title: pTH9142_ME_8mer_8645

source_name: C34D1.1, ME design


title: pTH9173_HK_8mer_8092

status: Public on Apr 23 2015

type: protein

city: Toronto

first: Kamesh

last: Narasimhan

state: Ontario

address: 160 college Street

country: Canada

institute: Donnelly Centre for Cellular and Biomolecular Research

hyb_protocol: After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. The VALUE column contains the median intensity for the 8mer sequence.  Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.   Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: efl-2, HK design

label_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

extract_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as AscI–SbfI fragments into pTH6838, a modified T7-driven GST expression vector.

tag: dbd source organism

value: Caenorhabditis elegans

tag: dbd

tag: platform_id_id design

value: HK


title: pTH9155_ME_8mer_7873

source_name: lin-48, ME design

value: ME


title: pTH9137_HK_8mer_8680

source_name: nhr-65, HK design


title: pTH9135_ME_8mer_10770

source_name: pop-1, ME design


title: pTH9135_HK_8mer_10754

source_name: pop-1, HK design


title: pTH9132_ME_8mer_8644

source_name: T27F2.4, ME design


title: pTH9125_HK_8mer_7630

source_name: egl-13, HK design


title: pTH9125_ME_8mer_7497

source_name: egl-13, ME design


title: pTH9132_HK_8mer_8678

source_name: T27F2.4, HK design


title: pTH9108_ME_8mer_7282

source_name: daf-12, ME design


title: pTH9116_HK_8mer_8677

source_name: lin-31, HK design


title: pTH9096_HK_8mer_7629

source_name: T07C12.11, HK design


title: pTH9096_ME_8mer_7229

source_name: T07C12.11, ME design


title: pTH9108_HK_8mer_7475

source_name: daf-12, HK design


title: pTH9085_ME_8mer_7138

source_name: nhr-42, ME design


title: pTH9089_HK_8mer_8676

source_name: ref-2, HK design


title: pTH9085_HK_8mer_7627

source_name: nhr-42, HK design


title: pTH9089_ME_8mer_7532

source_name: ref-2, ME design


title: pTH9116_ME_8mer_7290

source_name: lin-31, ME design


title: pTH9082_HK_8mer_10753

source_name: mab-23, HK design

value: DM


title: pTH9080_ME_8mer_7124

source_name: mnm-2, ME design


title: pTH9073_ME_8mer_7447

source_name: end-3, ME design

value: GATA


title: pTH9080_HK_8mer_7626

source_name: mnm-2, HK design


title: pTH9073_HK_8mer_8096

source_name: end-3, HK design


title: pTH9072_ME_8mer_7109

source_name: klf-3, ME design


title: pTH9072_HK_8mer_8506

source_name: klf-3, HK design


title: Hippocampus ApoD-KO Old, biological rep3

type: RNA

city: Valladolid

first: Diego

last: Sanchez

state: Valladolid

address: C/ Sanz y Forés 3

department: IBGM

country: Spain

institute: Universidad de Valladolid

hyb_protocol: 2.3  micrograms of the biotinylated and fragmented probes were hybridized to Affymetrix chips at 45ºC for 16 h, following the manufacturer's protocols.

scan_protocol: Following labeling and washes, the arrays were incubated with anti-biotin streptavidin-phycoeritrin antibody and were scanned with an Affymetrix GeneChip Scanner 7G.

data_processing: Analysis of differential gene expression was performed with FlexArray v1.6.1 program (Blazejczyk and others 2007), using the Affymetrix CEL files. Robust normalization using MAS 5.0 was performed to estimate a change p-value and its associated change call in gene expression for each probeset. Data pre-processing was carried out with the robust multiarray average algorithm (RMA) with background correction and normalization. Gene differential expression was evaluated with FlexArray by two sample comparisons with the cyberT-test, using a significance threshold of 1.2-fold change and a P value <0.05. False discovery rate (FDR) correction (5%) was performed using the Benjamini-Hochberg method. A Significance Analysis of Microarrays (SAM) algorithm using an unequal variance t-statistic was also employed to select genes robustly affected by age and/or genotype. Probe sets derived from non-annotated genes were not considered for the final discussion of differentially expressed genes.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse hippocampus, 655 days old

label_protocol: cDNA was synthesized and purified from 5 micrograms of each RNA sample with the One Cycle cDNA synthesis (Affymetrix, Santa Clara, CA). The generation, labeling and purification of cRNA were performed using the IVT kit (Affymetrix, Santa Clara, CA). Probe synthesis and hybridizations were performed at the Genomics facility of the Centro de Investigacion del Cancer (Salamanca, Spain).

growth_protocol: Mice were maintained in positive pressure-ventilated racks at 25±1ºC with 12 h light/dark cycle, fed ad libitum with a standard rodent pellet diet (Global Diet 2014; Harlan Inc., Indianapolis, IN, USA), and allowed free access to filtered and UV-irradiated water.

extract_protocol: Mouse brains were quickly removed following decapitation after CO2 anesthesia. Hippocampal and cortical regions selected for mRNA expression studies were rapidly sliced in cold PBS under a stereomicroscope, and stored at -80ºC. RNA was extracted with QIAzolTM Lysis Reagent (Qiagen) followed by a second purification step with RNeasy miniKit (Qiagen) The purified RNA quality was assayed using the Agilent 2100 Bioanalyzer. Equimolar amounts of total RNA from 2-3 randomly selected mice for each genotype, brain region and age were used to make pools. Three of these biological replicates per condition were used for hybridization with oligonucleotide microarrays.

tag: strain

tag: gender

value: Male

tag: tissue

value: Brain hippocampus

tag: genotype

value: ApoD-KO

tag: age

value: 655 days old


title: pTH9057_HK_8mer_7365

source_name: let-381, HK design


title: Hippocampus ApoD-KO Young, biological rep3

source_name: Mouse hippocampus, 100 days old

value: 100 days old


title: pTH9056_ME_8mer_8580

source_name: bed-3, ME design

value: zf-BED


title: Hippocampus WT Young, biological rep2

value: Wild type


title: Hippocampus ApoD-KO Old, biological rep1


title: Hippocampus ApoD-KO Old, biological rep2


title: pTH9056_HK_8mer_8660

source_name: bed-3, HK design


title: Hippocampus WT Old, biological rep1


title: Hippocampus WT Old, biological rep2


title: Hippocampus ApoD-KO Young, biological rep2


title: Hippocampus WT Old, biological rep3


title: Hippocampus ApoD-KO Young, biological rep1


title: pTH9057_ME_8mer_7066

source_name: let-381, ME design


title: pTH9052_HK_8mer_8548

source_name: F17A9.3, HK design


title: Cortex ApoD-KO Old, biological rep3

source_name: Mouse cortex, 655 days old

value: Brain cortex


title: Hippocampus WT Young, biological rep1


title: Cortex ApoD-KO Old, biological rep1


title: pTH8999_ME_8mer_8357

source_name: Y67D8A.3, ME design


title: Cortex WT Old, biological rep2


title: pTH9317_ME_8mer_7880

source_name: egrh-1, ME design


title: pTH9052_ME_8mer_7061

source_name: F17A9.3, ME design


title: Cortex ApoD-KO Young, biological rep3

source_name: Mouse cortex, 100 days old


title: pTH8999_HK_8mer_8341

source_name: Y67D8A.3, HK design


title: pTH8998_ME_8mer_8520

source_name: mab-3, ME design


title: Cortex ApoD-KO Old, biological rep2


title: Cortex WT Old, biological rep3


title: Hippocampus WT Young, biological rep3


title: Cortex WT Old, biological rep1


title: pTH8998_HK_8mer_8564

source_name: mab-3, HK design


title: Cortex ApoD-KO Young, biological rep2


title: pTH6106_HK_8mer_3463

source_name: nhr-182, HK design


title: pTH10927_ME_8mer_10556

source_name: tbx-43, ME design

value: T-box


title: pTH10927_HK_8mer_10572

source_name: tbx-43, HK design


title: pTH10823_ME_8mer_10398

source_name: B0310.2, ME design


title: Cortex WT Young, biological rep2


title: pTH10823_HK_8mer_10575

source_name: B0310.2, HK design


title: pTH10837_ME_8mer_10428

source_name: T22H9.4, ME design


title: pTH10837_HK_8mer_10444

source_name: T22H9.4, HK design


title: Cortex ApoD-KO Young, biological rep1


title: Cortex WT Young, biological rep1


title: pTH6106_ME_8mer_2364

source_name: nhr-182, ME design


title: pTH10816_HK_8mer_10569

source_name: dmd-6, HK design


title: Cortex WT Young, biological rep3


title: pTH10816_ME_8mer_10391

source_name: dmd-6, ME design


title: pTH10811_ME_8mer_10386

source_name: nhr-216, ME design


title: pTH10811_HK_8mer_10568

source_name: nhr-216, HK design


title: pTH10810_ME_8mer_10385

source_name: lsy-2, ME design


title: pTH10808_ME_8mer_10239

source_name: ztf-19, ME design


title: pTH10810_HK_8mer_10567

source_name: lsy-2, HK design


title: pTH10822_ME_8mer_10397

source_name: unc-120, ME design

value: SRF-TF


title: pTH10808_HK_8mer_10255

source_name: ztf-19, HK design


title: pTH10822_HK_8mer_10570

source_name: unc-120, HK design


title: pTH10807_ME_8mer_10238

source_name: F13H6.1, ME design


title: pTH10807_HK_8mer_10254

source_name: F13H6.1, HK design


title: pTH10805_HK_8mer_10252

source_name: ztf-16, HK design


title: pTH10805_ME_8mer_10236

source_name: ztf-16, ME design


title: pTH10802_ME_8mer_10270

source_name: K02D7.2, ME design


title: C2_F3

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: pool of 2 individuals

hyb_protocol: Hybridizations and washes were performed using Gene Expression Hybridization Kit (Agilent Technologies) following manufactures protocol

scan_protocol: Hybridized slides were scanned on Agilent DNA Microarray Scanner and signals were extracted and quality control was performed using Feature Extraction 10.7.3.1 Software (Agilent Technologies).

data_processing: Microarray data analysis was performed in R environment (version 2.15.1) using Bioconductor’s libraries limma and vsn.

organism: Danio rerio

source_name: 4 months old zebrafish liver

label_protocol: The total RNA was labelled with Cy-3 using Low Input Quick-Amp Labeling Kit One-Color (Agilent technologies) following manufacturers protocol

growth_protocol: AB line of zebrafish (Danio rerio) that was used in the experiments, originated from the Department of Aquaculture of Szent István University. Prior to the experiment, the parent generation was maintained in a recirculation system allowing continuous flow of water (ZebTec, Tecniplast Inc.) in a light regime of 14 h light/10 h dark. Parameters of the system water were as follows: temperature 25±0.5 °C, pH 7.4±0.2, conductivity: 525±50 µS. During the experimental period fish were maintained at 24-26 °C in a light regime of 14 h light/10 h dark.

