title: AMD1

description: Non-AMD1 and AMD1 represent a pair of twins with discordant AMD phenotypes.

scan_protocol: Performed by NimbleGen according to their standard protocol. Signal intensity data is extracted from the scanned images of each array using Roche NimbleGen NimbleScan software.

data_processing:
Log2 (MeDIP/input) ratios were computed and scaled to center the ratio data around zero using NimbleScan software. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

Using NimbleScan software, peak data files are generated from the p-value data files. NimbleScan software detects peaks by searching for at least 2 probes above a p-value minimum cutoff (-log10) of 2. Peaks within 500bp of each other are merged. Peak score was used to filtered positive peaks in each sample. Peaks were identified by comparing MeDIP DNA of AMD1 (Ch2) and Input DNA of AMD1 (ch1).

source_name: AMD1 input

extract_protocol: Genomic DNA was isolated from peripheral blood mononuclear cells (PBMCs) using the Qiagen DNeasy kit. MeDIP was performed according to the NimbleGen 'Sample Preparation Protocol for DNA Methylation Microarrays' (v3.0).

value: peripheral blood mononuclear cells

tag: phenotype

value: age-related macular degeneration (AMD)

tag: antibody

tag: sample type

value: input

source_name: AMD1, MeDIP

treatment_protocol: Immunoprecipitation with an antibody against 5-methyl cytidine (Ab10805).

value: 5-methyl cytidine

tag: antibody vendor

value: Abcam

tag: antibody catalog number

value: MeDIP


title: 293+avb3 adherent, uninfected vs. p66- infected 6hr

status: Public on Mar 18 2011

type: RNA

city: Milwaukee

first: Jenifer

last: Coburn

state: WI

address: 8701 Watertown Plank Rd.

department: ID/CBID

country: USA

institute: Medical College of Wisconsin

description:
adherent cells
293 + avb3 adherent

hyb_protocol: The two differently labeled cDNAs were mixed and hybridized using Pronto Microarray Hybridization Kit in a hybridization chamber (Corning, Corning, NY), with the same array slide for 38 to 42 hr according to manufacturer’s instruction.   After a series of washes using the buffers provided in the kit, slides were spun dry. The slides were scanned under two laser channels in a Scanarray 4000 scanner (Packard Bioscience, Meriden, CT).

scan_protocol: Images were overlaid and analyzed using Imagene (BioDiscovery, El Segundo, CA).   Raw gene expression was imported from Imagene to GeneSifter (GeneSifter.Net, VizX Labs, Seattle, WA) for analysis.

data_processing: Data from at least 3 biological replicate experiments were normalized using Lowess normalization and by the median of the raw intensities for all spots in each sample for each array.

molecule: total RNA

organism: Homo sapiens

source_name: uninfected 6 hr

label_protocol: 5 to 20 mg of total RNA from uninfected control and infected samples was used to generate cDNA labeled with aminoallyl (aa)-dUTP through a reverse transcription reaction using anchored oligo(dT) primers.  The purified aa-dUTP-labeled cDNAs were coupled in 10 µl 0.1 M NaHCO3 with either Cy3 or Cy5 NHS-ester dye. Cy-dye labeled cDNA was purified using a Cyscribe GFX column (Amersham Biosciences, Piscataway, NJ).

extract_protocol: Cells were washed with phosphate buffered saline (PBS) and harvested for RNA isolation.  The RNA was purified using RNeasy kit (Qiagen, Valencia, CA) with DNase digestion according to manufacturer’s manual. The quality of RNA was checked using a Bioanalyzer (Agilent, Santa Clara, CA).

tag: infection

value: uninfected

tag: time point

value: 6 hr

tag: cell line

value: transfected HEK-293 derivative expressing integrin avb3

source_name: infected with p66- B. burgdorferi 6 hr

value: infected with p66- B. burgdorferi


title: 293+avb3 adherent, uninfected vs. p66- infected 24hr

description:
adherent cells
293 + avb3 adherent

source_name: uninfected 24 hr

value: 24 hr

source_name: infected with p66- B. burgdorferi 24 hr


title: 293+avb3 adherent, uninfected vs. p66+ infected 3hr

description:
adherent cells
293 + avb3 adherent

source_name: infected with p66+ B. burgdorferi 3 hr

value: infected with p66+ B. burgdorferi

value: 3 hr

source_name: uninfected 3 hr


title: 293 adherent, uninfected vs. p66- infected 6hr

description:
adherent cells
293 adherent


title: 293+avb3 adherent, uninfected vs. p66- infected 3hr

description:
adherent cells
293 + avb3 adherent

source_name: infected with p66- B. burgdorferi 3 hr


title: 293 adherent, uninfected vs. p66- infected 3hr

description:
adherent cells
293 adherent


title: 293+avb3 adherent, uninfected vs. p66+ infected 6hr

description:
adherent cells
293 + avb3 adherent

source_name: infected with p66+ B. burgdorferi 6 hr


title: Non-AMD1

status: Public on Mar 21 2011

type: genomic

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

hyb_protocol: Performed by NimbleGen according to their standard protocol.

data_processing:
Log2 (MeDIP/input) ratios were computed and scaled to center the ratio data around zero using NimbleScan software. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

Using NimbleScan software, peak data files are generated from the p-value data files. NimbleScan software detects peaks by searching for at least 2 probes above a p-value minimum cutoff (-log10) of 2. Peaks within 500bp of each other are merged. Peak score was used to filtered positive peaks in each sample. Peaks were identified by comparing MeDIP DNA of non-AMD1 (Ch2) and Input DNA of non-AMD1 (ch1).

molecule: genomic DNA

source_name: Non-AMD1 input

tag: cell type

value: non-AMD

source_name: Non-AMD1, MeDIP


title: HMEC lifted, uninfected vs. p66+ infected 3hr

description:
lifted cells
HMEC lifted

value: HMEC


title: AMD2

description: Non-AMD2 and AMD2 represent a pair of twins with discordant AMD phenotypes.

data_processing:
Log2 (MeDIP/input) ratios were computed and scaled to center the ratio data around zero using NimbleScan software. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

Using NimbleScan software, peak data files are generated from the p-value data files. NimbleScan software detects peaks by searching for at least 2 probes above a p-value minimum cutoff (-log10) of 2. Peaks within 500bp of each other are merged. Peak score was used to filtered positive peaks in each sample. Peaks were identified by comparing MeDIP DNA of AMD2 (Ch2) and Input DNA of AMD2 (ch1).

source_name: AMD2 input

label_protocol: Performed by NimbleGen according to their standard protocol.

source_name: AMD2, MeDIP


title: HMEC lifted, uninfected vs. p66+ infected 1hr

description:
lifted cells
HMEC lifted

source_name: uninfected 1 hr

value: 1 hr

source_name: infected with p66+ B. burgdorferi 1 hr


title: Eahy adherent, uninfected vs. p66- infected 24 hr

description:
adherent cells
Eahy adherent


title: Eahy adherent, uninfected vs. p66- infected 6 hr

description:
adherent cells
Eahy adherent


title: 293 adherent, uninfected vs. p66+ infected 3hr

description:
adherent cells
293 adherent


title: Eahy adherent, uninfected vs. p66+ infected 24 hr

description:
adherent cells
Eahy adherent

source_name: infected with p66+ B. burgdorferi 24 hr


title: 293 adherent, uninfected vs. p66+ infected 6hr

description:
adherent cells
293 adherent


title: HMEC lifted, uninfected vs. p66- infected 1hr

description:
lifted cells
HMEC lifted

source_name: infected with p66- B. burgdorferi 1 hr


title: Control heart_age 8 months_BSIX_rep2

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description:
BSIX-8mo-2
Gene expression data of control B6 heart, age 8 months.

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybridization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

label: biotin

organism: Mus musculus

source_name: Control heart, B6, untreated, age 8 months

label_protocol: Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5; and Invitrogen manual for SuperScript One-Cycle cDNA Kit).

growth_protocol: The study was performed with 8-month-old apolipoprotein E (apoE)-deficient mice treated for 2 months with the anti-diabetic drug rosiglitazone. Control groups consisted of age-matched untreated apoE-deficient mice and non-transgenic B6 mice. All mice had free access to food and water. Mice were fed a rodent chow containing 7 % fat and 0.15 % cholesterol (Ain 93-based diet). At an age of 6 months, the treatment group of apoE-deficient mice received rosiglitazone (30 mg/kg/d) for 2 months. At an age of 8 months, cardiac function of all study groups was determined by echocardiography and hearts were isolated.

extract_protocol: Total RNA was isolated from heart tissue with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: For the microarray study, hearts were isolated from three study groups: (i) failing hearts from 8-month-old apoE-deficient mice with 2 months of rosiglitazone treatment (30 mg/kg/d), (ii) hearts from 8-month-old untreated apoE-deficient mice, and (iii) hearts from 8-month-old untreated B6 controls.

tag: strain/background

tag: genotype

value: wild type

tag: age

value: 8 months

tag: tissue

value: control heart

tag: treatment


title: 293 adherent, uninfected vs. p66+ infected 24hr

description:
adherent cells
293 adherent


title: 293 adherent, uninfected vs. p66- infected 24hr

description:
adherent cells
293 adherent


title: 293+avb3 adherent, uninfected vs. p66+ infected 24hr

description:
adherent cells
293 + avb3 adherent


title: Failing heart_apoE-deficient_2 months of rosiglitazone_age 8 months_rep2

description:
Apoe-rosiglitazone-2
Gene expression data of failing apoE-deficient heart with 2 months of rosiglitazone, age 8 months.

source_name: Failing heart, apoE-deficient, 2 months of rosiglitazone, age 8 months

value: apoE-deficient

value: failing heart

value: 2 months of rosiglitazone


title: Control heart_age 8 months_BSIX_rep1

description:
BSIX-8mo-1
Gene expression data of control B6 heart, age 8 months.


title: Eahy adherent, uninfected vs. p66- infected 3 hr

description:
adherent cells
Eahy adherent


title: Eahy adherent, uninfected vs. p66+ infected 6 hr

description:
adherent cells
Eahy adherent

source_name: uninfected 6 hr


title: Eahy adherent, uninfected vs. p66+ infected 3 hr

description:
adherent cells
Eahy adherent


title: Heart_apoE-deficient_age 8 months_rep2

description:
Apoe-8mo-2
Gene expression data of apoE-deficient heart, age 8 months.

