title: NCH_1436

status: Public on Jun 17 2009

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

institute: Salento University

description:
After image acquisition, the scanned 16-bit image was used to quantify the signal intensities using the ScanAnalyze program. GeneSpring (Silicon Genetics, Redwood City, CA) software was used for further analysis. To import data, a file for each sample containing information about its gene name, signal and detection for each gene, was created. After importing data several experiments defining parameters and normalization were tested. The fluorescent intensity of each DNA spot   (average of intensity of each pixel present within the spot) was calculated using local mean background subtraction. A signal was accepted if the intensity after background subtraction was at least 2.5-fold higher than its local background.
To minimize biases in RNA amplification only one round amplification was performed using similar incubations times and 200 ng of total RNA of good quality as template for the reverse transcription reaction. The quality and quantity of aRNA was monitored on agarose gel electrophoresis and by spectrophotometer. Typically, 10-20 ug of aRNA was generated from 200 ng of total RNA by one round of amplification and 10 ug of aRNA were employed for hybridization.

hyb_protocol: We used a custom 60-mer amino modified oligo- array, containing 724 probes, a lot of which specific for genes commonly altered in cancer. We labelled RNA using the SuperScript Indirect RNA Amplification System (Invitrogen, Karlsruhe, Germany). Slides was activated in 0,1%Triton X-100 for 5 min, then rinsed 2 times in 1mM HCl for 2 min, rinsed in 100mM KCl for 10 min and finally washed in dH2O at room temperature. After washing the slides were incubated in the blocking buffer (50mM ethanolamine, 0,1%SDS in 0.1M Tris pH 9) at 50°C for 15 min. Finally the slides were rinsed 1 min in dH2O and centrifuged at 200g for 5 min to avoid water stains on the slide surface. Hybridization was performed overnight in hybridization buffer (3X SSC, 50% formammide, 0,1% SDS), at 42 ºC in a humidity controlled hybridization chamber. A wash step in 2X SSC, 0.2% SDS was performed at 50° for 10 min, followed by two washes in 2X SSC for 10 min at room temperature, a final wash in 0.2X SSC for 10 min at room temperature and a centrifugation at 200g for 5 min to avoid any water stains on the slide surfaces.

scan_protocol: After hybridization, arrays were scanned using a confocal laser scanner (Affymetrix 428 scanner) at a resolution of 10 ?m. Data from the laser scans were collected as graphics (.tiff format) for each channel. To maximize the dynamic range of microarrays, the same arrays were scanned using different photo-multiplier settings (PMT). The use of different intensities allows the quantification of both the high and low copy expressed genes.

data_processing:
The images were combined and processed using the ScanAnalyze program (written by Michael Eisen, http://rana.Stanford.EDU/software/) and the positions on the images were assigned to grid coordinates for the matching of spot identity with average pixel intensity at that region. Background corrected, log converted intensity ratios were determined for each element of the array. The image processing analysis also extracted information regarding spot quality and assigned a quality score to each ratio measurement. The definition of the quality metric was based on the notion that unreliable data points usually result from weak target intensity, high local background, small target area, and inconsistent target intensity within a given target. Implementation of the quality metric enabled unified and universally applicable data filtering before downstream higher-level data analysis.
ScanAlyze data was imported in GeneSpring and GenePattern for further elaboration (Silicon Genetics, Redwood City, CA). To import data a file for each sample containing information about its gene name, signal and detection for each gene, was created. After importing data several experiments defining parameters and normalization were tested. Parameters are not numerical but define the sample nature or tissue type. The normalization of each sample was performed dividing each signal intensity by the 50th- percentile of all genes in that array. The normalization of each gene between samples was performed on the median of signal intensity of that gene in the reference sample.
Genes were also analyzed using GeneSpring for differential expression between sample classes. The software allow the data filtering upon signal intensity and detection value. To select differentially expressed genes we used several approaches: for two class matching we utilized the Scatter Plot selecting the genes with an expression fold >2. To identify differentially expressed genes in a multi class match we calculated the log2 of normalized data. In this way over-expressed genes was the ones with a value >0, while the down-expressed was the ones with a value <0. For statistical validation we used t-test with a p-value of 0.01.

label_protocol:
aRNA was chemically labeled with a NHS-cyanine dye using. Briefly, 10 ug
of aRNA was incubated at 85°C for 15 minutes with labeling buffer and either Cy5 or Cy3 in a
total volume of 20 ul prior to termination of the reaction by cooling on ice and addition of 5 ul
of stop buffer.

