title: 14227193 - 8P-2 vs 8C-2

description: effect of phenanthrene and sucrose

hyb_protocol: 8C-2 Cy5 / 8P-2 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: 14248932 - 2P-1 vs 2S-1

status: Public on Jun 28 2013

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: effect of phenanthrene and sucrose

hyb_protocol: 2S-1 Cy5 / 2P-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

molecule: total RNA

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: whole plant - Media   MS/2  hygrometry   60%  Temperature   22°C  Light   16h

extract_protocol: 2S-1:12.8ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:sucrose+phenanthrene-2h; compound based treatment (compound addition); sucrose+phenanthrene: quantity 3%, time 2hr. 3% sucrose+0.2mM phenanthrene

tag: ecotype

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

extract_protocol: 2P-1:20.3ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:phenanthrene-2h; compound based treatment (compound addition); phenanthrene: quantity 0.2mM time 2hr. solvent=DMSO


title: 14227199 - 24P-2 vs 24C-2

description: effect of phenanthrene and sucrose

hyb_protocol: 24C-2 Cy5 / 24P-2 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: 24C-2:4.8ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: harvest date

extract_protocol: 24P-2:3.6ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:phenanthrene-24h; compound based treatment (compound addition); phenanthrene: quantity 0.2mM time 24hr. solvent=DMSO


title: 14227194 - 8P-1 vs 8S-1

description: effect of phenanthrene and sucrose

hyb_protocol: 8S-1 Cy5 / 8P-1 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: 8S-1:10.5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:sucrose+phenanthrene-8h; compound based treatment (compound addition); sucrose+phenanthrene: quantity 3% time 8hour. 3% sucrose+0.2mM phenanthrene

extract_protocol: 8P-1:34.3ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:phenanthrene-8h; compound based treatment (compound addition); phenanthrene: quantity 0.2mM time 8hr. solvent=DMSO


title: 14248939 - 2S-2 vs 30S-2

description: effect of phenanthrene and sucrose

hyb_protocol: 30S-2 Cy5 / 2S-2 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: 30S-2:4.7ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:sucrose+phenanthrene-30min; compound based treatment (compound addition); sucrose+phenanthrene: quantity 3%, time 30min. 3% sucrose+0.2mM phenanthrene

extract_protocol: 2S-2:10.5ug. (Qiagen_RNeasy.pdf)


title: 14227192 - 8C-1 vs 8P-1

description: effect of phenanthrene and sucrose

hyb_protocol: 8P-1 Cy5 / 8C-1 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: 8C-1:14.3ug. (Qiagen_RNeasy.pdf)


title: Case 372C

type: genomic

city: Madrid

first: Francesco

last: Acquadro

state: Madrid

address: calle de Melchor Fernandez Almagro 3

department: Molecular Cytogenetics

country: Spain

institute: Centro Nacional de Investigaciones Oncologicas CNIO

hyb_protocol: The Hybridization process was performed according to the manufacturer's protocol (Agilent Inc. , Palo Alto, Ca)

scan_protocol: Image scanning was performed using an Agilent Scanner (Agilent G2565AA) and microarray data were extracted using Agilent Feature Extraction v10.1 software.

data_processing: Data analysis and visualization were performed using Agilent DNA Analytics v4.0.76 Software. Copy number altered regions were detected using the Z-score (set as 4) and ADM-2 (set as 6) statistics provided by DNA Analytics.

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary Bladder Cancer Sample

label_protocol: 500ug of DNA extracted from the cell lines was labeled using the Enzymatic labeling protocol from Agilent, while in the case of primary tumors we use the non enzymatic Protocol for DNA extracted from Paraffin Embedded samples ULS Labeling Protocol (Agilent Inc., Palo Alto, CA)

extract_protocol: DNA was isolated using a commercial kit, as described (DNeasy Blood & Tissue Kit; Qiagen, Hilden, Germany).

tag: gender

value: Female

tag: cell line

value: Primary Bladder Tumor Sample

tag: tumor stage

value: T3 tumor stage

tag: tumor grade

value: grade 3

source_name: Female DNA Pool

value: female

tag: sample type

value: pooled control (reference) DNA

tag: sample source

value: 20 healty donors


title: JON

source_name: JON Human Bladder Cancer Cell Line

value: Male

value: Bladder Cancer Cell Line


title: RT-4

source_name: RT-4 Human Bladder Cancer Cell Line


title: 15731_blood

city: Tartu

first: Tonu

last: Esko

address: Riia 23b

country: Estonia

institute: Estonian Genome Center, University of Tartu

hyb_protocol: Standard Illumina hybridization protocol

data_processing: MixUpMapper

label: biotin

source_name: whole-blood

extract_protocol: Whole peripheral blood RNA samples were collected using Tempus Blood RNA Tubes (Life Technologies,  NY, USA), and RNA was extracted using Tempus Spin RNA Isolation Kit (Life Technologies, NY, USA).  Quality was measured by NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, DE, USA) and  Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).

