title: freshly prepared FDCs from CFA+Pam immunized pLN

description:
from Balb/cAnNCrlCrlj wild type mice
WT CFA+Pam immunized pLN FDC

value: adult

value: lymph nodes

value: FDC purified from CFA+Pam immunized pLNs


title: in vitro pLN FDC LPS72h

status: Public on Jul 05 2010

type: RNA

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN

description: pLN FDC cultured with LPS for 72h

hyb_protocol: The labeled cRNA was hybridized with Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The image was quantified by using GCOS software.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse in vitro cultured FDC stimulated with LPS for 72h

label_protocol: RNA was subjected to biotinilated cRNA synthesis by using Target Labeling lit (Affymetrix).

growth_protocol: Balb/cAnNCrlCrlj wild type mice were maintained in specific pathogen-free conditions (SPF) at the animal facility of the Research Center for Allergy and Immunology. To culture FDCs, purified FDCs were cultured in D-MEM with 10% fetal calf serum (FCS), 0.02M HEPES, 0.2mM non-essential amino acids (NEAA), TNFα (5ng/ml) and anti-LTβR (1μg/ml).

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen).

treatment_protocol: To stimulate FDCs in vitro, the cells were were cultured without of with the following stimuli: Pam2CSK4 (100ng/ml), LPS (20µg/ml), all-trans-retinoic acid (RA, 40nM).

tag: strain

value: from Balb/cAnNCrlCrlj wild type mice, without immunization

tag: tissue

value: Adult mouse lymph nodes


title: in vitro pLN FDC Pam96h-2

department: Research Center for Allergy and Immunology

description: pLN FDC cultured with Pam2CSK4 for 96h

source_name: mouse in vitro cultured FDC stimulated with Pam2CK4 for 96h


title: LPS/obovatol treated BV-2 cells

city: Daegu

first: Kyoungho

last: Suk

address: 101 Dong-In, Joong-gu

department: Department of Pharmacology

country: South Korea

institute: Kyungpook National University School of Medicine

description: obovatol/LPS-treated sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Images were quantified using software program Illumina beadscan 3.2 (Illumina Inc., San Diego, CA) and BeadStudio v3.0 (Illumina Inc.).

source_name: mouse brain microglia

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The immortalized BV-2 murine microglia cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 5% heat-inactivated FBS, 50 μg/ml gentamicin at 37°C.

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: BV-2 cells were treated with LPS in the absence or presence of obovatol for 6 hr.


title: in vitro pLN FDC RA96h-2

description: pLN FDC cultured with RA for 96h

source_name: mouse in vitro cultured FDC stimulated with RA for 96h


title: in vitro pLN FDC RA+Pam96h-2

description: pLN FDC cultured with RA+Pam2CSK4 for 96h

source_name: mouse in vitro cultured FDC stimulated with RA+Pam2CSK4 for 96h


title: MSC-biological replicate #1

status: Public on Jul 03 2010

city: Verona

first: Mirco

last: Galiè

address: via Le Grazie, 8

department: Neuroscience, Biomedicine and Movement Sciences

country: Italy

institute: University of Verona

description: mesenchymal phenotype

hyb_protocol: 6 micrograms of biotin-labeled cDNA was hybridized overnight at 60°C on 96 oligonucleotide probes (excluded black, positive and negative controls) for cancer signal transduction related genes spotten on a nylon membrane.

scan_protocol: the hybridization results were revealed using Enhanced Chemoluminscence on a X-Ray film and then scannerized at 300dpi as .tiff image

data_processing: Data from arrays was analyzed using GEArray Expression Analysis Suite (Superarray Bioscience Corporation /Frederick, MD). Quantitative values of expression were corrected to the background, normalized with respect to the positive control genes included in the arrays, and reported as ratios to the mean values of normalization genes.

source_name: inguinal fat pad

label_protocol: cDNA was retrotranscribed from 1 microgram of total RNA template in presence of biotin-dUTP.

growth_protocol: HER-2 mammary tumors developed spontaneously in the mammary gland of female FVB/NeuT.233 mice, transgenic for the constitutively activated rat isoform of HER-2/neu (neu T) under MMTV promoter. BB1, A17, sB7 were established in culture from HER-2/neu spontaneous tumors. MSCs were isolated from inguinal adipose tissue of FVB mice. all cell lineages were cultured in DMEM mediun supplemented with 20% of foetal bovine serum.

extract_protocol: total RNA was extracted from cell cultures and tumor samples using QIAGEN mini-spin column and closely following manifacturers' instructions

treatment_protocol: tumors were excised when they reached 7-8 cm of major diameter, homogenized and undergon RNA extraction. A17, BB1, sB7 were cultured at confluence before RNA extraction. MSC were cultured at confuluence for less than 10 passages before RNA extraction.

tag: sample type

value: mesenchymal stem cells

tag: tumor type

value: non-tumor cell lineage

tag: phenotype

value: mesenchymal


title: MSC-biological replicate#3

description: mesenchymal phenotype


title: in vitro pLN FDC LPS5h

description: pLN FDC cultured with LPS for 5h

source_name: mouse in vitro cultured FDC stimulated with LPS for 5h


title: A17 tumor

description: mesenchymal phenotype

source_name: tumors arisen from subcoutaneous injection of BB1 cells


title: in vitro pLN FDC NS-2

description: pLN FDC cultured without stimulation

source_name: mouse in vitro cultured FDC, without stimulation


title: BB1 tumor

description: epithelial phenotype

source_name: tumors arisen from subcoutaneous injection of A17 cells

value: epithelial


title: BB1 cell- technical replicate #2

description: epithelial phenotype

source_name: cell lineage from mouse HER-2 transgenic mammary tumor

value: tumor cell lineage


title: untreated BV-2

description: untreated

treatment_protocol: BV-2 cells not treated.


title: in vitro pLN FDC RA96h-1

description: pLN FDC cultured with RA for 96h


title: LPS treated BV-2 cells

description: LPS-treated sample


title: in vitro pLN FDC Pam96h-1

description: pLN FDC cultured with Pam2CSK4 for 72h


title: sB7 cell

description: epithelial phenotype

value: cell lineage from mouse HER-2 transgenic mammary tumor


title: A17 cell-technical replicate #2

description: mesenchymla phenotype

value: mesenchymla


title: MSC-biological replicate #2

description: mesenchymal phenotype


title: BB1 cell-technical replicate #1

description: epithelial phenotype


title: A17 cell- technical replicate #1

description: mesenchymal phenotype


title: PAKH2O_3

city: Dallas

first: Andrew

last: Koh

state: TX

address: 5323 Harry Hines Boulevard

department: Pediatrics

country: USA

institute: University of Texas Southwestern Medical Center

description: Gene expression data from P. aeruginosa suspended in sterile water fed to adult C3H/HeN mice

hyb_protocol: 4-7 ug of fragmented cDNA were hybridized for 15 hours at 50C on a GeneChip P. aeruginosa Genome Array.  Genome arrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: P. aeruginosa Genome Arrays were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Intrachip normalizations were performed with Affymetrix Microarray Suite 5.0 software.  Statistical analysis and experimental comparisons were made with GeneSpring version 4.2.1 (Agilent Technologies).

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PAK from sterile water fed to mice

label_protocol: 12 ug of purified total RNA from cecal flushates or drinking water was converted to cDNA with Superscript II Reverse Transcriptase (Invitrogen) and a semi-random decamer, (NS)5 (Invitrogen).  cDNA was partially digested with Dnase I and end labeled with ddUTP-biotin (Enzo Life Sciences)

growth_protocol: Sterile water with 1500 units penicillin G/mL and P. aeruginosa strain PAK (107 cfu/mL) was stored in a sterile flask at RT for 24 hours.

extract_protocol: Hot acid phenol/chloroform (Ambion)  extraction protocol was utilized, followed by RQ1 Dnase (Promega) treatment and RNeasy cleanup protocol (Qiagen)

treatment_protocol: 6-8 wk old C3H/HeN mice were given antibiotic water (streptomycin, penicillin G for 4 days), then given P. aeruginosa strain PAK in sterile water with pencillin for 5 days.  Animals were euthanized and cecal contents (flushates) were recovered and immediately immersed in liquid nitrogen.

value: PAK

value: Drinking water


title: PAKH2O_1


title: PAKGIColoniz_3

description: Gene expression data from P. aeruginosa colonizing the gastrointestinal tracts of adult C3H/HeN

source_name: P. aeruginosa PAK from murine cecums (8 mice)

value: Murine cecal flushates


title: Protoperithecia (Cy5) vs Mycelia (Cy3) replicate 1 [MTP]

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers (53°C water bath). After hybridization, slides were washed sequentially.