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

value: brain tumour

tag: prognosis on survival data

value: Poor

tag: prognosis on neuroradiological data

tag: genemutated

value: PTEN

tag: overall survival (months)

value: F

tag: kps

tag: histology

value: Anaplastic astrocytoma

tag: grade

value: III

source_name: NOrmal tissue 96

label_protocol: same as for channel 1

extract_protocol: same as for channel 1

tag: Control normal tissue


title: NCH_1429

type: RNA

country: Italy

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: gender

tag: age

source_name: NOrmal tissue 102

tag: normal control brain tissue


title: NCH_1420

source_name: Normal tissue 67

tag: normal control tissue


title: NCH_1410

value: Good

tag: genemutated:

value: oligoastrocytoma

value: II

source_name: Normal tissue118

tag: Normal control brain tissue


title: NCH_1461

value: Anaplastic oligoastrocytoma

source_name: Normal tissue 101

tag: Control brain normal tissue


status: Public on Sep 01 2009

city: Charlotte

first: John

last: Zagorski

state: NC

address: 1542 Garden Terrace, 301

department: Emergency Medicine

country: USA

institute: Carolinas Medical Center

description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle outflow, biological rep2

hyb_protocol: 25 microg of fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 v2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned twice using an Agilent Gene Array Scanner G2500A

data_processing: The data were generated with Affymetrix GeneChip Operating Software using a scaling target of 500, user defined normalization of 1.0, no probe mask, no baseline, and default "parameter" settings.

label: biotin

organism: Rattus norvegicus

source_name: Gene expression data from right ventricle outflow RNA after 6 weeks of vehicle treatment.

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocols from 5 microgram total RNA (Carolinas Medical Center-modified Affymetrix "Expression Analysis Technical Manual", 2001 using Superscript II cDNA module, Affymetrix IVT module, Affymetrix/Qiagen sample clean-up module).

growth_protocol: Rat was euthanized 6 weeks after vehicle treatment. Heart was excised surgicaly and briefly perfused with saline buffer on a Langendorff heart perfusion apparatus. The right venticle was disected and separated into outflow tract (base) and apex samples. This sample is "O" for outflow tract.

extract_protocol: Heart tissue was snap frozen in liquid nitrogen and crushed to a fine powder with a mortar and pestle in liquid nitrogen. Aliquots of powders were homogenized in guanidinium isothiocyanate and extracted with acidic phenol/chloroform. Crude RNA was collected by ethanol precipitation and purified using Qiagen RNeasy spin columns.

treatment_protocol: Rat was injected in the right jugular vein with 0.15 ml/100 grams weight of 0.01% Tween-20 as "vehicle" control treatment

tag: strain

value: Sprague Dawley

value: male

tag: weight

value: approximately 350 grams at time of experiment


title: NCH_1457

tag: prognosis on survival data

tag: prognosis on neuroradiological data

value: M

value: astrocytoma

source_name: Normal tissue 100

tag: control normal brain tissue


title: NCH_1377

label_protocol:
aRNA was chemically labeled with a NHS-cyanine dye using. Briefly, 10 ug
of aRNA was incubated at 85°C for 15 minutes with labeling buffer and either Cy5 or Cy3 in a
total volume of 20 ul prior to termination of the reaction by cooling on ice and addition of 5 ul
of stop buffer. labeled with Cy5

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

value: Brain tumour bioptic

tag: overall survival (months)

tag: kps

source_name: Normal tissue 76

label_protocol: same as channel 1

extract_protocol: same as channel 1


title: NCH_1477

tag: histology

tag: grade

source_name: Normal tissue 107

tag: COntrol brain normal tissue


title: NCH_1474

tag: tissue

tag: gender

source_name: Normal tissue 104


title: NCH_1448

tag: age

source_name: NOrmal tissue 91

tag: control brain tissue


description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle apex, biological rep5

source_name: Gene expression data from right ventricle apex RNA after 6 weeks of vehicle treatment.

growth_protocol: Rat was euthanized 6 weeks after vehicle treatment. Heart was excised surgicaly and briefly perfused with saline buffer on a Langendorff heart perfusion apparatus. The right venticle was disected and separated into outflow tract (base) and apex samples. This sample is "A" for apex.


description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle outflow, biological rep4


description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle apex, biological rep1


description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle outflow, biological rep1


description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle apex, biological rep4.


title: NCH_1398

tag: genemutated:

source_name: NOrmal brain tissue 72

tag: normal control brain tissue


description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle apex, biological rep3.


title: NCH_1399

source_name: Normal Brain tissue 113

tag: Control Normal brain tissue


description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle apex, biological rep2.

tag: strain


description: Experimental pulmonary embolism: Week 6 vehicle control rat, heart right ventricle outflow, biological rep5

tag: weight


title: NCH_1443

tag: prognosis on survival data

source_name: Normal tissue 73

tag: Normal control brain tissue


title: NCH_1432

tag: prognosis on neuroradiological data

tag: genemutated

source_name: NOrmal tissue 87

tag: Control normal tissue


title: NCH_1397

value: brain tumor

tag: overall survival (months)

tag: kps

tag: histology

source_name: Normal tissue 70


title: NCH_1409

tag: tissue

value: brain tumour

tag: grade

source_name: NOrmal tissue 106

tag: Control normal brain tissue


title: NCH_1441

value: Poor

tag: gender

tag: age

source_name: Normal tissue 80

tag: Normal brain control tissue


title: NCH_1419

value: PTEN

source_name: Normal tissue 90

tag: normal control brain tissue


title: NCH_1437

tag: genemutated:

source_name: Normal tissue 78


title: NCH_1428

value: F

source_name: Normal tissue 110

tag: Normal control tissue


title: NCH_1384

tag: prognosis on survival data

value: Anaplastic astrocytoma

source_name: Normal tissue 62

tag: control brain tissue


title: NCH_1396

tag: prognosis on neuroradiological data

source_name: Normal tissue 114

tag: normal brain tissue


title: NCH_1380

source_name: Normal tissue 82


title: NCH_1386

value: III

source_name: Normal Tissue 61

tag: control normal tissue


title: NCH_1390

tag: overall survival (months)

source_name: Normal TIssue 79

tag: control normal brain tissue


title: NCH_1381

value: Good

tag: kps

tag: histology

source_name: Normal tissue 105

tag: COntrol normal tissue


title: NCH_1379

tag: tissue

tag: grade

source_name: Normal tissue 99


title: NCH_1349

tag: gender

tag: age

source_name: Normal Tissue 86

tag: normal control tissue


title: NCH_1355

tag: genemutated

source_name: Normal tissue 65


title: NCH_1367

source_name: Normal tissue 68

tag: normal control brain tissue


title: NCH_1374

tag: prognosis on survival data

tag: genemutated:

source_name: Normal brain tissue 85


title: NCH_1376

value: tumor brain

tag: prognosis on neuroradiological data

source_name: NOrmal tissue 63


title: NCH_1347

value: II

source_name: NOrmal Tissue 92


title: NCH_1348

source_name: NOrmal Tissue 66

tag: normal brain tissue


title: NCH_1344

source_name: Normal tissue 112

tag: Normal control brain tissue


title: NCH_1340

tag: overall survival (months)

value: oligoastrocytoma

source_name: Normal Tissue 84


title: NCH_1339

source_name: Normal tissue 83

tag: cotroll normal brain tissue


title: NCH_1331

tag: kps

source_name: Normal tissue 71


title: NCH_1368

tag: histology

source_name: NOrmal brain tissue 88


title: NCH_1329

source_name: Normal Tissue 115


title: NCH_1383

value: Anaplastic oligoastrocytoma

source_name: Normal tissue 106

tag: control normal tissue


title: NCH_1323

tag: tissue

source_name: Normal brain tissu 97


title: NCH_1375

tag: grade

source_name: Control brain tissue

tag: Normal brain tissue


title: NCH_1362

tag: gender

tag: age

source_name: NOrmal Tissue 94


title: NCH_1318

tag: genemutated

source_name: Normal Tissue64


title: NCH_1321

tag: Tumor brain tissue

source_name: Normal Tissue 93


title: NCH_1322

tag: prognosis on survival data

source_name: Normal tissue 81


title: NCH_1313

tag: tumour tissue


title: NCH_1314

tag: prognosis on neuroradiological data


title: NCH_1305

tag: genemutated:

tag: normal brain tissue


title: NCH_1300

tag: overall survival (months)


title: NCH_1290

source_name: Normal tissue 109


title: NCH_1281

tag: tumour brain bioptic tissue

source_name: Normal tissue 116

label_protocol: Same as for channel 1

extract_protocol: Same as for channel 1


title: NCH_1291

tag: kps

source_name: NOrmal tissue 89


title: NCH_1293

tag: histology

source_name: NOrmal tissue 117


title: NCH_1285

source_name: NOrmal tissue 97


title: NCH_1413

tag: Gliomatosis Cerebri type I tumor sample

source_name: NOrmal tissue 103


title: NCH_1280

tag: tissue

source_name: Normal tissue 111


title: NCH_1286

tag: grade

source_name: NOrmal Tissue 75


title: HPC-PB_donorAF13-66yrs

status: Public on Jun 12 2009

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: GeneChip Human Genome U133_Plus_2.0 (Affymetrix) were hybridized with 10 µg amplified RNA and washed with a fluidics station 450 (Affymetrix).

scan_protocol: GeneChip Human Genome U133_Plus_2.0 (Affymetrix) were scanned with GeneChip scanner 3000 (Affymetrix)

label: Biotin

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 66 years old).

label_protocol: 100 ng total RNA was amplified with GeneChip two-cycle cDNA synthesis kit (Affymetrix, High Wycombe, United Kingdom) according to the manufacturers instructions. Quality of amplified RNA was controlled by LabChip technology.

growth_protocol: Cells were isolated from fresh blood and immediately harvested for subsequent analysis.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Paisley, Scotland) according to the manufacturer´s instructions. RNA quality was controlled using the RNA 6000 Pico LabChip kit (Agilent, Waldbronn, Germany) and quantified with a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: HPC were collected from fresh umbilical cord blood (CB) or mobilized peripheral blood (PB) after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Heidelberg. Mononuclear cells were isolated after centrifugation on Ficoll-hypaque (Biochrom KG, Berlin, Germany). CD34+ cells were enriched with a monoclonal anti-CD34 antibody labeled using magnetic beads on an affinity column (Miltenyi Biotec, Bergisch-Gladbach, Germany). After additional staining with anti-CD34-APC (Becton Dickinson, San Jose, CA, [BD]) further purification was achieved using the FACS-Vantage-SE flow cytometry system. Staining with propidium iodide (PI) was performed to allow exclusion of non-viable cells. Reanalysis revealed purity higher than 95%.