tag: tissue

value: blood


title: 83097_blood

scan_protocol: Standard Illumina hybridization protocol


title: 79204_blood

label_protocol: Standard Illumina hybridization protocol


title: 40528_blood


title: 81276_blood


title: 88573_blood


title: 95187_blood


title: 49272_blood


title: 28793_blood


title: SW1710

source_name: SW1710 Human Bladder Cancer Cell Line


title: 70957_blood


title: 19682_blood


title: 87374_blood


title: 43377_blood


title: 41165_blood


title: 13628_blood


title: 91291_blood


title: DNA from breast tumor of patient 146

status: Public on Jun 29 2013

city: Bar Harbor

first: Edison

last: Liu

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

description: Hybridized to SNP 6.0

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

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

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software. Signal intensitites for individual SNPs were extracted and converted from CHP and CEL files using the Copy Number pipeline implemented into Partek software version 6.5

label: Biotin

source_name: DNA from breast tumor of patient 146

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood cells using the Qiagen DNA Blood Mini Kit. Genomic DNA from the tumors was extracted using the DNA/RNA AllPrep mini kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: Primary breast tumor

tag: patient


title: 81634_blood


title: DNA from Peripheral blood cells of patient 55

description: Hybridized to SNP 6.0

value: Peripheral blood cells


title: 70637_blood


title: DNA from Peripheral blood cells of patient 73

description: Hybridized to SNP 6.0


title: DNA from breast tumor of patient 73

description: Hybridized to SNP 6.0

source_name: DNA from breast tumor of patient 73


title: 45509_blood


title: 83327_blood


title: 22824_blood


title: 41984_blood


title: DNA from Peripheral blood cells of patient 122

description: Hybridized to SNP 6.0


title: DNA from Peripheral blood cells of patient 146

description: Hybridized to SNP 6.0


title: DNA from breast tumor of patient 55

description: Hybridized to SNP 6.0

source_name: DNA from breast tumor of patient 55


title: 80776_blood


title: 61531_blood


title: 38909_blood


title: 11843_blood


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title: 87878_blood


title: 9108_blood


title: 98099_blood


title: 52548_blood


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title: DNA from breast tumor of patient 122

description: Hybridized to SNP 6.0

source_name: DNA from breast tumor of patient 122


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title: 31885_blood


title: 15837_blood


title: 74582_blood


title: 5451_blood


title: 65062_blood


title: 67429_blood


title: 16320_blood


title: 25687_blood


title: 87696_blood


title: 5088_blood


title: 22283_blood


title: 39256_blood


title: 57223_blood


title: 55329_blood


title: 2314_blood


title: 9896_blood


title: 3196_blood


title: Spat_uninfected natural sanctuary site animal_Rep4

city: CAEN

first: christophe

last: lelong

address: Esplanade de la Paix

institute: UNICAEN

hyb_protocol: Hybridization was performed using the Agilent’s Gene expression hybridization kit as described by the purchaser with 1.65μg of aRNA samples labeled with Cy3. Subsequently, slides were washed with Gene expression wash buffer kit (Agilent Technologies), dried and stablilized in Stabilization and Drying solution (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 6.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. A matrix of gene expression levels was generated, where each row corresponds to a different gene and each column to one sample. The expression level of each gene was then logarithmically transformed, centered, and reduced, so that relative variations rather than absolute values were used for interpretation.

organism: Magallana gigas

source_name: Spat 2N Hatchery, sanctuary site uninfected

label_protocol: 200 ng of total RNA was indirectly labeled with Cy3 using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. Qiagen's RNeasy mini spin columns were used for purifying amplified RNA (aRNA) samples. After purification, aRNA amplification and dye incorporation rates were controlled using a ND-1000 spectrophotometer (Nanodrop Technologies) and were comprised respectively between 200 and 500 ng/μL (concentration) and between 20 and 50 pmol/μg aRNA (dye incorporation).

growth_protocol: Natural Field condition excepted for offshore structure (with low environmental conditions)

extract_protocol: Total RNA was extracted from the tissues with Tri-Reagent kit (Sigma) and subsequently cleaned with nucleospin RNA Clean-up (Macherev Nagel) isolation columns. After homogenisation of the N2 grinding powder in Tri-reagent and the first centrifugation, the aqueous phase was extracted to directly isolate the tota RNA on the column as described by the provide. RNA concentrations were measured using an ND-1000 spectrophotometer (Nanodrop Technologies) and RNA integrity was controlled on the Agilent bioanalyser using RNA 6000 nano kit (Agilent Technologies)

treatment_protocol: Oyster were sampled in July 2012, snap-frozen in liquid nitrogen, and stored at -80 degrees celsius for total RNA extraction. Measurement of the viral load

tag: spat

value: 2N Hatchery, sex indertermined


title: Spat_uninfected natural sanctuary site animal_Rep2


title: 46133_blood


title: 59081_blood


title: Spat_uninfected offshore condition animal_Rep3

source_name: Spat 2N Hatchery, offshore uninfected


title: Spat_uninfected offshore condition animal_Rep4


title: 46014_blood


title: Spat_uninfected natural sanctuary site animal_Rep1


title: 38023_blood


title: 20439_blood


title: 30681_blood


title: 52090_blood


title: 35435_blood


title: 59731_blood


title: 38120_blood


title: Spat_low viral load infected animal from Blainville_Rep4

source_name: Spat 2N Hatchery, Low infected


title: Spat_low viral load infected animal from Blainville_Rep3


title: 20075_blood


title: Spat_uninfected offshore condition animal_Rep2


title: Spat_high viral load infected animal from Blainville_Rep2

source_name: Spat 2N Hatchery, High infected


title: Spat_low viral load infected animal from Blainville_Rep1


title: 57613_blood


title: Spat_high viral load infected animal from Blainville_Rep4


title: Spat_uninfected offshore condition animal_Rep1


title: Spat_high viral load infected animal from Blainville_Rep3


title: 45711_blood


title: 79221_blood


title: 37764_blood


title: 88532_blood


title: 17222_blood


title: Spat_high viral load infected animal from Blainville_Rep1


title: Spat_low viral load infected animal from Blainville_Rep2


title: x324

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

hyb_protocol: Fragmentation, hybridization and washing for the spotted arrays were carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies ) and Gene Expression Wash Buffer Kit (Agilent Technologies) according to the manufacturer’s protocol in a low ozone environment.

