title: HCC 61

city: Heidelberg

first: Christof

middle: Simon

last: Schlaeger

state: BW

address: INF 580

department: Molecular Genetics (B060)

institute: DKFZ

description: Comparison of normal (Cy5-labeled) versus HCC DNA (Cy5-labeled). Whole-genome screening of DNA-copy number changes by array-based or matrix comparative genomic hybridization (matrix-CGH).

hyb_protocol: Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 h at 37°C. Slides were washed with 2x SSC/0.05% Tween-20 at 37°C for one cycle, 2x SSC/0.05% Tween-20 at 44°C for two cycles, 50% formamide/2x SSC/0.1% Tween-20 at 44°C for 3 cycles, 2x SSC/0.05% Tween-20 at 44°C for 2 cycles, and finally 1x PBS/0.05% Tween-20 at 25°C for two cycles. Slides were dried by centrifugation

scan_protocol: Arrays were scanned with an Agilent DNA microarray scanner (Agilent Technologies, Palo Alto, USA) Images were quantified using GenePix Pro 6.0 software (Axon Instruments, Burlingame, USA)

data_processing: Data were filtered consistently according to spot signal/local background ratio (>3.0 for aCGH; >2.0 for expression profiling), mean/median spot intensity (<0.3) and spot replicate standard deviation (<0.25), and normalized globally by print-tip loess

source_name: Pooled reference DNA from either 7 healthy males or females of the same sex compared to the sample

label_protocol: 300 ng of genomic DNA was labeled with Cy5 or Cy5 using the Bioprime Labelling Kit (Invitrogen, Karlsruhe, Germany) according to the manufactures' instructions

extract_protocol: Extraction of high molecular weight DNA and RNA from frozen HCC samples was carried out by ultracentrifugation in cesium chloride as previously described in van den Boom et al., 2003 Am J Pathol.

tag: human lymphocytes

source_name: Isolated genomic tumor DNA, derived from HCC tumor

tag: primary HCC derived from HFE


title: HCC 63

status: Public on Oct 15 2007

type: genomic

country: Germany

molecule: genomic DNA

organism: Homo sapiens


title: PLC

source_name: Isolated genomic tumor DNA, derived from cell line

tag: HBV-associated human hepatoma cell line


title: HuH7

tag: human hepatoma cell line


title: HCC 59

tag: primary HCC derived from alpha1-Antitrypsinmangel


title: Hep3B


title: HepG2

tag: human hepatoblastoma cell line


title: HCC 62


title: HCC 54

tag: HBV/HCV-derived primay HCC


title: HCC 55

tag: HBx-positiv primay HCC


title: HCC 50

tag: cryptogenic primay HCC


title: Bradyrhizobium japonicum 110spc4, induced with genistein, biological replicate 3

type: RNA

city: Dresden

first: Michael

last: Göttfert

address: Helmholtzstrasse 10

department: Biology

institute: Dresden University of Technology

description: Gene expression data of Bradyrhizobium japonicum grown with genistein for 8 hours.

hyb_protocol: Modification of Affymetrix protocol used for Escherichia coli. 1.8-2.5 µg of labeled cDNA was used.

scan_protocol: Standard Affymetrix protocol

data_processing: GeneChip Operating Software (GCOS) version 1.2 (Affymetrix), global scaling to a target intensity of 500.

label: biotin

molecule: total RNA

organism: Bradyrhizobium japonicum

label_protocol: 3 µg cDNA were labeled with biotin.

growth_protocol: After addition of genistein cells were grown for 8 hours at 28 °C.

extract_protocol: RNA was isolated as described by Lang et al. (2007) Mol Gen Genomics, submitted.

treatment_protocol: Genistein (1 µM end concentration) was added at an OD600 of 0.4-0.6.

tag: Genotype

value: wild type

tag: Growth condition

value: AG medium supplemented with genistein

tag: Induction time

value: 8 hours


title: HCC 47


title: HCC 51


title: HCC 48


title: HCC 49


title: HCC 45


title: HCC 60


title: HCC 52


title: Bradyrhizobium japonicum 110spc4, biological replicate 3

source_name: Bradyrhizobium japonicum grown with methanol for 8 hours

growth_protocol: After addition of methanol cells were grown for 8 hours at 28 °C.

treatment_protocol: Methanol (as solvent for genistein) was added at an OD600 of 0.4-0.6.

value: AG medium supplemented with methanol


title: HCC 56

tag: alcoholic derived primary HCC, Hbx-positive


title: HCC 57


title: HCC 53

tag: HBx-positive primay HCC


title: HCC 44


title: HCC 46


title: HCC 43


title: HCC 58


title: HCC 40


title: HCC 39


title: HCC 30

tag: alcoholic derived primary HCC


title: HCC 31


title: HCC 35


title: HCC 29


title: HCC 32


title: HCC 42


title: HCC 41


title: HCC 33


title: HCC 34


title: HCC 28


title: HCC 37


title: HCC 22

tag: HCV-derived primary HCC


title: HCC 26


title: HCC 23


title: HCC 21


title: HCC 38


title: HCC 36


title: HCC 17


title: HCC 18


title: HCC 19


title: HCC 20


title: HCC 27


title: HCC 24


title: HCC 25


title: HCC 12


title: HCC 13


title: HCC 15


title: HCC 6

tag: HBV-derived primary HCC


title: HCC 10

tag: human lymphocytes


title: HCC 14


title: HCC 16


title: HCC 7


title: SmutansUA159_anaerobic_rep4

status: Public on Oct 13 2007

city: Gainesville

first: Robert

middle: A

last: Burne

state: FL

address: 1600 SW Archer Rd. BOX 100424

department: Oral Biology

country: USA

institute: University of Florida

description: Streptococcus mutans wild-type grown in anaerobic conditions

hyb_protocol: Hybridizations were carried out in a Maui 4-chamber hybridization system (BioMicro Systems, Salt Lake City, Utah) for 17 h at 42ºC. The slides were then washed according to TIGR protocols (SOT# M008, version 2.1, 11/06).

scan_protocol: The slides were scanned using a GenePix Scanner (Axon Instruments Inc., Union City, CA).

data_processing: After the slides were scanned, single-channel images were loaded into TIGR Spotfinder software and overlayed. A spot grid was created according to TIGR specifications and manually adjusted to fit all spots within the grid, then the intensity values of each spot were measured. Data was normalized using Microarray data analysis software (MIDAS), by using LOWESS and Iterative Log Mean Centering with default settings.

organism: Streptococcus mutans

source_name: Streptoccocus mutans grown in anaerobic conditions

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications. The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2. SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields. Purified cDNAs were coupled with indocarbocyanine (Cy3)-dUTP

growth_protocol: grown in Brain Heart Infusion media in a Gaspak Plus anaerobe jar until OD600 of 0.4 was reached.

extract_protocol: RNA from S. mutans was isolated from 50 ml cultures that were grown under the desired conditions and harvested by centrifugation at 4ºC. Pelleted cells were resuspended in 400 ml of DEPC-treated water, 800 ml of RNA protect reagent (QIAGEN, Inc., Chatsworth, CA) was added, and the samples were incubated at room temperature for 5 min with vortexing for 10 s at one minute intervals. Cells were then pelleted, resuspended in 500 ml Tris-EDTA (50:10) buffer and transferred to 1.5 ml screw cap tubes containing sterile glass beads (0.1 mm avg. diam.; Biospec, Bartlesville, OK), 100 ml of 1% SDS and 650 ml of acid phenol:chloroform (5:1). The mixture was homogenized in a Bead Beater twice for 40 s and chilled on ice for 2 min between cycles. Samples were centrifuged for 30 min at maximum speed at 4ºC. Two additional hot acid phenol:chloroform extractions were performed followed by one extraction with chloroform:isoamyl-alcohol (24:1). RNA was precipitated in the presence of isopropanol and sodium acetate, pH 5, at -20ºC for 1 h, followed by multiple washes with 70% ethanol, one wash with 99% ethanol, and drying in vacuo. RNA was resuspended in DEPC-treated water and digested with DNAseI (Ambion, Austin, TX). The RNA was re-purified and treated on-column with DNaseI using the RNeasy mini kit (QIAGEN, Inc., Chatsworth, CA), as recommended by the supplier.

tag: Characteristics 	Strain UA159

source_name: S. mutans UA159 grown in 5% CO2

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications. The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2. SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields. Reference cDNA was coupled with indodicarbocyanine (Cy5)-dUTP (Amersham Biosciences, Piscataway, NJ).

growth_protocol:
Growth Media: Brain Heart Infusion
OD600: 0.6
Grown in 5% CO2 incubator

tag: Strain UA159


title: HCC 9


title: HCC 5


title: HCC 8


title: HCC 1


title: SmutansUA159_anaerobic_rep2

tag: S. mutans strain UA159


title: HCC 4


title: HCC 3


title: SmutansUA159_aerobic_rep4

description: Streptococcus mutans wild-type grown in aerobic conditions

source_name: Streptoccocus mutans grown in aerobic conditions

growth_protocol: grown in Brain Heart Infusion media in a shaking incubator until OD600 of 0.4 was reached.


title: HCC 11


title: HCC 2


title: SmutansUA159_aerobic_rep3


title: SmutansUA159_aerobic_rep1


title: SmutansUA159_anaerobic_rep3

tag: strain UA159


title: SmutansUA159_aerobic_rep2


title: SmutansUA159_anaerobic_rep1

growth_protocol:
Growth Media: Brain Heart Infusion
OD600: 0.4
Grown in 5% CO2 incubator


title: Medulloblastoma, biological rep3 (430A)

status: Public on Oct 12 2007

city: Cambridge

first: Junhao

last: Mao

state: MA

address: 16 Divinity Ave., BL 1048

department: MCB

institute: Harvard University

description: gene expression data in medulloblastoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized according to the standard Affymetrix protocol

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

data_processing: dChip

organism: Mus musculus

source_name: medulloblastoma from CAGGS-CreER;R26-SmoM2 mice

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

growth_protocol: CAGGS-CreER;R26-SmoM2 tumor mice were generated by crossing CAGGS-CreER males to R26-SmoM2 females.