extract_protocol: The RNA was isolated by Direct-zol RNA Miniprep (ZymoResearch) from liver from 10 individuals per exposure point from each of the two replicates. After RNA quality and quantity evaluation (Agilent Bioanalyzer, RNA 6000 Nano Kit, Eukaryote Assay), RNA from 3 individuals from same treatment, replicate and gender was pooled, DNase treated (Invitrogen DNaseI; 0.2 U/µg RNA) in 45 μl reactions and subsequently purified using RNeasy Mini Elute kit (Qiagen). Purified RNA was checked for integrity and quantity by Bioanalyzer.

treatment_protocol: 5-fuorouracil (5-FU) (CAS 51-21-8) was purchased from Sigma-Aldrich. Stock solution (100 mg/L) was prepared in dimethyl-sulfoxide (DMSO) and used for toxicity evaluation after dilution in clean system water (see parameters above). The nominal exposure concentrations were 0.01 and 1 a100 µg/L of 5-FU. The control group of fish was kept in the system water supplemented with 1μl/L of DMSO (vehicle control). All treatments including controls were conducted in duplicates (A and B).   The experiment was performed under the semistatic conditions with a complete renewal of exposure medium every three days. Chemical analyses of treatment medium samples were performed immediately after the medium exchange, at the end of the second day (48 h) and the end of the third day (72 h). At the age of 4 month part of F1 fish was sampled for gene expression analyses.

value: female

tag: agent

tag: dose

value: 1 µg/L

value: 4 months old

value: liver


title: C2_M2

description: pool of 3 individuals

value: male


title: C2_M3

description: pool of 3 individuals


title: C2_M1

description: pool of 3 individuals


title: C2_F2

description: pool of 3 individuals


title: C2_F4

description: individual fish


title: C1_F2

description: pool of 3 individuals


title: pTH10798_ME_8mer_10194

source_name: Y75B8A.6, ME design

value: Caenorhabditis elegans

value: zf-CXXC

value: ME


title: C1_F3

description: pool of 3 individuals


title: C1_M2

description: pool of 3 individuals


title: C1_M3

description: pool of 2 individuals


title: 550541A02 - mu775_BR1 vs. col_BR1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Look for potential targets of miR775 at Arabidopsis thaliana by the analysis of the transcriptome of a mutant not producing any more the miRNA.

hyb_protocol: col_BR1 Cy5 / mu775_BR1 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: Mapix, Cy3:532nm, pmt voltage 480V, laser power 35%; Cy5:635nm, pmt voltage 480V, laser power 30%.

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green). For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias. Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

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: aerial,seedling - Media=Arabidopsis compost hygrometry=glasshouse condition Temperature=glasshouse condition Light=LD glasshouse condition

extract_protocol: col_BR1:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: No treatment

tag: ecotype/background

tag: genotype/variation

value: wild type

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

value: seedling

extract_protocol: mu775_BR1:5ug. (Qiagen_RNeasy.pdf)

value: miR775 mutant


title: 550541A03 - col_BR2 vs. mu775_BR2

hyb_protocol: mu775_BR2 Cy5 / col_BR2 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.

extract_protocol: mu775_BR2:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: col_BR2:5ug. (Qiagen_RNeasy.pdf)


title: pTH10798_HK_8mer_10210

source_name: Y75B8A.6, HK design

value: HK


title: C1_M1

description: pool of 2 individuals


title: pTH10797_ME_8mer_10782

source_name: K11D2.4, ME design


title: C2_F1

description: pool of 3 individuals


title: pTH10797_HK_8mer_10766

source_name: K11D2.4, HK design


title: pTH10802_HK_8mer_10214

source_name: K02D7.2, HK design


title: 550541A01 - col_BR1 vs. mu775_BR1

hyb_protocol: mu775_BR1 Cy5 / col_BR1 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.


title: 546693A12 - mu775_BR2 vs. col_BR2

hyb_protocol: col_BR2 Cy5 / mu775_BR2 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.


title: pTH10796_HK_8mer_10191

source_name: hsf-1, HK design


title: pTH10796_ME_8mer_10268

source_name: hsf-1, ME design


title: Control_M3

description: pool of 2 individuals

value: DMSO

value: control


title: pTH10795_ME_8mer_10267

source_name: ztf-14, ME design


title: pTH10795_HK_8mer_10190

source_name: ztf-14, HK design


title: pTH10794_ME_8mer_10266

source_name: pax-2, ME design

value: PAX


title: pTH10794_HK_8mer_10189

source_name: pax-2, HK design


title: Control_M2

description: pool of 3 individuals


title: Control_F2

description: pool of 3 individuals


title: C1_F1

description: pool of 3 individuals


title: pTH10779_ME_8mer_10142

source_name: nhr-182, ME design


title: pTH10787_HK_8mer_10182

source_name: eyg-1, HK design

value: PAX,Homeobox


title: Control_F3

description: pool of 3 individuals


title: pTH10788_ME_8mer_10265

source_name: tbx-33, ME design

value: T-box


title: pTH10777_ME_8mer_10140

source_name: dmd-5, ME design

value: DM


title: pTH10787_ME_8mer_10264

source_name: eyg-1, ME design


title: pTH10779_HK_8mer_10158

source_name: nhr-182, HK design


title: pTH9082_ME_8mer_10769

source_name: mab-23, ME design


title: pTH10777_HK_8mer_10156

source_name: dmd-5, HK design


title: pTH10772_HK_8mer_10151

source_name: ceh-52, HK design

value: Homeobox


title: Control_M1

description: pool of 3 individuals

source_name: 4 months old zebrafish liver

value: 4 months old


title: Control_F1

description: pool of 3 individuals

value: female

value: liver


title: pTH10769_ME_8mer_10132

source_name: Y48G1C.6, ME design

value: Caenorhabditis elegans


title: pTH10788_HK_8mer_10183

source_name: tbx-33, HK design


title: pTH10769_HK_8mer_10148

source_name: Y48G1C.6, HK design


title: pTH10730_ME_8mer_10781

source_name: ceh-36, ME design


title: pTH10768_HK_8mer_10147

source_name: med-2, HK design

value: GATA


title: pTH10730_HK_8mer_10765

source_name: ceh-36, HK design


title: pTH10722_HK_8mer_10764

source_name: egrh-3, HK design


title: pTH10768_ME_8mer_10131

source_name: med-2, ME design

value: ME


title: pTH10721_HK_8mer_10126

source_name: ztf-9, HK design


title: pTH10721_ME_8mer_10261

source_name: ztf-9, ME design


title: pTH10722_ME_8mer_10780

source_name: egrh-3, ME design


title: pTH10718_ME_8mer_10259

source_name: egl-43, ME design


title: pTH10718_HK_8mer_10123

source_name: egl-43, HK design


title: pTH10772_ME_8mer_10553

source_name: ceh-52, ME design


title: pTH10716_HK_8mer_10121

source_name: ceh-37, HK design


title: pTH10716_ME_8mer_10257

source_name: ceh-37, ME design


title: pTH10714_HK_8mer_10119

source_name: nhr-142, HK design


title: pTH10707_HK_8mer_10112

source_name: elt-6, HK design


title: KO 3

city: Woodbury

first: Megan

last: Crow

state: New York

address: 500 Sunnyside Blvd

country: USA

institute: Cold Spring Harbor Laboratory

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Run on an Affymetrix GeneChip Scanner

data_processing: Quality control and analysis were carried out using the following bioconductor packages in R: oligo for preprocessing, RMA normalization, and various quality controls (including MA plots, box plots, and principal component analysis) and limma for statistical analysis

source_name: Dorsal root ganglion

label_protocol: Used Ambion WT Expression kit (TdT label)

extract_protocol: RNA extraction was performed with a two-step protocol consisting of phenol-chloroform extraction followed by clean-up and elution on Qiagen RNeasy MinElute columns. Care was taken to avoid batch effects by processing samples in matched groups.  Snap frozen tissues were transferred into 500 µL Trizol reagent (Invitrogen) in a fresh tube, and homogenized on ice in three 10 second bursts. Samples were lysed at room temperature for 10 minutes, then were transferred to Phase Lock Gel Heavy tubes (5 Prime), and 100 µL chloroform was added. Samples were shaken for 15 seconds and allowed to rest at room temperature for three minutes prior to centrifugation at 11300 RPM for 15 minutes at 4°C. The aqueous phase was transferred to an RNAse-free eppendorf tube, an equal volume of fresh 70% ethanol was added, and this was loaded onto columns for clean-up following manufacturer’s protocol.

value: HDAC4 Nav1.8 cKO

value: adult


title: pTH10717_ME_8mer_10258

source_name: syd-9, ME design


title: KO 2


title: KO 1


title: pTH10699_ME_8mer_10072

source_name: ceh-53, ME design


title: Wildtype 1

value: HDAC4 fl/fl


title: Mature leaves of wild-type_rep2

city: Kyoto

first: Mitsuhiro

last: Matsuo

address: 1-5 Hangi-cho, Shimogamo, Sakyoku

department: Graduate School of Life and Environmental Sciences

country: Japan

institute: Kyoto Prefectural University

hyb_protocol: Hybridization of cRNA on Affymetrix Arabidopsis ATH1 Genome Array [ATH1-121501] were performed according to the manufacturer's instruction.

scan_protocol: Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

data_processing: Summarized probe set signals were calculated by using Microarray Suite version 5.0 (MAS 5.0) with the Affymetrix GeneChip Expression Console Software.

source_name: Arabidopsis mature leaves, wild-type

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instruction (GeneChip Expression Analysis Technical Manual,  Affymetrix).

growth_protocol: Seedlings of wild-type and transgenic plant were grown on MS medium in the presence of 1.37% sucrose under continuous medium-light condition (80 µmol m-2s-1) at 20˚C for 2 weeks. And then, they were transferred to pots containing garden-soil including vermiculite and were further grown under short-day condition with the medium-light intensity at 20˚C for 3 weeks.

extract_protocol: Total RNA was isolated from the mature leaves using RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Mature leaves were harvested.

value: Mature leaf

value: Columbia

value: wild type


title: Mature leaves of wild-type_rep3


title: Wildtype 2


title: Mature leaves of wild-type_rep1


title: control 1, day 8, repeat 2

city: Victoria

first: Julian

middle: J.

last: Lum

state: BC

address: 2410 Lee Avenue

department: Deeley Research Centre

institute: BC Cancer Agency

hyb_protocol: An input of 20ng of total RNA was used to generate Cyanine-3 labeled cRNA. 600ng of Cy3-labeled cRNA (specific activity >15 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1ul Agilent fragmentation buffer and 5ul of 10X Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-026687 Whole Mouse Genome Microarray 4x44K v2 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 for 1min in acetonitrile.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution and data was processed with Agilent Feature Extraction 11.0.1.1.

source_name: Atg5fl/+ Cre+/- Thy1.1+ OTI+

label_protocol: Samples were prepared following the Agilent One-Color Microarray-Based Exon Analysis Low Input Quick Amp WT Labeling v1.0.  Total RNA is initially converted into cDNA using a mixture of T7 polymerase dT and T7 polymerase random primed reverse transcriptase reaction to synthesize first and second strand of cDNA. This cDNA then served as a template for cRNA synthesis by T7 RNA polymerase in the presence of Cyanine 3-labeled CTP (Cy3).