scan_protocol: Scanned using a Agilent G2565CA Microarray scanner

data_processing: Scanned images were quantified by Gene Pix Pro 6.0 (Molecular Devices). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were background corrected (normexp, offset=50), then within-array normalized by loess normalization method and between-array normalizatized by the quantile method. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed by calculating the median. The 92 samples were processed together with 154 other breast tumor samples. ComBat method was used for adjustment of the batch effects across the different spotting batches [PMID: 16632515]. In cases of multiple probes per gene symbol only the probe with the maximum mean (Cy5) intensity was kept. Missing expression values were imputed by k-nearest neighbors averaging (k = 10).

source_name: Breast tumor tissue

label_protocol: RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).

tag: group

value: Sporadic

value: Basal

source_name: Universal Human Reference RNA (Stratagene)

tag: reference


title: 27139_blood


title: x323

value: LumB

value: Universal Human Reference RNA (Stratagene)


title: 6313_blood


title: 56082_blood


title: 58664_blood


title: 32620_blood


title: 89840_blood


title: 96436_blood


title: x288


title: 25614_blood


title: x278


title: 37973_blood


title: 20681_blood


title: x291


title: Spat_uninfected natural sanctuary site animal_Rep3


title: x286


title: 90739_blood


title: x315


title: x274


title: x277


title: x281


title: x300


title: x301


title: 71374_blood


title: Plek2 KD 2

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

description: Sample name: 23-4

hyb_protocol: Standard Illumina protocol

scan_protocol: Illumina HiScan scanner

data_processing:
GeneSpring GX
GSGX Version = 1.9.0
Report Date = 41172.61709
Project = PJi-Sept20-12-M6v2
Group Set = PJi-Sept20-12-M6v2
Non-normalized data: (linked as supplementary file on Series record)
Analysis = PJi-Sept20-12-M6v2_nonorm_nobkgdsub
Normalization = none
Normalized data: see data table below
Analysis = PJi-Sept20-12-M6v2_quantile_bkgdsub
Normalization = quantile

organism: Mus musculus

source_name: Plek2 KD, TER119 negative fetal liver erythroid cells

label_protocol: Illumina® TotalPrep-96 RNA Amplification Kit, ambion catalog 4393543

growth_protocol: TER119 negative mouse fetal erythroblasts from E13.5 mouse fetal liver were transduced with control or plek2 shRNA and cultured at 37°C in Epo free medium for 24 hrs, which were then cultured in Epo containing medium for an additional 12 hours.

extract_protocol: RNAs isolated from these cells using RNeasy kit (Qiagen) were processed for hybridization to Illumina MouseWG-6 v2.0 microarrays.

tag: strain

value: TER119 negative, fetal liver erythroblasts

tag: genotype/variation

value: Plek2 knockdown


title: Plek2 KD 1

description: Sample name: 23


title: Control 3

description: Sample name: C5

source_name: Control, TER119 negative fetal liver erythroid cells

value: control


title: 96675_blood


title: 17826_blood


title: 24538_blood


title: 51010_blood


title: x280


title: Plek2 KD 3

description: Sample name: 23-5


title: Control 2

description: Sample name: C4


title: Control 1

description: Sample name: C


title: x265


title: 86983_blood


title: 97257_blood


title: x264


title: 27045_blood


title: 97170_blood


title: Mtb infected-42d-5

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: PHRI, NJMS, Rutgers the State University of NJ

description: Gene expression data from Mtb-infected mouse lungs

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute of UMDNJ was used for all the experiments

data_processing: Data from the scanned images were extracted using the software from Affymetrix and processed using PARTEK Genomics Suite for further analysis

source_name: Mouse lungs infected with Mtb for 42 days

label_protocol: Total RNA samples were reverse transcribed and labled with biotin as suggested by the array manufacturer (affymetrix)

growth_protocol: B6D2F1 mice were infected with Mtb CDC1551 at ~2log10 (on day 0). At28 days post infection, one group of infected mice were treated with Pyrazinamide at 150mg/kg.  Lung tissue from Uninfected, Untreated and PZA treated mice were isolated at Day 0, 28, 42 and 63 days post infection and used for total RNA isolation.

extract_protocol: Total RNA from the mouse lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) and purified using RNA mini prep columns (Qiagen, CA, USA) according to the instructions of the manufacturers

treatment_protocol: PZA, one of the first line anti-TB drugs, was used to treat one group of Mtb infected mice. The compound was used at 150mg/kg body weight, dissolved in distilled water and administered through gavage five days a weeks.  Treatment was started at 28 days post infection and continued up to 63 days post infection.

value: Lung

tag: infection

value: Mtb

tag: time

value: 42 dpi


title: Mtb infected-42d-6

scan_protocol: standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute of UMDNJ was used for all the experiments