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

treatment_protocol: 1mg/40g body weight tamoxifen injection @postnatal day 10 of CAGGS-CreER;R26-SmoM2 mice

tag: CAGGS-CreER;R26-SmoM2 in mixed background


title: Wild type cerebellum, biological rep2 (430A)

description: gene expression data in wild type cerebellum

source_name: adjacent wild type cerebellar tissue from CAGGS-CreER;R26-SmoM2 mice


title: Medulloblastoma, biological rep2 (430A)

description: gene expression data in medulloblastoma


title: Medulloblastoma, biological rep1 (430A)

description: gene expression data in medulloblastoma


title: Medulloblastoma, biological rep3 (430B)

description: gene expression data in medulloblastoma


title: Wild type cerebellum, biological rep1 (430A)


title: Medulloblastoma, biological rep1 (430B)

description: gene expression data in medulloblastoma


title: Medulloblastoma, biological rep2 (430B)

description: gene expression data in medulloblastoma


title: Wild type cerebellum, biological rep1 (430B)


title: Wild type cerebellum, biological rep2 (430B)


title: IFO0233 Phenelzine 15.9669285714286 hours (A092_A_Yeast-2_01-1)

city: Duarte

middle: R

last: Klevecz

state: CA

address: 1450 E. Duarte Rd.

institute: Beckman Research Institute of the City of Hope

description: 15.9669285714286 hours following inoculation

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner M10.

data_processing:
Results were quantified and analyzed using MicroArray Suite 6.1 and GCOS software. Matrix files have already been adjusted for differences in hybridization efficiency using a polynomial fit to the E. coli standards. This file can be obtained from the contact person, R. Klevecz.
The values for the E. coli and B. subtilis standards in the matrix file should NOT be used for any further adjustments to the data. Use the original standards in the CEL files for that purpose. Values in the matrix files were not adjusted for differences in the values of the B. subtilis standards The B. subtilis standards were added at the time of RNA isolation and should NOT be used at all except as described below.
Checking for relative constancy of RNA Recovery:
To test the possibility that differences in expression level might be due to differences in recovery of mRNA, B.subtilis poly-A standards were spiked into the cell pellet at the beginning of the RNA isolation procedure as a measure of recovery. This approach, while imperfect, gives at least some assurance that variations in total transcript levels for all transcripts in any one chip is not due to differences in recovery. It might also monitor the inherent bias in adjusting the input RNA to a constant level throughout the procedure as required by Affymetrix. No consistent trend in recovery was noted.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: IFO0233, Phenelzine

label_protocol: Purified total RNA samples were processed as recommended in the Affymetrix GeneChip Expression Analysis Technical Manual. RNA samples were adjusted to a final concentration of 1 mg/ml. Typically, 25-250 ng were loaded onto an RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) and analyzed in an Agilent Bioanalyzer 2100. Double-stranded cDNA was synthesized from 5 mg of total RNA using GeneChip Expression 3'-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix) and oligo(dT) primers containing a T7 RNA polymerase promoter. Double-stranded cDNA was used as a template to generate biotinylated cRNA using the GeneChip Expression 3'-Amplification Reagents for IVT Labeling. The biotin-labeled cRNA was fragmented to 35-200 bases following the Affymetrix protocol. Five micrograms of fragmented cRNA was hybridized to Yeast 2.0 Affymetrix arrays at 45°C for 16 h in an Affymetrix GeneChip Hybridization Oven 640. The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin (SAPE) on an Affymetrix Fluidics Station 450, followed by scanning on an Affymetrix GeneArray scanner.

growth_protocol: The fermenter was inoculated with 2 x 10^7 cells of the strain IFO0233 in 650 ml. Fermentative growth on glucose was observed during the first 12 h after inoculation. Oscillatory dynamics typically appear beginning 16 to 24 h after inoculation. To maintain oscillations, cultures are shifted from batch to continuous culture by medium addition and removal at a rate of 0.086/h. Once established, oscillatory dynamics remain largely unchanged for weeks to months. Normally, periodicity remains between 40 and 45 min. Dissolved oxygen levels and carbon dioxide release are the most accessible output from the oscillator and are characterized by a phase of high respiration followed by a shift to a low respiration phase. No difference in oscillation was seen in light or darkness. The oscillation is dependent on pH, aeration, and carbon dioxide. Oscillation occurs when glucose, ethanol, or acetaldehyde is used as a carbon source. Cell numbers are kept between 0.45 and 0.85 x 10^9/ml.

extract_protocol: For RNA isolation, the pellet was resuspended in 0.5 ml of RNA Later (cat. no. 7020; Ambion, Austin, TX ) containing 1% 2-mercaptoethanol. Cells were lysed by beating in a minibead beater (BioSpec Products, Bartlesville, OK) for 3 min with 0.5 ml of acid-washed glass beads (cat. no. G-8772; Sigma, St. Louis, MO). After the cell lysate was removed, the beads were washed three times with 0.5 ml of RLT buffer (Qiagen, Valencia, CA) containing 1% 2-mercaptoethanol by bead beater (1 min each wash). The cell lysate and washes were pooled. An equal volume of 70% ethanol was added, and RNA was purified with RNA easy columns (Qiagen) according to the manufacturer. DNA was digested on the columns according to the instructions. RNA was eluted in a total of 0.1 ml of RNase-free water. The final RNA samples were analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Typical total RNA yields were 20-40 mg with absorbance 260/280 ratios of 1.8-2.2.

treatment_protocol: For expression measurements, samples (0.5 ml) were taken every 4 min through an interval of 200 min. The cells were centrifuged, the supernatant was decanted, and the pellet was placed in a dry-ice acetone bath. The time from removal of the sample to freezing was less than 1 min. Samples were stored at -80°C

tag: Strain


title: IFO0233 Phenelzine 16.4336785714286 hours (A099_A_Yeast-2_01-1)

description: 16.4336785714286 hours following inoculation


title: IFO0233 Phenelzine 16.3003214285714 hours (A097_A_Yeast-2_01-1)

description: 16.3003214285714 hours following inoculation


title: IFO0233 Phenelzine 16.367 hours (A098_A_Yeast-2_01-1)

description: 16.367 hours following inoculation


title: IFO0233 Phenelzine 15.8335714285714 hours (A089_A_Yeast-2_02-1)

description: 15.8335714285714 hours following inoculation


title: IFO0233 Phenelzine 15.7668928571429 hours (A088_A_Yeast-2_02-1)

description: 15.7668928571429 hours following inoculation


title: IFO0233 Phenelzine 15.7002142857143 hours (A087_A_Yeast-2_01-1)

description: 15.7002142857143 hours following inoculation


title: IFO0233 Phenelzine 16.5003571428572 hours (A100_A_Yeast-2_01-1)

description: 16.5003571428572 hours following inoculation


title: IFO0233 Phenelzine 16.6337142857143 hours (A102_A_Yeast-2_01-1)

description: 16.6337142857143 hours following inoculation

growth_protocol: The fermenter was inoculated with 2 ´ 107 cells of the strain IFO0233 in 650 ml. Fermentative growth on glucose was observed during the first 12 h after inoculation. Oscillatory dynamics typically appear beginning 16 to 24 h after inoculation. To maintain oscillations, cultures are shifted from batch to continuous culture by medium addition and removal at a rate of 0.086/h. Once established, oscillatory dynamics remain largely unchanged for weeks to months. Normally, periodicity remains between 40 and 45 min. Dissolved oxygen levels and carbon dioxide release are the most accessible output from the oscillator and are characterized by a phase of high respiration followed by a shift to a low respiration phase. No difference in oscillation was seen in light or darkness. The oscillation is dependent on pH, aeration, and carbon dioxide. Oscillation occurs when glucose, ethanol, or acetaldehyde is used as a carbon source. Cell numbers are kept between 0.45 and 0.85 ´ 109/ml.


title: IFO0233 Phenelzine 16.1002857142857 hours (A094_A_Yeast-2_01-1)

description: 16.1002857142857 hours following inoculation


title: IFO0233 Phenelzine 15.4335 hours (A083_A_Yeast-2_01-1)

description: 15.4335 hours following inoculation


title: IFO0233 Phenelzine 16.0336071428572 hours (A093_A_Yeast-2_01-1)

description: 16.0336071428572 hours following inoculation


title: IFO0233 Phenelzine 15.1667857142857 hours (A079_A_Yeast-2_01-1)

description: 15.1667857142857 hours following inoculation


title: IFO0233 Phenelzine 16.2336428571429 hours (A096_A_Yeast-2_01-1)

description: 16.2336428571429 hours following inoculation


title: IFO0233 Phenelzine 16.5670357142857 hours (A101_A_Yeast-2_01-1)

description: 16.5670357142857 hours following inoculation


title: IFO0233 Phenelzine 15.3001428571429 hours (A081_A_Yeast-2_02-1)

description: 15.3001428571429 hours following inoculation


title: IFO0233 Phenelzine 15.5001785714286 hours (A084_A_Yeast-2_01-1)

description: 15.5001785714286 hours following inoculation


title: IFO0233 Phenelzine 16.1669642857143 hours (A095_A_Yeast-2_01-1)

description: 16.1669642857143 hours following inoculation


title: IFO0233 Phenelzine 15.2334642857143 hours (A080_A_Yeast-2_02-1)

description: 15.2334642857143 hours following inoculation

hyb_protocol: Standard Affymetrix Protocol


title: IFO0233 Phenelzine 15.1001071428571 hours (A078_A_Yeast-2_01-1)

description: 15.1001071428571 hours following inoculation


title: IFO0233 Phenelzine 15.6335357142857 hours (A086_A_Yeast-2_01-1)

description: 15.6335357142857 hours following inoculation


title: IFO0233 Phenelzine 15.0334285714286 hours (A077_A_Yeast-2_01-1)

description: 15.0334285714286 hours following inoculation


title: IFO0233 Phenelzine 15.90025 hours (A090_A_Yeast-2_02-1)

description: 15.90025 hours following inoculation


title: IFO0233 Phenelzine 15.3668214285714 hours (A082_A_Yeast-2_02-1)

description: 15.3668214285714 hours following inoculation


title: IFO0233 Phenelzine 15.5668571428571 hours (A085_A_Yeast-2_01-1)

description: 15.5668571428571 hours following inoculation


title: IFO0233 Phenelzine 14.7667142857143 hours (A073_A_Yeast-2_01-1)

description: 14.7667142857143 hours following inoculation

hyb_protocol: Standard Affymetrix protocol.


