title: glioma 711

city: Rotterdam

first: Lonneke

middle: AM

last: Gravendeel

state: South Holland

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Array hybridization was performed by AROS Applied Biotechnology AS (Arhus, Denmark) according to standard Affymetrix protocols in combination with Nugen WT-Ovation technology (FFPE V2 and Exon modules) (San Carlos, CA, USA) (n=55).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf

label: Biotin

source_name: FFPE glioma tissue

label_protocol: Sample labeling was performed by AROS Applied Biotechnology AS (Arhus, Denmark) according to standard Affymetrix protocols in combination with Nugen WT-Ovation technology (FFPE V2 and Exon modules) (San Carlos, CA, USA) (n=55).

extract_protocol: Five sections of 10 µm thick were cut from each tissue block. The High Pure RNA Paraffin Kit (Roche Applied Science, Mannheim, Germany) was used to isolate the RNA from the paraffin.

value: brain

value: glioma

tag: histological diagnosis

value: pilocytic astrocytoma

tag: grade

tag: survival (yrs)


title: UTI T2 biological rep4 [GU-30.CEL]

status: Public on Jul 01 2012

type: RNA

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

description:
GU-30.CEL
amplified into double-stranded cDNA with random hexamers tagged with a T7 promoter sequence

hyb_protocol: Hybridization was performed according to the manufacturers’ instructions

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner

data_processing:
Raw microarray data were normalized using quantile normalization and summarized using RMA as implemented in the affy package in Bioconductor. Differentially expressed genes were identified by analyzing the data using the MAANOVA package (Wu et al., 2003) (http://www.bioconductor.org/packages/bioc/1.8/html/maanova.html)
RMA signal intensity; significant changes in gene expression identified using a shrinkage based t test together with permutation.  A false discovery rate (FDR) of 0.05 was used to generate the significant gene list

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Bladder, 24h Infection

label_protocol: RNA that passed Bioanalyzer analysis was quantified and 100 ng used for cDNA synthesis. RNA-derived biotinylated sense-strand DNA was applied to the whole transcript Gene 1.0 ST Mouse Microarray and hybridization was performed according to the manufacturers’ instructions in an Affymetrix Fluidics Station 400.

growth_protocol: O/N LB culture of UPEC CFT073 at 37C was collected and concentrated into PBS by centrifugation and washes in PBS

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

treatment_protocol: Mice were catheterized using a sterile Teflon catheter and 40 microlitres of PBS containing 10^9 CFU was instilled transurethrally into the bladder. Whole bladders collected at 24h following infection

tag: Sex

value: female

tag: strain

tag: age

value: 10 wk


title: microRNA profile of case NPC326519

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels, BRB ArrayTools v.3.8.0 was used.

organism: Homo sapiens

source_name: Nasopharyngeal carcinoma

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: glioma 712

tag: tissue

tag: cell type


title: Steer ID# 103 High fat diet, subcutaneous fat

city: Edmonton

first: Josue

middle: Moura

last: Romao

state: Alberta

address: 116 St. and 85 Ave.

department: AFNS

country: Canada

institute: University of Alberta

description:
Sample name: 103BF
Raw data file:
253020810004_201012091611_S01_miRNA_107_Sep09_1_1.txt

hyb_protocol: The labeled RNA was hybridized with array slides with hybridization buffer and 10X GE blocking agent, and were incubated at 55ºC for ~20 hours. Finally, the arrays were washed with GE wash buffers.

scan_protocol: The arrays were scanned at 5 μM resolution on an Agilent G2565CA High Resolution Scanner (Agilent Technologies). Data was processed through Agilent’s Feature Extraction software version 10.7.3.1  using the protocol miRNA_107_Sep09

data_processing: The data was normalized to the 75th percentile using GeneSpring GX 11.5 (Agilent Technologies)

organism: Bos taurus

source_name: Subcutaneous fat (backfat), High fat diet

label_protocol: Total RNA (100 ng/sample) was firstly labeled with the AGILENT miRNA Complete Labeling and Hyb Kit (Version 2.1) by dephosphorylation with Calf Intestinal Phosphatase followed by denaturing and ligation with Cyanine3-pCp to the 3’ end.

extract_protocol: Total RNA extraction was performed by homogenizing the fat tissue samples with TRIZOL® (TRI reagent, Invitrogen, Carlsbad, CA, USA) following the manufactures instructions for samples with high fat content.

tag: diet

value: High fat diet

value: Subcutaneous fat


title: microRNA profile of case NPC326265


title: glioma 628

value: astrocytoma


title: glioma 629

value: glioblastoma


title: glioma 568

value: oligoastrocytoma


title: Steer ID# 202 High fat diet, subcutaneous fat

description:
Sample name: 202BF
Raw data file:
253020810004_201012091611_S01_miRNA_107_Sep09_1_3.txt


title: UTI T2 biological rep2 [GU-16.CEL]

description:
GU-16.CEL
amplified into double-stranded cDNA with random hexamers tagged with a T7 promoter sequence


title: UTI T2 biological rep1 [GU-7.CEL]

description:
GU-7.CEL
amplified into double-stranded cDNA with random hexamers tagged with a T7 promoter sequence


title: Steer ID# 303 High fat diet, subcutaneous fat

description:
Sample name: 303BF
Raw data file:
253020810004_201012091611_S01_miRNA_107_Sep09_2_2.txt


title: Steer ID# 302 High fat diet, subcutaneous fat

description:
Sample name: 302BF
Raw data file:
253020810004_201012091611_S01_miRNA_107_Sep09_2_1.txt


title: microRNA profile of case NPC326525


title: glioma 566


title: Steer ID# 109 High fat diet, subcutaneous fat

description:
Sample name: 109BF
Raw data file:
253020810004_201012091611_S01_miRNA_107_Sep09_1_2.txt


title: GBS Ctrl T24 biological rep5

description: amplified into double-stranded cDNA with random hexamers tagged with a T7 promoter sequence

data_processing: Raw microarray data were normalized using quantile normalization and summarized using RMA as implemented in the affy package in Bioconductor. Differentially expressed genes were identified by analyzing the data using the MAANOVA package (Wu et al., 2003) (http://www.bioconductor.org/packages/bioc/1.8/html/maanova.html). Significant changes in gene expression identified using a shrinkage based t test together with permutation.  A false discovery rate (FDR) of 0.1 was used to generate the significant gene list.

source_name: Bladder, 24h Control

growth_protocol: O/N THB culture of GBS at 37C was collected and concentrated into PBS by centrifugation and washes in PBS

treatment_protocol: Mice were catheterized using a sterile Teflon catheter and 40 microlitres of PBS containing 10^9 CFU was instilled transurethrally into the bladder. Whole bladders collected at 2h and 24h following infection

value: bladder

tag: gender


title: Steer ID# 410 Control diet, visceral fat

description:
Sample name: 410KF
Raw data file:
253020810003_201010151636_S01_miRNA_107_Sep09_2_4.txt

source_name: Visceral fat (perirenal fat), Control diet

value: Control diet

value: Visceral fat


title: GBS Ctrl T24 biological rep4


title: GBS Ctrl T24 biological rep3


title: glioma 565


title: glioma 536


title: glioma 420


title: microRNA profile of case NPC326159


title: Steer ID# 405 Control diet, visceral fat

description:
Sample name: 405KF
Raw data file:
253020810003_201010151636_S01_miRNA_107_Sep09_2_3.txt


title: Steer ID# 308 Control diet, visceral fat

description:
Sample name: 308KF
Raw data file:
253020810003_201010151636_S01_miRNA_107_Sep09_2_2.txt


title: microRNA profile of case NPC326149


title: Steer ID# 209 Control diet, visceral fat

description:
Sample name: 209KF
Raw data file:
253020810003_201010151636_S01_miRNA_107_Sep09_1_3.txt


title: microRNA profile of case NPC325956


title: Steer ID# 307 Control diet, visceral fat

description:
Sample name: 307KF
Raw data file:
253020810003_201010151636_S01_miRNA_107_Sep09_2_1.txt


title: Steer ID# 211 Control diet, visceral fat

description:
Sample name: 211KF
Raw data file:
253020810003_201010151636_S01_miRNA_107_Sep09_1_4.txt