title: PZA treated-42d-2

description: Gene expression data from Mtb-infected and PZA treated mouse lungs

source_name: Mtb infected mouse lungs treated with PZA-42 days post infection

tag: treatment

value: Pyrazinamide


title: PZA treated-63d-1

source_name: Mtb infected mouse lungs treated with PZA-63 days post infection

value: 63 dpi


title: x275


title: Mtb infected-63d-1

source_name: Mouse lungs infected with Mtb for 63days


title: Mtb infected-42d-2


title: x259


title: PZA treated-63d-2


title: 9006_blood

source_name: whole-blood


title: x253


title: x266


title: Mtb infected-63d-2

source_name: Mouse lungs infected with Mtb for 63 days


title: x254


title: 2838_blood


title: 84463_blood


title: Mtb infected-42d-3


title: PZA treated-42d-1


title: Mtb infected-42d-4


title: 97536_blood


title: x251


title: Mtb infected-42d-1


title: x310


title: UnInfected-1

description: Gene expression data from uninfected mouse lungs

source_name: Mouse lungs-uninfected

value: uninfected


title: x249


title: x250


title: 17911_blood

value: blood


title: UnInfected-2


title: 6740_blood


title: UnInfected-4


title: 72115_blood


title: 50014_blood


title: x213


title: x246


title: 81848_blood


title: x232


title: 80983_blood


title: UnInfected-3


title: x245


title: 66956_blood


title: x226


title: x221


title: 28611_blood


title: 17330_blood


title: 11669_blood


title: 70413_blood


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title: 59584_blood


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title: 70767_blood


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title: x142


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title: 78858_blood


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title: 49670_blood


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title: x097R


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title: x095R


title: 12985_blood


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title: 33875_blood


title: 2302_blood


title: 82899_blood


title: x083R


title: x078


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title: 56950_blood


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title: 33669_blood


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title: x056


title: 48765_blood


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title: x033R


title: x053


title: x039R


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title: 3308_blood


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title: x034R


title: 70011_blood


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title: x026R


title: 64699_blood


title: 1227_blood


title: x032


title: 84527_blood


title: 48465_blood


title: x049


title: x025R


title: x028R


title: 56376_blood


title: x051


title: x023


title: 31567_blood


title: 20094_blood


title: 20668_blood


title: 72111_blood


title: 87762_blood


title: x019


title: x013


title: x018


title: 71121_blood


title: 16665_blood


title: x022


title: x011


title: x012


title: 62807_blood


title: x010


title: x001


title: 7237_blood


title: 88618_blood


title: x014


title: x002


title: 46506_blood


title: 12446_blood


title: x007


title: 69917_blood


title: 51281_blood


title: 65139_blood


title: 48512_blood


title: x003


title: 37763_blood


title: 48hrs_fish3

city: Jerusalem

first: Amit

last: Cohen

address: Hebrew University

country: Israel

institute: huji

description: Biological replicate 3 of 3 after 48 hours E2 treatment. Control fish pool, untreated.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent Technologies G2505B scanner.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Danio rerio

source_name: Liver, E2 treated, 48 hrs

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Adult zebrafish raised under standard conditions of 25°C with a light/dark cycle of 14/10 hrs. Ten fish were kept in each aquarium (5L in volume) under static conditions.

extract_protocol: Total RNA was extracted using TRI reagent (Sigma) following the manufacturer's instructions.

treatment_protocol: Male zebrafish were exposed to 17β-estradiol (E2) (Sigma) by immersion. The concentration used was 5 μg/L (18 nM). E2 (dissolved in 50 % ethanol) was added and tissue samples were collected at each time point (4, 12, 24, 48 hrs) after treatment. Water was changed and E2 was refreshed once a day during the incubation period. Only ethanol was added to control (0 hrs) fish.

value: liver

tag: gender

value: male

tag: age

value: 3 months

value: 17β-estradiol (E2)

tag: time point

value: 48 hrs

tag: FISH identifier

source_name: Pooled livers

value: reference


title: 12hrs_fish3

description: Biological replicate 3 of 3 after 12 hours E2 treatment. Control fish pool, untreated.

source_name: Liver, E2 treated, 12 hrs

value: 12 hrs

tag: sample type


title: 24hrs_fish3

description: Biological replicate 3 of 3 after 24 hours E2 treatment. Control fish pool, untreated.

source_name: Liver, E2 treated, 24 hrs

value: 24 hrs


title: 67427_blood


title: 41557_blood


title: 31800_blood


title: 4hrs_fish3

description: Biological replicate 3 of 3 after 4 hours E2 treatment. Control fish pool, untreated.

source_name: Liver, E2 treated, 4 hrs

value: 4 hrs


title: 48hrs_fish1

description: Biological replicate 1 of 3 after 48 hours E2 treatment. Control fish pool, untreated.


title: 12hrs_fish2

description: Biological replicate 2 of 3 after 12 hours E2 treatment. Control fish pool, untreated.


title: 48hrs_fish2

description: Biological replicate 2 of 3 after 48 hours E2 treatment. Control fish pool, untreated.


title: 54138_blood


title: 86602_blood


title: 24hrs_fish2

description: Biological replicate 2 of 3 after 24 hours E2 treatment. Control fish pool, untreated.


title: 97430_blood


title: 46357_blood


title: 5141_blood


title: 55595_blood


title: 24hrs_fish1

description: Biological replicate 1 of 3 after 24 hours E2 treatment. Control fish pool, untreated.


title: 75602_blood


title: 89420_blood


title: 38148_blood


title: 93575_blood


title: 7036_blood


title: 61962_blood


title: 62913_blood


title: 4hrs_fish2

description: Biological replicate 2 of 3 after 4 hours E2 treatment. Control fish pool, untreated.


title: 25930_blood


title: 12hrs_fish1

description: Biological replicate 1 of 3 after 12 hours E2 treatment. Control fish pool, untreated.


title: 16284_blood


title: 9478_blood


title: wildtype

city: Aurora

first: Dennis

middle: R.

last: Roop

state: Colorado

department: Dermatology

institute: University of Colorado

description: gene expression data from newborn wildtype mice

hyb_protocol: A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip array. The array was hybridized overnight at 45 degrees celcius with rotation at 60 rpm then washed and stained with strepavidin, R-phycoererythrin conjugate stain. Signal amplification was done using biotinylated antistrepavidin.