extract_protocol: RNA was isolated with the Quigen RNAesy Kit following the manufacturer instruction.

treatment_protocol: cells were kept on ice during preparation for sorting, during sorting until cell lysis. Sorting was performed with Influx for live CD8+ Thy1.1+ cells at day 7 or 8 after influenza infection. 3.000 to 10.000 cells were gained for one sample.

value: spleen


title: pTH10714_ME_8mer_10256

source_name: nhr-142, ME design


title: pTH10699_HK_8mer_10088

source_name: ceh-53, HK design

value: HK


title: pTH10717_HK_8mer_10122

source_name: syd-9, HK design


title: pTH10696_HK_8mer_10085

source_name: Y44A6D.3, HK design

value: BrkDBD


title: pTH10656_ME_8mer_10067

source_name: hlh-12, ME design

value: HLH


title: pTH10696_ME_8mer_10069

source_name: Y44A6D.3, ME design


title: Wildtype 3


title: Mature leaves of oe18_rep2

source_name: Arabidopsis mature leaves, oe18

value: RRTF1 overexpressor


title: Atg5 KO, day 8, repeat 2

data_processing: data was processed with Agilent Feature Extraction 11.0.1.1.

source_name: Atg5 knockout CD8+ T cells


title: pTH10654_ME_8mer_10065

source_name: ceh-90, ME design

value: Homeobox


title: pTH10656_HK_8mer_10566

source_name: hlh-12, HK design


title: Atg5 KO, day 7, repeat 2

source_name: Atg5fl/fl Cre+/- Thy1.1+ OTI+

value: female


title: Mature leaves of oe18_rep1


title: pTH10654_HK_8mer_10081

source_name: ceh-90, HK design


title: Mature leaves of oe18_rep3


title: control 1, day 7, repeat 2


title: control 2, day 8, repeat 2

source_name: Atg5fl/fl Cre-/- Thy1.1+ OTI+


title: pTH10650_ME_8mer_10192

source_name: nhr-154, ME design


title: control 2, day 7, repeat 2


title: root of rrtf1

city: Jena

first: khabat

last: vahabi

state: Deutschland

address: Dornburger Straße 159

department: plant physiology

country: Germany

institute: Friedrich-Schiller-Universität

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip 3’ IVT Express Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA). In brief, 250 ng of total RNA were reverse transcribed into double-stranded copy DNA (cDNA) followed by an in vitro transcription generating biotin-labeled amplified RNA (aRNA). The length of the purified aRNA products was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA). Following fragmentation, 15 µg aRNA were hybridized to Affymetrix GeneChip Arabidopsis ATH1 Genome arrays for 16 h at 45 °C in a rotating chamber. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Summarized probe set signals were calculated by using the RMA (1) algorithm with the Affymetrix GeneChip Expression Console Software. After exporting into Microsoft Excel comparison fold changes were calculated. Probe sets with a fold change above 2.0 fold were considered as significantly regulated.

source_name: Arabidopsis root

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

growth_protocol: Arabidopsis thaliana Col-0 was used as WT. The T-DNA-inserted RRTF1 knockout mutant (SALK_150614) was obtained from NASC (http://arabidopsis.info/). Homozygote RRTF1 knockout plant was identified by PCR with gene specific primers (LP_SALK_150622: 5’-CGCGATGCTTTGTAGGAGTAG-3’, RP_SALK_150622: 5’-TGTCAGGGTTTTTCCAGTGAC-3’) and T-DNA left border primer Lba1 (5’-TGGTTCACGTAGTGGGCCATCG-3’).  For the RRTF1 (At4g34410) overexpression construct p35S-RRTF1, the RRTF1 coding region was amplified from RRTF1 cDNA clone (DKLAT4G34410), obtained from Arabidopsis Biological Resource Center (http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc /abrchome.htm). The PCR product was cloned into pCR®8/GW/TOPO® TA vector (Invitrogen), and then the insert was integrated into a binary vector, pB2GW7 containing CaMV 35S promoter, using Gateway LR recombination reaction system (Invitrogen). p35S-RRTF1 was transformed into Arabidopsis Col-0 via Agrobacterium tumefaciens strain GV3101 with floral-dip method. T1 plants were selected by spraying 1-2 weeks old seedlings with 0.1% BASTA (Bayer, Germany). T2- and T3-plant resistant to DL-phosphinothricin (50µM) (Sigma-Aldrich) on MS medium plate were used for physiological experiments.    The seedlings were grown on MS medium with 1.37% sucrose under short day conditions and low light intensity (30 µmol m-2s-1) at 20˚C for 14 days. Transcriptome analysis was performed for the rrtf1 knock-out line and a RRTF1-overlexpressor line (called oe18) in comparison to wild-type seedlings.

extract_protocol: Total RNA was isolated from both roots and shoots of WT seedlings using RNeasy Plant Mini Kit (Qiagen)

value: Columbia RRTF1 knockout plant

value: root

tag: genetic background

value: 14 days


title: root of oe18

treatment_protocol: The seedlings were grown on MS medium with 1.37% sucrose under short day conditions and low light intensity (30 µmol m-2s-1) at 20˚C for 14 days. Transcriptome analysis was performed for the rrtf1 knock-out line and a RRTF1-overlexpressor line (called oe18) in comparison to wild-type seedlings.

value: Columbia RRTF1 overexpressor


title: pTH10650_HK_8mer_10565

source_name: nhr-154, HK design

value: Caenorhabditis elegans


title: pTH10647_ME_8mer_10043

source_name: nhr-232, ME design

value: ME


title: root of wild-type

value: Columbia wild type


title: pTH10647_HK_8mer_10059

source_name: nhr-232, HK design


title: Atg5 KO, day 8, repeat 1


title: shoot of oe18

source_name: Arabidopsis shoot

value: shoot


title: pTH10645_ME_8mer_10041

source_name: nhr-7, ME design


title: shoot of rrtf1

value: Columbia


title: control 2, day 8, repeat 1


title: pTH10645_HK_8mer_10564

source_name: nhr-7, HK design


title: control 1, day 7, repeat 1

source_name: Atg5fl/+ Cre+/- Thy1.1+ OTI+


title: control 1, day 8, repeat 1


title: pTH10638_ME_8mer_10002

source_name: dmd-3, ME design

value: DM


title: celline_MYCN_GTML_p53ki/ki_3

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Applied Sciences

country: United Kingdom

institute: Northumbria University

description: Mouse Model Chesler Cell line p53ki/ki - Group 3

hyb_protocol: Approximately 750ng of each cRNA was hybridised using the standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: processed using beadarray R/Bioconductor package with quantile normalisation

source_name: Derived Cell line

label_protocol: Approximately 200ng of each RNA was amplified and Biotinylated using the Illumina TotalPrep RNA amplification kit (Applied Biosystems, Foster City, CA. USA), with the size distribution of cRNA being assessed using the Agilent Bioanalyser.

extract_protocol: RNA was extracted using the Qiagen AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) according to manufacturer's instructions.Quality control was performed using an Agilent 2100 Bioanalyser.

tag: model

value: MYCN

value: cells


title: pTH10640_ME_8mer_10036

source_name: dmd-4, ME design


title: shoot of wild-type


title: celline_MYCN_GTML_p53ki/ki_2


title: control 2, day 7, repeat 1

value: spleen


title: celline_MYCN_GTML_p53ki/ki_4


title: Atg5 KO, day 7, repeat 1


title: pTH10640_HK_8mer_10052

source_name: dmd-4, HK design

value: HK


title: pTH10638_HK_8mer_10018

source_name: dmd-3, HK design


title: celline_MYCN_GTML_p53ki/ki_1


title: pTH10633_ME_8mer_10779

source_name: R07H5.10, ME design


title: cellline_MYCN_GTML_p53ki/wt_3

description: Mouse Model Chesler Cell line p53ki/wt - Group 3


title: cellline_MYCN_GTML_p53ki/wt_1


title: MYC_mouse_model_6

description: Mouse Model Roussell - Group 3

source_name: Grafted cell population

value: MYC

value: WT


title: pTH10633_HK_8mer_10763

source_name: R07H5.10, HK design


title: pTH10630_ME_8mer_10008

source_name: lsy-27, ME design


title: pTH10630_HK_8mer_10024

source_name: lsy-27, HK design


title: pTH10629_HK_8mer_10023

source_name: ztf-3, HK design


title: pTH10624_ME_8mer_10034

source_name: Y61A9LA.9, ME design


title: pTH10624_HK_8mer_10050

source_name: Y61A9LA.9, HK design


title: MYC_mouse_model_4

description: Mouse Model Roussell - Group 3


title: pTH10629_ME_8mer_10007

source_name: ztf-3, ME design


title: cellline_MYCN_GTML_p53ki/wt_2


title: pTH10623_ME_8mer_10033

source_name: scrt-1, ME design


title: cellline_MYCN_GTML_4

description: Mouse Model Chesler Cell line - Group 3


title: MYC_mouse_model_3

description: Mouse Model Roussell - Group 3


title: cellline_MYCN_GTML_1

description: Mouse Model Chesler Cell line - Group 3


title: pTH10707_ME_8mer_10551

source_name: elt-6, ME design

value: GATA


title: MYC_mouse_model_1

description: Mouse Model Roussell - Group 3

value: mut


title: pTH10623_HK_8mer_10049

source_name: scrt-1, HK design


title: MYC_mouse_model_2

description: Mouse Model Roussell - Group 3


title: cellline_MYCN_GTML_3

description: Mouse Model Chesler Cell line - Group 3


title: MYC_mouse_model_5

description: Mouse Model Roussell - Group 3


title: pTH10042_ME_8mer_8910

source_name: nhr-5, ME design


title: primary_MYCN_GTML_p53ki/ki_5

description: Mouse Model Chesler Primary p53ki/ki - Group 3

source_name: Excised Primary Tumour

value: primary


title: pTH10042_HK_8mer_8926

source_name: nhr-5, HK design


title: pTH10041_ME_8mer_8909

source_name: ztf-29, ME design


title: Mouse Colon RNA diet LL BS1711

city: Palmerston North

first: Wayne

last: Young

address: Tennent Drive

country: New Zealand

institute: AgResearch

description:
LL Colon BS1711
Slide 12 - Array 1

hyb_protocol: The labelled samples and reference RNA were hybridized onto Agilent Technologies 44k whole mouse genome oligonucleotide arrays (G4122F) according to the manufacturer’s instructions (Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008, Agilent Technologies).

scan_protocol: The microarray slides were scanned using a DNA Microarray Scanner G2565CA (Agilent Technologies) according to the manufacturer’s instructions.

data_processing: The data was processed using limma in R 3.0.2.  Raw fluorescence values were loess normalised without background correction. Probes that did not pass automated quality control metrics such as spot uniformity, background uniformity, and spot replicate outliers were excluded from analyses.  Fluorescence values were log2 transformed and expressed as Cy3/Cy5.