source_name: Heart, apoE-deficient, untreated, age 8 months

value: heart


title: Failing heart_apoE-deficient_2 months of rosiglitazone_age 8 months_rep1

description:
Apoe-rosiglitazone-1
Gene expression data of failing apoE-deficient heart with 2 months of rosiglitazone, age 8 months.


title: Heart_apoE-deficient_age 8 months_rep1

description:
Apoe-8mo-1
Gene expression data of apoE-deficient heart, age 8 months.


title: Non-AMD2

data_processing:
Log2 (MeDIP/input) ratios were computed and scaled to center the ratio data around zero using NimbleScan software. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

Using NimbleScan software, peak data files are generated from the p-value data files. NimbleScan software detects peaks by searching for at least 2 probes above a p-value minimum cutoff (-log10) of 2. Peaks within 500bp of each other are merged. Peak score was used to filtered positive peaks in each sample. Peaks were identified by comparing MeDIP DNA of non-AMD2 (Ch2) and Input DNA of non-AMD2 (ch1).

source_name: Non-AMD2 input

value: peripheral blood mononuclear cells

value: input

source_name: Non-AMD2, MeDIP

value: 5-methyl cytidine

value: Abcam

value: MeDIP


title: APP_R6_rep2

city: Heidelberg

first: Ulrike

last: Müller

address: Im Neuenheimer Feld 364

department: Bioinformatics and Functional Genomics

country: Germany

institute: Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg

hyb_protocol: Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.

data_processing: The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Animals were kept under specific pathogen free housing conditions (SPF unit) according to the guidelines of the German Council on Animal Care.

extract_protocol: Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.

treatment_protocol: Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices were dissected.

value: prefrontal cortex from adult APP knock-out mouse

tag: genetic background

value: back-crossed to C57BL/6 for 6 generations

tag: gender

value: male


title: WT_R6_rep2

value: prefrontal cortex from adult wild-type mouse


title: APLP2_R1_rep2

value: prefrontal cortex from adult APLP2 knock-out mouse with mixed genetic background

value: back-crossed to C57BL/6 for 1 generation


title: WT_R6_rep1


title: APPsa_R6_rep2

value: prefrontal cortex from adult APPsa knock-in mouse


title: APLP2_R1_rep3


title: E3-GemKD

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

description: Doxycycline-induction of Geminin shRNA knockdown

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(2) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 1.3-fold in treated versus untreated samples (E/B >1.3) groups, ii) MBEI differences were larger than 30 (E-B > 30), iii) expression was claimed as “present (P)” in at least one sample in each experiment. Probe sets that showed a change in expression upon Geminin knockdown that met cutoff values in at least 2 of the 3 experiments were considered for further single gene validation.

source_name: neurectoderm derived from embryonic stem cells

label_protocol: standard Affymetrix protocol

growth_protocol: mouse ES cells were induced to undergo neural fate commitment by culture in N2B27 medium for 2 days

extract_protocol: Total RNA was isolated from GemKD cells differentiated in N2B27 medium for two days with or without 500ng Dox and used for microarray analysis with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

treatment_protocol: shRNAmir-mediated knockdown of Geminin was induced in GemKD cells by doxycycline addition

value: Geminin knockdown, shRNAmir #11

tag: cell line origin

value: derivative of ES-E14TG2a (ATCC)

value: 129P2 (formerly 129/Ola)


title: APP_R6_rep3


title: APPsa_R6_rep1


title: APLP2_R6_rep1

value: prefrontal cortex from adult APLP2 knock-out mouse


title: APP_R6_rep1


title: E2-uninduced (no Dox) control

description: uninduced (no Dox) control

value: neurectoderm derived from embryonic stem cells

value: control, shRNAmir #9


title: E18L-24

city: Beijing

first: Tingting

last: Li

address: 38 Xueyuan Rd

department: Medical informatics

country: China

institute: Peking University

description: gene expression data from layer skeletal muscle collected at embyonic day 18

hyb_protocol: Affymetrix Gene Chip array hybridization was carried out according to Affymetrix Expression Analysis Technical Manual by GeneTech Biotechnology Limited Company (Shanghai, China). Following labeled cRNA fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45℃ on Affymetrix Chicken Genome Array. Washing and staining were followed standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: RMA with CDF file annotated by Dai et al.

organism: Gallus gallus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Meat-type broiler eggs (commercial Arbor Acres) and egg-type layer eggs (White Leghorn) were incubated at 37.5°C.

extract_protocol: total RNA were isolated from skeletal muscles (pectoralis) collected from broilers and layers at the embryonic stages E10, E12, E14 and E18 with TRiZol reagent.

treatment_protocol: skeletal muscles (pectoralis) were collected from broilers and layers at E10, E12, E14 and E18 stages, immediately frozen in liquid nitrogen, and stored at -80°C until RNA isolation.

value: skeletal muscle

tag: breed

value: layer

value: embyonic day 18


title: APLP2_R6_rep2


title: E3-uninduced (no Dox) control

description: uninduced (no Dox) control

value: control, shRNAmir #11


title: WT_R6_rep3


title: E1-uninduced (no Dox) control

description: uninduced (no Dox) control


title: E18L-23

source_name: layer skeletal muscle collected at embyonic day 18


title: E2-GemKD

value: Geminin knockdown, shRNAmir #9


title: APPsa_R6_rep3

value: back-crossed to C57BL/6 for 6 generations


title: APLP2_R1_rep1

value: male


title: E18B-21

description: gene expression data from broiler skeletal muscle collected at embyonic day 18

value: broiler


title: E18B-19

source_name: broiler skeletal muscle collected at embyonic day 18


title: E14L-17

description: gene expression data from layer skeletal muscle collected at embyonic day 14

value: embyonic day 14


title: E18B-20


title: E14L-18

source_name: layer skeletal muscle collected at embyonic day 14


title: E14B-15

description: gene expression data from broiler skeletal muscle collected at embyonic day 14


title: E12L-11

description: gene expression data from layer skeletal muscle collected at embyonic day 12

value: embyonic day 12


title: E12L-12

source_name: layer skeletal muscle collected at embyonic day 12


title: E18L-22


title: E12L-10


title: E12B-08

description: gene expression data from broiler skeletal muscle collected at embyonic day 12


title: E1-GemKD


title: E12B-07

source_name: broiler skeletal muscle collected at embyonic day 12


title: E10L-05

description: gene expression data from layer skeletal muscle collected at embyonic day 10

value: embyonic day 10


title: E10L-06

source_name: layer skeletal muscle collected at embyonic day 10


title: E12B-09


title: E10B-02

description: gene expression data from broiler skeletal muscle collected at embyonic day 10


title: E14B-14

source_name: broiler skeletal muscle collected at embyonic day 14


title: E10B-03

source_name: broiler skeletal muscle collected at embyonic day 10


title: HMEC lifted, uninfected vs. p66- infected 3hr

description:
lifted cells
HMEC lifted

source_name: uninfected 3 hr

value: uninfected

value: 3 hr

value: HMEC

source_name: infected with p66- B. burgdorferi 3 hr

value: infected with p66- B. burgdorfericharacteristics_ch2 =


title: E10B-01


title: E14B-13


title: CP724,714-treated_MCF10A_36hour

city: Detroit

first: Aliccia

middle: B

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

institute: Karmanos Cancer Inst., Wayne State University

description: Replicate 1 of 1.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R.

source_name: MCF-10A cell line, CP724,714, 36 hours

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit.

growth_protocol: MCF-10A cells were cultured in Ham's F-12 medium supplemented with 0.1% bovine serum albumin, fungizone (0.5 µg/mL), gentamicin (5 µg/mL), ethanolamine (5 mmol/L), HEPES (10 mmol/L), transferrin (5 µg/mL), 3,3,'5-Triiodo-L-Thyronine (T3 ) (10 µmol/L), selenium (50 µmol/L), hydrocortisone (1 µg/mL), insulin (5 µg/mL, and 10 ng/ml epidermal growth factor (EGF).

extract_protocol: RNA was extracted every three hours from parallel cultures with the QIAGEN Rneasy Plus kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanylizer and the Agilent RNA 6000 Nano Kit.

treatment_protocol: Cells were treated with the addition of 1uM CP724,714 (Pfizer Inc, Groton, CT) to culture media for 45 hours total.

value: nontransformed breast epithelial cells

tag: treatment time

value: 36 hours


title: CP724,714-treated_MCF10A_45hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 45 hours

value: 45 hours


title: E10L-04

value: skeletal muscle

value: layer


title: CP724,714-treated_MCF10A_33hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 33 hours

value: 33 hours


title: E10_03_layer

description: microRNA expression profiles of layer skeletal muscle collected at embyonic day 10

hyb_protocol: Microarray hybridizations were performed by LC Sciences.

scan_protocol: Microarrays were scanned using Axon GenePix 4000B Microarray Scanner.

data_processing: Normalization is carried out using a cyclic LOWESS (Locally-weighted Regression) method. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed.

label_protocol: total RNAs were isolated from skeletal muscles (pectoralis) collected from broilers and layers at E10 stage. RNA samples from broiler and layer were labeled either with Cy3 or Cy5.

growth_protocol: Meat-type broiler eggs (commercial Arbor Acres) and egg-type layer eggs (White Leghorn) were incubated at 37.5°C for 10 days (E10).

treatment_protocol: skeletal muscles (pectoralis) were collected from broilers and layers at E10 stage, immediately frozen in liquid nitrogen, and stored at -80°C until RNA isolation.


title: CP724,714-treated_MCF10A_42hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 42 hours

value: 42 hours


title: CP724,714-treated_MCF10A_39hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 39 hours

value: 39 hours


title: InVitroCells_6h_Aldosterone10-9M_rep3

city: Tokyo

first: Takanobu

last: Yoshimoto

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Clinical and Molecular Endocrinology

country: Japan

institute: Tokyo Medical and Dental University Graduate School

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 4x44k (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cells with 10-9 M aldosterone 6hr replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Cells were lysed using QIAzol Lysis Reagent (Qiagen) and total RNA was then extracted acoording to the manufacturer's protocol. RNA samples were then purified using the RNeasy minikit (Qiagene).