scan_protocol: The stained array was scanned on the Agilent Genearray 2500 scanner

data_processing: The images were analyzed and quality control metrics were recorded using Affymetrix MAS 5.0 software

source_name: P0 whole skin

label_protocol: Labeling was done according to the the University of New Mexico Microarray core

growth_protocol: Whole skin was taken at P0

extract_protocol: RNA was extracted using the Rneasy kit from QIAGEN accoring to their specifications

tag: genotype

value: wildtype

value: FVB/N

value: whole skin


title: loricrin knockout

description: gene expression data from loricrin knockout mice

value: loricrin knockout

tag: tissue


title: loricrin knockout replicate


title: 29770_blood


title: 33251_blood


title: 72569_blood


title: 64313_blood


title: wildtype replicate


title: 81907_blood


title: E2A-PBX1-SNP_#32

status: Public on Jun 27 2013

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as failed. These failed loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, Methylated loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either methylated or failed) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167. Interarray normalization was performed independently for each channel using a quantile normalization, and after that the log(ratio) for each array was calculated as Log2 (HpaII signal) - Log2(MspI signal)

source_name: ALL Blast cells, MspI representation of genomic DNA

label_protocol: Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: cell type

value: ALL Blast cells

tag: all blast cells from

value: tumor cells obtained at diagnosis in childhood ALL with TCF3-PBX1 rearrangement

source_name: ALL Blast cells, HpaII representation of genomic DNA


title: E2A-PBX1-SNP_#25


title: TEL-AML1-SNP_#06

value: tumor cells obtained at diagnosis in childhood ALL with ETV6-RUNX1 rearrangement


title: E2A-PBX1-SNP_#09


title: E2A-PBX1-SNP_#24


title: 63570_blood

value: blood


title: E2A-PBX1-SNP_#35


title: E2A-PBX1-SNP_#23


title: E2A-PBX1-SNP_#34


title: Hyperdip>50-SNP_#113

value: tumor cells obtained at diagnosis in childhood ALL with high hyperdiploid karyotype


title: E2A-PBX1-SNP_#08


title: E2A-PBX1-SNP_#03


title: Hyperdip>50-SNP_#109


title: Hyperdip>50-SNP_#167


title: Hyperdip>50-SNP_#116


title: Hyperdip>50-SNP_#129


title: Hyperdip>50-SNP_#134


title: Hyperdip>50-SNP_#133


title: Hyperdip>50-SNP_#152


title: Hyperdip>50-SNP_#18


title: Hyperdip>50-SNP_#104


title: Hyperdip>50-SNP_#82


title: Hyperdip>50-SNP_#164


title: Hyperdip>50-SNP_#136


title: Hyperdip>50-SNP_#139


title: Hyperdip>50-SNP_#124


title: RD-ES_siHDGF VS RD-ES_NC

city: Guangzhou

first: yang

last: yang

address: 58, Zhongshan Road II, Guangzhou

country: China

institute: Sun Yat-sen University

description: To identify the genes regulated by HDGF in RD-ES cells

hyb_protocol: Cy5-dCTP for test samples and Cy3-dCTP for reference samples labeled double-stranded cDNA dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: The arrays were scanned by the LuxScan 10KA dual channels laser scanner and analyzed with the LuxScan 3.0 image analysis software (CapitalBio Corp., Beijing, China).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: RD-ES cells transfected with siHDGF

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: RD-ES cells were cultured in DMEM (high glucose) medium supplemented with 15% fetal bovine serum (FBS), 100 units/ml penicillin, and 100ug/ml streptomycin in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen Co., Carlsbad, CA) and purified with NucleoSpin® RNA clean-up Kit (MACHEREY-NAGEL, Germany). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Cells were transfected with specific siRNA directed against HDGF. Cells were harvested 48 hours post-transfection

tag: cell line

value: RD-ES

tag: transfected

value: siHDGF

source_name: RD-ES cells transfected with negative control siRNA

treatment_protocol: Cells were transfected with scrambled siRNA. Cells were harvested 48 hours post-transfection

value: control siRNA


title: 4hrs_fish1

description: Biological replicate 1 of 3 after 4 hours E2 treatment. Control fish pool, untreated.

value: liver

value: male

value: 3 months

value: 17β-estradiol (E2)