label_protocol: The RNA samples were amplified and labeled with cyanine-3 labeled CTP dye using the Agilent Quick-Amp Labeling Kit (5190-0424) as per the manufacturer's instructions (Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008, Agilent Technologies). Reference RNA was  amplified and labeled with cyanine-5 labeled CTP dye using the same kit.

growth_protocol: Pregnant C57 mice were fed a diet sufficent in Selenium and Folate (H), or a diet deficient in selenium and folate (L).  The resulting pups were then fed diets sufficent in Selenium and Folate (H), or deficient in selenium and folate (L)

extract_protocol: Total RNA was extracted colon or liver tissue using AllPrep® DNA/RNA/Protein mini kits (Qiagen, Cat number 80004) following manufacturer instructions.

treatment_protocol: The pups were fed from weaning to 12 weeks of age.  At the end of this period, the mice were euthanised and liver and colon tissue samples were collected.

tag: diet

value: deficient in selenium and folate during weaning and in utero (LL)

value: Colon

source_name: Mouse reference RNA_multi-organ

value: Multi-organ

tag: sample type

value: Mouse reference RNA


title: pTH10041_HK_8mer_8925

source_name: ztf-29, HK design

tag: dbd source organism

value: Caenorhabditis elegans


title: Mouse Colon RNA diet LH BS2271

description:
LH Colon BS2271
Slide 12 - Array 4

value: sufficient in selenium and folate during weaning but deficient in utero (LH)


title: Mouse Colon RNA diet HL BS1011

description:
HL Colon BS1011
Slide 12 - Array 3

value: deficient in selenium and folate during weaning but not in utero (HL)


title: primary_MYCN_GTML_p53ki/ki_3


title: Mouse Colon RNA diet HH BS731

description:
HH Colon BS731
Slide 12 - Array 2

value: sufficient in selenium and folate during weaning and in utero (HH)


title: pTH10040_ME_8mer_8908

source_name: slr-2, ME design

tag: dbd

value: ME


title: Mouse Colon RNA diet LH BS2201

description:
LH Colon BS2201
Slide 11 - Array 3


title: pTH10040_HK_8mer_8924

source_name: slr-2, HK design

tag: platform_id_id design


title: cellline_MYCN_GTML_2

description: Mouse Model Chesler Cell line - Group 3

source_name: Derived Cell line

value: MYCN

value: cells


title: primary_MYCN_GTML_p53ki/ki_4


title: Mouse Colon RNA diet HL BS1151

description:
HL Colon BS1151
Slide 11 - Array 2

tag: strain


title: pTH10038_HK_8mer_10760

source_name: gei-3, HK design

value: HK


title: primary_MYCN_GTML_p53ki/wt_5

description: Mouse Model Chesler Primary p53ki/wt - Group 3


title: Mouse Colon RNA diet LL BS1641

description:
LL Colon BS1641
Slide 10 - Array 3


title: Mouse Colon RNA diet HH BS591

description:
HH Colon BS591
Slide 10 - Array 4


title: Mouse Colon RNA diet HH BS871

description:
HH Colon BS871
Slide 11 - Array 1


title: primary_MYCN_GTML_p53ki/ki_1


title: primary_MYCN_GTML_p53ki/ki_2


title: Mouse Colon RNA diet HL BS1081

description:
HL Colon BS1081
Slide 10 - Array 1


title: pTH10037_HK_8mer_8921

source_name: T22C8.4, HK design


title: primary_MYCN_GTML_p53ki/wt_3


title: Mouse Colon RNA diet HL BS1501

description:
HL Colon BS1501
Slide 9 - Array 4


title: Mouse Colon RNA diet LH BS2621

description:
LH Colon BS2621
Slide 10 - Array 2


title: primary_MYCN_GTML_p53ki/wt_1


title: primary_MYCN_GTML_p53ki/wt_2


title: primary_MYCN_GTML_21

description: Mouse Model Chesler Primary - Group 3


title: pTH10038_ME_8mer_10776

source_name: gei-3, ME design


title: primary_MYCN_GTML_p53ki/wt_4


title: pTH10037_ME_8mer_8905

source_name: T22C8.4, ME design


title: Mouse Colon RNA diet HH BS661

description:
HH Colon BS661
Slide 9 - Array 3


title: pTH10034_HK_8mer_8918

source_name: nhr-66, HK design


title: pTH10031_ME_8mer_8947

source_name: mbr-1, ME design


title: Mouse Colon RNA diet LL BS2061

description:
LL Colon BS2061
Slide 9 - Array 2


title: pTH10031_HK_8mer_8963

source_name: mbr-1, HK design


title: primary_MYCN_GTML_20

description: Mouse Model Chesler Primary - Group 3


title: pTH10030_ME_8mer_8899

source_name: xbp-1, ME design


title: primary_MYCN_GTML_18

description: Mouse Model Chesler Primary - Group 3


title: primary_MYCN_GTML_19

description: Mouse Model Chesler Primary - Group 3


title: pTH10030_HK_8mer_8883

source_name: xbp-1, HK design


title: pTH10034_ME_8mer_8902

source_name: nhr-66, ME design


title: pTH10028_ME_8mer_8897

source_name: nhr-204, ME design


title: primary_MYCN_GTML_17

description: Mouse Model Chesler Primary - Group 3

source_name: Excised Primary Tumour


title: pTH10028_HK_8mer_8881

source_name: nhr-204, HK design


title: Mouse Colon RNA diet LH BS2551

description:
LH Colon BS2551
Slide 8 - Array 4

source_name: Mouse reference RNA_multi-organ


title: primary_MYCN_GTML_16

description: Mouse Model Chesler Primary - Group 3


title: pTH10027_ME_8mer_8896

source_name: M03D4.4, ME design


title: Mouse Colon RNA diet LL BS1781

description:
LL Colon BS1781
Slide 11 - Array 4


title: Mouse Colon RNA diet LH BS2341

description:
LH Colon BS2341
Slide 9 - Array 1


title: primary_MYCN_GTML_14

description: Mouse Model Chesler Primary - Group 3


title: Mouse Colon RNA diet LL BS1571

description:
LL Colon BS1571
Slide 8 - Array 1


title: Mouse Colon RNA diet HH BS521

description:
HH Colon BS521
Slide 8 - Array 2


title: primary_MYCN_GTML_15

description: Mouse Model Chesler Primary - Group 3


title: Mouse Colon RNA diet HH BS801

description:
HH Colon BS801
Slide 7 - Array 1


title: primary_MYCN_GTML_10

description: Mouse Model Chesler Primary - Group 3


title: primary_MYCN_GTML_13

description: Mouse Model Chesler Primary - Group 3


title: primary_MYCN_GTML_12

description: Mouse Model Chesler Primary - Group 3


title: Mouse Colon RNA diet HL BS1221

description:
HL Colon BS1221
Slide 7 - Array 2


title: primary_MYCN_GTML_11

description: Mouse Model Chesler Primary - Group 3


title: pTH10027_HK_8mer_8880

source_name: M03D4.4, HK design


title: Mouse Liver RNA diet HH BS427  rep2

description:
HH Liver BS427
Slide 6 - Array 2

value: Liver


title: pTH10026_HK_8mer_8879

source_name: F55C5.11, HK design


title: Mouse Colon RNA diet HL BS1291

description:
HL Colon BS1291
Slide 8 - Array 3


title: pTH10026_ME_8mer_8895

source_name: F55C5.11, ME design


title: primary_MYCN_GTML_7

description: Mouse Model Chesler Primary - Group 3

value: WT


title: pTH10024_HK_8mer_8877

source_name: F52B5.7, HK design


title: pTH10024_ME_8mer_8893

source_name: F52B5.7, ME design


title: pTH10021_ME_8mer_8890

source_name: daf-19, ME design


title: Mouse Liver RNA diet HL BS1406

description:
HL Liver BS1406
Slide 6 - Array 3


title: primary_MYCN_GTML_8

description: Mouse Model Chesler Primary - Group 3


title: Mouse Liver RNA diet LH BS2177

description:
LH Liver BS2177
Slide 6 - Array 4


title: primary_MYCN_GTML_6

description: Mouse Model Chesler Primary - Group 3


title: Mouse Liver RNA diet LL BS1756

description:
LL Liver BS1756
Slide 5 - Array 4


title: Slide 345466

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios  were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: Streptococcus pneumoniae D39 wild-type in M17 plus 0.5% fucose (FM17)

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences)

growth_protocol: Cells were grown to OD600 of 0.2 in FM17 and GM17

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006; Shafeeq et al., 2011). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

source_name: Streptococcus pneumoniae D39 wild-type in M17 plus 0.5% glucose (GM17)


title: Slide 345463

description: Sample 1


title: Mouse Liver RNA diet LH BS2316

description:
LH Liver BS2316
Slide 5 - Array 3


title: pTH10021_HK_8mer_8874

source_name: daf-19, HK design


title: primary_MYCN_GTML_5

description: Mouse Model Chesler Primary - Group 3


title: primary_MYCN_GTML_4

description: Mouse Model Chesler Primary - Group 3


title: Mouse Liver RNA diet LL BS1827

description:
LL Liver BS1827
Slide 6 - Array 1


title: Mouse Liver RNA diet HL BS1056

description:
HL Liver BS1056
Slide 5 - Array 2


title: pTH10015_HK_8mer_8868

source_name: che-1, HK design


title: pTH10015_ME_8mer_8884

source_name: che-1, ME design


title: pTH10013_ME_8mer_8802

source_name: nhr-168, ME design


title: Slide 344302

description: Sample 3

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown MM17 and GM17 medium, and harvested at OD600 of 0.2.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

value: wild type

tag: growth media


title: Slide 344301

description: Sample 2


title: pTH10013_HK_8mer_8786

source_name: nhr-168, HK design


title: Mouse Liver RNA diet HH BS496

description:
HH Liver BS496
Slide 5 - Array 1

tag: tissue


title: primary_MYCN_GTML_3

description: Mouse Model Chesler Primary - Group 3

source_name: Excised Primary Tumour


title: Slide 344300

description: Sample 1


title: Slide 343745

description: Sample 2

source_name: malR mutant

growth_protocol: Cells were grown in GM17 medium and harvested at OD600 of 0.20.

value: malR mutant

source_name: Wild type

value: Wild type


title: Slide 343744

description: Sample 1


title: Slide 347331

description: Sample 2

source_name: ccpA mutant

growth_protocol: Cells were grown in MM17 medium and harvested at OD600 of 0.20.