title: microRNA profile of case NPC325796


title: Primary Breast Tumor no brain metastasis 156399

city: Indianapolis

first: Sunil

last: Badve

state: IN

address: 350 West 11th street

department: Pathology

country: USA

institute: Indiana University

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

source_name: Primary Breast Tumor

label_protocol: standard Illumina protocol

extract_protocol: Trizol

tag: sentrix barcode

value: primary breast cancer tumor

tag: set

value: TRAINING

tag: date of birth

tag: menopausal status (1=pre, 2=post)

tag: type of cancer histology

tag: lobulare

tag: date of primary tumor diagnosis

tag: grading

tag: err

tag: pgr

tag: her2 ihc

tag: her2 fish

tag: induction chemotherapy (0=no, 1=yes)

tag: induction hormonal therapy with ta (0=no, 1=yes)

tag: induction hormonal therapy with ar (0=no, 1=yes)

tag: adjuvant chemotherapy (0=no, 1=yes)

tag: adjuvant hormonal therapy with tamox (0=no, 1=yes)

tag: adjuvant hormonal therapy with ia (0=no, 1=yes)

tag: adjuvant rtg therapy  (0=no, 1=yes)

tag: trastuzumab therapy (0=no, 1=yes)

tag: brain metasteses  (0=no, 1=yes)

tag: overall survival  (0=no, 1=yes)

tag: date of last information


title: microRNA profile of case NPC326153

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: glioma 515

tag: tissue

tag: cell type

tag: histological diagnosis

tag: grade

tag: survival (yrs)


title: glioma 446


title: glioma 467


title: microRNA profile of case NPC325628


title: GBS Ctrl T24 biological rep1

tag: strain

tag: gender

tag: age


title: Steer ID# 111 Control diet, visceral fat

description:
Sample name: 111KF
Raw data file:
253020810003_201010151636_S01_miRNA_107_Sep09_1_2.txt

tag: diet


title: Steer ID# 108 Control diet, visceral fat

description:
Sample name: 108KF
Raw data file:
253020810003_201010151636_S01_miRNA_107_Sep09_1_1.txt


title: GBS Ctrl T24 biological rep2


title: microRNA profile of case NPC325404


title: GBS UTI T24 biological rep4


title: GBS UTI T24 biological rep5


title: glioma 416

value: oligodendroglioma


title: GBS UTI T24 biological rep3


title: glioma 387


title: Steer ID# 410 Control diet, subcutaneous fat

description:
Sample name: 410BF
Raw data file:
253020810002_201010151644_S01_miRNA_107_Sep09_2_4.txt

source_name: Subcutaneous fat (backfat), Control diet


title: glioma 393


title: GBS UTI T24 biological rep1


title: microRNA profile of case NPC324910


title: microRNA profile of case NPC325344


title: Steer ID# 405 Control diet, subcutaneous fat

description:
Sample name: 405BF
Raw data file:
253020810002_201010151644_S01_miRNA_107_Sep09_2_3.txt


title: GBS UTI T24 biological rep2


title: microRNA profile of case NPC324597


title: microRNA profile of case NPC324587


title: glioma 336


title: GBS UTI T2 biological rep4

source_name: Bladder, 2h Infection


title: Steer ID# 307 Control diet, subcutaneous fat

description:
Sample name: 307BF
Raw data file:
253020810002_201010151644_S01_miRNA_107_Sep09_2_1.txt


title: glioma 353


title: GBS UTI T2 biological rep3


title: glioma 315


title: Steer ID# 211 Control diet, subcutaneous fat

description:
Sample name: 211BF
Raw data file:
253020810002_201010151644_S01_miRNA_107_Sep09_1_4.txt


title: Steer ID# 308 Control diet, subcutaneous fat

description:
Sample name: 308BF
Raw data file:
253020810002_201010151644_S01_miRNA_107_Sep09_2_2.txt


title: microRNA profile of case NPC324257


title: Steer ID# 209 Control diet, subcutaneous fat

description:
Sample name: 209BF
Raw data file:
253020810002_201010151644_S01_miRNA_107_Sep09_1_3.txt


title: glioma 293


title: microRNA profile of case NPC324229


title: GBS UTI T2 biological rep5


title: Steer ID# 111 Control diet, subcutaneous fat

description:
Sample name: 111BF
Raw data file:
253020810002_201010151644_S01_miRNA_107_Sep09_1_2.txt


title: GBS UTI T2 biological rep2


title: glioma 227


title: GBS UTI T2 biological rep1


title: glioma 286


title: Steer ID# 108 Control diet, subcutaneous fat

description:
Sample name: 108BF
Raw data file:
253020810002_201010151644_S01_miRNA_107_Sep09_1_1.txt


title: microRNA profile of case NPC324157


title: GNMT-WT mouse hepatocytes (sample 3)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

source_name: GNMT-WT mouse hepatocytes

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

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

treatment_protocol: At 3 weeks of age, Gnmt knockout and wild-type mice from the same litter were intraperitoneally injected with 10 mg AFB1/kg of body weight

value: hepatocytes

tag: genotype/variation

value: GNMT-WT

tag: agent

value: aflatoxin B1 (AFB1)


title: GNMT-WT mouse hepatocytes (sample 2)


title: GNMT-WT mouse hepatocytes (sample 1)


title: glioma 198

value: brain

value: glioma


title: GNMT-KO mouse hepatocytes (sample 3)

source_name: GNMT-KO mouse hepatocytes

value: GNMT-KO


title: microRNA profile of case NPC323786


title: glioma 183


title: microRNA profile of case NPC323973


title: microRNA profile of case NPC323692


title: glioma 174


title: glioma 209


title: microRNA profile of case NPC323838


title: glioma 206


title: glioma 143


title: microRNA profile of case NPC323341


title: microRNA profile of case NPC323339


title: E.albidus_8d_Zn_EC90_rep2

city: Aveiro

first: Sara

last: Novais

address: Campus de Santiago, Department of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

description:
SAMPLE 47
E.albidus gene expression after 8 days of exposure to zinc reproduction EC90

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit . 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-030589 Custom Gene Expression Array for Enchytraeus albidus 8x15k, 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 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies) using default parameters (protocol GE1_105_Dec08 and Grid: 030589_D_F_20101007) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Enchytraeus albidus

source_name: E. albidus_zinc EC90_8 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (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: Isolation of total RNA from each replicate was performed through the Trizol extraction method (Invitrogen, Belgium). This RNA followed a DNAse treatment (Fermentas, Germany) and further purification steps consisting of phenol/chloroform extractions. The quantity and purity of the isolated RNA were measured spectrophotometrically with nanodrop (NanoDrop ND-1000 Spectrophotometer) and its integrity was checked on a denaturing formaldehyde agarose gel electrophoresis.

treatment_protocol: Fifteen adult worms with well developed clitellum were introduced in the test vessels, each containing 25 g moist soil (control or spiked soil with Cd or Zn). The worms were exposed for 2, 4 and 8 days at 20C and a 16:8h photoperiod. Three biological replicates per exposure treatment  in each time point and 4 biologcal replicates of control conditions were used. At test end, animals of each replicate were carefully removed, rinsed in deionised water, stored in RNA later (Ambion, USA) containing criotubes and frozen in liquid Nitrogen. All the samples were stored at -80C till further analysis.

value: Whole body extracts

tag: developmental stage

value: Adult organisms with well developed clitellum


title: microRNA profile of case NPC323332


title: glioma 134

value: astrocytoma


title: OKER Tumoral cell line (sample 3)

description:
Oker_1(tube5)
We isolated a cell line derived from a hepatic tumour of GNMT-KO mice, OKER cells.

source_name: OKER Tumoral cell line

value: OKER tumor cells


title: E.albidus_8d_Zn_EC90_rep1

description:
SAMPLE 46
E.albidus gene expression after 8 days of exposure to zinc reproduction EC90


title: glioma 123

value: glioblastoma


title: microRNA profile of case NPC323032


title: microRNA profile of case NPC322762


title: E.albidus_8d_Zn_EC50_rep3

description:
SAMPLE 45
E.albidus gene expression after 8 days of exposure to zinc reproduction EC50

source_name: E. albidus_zinc EC50_8 days


title: GNMT-KO mouse hepatocytes (sample 1)


title: OKER Tumoral cell line (sample 2)

description:
Oker_1(tube4)
We isolated a cell line derived from a hepatic tumour of GNMT-KO mice, OKER cells.