title: IFO0233 Phenelzine 14.7000357142857 hours (A072_A_Yeast-2_01-1)

description: 14.7000357142857 hours following inoculation


title: IFO0233 Phenelzine 14.96675 hours (A076_A_Yeast-2_01-1)

description: 14.96675 hours following inoculation


title: IFO0233 Phenelzine 14.8333928571429 hours (A074_A_Yeast-2_01-1)

description: 14.8333928571429 hours following inoculation


title: IFO0233 Phenelzine 14.6333571428571 hours (A071_A_Yeast-2_01-1)

description: 14.6333571428571 hours following innoculation


title: IFO0233 Phenelzine 14.9000714285714 hours (A075_A_Yeast-2_01-1)

description: 14.9000714285714 hours following inoculation


title: T47D_MTVL_AG490_R5020_6h_ReplicateA

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were pre-hybridized  in prewarmed 5X SCC, 0.1% SDS and 0.1% BSA at 42ºC for 45 min, rinsed under milliQ water and spun dry using a centrifuge for 5 min at 1500 rpm. Labeled samples were redissolved in 42ºC prewarmed 12 microliter of Hybridization buffer A (50% formamide, 6X SSC, 0.5% SDS and 5X Denhardt’s applied to a glass coverslip, covered with the spotted glass slide. Arrays were incubated in a corning hybridization chamber for 18 hr at 42ºC in a humid environment (In Slide Out oven, Boeckel). Arrays were washed at room temperature using an orbital shaker for 10 min with a high stringency wash buffer (0.1X SSC, 0.1% SDS), twice for 10 min with a low stringency wash buffer (0.1X SSC), rinsed for 5 min in milliQ water and spun dry for 5 min at 1500 rpm using a centrifuge.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing:
Raw data were processed using LIMMA, a microarray statistical analysis package of Bioconductor (http://www.bioconductor.org, Dudoit et al. 2003) that runs in the R programming environment (Gentleman et al. 2004,  Wettenhall et al. 2004). Gene intensities were locally background subtracted using Normexp, taking mean of channel intensities and the median of background intensities. Spots with intensities smaller than two times the local background in both dye filter channels (Cy3 or Cy5), as well as control spots, were excluded from normalization and are left blank.
Expression ratios were calculated as R/G, where R and G are the red and green color intensities, respectively. Ratios were transformed to logarithm base 2. Locally weighted linear regression (Lowess) analysis was used as a normalization method. We applied a local Lowess to each print-tip group or subgrid to correct any systematic spatial variation on the array, between spotting needles or variability on slide surface, by adjusting the mean of the Log2Ratio values in each subgrid to zero. We adjust the variance across all subgrids with a scaling factor for normalization, applying a smoothing factor f=0.2 to each subgrid in order to homogenize the variance of the log2Ratio within each print-tip. Normalized Log2Ratios across all arrays were scaled so that every array has the same median intensity and same absolute standard deviation, in order to give the same weight to every gene on the array.
After normalization, replicated spots of the same gene were average.

source_name: T47D-MTVL human breast cancer cell line

label_protocol:
Linear T7-oligodT mediated mRNA amplification (described by Van Gelder et al. 1990 and Eberwine et al. 1992)
3 microgram of the in vitro amplified aRNA samples were reverse transcribed with 4 microliter 5X first strand buffer, 2 microliter 0.1 M DTT, 0.4 microliter low dT-dNTP mix (25 mM dA, dC, dG, 10 mM dT), 1.5 microliter Superscript II (Invitrogen) and 2 microliter 25 mM Cy3-dUTP or Cy5-dUTP (Amersham). The reaction was incubated at 42ºC for 2 hr, chilled on ice and quick spun to bring down condensation. To stop the reaction 1 microliter 1 M NaOH/20 mM EDTA, was added followed by 80 microliter MilliQ-H20 and 10 microliter 3M NaOAc pH 5. Labeled samples were purified with Quiaquick PCR purification columns (Qiagen) and eluted twice with 50 microliter EB (10 mM Tris pH 8.5). Labeling efficiency was calculated by quantification with Nanodrop, obtaining between 50-80 pmol/microliter of Cy3 or Cy5 labeled probes. Labeled samples for the same array were combined, 1 microliter 1 microgram/microliter Human Cot DNA (Invitrogen) was added, and the labeled mix was desiccated by Speed-Vac centrifugation.

growth_protocol: T47D-MTVL cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100 microg/ml streptomycin.

extract_protocol:
RNeasy mini kit (QUIAGEN, cat.no. 74104)
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol:
T47D-MTVL cells were serum-starved for 48 h and then were pre-treated with the JAK/STAT pathway inhibitor AG490 (Calbiochem) 1 h prior treatment with the progestin R5020 (PerkinElmer Life Sciences) 10 nM for 6 h.
In more detail, cells were plated in medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 24 h later medium was replaced by fresh medium without serum. After 2 days in serum-free conditions, cells were treated with progestin for 6 h at 37ºC. AG490 (50 microMolar) was added 1 h before hormone treatment.

tag: Human breast cancer cell line T47D modified to contain one stably integrated copy of Luciferase reporter gene driven by the Mouse Mammary Tumor Virus promoter, named T47D-MTVL (Truss, M., J. Bartsch, A. Schelbert, R. J. Hache, and M. Beato. 1995). Hormone induces binding of receptors and transcription factors to a rearranged nucleosome on the MMTV promoter in vivo. EMBO J. 14:1737-1751).

source_name: Universal human reference RNA Stratagene® (cat.no.740000)

tag: pool of ten different tumor cell lines from different human tissues Stratagene® (cat.no.740000)


title: T47D_MTVL_R5020_6h_ReplicateB

treatment_protocol: T47D-MTVL cells were plated in medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 24 h later medium was replaced by fresh medium without serum. After 2 days in serum-free conditions, cells were treated with the progestin R5020 (PerkinElmer Life Sciences) 10 nM for 6 h at 37ºC.


title: T47D_MTVL_R5020_6h_ReplicateA


title: IFO0233 Control 14.233 hours (A065_A_Yeast-2_01-1)

description: 14.233 hours following inoculation

source_name: IFO0233, Control


title: IFO0233 Control 14.367 hours (A067_A_Yeast-2_01-1)

description: 14.367 hours following inoculation


title: IFO0233 Control 13.833 hours (A059_A_Yeast-2_01-1)

description: 13.833 hours following inoculation


title: IFO0233 Control 14.3 hours (A066_A_Yeast-2_01-1)

description: 14.3 hours following inoculation

hyb_protocol: Our approach using the S98 chip and early experiments with the S2 chip are to use the Bacillus subtilis poly(A) standards spiked into the cell pellet at the beginning of the RNA isolation as a measure of both recovery and variations in amplification. This approach, although imperfect, gives at least some assurance that variations in total transcript levels for all transcripts in any one chip are not due to differences in recovery. It also overcomes the inherent bias in adjusting the input RNA to a constant level throughout the procedure.


title: T47D_MTVL_AG490_EtOH_6h_ReplicateB

hyb_protocol: Slides were pre-hybridized in prewarmed 5X SCC, 0.1% SDS and 0.1% BSA at 42ºC for 45 min, rinsed under milliQ water and spun dry using a centrifuge for 5 min at 1500 rpm. Labeled samples were redissolved in 42ºC prewarmed 12 microliter of Hybridization buffer A (50% formamide, 6X SSC, 0.5% SDS and 5X Denhardt’s applied to a glass coverslip, covered with the spotted glass slide. Arrays were incubated in a corning hybridization chamber for 18 hr at 42ºC in a humid environment (In Slide Out oven, Boeckel). Arrays were washed at room temperature using an orbital shaker for 10 min with a high stringency wash buffer (0.1X SSC, 0.1% SDS), twice for 10 min with a low stringency wash buffer (0.1X SSC), rinsed for 5 min in milliQ water and spun dry for 5 min at 1500 rpm using a centrifuge.

data_processing:
Raw data were processed using LIMMA, a microarray statistical analysis package of Bioconductor (http://www.bioconductor.org, Dudoit et al. 2003) that runs in the R programming environment (Gentleman et al. 2004, Wettenhall et al. 2004). Gene intensities were locally background subtracted using Normexp, taking mean of channel intensities and the median of background intensities. Spots with intensities smaller than two times the local background in both dye filter channels (Cy3 or Cy5), as well as control spots, were excluded from normalization and are left blank.
Expression ratios were calculated as R/G, where R and G are the red and green color intensities, respectively. Ratios were transformed to logarithm base 2. Locally weighted linear regression (Lowess) analysis was used as a normalization method. We applied a local Lowess to each print-tip group or subgrid to correct any systematic spatial variation on the array, between spotting needles or variability on slide surface, by adjusting the mean of the Log2Ratio values in each subgrid to zero. We adjust the variance across all subgrids with a scaling factor for normalization, applying a smoothing factor f=0.2 to each subgrid in order to homogenize the variance of the log2Ratio within each print-tip. Normalized Log2Ratios across all arrays were scaled so that every array has the same median intensity and same absolute standard deviation, in order to give the same weight to every gene on the array.
After normalization, replicated spots of the same gene were average.

treatment_protocol:
T47D-MTVL cells were serum-starved for 48 h and then were pre-treated with the JAK/STAT pathway inhibitor AG490 (Calbiochem) 1 h prior treatment with ethanol or the progestin R5020 (PerkinElmer Life Sciences) 10 nM for 6 h.
In more detail, cells were plated in medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 24 h later medium was replaced by fresh medium without serum. After 2 days in serum-free conditions, cells were treated with ethanol for 6 h at 37ºC. AG490 (50 microMolar) was added 1 h before hormone treatment.


title: IFO0233 Control 14.167 hours (A064_A_Yeast-2_01-1)

description: 14.167 hours following inoculation


title: T47D_MTVL_AG490_R5020_6h_ReplicateB


title: T47D_MTVL_EtOH_6h_ReplicateB

treatment_protocol: T47D-MTVL cells were plated in medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS (DCC/FBS), and 24 h later medium was replaced by fresh medium without serum. After 2 days in serum-free conditions, cells were treated with ethanol for 6 h at 37ºC.


title: IFO0233 Phenelzine 14.5666785714286 hours (A070_A_Yeast-2_01-1)

description: 14.5666785714286 hours following inoculation


title: IFO0233 Phenelzine 16.9671071428572 hours (A107_A_Yeast-2_01-1)

description: 16.9671071428572 hours following inoculation


title: IFO0233 Control 14.433 hours (A068_A_Yeast-2_01-1)

description: 14.433 hours following inoculation


title: IFO0233 Control 13.967 hours (A061_A_Yeast-2_01-1)

description: 13.967 hours following inoculation


title: IFO0233 Control 14.1 hours (A063_A_Yeast-2_01-1)

description: 14.1 hours following inoculation

hyb_protocol: Standard Affymetrix Protocol.


title: IFO0233 Control 14.5 hours (A069_A_Yeast-2_01-1)

description: 14.5 hours following inoculation

hyb_protocol: Standard Affymetrix protcol


title: IFO0233 Control 14.033 hours (A062_A_Yeast-2_01-1)

description: 14.033 hours following inoculation


title: Cultured ovary postnatal day 0 replicate 2

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Chip ID=phil-cultured-U34A-022703.  RNA from zero-day old rat ovaries cultured 7 days.