value: ccpA mutant

source_name: wild type


title: primary_MYCN_GTML_2

description: Mouse Model Chesler Primary - Group 3

value: primary


title: Slide 347330

description: Sample 1


title: primary_MYCN_GTML_9

description: Mouse Model Chesler Primary - Group 3


title: Mouse Liver RNA diet HL BS13372

description:
HL Liver BS13372
Slide 4 - Array 1

source_name: Mouse reference RNA_multi-organ

value: Multi-organ


title: Mouse Liver RNA diet HH BS707

description:
HH Liver BS707
Slide 4 - Array 4

value: Mouse reference RNA


title: Mouse Liver RNA diet LL BS2037

description:
LL Liver BS2037
Slide 4 - Array 3

value: deficient in selenium and folate during weaning and in utero (LL)


title: primary_MYCN_GTML_1

description: Mouse Model Chesler Primary - Group 3


title: Mouse Liver RNA diet LH BS2106

description:
LH Liver BS2106
Slide 4 - Array 2

value: sufficient in selenium and folate during weaning but deficient in utero (LH)


title: Mouse Liver RNA diet HH BS427 rep1

description:
HH Liver BS427
Slide 3 - Array 3


title: Mouse Liver RNA diet HL BS1126

description:
HL Liver BS1126
Slide 2 - Array 3

value: deficient in selenium and folate during weaning but not in utero (HL)


title: Mouse Liver RNA diet HH BS637

description:
HH Liver BS637
Slide 2 - Array 2

value: sufficient in selenium and folate during weaning and in utero (HH)


title: P493_shControl-3

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

description:
shControl_3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

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

organism: Homo sapiens

source_name: P493 cells

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: P493 cells

tag: treatment

value: pLKO shControl


title: Mouse Liver RNA diet LH BS2386

description:
LH Liver BS2386
Slide 2 - Array 4


title: Mouse Colon RNA diet LH BS2481

description:
LH Colon BS2481
Slide 7 - Array 3

value: Colon


title: P493_shTert-3

description:
shTert_3
replicate 3

value: pLKO shTERT


title: Mouse Liver RNA diet HL BS1197

description:
HL Liver BS1197
Slide 1 - Array 2

value: Liver


title: Mouse Liver RNA diet LH BS2596

description:
LH Liver BS2596
Slide 1 - Array 3


title: P493_shTert-2

description:
shTert_2
replicate 2


title: Mouse Liver RNA diet HL BS1267

description:
HL Liver BS1267
Slide 3 - Array 4


title: Mouse Liver RNA diet LL BS1546

description:
LL Liver BS1546
Slide 3 - Array 2


title: Mouse Liver RNA diet LH BS2527

description:
LH Liver BS2527
Slide 3 - Array 1


title: sample 77

city: Ulm

first: Jochen

last: Greiner

address: Helmholzstrasse 10

department: Internal Medicine III

institute: University Clinic Ulm

description: gene expression profiles from sorted AML patients samples

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: GM-CSF mobilized blood sample

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

growth_protocol: AML patient samples, no previous treatment

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

value: blood

tag: patient id

value: healthy 5

tag: disease status

value: healthy

tag: cd34 status

value: + plus

tag: cd38 status

value: - minus


title: P493_shTert-1

description:
shTert_1
replicate 1


title: P493_shControl-1

description:
shControl_1
replicate 1


title: Mouse Liver RNA diet LL BS1686

description:
LL Liver BS1686
Slide 2 - Array 1


title: P493_shControl-2

description:
shControl_2
replicate 2


title: Mouse Liver RNA diet LL BS1896

description:
LL Liver BS1896
Slide 1 - Array 4


title: sample 76

value: healthy 4


title: Mouse Colon RNA diet LL BS1921

description:
LL Colon BS1921
Slide 7 - Array 4

value: Multi-organ


title: Mouse Liver RNA diet HH BS566

description:
HH Liver BS566
Slide 1 - Array 1

value: Mouse reference RNA


title: sample 71

source_name: primary AML blood sample

value: patient 20

value: AML

tag: npm1 status

value: MUT


title: sample 69

value: patient 19


title: sample 72


title: sample 67

value: patient 18


title: sample 75

value: healthy 3


title: DC TNK2 tumor at T2, biological replicate 3

city: Cambridge

first: Lorena

last: Lerner

state: MA

address: 650 E. Kendall Street

institute: AVEO Oncology

description: Gene expression data from tumor generated by DC mouse model

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed using the affy package from Bioconductor 3.0

source_name: tumor material

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

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit following manufacturer's protocol

value: tumor

tag: dc gene

tag: cachexia status

value: no cachexia


title: sample 74

value: healthy 2


title: DC TNK2 tumor at T2, biological replicate 1


title: DC TNK2 tumor at T2, biological replicate 2


title: sample 66

value: blood


title: DC RSK2 tumor at T1, biological replicate 1


title: DC RSK2 tumor at T2, biological replicate 2


title: DC TNK2 tumor at T1, biological replicate 1


title: sample 64

value: WT


title: sample 70


title: DC RSK2 tumor at T1, biological replicate 2


title: DC RSK2 tumor at T3, biological replicate 1


title: DC RSK2 tumor at T2, biological replicate 1


title: DC TNK2 tumor at T1, biological replicate 2


title: sample 73

value: healthy 1

value: healthy


title: sample 65

value: + plus

value: - minus


title: DC TNK2 tumor at T1, biological replicate 3


title: DC RONd160 tumor at T3, biological replicate 2


title: sample 68


title: DC RSK2 tumor at T2, biological replicate 3


title: sample 63


title: sample 58

value: patient 16


title: DC RONd160 tumor at T1, biological replicate 1


title: sample 62


title: DC RON+MSP tumor at T3, biological replicate 1

value: RON+MSP


title: DC RON+MSP tumor at T3, biological replicate 2


title: DC RONd160 tumor at T1, biological replicate 3


title: sample 59


title: DC RONd160 tumor at T3, biological replicate 1


title: sample 60


title: DC RONd160 tumor at T2, biological replicate 1


title: sample 61


title: DC RONd160 tumor at T1, biological replicate 2


title: sample 56

value: patient 15


title: sample 55

value: AML


title: sample 57


title: DC RON+MSP tumor at T2, biological replicate 2


title: DC RON+MSP tumor at T2, biological replicate 1


title: sample 54


title: DC RON+MSP tumor at T1, biological replicate 2


title: 25R

type: genomic

description: Methylation data from a medulloblastoma tumor sample

hyb_protocol: Illumina

scan_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing:
Beta values were obtained using the R package minfi, performing background correction, normalisation to internal controls, and type I / type II correction using SWAN
The raw signal intensities can be found in the file matrixIntensitiesFinal.csv available on the series record. The Average Beta and Detection P-values are available in the Sample tables and on the series record in the file  matrixProcessed.csv.

label: Cy3 / Cy5

molecule: genomic DNA

source_name: Relapsed medulloblastoma tumor tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Extraction of DNA from fresh frozen tumor samples was performed using a Qiagen AllPrep Kit. Extraction of DNA from FFPE tumour samples was performed using a QIAamp DNA FFPE tissue kit

value: medulloblastoma tumor

tag: gender

value: M

tag: age class at diagnosis (infant < 4 yrs)

value: Non-infant

tag: pathology

value: CLA

tag: subgroup


title: DC PIP5K1B tumor at T3, biological replicate 2

value: tumor


title: sample 50

value: patient 13


title: sample 53

value: patient 14


title: DC RON+MSP tumor at T1, biological replicate 1

value: no cachexia


title: sample 49

value: blood

value: WT


title: DC PIP5K1B tumor at T2, biological replicate 3


title: sample 52


title: DC PIP5K1B tumor at T2, biological replicate 1


title: sample 48


title: DC PIP5K1B tumor at T3, biological replicate 1


title: DC PIP5K1B tumor at T2, biological replicate 2


title: 22R

value: LCA


title: 20D

source_name: Diagnostic medulloblastoma tumor tissue


title: 21D

value: F


title: 20R


title: 21R


title: 22D


title: sample 51

value: + plus


title: 23R


title: 17D


title: sample 47

value: - minus


title: DC PIP5K1B tumor at T1, biological replicate 1


title: 18R


title: DC MAP3K7 tumor at T3, biological replicate 2


title: 19R


title: DC MAP3K7 tumor at T2, biological replicate 2


title: DC MAP3K7 tumor at T2, biological replicate 1


title: MACs_d4_donor 1

city: Frankfurt

first: Fiona

last: O'Rourke

state: Hessen

address: Theodor Stern Kai 7

institute: University Hospital Frankfurt

description: Day4 RNA 23.2.11 EMB-2 21.2.11

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

label_protocol: Samples were labelled, washed and stained using the Labeling and HWS Kit from Affymetrix.

growth_protocol: MACs were isolated from periferal blood on fibronectin coated plates. At d4 after isolation non-adherent cells were removed. Adherent cells were isolated for analysis. OR At d5 after isolation cells were infected with B.h. MOI300 for 24hr. Infected cell were then re-seeded onto Matrigel coated plates, plates were incubated for up to 49days with regular, partial medium changes. HUVECs were seeded onto Matrigel coated plates and incubated for 12hr.

extract_protocol: RNA was amplified using the Ambion WT Expression Kit from Ambion applied for 100ng total RNA

treatment_protocol: d4 cells were dissociated from culture plates with EDTA, long term culture cells were proteolytically dissociated from Matrigel matrix using DISPASE

tag: donor id

value: donor 1

value: Myeloid Angiogenic Cells (MACs)

tag: time point

value: shortly after isolation (d4)


title: DC MAP3K7 tumor at T3, biological replicate 1

tag: strain


title: sample 43

tag: tissue

value: patient 12

value: AML

value: MUT


title: 19D

value: medulloblastoma tumor

value: M

value: Non-infant

value: CLA


title: MACs_d4_donor 3

description: Day4 RNA 2.3.11EMB-2,A28.2.11

value: donor 3

tag: cell type


title: sample 44

value: blood


title: sample 42

value: patient 11


title: sample 46


title: DC MAP3K7 tumor at T1, biological replicate 2

value: tumor

value: no cachexia


title: 15D

value: F

value: LCA


title: DC MAP3K7 tumor at T1, biological replicate 1


title: HUVEC_Matrigel

description: HUVEC Control RNA

value: human umbilical cord vein endothelial cells (HUVECs)


title: sample 40

value: - minus


title: MACs_d4_donor 2

description: Day4 RNA 2.3.11EMB-2,B 28.2.11

value: donor 2

value: Myeloid Angiogenic Cells (MACs)

value: shortly after isolation (d4)


title: sample 45

value: patient 12

value: AML

value: MUT


title: 18D

value: medulloblastoma tumor

value: Non-infant


title: MAC_+B.h._Matrigel_donor 3

description: Matrigel RNA 2.3.11EMB-2,A13.4.11

value: donor 3

tag: infected with

value: Bartonella henselae (B.h.)