title: microRNA profile of case NPC322680


title: E.albidus_8d_Zn_EC50_rep2

description:
SAMPLE 44
E.albidus gene expression after 8 days of exposure to zinc reproduction EC50


title: E.albidus_8d_Zn_EC50_rep1

description:
SAMPLE 43
E.albidus gene expression after 8 days of exposure to zinc reproduction EC50


title: glioma 119


title: E.albidus_8d_Cd_EC90_rep2

description:
SAMPLE 41
E.albidus gene expression after 8 days of exposure to cadmium reproduction EC90

source_name: E. albidus_cadmium EC90_8 days


title: OKER Tumoral cell line (sample 1)

description:
Oker_1(tube3)
We isolated a cell line derived from a hepatic tumour of GNMT-KO mice, OKER cells.


title: E.albidus_8d_Cd_EC90_rep3

description:
SAMPLE 42
E.albidus gene expression after 8 days of exposure to cadmium reproduction EC90


title: microRNA profile of case NPC322460


title: microRNA profile of case NPC322435


title: MFG

city: Seattle

first: YuFeng

last: Peng

state: WA

address: 1959 Pacific  Street

department: Rheumatology

institute: University of Washington

scan_protocol: Standard Illumina scan protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: spleen from MFG-E8 deficient mice

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

extract_protocol: RNA samples were extracted with Qiagen RNA easy kit

value: spleen

value: 4 month old

tag: genotype

value: MFG-E8 deficient


title: glioma 105


title: 'D' ODN for 48 hours - repeat 3 - mAdbID:115405

city: Hilden

first: Folkert

last: Steinhagen

address: Breddert 37

country: Germany

institute: National Cancer Institute

description: mAdb experiment ID: 115405

hyb_protocol: Hybridization Protocol Other: The probes were mixed, diluted in 5 ul DMSO plus 1.7 ul of 1 M NaHCO3 and hybridized to 36K human 60-mer oligonucleotide array slides (NCI Human Array Set Hs-OperonV3.0) at 42 C for 18 h in a MAUI hybridization system (BioMicro Systems) followed by washing, centrifugation and air drying.

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.46599;; 3.75164 Temperature: 26.632 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

data_processing:
BRB Array Tools Data Processing Protocol
Calculation Method: Gene expression analysis was performed using BRB Array Tools Version 3.8.1 developed by the NCI Biometric Research Branch (Bethesda, MD). Data were background-corrected, flagged values were removed, spots in which both signals were <100 were filtered, ratios were log base 2 transformed, and lowest intensity-dependant normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes. Analysis was restricted to genes present in >60% of the arrays after filtering. In toto, 29,039 features were reproducibly tracked in all microarrays.

source_name: Universal Human Reference RNA

label_protocol:
Cy3 Sample Labeling
Other: Ten microliters of cDNA was labeled with Cy3 reactive dyes (Amersham Biosciences, UK) diluted in 5 ul of DMSO plus 1.7 ul of 1 M NaHCO3 for 90 min in the dark.

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was extracted using TRIzol Reagent (Invitrogen) as specified by the manufacturer.

tag: sample type

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: 'D' ODN for 48 hours

label_protocol:
Cy5 Sample Labeling
Other: Ten microliters of cDNA was labeled with Cy5 reactive dyes (Amersham Biosciences, UK) diluted in 5 ul of DMSO plus 1.7 ul of 1 M NaHCO3 for 90 min in the dark.

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'D' (CpG-A) ODN
Treatment dose: 3 uM
Treatment time: 48 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'D' ODN for 1-48h.

tag: cell line

value: plasmacytoid dendritic cells (pDC)

tag: disease state

value: Leukemia

tag: treatment type

value: small molecule

value: TLR9 ligand 'D' (CpG-A) ODN

tag: treatment dose

value: 3 uM

tag: treatment time

value: 48 hours


title: B6

source_name: spleen from wild type mice

tag: tissue

value: wild type


title: E.albidus_8d_Cd_EC50_rep3

description:
SAMPLE 39
E.albidus gene expression after 8 days of exposure to cadmium reproduction EC50

source_name: E. albidus_cadmium EC50_8 days


title: glioma 112

source_name: FFPE glioma tissue

value: brain

tag: cell type

value: glioma

tag: histological diagnosis

tag: grade


title: microRNA profile of case NPC322405

source_name: Nasopharyngeal carcinoma

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: glioma 77

tag: survival (yrs)


title: E.albidus_8d_Cd_EC90_rep1

description:
SAMPLE 40
E.albidus gene expression after 8 days of exposure to cadmium reproduction EC90

value: Whole body extracts

tag: developmental stage

value: Adult organisms with well developed clitellum


title: E.albidus_8d_Cd_EC50_rep1

description:
SAMPLE 37
E.albidus gene expression after 8 days of exposure to cadmium reproduction EC50


title: 'K' ODN + anti-INFR for 9 hours - repeat 1 - mAdbID:111779

description: mAdb experiment ID: 111779

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47728;; 3.83648 Temperature: 28.9819 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'K' ODN + anti-INFR for 9 hours

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'K' (CpG-B) ODN; anti-type I IFNalpha/beta receptor chain2 (MMHAR-2, PBL) (anti-IFNR)
Treatment dose: 3 uM ('K' ODN); 5 ug/ml (anti-IFNR)
Treatment time: 9 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'K' ODN for 9 h. Blocking experiments using neutralizing mAb against anti-type I IFNalpha/beta receptor chain2 (MMHAR-2, PBL) (anti-IFNR) were performed identically for the duration of maximal gene expression. Anti-IFNR (5 ug/ml) was added 30 min prior to CpG administration.

tag: agent

value: 3 uM ('K' ODN); 5 ug/ml (anti-IFNR)

value: 9 hours


title: glioma 99

value: glioblastoma


title: glioma 98


title: glioma 104


title: microRNA profile of case NPC322300


title: 'D' ODN + anti-IFNR for 27 hours - repeat 2 - mAdbID:109374

description: mAdb experiment ID: 109374

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.5457;; 3.65667 Temperature: 30.1721 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'D' ODN + anti-INFR for 27 hours

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'D' (CpG-A) ODN; anti-type I IFNalpha/beta receptor chain2 (MMHAR-2, PBL) (anti-IFNR)
Treatment dose: 3 uM ('D' ODN); 5 ug/ml (anti-IFNR)
Treatment time: 27 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'D' ODN for 27 h. Blocking experiments using neutralizing mAb against anti-type I IFNalpha/beta receptor chain2 (MMHAR-2, PBL) (anti-IFNR) were performed identically for the duration of maximal gene expression. Anti-IFNR (5 ug/ml) was added 30 min prior to CpG administration.

value: 3 uM ('D' ODN); 5 ug/ml (anti-IFNR)

value: 27 hours

tag: sample type


title: 'D' ODN for 27 hours - repeat 4 - mAdbID:109463

description: mAdb experiment ID: 109463

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.54015;; 3.71493 Temperature: 27.9748 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: 'D' ODN for 27 hours

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'D' (CpG-A) ODN
Treatment dose: 3 uM
Treatment time: 27 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'D' ODN for 1-48h.

tag: cell line


title: E.albidus_8d_Cd_EC50_rep2

description:
SAMPLE 38
E.albidus gene expression after 8 days of exposure to cadmium reproduction EC50


title: 'K' ODN for 9 hours - repeat 5 - mAdbID:111777

description: mAdb experiment ID: 111777

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.44859;; 3.80169 Temperature: 30.8435 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'K' ODN for 9 hours

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'K' (CpG-B) ODN
Treatment dose: 3 uM
Treatment time: 9 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'K' ODN for 1-27 h.

