin_PAX_Y)

description: Heparin, PAXgene tube, replicate Y


title: PHA unstimulated, Tempus, replicate Y (Blood_PHA0_ABI_Y)

description: PHA unstimulated, Tempus RNA extraction method, replicate Y


title: PHA unstimulated, PAXgene, replicate U (Blood_PHA0_PAX_U)

description: PHA unstimulated, PAXgene RNA extraction method, replicate U


title: PHA stimulated, PAXgene, replicate S (Blood_PHA25_PAX_S)

description: PHA stimulated, PAXgene RNA extraction method, replicate S


title: PHA unstimulated, Tempus, replicate T (Blood_PHA0_ABI_T)

description: PHA unstimulated, Tempus RNA extraction method, replicate T


title: PHA stimulated, PAXgene, replicate T (Blood_PHA25_PAX_T)

description: PHA stimulated, PAXgene RNA extraction method, replicate T


title: PHA stimulated, Tempus, replicate S (Blood_PHA25_ABI_S)

description: PHA stimulated, Tempus RNA extraction method, replicate S


title: PHA unstimulated, Tempus, replicate U (Blood_PHA0_ABI_U)

description: PHA unstimulated, Tempus RNA extraction method, replicate U


title: PHA stimulated, Tempus, replicate T (Blood_PHA25_ABI_T)

description: PHA stimulated, Tempus RNA extraction method, replicate T


title: PHA unstimulated, PAXgene, replicate T (Blood_PHA0_PAX_T)

description: PHA unstimulated, PAXgene RNA extraction method, replicate T


title: PHA unstimulated, PAXgene, replicate S (Blood_PHA0_PAX_S)

description: PHA unstimulated, PAXgene RNA extraction method, replicate S


title: PHA stimulated, PAXgene, replicate R (Blood_PHA25_PAX_R)

description: PHA stimulated, PAXgene RNA extraction method, replicate R


title: PHA stimulated, PAXgene, replicate C (Blood_PHA25_PAX_C)

description: PHA stimulated, PAXgene RNA extraction method, replicate C


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep1

first: Kenneth

middle: David

last: Birnbaum

address: 12 Waverly Place

department: Biology

institute: New York University

description: Roots grown horizontally on square plates

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on an Affymetrix ATH1 GeneChip Arabidopsis Whole Genome Array in the Affymetrix Hybridization oven 640 following standard Affymetrix protocol. GeneChips were washed and stained using the 'EukGE-WS2v4_450' protocol in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner according to standard Affymetrix protocols.

data_processing: The data was normlized using MAS5 with a target intensity of 250

source_name: Stump of Root Cut at 70 mm Harvested 192 hours after the First Cut

label_protocol: Biotinylated cRNA from all isolated samples was prepared according to the standard two-cycle Affymetrix protocol from 50 ng total RNA

growth_protocol: Plants were grown for 4 days in long day (16hr light/8hr dark) 22 oC conditions in a Percival (Percival Scientific).  Plants were grown on agar in 1x MS  All plant lines are in the Col-0 background.

extract_protocol: Sets of 5 tissue samples were collected each in 2.5 ul of extraction buffer (XB) of the Pico Pure RNA Isolation Kit (Araturus), flash-frozen in liquid nitrogen and ground. At least 25 samples were pooled for each experimental replicate (4 replicates)

treatment_protocol: Seedlings at 4 dpg were transferred to a plate of 5% agar solid medium (1X MS salts, 0.5% sucrose) to ensure a hard support and the root tip was surgically excised under a dissecting microscope using a 30G sterile dental needle (ExelInt), with a cutting error of about 5 um. The plant was immediately returned to a standard 0.8% agar solid medium (1X MS salts, 0.5% sucrose) for recovery. For microarray analysis, 130 um of uncut tip or 70 um of regenerating stumps were manually excised with the 30G needle

tag: Genotype

tag: Root Meristematic Region


title: PHA stimulated, PAXgene, replicate J (Blood_PHA25_PAX_J)

description: PHA stimulated, PAXgene RNA extraction method, replicate J


title: Section of Root from 270 mm to 340 mm harvested immediately rep2

tag: Root Early Differention Region


title: Section of Root from 270 mm to 340 mm harvested immediately rep3


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep2


title: Liver_development_NL_rep2

city: Beijing

first: Tingting

last: Li

address: Hai Dian

department: Automatioon

country: China

institute: Tsinghua University

description: gene expression data from normal adult liver, 18 weeks after birth

hyb_protocol: The pooled RNA sample were labelled and hybridized to Mouse430 2.0 high-density oligonucleotide arrays (Affymetrix). One ug of total RNA was annealed to oligo(dT) and transcribed using SurperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), Labeling, hybridization, washing and signal scan on the microarrays were performed according to the manufacturer's instructions.