value: up to 49 days after infection


title: sample 41

value: blood

tag: patient id

value: patient 11

value: + plus


title: MAC_+B.h._Matrigel_donor 2

description: Matrigel RNA 2.3.11EMB-2,B19.4.11


title: DC MAP3K11 tumor at T3, biological replicate 1

value: tumor

value: cachexia


title: MAC_+B.h._Matrigel_donor 1

description: Matrigel RNA 23.2.11EMB-213.4.11

value: donor 1


title: DC MAP3K11 tumor at T2, biological replicate 1


title: DC MAP3K11 tumor at T3, biological replicate 2


title: sample 37

value: patient 10

tag: disease status

value: - minus

value: WT


title: 17R

value: M

value: LCA


title: sample 39

value: AML

tag: cd34 status

value: MUT


title: sample 36

tag: cd38 status


title: 10D

value: medulloblastoma tumor

value: Non-infant

value: DN

value: SHH


title: DC MAP3K11 tumor at T2, biological replicate 2


title: 24R

value: MBNOS


title: 13R

value: CLA

value: WNT


title: DC MAP3K11 tumor at T1, biological replicate 2

value: tumor


title: 16R


title: sample 35

value: blood

value: + plus

tag: npm1 status


title: 11D

value: F


title: 11R


title: DC MAP3K11 tumor at T1, biological replicate 1

tag: dc gene

value: cachexia


title: sample 38

value: patient 10

value: - minus

value: WT


title: 10R

value: M


title: sample 34

value: patient 9

value: AML


title: Monocyte Ly6Chi from Adult 2 months old Bone Marrow rep1

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

hyb_protocol: Target cRNA was hybridized to the Illumina Mouse WG6 v2 Beadchips.

scan_protocol: Arrays were scanned using BeadArray Scanner 500GX at the Biopolis Shared Facility, A*STAR, Singapore. Images were analyzed using the Illumina GenomeStudio Gene Expression v 1.9.0 software.

data_processing: Microarray data was normalized by quantile normalization using R version 3.1.2 and R package lumi version 2.18.0. Hierarchical clustering of samples was generated using Pearson’s correlation and complete agglomeration method. Differentially expressed genes (DEGs) were selected by using Linear Models for Microarray Data (Limma) and a False Discovery Rate (FDR) cut-off of 0.05.

label_protocol: Fifty ng of total RNA were used to prepare biotinylated cRNA using the TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre).

extract_protocol: Total RNA was extracted using the Life Technologies mirVana™ miRNA Isolation Kit (Ambion Inc, Austin, TX, USA). Agilent Bioanalyzer was used to assess RNA integrity and the RNA Integrity Number (RIN) was calculated. Only samples with a RIN ≥ 7 RNA were processed.

tag: strain background

tag: age

value: Adult 2 months

value: adult bone marrow

value: Monocyte Ly6Chi


title: 12R

value: medulloblastoma tumor

tag: gender

tag: age class at diagnosis (infant < 4 yrs)

value: Non-infant

value: LCA

value: SHH


title: 14R

tag: pathology

tag: subgroup

value: WNT


title: Monocyte Ly6Chi from Adult 2 months old Bone Marrow rep4


title: 9R

value: CLA


title: 9D

value: F

value: DN


title: Monocyte Ly6Chi from Adult 2 months old Bone Marrow rep3


title: 13D


title: Monocyte Ly6Chi from Adult 2 months old Bone Marrow rep2


title: cMoP from Adult 2 months old Bone Marrow rep2

value: Common Monocytes Progenitor (cMoP)


title: sample 33

value: blood

value: - minus


title: DC HER2 tumor at T3, biological replicate 1

value: tumor

tag: cachexia status

value: no cachexia


title: cMoP from Adult 2 months old Bone Marrow rep1


title: sample 30

value: patient 8

value: AML

value: + plus

value: WT


title: DC HER2 tumor at T2, biological replicate 1

tag: strain


title: DC HER2 tumor at T3, biological replicate 2

tag: tissue


title: DC HER2 tumor at T2, biological replicate 2


title: 8D

value: medulloblastoma tumor

value: M


title: MDP from Adult 2 months old Bone Marrow rep4

source_name: MDP from Adult 2 months old Bone Marrow

value: Adult 2 months

value: adult bone marrow

tag: cell type

value: monocyte-dendritic cell progenitors (MDPs)


title: 8R

value: Non-infant

value: CLA

value: SHH


title: DC HER2 tumor at T1, biological replicate 1


title: DC HER2 tumor at T1, biological replicate 2


title: sample 29


title: MDP from Adult 2 months old Bone Marrow rep1


title: Monocyte Ly6Chi from E14.5 Fetal liver rep3

source_name: Monocyte Ly6Chi from E14.5 Fetal liver

value: embryonic day E14.5

value: fetal liver

value: Monocyte Ly6Chi


title: MDP from Adult 2 months old Bone Marrow rep2


title: sample 28

value: blood


title: sample 27

value: - minus


title: sample 26

value: patient 7

value: MUT


title: DC FGFR3 tumor at T2, biological replicate 2

value: tumor

value: no cachexia


title: DC FGFR3 tumor at T3, biological replicate 1


title: DC FGFR3 tumor at T2, biological replicate 1


title: 5R

value: medulloblastoma tumor

value: F

value: Infant


title: sample 32

value: patient 9

value: AML

value: + plus

value: WT


title: DC FGFR3 tumor at T1, biological replicate 3


title: sample 25


title: sample 31


title: 7R

value: Non-infant

value: DN

value: SHH


title: Monocyte Ly6Chi from E14.5 Fetal liver rep2

value: embryonic day E14.5

value: fetal liver

value: Monocyte Ly6Chi


title: Monocyte Ly6Chi from E14.5 Fetal liver rep1


title: sample 24

value: blood

value: patient 7


title: 6D

value: CLA


title: 5D


title: cMoP from E14.5 Fetal liver rep2

source_name: cMoP from E14.5 Fetal liver

value: Common Monocytes Progenitor (cMoP)


title: D14 14T

city: Bergisch Gladbach

first: Jutta

last: Kollet

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyibiotec GmbH

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: co-cultured with EBV-LCL and IL2 in T75 flasks (T)

label_protocol: 100 ng total RNA  was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was isolated using the NucleoSpin® RNA kit (Macherey-Nagel)

treatment_protocol: NK cells were isolated from six individual healthy human donor buffy coats by magnetic separation (CD3 depletion followed by CD56 enrichment). Freshly isolated NK cells served as a control sample (d0). Isolated NK cells were then cultivated for 14 days in TexMACS GMP Medium (Miltenyi, Bergisch Gladbach, germany) supplemented with 5% AB human serum (Lifetechnologies, WI, USA) and 500 U/ml Proleukin S (Novartis, Nürnberg, Germany), either together with 100 Gy irradiated EBV-LCL feeder cells or without feeder cells. Feeder cell free expansion was performed manually in T75 flasks (I), while feeder cell based expansion was done manually in T75 flasks (T) or by the automated cell processing system CliniMACS Prodigy (P). All samples were lysed in RA1 buffer (Machery-Nagel, Düren, Germany) and stored at –20°C until RNA isolation.

tag: donor id

value: Donor 14

tag: donor status

value: healthy

value: blood-derived NK cells

tag: culture condition

value: cultivated with IL2 and EBV-LCL in T flasks


title: sample 23

tag: patient id

tag: disease status

value: AML

tag: cd34 status

value: - minus

value: MUT


title: 4D

value: medulloblastoma tumor

value: M

value: Infant


title: cMoP from E14.5 Fetal liver rep3

value: embryonic day E14.5


title: DC FGFR3 tumor at T1, biological replicate 1

value: tumor

tag: dc gene

value: no cachexia


title: D14 14P

source_name: co-cultured with EBV-LCL and IL2 in the CliniMACS Prodigy system (P)

value: cultivated with IL2 and EBV-LCL in CliniMACS Prodigy


title: cMoP from E14.5 Fetal liver rep1

tag: strain background

value: fetal liver


title: D14 14I

source_name: cultured with IL2 without feeder cells (I)

value: cultivated with IL2 in T flasks


title: DC FGFR2aIIIc tumor at T3, biological replicate 1


title: MP from E14.5 Fetal liver rep3

source_name: MP from E14.5 Fetal liver

tag: age

value: myeloid progenitors (MP)


title: sample 22

value: blood

value: patient 6

tag: cd38 status

tag: npm1 status

value: WT


title: DC FGFR2aIIIc tumor at T2, biological replicate 3


title: 7D

tag: gender

value: F

tag: age class at diagnosis (infant < 4 yrs)

value: Non-infant

tag: pathology

value: CLA

value: SHH


title: 3R

value: medulloblastoma tumor

value: DN

tag: subgroup


title: D14 d0

source_name: freshly isolated NK cells (d0)

value: Donor 14

value: healthy

value: blood-derived NK cells

value: freshly isolated


title: MP from E14.5 Fetal liver rep1

value: embryonic day E14.5

tag: tissue


title: sample 19

value: AML

value: + plus

value: - minus


title: sample 20

value: blood


title: 2R

value: M

value: Infant


title: DC FGFR2aIIIc tumor at T2, biological replicate 2

value: tumor

tag: strain

tag: cachexia status

value: no cachexia


title: sample 21

value: patient 6

value: WT


title: D13 14P

tag: donor id

value: Donor 13

tag: donor status

tag: cell type

value: cultivated with IL2 and EBV-LCL in CliniMACS Prodigy


title: D13 14T

tag: culture condition

value: cultivated with IL2 and EBV-LCL in T flasks


title: MP from E14.5 Fetal liver rep2

value: fetal liver

value: myeloid progenitors (MP)


title: DC FGFR2aIIIc tumor at T2, biological replicate 1


title: MDP from Adult 2 months old Bone Marrow rep3

value: Adult 2 months

value: adult bone marrow

value: monocyte-dendritic cell progenitors (MDPs)


title: 2D

value: medulloblastoma tumor

value: DN

value: SHH


title: 1R

value: M

value: CLA


title: DC FGFR3 tumor at T1, biological replicate 2

value: tumor


title: 1D

value: Infant


title: D13 14I

value: healthy

value: blood-derived NK cells

value: cultivated with IL2 in T flasks


title: MDP from E14.5 Fetal liver rep3

source_name: MDP from E14.5 Fetal liver

value: embryonic day E14.5


title: D13 d0

value: Donor 13

value: freshly isolated


title: sample 16

value: blood

tag: patient id

value: patient 5

tag: disease status

value: AML

tag: cd34 status

value: + plus

value: MUT


title: DC FGFR2aIIIc tumor at T1, biological replicate 1

tag: dc gene

value: no cachexia


title: D10 14T_2

value: Donor 10

value: cultivated with IL2 and EBV-LCL in T flasks


title: sample 17

value: - minus

tag: cd38 status


title: sample 18

tag: npm1 status


title: Monocyte Ly6Chi from E17.5 Dermis rep5

description: E17.5 SK Der_Mono_Ly6CHi_5

source_name: Monocyte Ly6Chi from E17.5 Dermis

tag: strain background

tag: age

value: embryonic day E17.5

value: fetal Dermis

value: Monocyte Ly6Chi


title: DC FGFR2aIIIb tumor at T3, biological replicate 2

value: tumor


title: sample 15


title: MDP from E14.5 Fetal liver rep2

value: fetal liver

value: monocyte-dendritic cell progenitors (MDPs)