scan_protocol: Hybridized microarrays were scanned and gridded with a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA)

data_processing: Normalized by background-subtracted mean-by-mean normalization of well measured spots, and statistically analyzed using a Bayesian analysis of gene expression levels with BAGEL software.

organism: Neurospora crassa

source_name: Reproductive structure

label_protocol: 2 µg of mRNA were primed with 0.5 µl of 100 µM MTP or Oligo-d(T) primer at 70°C for 10min, then reversed transcribed at 42°C for 2h in the presence of 400 U SuperScript II RTase (Invitrogen), and 0.8ul Amino-allyl dUTP/dNTP made from Sigma in mg aliquotes and dissolved in 20µl H2O-(DEPC) and mixed with 30µl of 100mM dATP, dTTP, dGTP, dCTP and 12µl 100mM dTTP;  25 µM Cy3/Cy5-label

growth_protocol: SCM media

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Constant light

tag: developmental stage

value: Protoperithecia

value: mat A FGSC#2489

tag: primer type

value: MTP

value: Mycelia


title: Protoperithecia (Cy5) vs Mycelia (Cy3) replicate 2 [MTP]


title: in vitro pLN FDC RA+Pam96h-1


title: FlowerPedicel_AC_rep2

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

institute: National Food Research Institute

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Buffer Kit (Agilent) were used according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned using an Agilent Technology Microarray Scanner at a resolution of 5 micro-meter.

data_processing: Raw data were subjected to per chip normalization to 75th percentile using Genespring ver.10.0 software (Agilent).

organism: Solanum lycopersicum

source_name: Ailasa craig, replicate 2

label_protocol: Labeled-cRNA was synthesized from 0.5 µg of total RNA using a Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instructions.

growth_protocol: Tomato plants were grown in a growth-room at 25 °C with a 16 h light and at 20 °C with a 8 h dark cycle.

extract_protocol: RNeasy Plant Mini Kit (Qiagen) was used according to the manufacturer’s instructions.

value: flower pedicel

tag: genotype/variation

value: Ailasa craig


title: PAKH2O_2


title: PAKGIColoniz_1


title: in vitro pLN FDC NS-1

description: pLN FDC cultured without stimulation

value: from Balb/cAnNCrlCrlj wild type mice, without immunization

value: Adult mouse lymph nodes


title: PAKGIColoniz_2


title: FlowerPedicel_MC-supp_rep2

source_name: MC-suppressed transformant, replicate 2

value: MC-suppressed transformant


title: FlowerPedicel_MC-supp_rep1

source_name: MC-suppressed transformant, replicate 1


title: FlowerPedicel_j_rep2

source_name: jointless mutant, replicate 2

value: jointless mutant


title: Mycelia (Cy5) vs Protoperithecia (Cy3) [MTP]


title: FlowerPedicel_AC_rep1

source_name: Ailasa craig, replicate 1


title: SC31-MSC_B

status: Public on Jul 02 2010

city: SAN DIEGO

first: JOEL GOTTESFELD ; JEANNE LORING ;

last: GULSAH ALTUN

email: joelg@scripps.edu, skusen@home2.scripps.edu, jloring@scripps.edu, gulsah@scripps.edu, gulsahaltun@gmail.com

state: CA

address: 3030 Science Park Rd. 3rd floor, room 3020

department: CHEMICAL PHYSIOLOGY

institute: THE SCRIPPS RESEARCH INSTITUTE

description: Bone marrow-derived mesenchymal stem cells, CD105+, CD34-,  SC31-MSC_B replicate 2

data_processing: The data were normalised using quantile normalisation with Illumina quantile normalization in Genome Studio.

organism: Homo sapiens

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion), quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

tag: cell type


title: FlowerPedicel_j_rep1

source_name: jointless mutant, replicate 1


title: SC41-MSC_B

description: Bone marrow-derived mesenchymal stem cells, CD105+, CD34-, SC41-MSC_B replicate 2


title: UreterPt1

description: Ureter tissue from Patient 1

source_name: Ureter tissue from Patient 1

tag: gender

value: male

value: Ureter tissue from Patient 1


title: SC31-MSC_A

description: Bone marrow-derived mesenchymal stem cells, CD105+, CD34-, SC31-MSC_A replicate 1


title: Pel_B

description: Human embryonic stem cell line differentiated fibroblast Pel_B replicate 2

tag: cell line


title: UreterPt2

description: Ureter tissue from Patient 2

source_name: Ureter tissue from Patient 2

tag: age

value: 47 years

value: female

value: Ureter tissue from Patient 2


title: SC30_B

description: Postmortem-derived primary dermal fibroblasts SC30_B replicate 2


title: SC41-MSC_A

description: Bone marrow-derived mesenchymal stem cells, CD105+, CD34-, SC41-MSC_A replicate 1


title: SC30_A

description: Postmortem-derived primary dermal fibroblasts SC30_A replicate 1


title: Pel_A

description: Human embryonic stem cell line differentiated fibroblast Pel_A replicate 1


title: NuFF_B

description: Primary cell line (Human foreskin fibroblasts) NuFF_B replicate 2


title: NuFF_A

description: Primary cell line (Human foreskin fibroblasts) NuFF_A replicate 1


title: MR90C2P27

description: Human induced pluripotent stem cell line MR90C2P27


title: MR90C2P28

description: Human induced pluripotent stem cell line MR90C2P28


title: Miz4_B

description: Human embryonic stem cell line Miz4_B replicate 2

value: Human embryonic stem cell line Miz4_B


title: IPSY2-1MSC-Ips1

description: Human induced pluripotent stem cell line IPSY2-1MSC-Ips1


title: Mel1_P51

description: Human embryonic stem cell line Mel1_P51

source_name: Human embryonic stem cell line Mel1_P51

value: Human embryonic stem cell line Mel1_P51


title: IPS-J1-12-BJ1-iPS12

description: Human induced pluripotent stem cell line IPS-J1-12-BJ1-iPS12


title: LungPt1

description: Lung tissue from Patient 1

source_name: Lung tissue from Patient 1

value: Lung tissue from Patient 1


title: LungPt2

description: Lung tissue from Patient 2

source_name: Lung tissue from Patient 2

value: Lung tissue from Patient 2


title: IMR90_B

description: Primary cell line IMR90_B replicate 2

source_name: Primary cell line IMR90_B replicate 2

value: Primary cell line IMR90_B


title: IPS-F-5-hFib2-Ips5

description: Human induced pluripotent stem cell line IPS-F-5-hFib2-Ips5


title: IMR90_A

description: Primary cell line IMR90_A replicate 1

source_name: Primary cell line IMR90_A replicate 1

value: Primary cell line IMR90_A


title: Mel1_P52

description: Human embryonic stem cell line Mel1_P52

source_name: Human embryonic stem cell line Mel1_P52

value: Human embryonic stem cell line Mel1_P52


title: HUVEC-BF5

description: Human Umbilical Vein Endothelial Cell Line HUVEC-BF5


title: HMSC-ad

description: Human Mesenchymal_Stem_Cells_adipose HMSC-ad


title: HMSC-bm

description: Human Mesenchymal_Stem_Cells_bone_marrow HMSC-bm


title: HS27_B

description: Primary cell line (Human foreskin fibroblasts) HS27_B replicate 2


title: HUVEC-BF4

description: Human Umbilical Vein Endothelial Cell Line  HUVEC-BF4


title: HES-2_B

description: Human embryonic stem cell line HES-2_B replicate 2

value: Human embryonic stem cell line HES-2_B


title: Miz4_A

description: Human embryonic stem cell line Miz4_A replicate 1

value: Human embryonic stem cell line Miz4_A


title: HSF6_B

description: Human embryonic stem cell line HSF6_B replicate 2

value: Human embryonic stem cell line HSF6_B


title: HES-2_A

description: Human embryonic stem cell line HES-2_A replicate 1

value: Human embryonic stem cell line HES-2_A


title: HSF6_A

description: Human embryonic stem cell line HSF6_A replicate 1

value: Human embryonic stem cell line HSF6_A


title: HumanKeratinocytes_A

description: Primary cell line human keratinocytes HumanKeratinocytes_A replicate 1


title: HDF_B

description: Human dermal fibroblast line HDF_B replicate 2

value: Human dermal fibroblast line HDF_B


title: HS27_A

description: Primary cell line (Human foreskin fibroblasts) HS27_A replicate 1


title: Spontaneous tumor

description: epithelial phenotype

source_name: HER-2 neu transgenic mammary tumor

value: HER-2 neu transgenic mammary tumor

value: epithelial


title: HDF_A

description: Human dermal fibroblast line HDF_A replicate 1

value: Human dermal fibroblast line HDF_A


title: hFib2-Ips5_B

description: Human induced pluripotent stem cell line hFib2-Ips5_B replicate 2


title: HumanKeratinocytes_B

description: Primary cell line human keratinocytes HumanKeratinocytes_B replicate 2