tag: Hematopoietic progenitor cells (HPC) were enriched within the CD34+ cell fraction (selection by magnetic beads and subsequent flow cytometric separation) from G-CSF mobilized blood from healthy donors for allogeneic blood stem cell transplantation.

tag: Donor was 66 years old


title: HPC-PB_donorAF12-64yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 64 years old).

tag: Donor was 64 years old


title: HPC-PB_donorAF22-27yrr

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 27 years old).

tag: Donor was 27 years old


title: HPC-CB_donorAF4-0yrs

source_name: Hematopoietic progenitor cells (HPC), human umbilical cord blood (CB, 0 years old).

tag: Hematopoietic progenitor cells (HPC) were enriched within the CD34+ cell fraction (selection by magnetic beads and subsequent flow cytometric separation) from fresh cord blood.

tag: (0 years old)


title: HPC-PB_donorAF17-53yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 53 years old).

tag: Donor was 53 years old


title: HPC-PB_donorAF20-60yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 60 years old).

tag: Donor was 60 years old


title: HPC-PB_donorAF1-28yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 28 years old).

tag: Donor was 28 years old


title: HPC-PB_donorAF16-42yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 42 years old).

tag: Donor was 42 years old


title: HPC-PB_donorAF9-35yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 35 years old).

tag: Donor was 35 years old


title: HPC-PB_donorAF6-42yrs


title: HPC-CB_donorAF5-0yrs


title: HPC-PB_donorAF15-38yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 38 years old).

tag: Donor was 38 years old


title: HPC-PB_donorAF2-49yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 49 years old).

tag: Donor was 49 years old


title: HPC-PB_donorAF21-59yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 59 years old).

tag: Donor was 59 years old


title: HPC-CB_donorAF3-0yrs


title: KO_BDNF_48h_4

status: Public on Sep 25 2008

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

country: Japan

institute: RIKEN

description: Primary culture from telencephalon of 6 Xbp1 -/- or 4 control mice at E12.5 was used for study. The neurons in 10 of 15 dishes in each group were stimulated with BDNF. On 4 DIV, neurons in 5 dishes (BDNF, 24hr) and 5 non-stimulated dishes were lysed to extract RNA. On 5 DIV, neurons in 5 dishes (BDNF, 48hr) were lysed.

hyb_protocol: Biotin-labeled cRNA sample was hybridized to Affymetrix GeneChip mouse Genome 430A2.0 Array according to manufacture's instruction.

scan_protocol: Hybridization signal on the chip was scanned using an HP GeneArray scanner (Hewlett-Packard).

data_processing: Data was processed by MAS5 software (Affymetrix).

organism: Mus musculus

source_name: telencephalon primary culture

label_protocol: Biotin-labeled cRNA for DNA microarray analysis was systhesized using Two Cycle cDNA Synthesis and IVT labeling Kit (Affymetrix).

growth_protocol: Cells were maintained in a serum-free medium containing 0.5 mM glutamine and B17.

extract_protocol: Total RNA was extracted using RNAeasy Micro Kit (Qiagen). Quantity and quality of RNA were measured using NanoDrop ND1000.

value: telencephalon primary culture

tag: embryonic day


title: KG-1_AC treatment_4 days_C/WE1_S3

status: Public on Nov 18 2008

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: Data processing will be described in detail in our website http://140.114.106.30/publication/wypeng/

hyb_protocol: Hybridization reactions were incubated in a humid chamber at 65℃ for 16 hrs, and labeled with fluorescence by using 3-DNA detection kit. (Genisphere). Subsequently, any unbound target was washed away with Corning UltraGAPSTM coated slides protocol.

scan_protocol: Barcode=12766562 "PMTGain=690	570" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.93	3.11" Temperature=29.3 "ScanPower=100	100"

data_processing: Raw image of spot intensity signal was converted into intensity-dependent MA plot, and subsequently system variance was adjusted by within-print tip LOWESS normalization and scale normalization. A set of loop design method was applied to microarray experi

source_name: KG-1 cells without  any treament for 4 days.

label_protocol: Fluorescent-labeled targets were made from 20 ug of total RNA. Samples were reverse-transcribed to cDNA by Superscript II RNase H reverse transcriptase (Invitrogen). The products were purified by passing through Microcon YM-30 column (Millipore). Target cDNA labeled with fluorescence by using 3-DNA detection kit. (Genisphere).

growth_protocol: Cells were grown in Iscove’s Modified Dulbecco’s Medium（IMDM）supplemented with 20% Heat-inactivated fetal bovine serum (Hyclone), penicillin (100 unit/ml),streptomycin (100 ug/ml),and L-Glutamine(4mM) in 75 cm2 tissue culture flasks at humidified incubator in 37℃ with 5% CO2.