title: NormalB-#14

source_name: Normal Bone Marrow B cells, MspI representation of genomic DNA

value: Mature B cells

source_name: Normal Bone Marrow B cells, HpaII representation of genomic DNA


title: Hyperdip>50-SNP_#158


title: Hyperdip>50-SNP_#126


title: Hyperdip>50-SNP_#115


title: Hyperdip>50-SNP_#107


title: Hyperdip>50-SNP_#108


title: Hyperdip>50-SNP_#127


title: Hyperdip>50-SNP_#163


title: Hyperdip>50-SNP_#117


title: Hyperdip>50-SNP_#121


title: Hyperdip>50-SNP_#160


title: NormalB-#16


title: NormalB-#7

value: ProB cells


title: NormalB-#15


title: NormalB-#18


title: NormalB-#13


title: NormalB-#6

value: PreB cells


title: NormalB-#5


title: NormalB-#9


title: NormalB-#11


title: NormalB-#8


title: NormalB-#10


title: NormalB-#3


title: NormalB-#19

value: Normal B cells


title: NormalB-#17


title: NormalB-#12


title: T-ALL-SNP-#27

value: T-lineage ALL


title: T-ALL-SNP-#90

value: ALL Blast cells


title: T-ALL-SNP-#101


title: T-ALL-SNP-#19


title: NormalB-#1


title: T-ALL-SNP-#25


title: T-ALL-SNP-#89


title: NormalB-#4


title: T-ALL-SNP-#15


title: T-ALL-SNP-#85


title: T-ALL-SNP-#74


title: NormalB-#2


title: T-ALL-SNP-#99


title: T-ALL-SNP-#92


title: T-ALL-SNP-#87


title: T-ALL-SNP-#26


title: T-ALL-SNP-#91

value: T-lineage ALL and early thymic progenitor immunophenotype


title: T-ALL-SNP-#73


title: T-ALL-SNP-#75


title: T-ALL-SNP-#71


title: T-ALL-SNP-#88


title: T-ALL-SNP-#80


title: T-ALL-SNP-#22


title: MLL-SNP-#13

value: tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement


title: Other-SNP-#110

value: B-precursor ALL with miscellaneous karyotype


title: T-ALL-SNP-#79


title: T-ALL-SNP-#96


title: T-ALL-SNP-#04


title: Hyperdip47-50-SNP-#38

value: B-precursor ALL with low hyperdiploid karyotype


title: T-ALL-SNP-#10


title: Hypodip-SNP-#06

value: B-precursor ALL with hypodiploid karyotype


title: Pseudodip-SNP-#11

value: B-precursor ALL with pseudodiploid karyotype


title: T-ALL-SNP-#28


title: MLL-SNP-#20


title: MLL-SNP-#21


title: Other-SNP-#102


title: Other-SNP-#116


title: Pseudodip-SNP-#08


title: Other-SNP-#113


title: T-ALL-SNP-#77


title: Other-SNP-#99


title: Pseudodip-SNP-#07


title: T-ALL-SNP-#8


title: Pseudodip-SNP-#12


title: Other-SNP-#07


title: Pseudodip-SNP-#10


title: Pseudodip-SNP-#09

value: tumor with alteration of ERG


title: Other-SNP-#122


title: Other-SNP-#125


title: Other-SNP-#152

value: tumor cells obtained at diagnosis in childhood ALL with CRLF2 rearrangement


title: Other-SNP-#140


title: Hyperdip47-50-SNP-#12


title: Other-SNP-#108


title: Other-SNP-#141


title: Hyperdip47-50-SNP-#15


title: Other-SNP-#112


title: Other-SNP-#101


title: Other-SNP-#129


title: BCR-ABL-SNP-#06

value: tumor cells obtained at diagnosis in childhood ALL with BCR-ABL1 rearrangement


title: Other-SNP-#126


title: Down-SNP-#21


title: Hyperdip47-50-SNP-#14


title: Hyperdip47-50-SNP-#07


title: BCR-ABL-SNP-#02


title: Other-SNP-#127


title: Other-SNP-#100


title: Pseudodip-SNP-#04


title: Down-SNP-#20


title: Other-SNP-#147


title: Other-SNP-#159


title: BCR-ABL-SNP-#04


title: BCR-ABL-SNP-#03


title: Hyperdip47-50-SNP-#02


title: BCR-ABL-SNP-#07


title: BCR-ABL-SNP-#13


title: BCR-ABL-SNP-#18


title: MLL-SNP-#29


title: BCR-ABL-SNP-#10


title: BCR-ABL-SNP-#12


title: BCR-ABL-SNP-#20


title: BCR-ABL-SNP-#16


title: BCR-ABL-SNP-#08


title: BCR-ABL-SNP-#11


title: MLL-SNP-#04


title: BCR-ABL-SNP-#01


title: BCR-ABL-SNP-#09


title: MLL-SNP-#17


title: BCR-ABL-SNP-#14


title: BCR-ABL-SNP-#05


title: MLL-SNP-#19


title: MLL-SNP-#05


title: BCR-ABL-SNP-#21


title: MLL-SNP-#15


title: MLL-SNP-#07


title: MLL-SNP-#09


title: MLL-SNP-#01


title: MLL-SNP-#06


title: MLL-SNP-#02


title: Hyperdip>50-SNP_#132

value: tumor cells obtained at diagnosis in childhood ALL with high hyperdiploid karyotype


title: MLL-SNP-#23


title: MLL-SNP-#22


title: MLL-SNP-#03


title: MLL-SNP-#18


title: TEL-AML1-SNP-#76

value: tumor cells obtained at diagnosis in childhood ALL with ETV6-RUNX1 rearrangement


title: MLL-SNP-#11


title: MLL-SNP-#12


title: TEL-AML1-SNP-#13


title: BCR-ABL-SNP-#17


title: TEL-AML1-SNP-#84


title: TEL-AML1-SNP-#87


title: TEL-AML1-SNP-#85


title: TEL-AML1-SNP-#25


title: TEL-AML1-SNP-#02


title: MLL-SNP-#10


title: MLL-SNP-#16


title: TEL-AML1-SNP-#36


title: MLL-SNP-#08


title: TEL-AML1-SNP-#11


title: TEL-AML1-SNP-#34


title: TEL-AML1-SNP-#77


title: TEL-AML1-SNP-#23


title: TEL-AML1-SNP-#114


title: TEL-AML1-SNP-#78


title: TEL-AML1-SNP-#14


title: TEL-AML1-SNP-#88


title: TEL-AML1-SNP-#58


title: TEL-AML1-SNP-#17


title: TEL-AML1-SNP-#18


title: E2A-PBX1-SNP-#08

value: tumor cells obtained at diagnosis in childhood ALL with TCF3-PBX1 rearrangement