title: D10 14I_2

value: healthy

value: blood-derived NK cells

value: cultivated with IL2 in T flasks


title: MDP from E14.5 Fetal liver rep1

value: embryonic day E14.5


title: sample 14

value: blood

value: patient 4

value: AML

value: WT


title: DC FGFR2aIIIb tumor at T2, biological replicate 2

value: no cachexia


title: D10 d0

value: Donor 10

value: freshly isolated


title: DC FGFR2aIIIb tumor at T3, biological replicate 1


title: Monocyte Ly6Chi from E16.5 total skin rep3

description: E16.5 SK_Mono_Ly6CHi_3

source_name: Monocyte Ly6Chi from E16.5 total skin

value: embryonic day E16.5

value: fetal skin


title: D10 14P_2

value: cultivated with IL2 and EBV-LCL in CliniMACS Prodigy


title: DC FGFR2aIIIb tumor at T1, biological replicate 2

value: tumor


title: sample 11

value: patient 3

value: - minus

value: + plus

value: MUT


title: Monocyte Ly6Chi from E17.5 Dermis rep1

description: E17.5 SK Der_Mono_Ly6CHi_1

value: embryonic day E17.5

value: fetal Dermis

value: Monocyte Ly6Chi


title: DC FGFR2aIIIb tumor at T2, biological replicate 1


title: sample 12

value: blood

value: patient 4


title: sample 13

value: AML

value: WT


title: D5 14T

value: Donor 5

value: healthy

value: blood-derived NK cells

value: cultivated with IL2 and EBV-LCL in T flasks


title: D5 14P

value: cultivated with IL2 and EBV-LCL in CliniMACS Prodigy


title: Monocyte Ly6Chi from E17.5 Dermis rep4

description: E17.5 SK Der_Mono_Ly6CHi_4


title: Monocyte Ly6Chi from E16.5 total skin rep2

description: E16.5 SK_Mono_Ly6CHi_2

value: embryonic day E16.5

value: fetal skin


title: DC FGFR2aIIIb tumor at T1, biological replicate 1

value: tumor

value: no cachexia


title: sample 10

value: patient 3

value: + plus

value: MUT


title: D5 d0

value: freshly isolated


title: sample 9

value: blood

value: - minus


title: Monocyte Ly6Chi from E16.5 total skin rep1

description: E16.5 SK_Mono_Ly6CHi_1

value: Monocyte Ly6Chi


title: DC FAK1 tumor at T1, biological replicate 1


title: DC FAK1 tumor at T2, biological replicate 1


title: sample 8

value: patient 2

value: AML


title: D2 d0

value: Donor 2

value: healthy


title: DC FAK1 tumor at T3, biological replicate 1


title: Macrophage from E17.5 Epidermis rep2

description: E17.5 Epi_Mac_2

source_name: Macrophage from E17.5 Epidermis

value: embryonic day E17.5

value: fetal Epidermis

value: Macrophage


title: Macrophage from E17.5 Dermis rep7

description: E17.5 Der_Mac_7

source_name: Macrophage from E17.5 Dermis

value: fetal Dermis


title: sample 6

source_name: primary AML blood sample


title: D2 14I

value: blood-derived NK cells

value: cultivated with IL2 in T flasks


title: D5 14I

value: Donor 5


title: Macrophage from E17.5 Dermis rep3

description: E17.5 Der_Mac_3


title: D2 14T

value: cultivated with IL2 and EBV-LCL in T flasks


title: Macrophage from E17.5 Epidermis rep1

description: E17.5 Epi_Mac_1


title: sample 5

value: + plus

value: MUT


title: Macrophage from E16.5 total skin rep8

description: E16.5 SK_Mac_8

source_name: Macrophage from E16.5 total skin

value: embryonic day E16.5

value: fetal skin


title: DC ErbB3 tumor at T3, biological replicate 1

source_name: tumor material

value: tumor

value: no cachexia


title: DC ErbB3 tumor at T3, biological replicate 3


title: DC FAK1 tumor at T1, biological replicate 2


title: sample 4

value: blood

value: patient 1

value: AML

value: - minus

value: WT


title: sample 7

value: patient 2


title: D2 14P

value: Donor 2

value: healthy

value: cultivated with IL2 and EBV-LCL in CliniMACS Prodigy


title: DC FGFR2aIIIc tumor at T1, biological replicate 2


title: Macrophage from E17.5 Dermis rep1

description: E17.5 Der_Mac_1

value: embryonic day E17.5

value: fetal Dermis

value: Macrophage


title: Macrophage from E17.5 Epidermis rep3

description: E17.5 Epi_Mac_3

value: fetal Epidermis


title: DC ErbB3 tumor at T3, biological replicate 2


title: D1 14T

value: Donor 1

value: blood-derived NK cells

value: cultivated with IL2 and EBV-LCL in T flasks


title: sample 3

value: + plus


title: DC ErbB3 tumor at T2, biological replicate 1

value: tumor

value: no cachexia


title: sample 2

value: blood

value: patient 1

value: AML


title: Macrophage from E16.5 total skin rep5

description: E16.5 SK_Mac_5

value: embryonic day E16.5

value: fetal skin


title: DC ErbB3 tumor at T1, biological replicate 2


title: D1 14P

value: healthy


title: D1 d0

value: freshly isolated


title: sample 1

value: - minus

value: WT


title: Macrophage from E16.5 total skin rep1

description: E16.5 SK_Mac_1

value: Macrophage


title: PBCS-4419

status: Public on Apr 22 2015

city: Tempe

first: Jie

last: Wang

state: Arizona

address: 1001 S. McAllister Ave.

department: Center for Personalized Diagnostics

institute: Arizona State University

description: The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.

hyb_protocol: Plasma hybridization was performed on TECAN HS 4800 Pro. 1. Protein Arrays were blocked with 5% milk PBST (0.2% Tween) for 1 hour at RT; 2. 150uL 1:50 diluted serum was applied to each slide with medium agitation 16 hrs at 4oC; 3. Slides were incubated with 150uL 1:500 dilution of Dylight649-linked anti-human secondary antibodies (Jackson Immunoresearch) in Milk PBST.

scan_protocol: Slides were scanned by TECAN PowerScanner at 50% gain, 50% laser and 10 μm resolution.

data_processing: 1. The background signal estimated by the 25th percentile of the negative control; 2. Normaliza the array data by median.

label: Serum sample are not labeled

source_name: Peripheral blood

label_protocol: No label was performed on the serum sample.

extract_protocol: Peripheral blood samples were drawn from the antecubital vein and serum was prepared according to a standardized protocol before freezing serum aliquots at -80oC

value: Plasma

tag: type

value: control

tag: array batch

tag: gender

value: Female


title: DC ErbB3 tumor at T1, biological replicate 1

tag: tissue

tag: strain


title: Macrophage from E16.5 total skin rep2

description: E16.5 SK_Mac_2


title: PBCS-4544


title: PBCS-3452


title: PBCS-2247


title: PBCS-1529


title: PBCS-1002


title: PBCS-1807


title: PBCS-1325


title: PBCS-2930


title: PBCS-1161


title: PBCS-4082


title: PBCS-640


title: PBCS-4032


title: PBCS-3771


title: PBCS-4512


title: PBCS-2858


title: PBCS-4128


title: PBCS-3234


title: PBCS-2991


title: N. fischeri in asphaltenes

city: Ensenada

first: RAFAEL

last: VAZQUEZ DUHALT

state: Baja California

address: Km 107 Carretera Tijuana-Ensenada

department: Bionanotechnology

country: Mexico

institute: Nanoscience and Nanotechnology Center-UNAM

description: Comparative transcriptome  of the genes expressed when the fungus grows in two different carbon sources

hyb_protocol: Labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC), to the arrays for 14 h at 42°C.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using optimal laser power and 5µm resolution. For each spot the Cy3 and Cy5 density mean value and the Cy3 and Cy5 background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing: Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean.  zi = (Ri – mean(R)) / sd(R)  Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.

organism: Aspergillus fischeri

source_name: mycelium grown in asphaltene

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Neosartorya fischerii was grown in flask (125 mL) with 50 mL of media with  agitation speed constant at 110 rpm and the temperature maintained at 37 °C.

extract_protocol: The micelium was frozen and broken with liquid nitrogen. The RNA extraction was performed using TRI reagent kit.  RNA quality was tested on an agarose gel.

treatment_protocol: The cultures were maintained by stirring at 110 rpm and the temperature manteined at 37°C. The cultures growth in glucose-peptone  were manteined by 24 hours, and the cultures growth in asphaltenes were manteined by 17 days.

value: Mycelium

source_name: mycelium grown in glucose-peptone


title: PBCS-3254


title: PBCS-2970


title: PBCS-2988


title: PBCS-3392


title: PBCS-3253


title: PBCS-3492


title: PBCS-3098


title: PBCS-106


title: PBCS-648


title: PBCS-2415


title: PBCS-923


title: PBCS-4356

value: BLBC


title: PBCS-863


title: PBCS-67


title: PBCS-250


title: PBCS-568


title: PBCS-189


title: PBCS-658


title: PBCS-654


title: PBCS-3890


title: PBCS-559


title: PBCS-1414


title: PBCS-994


title: PBCS-924


title: PBCS-1910


title: PBCS-647


title: PBCS-1247


title: PBCS-914


title: PBCS-3961


title: PBCS-4457


title: PBCS-4464


title: PBCS-3754


title: PBCS-4454


title: PBCS-1243


title: PBCS-2213


title: PBCS-2197


title: PBCS-2020


title: PBCS-1573


title: PBCS-1572


title: PBCS-886


title: PBCS-4067


title: PBCS-1498


title: PBCS-4102


title: PBCS-4492


title: PBCS-1860


title: PBCS-1233


title: PBCS-1211


title: PBCS-2006


title: PBCS-2192


title: PBCS-1864


title: PBCS-1293


title: PBCS-3226


title: PBCS-1736


title: PBCS-3191


title: PBCS-3560


title: PBCS-3486


title: PBCS-1074


title: PBCS-1754


title: PBCS-4470


title: PBCS-3425


title: PBCS-1023


title: PBCS-3227


title: PBCS-906


title: PBCS-603


title: PBCS-684


title: PBCS-506


title: PBCS-447


title: PBCS-1089


title: PBCS-178


title: PBCS-231


title: PBCS-110


title: PBCS-4544


title: PBCS-4082


title: PBCS-4128


title: PBCS-1529


title: PBCS-1161


title: PBCS-2858


title: PBCS-640


title: PBCS-4512


title: PBCS-2247


title: PBCS-3771


title: PBCS-4032


title: PBCS-1325


title: PBCS-1002


title: PBCS-2930


title: PBCS-4419


title: PBCS-1807


title: PBCS-2988


title: PBCS-3254


title: PBCS-3452


title: PBCS-2991


title: PBCS-3234


title: PBCS-2970


title: PBCS-3492


title: PBCS-3392


title: PBCS-3253


title: D1 14I

tag: donor id

value: Donor 1

value: blood-derived NK cells

value: cultivated with IL2 in T flasks


title: PBCS-3098


title: PBCS-647


title: PBCS-924


title: PBCS-106


title: PBCS-994


title: PBCS-559


title: PBCS-1910


title: PBCS-1247


title: PBCS-568


title: PBCS-648


title: PBCS-923


title: PBCS-658


title: PBCS-67


title: PBCS-654


title: PBCS-914


title: PBCS-250


title: PBCS-4464


title: PBCS-3890


title: PBCS-4356


title: PBCS-4454


title: PBCS-3961


title: PBCS-189


title: PBCS-4457


title: PBCS-1414


title: PBCS-863


title: PBCS-2415


title: PBCS-2213


title: PBCS-1572


title: PBCS-3754


title: PBCS-2197


title: PBCS-1573


title: PBCS-1498


title: PBCS-4492


title: PBCS-2020


title: PBCS-4102


title: PBCS-4470


title: PBCS-3560


title: PBCS-3425


title: PBCS-3486


title: PBCS-4067


title: PBCS-1754


title: PBCS-3227


title: PBCS-3226


title: PBCS-1293


title: PBCS-1864


title: PBCS-1860


title: PBCS-2006


title: PBCS-3191


title: PBCS-2192


title: PBCS-1074


title: PBCS-1089


title: PBCS-1233


title: PBCS-684


title: PBCS-906


title: PBCS-886


title: PBCS-506


title: PBCS-1736


title: LnCaP nicotine-treated replicate #3

city: bethesda

first: Stefan

last: Ambs

state: md

address: 37 convent cir

institute: NIH

description: Gene expression data from LnCaP treated with nicotine

hyb_protocol: the cRNA was fragmented and hybridized overngiht to Affymetrix GeneCip HG-U133 A2.0 arrays