scan_protocol: Primary image analysis of the arrays was performed using GENECHIP 3.2 (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed and normalized with RMA software using default settings.

growth_protocol: Mouse embryos at various stages of gestation were obtained by mating random-bred C57/B6 animals. Noon of the following day of vaginal plug appearance was considered to be embryonic day 0.5. The C57/B6 mouse strains were bred and maintained to obtain embryos at National Institute of Biological Sciences (NIBS) at Beijing. All animal experiments in this study were approved by the Institutional Animal Care and Use Committee (IACUC) of NIBS.

extract_protocol: Total RNA was extracted using TRIZol reagent according to the manufacturer's instruction from Invitrogen.

treatment_protocol: Fetal liver tissue from C57/B6 mice of E11.5 (n=12), E12.5 (n=9), E13.5 (n=9), E14.5 (n=6), E15.5 (n=6), E16.5 (n=3), E17.5 (n=3), E18.5 (n=3),  the birth day (n=3), 3 days (n=3), 7 days (n=3), 14 days (n=3) and 21 days (n=3) after birth, as well as liver from mature mice, 18 weeks after birth  (n=3), were prepared under the binocular microscope and pooled.


title: PHA unstimulated, PAXgene, replicate C (Blood_PHA0_PAX_C)

description: PHA unstimulated, PAXgene RNA extraction method, replicate C


title: PHA stimulated, Tempus, replicate R (Blood_PHA25_ABI_R)

description: PHA stimulated, Tempus RNA extraction method, replicate R


title: PHA unstimulated, Tempus, replicate S (Blood_PHA0_ABI_S)

description: PHA unstimulated, Tempus RNA extraction method, replicate S


title: Liver_development_Day3_rep2

description: gene expression data from young liver, 3 days after birth

source_name: young liver, 3 days after birth

label_protocol: One ug of total RNA was annealed to oligo(dT) and transcribed using SurperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), Labeling, hybridization, washing and signal scan on the microarrays were performed according to the manufacturer's instructions.


title: Liver_development_Day0_rep1

description: gene expression data from young liver, the day of birth

source_name: young liver, the day of birth


title: Liver_development_Day21_rep2

description: gene expression data from young liver, 21 days after birth

source_name: young liver, 21 days after birth


title: PHA unstimulated, PAXgene, replicate R (Blood_PHA0_PAX_R)

description: PHA unstimulated, PAXgene RNA extraction method, replicate R


title: Liver_development_Day21_rep1


title: PHA unstimulated, PAXgene, replicate J (Blood_PHA0_PAX_J)

description: PHA unstimulated, PAXgene RNA extraction method, replicate J


title: Liver_development_Day7_rep1

description: gene expression data from young liver, 7 days after birth

source_name: young liver, 7 days after birth


title: PHA unstimulated, Tempus, replicate R (Blood_PHA0_ABI_R)

description: PHA unstimulated, Tempus RNA extraction method, replicate R


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep3

city: New York


title: PHA stimulated, Tempus, replicate J (Blood_PHA25_ABI_J)

description: PHA stimulated, Tempus RNA extraction method, replicate J


title: PHA unstimulated, Tempus, replicate J (Blood_PHA0_ABI_J)

description: PHA unstimulated, Tempus RNA extraction method, replicate J


title: Liver_development_Day0_rep2


title: Liver_development_NL_rep1

source_name: normal adult liver, 18 weeks after birth


title: PHA stimulated, Tempus, replicate C (Blood_PHA25_ABI_C)

description: PHA stimulated, Tempus RNA extraction method, replicate C


title: PHA unstimulated, Tempus, replicate C (Blood_PHA0_ABI_C)