title: E2A-PBX1-SNP-#09


title: E2A-PBX1-SNP-#24


title: TEL-AML1-SNP-#06


title: TEL-AML1-SNP-#43


title: TEL-AML1-SNP-#19


title: TEL-AML1-SNP-#05


title: Hyperdip>50-SNP-#113


title: E2A-PBX1-SNP-#32


title: TEL-AML1-SNP-#03


title: E2A-PBX1-SNP-#23


title: TEL-AML1-SNP-#38


title: Hyperdip>50-SNP-#108


title: E2A-PBX1-SNP-#25


title: Hyperdip>50-SNP-#129


title: Hyperdip>50-SNP-#107


title: Hyperdip>50-SNP-#82


title: E2A-PBX1-SNP-#03


title: Hyperdip>50-SNP-#124


title: Hyperdip>50-SNP-#18


title: Hyperdip>50-SNP-#134


title: E2A-PBX1-SNP-#34


title: E2A-PBX1-SNP-#35


title: Hyperdip>50-SNP-#132


title: TEL-AML1-SNP-#20


title: Hyperdip>50-SNP-#116


title: TEL-AML1-SNP-#27


title: Hyperdip>50-SNP-#127


title: Hyperdip>50-SNP-#109


title: Hyperdip>50-SNP-#104


title: Hyperdip>50-SNP-#152


title: Hyperdip>50-SNP-#136


title: Hyperdip>50-SNP-#139


title: Hyperdip>50-SNP-#117


title: Hyperdip>50-SNP-#163


title: Hyperdip>50-SNP-#121


title: Hyperdip>50-SNP-#158


title: Hyperdip>50-SNP-#164


title: Hyperdip>50-SNP-#133


title: Hyperdip>50-SNP-#160


title: Hyperdip>50-SNP-#126


title: Hyperdip>50-SNP-#167


title: testes aly[5] rep3

city: Cardiff

first: Helen

last: White-Cooper

address: Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

description: gene expression from aly mutant testes

hyb_protocol: Hybridisation was perfomed in GeneChip Hybridisation Oven 640, and washed with wash with GeneChip Fluidic Station 400

scan_protocol: scanning and quality control with GeneChip Scanner 3000 7G

data_processing: raw data were generated with GCOS/AGCC software. Data were normalised with an RMA normalisation across replicates

organism: Drosophila melanogaster

source_name: adult testes_aly mutant individuals

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

growth_protocol: Flies were grown on standard cornmeal yeast sucrose agar medium, and collected for dissection within one day of eclosion

extract_protocol: RNA easy (Qiagen) extraction of total RNA according to the manufacturer's instructions

treatment_protocol: Testes were manually dissected in testis buffer, snap frozen in liquid nitrogen, and stored at -80C until sufficient sample had been collected. Samples were processed into 350ul  lysis buffer (RLT+b-ME) then shipped on dry ice to the microarray facility in Glasgow university.

value: adult testis

tag: culture temperature


title: testes aly[5] rep1

description: gene expression from aly mutant testes


title: testes tinRNAi rep3

description: gene expression from normal testes

source_name: adult testes_tinRNAi individuals (control)

value: w; tinRNAi/+; bamGal4VP16/+


title: Hyperdip>50-SNP-#115


title: Y31314 (T8)

city: Vandoeuvre-lès-Nancy

first: Marc

last: Derive

address: 9, av de la Forêt de Haye

institute: Inserm U1116

hyb_protocol: Following fragmentation,4.4 ug of cDNA were hybridized for 18hr at 45°C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using the Gene chip Scanner 3000 affymetrix

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Macaca fascicularis

label_protocol: Biotinylated cDNA were prepared according to the standard NuGEN Ovation® Whole Blood Solution with Biotin kit protocol from 50 ng total RNA .

extract_protocol: Total RNA extraction was performed using the PAXgene Blood RNA (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Collection blood on PAXgene tube

value: Blood

tag: time (h)

tag: subject


title: Y31308 (T8)

source_name: peptide control, T8

value: peptide control


title: testes aly[5] rep2

description: gene expression from aly mutant testes

tag: genotype/variation


title: Y31312 (T8)


title: Y31307 (T8)


title: testes Nxt1 rep3

description: gene expression from Nxt1 mutant testes

source_name: adult testes_Nxt1 mutant individuals


title: testes Nxt1 rep2

description: gene expression from Nxt1 mutant testes


title: testes tinRNAi rep2

description: gene expression from normal testes


title: Y31310 (T8)


title: Y31309 (T8)


title: testes tinRNAi rep1

description: gene expression from normal testes


title: Y31311 (T8)


title: testes Nxt1 rep1

description: gene expression from Nxt1 mutant testes


title: Y31313 (T8)


title: Y31312 (T4)


title: Y31301 (T8)

source_name: Vehicle, T8

value: Vehicle


title: Y31302 (T8)


title: Y31313 (T4)


title: Y31304 (T8)


title: Y31303 (T8)


title: Y31304 (T4)

source_name: Vehicle, T4


title: Y31314 (T2)


title: Y31310 (T4)


title: Y31307 (T4)

source_name: peptide control, T4


title: Y31301 (T4)


title: Y31306 (T8)


title: Y31305 (T4)


title: Y31302 (T4)


title: Y31306 (T4)


title: Y31311 (T4)


title: Y31308 (T4)


title: Y31311 (T2)


title: Y31303 (T4)


title: Y31309 (T4)


title: Y31305 (T8)


title: Y31313 (T2)


title: Y31309 (T2)


title: Y31312 (T2)


title: Y31308 (T2)

source_name: peptide control, T2


title: Y31307 (T2)


title: Y31310 (T2)


title: Y31303 (T2)

source_name: Vehicle, T2


title: Y31305 (T2)