value: plasmacytoid dendritic cells (pDC)

tag: disease state

value: TLR9 ligand 'K' (CpG-B) ODN


title: Untreated Control - repeat 6 - mAdbID:109029

description: mAdb experiment ID: 109029

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.54015;; 3.57159 Temperature: 29.0429 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: Untreated Control

value: Leukemia


title: glioma 63


title: microRNA profile of case NPC321870


title: microRNA profile of case NPC321652


title: microRNA profile of case NPC321552


title: E.albidus_8d_Control_rep4

description:
SAMPLE 36
E.albidus gene expression after 8 days under control conditions

source_name: E. albidus_control_8 days


title: 'D' ODN for 27 hours- repeat 5 - mAdbID:109027

description: mAdb experiment ID: 109027

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.55124;; 3.53367 Temperature: 30.4773 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

tag: treatment type

value: small molecule

value: TLR9 ligand 'D' (CpG-A) ODN


title: E.albidus_8d_Control_rep2

description:
SAMPLE 34
E.albidus gene expression after 8 days under control conditions


title: E.albidus_8d_Control_rep3

description:
SAMPLE 35
E.albidus gene expression after 8 days under control conditions


title: glioma 473

value: astrocytoma


title: glioma 441

value: oligoastrocytoma


title: 'K' ODN + anti-INFR for 9 hours - repeat 2 - mAdbID:108040

description: mAdb experiment ID: 108040

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.48558;; 3.69736 Temperature: 26.2047 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: TLR9 ligand 'K' (CpG-B) ODN; anti-type I IFNalpha/beta receptor chain2 (MMHAR-2, PBL) (anti-IFNR)

tag: treatment dose


title: glioma 619

value: brain

value: glioma

value: oligodendroglioma


title: 'D' ODN + anti-IFNR for 27 hours - repeat 1 - mAdbID:108977

description: mAdb experiment ID: 108977

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.49391;; 3.66962 Temperature: 25.9911 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: TLR9 ligand 'D' (CpG-A) ODN; anti-type I IFNalpha/beta receptor chain2 (MMHAR-2, PBL) (anti-IFNR)

tag: treatment time


title: microRNA profile of case NPC321518


title: 'K' ODN for 9 hours - repeat 4 - mAdbID:108037

description: mAdb experiment ID: 108037

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.53275;; 4.09873 Temperature: 29.0735 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: 3 uM

value: 9 hours


title: E.albidus_4d_Zn_EC90_rep3

description:
SAMPLE 32
E.albidus gene expression after 4 days of exposure to zinc reproduction EC90

source_name: E. albidus_zinc EC90_4 days

tag: tissue

value: Whole body extracts

value: Adult organisms with well developed clitellum


title: microRNA profile of case NPC321979


title: E.albidus_8d_Control_rep1

description:
SAMPLE 33
E.albidus gene expression after 8 days under control conditions


title: glioma 380

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

tag: cell type

value: glioblastoma


title: microRNA profile of case NPC321467

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).


title: glioma 445

tag: histological diagnosis


title: GNMT-KO mouse hepatocytes (sample 2)

source_name: GNMT-KO mouse hepatocytes

tag: strain

value: hepatocytes

tag: genotype/variation

value: GNMT-KO

value: aflatoxin B1 (AFB1)


title: microRNA profile of case NPC321433

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)


title: E.albidus_8d_Zn_EC90_rep3

description:
SAMPLE 48
E.albidus gene expression after 8 days of exposure to zinc reproduction EC90

source_name: E. albidus_zinc EC90_8 days


title: microRNA profile of case NPC321033

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC321342


title: microRNA profile of case NPC320840


title: glioma 259

tag: grade

tag: survival (yrs)


title: glioma 291


title: glioma 258


title: E.albidus_4d_Zn_EC90_rep1

description:
SAMPLE 30
E.albidus gene expression after 4 days of exposure to zinc reproduction EC90

tag: developmental stage


title: E.albidus_4d_Zn_EC90_rep2

description:
SAMPLE 31
E.albidus gene expression after 4 days of exposure to zinc reproduction EC90


title: E.albidus_4d_Zn_EC50_rep2

description:
SAMPLE 28
E.albidus gene expression after 4 days of exposure to zinc reproduction EC50

source_name: E. albidus_zinc EC50_4 days


title: 'K' ODN for 3 hours - repeat 2 - mAdbID:107294

description: mAdb experiment ID: 107294

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.46385;; 4.2848 Temperature: 26.7541 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

tag: sample type

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: 'K' ODN for 3 hours

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'K' (CpG-B) ODN
Treatment dose: 3 uM
Treatment time: 3 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'K' ODN for 1-27 h.

tag: cell line

value: plasmacytoid dendritic cells (pDC)

value: Leukemia

value: small molecule

tag: agent

value: TLR9 ligand 'K' (CpG-B) ODN

value: 3 hours


title: D122 for 27 hours (D control) - repeat 2 - mAdbID:105012

description: mAdb experiment ID: 105012

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.48827;; 4.1963 Temperature: 28.6767 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: D122 for 27 hours (D control)

treatment_protocol:
Treatment type: small molecule
Agent: D122
Treatment dose: 3 uM
Treatment time: 27 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM respective control ODNs for the duration of maximal gene expression (D122 for 27 h).

tag: disease state

tag: treatment type

tag: treatment dose

value: 27 hours

source_name: Universal Human Reference RNA


title: E.albidus_4d_Cd_EC90_rep3

description:
SAMPLE 26
E.albidus gene expression after 4 days of exposure to cadmium reproduction EC90

source_name: E. albidus_cadmium EC90_4 days

tag: tissue


title: ODN1612 for 9 hours (K Control)- repeat 2 - mAdbID:105011

description: mAdb experiment ID: 105011

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.47606;; 4.43129 Temperature: 27.7001 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: ODN1612 for 9 hours (K control)

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand ODN1612
Treatment dose: 3 uM
Treatment time: 9 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM respective control ODNs for the duration of maximal gene expression (ODN1612 for 9 h).

tag: cell type

value: TLR9 ligand ODN1612

tag: treatment time


title: D122 for 27 hours (D control) - repeat 1 - mAdbID:105010

description: mAdb experiment ID: 105010

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.44554;; 4.29395 Temperature: 26.0216 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.


title: E.albidus_4d_Zn_EC50_rep3

description:
SAMPLE 29
E.albidus gene expression after 4 days of exposure to zinc reproduction EC50

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).


title: ODN1612 for 9 hours (K Control)- repeat 1 - mAdbID:105013

description: mAdb experiment ID: 105013

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.50047;; 3.82702 Temperature: 29.5007 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.


title: E.albidus_4d_Zn_EC50_rep1

description:
SAMPLE 27
E.albidus gene expression after 4 days of exposure to zinc reproduction EC50


title: Untreated Control - repeat 4 - mAdbID:104688

description: mAdb experiment ID: 104688

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.4547;; 4.10474 Temperature: 25.8995 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.


title: glioma 253

source_name: FFPE glioma tissue

value: brain

value: glioma

tag: histological diagnosis


title: E.albidus_4d_Cd_EC90_rep2

description:
SAMPLE 25
E.albidus gene expression after 4 days of exposure to cadmium reproduction EC90


title: 'D' ODN for 48 hours - repeat 2 - mAdbID:104686

description: mAdb experiment ID: 104686

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.5383;; 3.60858 Temperature: 29.928 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'D' ODN for 48 hours

value: TLR9 ligand 'D' (CpG-A) ODN

value: 3 uM

value: 48 hours


title: glioma 256

value: glioblastoma


title: E.albidus_4d_Cd_EC90_rep1

description:
SAMPLE 24
E.albidus gene expression after 4 days of exposure to cadmium reproduction EC90

value: Whole body extracts

value: Adult organisms with well developed clitellum


title: glioma 199


title: microRNA profile of case NPC320836

source_name: Nasopharyngeal carcinoma

tag: survival status  (1-death,0-survival)


title: microRNA profile of case NPC320046

tag: gender  (1-male,2-female)


title: microRNA profile of case NPC319735

tag: age (years)


title: microRNA profile of case NPC319543

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: microRNA profile of case NPC319124


title: glioma 194

value: astrocytoma

tag: grade


title: 'D' ODN for 48 hours - repeat 1 - mAdbID:104684

description: mAdb experiment ID: 104684

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.50963;; 4.04675 Temperature: 29.5923 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.