title: hFib2-Ips5_A

description: Human induced pluripotent stem cell line hFib2-Ips5_A replicate 1


title: H9_A1

description: Human embryonic stem cell line H9 replicate 1

value: Human embryonic stem cell line H9


title: H9_A2

description: Human embryonic stem cell line H9 replicate 2


title: Gottesfeld_4078.1A2_2

description: Human induced pluripotent stem cell line Gottesfeld_4078.1A2_2 replicate 2


title: Gottesfeld_8.2A4R_1

description: Human induced pluripotent stem cell line Gottesfeld_8.2A4R_1 replicate 1


title: ES4CL2_A

description: Human induced pluripotent stem cell line ES4CL2 replicate 1


title: Gottesfeld_8.2A4R_2

description: Human induced pluripotent stem cell line Gottesfeld_8.2A4R_2 replicate 2


title: Gottesfeld_3816.5_2

description: Human induced pluripotent stem cell line Gottesfeld_3816.5_2 replicate 2


title: BladderPt2

description: Bladder tissue from patient 2

source_name: Bladder tissue from patient 2

value: 47 years

value: female

value: Bladder tissue from patient 2


title: BG03_B

description: Human embryonic stem cell line BG03 replicate 2

value: Human embryonic stem cell line BG03


title: AdrenalPt1

description: Adrenal tissue from patient 1

source_name: Adrenal tissue from patient 1

value: male

value: Adrenal tissue from patient 1


title: BladderPt1

description: Bladder tissue from patient 1

source_name: Bladder tissue from patient 1

value: Bladder tissue from patient 1


title: BG01_A

description: Human embryonic stem cell line BG01 replicate 1

value: Human embryonic stem cell line BG01


title: BG01_B

description: Human embryonic stem cell line BG01 replicate 2


title: AdrenalPt2

description: Adrenal tissue from patient 2

source_name: Adrenal tissue from patient 2

value: Adrenal tissue from patient 2


title: Gottesfeld_3816.5_1

description: Human induced pluripotent stem cell line Gottesfeld_3816.5_1 replicate 1


title: BG03_A

description: Human embryonic stem cell line BG03 replicate 1


title: C57Bl/6 x Sv129 P21, ERRβ -/- knockout retina, 1

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N. Broadway, Suite 351

department: Neuroscience

institute: The Johns Hopkins University

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

label: Biotin

source_name: C57Bl/6 x Sv129 P21, ERRβ -/- knockout, 2 pooled retinas

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual).

growth_protocol: Standard chow, 12:12 light:dark cycle.

extract_protocol: RNeasy Kit (QIAGEN).

treatment_protocol: Microdissection into RNAlater (Ambion).

value: C57Bl/6 x Sv129 ERRβ -/- knockout

tag: sex

value: Mixed


title: AdiposePt1

description: Adipose tissue from patient 1

source_name: Adipose tissue from patient 1

value: Adipose tissue from patient 1


title: BG02_B

description: Human embryonic stem cell line BG02 replicate 2

value: Human embryonic stem cell line BG02


title: ES4CL2_B

description: Human induced pluripotent stem cell line ES4CL2 replicate 2


title: C57Bl/6 P21, wildtype retina, 3

source_name: C57Bl/6 P21, wildtype, 2 pooled retinas

value: C57Bl/6 wildtype


title: Gottesfeld_4078.1B3_2

description: Human induced pluripotent stem cell line Gottesfeld_4078.1B3_2 replicate 2


title: BG02_A

description: Human embryonic stem cell line BG02 replicate1


title: HUVEC_Ad-ICAP1_36hrs_rep2

city: Mannheim

first: Andreas

last: Fischer

address: Ludolf-Krehl-Str. 13-17

department: Joint Research Division Vascular Biology

country: Germany

institute: German Cancer Research Center and Medical Faculty Mannheim, Heidelberg University

description: biological replicate 3

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 50 ng cRNA/µl, unsealed in a wet chamber for 20 h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio v. 3. For analysis duplicates were averaged and the expression fold change of Notch1 or ICAP1 expressing cells to the GFP expressing control was calculated

label_protocol: Biotin-labeled cRNA were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Proc. Natl. Acad. Sci. U. S. A. (1992) 89:3010–3014). In brief, 250 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion, Inc., Austin, TX). Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were cultured in gelatine coated 6-well plates with ECGM2 medium including Supplement Mix (PromoCell) and 10% FCS. Cells were grown as a confluent monolayer and transduced with adenovirus with an MOI of 50. 36 h later RNA was harvested.

extract_protocol: RNA was isolated using the Rneasy kit (Qiagen) according to the instructions of the manufacturer. Optional steps of the protocol were skipped and no optional supplements to the buffers were used. The quality of total RNA was checked by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples had RNA index values greater than 8.5. RNA concentrations were determined using the NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE).


title: C57Bl/6 x Sv129 P21, ERRβ -/- knockout retina, 2


title: HUVEC_Ad-ICAP1_36hrs_rep1

description: biological replicate 3

value: Human umbilical vein endothelial cells (HUVEC)


title: C57Bl/6 x Sv129 P21, ERRβ -/- knockout retina, 3


title: Gottesfeld_4078.1A2_1

description: Human induced pluripotent stem cell line Gottesfeld_4078.1A2_1 replicate 1


title: HUVEC_Ad-NOTCH1-ICD_36hrs_rep2

description: biological replicate 2


title: AdiposePt2

description: Adipose tissue from patient 2

source_name: Adipose tissue from patient 2

value: Adipose tissue from patient 2


title: HUVEC_Ad-NOTCH1-ICD_36hrs_rep1

description: biological replicate 2


title: Gottesfeld_4078.1B3_1

description: Human induced pluripotent stem cell line Gottesfeld_4078.1B3_1 replicate 1


title: HUVEC_Ad-GFP_36hrs_rep2

description: biological replicate 1

source_name: GFP


title: HUVEC_Ad-GFP_36hrs_rep1

description: biological replicate 1


title: BRD7 shRNA 1 expressing BJ cells treated with nutlin-3a for 6 hours vs control

status: Public on Jul 01 2010

city: Boston

first: Anna

middle: E

last: Burrows

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Further data analysis material is available upon request.

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions (Agilent Two-Color Gene Expression Array) for 17 hours at 65C.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction.

source_name: Primay middle passage human BJ fibroblasts stably expressing BRD7 shRNA from the MSCV-mir30 based expression vector treated with 8uM nutlin-3a for 6 hours

label_protocol: 1.5ug of total RNA were harvested and primed and labeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with either cyanine 3-CTP (Cy3) or cyanine-5-CTP (Cy5).

growth_protocol: BJ  fibroblasts were grown in DMEM media (invitrogen) with 15% FBS under low oxygen (3%) conditions. Mid-passage BJs (approximately PD 45) were infected with retroviruses expressing either FF2 control shRNA or BRD7 shRNAs from an MSCV-mir30 shRNA expression vector and were selected for 5 days with 1ug/ml puromycin (Clontech).

extract_protocol: Total RNA was harvested using an RNAeasy Mini Kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: Cells were either untreated or treated with 8uM nutlin-3a (Cayman Chemicals) for 6 hours and then harvested.

value: human foreskin BJ fibroblasts

source_name: Primay middle passage human BJ fibroblasts stably expressing control FF2 shRNA from the MSCV-mir30 based expression vector treated with 8uM nutlin-3a for 6 hours


title: LCL, 900uM H2O2 at T24

status: Public on Jun 30 2010

city: Washington

first: Kimberly

last: Chapman

state: DC

address: 111 Michigan Ave NW

department: genetics

institute: Children's National

description: Gene expression data from pooled RNA for 900uM hydrogen peroxide treatment T24 hours

hyb_protocol: Resultant cRNA was hybridized to the Affymetrix Human Gene 1.0 ST expression microarray (Affymetrix, Santa Clara, CA) according to manufacturer's directions.