hyb_protocol: standard Affymetrix procedure

scan_protocol: chips were scanned using Agilent GeneArray Scanner G2500A

data_processing: Auto-scale ON (1-1000).  Scaling = all probe sets.  The microarray image data were converted to numerical data with GeneChip Operating Software using a scaling factor of 125, and then imported into the GeneSpring program (Agilent Technologies, Palo Alto, CA).

organism: Rattus norvegicus

source_name: 0-day rat ovary cultured 7 days

label_protocol: standard Affymetrix procedures

extract_protocol: About 20 ovaries with the same treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturers instructions (Sigma, St. Louis, MO).  Two independent RNA samples were analysed for each treatment group.

treatment_protocol: Female day P0 rat pups were euthanized and rat ovaries were removed according to IACUC-approved animal use protocols. Whole ovaries were cultured as previously described (Nilsson, Parrott et al. 2001) on floating filters (0.4 um Millicell-CM, Millipore, Bedford, MD) in 0.5 ml Dulbecco's Modified Eagle's Medium (DMEM)-Ham's F-12 medium (1:1, vol/vol) containing 0.1 % bovine serum albumin (BSA, Sigma, St. Louis, MO), 0.1% Albumax (Gibco BRL, Gaithersburg, MD), 27.5 ?g/ml transferrin, 200 ng/ml insulin (human recombinant, Sigma), and 0.05 mg/ml L-ascorbic acid (Sigma) in a 4-well culture plate (Nunc plate, Applied Scientific, South San Francisco, CA). Medium was supplemented with penicillin and streptomycin to prevent bacterial contamination.

tag: ovaries dissected from 0-day old Sprague-Dawley rats and cleaned of ovarian bursaand cultured for 7 days


title: IFO0233 Phenelzine 16.9004285714286 hours (A106_A_Yeast-2_02-1)

description: 16.9004285714286 hours following inoculation


title: T47D_MTVL_EtOH_6h_ReplicateA


title: IFO0233 Control 13.9 hours (A060_A_Yeast-2_01-1)

description: 13.9 hours following inoculation


title: T47D_MTVL_AG490_EtOH_6h_ReplicateA


title: IFO0233 Phenelzine 16.83375 hours (A105_A_Yeast-2_01-1)

description: 16.83375 hours following inoculation


title: IFO0233 Phenelzine 16.7670714285714 hours (A104_A_Yeast-2_01-1)

description: 16.7670714285714 hours following inoculation


title: Ovary postnatal day 0 replicate 2

description: Chip ID=Phil-PO-RGu34A-072403.  RNA from zero-day old rat ovaries.

source_name: 0-day rat ovary

treatment_protocol: Female day P0 rat pups were euthanized and rat ovaries were removed according to IACUC-approved animal use protocols.

tag: ovaries dissected from 0-day old Sprague-Dawley rats and cleaned of ovarian bursa.


title: Ovary postnatal day 4 replicate 2

description: Chip ID=Phil-P4-RGu34A-072403.  RNA from four-day old rat ovaries.

source_name: P4-day rat ovary

treatment_protocol: Female day P4 rat pups were euthanized and rat ovaries were removed according to IACUC-approved animal use protocols.

tag: ovaries dissected from P4-day old Sprague-Dawley rats and cleaned of ovarian bursa.


title: IFO0233 Phenelzine 16.7003928571429 hours (A103_A_Yeast-2_01-1)

description: 16.7003928571429 hours following inoculation


title: Cultured ovary postnatal day 0 replicate 1

description: Chip ID=Phil-Cult.Ovary-RGu34A-082603.  RNA from zero-day old rat ovaries cultured 7 days.

tag: ovaries dissected from 0-day old Sprague-Dawley rats and cleaned of ovarian bursa and cultured for 7 days


title: 22 weeks after first infliximab injection (01-22w-70)

status: Public on Oct 10 2007

city: Kawagoe-shi, Saitama

first: Tsutomu

last: Takeuchi

address: 1981 Tsujido-machi, Kamoda

department: Department of Internal Medicine

country: Japan

institute: Saitama Medical University

description: no additional information

hyb_protocol: Competitive hybridization of Cy3-labeled reference and Cy5-labeled sample cDNA on the microarray was carried out according to Brown and Yanofsky[10] with chamber systems (Agilent Technologies, Palo Alto, CA).

scan_protocol: Slides were scanned five times with five different power ranges using ScanArray 5000 (PerkinElmer, Boston, MA).

data_processing: The data was converted from tif image data to signal using ImaGene software (BioDiscovery, El Segundo, CA) for further statistical analysis.  Five file data of each four spot data corresponding each gene were merged to establish the single representative data for each gene (Patent pending: PCT/JP03/06677).

label_protocol: Then total RNA (1 mg) from patients was transcribed and amplified to produce amplified sample RNA (aRNA) using the MessageAmp aRNA kit according to the manufacturer’s instructions.  Next, an external control RNA mixture (LD, GP, and RL) was added to both the sample and reference aRNA (9 mg each).  These mixed sample and reference aRNA were labeled using SuperScript II kit (Invitrogen, Carlsbad, CA) with random hexamer (TaKaRa, Kyoto, Japan) with Cy3-dUTP and Cy5-dUTP (PerkinElmer, Boston, MA), respectively.

extract_protocol: The blood (2.5 ml x 2 tubes) was drawn using PAXgene tubes (QIAGEN, Hilden, Germany).  The total RNA extraction and purification were carried out according to the manufacturer’s protocol.

tag: Gender

value: female, Age:61 years, ACR score at 14 weeks after first infliximab injection:70%

source_name: Reference RNA

tag: healthy volunteers


title: 22 weeks after first infliximab injection (04-22w-70)

description: no additional information

value: female, Age:51 years, ACR score at 14 weeks after first infliximab injection:70%


title: Ovary postnatal day 0 replicate 1

description: Chip ID=phil_P0_U34A_102502.  RNA from zero-day old rat ovaries.


title: 22 weeks after first infliximab injection (11-22w-50)

description: no additional information

value: female, Age:60 years, ACR score at 14 weeks after first infliximab injection:50%


title: 22 weeks after first infliximab injection (12-22w-50)

description: no additional information

value: female, Age:52 years, ACR score at 14 weeks after first infliximab injection:50%


title: 22 weeks after first infliximab injection (13-22w-20)

description: no additional information

value: female, Age:45 years, ACR score at 14 weeks after first infliximab injection:20%


title: 22 weeks after first infliximab injection (08-22w-50)

description: no additional information


title: 22 weeks after first infliximab injection (09-22w-50)

description: no additional information

value: female, Age:58 years, ACR score at 14 weeks after first infliximab injection:50%


title: 22 weeks after first infliximab injection (10-22w-20)

description: no additional information

value: female, Age:66 years, ACR score at 14 weeks after first infliximab injection:20%


title: 22 weeks after first infliximab injection (03-22w-50)

description: no additional information

value: female, Age:51 years, ACR score at 14 weeks after first infliximab injection:50%


title: 22 weeks after first infliximab injection (16-22w-50)

description: no additional information

value: male, Age:62 years, ACR score at 14 weeks after first infliximab injection:50%


title: 22 weeks after first infliximab injection (15-22w-20)

description: no additional information

value: male, Age:42 years, ACR score at 14 weeks after first infliximab injection:20%


title: Ovary postnatal day 4 replicate 1

description: Chip ID=phil_P4_U34A_102502.  RNA from four-day old rat ovaries.


title: 22 weeks after first infliximab injection (05-22w-20)

description: no additional information

value: male, Age:34 years, ACR score at 14 weeks after first infliximab injection:20%


title: 22 weeks after first infliximab injection (06-22w-20)

description: no additional information

value: female, Age:51 years, ACR score at 14 weeks after first infliximab injection:20%


title: 22 weeks after first infliximab injection (18-22w-0)

description: no additional information

value: female, Age:53 years, ACR score at 14 weeks after first infliximab injection:0%


title: 22 weeks after first infliximab injection (07-22w-20)

description: no additional information

value: female, Age:60 years, ACR score at 14 weeks after first infliximab injection:20%


title: 14 weeks after first infliximab injection (01-14w-70)

description: no additional information


title: 14 weeks after first infliximab injection (16-14w-50)

description: no additional information


title: 22 weeks after first infliximab injection (14-22w-0)

description: no additional information

value: female, Age:60 years, ACR score at 14 weeks after first infliximab injection:0%


title: 22 weeks after first infliximab injection (02-22w-0)

description: no additional information

value: female, Age:63 years, ACR score at 14 weeks after first infliximab injection:0%


title: 22 weeks after first infliximab injection (17-22w-0)

description: no additional information

value: female, Age:52 years, ACR score at 14 weeks after first infliximab injection:0%


title: 14 weeks after first infliximab injection (04-14w-70)

description: no additional information


title: 14 weeks after first infliximab injection (12-14w-50)

description: no additional information


title: 14 weeks after first infliximab injection (09-14w-50)

description: no additional information


title: 14 weeks after first infliximab injection (03-14w-50)

description: no additional information


title: 14 weeks after first infliximab injection (11-14w-50)

description: no additional information


title: 14 weeks after first infliximab injection (10-14w-20)

description: no additional information


title: 14 weeks after first infliximab injection (13-14w-20)

description: no additional information


title: 14 weeks after first infliximab injection (15-14w-20)

description: no additional information


title: 14 weeks after first infliximab injection (08-14w-50)

description: no additional information


title: 14 weeks after first infliximab injection (07-14w-20)

description: no additional information


title: 14 weeks after first infliximab injection (06-14w-20)

description: no additional information


title: 14 weeks after first infliximab injection (05-14w-20)

description: no additional information


title: sDf135_hT2

status: Public on Oct 11 2007

city: Vancouver

first: Martin

middle: Richard

last: Jones

state: BC

address: Room 419 NCE Building 2125 East Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

description: no additional information

scan_protocol: The scanner used was an Axon Scanner (Model # 4000B) .  see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Segmentation analysis based on the DNACopy package  Segmentation GFF file  Genome annotation GFF file

organism: Caenorhabditis elegans

source_name: whole animal, mixed stage

label_protocol: Cy3 and Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. Mutant DNA samples were labelled with Cy3 and the wild type DNA sample (VC196) was labelled with Cy5. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

growth_protocol: Nematodes were grown at 200C on 150mm NGM agar plates seeded with Escherichia coli strain OP50.

extract_protocol: Animals were harvested and treated with a standard protienase K digestion. Samples were extracted using a standard phenol/chloroform protocol, treated with RNAse A for 1 hour and subjected to a second round of phenol/chloroform extraction. DNA was resuspended in water and quantified.