treatment_protocol: After the treatment with or without aldostreone, cells were drirectly lysed with QIAzol Lysis Reagent (Qiagene) and then scraped off.

value: MR-Eahy

tag: agent

value: aldosterone


title: E10_02_layer


title: InVitroCells_6h_w/oAldo_rep3

source_name: cells without aldosterone 6hr replicate 3


title: InVitroCells_6h_Aldosterone10-9M_rep2

source_name: cells with 10-9 M aldosterone 6hr replicate 2


title: InVitroCells_6h_w/oAldo_rep2

source_name: cells without aldosterone 6hr replicate 2


title: CP724,714-treated_MCF10A_27hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 27 hours

value: 27 hours


title: CP724,714-treated_MCF10A_18hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 18 hours

value: 18 hours


title: InVitroCells_6h_w/oAldo_rep1

source_name: cells without aldosterone 6hr replicate 1


title: CP724,714-treated_MCF10A_21hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 21 hours

value: 21 hours


title: CP724,714-treated_MCF10A_12hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 12 hours

value: 12 hours


title: CP724,714-treated_MCF10A_15hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 15 hours

value: 15 hours


title: CP724,714-treated_MCF10A_30hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 30 hours

value: 30 hours


title: Rice Stem-control

city: Hangzhou

first: Guoxin

last: zhou

state: Zhejiang

address: Kaixuan Road 268

institute: Zhejiang University, Institute of Insect Science

description: total RNA

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

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Results of the comparison analysis are provided in the 'full_matrix.txt' supplementary file on the Series record.

organism: Oryza sativa

source_name: rice stem

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

growth_protocol:
Pregerminated seeds of rice cv. Xiushui 11 were sown in a greenhouse. After 20–25 d, seedlings were transplanted into small clay pots (8 cm diameter × 10 cm height; one or three plants per pot) or larger clay pots (15 cm diameter × 15 cm height; 15 plants per pot). Plants were watered daily, and 10 ml nutrient solution (urea, 1 g L-1) was applied to each pot weekly. All plants were grown in a greenhouse at 28 ± 2 °C with a 12 h photoperiod and 70–80% RH. Twenty-five to 30 d after transplanting, plants were used for experiments.
Larvae of C. suppressalis were collected from a rice field in Hangzhou and maintained on Xiushui 11 rice seedlings in a controlled climate room at 26 ± 2 °C with a 12 h photoperiod and 80% RH. Third instar larvae were used in experiments.

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

treatment_protocol: Pots with one, three or fifteen plants were used (see details for each experiment). Plants were individually infested with a third instar SSB larvae that had been starved for 2 h. Control plants were kept insect-free. All plants were placed in a controlled climate room maintained at 26 ± 2 °C, a 12 h photoperiod and 80% RH. The onset of herbivore infestation was defined as the time that half of the larval body entered the stem. Samples were harvested at different times after the start of treatment (see details for each experiment).

value: dechorionated embryo


title: InVitroCells_6h_Aldosterone10-9M_rep1

source_name: cells with 10-9 M aldosterone 6hr replicate 1


title: E10_01_layer

source_name: layer skeletal muscle collected at embyonic day 10

value: embyonic day 10


title: Rice stem_SSB infested by 24 h-Rep2

description: total RNA

source_name: rice stem infested by SSB larvae for 24 h


title: Rice stem_SSB infested by 24 h-Rep1

description: total RNA


title: CP724,714-treated_MCF10A_9hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 9 hours

value: nontransformed breast epithelial cells

value: 9 hours


title: CP724,714-treated_MCF10A_6hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 6 hours

value: 6 hours


title: E10_02_broiler

description: microRNA expression profiles of broiler skeletal muscle collected at embyonic day 10

value: skeletal muscle

value: broiler


title: germinated pollen grains 2, biological rep 2

first: liqin

last: wei

address: 20 nanxincun, Xiangshan, Haidian distict

department: Research Center for Molecular & Developmental Biology

institute: Institute of Botany, Chinese Academy of Sciences

description: Gene expression data from rice germinated pollen grains

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

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

source_name: rice germinated pollen grains (GPG)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: room temperature ( 30 °C)

extract_protocol: total RNA was isolated by RNAplant reagent ((Tiangen Biotech))and  purified by Qiagen RNeasy kit.

tag: sample type

value: rice germinated pollen grains (GPG)

tag: subspecies

value: Oryza sativa L. ssp. Japonica

tag: collection protocol

value: fresh mature pollen gains are transferred into a liquid germination medium (20% sucrose, 10% polyethylene glycol 4000, 3 mM Ca(NO3)2 4H2O, 40 mg/liter H3BO3, 3 mg/liter vitamin B1) and cultured for about 10 min at room temperature ( 30C) to generate synchronously germinated rice pollen grains (GPGs).

value: germinated pollen grains in vitro


title: CP724,714-treated_MCF10A_0hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, untreated

value: 0 hours


title: germinated pollen grains 3, biological rep 3


title: mature pollen grains 2, biological rep 2

description: Gene expression data from rice mature pollen grains

source_name: rice mature tricellular pollen (MPG)

growth_protocol: natural growth season in Beijing (39°54'N, 116°24'E).

extract_protocol: total RNA was isolated by RNAplant reagent ((Tiangen Biotech))and  purified by Qiagen RNeasy kit

value: rice mature tricellular pollen (MPG)

value: mautre pollen grains are collected by shaking panicles gently during flowering.

value: pollen grains after anther dehiscence


title: germinated pollen grains 1, biological rep 1

value: fresh mature pollen gains are transferred into a liquid germination medium (20% sucrose, 10% polyethylene glycol 4000, 3 mM Ca(NO3)2 4H2O, 40 mg/liter H3BO3, 3 mg/liter vitamin B1) and cultured for about 10 min at room temperature ( 30C) to generate synchronously germinated rice pollen grains.


title: CP724,714-treated_MCF10A_3hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 3 hours

value: 3 hours


title: mature pollen grains 3, biological rep 3


title: mature pollen grains 1, biological rep1


title: E10_03_broiler

source_name: broiler skeletal muscle collected at embyonic day 10


title: APLP2_R6_rep3

value: prefrontal cortex from adult APLP2 knock-out mouse

value: back-crossed to C57BL/6 for 6 generations

value: male


title: E10_01_broiler

value: embyonic day 10


title: CP724,714-treated_45hour

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: SUM-225 cell line

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: SUM-225 cells were cultured in Ham's F-12 medium supplemented with 5% fetal bovine serum, insulin (5 µg/ml) and hydrocortisone (1 µg/mL)

value: breast cancer-derived cell line with HER-2 amplification and over expression

tag: time


title: tricellular pollen 2, biological rep2

description: Gene expression data from rice tricellular pollen

source_name: rice immature tricellular pollen (TCP)

value: rice immature tricellular pollen (TCP)

value: crach gently the anther in 0.4 M mannitol at 4C, remove the anther wall and fragment, and the grains are collected  by centrifugation (500 g, 5min, 4C).

value: pollen granins after PM (Pollen Mitosis) but dehydroded


title: tricellular pollen 3, biological rep3

value: Oryza sativa L. ssp. Japonica


title: CP724,714-treated_MCF10HER2_45hour

description:
The MCF-10HER-2 cell line is derived from the nontransformed breast epithelial cell line MCF-10A and is transduced to stably overexpress the HER-2 oncogene.
Replicate 1 of 1.

source_name: MCF-10HER-2 cell line, CP724,714, 45 hours

growth_protocol: MCF-10HER-2 cells were cultured in Ham's F-12 medium supplemented with 0.1% bovine serum albumin, fungizone (0.5 µg/mL), gentamicin (5 µg/mL), ethanolamine (5 mmol/L), HEPES (10 mmol/L), transferrin (5 µg/mL), 3,3,'5-Triiodo-L-Thyronine (T3 ) (10 µmol/L), selenium (50 µmol/L), hydrocortisone (1 µg/mL), and 10 ng/ml epidermal growth factor (EGF).

tag: cell line

value: nontransformed breast epithelial cells stably overexpressing HER-2

value: 45 hours


title: CP724,714-treated_MCF10HER2_42hour

source_name: MCF-10HER-2 cell line, CP724,714, 42 hours

tag: cell type

value: 42 hours


title: CP724,714-treated_42hour

description: replicate 1


title: CP724,714-treated_MCF10HER2_36hour

source_name: MCF-10HER-2 cell line, CP724,714, 36 hours

value: 36 hours


title: CP724,714-treated_MCF10HER2_39hour

source_name: MCF-10HER-2 cell line, CP724,714, 39 hours

value: 39 hours


title: CP724,714-treated_MCF10HER2_33hour

source_name: MCF-10HER-2 cell line, CP724,714, 33 hours

value: 33 hours


title: bicellular pollen 3, biological rep3

description: Gene expression data from rice bicellular pollen

source_name: rice bicellular pollen (BCP)

value: rice bicellular pollen (BCP)

value: crach gently the anther in 0.4 M mannitol at 4C, remove the anther wall and fragment, and the pollen grains are isolated through 25%/35%/45%/80% Percoll step gradient, the bicellular pollen was distributed in the fraction of 35%/45%.

value: pollen granins before PM (Pollen Mitosis) and after PM (Pollen Mitosis)


title: tricellular pollen 1, biological rep1


title: CP724,714-treated_MCF10HER2_30hour

source_name: MCF-10HER-2 cell line, CP724,714, 30 hours

value: 30 hours


title: CP724,714-treated_27hour

description: replicate 1


title: CP724,714-treated_24hour

description: replicate 1


title: CP724,714-treated_33hour

description: replicate 1


title: CP724,714-treated_MCF10HER2_27hour

source_name: MCF-10HER-2 cell line, CP724,714, 27 hours

value: 27 hours


title: CP724,714-treated_36hour

description: replicate 1


title: CP724,714-treated_30hour

description: replicate 1


title: bicellular pollen 2, biological rep2


title: CP724,714-treated_MCF10HER2_24hour

source_name: MCF-10HER-2 cell line, CP724,714, 24 hours

value: 24 hours


title: uninucleate microspores 2, biological rep2

description: Gene expression data from rice uniucleate microspores

source_name: rice uninucleate microspores (UNM)

value: rice uninucleate microspores (UNM)

value: crach gently the anther in 0.4 M mannitol at 4C, remove the anther wall and fragment, and the microspores are collected  by centrifugation (500 g, 5min, 4C).