title: E.albidus_4d_Cd_EC50_rep3

description:
SAMPLE 23
E.albidus gene expression after 4 days of exposure to cadmium reproduction EC50

source_name: E. albidus_cadmium EC50_4 days


title: microRNA profile of case NPC319123


title: Untreated Control - repeat 3 - mAdbID:103662

description: mAdb experiment ID: 103662

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.52794;; 4.26344 Temperature: 29.8669 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: plasmacytoid dendritic cells (pDC)


title: Untreated Control - repeat 5 - mAdbID:103663

description: mAdb experiment ID: 103663

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.52184;; 4.43434 Temperature: 29.3176 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: Leukemia


title: E.albidus_4d_Control_rep4

description:
SAMPLE 20
E.albidus gene expression after 4 days under control conditions

source_name: E. albidus_control_4 days


title: E.albidus_4d_Cd_EC50_rep2

description:
SAMPLE 22
E.albidus gene expression after 4 days of exposure to cadmium reproduction EC50


title: 'D' ODN for 27 hours - repeat 3 - mAdbID:103661

description: mAdb experiment ID: 103661

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.52794;; 3.85449 Temperature: 30.4468 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'D' ODN for 27 hours

value: small molecule


title: Untreated Control - repeat 2 - mAdbID:104006

description: mAdb experiment ID: 104006

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.51268;; 4.24512 Temperature: 29.2871 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: Untreated Control


title: E.albidus_4d_Cd_EC50_rep1

description:
SAMPLE 21
E.albidus gene expression after 4 days of exposure to cadmium reproduction EC50


title: E.albidus_4d_Control_rep3

description:
SAMPLE 19
E.albidus gene expression after 4 days under control conditions


title: glioma 257

value: oligodendroglioma

tag: survival (yrs)


title: Rat PCCl3 thyroid cells expressing Engr HDm (-Dox) vs non-expressing cells (+Dox)_1

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: Samples were hybridized onto Rat MI ReadyArray (Microarrays Inc., Alabama USA).

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 5xSSC, SDS 0.1%, HEPES 24mM, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Cyanine-labeled cRNA samples were mixed with 30 µg of human cot-1, incubated for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, slides were washed twice for 2 min at 60°C with 2xSSC, 0.03% SDS, once for 2 min at 60°C with 2xSSC, and finally briefly washed in 0.2xSSC at room temperature. They were dried by centrifugation at 800 rpm for 13 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and expression levels were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing: A non-linear Lowess (locally weighted scatter plot) normalization method was carried out. VALUE is the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2.

organism: Rattus norvegicus

source_name: Rat PCCl3_expressing Engr HDm (–Dox)

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Applied Biosystems/Ambion, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30 min in 50% DMSO at room temperature in a dark environment.

growth_protocol: Clones of PCCl3 cells stably transformed with a pEFIN4 expression construct were selected in culture medium supplemented with 400 µg/mL of Geneticin (Gibco) and maintained afterwards in the presence of 200 µg/mL of Geneticin. For the isolation of tTA-expressing clones transformed with the pTRE2hyg construct driving the conditional expression of Engr-HD or Engr-HDm, cells were transfected in culture medium supplemented with 200 µg/mL of  Geneticin and 2 µg/mL of doxycycline (Sigma-Aldrich) and then selected in the presence of  200 µg/mL of  both Geneticin and hygromycin (HygroGold, InvivoGen) and 2 µg/mL of doxycycline.

extract_protocol: Total RNA was obtained from cells at 50 % confluency maintained in the absence of doxycycline for one week using the RNeasy mini kit from Invitrogen.

treatment_protocol: Transformed PCCl3 cells harbouring the Engr-HDm-producing construct were grown in the continuous presence of doxycycline, then cell population was split into two pools and maintained in culture for a further 10 days period, either in the presence or in the absence of the agent.

value: rat thyroid cells

tag: transformed with

value: Engr-HDm-producing construct

tag: culture

value: in the absence of doxycycline (expressing Engr-HDm)

source_name: Rat PCCl3_not expressing Engr HDm (+Dox)

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Applied Biosystems/Ambion Austin, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30 min in 50% DMSO at room temperature in a dark environment.

value: in the presence of doxycycline (not expressing Engr-HDm)


title: microRNA profile of case NPC319114


title: Rat PCCl3 thyroid cells expressing Engr HDm (-Dox) vs non-expressing cells (+Dox)_2

tag: cell line


title: 'D' ODN for 9 hours - repeat 2 - mAdbID:103552

description: mAdb experiment ID: 103552

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.51878;; 4.48317 Temperature: 28.7378 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

tag: sample type

source_name: 'D' ODN for 9 hours

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'D' (CpG-A) ODN
Treatment dose: 3 uM
Treatment time: 9 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'D' ODN for 1-48h.

tag: agent

value: 9 hours


title: glioma 55

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

value: brain

value: glioma


title: E.albidus_4d_Control_rep2

description:
SAMPLE 18
E.albidus gene expression after 4 days under control conditions

tag: developmental stage


title: 'D' ODN for 27 hours - repeat 2 - mAdbID:103660

description: mAdb experiment ID: 103660

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.53099;; 3.72021 Temperature: 30.7825 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

tag: disease state

tag: treatment type

value: TLR9 ligand 'D' (CpG-A) ODN

tag: treatment dose

value: 3 uM

value: 27 hours


title: glioma 40

tag: tissue

tag: cell type


title: glioma 8

tag: histological diagnosis


title: microRNA profile of case NPC318256

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)


title: microRNA profile of case NPC316103

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: E.albidus_2d_Zn_EC90_rep3

description:
SAMPLE 16
E.albidus gene expression after 2 days of exposure to zinc reproduction EC90

source_name: E. albidus_zinc EC90_2 days

value: Whole body extracts

value: Adult organisms with well developed clitellum


title: E.albidus_4d_Control_rep1

description:
SAMPLE 17
E.albidus gene expression after 4 days under control conditions


title: 'D' ODN for 3 hours - repeat 1 - mAdbID:103551

description: mAdb experiment ID: 103551

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.49132;; 4.17798 Temperature: 27.2118 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: 'D' ODN for 3 hours

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'D' (CpG-A) ODN
Treatment dose: 3 uM
Treatment time: 3 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'D' ODN for 1-48h.

tag: treatment time

value: 3 hours


title: microRNA profile of case NPC315979


title: 'K' ODN for 1 hour - repeat 3 - mAdbID:103550

description: mAdb experiment ID: 103550

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.4547;; 3.65917 Temperature: 25.4112 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'K' ODN for 1 hour

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'K' (CpG-B) ODN
Treatment dose: 3 uM
Treatment time: 1 hour
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'K' ODN for 1-27 h.

value: plasmacytoid dendritic cells (pDC)

value: Leukemia

value: TLR9 ligand 'K' (CpG-B) ODN

value: 1 hour


title: E.albidus_2d_Zn_EC50_rep2

description:
SAMPLE 12
E.albidus gene expression after 2 days of exposure to zinc reproduction EC50

source_name: E. albidus_zinc EC50_2 days


title: Untreated Control - repeat 1 - mAdbID:103509

description: mAdb experiment ID: 103509

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.50963;; 4.4557 Temperature: 27.9138 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: Universal Human Reference RNA


title: E.albidus_2d_Zn_EC90_rep2

description:
SAMPLE 15
E.albidus gene expression after 2 days of exposure to zinc reproduction EC90

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).


title: E.albidus_2d_Zn_EC50_rep3

description:
SAMPLE 13
E.albidus gene expression after 2 days of exposure to zinc reproduction EC50


title: 'D' ODN for 3 hours - repeat 3 - mAdbID:103440

description: mAdb experiment ID: 103440

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.51268;; 4.30921 Temperature: 29.1345 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: small molecule


title: Rat PCCl3 thyroid cells expressing Engr HD (-Dox) vs non-expressing cells (+Dox)_1

source_name: Rat PCCl3_expressing Engr HD (–Dox)

treatment_protocol: Transformed PCCl3 cells harbouring the Engr-HD-producing construct were grown in the continuous presence of doxycycline, then cell population was split into two pools and maintained in culture for a further 10 days period, either in the presence or in the absence of the agent.