title: 2 weeks after first infliximab injection (04-02w-70)

description: no additional information


title: 14 weeks after first infliximab injection (14-14w-0)

description: no additional information


title: 14 weeks after first infliximab injection (17-14w-0)

description: no additional information


title: Mdr2-KO heterozygote, 16 month old mouse 1

city: Ramat-Gan

first: Mark

last: Katzenellenbogen

address: Ramat-Gan 52900, Israel

department: THE FACULTY OF LIFE SCIENCE, BIOINFORMATICS AND MICROARRAY UNIT

country: Israel

institute: Bar Ilan University

description: According to paper: Molecular mechanisms of liver carcinogenesis in the Mdr2-knockout mice

hyb_protocol: The sample hybridization was performed according the Affymetrix protocols: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: The stained array was scanned on the Affymetrix scanner, the GCOS (Gene Operating System) generated the numerical data from the scanned intensities using the MAS 5 software (MicroArray suite 5.0; Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Mdr2-KO heterozygous mouse, 16 month old mouse, liver tissue sample

label_protocol: The sample labeling was performed according the Affymetrix protocols: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

extract_protocol: Total RNA was isolated from frozen liver tissues with Trizol reagent (Invitrogen, Carlsbad, CA) as described by the manufacturer

tag: Genotype

value: Mdr2-KO heterozygous mouse

tag: Age

value: 16 month


title: Mdr2-KO, 16 month old mouse 6 tumor 1

source_name: Mdr2-KO mouse, 16 month old mouse, liver tumor 1

value: Mdr2-KO homozygous mouse


title: sDp8_eT1

description: no additional information

hyb_protocol: see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.


title: Mdr2-KO heterozygote, 16 month old mouse 3


title: Mdr2-KO, 16 month old mouse 5 tumor 2

source_name: Mdr2-KO mouse, 16 month old mouse, liver tumor 2


title: sDf128_hT2

description: no additional information


title: sDf130_hT2

description: no additional information


title: Mdr2-KO heterozygote, 16 month old mouse2


title: 14 weeks after first infliximab injection (02-14w-0)

description: no additional information


title: Mdr2-KO, 16 month old mouse 6 tumor 2


title: Mdr2-KO, 16 month old mouse 5 tumor 1


title: nDf20_eT1

description: no additional information


title: sDf127_hT2

description: no additional information


title: sDf125_hT2

description: no additional information


title: 2 weeks after first infliximab injection (16-02w-50)

description: no additional information


title: 2 weeks after first infliximab injection (01-02w-70)

description: no additional information

value: female, Age:61 years, ACR score at 14 weeks after first infliximab injection:70%


title: 2 weeks after first infliximab injection (12-02w-50)

description: no additional information

value: female, Age:52 years, ACR score at 14 weeks after first infliximab injection:50%


title: 14 weeks after first infliximab injection (18-14w-0)

description: no additional information


title: HEEC_individual control_replicate 5

city: Uppsala

first: Carolina

last: Bredhult

address: Uppsala University Hospital

department: Women's and Children's Health

country: Sweden

institute: Uppsala University

description: Biological replicate 5 of 5. Control HEEC vs pooled control HEEC from replicate 1-5, harvested after passage 2.

hyb_protocol: Pre-hybridization buffer (5 x sodium chloride sodium citrate [SSC, VWR International AB, Stockholm, Sweden], 5 x Denhardt’s solution [Sigma-Aldrich Sweden AB, Stockholm, Sweden], 0.02 µg/µl tRNA [Invitrogen AB, Lidingö, Sweden], 0.5% sodiumdodecylsulfate [SDS, VWR International AB, Stockholm, Sweden] and 50% formamide [Sigma-Aldrich Sweden AB, Stockholm, Sweden]) was applied to each array under a hybrislip (22 x 60 mm, Sigma-Aldrich Sweden AB, Stockholm, Sweden). Incubation was performed in an Hybridization Cassette ArrayIt™ (TeleChem International Inc ArrayIt, Sunnyvale, CA, USA) at 42°C for 45 min at 100% humidity in a Heating Circulator model 8201 (PolyScience, Niles, Il, USA). Each array was then transferred to a 50 ml centrifugation tube containing double distilled water. The arrays were washed five times by repeatedly turning the tubes upside down for 30 seconds each time. Hybridization and post-hybridization washes of the slides were performed using the Pronto! Hybridization Kit (Corning Life Sciences, Noricon AB, Helsingborg, Sweden). The Hybridization Cassette ArrayIt™ and Erie Scientific Lifterslip (25 x 60 mm, Histolab, Västra Frölunda, Sweden) were used for hybridization of the slides at 42°C for 18-20 hours. After hybridization, the slides were washed in the three wash buffers described in the Pronto! Hybridization Kit.

scan_protocol: The slides were scanned in a ScanArray Express HT microarray scanner ([Packard BioScience] Perkin Elmer Life Sciences Inc, Boston, MA, USA). The scanning was performed at two different voltage values for the photo multiplier tube to get a wide dynamic range of signals (high or low). The laser value default was 99%. The tiff files from the scanned arrays were gridded using the software Spotreader v 1.3.1 (Niles Scientific, Portola Valley, CA, USA).

data_processing: The BioArray Software Environment BASE (Saal et al., 2002) and the Linnaeus Center of Bioinformatics Data Warehouse (LCB-DWH) (Ameur et al., 2006) were used for microarray data storage and analysis. Data was normalized using local background subtraction and within arrays using the print-tip lowess method (Yang et al., 2002).

source_name: Primary culture HEEC, obtained in proliferative phase, individual 5, control exposed 24 h

label_protocol: For each treatment and biological replicate, 500 ng isolated RNA was amplified and labelled using the Low RNA Input Linear Amplification Kit PLUS, Two-colour (Agilent Technologies Sweden AB, Kista, Sweden) and then purified using the RNeasy MinElute Cleanup Kit (Qiagen AB, Solna, Sweden). The amplification and labelling reactions were performed using the polymerase chain reaction (PCR) instrument model PTC-100 (MJ Research Inc, Waltham, MA, USA). Dye swaps were performed between the individuals to avoid dye bias between RNA from o,p’-DDT treated and untreated HEEC, and for the individual controls and the control pool. After the labelling reaction, the Nanodrop ND-1000 Spectrophotometer was used to measure the incorporation of Cy dye.

growth_protocol: HEEC were kept in 25 cm2 culture flasks (Fischer Scientific GTF, Västra Frölunda, Sweden) and grown in Microvascular Endothelial Cell Medium-2 (EGM™-2MV Bulletkit®; In vitro Sweden AB, Stockholm, Sweden) at 37ºC in an atmosphere of 5% CO2 in humidified air. Four culture flask per treatment alternative and culture (biological replicate) were used.

extract_protocol: Total RNA extracted using RNeasy Mini Kit spin protocol (Qiagen AB, Solna, Sweden) and QiaShredder homogenizers (Qiagen AB, Solna, Sweden) according to manufacturer's instructions.

treatment_protocol: At subconfluency in passage 2, HEEC in four culture flasks per culture (biological replicate) were exposed to 50 µM o,p'-DDT for 24h. Control HEEC in four culture flasks per culture were exposed to fresh culture medium containing 0.21% DMSO. As an additional control, cells in eight culture flasks per culture were also exposed to fresh culture medium containing 0.21% DMSO. Of these eight flasks, HEEC in four culture flasks per culture (biological replicate) were used for a common control pool av control samples from all five biological replicates.

tag: Female of fertile age

tag: Tissue

value: endometrium

tag: Cells

value: endothelial cells

tag: Menstrual cycle phase

value: proliferative

source_name: Primary culture HEEC, obtained in proliferative phase, individual 1-5, pooled control exposed 24 h


title: 2 weeks after first infliximab injection (11-02w-50)

description: no additional information

value: female, Age:60 years, ACR score at 14 weeks after first infliximab injection:50%


title: 2 weeks after first infliximab injection (09-02w-50)

description: no additional information

value: female, Age:58 years, ACR score at 14 weeks after first infliximab injection:50%


title: HEEC_individual control_replicate 4

description: Biological replicate 4 of 5. Control HEEC vs pooled control HEEC from replicate 1-5, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 4, control exposed 24 h


title: 2 weeks after first infliximab injection (08-02w-50)

description: no additional information


title: 2 weeks after first infliximab injection (03-02w-50)

description: no additional information

value: female, Age:51 years, ACR score at 14 weeks after first infliximab injection:50%


title: HEEC_individual control_replicate 3

description: Biological replicate 3 of 5. Control HEEC vs pooled control HEEC from replicate 1-5, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 3, control exposed 24 h


title: Mdr2-KO, 16 month old mouse 4 tumor

source_name: Mdr2-KO mouse, 16 month old mouse, liver tumor


title: HEEC_individual control_replicate 2

description: Biological replicate 2 of 5. Control HEEC vs pooled control HEEC from replicate 1-5, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 2, control exposed 24 h


title: Mdr2-KO, 16 month old mouse 3 tumor


title: Mdr2-KO, 16 month old mouse 6

source_name: Mdr2-KO mouse, 16 month old mouse, liver non-tumorous tissue sample


title: 2 weeks after first infliximab injection (06-02w-20)

description: no additional information

value: female, Age:51 years, ACR score at 14 weeks after first infliximab injection:20%


title: 2 weeks after first infliximab injection (10-02w-20)

description: no additional information

value: female, Age:66 years, ACR score at 14 weeks after first infliximab injection:20%


title: 2 weeks after first infliximab injection (15-02w-20)

description: no additional information

value: male, Age:42 years, ACR score at 14 weeks after first infliximab injection:20%


title: 2 weeks after first infliximab injection (05-02w-20)

description: no additional information

value: male, Age:34 years, ACR score at 14 weeks after first infliximab injection:20%


title: 2 weeks after first infliximab injection (07-02w-20)

description: no additional information

value: female, Age:60 years, ACR score at 14 weeks after first infliximab injection:20%


title: HEEC_individual control_replicate 1

description: Biological replicate 1 of 5. Control HEEC vs pooled control HEEC from replicate 1-5, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 1, control exposed 24 h


title: Mdr2-KO, 16 month old mouse 4


title: 2 weeks after first infliximab injection (17-02w-0)

description: no additional information

value: female, Age:52 years, ACR score at 14 weeks after first infliximab injection:0%


title: 2 weeks after first infliximab injection (18-02w-0)

description: no additional information

value: female, Age:53 years, ACR score at 14 weeks after first infliximab injection:0%