description: PHA unstimulated, Tempus RNA extraction method, replicate C


title: Liver_development_Day14_rep1

description: gene expression data from young liver, 14 days after birth

source_name: young liver, 14 days after birth


title: Section of Root from 270 mm to 340 mm harvested immediately rep1

description: Roots grown horizontally on square plates


title: Liver_development_Day3_rep1


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep5

source_name: Stump of Root Cut at 70 mm Harvested 22 hrs after the First Cut


title: Arabidopsis Root from tip to 130 mm proximal to tip (cut 8dpg) rep1

source_name: Root tip of 8 dpg seedling harvested immediated

tag: Root promeristem and cap


title: Liver_development_E15.5_rep2

description: gene expression data from fetal liver, embryonic day 15.5

source_name: fetal liver, embryonic day 15.5


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep1


title: Liver_development_E16.5_rep2

description: gene expression data from fetal liver, embryonic day 16.5

source_name: fetal liver, embryonic day 16.5


title: Liver_development_E15.5_rep1


title: Liver_development_E13.5_rep2

description: gene expression data from fetal liver, embryonic day 13.5

source_name: fetal liver, embryonic day 13.5


title: Liver_development_E16.5_rep1


title: Liver_development_E17.5_rep2

description: gene expression data from fetal liver, embryonic day 17.5

source_name: fetal liver, embryonic day 17.5


title: Arabidopsis Root from tip to 130 mm proximal to tip (cut 8dpg) rep2


title: Arabidopsis Root from tip to 130 mm proximal to tip (cut 8dpg) rep3


title: Liver_development_E17.5_rep1


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep3


title: Liver_development_E18.5_rep1

description: gene expression data from fetal liver, embryonic day 18.5

source_name: fetal liver, embryonic day 18.5


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep4


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep2


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep4

source_name: Stump of Root Cut at 70 mm Harvested 13 hrs after the First Cut


title: patient_1_b

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

institute: Duke University Medical Center

description: In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1.  For patient #1, we had 3 lesions from the extremity region harboring the  melanoma disease.

hyb_protocol: labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols

scan_protocol: Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000

data_processing: Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method.  RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities.  Normalization was done using quantile normalization.  Expression values were then transformed by taking Logarithm base 2

source_name: melanoma

label_protocol: one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA

extract_protocol: Tissue was homogenized and RNA isolated using Qiagen Rneasy kit.  A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue.  Each RNA isolation included treatment with Dnase to minimize genomic DNA.

treatment_protocol: Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch.  The samples were snap frozen and stored at -133°C until ready for further analysis.  All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.

tag: punch biopsy

tag: in-transit disease


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep3


title: Liver_development_E14.5_rep2

description: gene expression data from fetal liver, embryonic day 14.5

source_name: fetal liver, embryonic day 14.5


title: ADH-1 ip LPAM ILI 4hrs post ILI sample A

description: gene expression data from melanoma xenografts following ILI with melphalan

hyb_protocol: Cleaned and fragmented cRNA was hybridized to the Affymetrix Human U133 plus 2 genechip for 16 hrs at 45C followed by washing and staining according to Affymetrix instructions

scan_protocol: Hybridized probe arrays were stained according to Affymetrix protocols (streptavidin phycoerythrin conjugate) and scanned with the GeneChip Scanner

data_processing: The amount of light emitted is directly proportional to the amount of target bound to each location on the probe array.  Expression values were generated by calculating the difference between the perfect match signal and the mismatch signal for each probe using the Affymetrix GeneChip Operating System.

source_name: human-derived melanoma cells grown in rat as xenograft

label_protocol: cDNA was synthesized from the total RNA and, using an Affymetrix recommended IVT protocol, biotin-labeled cRNA was generated from the cDNA.  Prior to hybridization the cRNA was fragmented.

growth_protocol: Cells used to generate xenograft in rat were grown in Iscove MEM with 10%FBS, 1% Pen/Strep and 2mM L-glutamine added;  37C, 5% CO2; Cells were prepared in PBS plus matrigel at a ratio of 2:1 and 4 million cells were injected per rat.

extract_protocol: RNA was isolated using Qiagen Rneasy plus kit.  RNA quality was assessed using Agilent bioanalyzer prior to labeling and hybridization.