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

data_processing: RMA

label_protocol: GeneChip Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix, Santa Clara, CA)

growth_protocol: Lymphoblastoid cells were maintained at a density of 1x10^6 cells/mL in RPMI 1640 media (Gibco, Carlsbad, CA) with 15% fetal calf serum (Hyclone Laboratories, Logan, UT), 2 mmol per liter of L-glutamine (Gibco, Carlsbad, CA), and 100 units per milliliter of penicillin-streptomycin (BioWhittaker, Switzerland)

extract_protocol: Cells were lysed using Qiashredder (Qiagen, Valencia, CA) and total RNA was isolated by Qiagen RNeasy purification kit (Qiagen, Valencia, CA). The total RNA from each cell line was pooled for each time and treatment.

treatment_protocol: Four lymphoblastoid cell lines (GM07055, GM12057, GM14569, and GM14467) were cultured at 1 x10^6 cells/mL into 17 aliquots  (a total of 68 samples). Twenty-four hours later,  one culture was collected from each cell line and total RNA prepared, this was equally pooled and prepared for microarray analysis (time zero, treatment zero).  Each cell line was then treated with a 9 (4 cultures), 90 (4 cultures), or 900 uM hydrogen peroxide bolus (4 cultures) or water (4 cultures).  Four, 12, 24 or 48 hours following the hydrogen peroxide bolus, cells were collected for each cell line of each treatment.

value: pooled lymphoblastoid cell lines (GM07055, GM14569, GM14467, and GM12057)

tag: agent

tag: time


title: LCL, no treatment at T0

description: Gene expression data from pooled RNA for 0 treatment T0 hours

source_name: pooled RNA for 0 treatment T0 hours

value: no treatment

value: 0 h


title: XenopusTail-T3-48h-rep2

city: Flagstaff

first: Brian

middle: Thomas

last: Searcy

state: AZ

address: P.O. Box 5640, Northern Arizona University

department: Dept of Biological Sciences

institute: Northern Arizona University

hyb_protocol: Standard Affymetrix Xenopus protocol was used according to manufacturer's instructions

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

data_processing: The data was pre-processed/normalized using the GCRMA algorithm

organism: Xenopus laevis

source_name: Xenopus laevis tail total RNA, stage 51-54 animals,  whole animal exposed to 48h  T3

label_protocol: Samples were labeled using the unmodified Affymetrix labeling protocol

growth_protocol: Stage 54 Xenopus laevis larvae were maintained in 500 ml glass containers at 20C in FETAX. 2/container.

extract_protocol: mRNA was extracted using Qiagen mini-kit RNAeasy protocol according to manufacturer's instructions

treatment_protocol: At time zero  vehicle or 20 nM T3 suspended in vehicle was added to the water, tails were collected at 48 h (vehicle), 6 h (T3) and 48 h (T3).  Tails were removed, and RNA extracted from pools of three tails/array.  Three arrays of pooled tails from each treatment were hybridized.

value: tail

tag: stage

value: stage 54 tadpoles (larvae)


title: XenopusTail-T3-48h-rep3


title: XenopusTail-T3-6h-rep1

source_name: Xenopus laevis tail total RNA, stage 51-54 animals,  whole animal exposed to 6h  T3


title: XenopusTail-T3-48h-rep1


title: LCL, 900uM H2O2 at T48

description: Gene expression data from pooled RNA for 900uM hydrogen peroxide treatment T48 hours


title: LCL, 90uM H2O2 at T24

description: Gene expression data from pooled RNA for 90 uM hydrogen peroxide treatment T24 hours

value: 90uM H2O2


title: LCL, 90uM H2O2 at T12

description: Gene expression data from pooled RNA for 90 uM hydrogen peroxide treatment T12 hours


title: C57Bl/6 P21, wildtype retina, 2


title: XenopusTail-T3-6h-rep2


title: LCL, 9uM H2O2 at T48

description: Gene expression data from pooled RNA for 9 uM hydrogen peroxide treatment T48 hours

value: 9uM H2O2


title: FF_14

status: Public on May 27 2010

city: Zeist

first: Marijana

last: Radonjic

address: Utrechtseweg 48

country: Netherlands

institute: TNO

description: gene expression data of ApoE3L.CETP mice liver samples treated with fenofibrate (FF)

hyb_protocol: For the hybridization 15 μg cRNA is used for further fragmentation and finally 10 μg for the hybridizations. The Affymetrix Mouse Genome 430-2.0 Arrays Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix 3’ IVT-Express labeling Kit.

scan_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrix protocols are strictly followed. The Affymetrix Command Console (v1.1) and Expression Console software (v1.1) are used to measure the performance of the washing, staining and scanning of the chips.

data_processing:
Raw signal intensities (from CEL files)were normalized using the GCRMA algorithm (gc-rma slow) using Management and Analysis Database for MicroArray eXperiments (MADMAX) software.
For annotation of probes and summarization of signals from probes representing one gene the MNBI custom CDF annotation file was used (based on EntrezGene, version 11.0.2 (file Matrix_customCDF - used for analysis and drawing conclusions). Genes were filtered for expression above 5 in 3 or more samples, resulting in a set of 11587 genes that was used for further analysis.

source_name: ApoE3L.CETP mice liver

label_protocol: The Affymetrix 3’ IVT-Express labeling Kit (#901229) is used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng is used for the labeling experiments.

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

value: APOE*3-Leiden.CETP (E3L)

value: liver

value: fenofibrate


title: LCL, no treatment at T12

description: Gene expression data from pooled RNA for 0 treatment T12 hours

source_name: pooled RNA for 0 treatment T12 hours


title: LCL, 90uM H2O2 at T48

description: Gene expression data from pooled RNA for 90 uM hydrogen peroxide treatment T48 hours


title: LCL, 9uM H2O2 at T12

description: Gene expression data from pooled RNA for 9 uM hydrogen peroxide treatment T12hours


title: LCL, 90uM H2O2 at T4

description: Gene expression data from pooled RNA for 90 uM hydrogen peroxide treatment T4 hours

value: 4 h


title: LCL, no treatment at T24

description: Gene expression data from pooled RNA for 0 treatment T24 hours

source_name: pooled RNA for 0 treatment T24 hours


title: LCL, no treatment at T48

description: Gene expression data from pooled RNA for 0 treatment T48 hours

source_name: pooled RNA for 0 treatment T48 hours


title: FF_11


title: XenopusTailVehicle-rep3

source_name: Xenopus laevis tail total RNA, stage 51-54 animals,  whole animal exposed to 48h vehicle

value: vehicle


title: FF_13


title: FF_10


title: LCL, 9uM H2O2 at T24

description: Gene expression data from pooled RNA for 9 uM hydrogen peroxide treatment T24 hours


title: LCL, 900uM H2O2 at T4

description: Gene expression data from pooled RNA for 900uM hydrogen peroxide treatment T4 hours


title: XenopusTailVehicle-rep2


title: XenopusTailVehicle-rep1


title: control_4

description: gene expression data of ApoE3L.CETP mice liver samples (control)

value: control


title: control_1


title: control_3


title: LCL, 9uM H2O2 at T4

description: Gene expression data from pooled RNA for 9 uM hydrogen peroxide treatment T4 hours

source_name: pooledRNA for 9 uM hydrogen peroxide treatment T4 hours


title: control_2


title: XenopusTail-T3-6h-rep3


title: control_5


title: LCL, 900uM H2O2 at T12

description: Gene expression data from pooled RNA for 900uM hydrogen peroxide treatment T12 hours


title: control_6


title: FF_8


title: FF_9


title: C57Bl/6 P21, wildtype retina, 1

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

value: C57Bl/6 wildtype

value: Mixed


title: LCL, no treatment at T4

description: Gene expression data from pooled RNA for 0 treatment T4 hours

source_name: pooled RNA for 0 treatment T4 hours


title: normal prostate: N8

status: Public on May 25 2010

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

description:
technical replicate: N8_DS
technical replicate: N8_NORM

hyb_protocol: Equal amounts (0.75 ug) of labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays representing 18K human unique genes and transcripts (Human 1A Glass Oligo Array, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSPE wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B

data_processing: Images were analyzed using Feature Extraction software (Agilent Technologies) version 7.6. Output files containing feature and background intensities and the related statistical parameters for red and green signals were then loaded into the Resolver SE System (Rosetta Biosoftware, Seattle, WA) together with the scan images and the pattern file. Data processing and normalization were performed using the Agilent Human 22k platform-specific error model. Replicated expression profiles were combined to form log10 expression ratios to measure the modulation in the sample compared to the reference.

source_name: normal prostate

label_protocol: RNA isolated from each tissue and from a commercial pool of RNA from organ donor healthy prostates (Becton Dickinson) was amplified by means of the Amino Allyl MessageAmp I aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns.

extract_protocol: All the samples were homogenized (Ultra – TurraxT8, Ika – Werke, Staufen, Germany) and total RNA was isolated by using TriReagent (Sigma Aldrich). TotRNA quality was checked by means of RNA 6000 pico chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.