value: uniucleate microspores released from tetrad


title: uninucleate microspores 1, biological rep1


title: uninucleate microspores 3, biological rep3


title: Root 3, biological rep3

description: Gene expression data from rice roots

source_name: Rice root

growth_protocol: Rice  seeds were germinated and grown in a growth container for two weeks (28?, 16 h light, 8 h dark, photo intensity 240 ?m photos m-2s-1).

value: Rice root

value: the seedling root were cutted and harvested from two-week seeding

value: two-week old rice root


title: CP724,714-treated_39hour

description: replicate 1

value: breast cancer-derived cell line with HER-2 amplification and over expression


title: bicellular pollen 1, biological rep1

value: Oryza sativa L. ssp. Japonica


title: CP724,714-treated_MCF10HER2_21hour

source_name: MCF-10HER-2 cell line, CP724,714, 21 hours

value: nontransformed breast epithelial cells stably overexpressing HER-2

value: 21 hours


title: CP724,714-treated_MCF10HER2_18hour

source_name: MCF-10HER-2 cell line, CP724,714, 18 hours

value: 18 hours


title: CP724,714-treated_18hour

description: replicate 1


title: Root 2, biological rep2

description: Gene expression data from rice roots


title: CP724,714-treated_MCF10HER2_15hour

source_name: MCF-10HER-2 cell line, CP724,714, 15 hours

value: 15 hours


title: CP724,714-treated_MCF10HER2_12hour

source_name: MCF-10HER-2 cell line, CP724,714, 12 hours

value: 12 hours


title: Leaf 3, biological rep3

description: Gene expression data from rice leaves

source_name: Rice leaf

growth_protocol: Rice were germinated and grown in soil.

value: Rice leaf

value: the flag leaf were harvested from rice plants during grain filling

value: flag leaf during rice grain filling (about 110-120 days after germination)


title: Root 1, biological rep1

description: Gene expression data from rice roots


title: CP724,714-treated_21hour

description: replicate 1

source_name: SUM-225 cell line


title: Leaf 2, biological rep2

description: Gene expression data from rice leaves


title: E14L-16

source_name: layer skeletal muscle collected at embyonic day 14

value: skeletal muscle

value: layer

value: embyonic day 14


title: CP724,714-treated_MCF10HER2_9hour

source_name: MCF-10HER-2 cell line, CP724,714, 9 hours

value: 9 hours


title: CP724,714-treated_9hour

description: replicate 1

value: 9 h


title: CP724,714-treated_6hour

description: replicate 1

value: 6 h


title: CP724,714-treated_MCF10HER2_3hour

source_name: MCF-10HER-2 cell line, CP724,714, 3 hours

value: 3 hours


title: CP724,714-treated_MCF10HER2_6hour

source_name: MCF-10HER-2 cell line, CP724,714, 6 hours

value: 6 hours


title: Dendritic Exosomes_#8

status: Public on Mar 17 2011

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

description: Expression of miRNAs from Dendritic exosomes

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55C in a hybridization oven  (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v2.0 (miRNA Microarray System Protocol, Agilent Technologies).

data_processing: Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 10.7.3.1 and protocol miRNA_105_Jan09

source_name: Dendritic Exosomes

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

growth_protocol: The human Jurkat-derived T-cell lines J77cl20 and the lymphoblastoid B-cell lines Raji (Burkitt lymphoma), were cultured in RPMI (Sigma) containing 10% fetal bovine serum (Invitrogen). To generate Dendritic cells, monocytes from healthy donors were cultured for 6 days in the presence of IL4 and GMCSF

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) and the miRNeasy® mini kit (Quiagen),

treatment_protocol: Donor cells were cultured in RPMI-1640 supplemented with 10% FBS (depleted of bovine exosomes by overnight centrifugation at 100000g), and exosomes were prepared from cell supernatants by several centrifugation and filtration steps . Briefly, cells were centrifuged (320g for 5 min) and the supernatant filtered through 0.22 μm membranes. Exosomes were pelleted by ultracentrifugation at 100000g for 60 min at 4C (Beckman Coulter Optima L-100 XP).

tag: origin

value: Exosome

value: Dendritic


title: Raji Exosomes_#9

description: Expression of miRNAs from Raji exosomes

source_name: Raji Exosomes

value: Raji


title: Jurkat Exosomes_#10

description: Expression of miRNAs from Jurkat exosomes

source_name: Jurkat Exosomes

value: Jurkat


title: Jurkat Cells_#10

description: Expression of miRNAs from Jurkat cells

source_name: Jurkat Cells

value: Whole cell


title: Raji Cells_#9

description: Expression of miRNAs from Raji cells

source_name: Raji Cells


title: CP724,714-treated_3hour

description: replicate 1

value: breast cancer-derived cell line with HER-2 amplification and over expression

value: 3 h


title: callus cell 2, biological rep2

description: Gene expression data from rice callus cells

source_name: Rice calli

growth_protocol: Rice seeds were induced in N6 solid medium containing 2,4-D (2 mg/l) at 25C for approximate one month.

value: Rice calli

value: Oryza sativa L. ssp. Japonica

value: the callus cell was collected directly.

value: one-month fresh rice calli


title: CP724,714-treated_MCF10HER2_0hour

source_name: MCF-10HER-2 cell line, untreated

value: nontransformed breast epithelial cells stably overexpressing HER-2

value: 0 hours


title: CP724,714-treated_0hour

description: replicate 1

value: 0 h


title: Leaf 1, biological rep1

description: Gene expression data from rice leaves

value: Rice leaf

value: the flag leaf were harvested from rice plants during grain filling

value: flag leaf during rice grain filling (about 110-120 days after germination)


title: callus cell 3, biological rep3


title: Dendritic Cells_#8

description: Expression of miRNAs from Dendritic cells

source_name: Dendritic Cells


title: callus cell 1, biological rep1


title: Dendritic Exosomes_#1

value: Exosome


title: Jurkat Exosomes_#7


title: Dendritic Cells_#1

value: Dendritic


title: Jurkat Exosomes_#5


title: Jurkat Cells_#6

description: Expression of miRNAs from Jurkat cells


title: Jurkat Cells_#5

description: Expression of miRNAs from Jurkat cells


title: Raji Cells_#2

description: Expression of miRNAs from Raji cells

value: Raji


title: Raji Exosomes_#4

description: Expression of miRNAs from Raji exosomes


title: Raji Cells_#3

description: Expression of miRNAs from Raji cells


title: Raji Exosomes_#2

description: Expression of miRNAs from Raji exosomes


title: CP724,714-treated_MCF10A_24hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, CP724,714, 24 hours

value: nontransformed breast epithelial cells

value: 24 hours


title: Skin_Footpads_M. leprae non-infected_12 month_rep2

city: Seoul

first: Tae Hoon

last: Kim

state: Socho-gu

address: 505 Bonpo-dong

department: Pathology

country: South Korea

institute: Medical College of the Catholic University

description: Replicate 2 of 3 in Control

data_processing: Gene Expression data was extracted and processed using Illumina Beadstudio.

label: Biotin

source_name: Skin of M. lepare non-infected footpads

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

extract_protocol: Total RNA was isolated using a TRIZOL Reagent (Invitrogen) following manufacturer's instructions.

treatment_protocol: M. leprae non-infected footpads: PBS (subcutaneous injection), M. leprae-infected footpads: 2´10^6 bacteria (subcutaneous injection)

tag: strain

value: BALB/c

tag: genotype/variation

value: skin

tag: experimental period

value: 12 months


title: TH-MYCN_mad552

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: primary tumor

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The RMA method was applied to CEL files using Partek Genomics Suite 6.4 (St. Louis, Mo)

source_name: neuroblastoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

extract_protocol: RNA was extracted from TH-MYCN mouse tumors using Trizol reagent (Invitrogen)

tag: tissue

value: neuroblastoma

tag: genotype

value: TH-MYCN


title: TH-MYCN_mad563

description: primary tumor


title: TH-MYCN_mad554

description: primary tumor


title: TH-MYCN_mad562

description: primary tumor


title: TH-MYCN_mad553

description: primary tumor


title: TH-MYCN_mad548

description: primary tumor


title: TH-MYCN_mad558

description: primary tumor


title: Skin_Footpads_M. leprae non-infected_12 month_rep1

description: Replicate 1 of 3 in Control


title: Skin_Footpads_M. leprae infected_12 month_rep3

description: Replicate 3 of 3 in Sample

source_name: Skin of M. lepare infected footpads


title: TH-MYCN_mad559

description: primary tumor


title: TH-MYCN_mad561

description: primary tumor


title: Skin_Footpads_M. leprae infected_12 month_rep1

description: Replicate 1 of 3 in Sample


title: TH-MYCN_mad565

description: primary tumor


title: TH-MYCN_mad551

description: primary tumor


title: TH-MYCN_mad550

description: primary tumor


title: TH-MYCN_mad549

description: primary tumor


title: TH-MYCN_mad564

description: primary tumor


title: Skin_Footpads_M. leprae infected_12 month_rep2

description: Replicate 2 of 3 in Sample


title: TH-MYCN_mad560

description: primary tumor


title: TH-MYCN_mad555

description: primary tumor


title: TH-MYCN_mad556

description: primary tumor


title: Skin_Footpads_M. leprae non-infected_12 month_rep3

description: Replicate 3 of 3 in Control


title: CP65.M

city: Goettingen

first: Marian

last: Grade

address: Robert-Koch-Str. 40

department: Surgery

institute: University Medical Center Goettingen, Georg-August-University

description: Human pretherapeutic colon cancer patient biopsy sample CP65.M

hyb_protocol: Expression profiling was carried out on National Cancer Institute oligonucleotide arrays (21,543 features) using the Operon V2 oligo set. Briefly, 20 ug of Cy3-labeled test cDNA and 20 ug of Cy5-labeled reference cDNA were hybridized at 42C overnight in specifically designed hybridization cassettes (TeleChem International, Sunnyvale, CA).

scan_protocol: After hybridization, slides were washed and scanned on an Axon scanner using GenePixPro (3.0) software (Axon Instruments, Union City, CA).