treatment_protocol: When tumors had reached ~1cm diameter treatment started.  Animals were given either ADH-1 (100mg/kg) or saline via ip injection 1 hour prior to start of Isolated Limb Infusion (ILI) with either melphalan (LPAM) or saline.  4 hour time point samples were harvested 4 hours after the completion of ILI.  All other animals were given a second dose of ADH-1 (100mg/kg) 24hrs after the first.  24 hour time point tissue was harvested 1 hour later.  Remaining animals were given 2 more doses of ADH-1 (100mg/kg) over next 24hrs and tumor was harvested 1hr following final dose.  Rats were anesthetized for tumor harvest and were humanely euthanized at the end of the study following an IACUC approved protocol.  Harvested tumor was frozen immediately in liquid nitrogen and stored at -80C until ready for processing.

tag: human melanoma-derived cell lines injected into hind limb of Crl:NIH Rnu Nude Rat


title: ADH-1 ip LPAM ILI 24hrs post ILI sample B


title: Liver_development_E14.5_rep1


title: ADH-1 ip LPAM ILI 4hrs post ILI sample B


title: patient_1_c


title: Saline ip LPAM ILI 4hrs post ILI


title: ADH-1 ip LPAM ILI 24hrs post ILI sample A


title: patient_1_a


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep2


title: ADH-1 ip saline ILI 24hrs post ILI sample B

description: gene expression data from melanoma xenografts following ILI with saline


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 5 hrs Taking 70 mm of Stump (4dpg) rep3

source_name: Stump of Root Cut at 70 mm Harvested 5 hrs after the First Cut


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 5 hrs Taking 70 mm of Stump (4dpg) rep4


title: Liver_development_E13.5_rep1


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep1


title: ADH-1 ip saline ILI 24hrs post ILI sample A


title: Liver_development_E11.5_rep2

description: gene expression data from fetal liver, embryonic day 11.5

source_name: fetal liver, embryonic day 11.5


title: Saline ip saline ILI 24hrs post ILI sample A


title: Liver_development_E12.5_rep2

description: gene expression data from fetal liver, embryonic day 12.5

source_name: fetal liver, embryonic day 12.5


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (4dpg) rep3

source_name: Stump of Root Cut at 70 mm Harvested Immediately After First Cut


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 5 hrs Taking 70 mm of Stump (4dpg) rep1


title: Saline ip saline ILI 48hrs post ILI


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (4dpg) rep2


title: Liver_development_E11.5_rep1


title: Saline ip LPAM ILI 24hrs post ILI sample B


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (4dpg) rep4


title: Saline ip LPAM ILI 48hrs post ILI


title: ADH-1 ip LPAM ILI 48hrs post ILI


title: Saline ip saline ILI 4hrs post ILI sample B


title: Liver_development_E12.5_rep1


title: Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep3

source_name: Root tip of 4 dpg seedling harvested immediated


title: Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep4


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 5 hrs Taking 70 mm of Stump (4dpg) rep2


title: Saline ip saline ILI 24hrs post ILI sample B


title: Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep2


title: Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep1


title: ADH-1 ip saline ILI 4hrs post ILI sample A


title: ADH-1 ip saline ILI 4hrs post ILI sample B


title: ADH-1 ip saline ILI 48hrs post ILI


title: Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (4dpg) rep1


title: HaCaT_siSMAD3_0h

status: Public on Oct 29 2008

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

description: Gene expression data from HaCaT cells transfected with SMAD3 siRNA, without stimulation

hyb_protocol: Array hybridization was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

scan_protocol: Array scanning was performed as described previously (Ishii et al, Genomics 68:136-143, 2000)

data_processing: Microarray Suite software 5.0 (Affymetrix) was used to calculate the average difference (AD) for each gene probe set, which was shown as an intensity value of the gene expression (Ishii et al, Genomics 68:136-143, 2000).

source_name: HaCaT cells, Smad3 siRNA transfected, without TGF-beta

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and a T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeled cRNA by using a BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to the manufacturer’s instructions (Ishii et al, Genomics 68:136-143, 2000).

growth_protocol: HaCaT cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM #11965, GIBCO/Invitrogen, CA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml of penicillin G, and 100 microgram/ml of streptomycin. Cells were grown in a humidified atmosphere with 5% CO2 at 37 oC.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen).