value: normal prostate from the peripheral gland zone

tag: tag type

value: BA

tag: reference


title: prostate cancer: 47

description:
technical replicate: 47_DS
technical replicate: 47_NORM

source_name: prostate cancer

tag: disease

value: prostate cancer

tag: ets group

tag: gleason grade

value: commercial pool of RNA from organ donor healthy prostates (Becton Dickinson)


title: prostate cancer: 46

description:
technical replicate: 46_DS
technical replicate: 46_NORM

source_name: commercial pool of RNA from organ donor healthy prostates


title: normal prostate: N1

description:
technical replicate: N1_DS
technical replicate: N1_NORM

tag: tissue

value: TL


title: normal prostate: N5

description:
technical replicate: N5_DS
technical replicate: N5_NORM

value: VG


title: normal prostate: N12

description:
technical replicate: N12_DS
technical replicate: N12_NORM

value: GB


title: normal prostate: N11

description:
technical replicate: N11_DS
technical replicate: N11_NORM

value: GA


title: prostate cancer: 40

description:
technical replicate: 40_DS
technical replicate: 40_NORM


title: normal prostate: N3

description:
technical replicate: N3_DS
technical replicate: N3_NORM

value: MG


title: prostate cancer: 43

description:
technical replicate: 43_DS
technical replicate: 43_NORM


title: prostate cancer: 41

description:
technical replicate: 41_DS
technical replicate: 41_NORM


title: normal prostate: N9

description:
technical replicate: N9_DS
technical replicate: N9_NORM

value: CM


title: normal prostate: N10

description:
technical replicate: N10_DS
technical replicate: N10_NORM

value: CG


title: normal prostate: N13

description:
technical replicate: N13_DS
technical replicate: N13_NORM

value: D


title: normal prostate: N4

description:
technical replicate: N4_DS
technical replicate: N4_NORM

value: FI


title: normal prostate: N7

description:
technical replicate: N7_DS
technical replicate: N7_NORM

value: ZP


title: normal prostate: N6

description:
technical replicate: N6_DS
technical replicate: N6_NORM

value: CD


title: prostate cancer: 16

description:
technical replicate: 16_DS
technical replicate: 16_NORM

tag: commercial pool of RNA from organ donor healthy prostates (Becton Dickinson)


title: normal prostate: N2

description:
technical replicate: N2_DS
technical replicate: N2_NORM


title: prostate cancer: 45

description:
technical replicate: 45_DS
technical replicate: 45_NORM


title: prostate cancer: 51

description:
technical replicate: 51_DS
technical replicate: 51_NORM


title: normal prostate: N14

description:
technical replicate: N14_DS
technical replicate: N14_NORM

value: PS


title: prostate cancer: 6

description:
technical replicate: 6_DS
technical replicate: 6_NORM


title: prostate cancer: 12

description:
technical replicate: 12_DS
technical replicate: 12_NORM


title: prostate cancer: 52

description:
technical replicate: 52_DS
technical replicate: 52_NORM

value: NoETS


title: prostate cancer: 13

description:
technical replicate: 13_DS
technical replicate: 13_NORM


title: prostate cancer: 36

description:
technical replicate: 36_DS
technical replicate: 36_NORM


title: prostate cancer: 50

description:
technical replicate: 50_DS
technical replicate: 50_NORM


title: prostate cancer: 9

description:
technical replicate: 9_DS
technical replicate: 9_NORM


title: prostate cancer: 35

description:
technical replicate: 35_DS
technical replicate: 35_NORM


title: prostate cancer: 31

description:
technical replicate: 31_DS
technical replicate: 31_NORM


title: prostate cancer: 32

description:
technical replicate: 32_DS
technical replicate: 32_NORM


title: prostate cancer: 34

description:
technical replicate: 34_DS
technical replicate: 34_NORM


title: prostate cancer: 7

description:
technical replicate: 7_DS
technical replicate: 7_NORM


title: prostate cancer: 21

description:
technical replicate: 21_DS
technical replicate: 21_NORM


title: prostate cancer: 25

description:
technical replicate: 25_DS
technical replicate: 25_NORM


title: prostate cancer: 26

description:
technical replicate: 26_DS
technical replicate: 26_NORM


title: prostate cancer: 18

description:
technical replicate: 18_DS
technical replicate: 18_NORM


title: prostate cancer: 70

description:
technical replicate: 70_DS
technical replicate: 70_NORM


title: prostate cancer: 10

description:
technical replicate: 10_DS
technical replicate: 10_NORM


title: prostate cancer: 49

description:
technical replicate: 49_DS
technical replicate: 49_NORM


title: prostate cancer: 29

description:
technical replicate: 29_DS
technical replicate: 29_NORM


title: prostate cancer: 19

description:
technical replicate: 19_DS
technical replicate: 19_NORM


title: prostate cancer: 67

description:
technical replicate: 67_DS
technical replicate: 67_NORM


title: prostate cancer: 20

description:
technical replicate: 20_DS
technical replicate: 20_NORM


title: prostate cancer: 27

description:
technical replicate: 27_DS
technical replicate: 27_NORM


title: prostate cancer: 24

description:
technical replicate: 24_DS
technical replicate: 24_NORM


title: prostate cancer: 4

description:
technical replicate: 4_DS
technical replicate: 4_NORM


title: prostate cancer: 3

description:
technical replicate: 3_DS
technical replicate: 3_NORM


title: prostate cancer: 8

description:
technical replicate: 8_DS
technical replicate: 8_NORM


title: prostate cancer: 66

description:
technical replicate: 66_DS
technical replicate: 66_NORM


title: prostate cancer: 69

description:
technical replicate: 69_DS
technical replicate: 69_NORM


title: prostate cancer: 68

description:
technical replicate: 68_DS
technical replicate: 68_NORM


title: prostate cancer: 22

description:
technical replicate: 22_DS
technical replicate: 22_NORM


title: prostate cancer: 15

description:
technical replicate: 15_DS
technical replicate: 15_NORM


title: prostate cancer: 64

description:
technical replicate: 64_DS
technical replicate: 64_NORM


title: prostate cancer: 63

description:
technical replicate: 63_DS
technical replicate: 63_NORM


title: prostate cancer: 48

description:
technical replicate: 48_DS
technical replicate: 48_NORM


title: prostate cancer: 39

description:
technical replicate: 39_DS
technical replicate: 39_NORM


title: prostate cancer: 11

description:
technical replicate: 11_DS
technical replicate: 11_NORM


title: prostate cancer: 33

description:
technical replicate: 33_DS
technical replicate: 33_NORM


title: prostate cancer: 37

description:
technical replicate: 37_DS
technical replicate: 37_NORM


title: prostate cancer: 23

description:
technical replicate: 23_DS
technical replicate: 23_NORM


title: prostate cancer: 17

description:
technical replicate: 17_DS
technical replicate: 17_NORM

value: CRYO


title: prostate cancer: 5

description:
technical replicate: 5_DS
technical replicate: 5_NORM


title: MLN120B Treated HBL-1 - 8 hrs - mAdbID:95901

status: Public on Jan 11 2010

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 95901

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505B US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 9.5.3.1
Protocol_Name: GE2-v5_95_Feb07 (Read Only)

source_name: Untreated HBL-1 cells

label_protocol:
Cy3 Labeling Protocol
Other: 2 ug total RNA were labeled with Cy3.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

value: blood

tag: disease state

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: MLN120B Treated HBL-1 - 8 hr

label_protocol:
Cy5 Labeling Protocol
Other: 2 ug total RNA were labeled with Cy5.

treatment_protocol:
Treatment type: compound
Agent: MLN120B
Treatment dose: 25 umol/L
Treatment time: 8 hours
In-vitro treatment: HBL-1 cells were incubated with 25 µmol/L MLN120B (Millennium Pharmaceuticals, Cambridge, MA) for 8 hours.


title: prostate cancer: 30

description:
technical replicate: 30_DS
technical replicate: 30_NORM


title: MLN120B Treated HBL-1 - 3 hrs - mAdbID:99297

description: mAdb experiment ID: 99297

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: MLN120B Treated HBL-1 - 3 hr

treatment_protocol:
Treatment type: compound
Agent: MLN120B
Treatment dose: 25 umol/L
Treatment time: 3 hours
In-vitro treatment: HBL-1 cells were incubated with 25 µmol/L MLN120B (Millennium Pharmaceuticals, Cambridge, MA) for 3 hours.


title: MLN120B Treated HBL-1 - 6 hrs - mAdbID:99298

description: mAdb experiment ID: 99298

source_name: MLN120B Treated HBL-1 - 6 hr

treatment_protocol:
Treatment type: compound
Agent: MLN120B
Treatment dose: 25 umol/L
Treatment time: 6 hours
In-vitro treatment: HBL-1 cells were incubated with 25 µmol/L MLN120B (Millennium Pharmaceuticals, Cambridge, MA) for 6 hours.