data_processing: Median signal intensities from the Feature Extraction Software were converted to log2 lowess normalized M-values (sample over control) which were again quantile normalized using the R package “limma”.

source_name: Pretherapeutic colon cancer patient biopsy

label_protocol: The amount of material was in the range of 24 to 370 mg. RNA extraction was done using TRIZOL (Invitrogen, Carlsbad, CA) according to standard procedures and resulted in RNA amounts that averaged 207 ug; 20 ug of total RNA were reverse transcribed into cDNA using random primers and reverse transcriptase. After incorporation of aminoallyl-dUTP followed by chemical coupling of Cy3 (Amersham, Piscataway, NJ), cDNA quantification and labeling efficiency was determined using the Nanodrop quantification device (Nanodrop, Rockland, DE). Control cDNA was generated by labeling of a reference mRNA pool (Stratagene, La Jolla, CA) as mentioned above using Cy5 (Amersham).

growth_protocol: Biospies from patients not cell lines were used for analyses

extract_protocol: Patients and sample collection. For this study, we collected tumor specimens from 73 patients with primary adenocarcinomas of the colon who were treated at the Department of General Surgery, University Medical Center, Gottingen, Germany. All tumors were located at least 16 cm above the anocutaneous verge and were classified based on the WHO histopathologic typing of colorectal cancers. After surgery, tumor resections were immediately stored on ice and then inspected by an experienced pathologist. Consistent with standard procedures, samples were only considered when the tissue contained at least 70% of tumor cells. Representative sections were macrodissected from the tumors and snapfrozen in liquid nitrogen. When possible, a representative biopsy of normal colonic mucosa was also obtained (n = 30).

treatment_protocol: No treatment prior to expression profiling analysis was performed.

tag: pid

value: mucosa

tag: age

tag: sex

value: m

tag: uiccstage

value: III

tag: t

tag: n

tag: nodal-count

tag: r

tag: g

molecule: polyA RNA

source_name: reference mRNA pool from Stratagene

value: reference mRNA pool


title: CP67.M

description: Human pretherapeutic colon cancer patient biopsy sample CP67.M

tag: sample type


title: CP62.M

description: Human pretherapeutic colon cancer patient biopsy sample CP62.M


title: CP56.M

description: Human pretherapeutic colon cancer patient biopsy sample CP56.M


title: CP73.M

description: Human pretherapeutic colon cancer patient biopsy sample CP73.M


title: CP68.M

description: Human pretherapeutic colon cancer patient biopsy sample CP68.M


title: CP53.M

description: Human pretherapeutic colon cancer patient biopsy sample CP53.M


title: CP46.M

description: Human pretherapeutic colon cancer patient biopsy sample CP46.M


title: CP42.M

description: Human pretherapeutic colon cancer patient biopsy sample CP42.M


title: CP44.M

description: Human pretherapeutic colon cancer patient biopsy sample CP44.M

value: f


title: CP39.M

description: Human pretherapeutic colon cancer patient biopsy sample CP39.M


title: CP40.M

description: Human pretherapeutic colon cancer patient biopsy sample CP40.M


title: CP51.M

description: Human pretherapeutic colon cancer patient biopsy sample CP51.M


title: CP38.M

description: Human pretherapeutic colon cancer patient biopsy sample CP38.M


title: CP724,714-treated_12hour

description: replicate 1

source_name: SUM-225 cell line

tag: cell type

value: breast cancer-derived cell line with HER-2 amplification and over expression

tag: treatment

tag: time

tag: cell line


title: CP724,714-treated_15hour

description: replicate 1


title: CP22.M

description: Human pretherapeutic colon cancer patient biopsy sample CP22.M

value: II


title: CP23.M

description: Human pretherapeutic colon cancer patient biopsy sample CP23.M


title: CP24.M

description: Human pretherapeutic colon cancer patient biopsy sample CP24.M


title: CP69.T

description: Human pretherapeutic colon cancer patient biopsy sample CP69.T

value: tumor


title: CP70.T

description: Human pretherapeutic colon cancer patient biopsy sample CP70.T


title: CP11.M

description: Human pretherapeutic colon cancer patient biopsy sample CP11.M


title: CP72.T

description: Human pretherapeutic colon cancer patient biopsy sample CP72.T


title: CP66.T

description: Human pretherapeutic colon cancer patient biopsy sample CP66.T


title: CP10.M

description: Human pretherapeutic colon cancer patient biopsy sample CP10.M


title: CP71.T

description: Human pretherapeutic colon cancer patient biopsy sample CP71.T


title: CP65.T

description: Human pretherapeutic colon cancer patient biopsy sample CP65.T


title: CP25.M

description: Human pretherapeutic colon cancer patient biopsy sample CP25.M


title: CP64.T

description: Human pretherapeutic colon cancer patient biopsy sample CP64.T


title: CP01.M

description: Human pretherapeutic colon cancer patient biopsy sample CP01.M


title: CP28.M

description: Human pretherapeutic colon cancer patient biopsy sample CP28.M


title: CP14.M

description: Human pretherapeutic colon cancer patient biopsy sample CP14.M


title: CP73.T

description: Human pretherapeutic colon cancer patient biopsy sample CP73.T


title: CP67.T

description: Human pretherapeutic colon cancer patient biopsy sample CP67.T


title: CP60.T

description: Human pretherapeutic colon cancer patient biopsy sample CP60.T


title: CP06.M

description: Human pretherapeutic colon cancer patient biopsy sample CP06.M


title: CP20.M

description: Human pretherapeutic colon cancer patient biopsy sample CP20.M


title: CP68.T

description: Human pretherapeutic colon cancer patient biopsy sample CP68.T


title: CP61.T

description: Human pretherapeutic colon cancer patient biopsy sample CP61.T


title: CP31.M

description: Human pretherapeutic colon cancer patient biopsy sample CP31.M


title: CP18.M

description: Human pretherapeutic colon cancer patient biopsy sample CP18.M


title: CP29.M

description: Human pretherapeutic colon cancer patient biopsy sample CP29.M


title: CP63.T

description: Human pretherapeutic colon cancer patient biopsy sample CP63.T


title: CP09.M

description: Human pretherapeutic colon cancer patient biopsy sample CP09.M


title: CP62.T

description: Human pretherapeutic colon cancer patient biopsy sample CP62.T


title: CP58.T

description: Human pretherapeutic colon cancer patient biopsy sample CP58.T


title: CP57.T

description: Human pretherapeutic colon cancer patient biopsy sample CP57.T


title: CP56.T

description: Human pretherapeutic colon cancer patient biopsy sample CP56.T


title: CP53.T

description: Human pretherapeutic colon cancer patient biopsy sample CP53.T


title: CP47.T

description: Human pretherapeutic colon cancer patient biopsy sample CP47.T


title: CP52.T

description: Human pretherapeutic colon cancer patient biopsy sample CP52.T


title: CP49.T

description: Human pretherapeutic colon cancer patient biopsy sample CP49.T


title: CP50.T

description: Human pretherapeutic colon cancer patient biopsy sample CP50.T


title: CP48.T

description: Human pretherapeutic colon cancer patient biopsy sample CP48.T


title: CP51.T

description: Human pretherapeutic colon cancer patient biopsy sample CP51.T


title: CP46.T

description: Human pretherapeutic colon cancer patient biopsy sample CP46.T


title: CP44.T

description: Human pretherapeutic colon cancer patient biopsy sample CP44.T


title: CP38.T

description: Human pretherapeutic colon cancer patient biopsy sample CP38.T


title: CP42.T

description: Human pretherapeutic colon cancer patient biopsy sample CP42.T


title: CP41.T

description: Human pretherapeutic colon cancer patient biopsy sample CP41.T


title: CP45.T

description: Human pretherapeutic colon cancer patient biopsy sample CP45.T


title: CP39.T

description: Human pretherapeutic colon cancer patient biopsy sample CP39.T


title: CP59.T

description: Human pretherapeutic colon cancer patient biopsy sample CP59.T


title: CP35.T

description: Human pretherapeutic colon cancer patient biopsy sample CP35.T


title: CP37.T

description: Human pretherapeutic colon cancer patient biopsy sample CP37.T


title: CP33.M

description: Human pretherapeutic colon cancer patient biopsy sample CP33.M


title: CP32.T

description: Human pretherapeutic colon cancer patient biopsy sample CP32.T


title: CP30.T

description: Human pretherapeutic colon cancer patient biopsy sample CP30.T


title: CP40.T

description: Human pretherapeutic colon cancer patient biopsy sample CP40.T


title: CP34.T

description: Human pretherapeutic colon cancer patient biopsy sample CP34.T


title: CP36.T

description: Human pretherapeutic colon cancer patient biopsy sample CP36.T


title: CP43.T

description: Human pretherapeutic colon cancer patient biopsy sample CP43.T


title: CP29.T

description: Human pretherapeutic colon cancer patient biopsy sample CP29.T


title: CP28.T

description: Human pretherapeutic colon cancer patient biopsy sample CP28.T


title: CP33.T

description: Human pretherapeutic colon cancer patient biopsy sample CP33.T


title: CP31.T

description: Human pretherapeutic colon cancer patient biopsy sample CP31.T


title: CP25.T

description: Human pretherapeutic colon cancer patient biopsy sample CP25.T


title: CP27.T

description: Human pretherapeutic colon cancer patient biopsy sample CP27.T


title: CP26.T

description: Human pretherapeutic colon cancer patient biopsy sample CP26.T


title: CP24.T

description: Human pretherapeutic colon cancer patient biopsy sample CP24.T


title: CP23.T

description: Human pretherapeutic colon cancer patient biopsy sample CP23.T


title: CP21.T

description: Human pretherapeutic colon cancer patient biopsy sample CP21.T


title: CP20.T

description: Human pretherapeutic colon cancer patient biopsy sample CP20.T


title: CP22.T

description: Human pretherapeutic colon cancer patient biopsy sample CP22.T


title: CP19.T

description: Human pretherapeutic colon cancer patient biopsy sample CP19.T


title: CP16.T

description: Human pretherapeutic colon cancer patient biopsy sample CP16.T


title: CP17.T

description: Human pretherapeutic colon cancer patient biopsy sample CP17.T


title: CP15.T

description: Human pretherapeutic colon cancer patient biopsy sample CP15.T


title: CP18.T

description: Human pretherapeutic colon cancer patient biopsy sample CP18.T


title: CP13.T

description: Human pretherapeutic colon cancer patient biopsy sample CP13.T


title: CP12.T

description: Human pretherapeutic colon cancer patient biopsy sample CP12.T


title: CP14.T

description: Human pretherapeutic colon cancer patient biopsy sample CP14.T


title: CP11.T

description: Human pretherapeutic colon cancer patient biopsy sample CP11.T


title: CP08.T

description: Human pretherapeutic colon cancer patient biopsy sample CP08.T


title: CP09.T

description: Human pretherapeutic colon cancer patient biopsy sample CP09.T


title: CP54.T

description: Human pretherapeutic colon cancer patient biopsy sample CP54.T


title: CP10.T

description: Human pretherapeutic colon cancer patient biopsy sample CP10.T


title: Patient with SCOS 12

city: Münster

first: Frank

last: Tüttelmann

address: Vesaliusweg 12-14

department: University of Münster

institute: Institute of Human Genetics

hyb_protocol: according to standard protocol Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis (Version 4.0; June 2006)