treatment_protocol: Cells were stimulated with TGF-beta3 in growth medium for the indicated times.

tag: immortalized keratinocyte cell line


title: HaCaT_siSMAD2_24h

description: Gene expression data from HaCaT cells transfected with SMAD2 siRNA, treated with 1ng/ml TGF-beta for 24 hours

source_name: HaCaT cells, Smad2 siRNA transfected, stimulated with TGF-beta for 24hrs


title: HaCaT_siTFAP2A_24h

description: Gene expression data from HaCaT cells transfected with TFAP2A siRNA, treated with TGF-beta for 24 hours

source_name: HaCaT cells, TFAP2A siRNA transfected, stimulated with TGF-beta3 for 24 hours

treatment_protocol: Cells were stimulated with 3ng/ml (120pM) of TGF-beta3 in growth medium for the indicated times.

tag: immmortalized keratinocyte cell line


title: HaCaT_siTFAP2A_0h

description: Gene expression data from HaCaT cells transfected with TFAP2A siRNA, without TGF-beta stimulation

source_name: HaCaT cells, TFAP2A siRNA transfected, without TGF-beta3 stimulation


title: HaCaT_siSMAD2_0h

description: Gene expression data from HaCaT cells transfected with SMAD2 siRNA, without stimulation

source_name: HaCaT cells, Smad2 siRNA transfected, without TGF-beta


title: HaCaT_siCont_0h

description: Gene expression data from HaCaT cells transfected with control siRNA, without TGF-beta stimulation

source_name: HaCaT cells, control siRNA transfected, without TGF-beta3 stimulation


title: HaCaT_siSMAD3_1.5h

description: Gene expression data from HaCaT cells transfected with SMAD3 siRNA, treated with 1ng/ml TGF-beta for 1.5 hours

source_name: HaCaT cells, Smad3 siRNA transfected, stimulated with TGF-beta for 1.5hrs


title: HaCaT_siETS1_1.5h

description: Gene expression data from HaCaT cells transfected with ETS1 siRNA, treated with TGF-beta for 1.5 hours

source_name: HaCaT cells, ETS1 siRNA transfected, stimulated with TGF-beta3 for 1.5 hours


title: HaCaT_siCont_24h

description: Gene expression data from HaCaT cells transfected with control siRNA, treated with TGF-beta for 24 hours

source_name: HaCaT cells, control siRNA transfected, stimulated with TGF-beta3 for 24 hours


title: HaCaT_siTFAP2A_1.5h

description: Gene expression data from HaCaT cells transfected with TFAP2A siRNA, treated with TGF-beta for 1.5 hours

source_name: HaCaT cells, TFAP2A siRNA transfected, stimulated with TGF-beta3 for 1.5 hours


title: HaCaT_6h

description: Gene expression data from HaCaT cells treated with TGF-beta for 6 hours

source_name: HaCaT cells stimulated with TGF-beta3 for 6 hours


title: HaCaT_siSMAD3_24h

description: Gene expression data from HaCaT cells transfected with SMAD3 siRNA, treated with 1ng/ml TGF-beta for 24 hours

source_name: HaCaT cells, Smad3 siRNA transfected, stimulated with TGF-beta for 24hrs


title: HaCaT_siSMAD2_1.5h

description: Gene expression data from HaCaT cells transfected with SMAD2 siRNA, treated with 1ng/ml TGF-beta for 1.5 hours

source_name: HaCaT cells, Smad2 siRNA transfected, stimulated with TGF-beta for 1.5hrs


title: HaCaT_siETS1_24h

description: Gene expression data from HaCaT cells transfected with ETS1 siRNA, treated with TGF-beta for 24 hours

source_name: HaCaT cells, ETS1 siRNA transfected, stimulated with TGF-beta3 for 24 hours


title: HaCaT_0h

description: Gene expression data from HaCaT cells without TGF-beta stimulation

source_name: HaCaT cells without TGF-beta3 stimulation


title: HaCaT_siCont_1.5h

description: Gene expression data from HaCaT cells transfected with control siRNA, treated with TGF-beta for 1.5 hours

source_name: HaCaT cells, control siRNA transfected, stimulated with TGF-beta3 for 1.5 hours