title: HEEC_o,p'-DDT-exposed_replicate 5

description: Biological replicate 5 of 5. o,p'-DDT exposed HEEC vs control HEEC, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 5, o,p'-DDT exposed 24 h


title: 2 weeks after first infliximab injection (14-02w-0)

description: no additional information

value: female, Age:60 years, ACR score at 14 weeks after first infliximab injection:0%


title: HEEC_o,p'-DDT-exposed_replicate 3

description: Biological replicate 3 of 5. o,p'-DDT exposed HEEC vs control HEEC, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 3, o,p'-DDT exposed 24 h


title: 2 weeks after first infliximab injection (13-02w-20)

description: no additional information

value: female, Age:45 years, ACR score at 14 weeks after first infliximab injection:20%


title: HEEC_o,p'-DDT-exposed_replicate 4

description: Biological replicate 4 of 5. o,p'-DDT exposed HEEC vs control HEEC, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 4, o,p'-DDT exposed 24 h


title: Mdr2-KO, 16 month old mouse 3

value: Mdr2-KO homozygous mouse

value: 16 month


title: 2 weeks after first infliximab injection (02-02w-0)

description: no additional information

value: female, Age:63 years, ACR score at 14 weeks after first infliximab injection:0%


title: Baseline (04-0-70)

description: no additional information

source_name: Pre-treated

value: female, Age:51 years, ACR score at 14 weeks after first infliximab injection:70%


title: Baseline (01-0-70)

description: no additional information

value: female, Age:61 years, ACR score at 14 weeks after first infliximab injection:70%

source_name: Reference RNA


title: Baseline (16-0-50)

description: no additional information

value: male, Age:62 years, ACR score at 14 weeks after first infliximab injection:50%


title: Mdr2-KO, 16 month old mouse 5


title: Mdr2-KO, 16 month old mouse 2


title: HEEC_o,p'-DDT-exposed_replicate 2

description: Biological replicate 2 of 5. o,p'-DDT exposed HEEC vs control HEEC, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 2, o,p'-DDT exposed 24 h

value: endometrium

value: endothelial cells

value: proliferative


title: Baseline (11-0-50)

description: no additional information

value: female, Age:60 years, ACR score at 14 weeks after first infliximab injection:50%


title: Baseline (12-0-50)

description: no additional information

value: female, Age:52 years, ACR score at 14 weeks after first infliximab injection:50%


title: Mdr2-KO, 16 month old mouse 1


title: HEEC_o,p'-DDT-exposed_replicate 1

description: Biological replicate 1 of 5. o,p'-DDT exposed HEEC vs control HEEC, harvested after passage 2.

source_name: Primary culture HEEC, obtained in proliferative phase, individual 1, o,p'-DDT exposed 24 h


title: Baseline (09-0-50)

description: no additional information

value: female, Age:58 years, ACR score at 14 weeks after first infliximab injection:50%


title: Baseline (08-0-50)

description: no additional information


title: Baseline (06-0-20)

description: no additional information

value: female, Age:51 years, ACR score at 14 weeks after first infliximab injection:20%


title: Baseline (07-0-20)

description: no additional information

value: female, Age:60 years, ACR score at 14 weeks after first infliximab injection:20%


title: Baseline (15-0-20)

description: no additional information

value: male, Age:42 years, ACR score at 14 weeks after first infliximab injection:20%


title: Baseline (03-0-50)

description: no additional information

value: female, Age:51 years, ACR score at 14 weeks after first infliximab injection:50%


title: Baseline (10-0-20)

description: no additional information

value: female, Age:66 years, ACR score at 14 weeks after first infliximab injection:20%


title: Baseline (13-0-20)

description: no additional information

value: female, Age:45 years, ACR score at 14 weeks after first infliximab injection:20%


title: Baseline (17-0-0)

description: no additional information

value: female, Age:52 years, ACR score at 14 weeks after first infliximab injection:0%


title: Baseline (05-0-20)

description: no additional information

value: male, Age:34 years, ACR score at 14 weeks after first infliximab injection:20%


title: Baseline (18-0-0)

description: no additional information

value: female, Age:53 years, ACR score at 14 weeks after first infliximab injection:0%


title: Baseline (02-0-0)

description: no additional information

value: female, Age:63 years, ACR score at 14 weeks after first infliximab injection:0%


title: Baseline (14-0-0)

description: no additional information

value: female, Age:60 years, ACR score at 14 weeks after first infliximab injection:0%


title: DC_15_Ab6hr

status: Public on Oct 06 2007

city: Branford

first: James

middle: Andrew

last: Whitney

state: CT

address: 36 East Industrial Road

institute: CGI Pharmaceuticals Inc.

description: The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response.  We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors.  These events were triggered at least in part by activation of the beta-catenin pathway.  However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.

hyb_protocol: Arrays were equilibrated with hybridization cocktail (including hybridization controls, as well as fragmented sample cRNA) and incubated with Human Genome U95Av2 arrays (Affymetrix, Santa Clara, CA) in an Affymetrix Hybridization Oven 640 for 16 hours, at 45 C, per manufacturer's protocol.

scan_protocol: Hybridized arrays were washed, stained with Streptavidin Phycoerythrin (SAPE) using an Affymetrix Fluidics Station 400 and scanned with a GeneArray Scanner GS2500, per manufacturer's instructions.

data_processing: Raw data correction and normalization was performed using Affymetrix Microarray Suite 5.0 for background and PM/MM corrections.

source_name: dendritic cells, cluster disruption and Anti E-cadherin, 6 hours

label_protocol: Biotin-labeled cRNA was generated using the Enzo BioArray RNA transcript labeling kit from Affymetrix, followed by sample cleanup using the GeneChip Sample Cleanup Module.

growth_protocol: CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies.  For maturation, X-VIVO + 1x cytokines was supplemented with additional bacterial (DH5alpha) or LPS (250 ng/ml) or by physical disruption of the clusters with repetitive pipeting (CD). For antibody blocking experiment, 5 ug/ml of anti-human E-cadherin antibody was added in the media before the clusters were disrupted.

extract_protocol: Total RNA from human CD34+ DCs was isolated using RNeasy kits (Qiagen), followed by cDNA synthesis (5 mg RNA per sample) using the SuperScript system (Invitrogen), per manufacturer's instructions.  Labeled cRNA was then fragmented according to Affymetrix instructions, and stored at -20 C until ready to hybridize.

treatment_protocol: Clusters of Langerhans cells were treated with 5 ug/ml of anti-human E-cadherin antibody prior to disruption with repetitive pipeting.  Samples were harvested 6 hours later for microarray analysis.

tag: Human Langerhans cells were produced from CD34+ stem cells cultured as described in the Growth Protocol section.


title: DC_17_Ab36hr

source_name: dendritic cells, cluster disruption and Anti E-cadherin, 36 hours

treatment_protocol: Clusters of Langerhans cells were treated with 5 ug/ml of anti-human E-cadherin antibody prior to disruption with repetitive pipeting.  Samples were harvested 36 hours later for microarray analysis.


title: DC_14_B36hr

source_name: dendritic cells, stimulated by bacteria, 36 hours

treatment_protocol: Clusters of Langerhans cells, grown as described in the Growth Protocol section,  were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml).  For this sample, cells were harvested for microarray analysis after 36 hours of treatment.


title: DC_11_B6hr

source_name: dendritic cells, stimulated by bacteria, 6 hours

treatment_protocol: Clusters of Langerhans cells, grown as described in the Growth Protocol section,  were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml).  For this sample, cells were harvested for microarray analysis after 6 hours of treatment.


title: DC_13_B18hr

source_name: dendritic cells, stimulated by bacteria, 18 hours

treatment_protocol: Clusters of Langerhans cells, grown as described in the Growth Protocol section,  were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml).  For this sample, cells were harvested for microarray analysis after 18 hours of treatment.


title: DC_16_Ab12hr

source_name: dendritic cells, cluster disruption and Anti E-cadherin, 12 hours

treatment_protocol: Clusters of Langerhans cells were treated with 5 ug/ml of anti-human E-cadherin antibody prior to disruption with repetitive pipeting.  Samples were harvested 12 hours later for microarray analysis.


title: DC_12_B12hr

source_name: dendritic cells, stimulated by bacteria, 12 hours

treatment_protocol: Clusters of Langerhans cells, grown as described in the Growth Protocol section,  were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml).  For this sample, cells were harvested for microarray analysis after 12 hours of treatment.


title: DC_10_B3hr

source_name: dendritic cells, stimulated by bacteria, 3 hours

treatment_protocol: Clusters of Langerhans cells, grown as described in the Growth Protocol section,  were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml).  For this sample, cells were harvested for microarray analysis after 3 hours of treatment.


title: DC_5_CD6hr

source_name: dendritic cells, cluster disruption, 6 hours

treatment_protocol: For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 6 hours later for microarray analysis.


title: DC_9_B1hr

source_name: dendritic cells, stimulated by bacteria, 1 hours

treatment_protocol: Clusters of Langerhans cells, grown as described in the Growth Protocol section,  were stimulated to mature with the addition of additional bacterial (DH5alpha) or LPS (250 ng/ml).  For this sample, cells were harvested for microarray analysis after one hour of treatment.


title: DC_6_CD12hr

source_name: dendritic cells, cluster disruption, 12 hours

treatment_protocol: For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 12 hours later for microarray analysis.


title: DC_4_CD3hr

source_name: dendritic cells, cluster disruption, 3 hours

treatment_protocol: For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 3 hours later for microarray analysis.


title: DC_1_CT0hr

description: The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response.  We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors.  These events were triggered at least in part by activation of the -catenin pathway.  However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.

source_name: dendritic cells, control, 0 hours

growth_protocol: CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 104 U/mg), 2.5 ng/ml TNF- (2 x 107 U/mg), 0.5 ng/ml TGF-ß1 (2 x 107 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies.

treatment_protocol: For this sample, clusters of Langerhans cells were harvested at 0 hours for microarray analysis.