value: rat thyroid cells

tag: transformed with

value: Engr-HD-producing construct

value: absence of doxycycline (expressing Engr-HD)

source_name: Rat PCCl3_not expressing Engr HD (+Dox)

value: presence of doxycycline (not expressing Engr-HD)


title: E.albidus_2d_Zn_EC90_rep1

description:
SAMPLE 14
E.albidus gene expression after 2 days of exposure to zinc reproduction EC90


title: Rat PCCl3 thyroid cells expressing Engr HD (-Dox) vs non-expressing cells (+Dox)_2

tag: culture

value: in the absence of doxycycline (expressing Engr-HD)

value: in the presence of doxycycline (not expressing Engr-HD)


title: glioma 92

source_name: FFPE glioma tissue

value: brain

value: glioma

value: glioblastoma

tag: grade

tag: survival (yrs)


title: microRNA profile of case NPC315578


title: microRNA profile of case NPC315807


title: microRNA profile of case NPC315505


title: microRNA profile of case NPC314985


title: 'K' ODN for 9 hours - repeat 3 - mAdbID:103289

description: mAdb experiment ID: 103289

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.51878;; 4.36415 Temperature: 28.7988 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'K' ODN for 9 hours

tag: cell line

tag: agent

value: 3 uM

value: 9 hours

tag: sample type


title: 'D' ODN for 1 hour - repeat 3 - mAdbID:103406

description: mAdb experiment ID: 103406

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.49437;; 4.22987 Temperature: 27.1203 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: 'D' ODN for 1 hour

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'D' (CpG-A) ODN
Treatment dose: 3 uM
Treatment time: 1 hour
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'D' ODN for 1-48h.

tag: disease state

tag: treatment type

value: TLR9 ligand 'D' (CpG-A) ODN


title: microRNA profile of case NPC320565

source_name: Nasopharyngeal carcinoma


title: 'K' ODN for 27 hours - repeat 3 - mAdbID:103436

description: mAdb experiment ID: 103436

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.47;; 3.79 Temperature: 25.5 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'K' ODN for 27 hours

treatment_protocol:
Treatment type: small molecule
Agent: TLR9 ligand 'K' (CpG-B) ODN
Treatment dose: 3 uM
Treatment time: 27 hours
In-vitro treatment: The pDC cell line CAL-1 was grown in complete medium (RPMI 1640; Lonza) supplemented with 2mM L-Glutamin, 1mM sodium pyruvate, 10mM HEPES, 1x MEM NEAA (all Gibco) to which 10% heat-inactivated fetal bovine serum (Lonza) was added. Typically cells were maintained in a 150cm2 flask with a density of 1-2.4 x 106 cells / ml and washed every 3 days. Before stimulation of cells for microarray analysis, cells were cultured for 3 days at 37 C in a 5% CO2 air incubator. Cells were then washed and plated in a 75cm2 flask (30 x 106/ 15 ml (80% confluence)), and rested over night before being stimulated with 3uM 'K' ODN for 1-27 h.

value: plasmacytoid dendritic cells (pDC)

value: Leukemia

tag: treatment dose

value: 27 hours


title: E.albidus_2d_Cd_EC90_rep2

description:
SAMPLE 9
E.albidus gene expression after 2 days of exposure to cadmium reproduction EC90

source_name: E. albidus_cadmium EC90_2 days

tag: tissue

value: Whole body extracts

tag: developmental stage

value: Adult organisms with well developed clitellum


title: microRNA profile of case NPC314856

tag: survival status  (1-death,0-survival)


title: microRNA profile of case NPC313343

tag: gender  (1-male,2-female)


title: microRNA profile of case NPC312797

tag: age (years)


title: microRNA profile of case NPC313093

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: E.albidus_2d_Cd_EC50_rep3

description:
SAMPLE 7
E.albidus gene expression after 2 days of exposure to cadmium reproduction EC50

source_name: E. albidus_cadmium EC50_2 days


title: E.albidus_2d_Cd_EC90_rep3

description:
SAMPLE 10
E.albidus gene expression after 2 days of exposure to cadmium reproduction EC90


title: E.albidus_2d_Control_rep4

description:
SAMPLE 4
E.albidus gene expression after 2 days under control conditions

source_name: E. albidus_control_2 days


title: 'D' ODN for 9 hours - repeat 3 - mAdbID:103438

description: mAdb experiment ID: 103438

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.50658;; 4.42213 Temperature: 28.6462 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

tag: cell type

value: small molecule

tag: treatment time


title: 'K' ODN for 9 hours - repeat 2 - mAdbID:102744

description: mAdb experiment ID: 102744

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.52794;; 4.34278 Temperature: 29.7143 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: TLR9 ligand 'K' (CpG-B) ODN


title: 'K' ODN for 27 hours - repeat 2 - mAdbID:102880

description: mAdb experiment ID: 102880

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.47301;; 3.7965 Temperature: 25.6554 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.


title: E.albidus_2d_Cd_EC90_rep1

description:
SAMPLE 8
E.albidus gene expression after 2 days of exposure to cadmium reproduction EC90


title: patient 39

city: angers

first: frederique

last: savagner

address: 4 rue larrey

country: France

institute: Inserm

description: paired control tissue

hyb_protocol: The microarrays were first incubated at 50°C in a 50mM Ethanolamine - 100mM Tris base – SDS 0.1% solution for 15 minutes, and in a SSC 4x – 0.1% SDS solution for 15 minutes. The microarrays were then pre-hybridized 1 hour at 42°C. For each test, 20 µg of Cy3 labelled fragmented and hybridization mix resuspended samples were mixed with 20 µg of Cy5 labelled fragmented and hybridization mix resuspended reference. These mixes were denatured 2 minutes at 100°C and incubated 10 minutes at 37°C before hybridization. The microarrays were hybridized overnight at 42°C.

scan_protocol: The microarrays were scanned at 10 µM /pixel resolution with the Perkin Scanner (Waltham, MS, USA).

data_processing:
The signal intensities were extracted with the Genepix Pro 5.1 image_analysis software (Axon Instruments, Sunnyvale, CA).
The Genespring GX software (version 7) was used to analyse the microarrays data. We first applied a “per spot and per chip” lowess normalisation on the data, normalising each chip to the median of the spots (50th percentile) and each gene to the median of the replicates (cut off in raw signal = 50).

source_name: thyroid tumor

label_protocol: The Cy3 (test) and Cy5 (reference) label were performed using the Amino Allyl MessageAmp™ II CyDye™ aRNA Amplification kit (Ambion, Cambridgeshire, UK) and the RNA fragmentation Reagents kit (Ambion).

growth_protocol: Human thyroid tissues.

extract_protocol: The total RNA were extracted using a trizol® Reagent extraction procedure. RNA quality was checked on a bionalyzer and considered when RIN> 8

treatment_protocol: Human tumoral and paired control tissues.

value: Papillary Thyroid Tumor

tag: individual

value: patient 39

source_name: normal thyroid tissue

value: pool of paired control normal thyroid tissue


title: patient 38

description: paired control tissue

value: patient 38


title: patient 37

description: paired control tissue

value: patient 37


title: E.albidus_2d_Cd_EC50_rep2

description:
SAMPLE 6
E.albidus gene expression after 2 days of exposure to cadmium reproduction EC50

treatment_protocol: Fifteen adult worms with well developed clitellum were introduced in the test vessels, each containing 25 g moist soil (control or spiked soil with Cd or Zn). The worms were exposed for 2, 4 and 8 days at 20C and a 16:8h photoperiod. Three biological replicates per exposure treatment  in each time point and 4 biologcal replicates of control conditions were used. At test end, animals of each replicate were carefully removed, rinsed in deionised water, stored in RNA later (Ambion, USA) containing criotubes and frozen in liquid Nitrogen. All the samples were stored at -80C till further analysis.