extract_protocol: RNA samples were prepared using Trizol reagent (Invitrogen) and further purified by RNeasy kit (Qiagen). Total RNA yield was measured with UV absorbance at 260 nm and RNA quality was measured by Agilent 2100 bioanalyzer.

treatment_protocol: 5ml of KG-1 cells (2 × 105 cells/ml) were grown in T25 flask. Aqueous or methanol extracts of A.camphorata were added to culture medium, and then replenish with flash medium and A.camphorata extracts on 2 days. Cell number was counted in triplicate on days 2, 4, 6, and 8 by Coulter Z1 Counter (Beckman Coulter TM), Cell viability was examined with a trypan-blue dye exclusion method.

tag: strain

tag: gender

value: male

tag: age

value: 45 days

tag: tissue

value: acute myelogenous leukemia

source_name: KG-1 cells treated with AC Water extracts for 4 days.


title: HPC-PB_donorAF18-73yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 73 years old).

tag: Hematopoietic progenitor cells (HPC) were enriched within the CD34+ cell fraction (selection by magnetic beads and subsequent flow cytometric separation) from G-CSF mobilized blood from healthy donors for allogeneic blood stem cell transplantation.

tag: Donor was 73 years old


title: KG-1_AC treatment_4 days_ME/C_S7

scan_protocol: Barcode=12766908 "PMTGain=680	550" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.91	3.14" Temperature=25.88 "ScanPower=100	100"

source_name: KG-1 cells treated with AC Methanol extracts for 4 days.

source_name: KG-1 cells without any treatment for 4 days.

label_protocol: Fluorescent-labeled targets were made from 20 ug of total RNA. Samples were reverse-transcribed to cDNA by Superscript II RNase H reverse transcriptase (Invitrogen). The products were purified by passing through Microcon YM-30 column (Millipore). Target c


title: KG-1_AC treatment_4 days_M/W_S8

scan_protocol: Barcode=12766906 "PMTGain=650	640" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.91	3.13" Temperature=29.3 "ScanPower=100	100"

source_name: KG-1 cells treated with Methanol only for 4 days.

source_name: KG-1 cells treated with Water only for 4 days.


title: KG-1_AC treatment_4 days_WE1/M_S2

scan_protocol: Barcode=12766561 "PMTGain=540	670" Scanner=GenePix 4100A 01 [100641] "LaserPower=3.12	2.96" Temperature=27.83 "ScanPower=100	100"

source_name: KG-1 cells treated with AC water extracts for 4 days.


title: KO_BDNF_48h_5


title: KG-1_AC treatment_4 days_ME1/ME2_S9.

scan_protocol: Barcode=12767248 "PMTGain=670	550" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.9	3.14" Temperature=25.88 "ScanPower=100	100"


title: HPC-CB_donorAF8-0yrs

source_name: Hematopoietic progenitor cells (HPC), human umbilical cord blood (CB, 0 years old).

tag: Hematopoietic progenitor cells (HPC) were enriched within the CD34+ cell fraction (selection by magnetic beads and subsequent flow cytometric separation) from fresh cord blood.


title: HPC-PB_donorAF14-39yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 39 years old).

tag: Donor was 39 years old


title: KG-1_AC treatment_4 days_M/ME_S1

scan_protocol: Barcode=12766557 "PMTGain=720	580" Scanner=GenePix 4100A 01  [100641] "LaserPower=2.93	3.11" Temperature=30.27 "ScanPower=100	100"

data_processing: Raw image of spot intensity signal was converted into intensity-dependent MA plot, and subsequently system variance was adjusted by within-print tip LOWESS normalization and scale normalization. A set of loop design method was applied to microarray experiments. In ours microarray system, the average signal intensity was > 4 times signal to noise ratio (SNR value).Correlation between gene expression profiles were measured using centered Pearson correlation coefficient, and hierarchical cluster analysis were perform based on an average linkage clustering algorithm.


title: KG-1_AC treatment_4 days_WE2/W_S5

scan_protocol: Barcode=12766564 "PMTGain=790	550" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.91	3.12" Temperature=31.25 "ScanPower=100	100"


title: HPC-PB_donorAF19-28yrs

source_name: Hematopoietic progenitor cells (HPC), mobilized peripheral blood of healthy donors (PB, 28 years old).


title: KO_BDNF_48h_3


title: KG-1_AC treatment_4 days_W/C_S4

scan_protocol: Barcode=12766905 "PMTGain=590	580" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.89	3.15" Temperature=29.3 "ScanPower=100	100"

source_name: KG-1 cells treated with water only for 4 days.

source_name: KG-1 cells without any treament for 4 days.


title: KG-1_AC treatment_4 days_M/WE2_S6

scan_protocol: Barcode=12766907 "PMTGain=660	610" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.89	3.14" Temperature=29.3 "ScanPower=100	100"


title: WT_BDNF_24h_3


title: KO_BDNF_48h_2


title: WT_basal_2


title: WT_BDNF_24h_4


title: WT_basal_4


title: KO_BDNF_48h_1


title: WT_basal_1


title: WT_basal_5


title: WT_BDNF_48h_5


title: WT_BDNF_48h_4


title: WT_BDNF_24h_1


title: WT_BDNF_48h_3


title: WT_BDNF_24h_2


title: KO_basal_3

label_protocol: Biotin-labeled cRNA for DNA microarray amalysis was synthesized using Two Cycle cDNA Synthesis and IVT labeling Kit (Affymetrix).