title: DC_2_CT36hr

source_name: dendritic cells, control, 36 hours

growth_protocol: CD34+ stem cells were immunomagnetically purified from leukapheresis products with either a midi-MACS system (CD34 progenitor cell isolation kit or multisort kit) following the protocol of the manufacturer (Miltenyi Biotec, Auburn, CA) or a Baxter Isolex device (Baxter, Deerfield, IL). Cells were thawed and cultured at 1 x 104/ml/well in 24-well plates in media prepared as follows: X-VIVO 15 containing 100 ng/ml GM-CSF (5.6 IU/mg), 20 ng/ml stem cell factor (5 x 10E4 U/mg), 2.5 ng/ml TNF- (2 x 10E7 U/mg), 0.5 ng/ml TGF-ß1 (2 x 10E7 U/mg), and 100 ng/ml Flt3 ligand (Flt3L). All cytokines were purchased from PeproTech (Rocky Hill, NJ), except for GM-CSF and Flt3L, which were obtained from Immunex (Seattle, WA). Cultures were incubated at 37°C with 5% CO2 in a humidified environment for 7–10 days without feeding or replating; by this time total cell number had increased by 50- to 100-fold. Clusters were purified by gently harvesting cells with a pipette and layering on top of 6 ml of 7.5% BSA (Sigma, St. Louis, MO) in 15-ml tubes: up to eight wells were loaded per column. No adherent cells remained in the wells upon harvesting. After 30 min on ice, single cells in suspension were removed by aspirating the BSA columns until 3.5 ml remained. Clusters were concentrated by centrifugation at 300 x g, resuspended in growth media, and cultured at 5 x 105 cells/ml/well in 24-well plates for 1-2 days for maturation studies.

treatment_protocol: For this sample, clusters of Langerhans cells were harvested at 36 hours for microarray analysis.

tag: Human Langerhans cells produced from CD34+ stem cells cultured as described in the Growth Protocol section, were incubated for 36 hours without maturation stimulus.


title: DC_7_CD18hr

source_name: dendritic cells, cluster disruption, 18 hours

treatment_protocol: For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 18 hours later for microarray analysis.


title: Day 5 DC etanercept rep3

city: NYC

first: Lisa

middle: Caithleen

last: Zaba

state: NY

address: 1230 York Avenue

department: Dermatology

institute: Rockefeller University

description: single amp

hyb_protocol: Quiagen single amplification protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A.

data_processing: GC-RMA normalization to the median

source_name: Day 5 DC etanercept

label_protocol: Quiagen single amplification protocol

growth_protocol: GMCSF and IL-4 for 5 days

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol

treatment_protocol: GMCSF, IL-4, and Etanercept 10ug/mL for 5 days

tag: Buffy 3


title: DC_3_CD1hr

source_name: dendritic cells, cluster disruption, 1 hour

treatment_protocol: For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested at 1 hour for microarray analysis.


title: Day 5 DC control rep1

description: single amp

source_name: Day 5 DC control

tag: Buffy 1


title: Day 5 DC etanercept rep2

description: single amp

tag: Buffy 2


title: BY4742, 0.1MPa, 24C (D)

status: Public on Oct 05 2007

city: Yokosuka

first: Fumiyoshi

last: Abe

state: Kanagawa

address: 2-15 Natsushima-cho

department: Extremobiosphre Research Center

institute: Japan Agency for Marine-Earth Science and Technology

description:
Total RNA from RPB1 wild type strain growing at 30C in rich media in day A (N1).
Robust Multiarray Average (RMA) using quantile normalization (see: Bolstad B et all. 2003. A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19: 185-193) and gene calls generated using the RMA algorithm (Irizarry RA. et all. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64).

hyb_protocol: As described previously: Nuwaysir EF, et all. 2002. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12:1749-55.

scan_protocol: with GenePix

data_processing: RMA(Robust Multichip Average)

label: bio-11-CTP and bio-16 UTP


title: Day 5 DC control rep2

description: single amp


title: Day 5 DC control rep3

description: single amp


title: Patients 5 and 6

city: Pointe-Claire

first: Daniel

last: Cyr

state: Québec

address: 245, Boulevard Hymus

institute: INRS-Institut Armand-Frappier

description: Only the gene expression of the caput of the epididymis were compared between the fertile and the infertile patient.

hyb_protocol: 0.75 mg of cRNA were hybridized to the Agilent oligo microarray (Agilent-012097 Human 1A Microarray (V2) G4110B) using the In Situ Hybridization Kit Plus (Agilent Technologies) according to the protocol provided by the manufacturer.

scan_protocol: GeneChips were scanned using the ScanArray Express scanner (Perkin Elmer, Woodbridge, Canada).

data_processing: Fluorescence ratios were extracted using ScanArray Express Software (Perkin Elmer) and were analyzed using GeneSpring software 6.1 (Agilent technologies). Data was normalized using a locally weighted regression Lowess method and genes were considered differentially expressed in sample 1 versus sample 2 if there was at least a 2-fold change.

label: Cyanine 5

source_name: Patient 5

label_protocol: Fluorescent cRNA were prepared from 500 ng total RNA using the Low RNA Input Linear Amplification Kit (Agilent Technologies, Mississauga , Ontario). As a last step of the extraction procedure, the cRNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

extract_protocol: RNA was extracted using Absolutely RNA RT-PCR Miniprep Kit (Stratagene, La Jolla, CA) according to the manufacturer's instructions.

tag: male, non-obstructive azoospermic patient, 40-years-old

label: Cyanine 3

source_name: Patient 6

tag: male, patient with active spermatogenesis suffering from localized testicular cancer (to the tunica albuginea), 50-years-old.


title: BY4742, 0.1MPa, 15C (F)

label_protocol: As described previously: Nuwaysir EF, et all. 2002. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12:1749-55.


title: Patients 3 and 4

data_processing: Fluorescence ratios were extracted using ScanArray Express Software (Perkin Elmer) and were analyzed using GeneSpring software 6.1 (Agilent technologies). To account for dye swap, the channels measurements were swapped. The data are therefore expressed as infertile-cyanine 5/fertile-cyanine 3. Data was normalized using a locally weighted regression Lowess method and genes were considered differentially expressed in sample 1 versus sample 2 if there was at least a 2-fold change.

source_name: Patient 3

tag: male, non-obstructive azoospermic patient, 32-years-old

source_name: Patient 4

tag: male, patient with active spermatogenesis suffering from localized testicular cancer (to the tunica albuginea), 36-years-old.


title: Patients 1 and 2 (not swapped)

source_name: Patient 1

tag: male, non-obstructive azoospermic patient, 42-years-old

source_name: Patient 2

tag: male, patient with active spermatogenesis suffering from localized testicular cancer (to the tunica albuginea), 29-years-old.


title: Patients 1 and 2


title: Patients 7 and 8

data_processing: Fluorescence ratios were extracted using ScanArray Express Software (Perkin Elmer) and were analyzed using GeneSpring software 6.1 (Agilent technologies). To account for dye swap, the channels measurements were swapped. The data are therefore expressed as infertile-cyanine 5/fertile-cyanine 3.Data was normalized using a locally weighted regression Lowess method and genes were considered differentially expressed in sample 1 versus sample 2 if there was at least a 2-fold change.

source_name: Patient 7

tag: male, non-obstructive azoospermic patient, 34-years-old

source_name: Patient 8

tag: male, patient with active spermatogenesis suffering from localized testicular cancer (to the tunica albuginea), 40-years-old.


title: KO_mechanical_ventilation_3

status: Public on Oct 04 2007

city: Baltimore

first: Dmitry

middle: N

last: Grigoryev

state: MD

institute: JHU

description: Left lung lobe

hyb_protocol: Affymetrix

scan_protocol: Agilent

data_processing: GCOS 1.4

source_name: Lung

label_protocol: Affymetrix

extract_protocol: Affymetrix

tag: KO


title: Day 5 DC etanercept rep1

description: single amp


title: KO_mechanical_ventilation_1

description: Left lung lobe


title: Stroma normal breast (Nstr122204)

city: Boston

first: Andrea

last: Richardson

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description: expression of breast tissue

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16hr at 45c on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the affymetrix fludics station 400

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

data_processing: dCHIP with default settings

source_name: stroma

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

growth_protocol: RNA extraction, cRNA sythesis and Hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64(2004), pp. 64-71

tag: normal


title: KO_spontaneous_ventilation_3

description: Left lung lobe


title: BY4742, 25MPa, 24C (E)


title: DC_8_CD36hr

source_name: dendritic cells, cluster disruption, 36 hours

treatment_protocol: For this sample, clusters of Langerhans cells were disrupted with repetitive pipeting, and harvested 36 hours later for microarray analysis.


title: KO_spontaneous_ventilation_1

description: Left lung lobe


title: KO_spontaneous_ventilation_2

description: Left lung lobe


title: WT_mechanical_ventilation_3

description: Left lung lobe

tag: WT


title: WT_spontaneous_ventilation_1

description: Whole lung


title: WT_spontaneous_ventilation_2

description: Left lung lobe


title: WT_mechanical_ventilation_1

description: Left lung lobe


title: KO_mechanical_ventilation_2

description: Left lung lobe


title: WT_mechanical_ventilation_2

description: Left lung lobe


title: WT_spontaneous_ventilation_3

description: Left lung lobe


title: Sample 1D, 30 min

city: Lund

first: Carina

last: Strand

address: Barngatan 2B

department: IKVL, Oncology

institute: Lund University

description: Six breast cancer samples were used, each sample were divided in four and the pieces were left in room temperature for four different time periods (50 sec, 2-3 min, 10 min, 30 min)

hyb_protocol: Hybridizations were performed in 4 x SSC, 0.1% SDS, 0,5 NOTE human 0,8-1,0 µg/µl Cot-1 DNA at 42degC overnight. Arrays were washed three times 4xSSC RT, twice 2xSSC / 0.1% SDS at 42degC, one time 0.2xSSC, and one time 0.1xSSC RT.

scan_protocol: Arrays were scanned in Agilent scanner (Agilent Technologies)

data_processing: Image analysis was performed using Genepix v4.0. Result files were uploaded into BASE where they were filtered and normalized.

source_name: breast cancer sample Ca18269

label_protocol: Direct labeled by random priming (Promega, Pronto)

extract_protocol: Trizol (Invitrogen) followed by Qiaex (Qiagen). RNA integrity was checked on a Bioanalyzer (Agilent).

tag: 30 min

tag: female

source_name: Human Reference RNA (Stratagene)

extract_protocol: Stratagene

tag: pool of 10 cell lines


title: Sample 1A, 50 sec

source_name: breast cancer sampleCa18269

tag: 50 sec


title: Sample 1C, 10 min

tag: 10 min


title: Sample 2B, 2-3 min

source_name: breast cancer sample Ca18245

tag: 2-3 min


title: Sample 1B, 2-3 min


title: Sample 2D, 30 min

source_name: breast cancer sampleCa18245


title: Sample 3D, 30 min

source_name: breast cancer sampleCa18230


title: Sample 2A, 50 sec


title: Sample 5C, 10 min

source_name: breast cancer sample Ca18165


title: Sample 4D, 30 min

source_name: breast cancer sample Ca18193


title: Sample 4C, 10 min

source_name: breast cancer sampleCa18193


title: Sample 3B, 2-3 min

source_name: breast cancer sample Ca18230


title: Sample 2C, 10 min


title: Sample 4B, 2-3 min


title: Sample 3C, 10 min


title: Sample 4A, 50 sec


title: Sample 5D, 30 min

source_name: breast cancer sampleCa18165


title: myb98_rep4

city: Chicago

first: Matthew

last: Jones-Rhoades

state: IL

address: W519, 929 E. 57th Street

institute: University of Chicago

description: total RNA from myb98 ovules

hyb_protocol: hybridization protocol for eukaryotic cRNA target (Affymetrix)

scan_protocol: Chips were scanned by an Affymetrix Scanner 7G with GeneChip Operational System (Affymetrix)

data_processing: bg.adjust and quantile.normalize functions of affy R package were used on PM values

organism: Arabidopsis thaliana

source_name: stage 14 ovules

label_protocol: Oligo-DT selection, Reverse transcription, second strand synthesis, biotin labeling (Bioprime kit)

extract_protocol: Total RNA was purified from dissected uvules by RNAqueous -micro spin columns (Ambion)

tag: Ecotype

value: Columbia

tag: 1 month old plant


title: Sample 5A, 50 sec


title: myb98_rep2

description: total RNA from myb98 ovules


title: LmrR Lactococcus lactis MG1363 (slide176539 rep1)

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: LmrR is a negative transcriptional regulator of the expression of the Multidrug ABC transporter LmrCD in Lactococcus lactis

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner. Quantification of the signal of the spots on slides was done with ArrayPro 4.5

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (PMID: 15130795).