scan_protocol: Scanned on an Agilent G2565CA scanner

data_processing: Agilent Feature Extraction Software (v 10.7)

source_name: Patient with SCOS 12

extract_protocol: genomic DNA extracted from peripheral blood by standard methods

tag: source

value: peripheral blood

tag: disease state

value: bilateral Sertoli-cell-only syndrome

source_name: Promega Human Genomic DNA


title: CP55.T

description: Human pretherapeutic colon cancer patient biopsy sample CP55.T

tag: tissue


title: Patient with SCOS 11

source_name: Patient with SCOS 11

label_protocol: according to standard protocol Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis (Version 4.0; June 2006)


title: Patient with SCOS 14

source_name: Patient with SCOS 14


title: CP07.T

description: Human pretherapeutic colon cancer patient biopsy sample CP07.T

tag: pid


title: Patient with SCOS 15

source_name: Patient with SCOS 15


title: CP05.T

description: Human pretherapeutic colon cancer patient biopsy sample CP05.T

tag: age


title: Patient with SCOS 13

source_name: Patient with SCOS 13


title: CP06.T

description: Human pretherapeutic colon cancer patient biopsy sample CP06.T

tag: sex


title: Patient with SCOS 5

source_name: Patient with SCOS 5


title: CP03.T

description: Human pretherapeutic colon cancer patient biopsy sample CP03.T

tag: uiccstage


title: Patient with SCOS 6

source_name: Patient with SCOS 6


title: Patient with SCOS 17

source_name: Patient with SCOS 17


title: Patient with SCOS 7

source_name: Patient with SCOS 7


title: Patient with SCOS 9

source_name: Patient with SCOS 9


title: Patient with SCOS 3

source_name: Patient with SCOS 3


title: CP02.T

description: Human pretherapeutic colon cancer patient biopsy sample CP02.T

tag: t


title: Patient with SCOS 4

source_name: Patient with SCOS 4


title: CP01.T

description: Human pretherapeutic colon cancer patient biopsy sample CP01.T

tag: n


title: Patient with SCOS 2

source_name: Patient with SCOS 2


title: Patient with SCOS 8

source_name: Patient with SCOS 8


title: Patient with SCOS 10

source_name: Patient with SCOS 10


title: Patient with OAT 29

source_name: Patient with OAT 29

value: idiopathic severe oligozoospermia


title: Live M. leprae infected peritoneal macrophage 6

description: Replicate 6 of 8

hyb_protocol: Used 'Gene Expression Hyb Kit (Agilent).' Followed manufacturer's protocol

scan_protocol: Used GenePix 4000B laser scanner (Axon Instrument) with 5 um resolution. Images were quantified using Agilent Feature Extraction Software (version 9.5.3).

data_processing:
Agilent Feature Extraction Software (v 9.5.3) was used for background subtraction and LOWESS normalization.
The data were then analyzed by GeneSpring. In processes using GeneSpring, we set step called as flagged data removal to ignore or eliminate low signal, abnormal spot, or inappropriate signal affected by background signal etc. Due to various reasons, the Flag indicates incorrect signal of spots. Flag is marked with three codes (A, M, and P) and No. The spot value flagged with “A” is not used to analyze microarray data using GeneSpring, TM4, Cluster by Eisen lab, GSEA and etc. Finally, “No” means NO DATA.

label: Cy 3

source_name: PBS injected peritoneal macrophage 14

label_protocol: Used 'Low Input Quick Amp Labeling Kit (Agilent).' Followed manufacturer's protocol

extract_protocol: total RNA was extracted using Trizol (Invitrogen). Followed manufacturer's protocol

treatment_protocol: Control: PBS (intraperitoneal injection), Sample 1: Heat-killed M. leprae (2´10^6 bacilli intraperitoneal injection), and Sample 2: Live M. leprae (2´10^6 bacilli intraperitoneal injection)

tag: primary cells

value: Peritoneal Macrophage

tag: strain

value: BALB/c nu/nu

tag: genotype/variation

tag: experimental period

value: 2 weeks after injection

label: Cy 5

source_name: Live M.leprae injected peritoneal macrophage 6


title: Patient with SCOS 16

source_name: Patient with SCOS 16

source_name: Promega Human Genomic DNA


title: Live M. leprae infected peritoneal macrophage 7

description: Replicate 7 of 8

source_name: PBS injected peritoneal macrophage 15

source_name: Live M.leprae injected peritoneal macrophage 7


title: Patient with OAT 27

source_name: Patient with OAT 27


title: Patient with SCOS 1

source_name: Patient with SCOS 1


title: Live M. leprae infected peritoneal macrophage 4

description: Replicate 4 of 8

source_name: PBS injected peritoneal macrophage 12

source_name: Live M.leprae injected peritoneal macrophage 4


title: Live M. leprae infected peritoneal macrophage 3

description: Replicate 3 of 8

source_name: PBS injected peritoneal macrophage 11

source_name: Live M.leprae injected peritoneal macrophage 3


title: Live M. leprae infected peritoneal macrophage 1

description: Replicate 1 of 8

source_name: PBS injected peritoneal macrophage 9

source_name: Live M.leprae injected peritoneal macrophage 1


title: Patient with OAT 26

source_name: Patient with OAT 26


title: Live M. leprae infected peritoneal macrophage 5

description: Replicate 5 of 8

source_name: PBS injected peritoneal macrophage 13

source_name: Live M.leprae injected peritoneal macrophage 5


title: Live M. leprae infected peritoneal macrophage 8

description: Replicate 8 of 8

source_name: PBS injected peritoneal macrophage 16

source_name: Live M.leprae injected peritoneal macrophage 8


title: Heat-killed M. leprae infected peritoneal macrophage 7

description: Replicate 7 of 8

source_name: PBS injected peritoneal macrophage 7

source_name: Heat-killed M.leprae injected peritoneal macrophage 7


title: Patient with OAT 22

source_name: Patient with OAT 22

source_name: Promega Human Genomic DNA


title: Heat-killed M. leprae infected peritoneal macrophage 8

description: Replicate 8 of 8

source_name: PBS injected peritoneal macrophage 8

source_name: Heat-killed M.leprae injected peritoneal macrophage 8


title: Patient with OAT 23

source_name: Patient with OAT 23


title: Heat-killed M. leprae infected peritoneal macrophage 4

description: Replicate 4 of 8

source_name: PBS injected peritoneal macrophage 4

source_name: Heat-killed M.leprae injected peritoneal macrophage 4


title: Patient with OAT 28

source_name: Patient with OAT 28


title: Heat-killed M. leprae infected peritoneal macrophage 5

description: Replicate 5 of 8

source_name: PBS injected peritoneal macrophage 5

source_name: Heat-killed M.leprae injected peritoneal macrophage 5


title: Live M. leprae infected peritoneal macrophage 2

description: Replicate 2 of 8

source_name: PBS injected peritoneal macrophage 10

source_name: Live M.leprae injected peritoneal macrophage 2


title: Patient with OAT 20

source_name: Patient with OAT 20


title: Patient with OAT 21

source_name: Patient with OAT 21


title: Patient with OAT 25

source_name: Patient with OAT 25


title: Patient with OAT 18

source_name: Patient with OAT 18


title: Patient with OAT 14

source_name: Patient with OAT 14


title: Patient with OAT 19

source_name: Patient with OAT 19


title: Heat-killed M. leprae infected peritoneal macrophage 3

description: Replicate 3 of 8

source_name: PBS injected peritoneal macrophage 3

source_name: Heat-killed M.leprae injected peritoneal macrophage 3


title: Patient with OAT 16

source_name: Patient with OAT 16

source_name: Promega Human Genomic DNA


title: Patient with OAT 17

source_name: Patient with OAT 17


title: Patient with OAT 5

source_name: Patient with OAT 5


title: Patient with OAT 13

source_name: Patient with OAT 13


title: CP04.T

description: Human pretherapeutic colon cancer patient biopsy sample CP04.T

source_name: Pretherapeutic colon cancer patient biopsy

tag: nodal-count

tag: r

tag: g

source_name: reference mRNA pool from Stratagene

tag: sample type


title: Heat-killed M. leprae infected peritoneal macrophage 2

description: Replicate 2 of 8

source_name: PBS injected peritoneal macrophage 2

source_name: Heat-killed M.leprae injected peritoneal macrophage 2


title: 88h sample 1

city: Fort Collins

first: Andrey

last: Ptitsyn

state: CO

address: 1682 Canpus Delivery

department: Center for Bioinformatics

institute: Colorado State University

hyb_protocol: The Agilent® Aedes aegypti microarray described in Xi et al [33] and Nene et al [16] was used.  Each array contained 45,220 features, 43,803 of which correspond to 21,494 unique Ae. aegypti oligonucleotides replicated twice (20,692), thrice (793) or four times (10). The remaining features hybridized to oligonucleotides contained in the Agilent RNA Spike-In® kit for quality control.  Hybridizations were conducted with the Agilent Technologies® In Situ Hybridization kit at 60oC according to the manufacturer’s instructions.