title: 'D' ODN for 27 hours - repeat 1 - mAdbID:102883

description: mAdb experiment ID: 102883

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.50352;; 4.45875 Temperature: 27.8832 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'D' ODN for 27 hours


title: 'K' ODN for 1 hour - repeat 2 - mAdbID:102884

description: mAdb experiment ID: 102884

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.50963;; 4.40382 Temperature: 28.4936 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: 1 hour


title: 'K' ODN for 3 hours - repeat 3 - mAdbID:102725

description: mAdb experiment ID: 102725

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 33;; 33 LaserPower: 3.50315;; 3.91007 Temperature: 25.6249 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'K' ODN for 3 hours

value: 3 uM

value: 3 hours


title: patient 36

description: paired control tissue

value: patient 36


title: E.albidus_2d_Cd_EC50_rep1

description:
SAMPLE 5
E.albidus gene expression after 2 days of exposure to cadmium reproduction EC50


title: CCR9+

city: New York

first: Zeynep

middle: H.

last: Gumus

state: NY

address: 1300 York Ave

department: Physiology and Biophysics

institute: Cornell University

description: control

scan_protocol: Briefly, 1 micrograms of total RNA for each sample is reverse transcribed to first strand cDNA using the High Capacity cDNA reverse transcription kit (Applied BioSystems, Foster City, CA) following manufacturer  s protocol. Sample was prepared to dispense into the SmartChip by combining the cDNA and the SYBR green I master mix at a concentration of 1ng/ul. SmartChip pre-loaded with primers specific to 1293 genes in quadruplicate was placed on the dispensing platform in the sample dispenser. One hundred nano liters of master mix containing the target was dispensed into three wells and one well per gene respectively. Once the dispensing is complete the SmartChip is sealed and placed in the SmartChip real-time instrument  s chip drawer and cycled for 40 times followed by melting curve analysis.

data_processing: mRNA transcript level of each gene was analyzed by using Wafergen's qPCR software by setting thresholds within the phase of the PCR determining the cycle number at which the threshold was reached (Ct). Each gene is normalized by using the global means methodology to generate a delta Ct value for both the sample and the control. Delta delta Ct was generated by subtracting sample delta Ct from control delta Ct. Fold change is determined by following the formula FC=2^-(delta delta Ct)

source_name: CRC cells

label_protocol: Gene Expression profiling was quantified by RT-PCR using SYBR green  technology

growth_protocol: Cells cultured in stem cell media

extract_protocol: Total RNA isolated with Trizol

treatment_protocol: Recombinant CCL25 added to media.

value: early scell typee colorectal cancer stem cells

tag: facs-sorted


title: patient 35

description: paired control tissue

value: patient 35


title: CCR9-


title: E.albidus_2d_Control_rep3

description:
SAMPLE 3
E.albidus gene expression after 2 days under control conditions


title: E.albidus_2d_Control_rep1

description:
SAMPLE 1
E.albidus gene expression after 2 days under control conditions


title: 'D' ODN for 3 hours - repeat 2 - mAdbID:102741

description: mAdb experiment ID: 102741

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.51878;; 4.49843 Temperature: 28.5241 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: 'D' ODN for 3 hours

value: plasmacytoid dendritic cells (pDC)

value: Leukemia

value: TLR9 ligand 'D' (CpG-A) ODN


title: glioma 130

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

value: brain

value: glioma

tag: histological diagnosis

value: glioblastoma

tag: grade

tag: survival (yrs)


title: E.albidus_2d_Control_rep2

description:
SAMPLE 2
E.albidus gene expression after 2 days under control conditions

value: Whole body extracts

value: Adult organisms with well developed clitellum


title: 'K' ODN for 27 hours - repeat 1 - mAdbID:101482

description: mAdb experiment ID: 101482

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47758;; 3.68603 Temperature: 28.1579 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

tag: cell line

value: small molecule

tag: agent

value: TLR9 ligand 'K' (CpG-B) ODN

value: 27 hours

source_name: Universal Human Reference RNA

tag: sample type


title: 'D' ODN for 1 hour - repeat 2 - mAdbID:102722

description: mAdb experiment ID: 102722

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 10;; 10 LaserPower: 3.51878;; 4.52895 Temperature: 28.28 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

tag: disease state

tag: treatment type

tag: treatment dose

value: 3 uM

value: 1 hour


title: 'K' ODN for 1 hour - repeat 1 - mAdbID:101301

description: mAdb experiment ID: 101301

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.46324;; 3.68999 Temperature: 28.5241 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'K' ODN for 1 hour


title: Drosophila Wolbachia Infected Testes Replicate 3

city: Wuhan

first: Jialin

last: Wang

address: no.152 Luoyu Road

institute: Central China Normal University

description:
Biological replicate 3 of 3. Wolbachia strain wMel infected Drosophila larval testes, dissected at the 3rd instar.
Biological replicate 3 of 3. Control Drosophila larval testes, tetracycline treated, dissected at the 3rd instar after several generations

hyb_protocol: The Cy5/Cy3 labeled DNA in 80 μL hybridization solution (3×SSC, 0.2% SDS, 5×Denhart's, 25% formamide) was hybridized to 15K Drosophila Genome Array at 42°C overnight

scan_protocol: The GeneChips were used for scanning using LuxScan 10KA (CapitalBio)

data_processing: The data was normalized and analyzed by using LuxScan 3.0 software (CapitalBio)

organism: Drosophila melanogaster

source_name: Wolbachia infected larval testes

label_protocol: 2 ug cRNA was reverse transcribed to cDNA and the cDNA was used as the template for Cy5/Cy3 labeled DNA synthesis with Cy5/Cy3-dCTP

extract_protocol: Total RNA extracted using Trizol according to manufacturer's instructions

tag: infection

value: Wolbachia wMel strain

tag: tissue

value: testes

tag: developmental stage

value: 3rd instar larva

source_name: 3rd instar larval testes

tag: treatment

value: tetracycline


title: TYKnu

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

description: Baseline profiling of TYKnu cells

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).

source_name: TYKnu cells

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: TYKnu

tag: cell type

value: ovarian cancer cells


title: TYKnuCisR

description: Baseline profiling of TYKnuCisR cells

source_name: TYKnuCisR cells

value: TYKnuCisR


title: 'K' ODN for 3 hours - repeat 1 - mAdbID:101304

description: mAdb experiment ID: 101304

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.45134;; 3.68969 Temperature: 28.7683 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

value: plasmacytoid dendritic cells (pDC)

value: Leukemia

tag: treatment time

value: 3 hours


title: patient 33

description: paired control tissue

value: Papillary Thyroid Tumor

tag: individual

value: patient 33

value: pool of paired control normal thyroid tissue


title: 'K' ODN for 9 hours - repeat 1 - mAdbID:101308

description: mAdb experiment ID: 101308

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4727;; 3.59722 Temperature: 26.2658 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'K' ODN for 9 hours

value: small molecule

value: TLR9 ligand 'K' (CpG-B) ODN

value: 9 hours


title: patient 32

description: paired control tissue

value: patient 32


title: 'D' ODN for 9 hours - repeat 1 - mAdbID:101307

description: mAdb experiment ID: 101307

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48;; 3.61 Temperature: 26.33 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: 'D' ODN for 9 hours

value: TLR9 ligand 'D' (CpG-A) ODN

value: 3 uM


title: TOV21G

description: Baseline profiling of TOV21G cells

source_name: TOV21G cells


title: TOV112D

description: Baseline profiling of TOV112D cells

source_name: TOV112D cells


title: E.albidus_2d_Zn_EC50_rep1

description:
SAMPLE 11
E.albidus gene expression after 2 days of exposure to zinc reproduction EC50

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

source_name: E. albidus_zinc EC50_2 days

value: Whole body extracts

value: Adult organisms with well developed clitellum


title: patient 34

description: paired control tissue

source_name: thyroid tumor

value: patient 34


title: Replication timing of normal growing IMR90 cells

type: genomic

city: Tallahassee

first: Benjamin

last: Pope

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 2.5 kb across the human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

molecule: genomic DNA

source_name: Early-replicating DNA of normal IMR90 cells

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

growth_protocol: DMEM supplemented with 10% FBS and antibiotics in 5% oxygen

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

treatment_protocol: 100 nM 4OHT for 6 days in ER:Ras-expressing IMR90 cells to induced ER:Ras

value: lung embryonic fibroblasts

value: normal IMR90 cells

tag: gender

value: F

source_name: Late-replicating DNA of normal IMR90 cells


title: patient 30

description: paired control tissue

scan_protocol: The microarrays were scanned at 10 µM /pixel resolution with the Perkin Scanner (Waltham, MS, USA).