title: KO_BDNF_24h_5


title: WT_basal_3


title: WT_BDNF_48h_2

label_protocol: Biotin-labeled cRNA for DNA microarray analysis was synthesized using two-cycle cDNA synthesis and IVT labelling kit (Affymetrix).


title: WT_BDNF_48h_1


title: KO_BDNF_24h_2


title: KO_basal_2


title: KO_basal_4


title: WT_BDNF_24h_5


title: KO_BDNF_24h_3


title: KO_basal_5


title: Dld_hypothalamus_4

status: Public on Sep 08 2008

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: Biological replicate 4 of 4: treated hypothalamus

hyb_protocol: Agilent one color protocol (One-Color Microarray-Based Gene Expression Analysis (v 5.5) (G4140-90040) www.agilent.com)

data_processing: Normalized signal intensity; specifically, Lowess normalization in JMP genomics, smooting factor set at 0.2

organism: Micropterus salmoides

source_name: treated hypothalamus; 7 days

extract_protocol: RNA STAT60 protocol (Tel-test, Friendswood, TX).

treatment_protocol: LMB i.p. injected with diedrin for 7 days

tag: Sex

value: female

value: Hypothalamus

tag: agent

value: 10mg/kg diedrin


title: Dld_hypothalamus_1

description: Biological replicate 1 of 4: treated hypothalamus

scan_protocol: Agilent one color protocol (One-Color Microarray-Based Gene Expression Analysis (v 5.5) (G4140-90040) www.agilent.com)


title: Dld_hypothalamus_2

description: Biological replicate 2 of 4: treated hypothalamus

label_protocol: Agilent one color protocol (One-Color Microarray-Based Gene Expression Analysis (v 5.5) (G4140-90040) www.agilent.com)


title: Dld_hypothalamus_3

description: Biological replicate 3 of 4: treated hypothalamus


title: CTRL_hypothalamus_3

description: Biological replicate 3 of 4: control hypothalamus

source_name: control hypothalamus; 7 days

treatment_protocol: control


title: KO_basal_1


title: Liver_0.1mg/l_rep3

status: Public on Aug 15 2008

city: Wilrijk

first: An

last: Hagenaars

state: Antwerp

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

description: The array was hybridized with liver cDNA of control carps vs liver cDNA of carps exposed to 0.1mg/l PFOS.

hyb_protocol: Prior to hybridization the arrays were prehybridized in a solution containing 50% formamide, 20 × SSC, 10% SDS and 20 mg/mL BSA for 1 h at 42 °C, after which the array was washed in demineralized water and isopropanol. Slides were dried using N2. Precipitated targets were dissolved in hybridization solution (50% formamide, 20 × SSC, 10%SDS, 20 mg/mL BSA and 10 mg/mL sheared salmon sperm). This target mixture was heat denatured for 5 min at 95 °C and added to the microarray under a glass coverslip. The array was then incubated at 42 °C in a hybridization chamber (Genetix Ltd, Hampshire, UK) for 16–18 h.After hybridization the arrays were submerged in 2 × SSC + 0.1% SDS at 42 °C to remove the coverslip, 2 × SSC + 0.1% SDS for 5 min at 42 °C, two washes of 0.1 × SSC + 0.1% SDS at room temperature of 10 min each and three washes of 0.1 × SSC at room temperature of 15 s, 2 min and 1 min, respectively. After submerging in 0.01 × SSC for 15 s, the arrays were rinsed in demineralized water and isopropanol for 1 min each. Arrays were dried using compressed N2.

scan_protocol: Microarrays were scanned at 532 and 635 nm using the Genepix Personal 4100A confocal scanner (Genetix Ltd, Hampshire, UK). The photomultiplier tube voltage (PMT) was adjusted for each slide to obtain an overall ratio close to one. The images were analyzed using the Genepix Pro software (Axon Instruments, Union City, CA, USA) for spot identification and for quantification of the fluorescent signal intensities.

data_processing: Further analysis was performed in a database (www.islab.ua.ac.be/base/), a microarray analysis method developed by the Intelligent Systems Laboratory (University of Antwerp, Antwerp, Belgium). The fluorescent signal intensity for each spot (average of intensity of each pixel present within the spot) was calculated and background (BG) corrected. Spots for which the mean foreground signal was smaller than the mean local BG+2SD (SD, Standard Deviation) deviation were filtered out. Spots with oversaturated signal intensities were also excluded from further analyses. The Cy5/Cy3 ratio was calculated for each spot, transformed into a logarithmic value (log2) and normalized using Locally Weighed Scatterplot Smoothing (Lowess) with a smoothing parameter of 0.33. The quality of individual microarrays was evaluated using the Lucidea ScoreCard references which provide essential information on cDNA labeling efficiency, sensitivity and intra-array variability.