title: BRCA2 Breast tumor 5216 RNA

status: Public on Dec 16 2009

city: Brisbane

first: Nic

last: Waddell

address: St Lucia

country: Australia

institute: Queensland Centre for Medical Genomics

description: no additional information

scan_protocol: Standard Illumina scanning protocol, but slides were scaned at factor of 2

data_processing: The data were normalised using quantile normalisation

source_name: familial breast tumour with >50% tumour cells, kConFab (Kathleen Cuningham Foundation Consortium for research into Familial Breast cancer)

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: Breast Tumour

tag: mutation status


title: BRCA2 Breast tumor B1615A RNA

description: no additional information


title: BRCA2 Breast tumor 18413 RNA

description: no additional information


title: BRCA2 Breast tumor 98-11684 RNA

description: no additional information


title: BRCA2 Breast tumor 98-01436 RNA

description: no additional information


title: MLN120B Treated HBL-1 - 16 hrs - mAdbID:95902

description: mAdb experiment ID: 95902

source_name: MLN120B Treated HBL-1 - 16 hr

treatment_protocol:
Treatment type: compound
Agent: MLN120B
Treatment dose: 25 umol/L
Treatment time: 16 hours
In-vitro treatment: HBL-1 cells were incubated with 25 µmol/L MLN120B (Millennium Pharmaceuticals, Cambridge, MA) for 16 hours.


title: MLN120B Treated HBL-1 - 12 hrs - mAdbID:99299

description: mAdb experiment ID: 99299

source_name: MLN120B Treated HBL-1 - 12 hr

treatment_protocol:
Treatment type: compound
Agent: MLN120B
Treatment dose: 25 umol/L
Treatment time: 12 hours
In-vitro treatment: HBL-1 cells were incubated with 25 µmol/L MLN120B (Millennium Pharmaceuticals, Cambridge, MA) for 12 hours.


title: BRCA2 Breast tumor 14659 RNA

description: no additional information


title: BRCA2 Breast tumor 3586 RNA

description: no additional information


title: MLN120B Treated HBL-1 - 4 hrs - mAdbID:95900

description: mAdb experiment ID: 95900

source_name: MLN120B Treated HBL-1 - 4 hr

treatment_protocol:
Treatment type: compound
Agent: MLN120B
Treatment dose: 25 umol/L
Treatment time: 4 hours
In-vitro treatment: HBL-1 cells were incubated with 25 µmol/L MLN120B (Millennium Pharmaceuticals, Cambridge, MA) for 4 hours.


title: MLN120B Treated HBL-1 - 24 hrs - mAdbID:99300

description: mAdb experiment ID: 99300

source_name: MLN120B Treated HBL-1 - 24 hr

treatment_protocol:
Treatment type: compound
Agent: MLN120B
Treatment dose: 25 umol/L
Treatment time: 24 hours
In-vitro treatment: HBL-1 cells were incubated with 25 µmol/L MLN120B (Millennium Pharmaceuticals, Cambridge, MA) for 24 hours.


title: BRCA2 Breast tumor B1280A RNA

description: no additional information


title: BRCA1 Breast tumor 30866 RNA

description: no additional information


title: MLN120B Treated HBL-1 - 2 hrs - mAdbID:95899

description: mAdb experiment ID: 95899

source_name: MLN120B Treated HBL-1 - 2 hr

treatment_protocol:
Treatment type: compound
Agent: MLN120B
Treatment dose: 25 umol/L
Treatment time: 2 hours
In-vitro treatment: HBL-1 cells were incubated with 25 µmol/L MLN120B (Millennium Pharmaceuticals, Cambridge, MA) for 2 hours.


title: BRCA2 Breast tumor 14045 RNA

description: no additional information


title: BRCA2 Breast tumor 00-10408 RNA

description: no additional information


title: BRCA1 Breast tumor 20034 RNA

description: no additional information


title: BRCA2 Breast tumor 80654 RNA

description: no additional information


title: BRCA2 Breast tumor 61542 RNA

description: no additional information


title: BRCA2 Breast tumor 864 RNA

description: no additional information


title: BRCA2 Breast tumor 1003813 RNA

description: no additional information


title: BRCA2 Breast tumor 16412 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 21349 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 70036 RNA

description: no additional information


title: BRCA2 Breast tumor 1006583 RNA

description: no additional information


title: BRCA1 Breast tumor 10164 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 70425 RNA

description: no additional information


title: BRCA1 Breast tumor 20091 RNA

description: no additional information


title: BRCA1 Breast tumor 30130 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 60584 RNA

description: no additional information


title: BRCA2 Breast tumor 1003803 RNA

description: no additional information


title: BRCA1 Breast tumor 60097 RNA

description: no additional information


title: BRCA2 Breast tumor 51334 RNA

description: no additional information


title: BRCA2 Breast tumor 90210 RNA

description: no additional information


title: BRCA2 Breast tumor 30184 RNA

description: no additional information


title: BRCA1 Breast tumor 71067 RNA

description: no additional information


title: BRCA1 Breast tumor 60034 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 30193 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 50467 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 67 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 20069 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 20031 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 50260 RNA

description: no additional information


title: BRCA1 Breast tumor 90385 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 12655 RNA

description: no additional information


title: BRCA1 Breast tumor 61699 RNA

description: no additional information


title: BRCA2 Breast tumor 70266 RNA

description: no additional information


title: BRCA2 Breast tumor 62018 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 90590 RNA

description: no additional information


title: BRCA1 Breast tumor 70020 RNA

description: no additional information


title: Genotyping data from one mother of a patient with unexplained mental retardation and a deletion of Shank2 gene

status: Public on May 01 2010

type: genomic

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: We identified genome-wide CNV using Affymetrix Genotyping Console (GTC), which uses a Hidden Markov Model (HMM) algorithm to calculate copy numbers.

label: Standard Affymetrix protocol

molecule: genomic DNA

source_name: genomic DNA from whole blood

label_protocol: Standard Affymetrix protocol

extract_protocol: Standard DNA isolation Kit from whole blood with promega maxwell-technology.

tag: relation to patient

value: mother

value: whole blood


title: BRCA1 Breast tumor 70672 RNA

description: no additional information


title: Genotyping data from one patient with unexplained mental retardation and a deletion of Shank2 gene

value: a deletion on 11q13.3-q13.4 in one patients with severe mental retardation

tag: subject

value: patient


title: BRCA2 Breast tumor 70047 RNA

description: no additional information


title: prostate cancer: 14

description:
technical replicate: 14_DS
technical replicate: 14_NORM

value: prostate cancer

value: commercial pool of RNA from organ donor healthy prostates (Becton Dickinson)


title: non-BRCA1/2 Breast tumor 20021 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 60681 RNA

description: no additional information


title: unknown Breast tumor 30348 RNA

description: no additional information

value: unknown


title: BRCA1 Breast tumor 20030 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 70260 RNA

description: no additional information


title: Genotyping data from one father of a patient with unexplained mental retardation and a deletion of Shank2 gene

value: father


title: BRCA2 Breast tumor 51010 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 60312 RNA

description: no additional information


title: BRCA2 Breast tumor 60776 RNA

description: no additional information


title: BRCA1 Breast tumor 80553 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 50528 RNA

description: no additional information


title: BRCA2 Breast tumor 50018 RNA

description: no additional information


title: BRCA1 Breast tumor 70441 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 41413 RNA

description: no additional information


title: BRCA2 Breast tumor 50642 RNA

description: no additional information


title: BRCA1 Breast tumor 60289 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 90473 RNA

description: no additional information


title: BRCA2 Breast tumor 20444 RNA

description: no additional information


title: BRCA2 Breast tumor 20405 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 50979 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 70295 RNA

description: no additional information


title: BRCA1 Breast tumor 40515 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 60450 RNA

description: no additional information


title: BRCA2 Breast tumor 20447 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 50567 RNA

description: no additional information


title: BRCA1 Breast tumor 80607 RNA

description: no additional information


title: non-BRCA1/2 Breast tumor 70887 RNA

description: no additional information


title: Picea_C3_F2_xylem

status: Public on Oct 10 2009

city: Vancouver

first: Dr. Kermit

last: Ritland

state: BC

address: 2424 Main Mall

department: Forest Sciences

country: Canada

institute: University of British Columbia

description: Picea_C3_F2_xylem is a required hybridization of a series of 15 cross-species microarray hybridizations from the xylem source of tissue in accordance with a modified loop design (Hybridization date:Sept. 2, 08).