scan_protocol: Hybridization signals were visualized using phycoerythrin-conjugated streptavidin and scanned using a GeneChip scanner 3000 7G

data_processing: R/bioconductor

source_name: LnCaP nicotine-treated replicate #3

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

growth_protocol: cells were cultured according to ATCCC instruction

extract_protocol: total RNA from tissues and cultured cells was isolated by TRIzol(Invitrogen) according to the manufacturer instructions

treatment_protocol: Nicotine tartrate obtained from Sigma and treated cells in 100uM for 24hours

tag: cell line

value: LnCaP

tag: smoking

value: nicotine-treated


title: PBCS-1023


title: PBCS-603


title: PBCS-4419


title: PBCS-4082


title: PBCS-4128


title: PBCS-4544


title: PBCS-4032


title: PBCS-4512


title: PBCS-3771


title: PBCS-640


title: PBCS-110


title: PBCS-178


title: PBCS-1161


title: PBCS-447


title: PBCS-231


title: 22RV1 untreated replicate #1

description: Gene expression data from 22RV1 untreated

source_name: 22RV1 untreated replicate #1

value: untreated


title: LnCaP nicotine-treated replicate #2

source_name: LnCaP nicotine-treated replicate #2


title: LnCaP untreated replicate #1

description: Gene expression data from LnCaP untreated

source_name: LnCaP untreated replicate #1


title: LnCaP untreated replicate #3

source_name: LnCaP untreated replicate #3


title: 22RV1 nicotine-treated replicate #2

description: Gene expression data from 22RV1 treated with nicotine

source_name: 22RV1 nicotine-treated replicate #2


title: PBCS-2930


title: 22RV1 nicotine-treated replicate #1

source_name: 22RV1 nicotine-treated replicate #1


title: LnCaP nicotine-treated replicate #1

source_name: LnCaP nicotine-treated replicate #1


title: 22RV1 untreated replicate #3

source_name: 22RV1 untreated replicate #3


title: PBCS-2858


title: LnCaP untreated replicate #2

source_name: LnCaP untreated replicate #2


title: Smoking-23

description: Gene expression data from never smoker of prostate cancer

data_processing: R/bioconductor and Partek

source_name: never smoking

value: prostate

value: never smoking


title: Smoking-24


title: PBCS-1529


title: 22RV1 nicotine-treated replicate #3

source_name: 22RV1 nicotine-treated replicate #3


title: 22RV1 untreated replicate #2

source_name: 22RV1 untreated replicate #2


title: PBCS-1325


title: PBCS-2247


title: Smoking-21


title: Smoking-22


title: Smoking-20


title: PBCS-1002


title: Smoking-18


title: PBCS-1807


title: Smoking-17

description: Gene expression data from past smoker of prostate cancer

source_name: past smoking

value: past smoking


title: PBCS-3234

source_name: Peripheral blood


title: PBCS-3452


title: PBCS-2991


title: PBCS-2970


title: PBCS-3392


title: PBCS-3254


title: PBCS-2988


title: Smoking-14


title: PBCS-3253


title: Smoking-16


title: Smoking-15


title: Smoking-8

description: Gene expression data from current smoker of prostate cancer

source_name: current smoking

value: current smoking


title: PBCS-3098


title: Smoking-11


title: PBCS-1243


title: PBCS-3492


title: PBCS-647


title: Smoking-9


title: PBCS-924


title: PBCS-559


title: PBCS-994


title: Smoking-4


title: PBCS-914


title: Smoking-5


title: LCM never smoker #5


title: Smoking-12


title: LCM never smoker #4


title: Smoking-6


title: Smoking-13


title: PBCS-1910


title: Smoking-7


title: PBCS-1414


title: Smoking-10


title: LCM never smoker #3


title: LCM never smoker #2


title: PBCS-1247


title: PBCS-923


title: LCM never smoker #1


title: LCM current smoker #4


title: PBCS-1211


title: PBCS-2415


title: PBCS-568


title: PBCS-189


title: PBCS-863


title: PBCS-658


title: PBCS-648


title: LCM current smoker #2


title: PBCS-250


title: PBCS-654


title: LCM current smoker #3


title: PBCS-3890


title: TRAMP mouse 250 microgram nicotine-treated #5

description: Gene expression data from mouse treated with 250 microgram nicotine

hyb_protocol: hybridized for 17 hr at 45C on Affymetrix GeneChip mouse gene 1.0 st array

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

label_protocol: Amplify 250 ng of RNA using the Ambion WT Expression Kit (per directions) Fragment and label 5.5 ug of ssDNA using Affymetrix GeneChip WT Terminal Labeling and controls kit

growth_protocol: Male TRAMP mice were bred at the Assisted Reproduction Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.

extract_protocol: Trizol extraction as per manufacturer instructions. Check quality with Agilent Bioanalyzer

treatment_protocol: Beginning at 8 to 9 weeks of age, TRAMP mice received either tap water or a solution of 250 µg/ml of nicotine [nicotine tartrate salt (Sigma-Aldrich, St. Louis, MO)] in tap water

value: 250 microgram nicotine-treated


title: TRAMP mouse 250 microgram nicotine-treated #3


title: LCM current smoker #1


title: 4T1 Cl1_03022013

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

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

source_name: 4T1 MMP3-low

label_protocol: Standard Illumina label protocol

growth_protocol: All cells were grown in RPMI containing 10% FBS in 5% CO2 incubator

extract_protocol: RNA was harvested using Qiagen RNA extraction kit

treatment_protocol: Cells were transfected with mouse shRNA for MMP3 and corresponding scrambled control vector


title: TRAMP mouse 250 microgram nicotine-treated #4


title: 4T1 Cl1_03192013


title: 4T1 NC_03192013

source_name: 4T1 scrambled control


title: 4T1 NC_02272013


title: PBCS-4457


title: 4T1 NC_03022013


title: TRAMP mouse 250 microgram nicotine-treated #1


title: 4T1 Cl1_02272013


title: TRAMP mouse untreated #5

description: Gene expression data from mouse treated with water

source_name: TRAMP mouse untreated #5


title: TRAMP mouse untreated #4

source_name: TRAMP mouse untreated #4


title: PBCS-4356


title: PBCS-3754


title: PBCS-3961


title: PBCS-2213


title: PBCS-2197


title: PBCS-4464


title: TRAMP mouse untreated #3

source_name: TRAMP mouse untreated #3


title: PBCS-4454


title: TRAMP mouse untreated #2

source_name: TRAMP mouse untreated #2


title: PBCS-2020


title: TRAMP mouse untreated #1

source_name: TRAMP mouse untreated #1


title: Trem2-Cu12

city: Saint Louis

first: Marco

last: Colonna

state: MO

address: 660 S Euclid Ave.

department: Pathology and Immunology

institute: Washinton University School of Medicine

description:
Sample name: 23826
TREM2 4 week cuprizone
gene expression from purifed microglia

hyb_protocol: Samples are prepared using a Nugen Ovation Pico SL kit.

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

data_processing: Data were analyzed using GenePattern (Broad Institute)

label: Biotin

source_name: microglia

label_protocol: Biotinylated cRNA were prepared using a Nugen Encore Biotin kit from 2 ng total RNA.

growth_protocol: 8-12 weeks C57BL/6  or TREM2-/- male mice

extract_protocol: Microglia were FACS sorted directly into RLT buffer (Qiagen). A Rneasy micro kit (Qiagen) was used for subsquent RNA extraction.

treatment_protocol: C57BL/6 or TREM2-/- mice were fed on a 0.2% curpizone diet for 4 or 12 weeks to induce demyelination. Separate groups of mice were fed with a normal diet after cuprizone feeding for 2 weeks to allow recovery.

value: male

value: 8-12 weeks

tag: genotype/variation

tag: agent

value: cuprizone

tag: time

value: 4 weeks

tag: cell type

value: microglia


title: PBCS-1243

value: Plasma

value: BLBC

value: Female


title: PBCS-1573


title: WT-Cu12+2

description:
Sample name: 23827
WT 12 week cuprizone followed with 2 weeks recovery
gene expression from purifed microglia

value: WT

value: 12 weeks followed with 2 weeks recovery


title: PBCS-1498


title: PBCS-1572


title: PBCS-1754


title: PBCS-4470


title: PBCS-4492


title: PBCS-4067


title: PBCS-3560


title: Trem2-Cu12+2

description:
Sample name: 23829
TREM2 12 week cuprizone followed with 2 weeks recovery
gene expression from purifed microglia


title: WT-Cu12

description:
Sample name: 23824
WT 12 week cuprizone
gene expression from purifed microglia

value: 12 weeks


title: PBCS-3425


title: PBCS-3227


title: PBCS-3226


title: WT-Cu4

description:
Sample name: 23165
WT 4 week cuprizone
gene expression from purifed microglia


title: Trem2-Cu4+2

description:
Sample name: 23169
TREM2 4 week cuprizone followed with 2 weeks recovery
gene expression from purifed microglia

value: 4 weeks followed with 2 weeks recovery


title: PBCS-3191

description: The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.


title: PBCS-886


title: PBCS-2192


title: PBCS-3486


title: PBCS-1864


title: PBCS-2006


title: PBCS-4102


title: PBCS-1736


title: PBCS-1860


title: PBCS-1293


title: WT-Cu4+2

description:
Sample name: 23166
WT 4 week cuprizone followed with 2 weeks recovery
gene expression from purifed microglia


title: PBCS-1233


title: Trem2-Cu4

description:
Sample name: 23168
TREM2 4 week cuprizone
gene expression from purifed microglia


title: PBCS-1211


title: PBCS-1089


title: PBCS-106

value: control


title: WT-Ctl

description:
Sample name: 23164
WT control
gene expression from purifed microglia


title: PBCS-1074