organism: Cyprinus carpio

label_protocol: Aminoallyl labeled cDNA was covalent coupled with Cy5 mono NHS esters (Amersham Biosciences, Roosendaal, The Netherlands).

extract_protocol: Total liver RNA was extracted by application of the Trizol-RNA-extraction procedure (Gibco BRL, Life Technologies, Merelbeke, Belgium).

value: 6 months

value: liver

label_protocol: Aminoallyl labeled cDNA was covalent coupled with Cy3 mono NHS esters (Amersham Biosciences, Roosendaal, The Netherlands).


title: Liver_0.5mg/l_rep3


title: Liver_0.1mg/l_rep2


title: KO_BDNF_24h_4


title: KO_BDNF_24h_1


title: Liver_0.5mg/l_rep1


title: Liver_1mg/l_rep1

description: The array was hybridized with liver cDNA of control carps vs liver cDNA of carps exposed to 1mg/l PFOS.


title: CTRL_hypothalamus_1

description: Biological replicate 1 of 4: control hypothalamus


title: Liver_0.5mg/l_rep2


title: Liver_1mg/l_rep3


title: CTRL_hypothalamus_2

description: Biological replicate 2 of 4: control hypothalamus


title: Liver_0.1mg/l_rep1


title: CTRL_hypothalamus_4

description: Biological replicate 4 of 4: control hypothalamus


title: Cipro treated S. aureus cells 30 min replicate 5

status: Public on Nov 30 2006

city: San Diego

first: Marcus

last: Jones

state: CA

address: 4120 Torrey Pines Road

institute: JCVI

description: Flip dye replicate. Cipro treated S. aureus cells 30 min

hyb_protocol: Epoxy-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42°C for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were denatured to 95ºC prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42°C.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature"""""""""""""""""""""""""""""""

scan_protocol: Scanned on Axon GenePix 4000 scanner

data_processing: ratio statisitics normalized and inslide replicate analysis

organism: Staphylococcus aureus

source_name: Total RNA from wild type bacteria at 0hr with Cipro labeled with Cyanine-3 (green).

label_protocol: [2 ug] of total RNA were reverse transcribed to cDNA at 42°C overnight with powerscript (BD Clonetech), a 25mM 2:1 dUTP mix (Ambion)  and Rnase Out (Invitrogen). RNA was degraded with NaOH and purified with MinElute PCR columns (Qiagen)."""""""""""""""""""""""""""""""

extract_protocol: Qiagen RNA extraction protocol

tag: Strain 8325

source_name: Total RNA from cells treated  with Cipro for 30 min labeled with Cyanine-5 (red).


title: Cipro treated S. aureus cells 30 min replicate 6

hyb_protocol: Epoxy-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42°C for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were denatured to 95ºC prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42°C.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature"""""""""""""""

label_protocol: [2 ug] of total RNA were reverse transcribed to cDNA at 42°C overnight with powerscript (BD Clonetech), a 25mM 2:1 dUTP mix (Ambion)  and Rnase Out (Invitrogen). RNA was degraded with NaOH and purified with MinElute PCR columns (Qiagen)."""""""""""""""


title: Cipro treated S. aureus cells 30 min replicate 4


title: Cipro treated S. aureus cells 120 min replicate 4

description: Flip dye replicate. Cipro treated S. aureus cells 120 min

source_name: Total RNA from cells treated  with Cipro for 120 min labeled with Cyanine-5 (red).


title: SLE CD4 T cells 13

status: Public on Mar 01 2008

city: Dallas

first: Laurie

middle: S

last: Davis

state: TX

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

description: Gene expression data from freshly sorted cells

hyb_protocol: Following fragmentation, hybridization was carried out according to the Affymetrix Expression Analysis Technical Manual; only samples passing stringent quality control guidelines were assessed

scan_protocol: Affymetrix arrays were scanned using the Affymetrix GeneChip Scanner 3000 System

data_processing: Data was analyzed with Microarray Suite version 5.0 (MAS 5.0) software using the Affymetrix default analysis settings and global scaling normalization methods.

source_name: Peripheral blood from individuals with systemic lupus erythematosus

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix protocol from at least 5 ug of high quality RNA

extract_protocol: Qiagen Rneasy mini column; only high quality RNA samples as assessed by BioAnalyzer were hybridized to the GeneChips

treatment_protocol: PBMC were isolated, tagged with fluorochrome-conjugated antibodies to CD3, CD4, CD19 and CD33 for 30 min. PBMC were sorted into subsets on a Cytomation MoFlo cytometer into individual subsets. Purity of the populations was confirmed after sorting.

tag: SLE patient


title: Cipro treated S. aureus cells 120 min replicate 3


title: Cipro treated S. aureus cells 30 min replicate 2


title: Cipro treated S. aureus cells 120 min replicate 1


title: Cipro treated lexA S. aureus cells 30 min replicate 2

description: Flip dye replicate. Cipro treated S. aureus wt and lexA mutant cells 120 min

hyb_protocol: Epoxy-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42°C for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were denatured to 95ºC prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42°C.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature"""

data_processing: LOWESS normalized and inslide replicate analysis"""

source_name: Total RNA from wildtype bacteria  treated  with Cipro for 120 min labeled with Cyanine-3 (green).