hyb_protocol: The slide was pre-washed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 x 1.5 mm glass coverslip. First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array900 kit (Genisphere, Hatfield, USA):2X SDS Buffer; LNA dT blocker; and nuclease-free water. The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation. Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array900 kit (Genisphere, Hatfield, USA):2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer, and nuclease-free water. Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning consistently performed with 90% laser power, and the photomultiplier tube (PMT) percentages of 76 % for Cy3 channel, and 75% Cy5 channel. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from Picea_C3_F2_xylem hybridization together with 14 other microarray hybridizations of the xylem tissue were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays (and within as well as between arrays to arrive at the expression levels per individual basis). A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to 15 microarray slides. The model contained a fixed effect for species and random effect for individuals within species. For each gene-by-treatment(biological replicates), P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

organism: Picea abies

source_name: C3: Third biological replicate of Norway spruce

label_protocol: Used Genisphere Array900 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 25 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen);1.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546/Oyster-550 or Cy5/Alexa Fluor 647/Oyster-650;Cy5/Alexa Fluor 647/Oyster-650 dye-labeled; hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 10 min; and neutralized in 2 M Tris-HCl (pH 7.5).

extract_protocol:
Total RNA extraction used a modified version of the protocol described by Kolosova et al. (2004) Biotechniques 36: 821-824.
The extracted RNA was quantified and quality checked using spectrophotometry and agarose gel electrophoresis; in respect to the wavelength of maximum absorption at 260 nm and 280 nm and the presence of sharp bright bands of 28s and 18s ribosomal subunits at ~4.5 kb and ~1.9 kb on 1% agarose gel.

treatment_protocol: Scraped xylem pooled from various shoots of the individual tree was flash-frozen on the field by liquid nitrogen and kept in -80 ºC freezer until extraction.

tag: species

value: Norway spruce (P. abies)

value: Xylem tissue sampled from the shoots of mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC (collection established 1977).

organism: Picea jezoensis

source_name: F2: Second biological replicate of jezo spruce

label_protocol: Used Genisphere Array900 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 25 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 1.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546/Oyster-550 or Cy5/Alexa Fluor 647/Oyster-650; Cy3/Alexa Fluor 546/Oyster-550 dye-labeled; hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 10 min; and neutralized in 2 M Tris-HCl (pH 7.5).

value: jezo spruce (P. jezoensis)


title: non-BRCA1/2 Breast tumor 61761 RNA

description: no additional information

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays


title: vertical growth phase melanoma_46_DS

status: Public on Sep 30 2009

description: technical replicate of 46_NORM

hyb_protocol: Equal amounts (0.75 ug) of labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays representing 41K human unique genes and transcripts (Human Whole Genome Oligo Microarray Array, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSPE wash procedure. For each sample, a dye-swap replicate was performed.

data_processing:
Images were analyzed using Feature Extraction software (Agilent Technologies) version 7.6. Output files containing feature and background intensities and the related statistical parameters for red and green signals were then loaded into the Resolver SE System (Rosetta Biosoftware, Seattle, WA) together with the scan images and the Agilent Human Whole Genome pattern file. Data processing and normalization were performed using the Agilent Human Whole Genome platform-specific error model.  The Log10 (test/ref) ratios are reported in the Sample VALUE column in the data table below.

The final, processed data (those that form the basis of the conclusions of the study) are contained in the file named all_vs_average_nevi.txt which has been linked as a supplementary file on the Series GSE12391 record. Experiments (displastic nevi, melanoma, melanoma metastasis samples) were combined to form ratio experiments, by applying the ratio split with common reference option and calculating ratios over the average of non tumor samples (CMN).
More details: Replicated expression profiles were combined to form ratio experiments where each gene is associated to an expression fold-change and a p-value to assess the statistical significance of its modulation in the sample compared to the reference. New ratio experiments were also built by applying the “ratio split with common reference” option and calculating ratios over the average of non tumor samples (CMN). A “weight by error” divisive clustering algorithm available within the Rosetta Resolver system (with cosine correlation as similarity metrics) was applied to such new ratios to compare their expression profiles. At the same time, data treatment with the LIMMA (LInear Models for MicroArray data) package available within Bioconductor (http://www.bioconductor.org/) was also performed applying normexp background calculation, lowess within-array and A-quantile between-array normalization methods.

source_name: commercial human universal reference

label_protocol: RNA isolated from each fresh tissue and from the human universal reference (BD™ Human Universal Reference Total RNA, Clontech, Palo Alto, CA) was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Two rounds of amplification were performed to obtain the necessary quantity of aaRNA for labeling. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis (in the second round of amplification), cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns.

extract_protocol: All the samples were homogenized (Ultra – TurraxT8, Ika – Werke, Staufen, Germany) with 600 ul of RNA lysis buffer plus 1% 2-mercaptoethanol, and total RNA was isolated by using RNeasy Mini Kit (Qiagen, Dusseldorf, Germany). TotRNA quality was checked by means of RNA 6000 pico chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.

tag: Clontech human universal reference

source_name: melanoma Clark's level V

tag: Gender

value: Male

tag: Age


title: vertical growth phase melanoma_44_DS

description: technical replicate of 44_NORM

value: Female


title: vertical growth phase melanoma_42_DS

description: technical replicate of 42_NORM

source_name: melanoma Clark's level IV


title: vertical growth phase melanoma_45_DS

description: technical replicate of 45_NORM


title: vertical growth phase melanoma_41_DS

description: technical replicate of 41_NORM


title: vertical growth phase melanoma_43_DS

description: technical replicate of 43_NORM


title: radial growth phase melanoma_32_DS

description: technical replicate of 32_NORM

source_name: melanoma Clark's level II


title: vertical growth phase melanoma_40_DS

description: technical replicate of 40_NORM


title: radial growth phase melanoma_29_DS

description: technical replicate of 29_NORM


title: vertical growth phase melanoma_42

description: technical replicate of 42_DS


title: vertical growth phase melanoma_39_DS

description: technical replicate of 39_NORM


title: vertical growth phase melanoma_41

description: technical replicate of 41_DS


title: vertical growth phase melanoma_40

description: technical replicate of 40_DS


title: vertical growth phase melanoma_36_DS

description: technical replicate of 36_NORM

source_name: melanoma Clark's level III


title: vertical growth phase melanoma_38_DS

description: technical replicate of 38_NORM


title: radial growth phase melanoma_33_DS

description: technical replicate of 33_NORM


title: BRCA1 Breast tumor 11396 RNA

description: no additional information


title: vertical growth phase melanoma_45

description: technical replicate of 45_DS


title: vertical growth phase melanoma_46

description: technical replicate of 46_DS


title: radial growth phase melanoma_7b_DS

description: technical replicate of 7b_NORM


title: vertical growth phase melanoma_9b_DS

description: technical replicate of 9b_NORM


title: vertical growth phase melanoma_43

description: technical replicate of 43_DS


title: radial growth phase melanoma_31_DS

description: technical replicate of 31_NORM


title: vertical growth phase melanoma_38

description: technical replicate of 38_DS


title: vertical growth phase melanoma_34_DS

description: technical replicate of 34_NORM


title: vertical growth phase melanoma_44

description: technical replicate of 44_DS


title: vertical growth phase melanoma_39

description: technical replicate of 39_DS


title: vertical growth phase melanoma_9b

description: technical replicate of 9b_DS


title: vertical growth phase melanoma_36

description: technical replicate of 36_DS


title: vertical growth phase melanoma_35_DS

description: technical replicate of 35_NORM


title: 3H LPS, patient 91, responder

status: Public on Dec 01 2008

city: Amsterdam

first: Oscar

middle: Leonard

last: Volger

state: Noor Holland

address: Meibergdreef 15

department: Cardiology

institute: Academic Medical Center

description:
patient: Caucasian patients were included who underwent percutaneous coronary intervention (PCI) of a total coronary occlusion. Exclusion criteria were previous myocardial infarction, cardiac surgery, depressed left ventricular function, diabetes mellitus, neoplastic or inflammatory disease. Invasive coronary collateral flow index (CFI) measurements were then performed. Patients were dichotomized as either sufficient (CFI>0.37) or insufficient (CFI≤0.37) collateral responders (0.37 was the median CFI of this patient group).
tissue: mononuclear cells were collected from 50 ml of arterial blood using Ficoll separation

hyb_protocol: 750ng of biotinylated cRNA was hybridized onto the HumanRef-8 Expression BeadChips according to the manufacturer's specifications.

scan_protocol: According to the manufacturer, performed by ServiceXS (http://www.servicexs.com).

data_processing: Gene expression analysis was performed by using Illumina's Beadstudio v3 software, followed by a quantile inter-array normalization (R, Bioconductor).

source_name: arterial blood mononuclear cells activated by LPS, responder

label_protocol: Default in vitro transcription to produced Biotinylated antisense aRNA by using the Illumina Totalprep RNA amplification kit (#IL1791, Ambion).