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: Wild Type

label_protocol: Subsequently, single-strand reverse transcription (amplification) and indirect labeling of 20 μg of total RNA, with either Cy3 or Cy5 dye, were performed (including a sample in which the dyes were swapped to correct for dye-specific effects). Labeled cDNA samples were hybridized to microarray slides of L. lactis MG1363 spotted in duplicate as described (van Hijum et al., 2005;den Hengst et al., 2005b)

extract_protocol: DNA microarray experiments were essentially performed as described (van Hijum et al., 2005;den Hengst et al., 2005c). Briefly, RNA was isolated from two separately grown replicate cultures of L. lactis NZ9000 and the two L. lactis NZ9000 ΔlmrR strains. Strains were grown in GM17 medium and harvested at an OD660 of 1 (late log phase)..

tag: Wild Type At OD600=1

source_name: lmrR mutant

tag: Mutant At OD600=1


title: Sample 6D, 30 min

source_name: breast cancer sample Ca18146


title: Sample 5B, 2-3 min


title: Sample 6C, 10 min


title: LmrR Lactococcus lactis MG1363 (slide176538 rep2)


title: LmrR Lactococcus lactis MG1363 (slide176539 rep2)


title: LmrR Lactococcus lactis MG1363 (slide176537 rep2)


title: LmrR Lactococcus lactis MG1363 (slide176536 rep2)


title: LmrR Lactococcus lactis MG1363 (slide176537 rep1)


title: LmrR Lactococcus lactis MG1363 (slide176536 rep1)


title: myb98_rep1

description: total RNA from myb98 ovules


title: myb98_rep3

description: total RNA from myb98 ovules


title: Sample 3A, 50 sec


title: Sample 6B, 2-3 min


title: dif1_rep3

description: total RNA from dif1 ovules


title: Sample 6A, 50 sec


title: LmrR Lactococcus lactis MG1363 (slide176538 rep1)


title: dif1_rep4

description: total RNA from dif1 ovules


title: wild_type_rep3

description: total RNA from wild type ovules


title: irrigated root vs drought stressed root (slide 152)

status: Public on Oct 03 2007

city: Lubbock

first: Paxton

last: Payton

state: TX

address: 3810 4th Street

institute: USDA-ARS

description: For processed data, expression data were subjected to LOWESS normalization and a Benjamini and Hochberg multiple testing correction. Differential expression was defined as >2 fold change in expression level at p <0.05 in at least 4 of 6 replicate hybridizations of 3 biological replicates in dye-swap comparisons.

hyb_protocol: Hybridizations were carried out at 55ºC for 18h in a dark, circulating waterbath. Performer: Paxton Payton

scan_protocol: The hybridized arrays were scanned using Axon 4000B laser scanner. Feature extraction and quantification was performed GenePix Pro 6.0. Data was analyzed using GeneSpring 7.0 (Agilent Technologies, Santa Clara, CA). Performer: Paxton Payton

data_processing: Data from 3 biological replicated in dye-swap comparisons (5-6 hybridizations per tissue) were analyzed using GeneSpring 7.0 (Agilent Technologies, Santa Clara, CA). Performer: Paxton Payton

organism: Gossypium hirsutum

source_name: drought-stressed root Cy3

label_protocol: Target RNA (25 µg), quantified using ND-1000 Spectrophotometer (Nanodrop Technologies, Inc., Wilmington, DE), was labeled using the amino-allyl MessageAmp labeling kit (Ambion, Austin, TX). Hybridizations were carried out at 55ºC for 18h. The hybridized chips were scanned using Axon 4000B laser scanner. Data was analyzed using GeneSpring 7.0 (Agilent Technologies, Santa Clara, CA). Performer: Paxton Payton

growth_protocol: Cotton plants were grown under greenhouse conditions (30ºC/25ºC, day/night) for 8 weeks. Plants were fertilized twice weekly with 50% Hoagland’s solution. Performer: Paxton Payton

extract_protocol: Total RNA was isolated using the modified hot-borate method of Wilkins and Smart (1996). The youngest, near fully expaned leaf (4th leaf from the apical meristem) was sampled from each plant and immediately frozen in liquid nitrogen. Root tissue was harvested by sampling lateral roots in two sequential steps of flash freezing in liquid nitrogen. Performer: J.R. Quilantan

treatment_protocol: Parameter Growth Condition = greenhouse/USDA-ARS Cropping Systems Research Laboratory/Lubbock, TX USA. Water-deficit stress was imposed by withholding irrigation and leaf water potential measured with a pressure bomb. At the time of leaf and root tissue harvest, leaf water potentials averaged -8.7 Bars (+ 0.37 SE) for fully irrigated control plants and -23.1 Bars (+ 0.28 SE) for stressed plants, and leaf photosynthetic rates had decreased approximately to 60% of the rates seen in the irrigated controls. Performer: Paxton Payton

tag: Parameter Accession number or name = FiberMax989; Parameter Species = Gossypium hirsutum; Parameter Polyploid level = 4x; Parameter Tissue type = leaf; Parameter Transgenes = none; Performer

value: Paxton Payton

source_name: irrigated root Cy5

treatment_protocol: Parameter Growth Condition = greenhouse/USDA-ARS Cropping Systems Research Laboratory/Lubbock, TX USA. Plants were irrigated thrice weekly and fertilized twice weekly with 50% Hoagland’s solution. Performer: Paxton Payton


title: irrigated root vs drought stressed root (slide 157)

source_name: irrigated root Cy3

tag: Parameter Accession number or name = FiberMax989; Parameter Species = Gossypium hirsutum; Parameter Polyploid level = 4x; Parameter Tissue type = root; Parameter Transgenes = none; Performer

source_name: drought-stressed root Cy5


title: irrigated root vs drought stressed root (slide 159)


title: irrigated root vs drought stressed root (slide 166)


title: irrigated leaf vs drought stressed leaf (slide 156)

source_name: drought-stressed leaf Cy3

source_name: irrigated leaf Cy5


title: Human cancer, melanoma metastasis (Met Nr 66/2)

status: Public on Oct 02 2007

city: cambridge

first: steve

last: shen

address: 77 mass ave

institute: MIT

description: human clinical tumor tissue sample

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on one U133A human chip and one test chip. 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: raw data (CEL file) were normalized with RMA and further analyzied with GenePatter comparative marker selection module.

source_name: melanoma clinical sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (701025, Revision 3).

extract_protocol: Rneasy mini kit

tag: Genotype

value: melanoma metastasis

tag: Age


title: Human cancer, melanoma metastasis (Met Nr 92/3)

description: human clinical tumor tissue sample


title: irrigated leaf vs drought stressed leaf (slide 151)


title: irrigated root vs drought stressed root (slide 165)


title: Human cancer, melanoma metastasis (Met Nr 105/2)

description: human clinical tumor tissue sample


title: wild_type_rep1

description: total RNA from wild type ovules


title: Human cancer, melanoma metastasis (Met Nr 104/4)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 104/3)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 102/2)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 69/3)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 99/4)

description: human clinical tumor tissue sample


title: dif1_rep2

description: total RNA from dif1 ovules


title: wild_type_rep4

description: total RNA from wild type ovules


title: Human cancer, melanoma metastasis (Met Nr 69/6)

description: human clinical tumor tissue sample


title: irrigated leaf vs drought stressed leaf (slide 162)


title: Human cancer, melanoma metastasis (Met Nr 105/4)

description: human clinical tumor tissue sample


title: wild_type_rep2

description: total RNA from wild type ovules


title: Human cancer, melanoma metastasis (Met Nr 105/3)

description: human clinical tumor tissue sample


title: dif1_rep1

description: total RNA from dif1 ovules


title: Human cancer, melanoma metastasis (Met Nr 105/1)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 89/3)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 105/6)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 89/1)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 92/5)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 88/5)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 69/5)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 91/2)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 92/6)

description: human clinical tumor tissue sample


title: Mapping drought-stress related genes in cotton

hyb_protocol: Hybridizations were carried out at 55ºC for 18h in a dark, circulating waterbath.  Performer: Paxton Payton

source_name: irrigated leaf Cy3

growth_protocol: Cotton plants were grown under greenhouse conditions (30ºC/25ºC, day/night) for 8 weeks. Plants were fertilized twice weekly with 50% Hoagland’s solution.  Performer: Paxton Payton

treatment_protocol: Parameter Growth Condition = greenhouse/USDA-ARS Cropping Systems Research Laboratory/Lubbock, TX USA. Plants were irrigated thrice weekly  and fertilized twice weekly with 50% Hoagland’s solution. Performer: Paxton Payton

source_name: drought-stressed leaf Cy5


title: Human cancer, melanoma metastasis (Met Nr 91/1)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 69/4)

description: human clinical tumor tissue sample


title: irrigated leaf vs drought stressed leaf (slide 164)


title: Human cancer, melanoma metastasis (Met Nr 104/2)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 68/6)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 69/2)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 68/2)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 67/5)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 65/3)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 65/4)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 105/5)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 69/1)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 67/4)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 64/3)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 64/4)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 66/6)

description: human clinical tumor tissue sample


title: Human cancer, melanoma metastasis (Met Nr 64/1)

description: human clinical tumor tissue sample