scan_protocol: Hybridization intensities were determined with an Axon GenePix 4100AL scanner at 635nm for Cy-5 and at 532nm for Cy3, and images were analyzed with Gene Pix Pro 6.0 software.  The quality of the hybridization was assessed with Gene Pix software for control, feature and replicate quality control software packages.  Two of the 26 arrays that were processed failed to pass the quality control screens.  Both were repeated from the original RNA and passed on the second attempt

data_processing:
Values from all 1,417 spots that hybridize to the probes in the Agilent® RNA Spike-In kit were removed.  Median background values at 635nm were subtracted from median spot values and the same was repeated for background and spot values at 532 nm.  Background corrected values were then transformed to relative intensities using the formula: M = log2(Cy5/Cy3), so that all Cy3 values from 72 – 104 hours were standardized against the same pool of Cy5 labelled RNA from the 24 hr timepoint. This experiment layout has been chosen to standardise the impact of technical variation on different time points. The chosenned reference point is the same for all microarrays and placed far ahead of the starting point for the time series to allow sufficient numbers of genes differentially expressed in comparison to the Cy5 control at any point of the time series. Thus estimates of RNA quantities for each of the 21,494 Ae. aegypti gene features was estimated from 2-4 technical replicates and two biological replicates.
Analysis of periodicity
We composed 48h gene expression profiles out of a series of observation covering continuous 32h period with 2 independent replicates for each time point sampled every 4h. The technical replicates were processed as separate entities, rather than averaged.  The two biological replicates we considered as two independent timelines. The first six time points of each were concatenated to construct a continuous 48 hour time line used in analysis of periodicity. This experimental design reconstructing two consecutive periods from two simultaneously processed independent timelines has been approbated in previous studies [36].  The reconstructed time series starts with the first time point at 9am. The experiment design with numbers of replicates and time of sample collection is given in Supplemental Table 1 (see Additional File 1).
Expression profiles were smoothed using a 3rd degree polynomial procedure and median-subtracted using the seven-point Savitzky-Golay algorithm [52]. To take advantage of all points in the time series a single-pass smoothing was applied in a circular manner, with the last points contributing to smoothing of the starting points. The same smoothing and median subtraction procedure was applied to all data sets.

organism: Aedes aegypti

source_name: 24h control point

label_protocol: The Agilent RNA Spike-In® kit provided two-colored standards in all experiments.  RNA (500 ng) was placed in a 200 uL tube along with two uL of either Diluted Spike A or B and 1.2uL of T7 Promoter Primer Mix.  RNA from 24 hour old heads was labeled with Cyanine 5-CTP while RNA from all heads collected at later time points were labeled with Cyanine 3-CTP using the Agilent Technologies® low input linear amplification RNA labeling kit according to the manufacturer’s instructions. The RNeasy Mini-kit (QIAGEN Inc.) was used to purify the labeled / amplified cRNA. The purified cRNA was eluted in 30 µL RNase-free water and quantified in pmol/µL using a Nanodrop® spectrophotometer.  We did not proceed to the hybridization steps if the total yield was <825 ng or if the specific activity was <8.0 pmol Cy3 or Cy5 per µg cRNA.

extract_protocol: The RNeasy Midi-kit (QIAGEN Inc. Valencia, CA) was used to isolate total RNA according to manufacturer’s instructions.  RNA was eluted in 150 μL DEPC—ddH2O into a 1.5 mL DEPC-treated tube.  RNA concentration was read on a Nanodrop® spectrophotometer and the tube was maintained at -80°C.

tag: time point

source_name: 88h sample 1


title: Heat-killed M. leprae infected peritoneal macrophage 1

description: Replicate 1 of 8

source_name: PBS injected peritoneal macrophage 1

source_name: Heat-killed M.leprae injected peritoneal macrophage 1


title: Liver, Persimmon peel extract administrated for 12weeks #4

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description: No additional information

hyb_protocol: Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

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

organism: Rattus norvegicus

source_name: Liver, fed PP extract containing diet for 12 weeks

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using ISOGEN (Nippon Gene Co., Ltd., Toyama, Japan), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

tag: protocol

value: Goto-Kakizaki (GK)

tag: gender

value: male

value: 18 weeks

value: liver


title: 92h sample 1

source_name: 92h sample 1


title: Patient with OAT 2

source_name: Patient with OAT 2

tag: source

tag: disease state


title: 88h sample 2

source_name: 88h sample 2


title: KO-injury-5

city: London

first: Adam

last: Giangreco

address: 5 University Street

department: Respiratory Research

country: United Kingdom

institute: UCL

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent Mouse Oligo Arrays (catalogue number G4122F). 2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol The hybridisation was performed for 17 h at 65 ºC at 10 rpm. Slides were them washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325) and 1 min at 22 ºC in Wash Solution 2, pre-warmed to 37 ºC (catalogue number 5188-5326). Slides were incubated for 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505B US45102871 (ChipScan software version A.7.0.1), scan region 61 X 21.6mm, scan resolution 5 micron single pass, extended dynamic range selected (XDR Hi 100%; XDR Lo 10%).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version. 9.1.3.1 (protocol GE1-v5_91_0806). The VALUE column came from the gProcessedSignal column of the result table.

source_name: Myd88 KO polidocanol injury tissue 5

label_protocol: 600 ng RNA and 3 µl Agilent One-Color RNA Spike-In RNA were labelled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacture’s instructions as follows: 1.2 µl T7 Promoter Primer was added to 600 ng RNA and 3 µl spike in control and denatured at 65 ºC. First Strand Buffer, DTT, dNTP MMLV and RNaseOut was added. The cDNA was synthesised during the following incubation step (2h at 40 ºC). After 10 min denaturation at 65 ºC and the addition of Cy-labelled CTP, Transcription Buffer, DTT, NTP, PEG, RNaseOUT, Inorganic Phosphatase, and T7 RNA Polymerase the synthesis of the fluorescent labelled cRNA was performed during the second incubation step (2 h at 40 ºC). The labelled cRNA was purified with the Qiagen RNeasy Mini Kit according to Manufacturer’s protocol.

growth_protocol: Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit. The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.

treatment_protocol: Mice were used as control or exposed to intratracheal 2% polidocanol 3 days prior to collection (injury).  Mice were culled by pentobarbitol overdose and exsanguinated.  Whole trachea was isolated, excess connective tissue removed, and immediately processed for RNA purification

value: myd88 KO

tag: age

value: 4 month

tag: weight

tag: tissue

value: whole trachea


title: Heat-killed M. leprae infected peritoneal macrophage 6

description: Replicate 6 of 8

source_name: PBS injected peritoneal macrophage 6

source_name: Heat-killed M.leprae injected peritoneal macrophage 6


title: Liver, Persimmon peel extract administrated for 12weeks #2

description: No additional information

value: fed PP extract containing diet for 12 weeks


title: WT-injury-5

source_name: wild type polidocanol injury tissue 5


title: WT-control-5

source_name: wild type control tissue  5


title: Patient with OAT 4

source_name: Patient with OAT 4

source_name: Promega Human Genomic DNA


title: WT-injury-4

source_name: wild type polidocanol injury tissue 4

value: 4 months


title: Liver, Persimmon peel extract administrated for 12weeks #3

description: No additional information


title: Liver, Control #4

description: No additional information

source_name: Liver, fed control AIN-93G diet for 12 weeks

value: fed control AIN-93G diet for 12 weeks


title: 84h sample 1

source_name: 24h control point

source_name: 84h sample 1


title: KO-control-3

source_name: Myd88 KO control tissue  3

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit. The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit

treatment_protocol: Mice were used as control or exposed to intratracheal 2% polidocanol 3 days prior to collection (injury).  Mice were culled by pentobarbitol overdose and exsanguinated.  Whole trachea was isolated, excess connective tissue removed, and immediately processed for RNA purification.

value: Myd88 KO


title: KO-control-4

source_name: Myd88 KO control tissue  4


title: WT-control-4

source_name: wild type control tissue  4


title: 84h sample 2

source_name: 84h sample 2


title: Liver, Persimmon peel extract administrated for 12weeks #1

description: No additional information

source_name: Liver, fed PP extract containing diet for 12 weeks


title: KO-control-5

source_name: Myd88 KO control tissue  5


title: 80h sample 2

source_name: 80h sample 2


title: 80h sample 1

source_name: 80h sample 1


title: Patient with OAT 6

source_name: Patient with OAT 6

value: peripheral blood


title: Liver, Control #2

description: No additional information


title: KO-control-2

source_name: Myd88 KO control tissue  2

value: trachea


title: KO-injury-2

source_name: Myd88 KO polidocanol injury tissue 2


title: WT-injury-3

source_name: wild type polidocanol injury tissue 3


title: Liver, Control #3

description: No additional information


title: KO-injury-4

source_name: Myd88 KO polidocanol injury tissue 4


title: WT-control-3

source_name: wild type control tissue  3


title: WT-control-2

source_name: wild type control tissue  2


title: WT-injury-2

source_name: wild type polidocanol injury tissue 2


title: Liver, Control #1

description: No additional information

source_name: Liver, fed control AIN-93G diet for 12 weeks


title: KO-injury-1

source_name: Myd88 KO polidocanol injury tissue 1


title: KO-injury-3

source_name: Myd88 KO polidocanol injury tissue 3


title: Patient with OAT 7

source_name: Patient with OAT 7

value: idiopathic severe oligozoospermia

source_name: Promega Human Genomic DNA


title: 76h sample 1

source_name: 24h control point

source_name: 76h sample 1


title: 92h sample 2

source_name: 92h sample 2


title: 72h sample 1

source_name: 72h sample 1


title: 76h sample 2

source_name: 76h sample 2


title: 72h sample 2

source_name: 72h sample 2


title: WT-control-1

source_name: wild type control tissue  1


title: Patient with OAT 3

source_name: Patient with OAT 3


title: KO-control-1

source_name: Myd88 KO control tissue  1


title: WT-injury-1

source_name: wild type polidocanol injury tissue 1


title: Patient with OAT 24

source_name: Patient with OAT 24


title: Patient with OAT 1

source_name: Patient with OAT 1


title: Patient with OAT 15

source_name: Patient with OAT 15


title: Patient with OAT 11

source_name: Patient with OAT 11


title: RC_pool_H_r3_Sty

city: Bologna

first: Giampaolo

last: Ricci

state: BO

address: Massarenti 9

department: Pediatric Allergologic Center

country: Italy

institute: University of Bologna

description: Hybridized to 250K_Sty

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G

data_processing: Probe intensity data was taken directly from the CEL file and used to calculate a Relative Allele Signal (RAS) score by the MPAM algorithm implemented in the SNP-MaP script (http://sgdp.iop.kcl.ac.uk/oleo/affy). This method calculates the average of RAS1 (sense) and RAS2 (antisense) values as a quantitative index of allele frequencies in pooled DNA