extract_protocol: mRNA was extracted from 10 and 10 patients from the extreme ends of the spectrum (very high vs. very low CFI), by using Trizol (Invitrogen) with an RNEasy Micro column cleanup (Qiagen), who were matched for age, sex, medication and other factors that influence collateral artery growth.

treatment_protocol: Subsequently, monocytes were negatively isolated using immunomagnetic beads for stimulation with 10ng/ml LPS for 3h.

tag: race

value: Caucasian

tag: cell type

value: mononuclear cells

tag: treatment

value: LPS

value: chronic coronary occlusion

tag: collateral flow response

value: sufficient


title: vertical growth phase melanoma_35

description: technical replicate of 35_DS


title: 3H LPS, patient 95, responder

value: blood

tag: disease


title: radial growth phase melanoma_31

description: technical replicate of 31_DS


title: radial growth phase melanoma_7b

description: technical replicate of 7b_DS


title: radial growth phase melanoma_33

description: technical replicate of 33_DS


title: 3H LPS, patient 90, nonresponder

source_name: arterial blood mononuclear cells activated by LPS, nonresponder

value: insufficient


title: 3H LPS, patient 89, nonresponder


title: 3H LPS, patient 85, nonresponder


title: radial growth phase melanoma_29

description: technical replicate of 29_DS


title: vertical growth phase melanoma_34

description: technical replicate of 34_DS


title: 3H LPS, patient 88, responder


title: 3H LPS, patient 87, responder


title: 3H LPS, patient 84, nonresponder


title: 3H LPS, patient 71, nonresponder


title: 3H LPS, patient 72, responder


title: 3H LPS, patient 67, responder


title: 3H LPS, patient 55, nonresponder


title: 3H LPS, patient 80, responder


title: 3H LPS, patient 83, responder


title: 3H LPS, patient 73, nonresponder


title: 3H LPS, patient 82, responder


title: 3H LPS, patient 77, responder


title: 3H LPS, patient 69, nonresponder


title: Gene expression profiles of HL-60 cells exposed to benzene (IC50) [sample 2]

status: Public on Aug 08 2008

city: Seoul

first: Sailendra

middle: Nath

last: Sarma

address: P.O. Box 131, Cheongryang

institute: Korea Institute of Science and Technology

description: HL-60 cells were treated with 8.75 mM benzene for 3 h, and the RNA was subjected to microarray analysis.

hyb_protocol: Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). This was followed by the coupling of the Cy3 dye for the controls (DMSO) or Cy5 dye for the treated samples. Hybridization was performed in a hybridization oven at 62℃ for 12 h. After washing (2× SSC/0.1% SDS for 2 min at 58℃, 1× SSC for 2 min at RT and 0.2× SSC for 3 min at RT), the slide was dried by centrifugation at 800 rpm for 3 min at RT.

scan_protocol: Hybridization images on the slides were scanned by ScanArray Lite (PerkinElmer Life Sciences, USA). Scanned images were analyzed with GenePix 3.0 software (Axon Instruments, USA) to obtain gene expression ratios.

data_processing: The fluorescent intensity of each spot was calculated by local median background subtraction. The robust scatter-plot smoother LOWESS function was used to perform intensity dependent normalization for the gene expression. Scatter plot analysis was made by Microsoft Excel 2003. Significance Analysis of Microarray (SAM) was performed for the selection of the genes with significant gene expression changes (Tusher et al., 2001). Computing a p-value for each gene assessed the statistical significance of the differential expression of genes. To determine the p-value, a permutation procedure was used and for each permutation, two-sample t statistics were computed for each gene. Genes were considered differentially expressed when logarithmic gene expression ratios in three independent hybridizations were more than 1.5 or less than 0.66, i.e., 1.5-fold difference in expression level, and when the p-values were less than 5.

source_name: HL-60 cells treated with DMSO for 3 h

label_protocol: Gene expression analysis was conducted on the RNA samples using 35 K whole human genome microarray (Operon Biotechnologies, Inc. Germany). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy3 dye for the controls (DMSO).

extract_protocol: Total RNA was extracted from the HL-60 cells treated to DMSO for 3 h using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

tag: cell line

value: human promyelocytic leukemia cells

value: DMSO

tag: treatment time

value: 3 h

source_name: HL-60 cells treated with benzene (IC50) for 3 h

label_protocol: Gene expression analysis was conducted on the RNA samples using 35 K whole human genome microarray (Operon Biotechnologies, Inc. Germany). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy5 dye for the treated samples.

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC50 dose of benzene for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

tag: treament

value: benzene

tag: treament dose

tag: treament time

value: 3 hr


title: Gene expression profiles of HL-60 cells exposed to benzene (IC50) [sample 3]


title: K14E6_skin

status: Public on Sep 01 2008

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

description: Pooled total RNA from three transgenic mice

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, then, 15 μg of the fragmentation product were used to prepare 300 μl hybridization cocktail (100mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20, 0.1 mg ml-1 of HS DNA, and 0.5 mg ml-1 acetylated bovine serum albumine). The cocktails were heated to 95°C and hybridized in the Mouse Genome 430A 2.0 Array (Affymetrix Inc.) for 16 hours at 45ºC .After hybridization, arrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: The GeneChip Scanner 3000 7G  (Affymetrix, Santa Clara CA) was used to collect fluorescence signal of 11um feature size resolution after excitation at 570 nm. GCOS software (Affymetrix, Santa Clara CA) was used to obtain intensity signal and quality data of the scanned arrays.

data_processing: Chip scanning and expression analyisis of the .CHP files was performed using the MAS 5.0 software

source_name: K14E6_skin_pool of 3 mice

label_protocol: The quality and size distribution of the RNA were assessed with the RNA Nano Lab on a Chip kit (Agilent Technologies), which yielded RNA integrity numbers (RIN) from 6.5 to 9.2.  Total RNA collected from skin or cervical tissue from three female mice of each condition were pooled. Briefly, 3 μg of the total pooled RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer. Second strand cDNA synthesis was followed by an in vitro transcription reaction in which biotinylated CTP and UTP were incorporated to the generated transcripts.

extract_protocol: Collected tissues were homogenized by mortar in liquid nitrogen, total RNA was extracted using TRIZOL reagent (InVitrogen) and purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Tissue was immediately frozen in liquid nitrogen for later RNA isolation using Trizol.

tag: FVB type 6-week-old virgin female mice were employed. All mice were sacrificed and shaved with razor. After sacrifice dorsal skin (approx. 1cm2) was removed and immediately frozen in liquid nitrogen for later RNA isolation.


title: 3H LPS, patient 81, nonresponder

tag: tissue


title: Gene expression profiles of HL-60 cells exposed to benzene (IC50) [sample 1]


title: Mc DKK1 2hrs - mAdbID:60962

status: Public on Nov 30 2006

first: Vincent

last: Hearing

address: Bldg 37  Rm 2132

department: National Cancer Institute

institute: National Institutes of Health

description: mAdb experiment ID: 60962

hyb_protocol: NCI cDNA Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42øC for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ¶l COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100øC for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42øC just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42øC in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: control

label_protocol: Cy5 Sample Labeling Protocol - generic

growth_protocol:
Sample Growth Protocol
Other: Neonatal human foreskin melanocytes were obtained from Cascade Biologics, Inc. (Portland, OR). Melanoctye cultures were grown in melanocyte growth medium (MGM) consisting of Medium 154 (Cascade Biologics, Inc.) and HMGS (Cascade Biologics, Inc.). Melanocytes from the third and fifth passages were used in the experiments.

extract_protocol:
Sample Extraction Protocol
Other: Used an RNeasy mini kit (Qiagen, Valencia, CA)

tag: Tissue

value: skin

tag: Cell type

value: Normal human melanocytes

label_protocol: Cy3 Sample Labeling Protocol - generic

treatment_protocol:
Treatment type: compound
Agent: recombinant human dickkopf 1 (rhDKK1)
Treatment dose: 50 ng/ml
Treatment time: 5 days
Treatment temperature: 37 C


title: FVB_non_transgenic_skin

description: Pooled total RNA from three non-transgenic mice

source_name: FVB_non_transgenic_skin_pool of 3 mice


title: L-ZR-75-1

status: Public on Nov 07 2005

city: Durham

first: Joseph

middle: R.

last: Nevins

state: NC

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

institute: Duke University

description: Microarray analysis of breast cancer cell lines

data_processing: Affymetrix Microarray Suite version 5.0

source_name: RNA from growing cell lines

tag: breast cancer cell line


title: K-T-47D


title: radial growth phase melanoma_32

description: technical replicate of 32_DS

tag: Gender

tag: Clontech human universal reference


title: 3H LPS, patient 92, nonresponder

tag: race