label_protocol: [2 ug] of total RNA were reverse transcribed to cDNA at 42°C overnight with powerscript (BD Clonetech), a 25mM 2:1 dUTP mix (Ambion)  and Rnase Out (Invitrogen). RNA was degraded with NaOH and purified with MinElute PCR columns (Qiagen)."""

source_name: Total RNA from lexA bacteria  treated  with Cipro for 120 min labeled with Cyanine-5 (red).


title: Cipro treated S. aureus cells 30 min replicate 1


title: Cipro treated S. aureus cells 120 min replicate 2


title: Cipro treated S. aureus cells 30 min replicate 3


title: Cipro treated lexA S. aureus cells 30 min replicate 1

description: Flip dye replicate. Cipro treated S. aureus wt and lexA mutant cells 30 min

source_name: Total RNA from wild type bacteria  treated  with Cipro for 30 min labeled with Cyanine-3 (green).

source_name: Total RNA from lexA mutant bacteria  treated  with Cipro for 30 min labeled with Cyanine-5 (red).


title: mouse_heart_femaleVSmale_2months_rep1

status: Public on Jul 09 2006

city: Berlin

first: Joerg

last: Isensee

address: Hessische Str. 3-4

department: Center for Cardiovascular Research

institute: Charite Berlin

description: Image analysis was performed with Feature Extraction software 7.1.1 (Agilent)

hyb_protocol: Samples were vacuum-centrifuged and resuspended in 7.5 μl nuclease-free water, 2.5 μl deposition control targets (Agilent) and 15 μl DIG hybridisation buffer (Roche). Denatured samples (98°C, 2 min) were hybridised on cDNA microarrays (Agilent) in a humidified chamber at 42°C for 15 h.

scan_protocol: Agilent Microarray scanner (G2565BA)

data_processing: Linear and LOWESS dye normalization

source_name: mouse whole heart, 2 months old, female pool

label_protocol: For reverse transcription (Superscript III, Invitrogen) in the presence of cyanine dye (Cy3 or Cy5) coupled dCTP (Amersham) 50 μg total RNA was used in a 30 µl reaction. Labelled cDNAs were combined with 380 μl TE (10 mM Tris, 1 mM EDTA), 20 μg mouse  Cot1 DNA and 20 μg Oligo(dA) and purified with a Microcon YM-30 column (Millipore).

extract_protocol: TRIzol® (Invitrogen) method

value: 2 months

value: heart

tag: pool

source_name: mouse whole heart, 2 months old, male pool


title: mouse_heart_maleVSfemale_2months_rep4


title: mouse_heart_maleVSfemale_8months_rep2

source_name: mouse whole heart, 8 months old, male pool

value: 8 months

source_name: mouse whole heart, 8 months old, female pool


title: mouse_heart_maleVSfemale_2months_rep2


title: mouse_heart_femaleVSmale_8months_rep1


title: mouse_heart_maleVSfemale_8months_rep4


title: mouse_heart_femaleVSmale_8months_rep3


title: Cipro treated lexA S. aureus cells 30 min replicate 3

source_name: Total RNA from wildtype bacteria  treated  with Cipro for 30 min labeled with Cyanine-3 (green).

source_name: Total RNA from lexA bacteria  treated  with Cipro for 30 min labeled with Cyanine-5 (red).


title: mouse_heart_femaleVSmale_2months_rep3


title: 24h2

status: Public on Jun 01 2006

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

description: cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture’s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software.

scan_protocol: Scanned with a GenePix 4000B scanner, and gridded with GenePix Pro 4.0 software

data_processing: The data was filtered so that only spots with a signal intensity of two-fold above background in at least one channel, flagged good (0) and with a diameter above 70 were given a relative expression value: PGJ2-treated vs. control.  The data was then normalized globally so the median log ratios for each experiment were equal to zero.

growth_protocol: Human neuroblastoma SK-N-SH cells were maintained at 37oC and 5% CO2 in minimal essential media (MEM) with Eagle's salts containing 2mM L-glutamine, 1mM sodium pyruvate, 0.4% MEM vitamins, 0.4% MEM nonessential amino acids, 100 units/ml penicillin, 100μg/ml streptomycin and 5% normal fetal bovine serum. These cells are derived from peripheral tissue.

extract_protocol: Quiagen RNeasy Mini kit (Valencia, CA)

treatment_protocol: Cells were treated at 37oC for 24 hours with 20uM of PGJ2 (Cayman Chemical Co., Ann Arbor, Michigan) in DMSO. The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.

tag: Human neuroblastoma SK-N-SH cells treated with 20uM PGJ2 for 24 hours

source_name: untreated SK-N-SH cells

treatment_protocol: Cells were treated at 37oC for 24 hours with vehicle (0.5% DMSO).  The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.

tag: Human neuroblastoma SK-N-SH cells untreated


title: Liver_1mg/l_rep2