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood samples from allergic / asthmatic children using the Nucleospin DNA kit (Macherey & Nagel, Duren, Germany) and individual DNA concentration was determined in triplicate with the Quant-iT Pico-Green dsDNA Assay Kit (Invitrogen, Milan, Italy).

value: Rhinoconjunctivitis

tag: pool

value: H

tag: replicate


title: RC_pool_F_r3_Sty

description: Hybridized to 250K_Sty

value: F


title: RC_pool_G_r3_Sty

description: Hybridized to 250K_Sty

value: G


title: Asthma_pool_C_r3_Nsp

description: Hybridized to 250K_Nsp

value: Asthma

value: C


title: Asthma_pool_D_r3_Nsp

description: Hybridized to 250K_Nsp

value: D


title: Patient with OAT 10

source_name: Patient with OAT 10


title: Adult Normal Skin   (commercial)

description:
This sample is purchase from Biochain Company.  (Cat#C1234218)
Control RNA(Skin)_rep1

hyb_protocol: The labelled cDNAs are resuspended in 10ul of hybridization solution (GenoCheck, Korea), and are placed on Roche NimbleGen Human Whole genome 12-plex array (Roche NimbleGen Inc., WI) and covered by a NimbleGen H12 mixer (Roche NimbleGen Inc., WI).

scan_protocol: These arrays are scanned using Axon GenePix 4000B scanner with associated software (Molecular Devices Corp.)

data_processing: Each signal intensity of genes is processed with RMA (Robust Multi-array Average) and quantile normalization using NimbleScan Version 2.4 (Roche NimbleGen Inc.,WI).

source_name: Normal Skin  (Commercial)

label_protocol: Each total RNA sample is labelled with Cy3 using SuperScript II (Invitrogen, CA).

extract_protocol: Total RNA is extracted from the Human sample using the TRI reagent (MRC, OH) according to the manunfacturer's instructions.

value: Skin

tag: origin

value: unknown


title: Patient with OAT 9

source_name: Patient with OAT 9

source_name: Promega Human Genomic DNA


title: Asthma_pool_D_r3_Sty

description: Hybridized to 250K_Sty


title: RC_pool_H_r3_Nsp

description: Hybridized to 250K_Nsp


title: RC_pool_G_r3_Nsp

description: Hybridized to 250K_Nsp


title: Asthma_pool_B_r3_Sty

description: Hybridized to 250K_Sty

value: B


title: Asthma_pool_C_r3_Sty

description: Hybridized to 250K_Sty


title: RC_pool_E_r3_Sty

description: Hybridized to 250K_Sty

value: E


title: RC_pool_F_r3_Nsp

description: Hybridized to 250K_Nsp


title: Asthma_pool_A_r3_Sty

description: Hybridized to 250K_Sty

value: A


title: Patient with OAT 8

source_name: Patient with OAT 8


title: RC_pool_G_r2_Nsp

description: Hybridized to 250K_Nsp


title: Asthma_pool_B_r3_Nsp

description: Hybridized to 250K_Nsp


title: RC_pool_H_r2_Nsp

description: Hybridized to 250K_Nsp


title: Asthma_pool_A_r3_Nsp

description: Hybridized to 250K_Nsp


title: RC_pool_F_r2_Nsp

description: Hybridized to 250K_Nsp


title: RC_pool_G_r2_Sty

description: Hybridized to 250K_Sty


title: Tissue 4 (MB4) - 04

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 4 (MB4) - 04
GTC2MB-04_rep1

source_name: MB patient

value: Skin biopsy

value: Philippines


title: Asthma_pool_C_r2_Nsp

description: Hybridized to 250K_Nsp

value: peripheral blood


title: Asthma_pool_B_r2_Nsp

description: Hybridized to 250K_Nsp


title: Asthma_pool_D_r2_Nsp

description: Hybridized to 250K_Nsp


title: RC_pool_E_r3_Nsp

description: Hybridized to 250K_Nsp


title: RC_pool_H_r2_Sty

description: Hybridized to 250K_Sty


title: Tissue 2 (MB2) - 02

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 2 (MB2) - 02
GTC2MB-02_rep1


title: Tissue 3 (MB3) - 03

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 3 (MB3) - 03
GTC2MB-03_rep1


title: Tissue 1 (MB1) - 01

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 1 (MB1) - 01
GTC2MB-01_rep1


title: 13912899 - RNAi3 vs WT2 3

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: Identification of effector genes that act downstream of AtTCTP, using knockout ( tctp-2), RNAi expressing line (35S::RNAi-AtTCTP) and over expressing line (35S::AtTCTP)

hyb_protocol: WT2 3 Cy5 / RNAi3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: WT2 3

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - Media: MS medium for 7 days. Plants were subsquently transferred on soil. Hygrometry: 50%/70% (day/night) Temperature: 22°C Light: 200 µE m-2 s-1

treatment_protocol: no treatment

tag: strain

value: columbia

tag: dev.stage (boyes et al. plant cell 2001)

growth_protocol: leaf - Media: MS medium + basta 10 µg/mL for 7 days. Plants were subsquently transferred on soil. Hygrometry: 50%/70% (day/night) Temperature: 22°C Light: 200 µE m-2 s-1

value: columbia mutant (35s::RNAi-AtTCTP)


title: Asthma_pool_D_r2_Sty

description: Hybridized to 250K_Sty


title: Asthma_pool_A_r2_Nsp

description: Hybridized to 250K_Nsp


title: Tissue 6 (BT6) - 006

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 6 (BT6) - 006
GTC2BT-006_rep 1

source_name: BT patient


title: Tissue 6 (MB6) - 06

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 6 (MB6) - 06
GTC2MB-06_rep1


title: 13912898 - WT2 3 vs RNAi3

hyb_protocol: RNAi3 Cy5 / WT2 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Asthma_pool_C_r2_Sty

description: Hybridized to 250K_Sty


title: Tissue 5 (MB5) - 05

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 5 (MB5) - 05
GTC2MB-05_rep1


title: BC009_16_1

type: mixed

city: Princeton

first: Bess

last: Ward

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

description: English Channel time series N uptake study

hyb_protocol: hybridization at 65 oC using Agilent hybridization solution

scan_protocol: Arrays were scanned on an Agilent High-Resolution C Scanner

data_processing: Data were analyzed using GenePix Pro (Version 6.0)

organism: marine metagenome

source_name: ST-80 4 L seawater from 1 m depth at Station L4 in the English Channel collected 6 July 2004

label_protocol: Targets were linearly ampified using Klenow and the dNTP mix included dUaa.  The amplified product was post labeled by conjugation of Cy3 to the dUaa

extract_protocol: DNA was extracted using the Gentra PureGene cell culture protocol (Qigen); RNA was extracted using the RNAqueous kit (Ambion)

treatment_protocol: Water was filtered onto 0.2 µm sterivex filters and immediately frozen at -80oC  until extraction

value: particulate material from ~4 L of surface seawater

tag: hybd material

value: 200 ng nitrate reductase PCR product from cDNA

molecule: other

organism: synthetic construct

source_name: 20-mer internal standard

label_protocol: Targets were linearly ampified using Klenow and the dNTP mix included dUaa.  The amplified product was post labeled by conjugation of Cy5 to the dUaa

extract_protocol: not applicable

value: 20-mer internal standard


title: 13913502 - RNAi4 vs WT2 4

hyb_protocol: WT2 4 Cy5 / RNAi4 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT2 4


title: Tissue 4 (BT4) - 004

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 4 (BT4) - 004
GTC2BT-004_rep 1


title: Tissue 5 (BT5) - 005

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 5 (BT5) - 005
GTC2BT-005_rep 1


title: Asthma_pool_A_r2_Sty

description: Hybridized to 250K_Sty


title: RC_pool_H_r1_Nsp

description: Hybridized to 250K_Nsp

value: Rhinoconjunctivitis

value: H


title: RC_pool_G_r1_Nsp

description: Hybridized to 250K_Nsp

value: G


title: Tissue 3 (BT3) - 003

description:
This sample is diagnosed with BT according to classification of Ridley and Jopling, and is collected from tha same patient labelled as Blood 3 (BT3) - 003
GTC2BT-003_rep 1


title: Asthma_pool_B_r2_Sty

description: Hybridized to 250K_Sty

value: Asthma


title: RC_pool_F_r1_Nsp

description: Hybridized to 250K_Nsp

value: F


title: RC_pool_E_r2_Sty

description: Hybridized to 250K_Sty


title: RC_pool_E_r1_Nsp

description: Hybridized to 250K_Nsp


title: 13832672 - WT2 4 vs RNAi4

hyb_protocol: RNAi4 Cy5 / WT2 4 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: RC_pool_E_r2_Nsp

description: Hybridized to 250K_Nsp


title: Asthma_pool_D_r1_Nsp

description: Hybridized to 250K_Nsp

value: D


title: Patient with OAT 12

source_name: Patient with OAT 12

value: idiopathic severe oligozoospermia


title: RC_pool_F_r2_Sty

description: Hybridized to 250K_Sty


title: RC_pool_G_r1_Sty

description: Hybridized to 250K_Sty


title: Asthma_pool_C_r1_Nsp

description: Hybridized to 250K_Nsp

value: C


title: BC009_13_1

source_name: ST-65 4 L seawater from 1 m depth at Station L4 in the English Channel collected 7 June 2004


title: RC_pool_H_r1_Sty

description: Hybridized to 250K_Sty


title: BC009_12_1

source_name: ST-41 4 L seawater from 1 m depth at Station L4 in the English Channel collected 26 April 2004


title: BC009_12_2

source_name: ST-47 4 L seawater from 1 m depth at Station L4 in the English Channel collected 10 May 2004


title: RC_pool_E_r1_Sty

description: Hybridized to 250K_Sty

value: E


title: Asthma_pool_B_r1_Nsp

description: Hybridized to 250K_Nsp

value: B