value: Oncocytic tumor

value: patient 30

source_name: normal thyroid tissue


title: patient 31

description: paired control tissue

value: Papillary Thyroid Tumor

value: patient 31


title: microRNA profile of case NPC316871

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

source_name: Nasopharyngeal carcinoma

tag: survival status  (1-death,0-survival)

tag: gender  (1-male,2-female)

tag: age (years)

tag: stage  (1-stage i,2-stage ii,3-stage iii,4-stage iv)


title: Replication timing of Ras-induced senescent IMR90 cells

source_name: Early-replicating DNA of Ras-induced senescent IMR90 cells

value: Ras-induced senescent IMR90 cells

source_name: Late-replicating DNA of Ras-induced senescent IMR90 cells


title: Drosophila Wolbachia Infected Testes Replicate 2

description:
Biological replicate 2 of 3. Wolbachia strain wMel infected Drosophila larval testes, dissected at the 3rd instar.
Biological replicate 2 of 3. Control Drosophila larval testes, tetracycline treated, dissected at the 3rd instar after several generations

value: Wolbachia wMel strain

value: testes

value: 3rd instar larva

value: tetracycline


title: 'D' ODN for 1 hour - repeat 1 - mAdbID:101300

description: mAdb experiment ID: 101300

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48;; 3.64 Temperature: 26.78 Scanning Protocol Other: Arrays were scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 6.0 Software Tool (Axon Instruments) using GAL files provided by the manufacturer at http://madb.nci.nih.gov/.

source_name: Universal Human Reference RNA

value: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: 'D' ODN for 1 hour

tag: cell line

value: plasmacytoid dendritic cells (pDC)

value: Leukemia

value: small molecule

tag: agent

value: TLR9 ligand 'D' (CpG-A) ODN

value: 1 hour


title: microRNA profile of case NPC318513


title: Drosophila Wolbachia Infected Testes Replicate 1

description:
Biological replicate 1 of 3. Wolbachia strain wMel infected Drosophila larval testes, dissected at the 3rd instar.
Biological replicate 1 of 3. Control Drosophila larval testes, tetracycline treated, dissected at the 3rd instar after several generations

source_name: Wolbachia infected larval testes

source_name: 3rd instar larval testes


title: patient 28

description: paired control tissue

value: patient 28

value: pool of paired control normal thyroid tissue


title: patient 29

description: paired control tissue

value: Oncocytic tumor

value: patient 29


title: T8

description: Baseline profiling of T8 cells

source_name: T8 cells

value: ovarian cancer cells


title: Ejaculate not resulting in oocyte fertilization, F46

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

institute: University Hospital Hamburg-Eppendorf

hyb_protocol: Hybridization was conducted for 20h at 37°C, and arrays were washed in 1x TNT (10 min, RT) and 1x TNT (60 min, 46°C). Staining with Cy5-Streptavidin was done for 30 min at RT. Then, arrays were washed 2 times with 1x TNT for 10 min and 0.2x SSPE for 30s. They were spin-dried in a centrifuge at 2000 rpm for 2 min.

scan_protocol: Scanning was done on a ScanArray Gx Scanner (Perkin Elmer) at PMT 70/LP 90% setting and 5um resolution. Images were acquired with the ScanArray Express 3.0 software (Perkin Elmer).

data_processing: Scan images were converted to raw values by the CodeLink Expression analysis software (GE Healthcare, USA). Genes with lower than 5th percentile expression values over all samples were removed. Normalization was by quantile normalization using the Bioconducter package 'affy'.

source_name: ejaculate after 30 min liquefaction

label_protocol: 50 - 500 ng total RNA were amplified with the MessageAmp III Kit (Ambion, USA), and Biotin-UTP was incorporated as a label.

extract_protocol: RNA was extracted from the ejaculates by a specially designed two-fold genomic DNA pre-elimination protocol (Rneasy Micro). Details are to be found under http://www.dr-spiess.de/supp/MHRCappallo2011/RNA.pdf.

treatment_protocol: Human ejaculates were liquefied for 30 min at 37°C, and an aliquot of 1 mL was washed once by centrifugation in PBS (500 g).

value: ejaculate

tag: ivf outcome

value: no oocyte fertilization

tag: motility (a+b) [%]

tag: ejaculate volume

tag: concentration [10e6/ml]

tag: oocytes in metaphase ii

tag: age of woman [years]

tag: fertilisation ratio [%] (2pn/mii)

tag: cumulative embryo score

tag: pregnancies


title: patient 26

description: paired control tissue

tag: tissue

tag: individual

value: patient 26


title: Ejaculate resulting in oocyte fertilization, F50

value: oocyte fertilization


title: patient 27

description: paired control tissue

value: patient 27


title: SKOV6

description: Baseline profiling of SKOV6 cells

source_name: SKOV6 cells

tag: cell type


title: SKOV4

description: Baseline profiling of SKOV4 cells

source_name: SKOV4 cells


title: Ejaculate not resulting in oocyte fertilization, F35


title: 14269057 - prgh 12h RB2 vs Mock 12h RB2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: What is the transcriptomic reprogramming after Salmonella infection, What is the importance of the T3SS in the plant infection, Are there differences in gene expression between the 2 bacterial strains? What are the functions of these genes,

hyb_protocol: Mock 12h RB2 Cy5 / prgh 12h RB2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Experiments were designed with the statistics group of the Unité de Recherche en Génomique Végétale. 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. Differential analysis was based on the log ratios averaged on the dye-swap: The technical replicates were averaged to get one log-ratio per biological replicat and these values were used to performed a paired t-test. A trimmed variance is calculated from spots which do not displaying extreme variance (see details in Gagnot  et al. 2008). The raw P-values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate in order to keep a strong control of the false positives in a multiple-comparison context. We considered as being differentially expressed the probes with a Bonferroni P-value < 0.05.

organism: Arabidopsis thaliana

source_name: Mock 12h RB2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) 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: whole plant - 14 days-old Arabidopsis seedlings grown in MS/2 agar + 1% sugar (pH 5,7) in long day at 22°C were transfered in liquid MS/2 (pH 5,7) without sugar a day before treatment. 3 seedlings / well in 6 well plates with 5 ml media. The treatment consists in the addition of Salmonella Typhimurium 14028 (wild type) and St 14028 prgH mutant. Bacterial solutions were prepared in 10 mM MgCl2 and added to the media to a final concentration of OD600=0,2. Mock treatment was done by adding equal volume of MgCl2. Treatments were started at 9 am, seedlings were placed back in the rotonde and samples were taken at 2,4 6,12, and 24 hours post inoculation. Three replicates per treatment were frozen in liquid nitrogen and kept at -80°C.

extract_protocol: Mock 12h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:control 12h - pathogen - pathogen infection,mgcl2 10mm:time 12hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

tag: cultivar/ecotype

value: columbia mutant (col0)

tag: harvest date

tag: treatment

value: control 12h,mgcl2 10mm

tag: time

source_name: prgh 12h RB2

extract_protocol: prgh 12h RB2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Salmonella mutant 12h - pathogen - pathogen infection,salmonella typhimurium:time 12hour . addition of bacterial solution (in MgCl2 10 mM) at OD600 nm= 0,2 with salmonella WT 14028 or Salmonella mutant prgh or mock treatment (MgCl2 10 mM same volume) to liquid medium.

value: Salmonella mutant 12h,salmonella typhimurium


title: Ejaculate not resulting in oocyte fertilization, F55


title: patient 25

description: paired control tissue

source_name: thyroid tumor

value: patient 25


title: patient 24

description: paired control tissue

value: patient 24


title: patient 23

description: paired control tissue

value: patient 23