title: Y31302 (T2)


title: Y31312 (T0)


title: Y31311 (T0)


title: Y31313 (T0)


title: Y31304 (T2)


title: Y31310 (T0)


title: Y31306 (T2)


title: Y31314 (T0)


title: Y31302 (T0)

source_name: Vehicle, T0


title: Y31307 (T0)

source_name: peptide control, T0


title: Y31301 (T2)


title: Y31309 (T0)


title: Y31301 (T0)


title: Y31303 (T0)


title: Y31304 (T0)


title: Y31305 (T0)


title: Overexpression of miR-100 in stable miR-125b-expressing Reh cells, rep3

city: Rotterdam

first: Farhad

last: Akbari Moqadam

state: N/A = Not Applicable

address: dr. Molewaterplein 50

country: Netherlands

institute: ErasmusMC - department of Pediatric Oncology-Hematology

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.

source_name: ETV6-RUNX1-positive Reh leukemic cells

label_protocol: The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.

growth_protocol: Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.

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

treatment_protocol: The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of  miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.

value: Reh

value: overexpressing miR-125b plus miR-100


title: Y31306 (T0)


title: Overexpression of miR-99a and miR-100 in stable miR-125b-expressing Reh cells, rep2

value: overexpressing miR-125b plus miR-99a and miR-100


title: Overexpression of miR-99a and miR-100 in stable miR-125b-expressing Reh cells, rep1


title: Overexpression of miR-99a and miR-100 in stable miR-125b-expressing Reh cells, rep3


title: Overexpression of miR-100 in stable miR-125b-expressing Reh cells, rep2


title: Overexpression of miR-100 in stable miR-125b-expressing Reh cells, rep1


title: Y31308 (T0)


title: Overexpression of miR-99a in stable miR-125b-expressing Reh cells, rep3

value: overexpressing miR-125b plus miR-99a


title: Y31314 (T4)


title: Overexpression of miR-99a in stable miR-125b-expressing Reh cells, rep2


title: Overexpression of scrambled miR-control in stable miR-125b-expressing Reh cells, rep2

value: overexpressing miR-125b plus scrambled miR-control


title: Overexpression of miR-99a in stable miR-125b-expressing Reh cells, rep1


title: Overexpression of scrambled miR-control in stable miR-125b-expressing Reh cells, rep1


title: OEC-BC14

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and target value scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Healthy donor

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3'IVT Express Kit and Affymetrix Hybridization Wash and Stain Kit from 100 ng total RNA.

growth_protocol: Mononuclear cells from peripheral blood were plated in endothelial growth medium for 4 weeks with medium change every second day. Outgrowth of OECs occured between week 3 and 4. OEC clones were isolated and cultured until they became senescent.

extract_protocol: mRNA was isolated according to the manufacturer's instructions using the Rneasy Kit from Qiagen.

treatment_protocol: For microarray analysis, OEC clones were harvested at passage 4 or 5. Cells were pelleted and pellet was stored at -80°C.

tag: diagnosis

value: Healthy donor

value: outgrowth endothelial cells (OEC)

value: male

value: 26 years


title: LDS-OEC5

source_name: Loeys-Dietz syndrome (LDS)

value: Loeys-Dietz syndrome (LDS)

value: 27 years


title: OEC-BC401

value: female

value: 29 years


title: OEC-BC248

value: 52 years


title: LDS-OEC1

value: 50 years


title: NormalB_#14

value: Mature B cells


title: LDS-OEC11


title: NormalB_#13


title: NormalT_#6

source_name: Normal T lymphocyte cells, MspI representation of genomic DNA

value: Normal T lymphocyte cells

source_name: Normal T lymphocyte cells, HpaII representation of genomic DNA


title: NormalB_#17

source_name: Normal Bone Marrow B cells, MspI representation of genomic DNA

source_name: Normal Bone Marrow B cells, HpaII representation of genomic DNA


title: NormalT_#3


title: NormalT_#1


title: NormalB_#11

value: ProB cells


title: NormalT_#5


title: NormalB_#18


title: NormalB_#19

value: Normal B cells


title: NormalT_#8


title: NormalT_#7


title: NormalT_#4


title: NormalB_#15


title: NormalT_#2


title: NormalB_#7


title: NormalB_#12


title: NormalB_#10


title: NormalB_#16


title: NormalB_#8


title: NormalB_#6

value: PreB cells


title: NormalB_#5


title: NormalB_#9


title: NormalB_#4


title: T-ALL-SNP_#15

source_name: ALL Blast cells, MspI representation of genomic DNA

value: ALL Blast cells

value: T-lineage ALL

source_name: ALL Blast cells, HpaII representation of genomic DNA


title: NormalB_#3


title: NormalB_#2


title: NormalB_#1


title: Non-adherent_biological_repl_2

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

institute: Radboud University Medical Centre

description:
nAdh2
Gene expression of planktonic (non-adherent) M. catarrhalis BBH18, biological replicate 2

hyb_protocol: 2 µg of labeled cDNA was applied to 4x72K custom design NimbleGen arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).

scan_protocol: Array images were acquired with a NimbleGen MS200 scanner following their standard operation protocol, using the autogain function per subarray.

data_processing: Raw data was normalized using Arraystar (DNASTAR) software with Quantile RMA normalization.

label: 5'Cy3-labeled random nonamers

organism: Moraxella catarrhalis

source_name: M. catarrhalis BBH18 not bound to Detroit 562 (planktonic)

label_protocol: Total RNA was labeled according to standard Nimblegen gene expression array protocols.

growth_protocol: M. catarrhalis BBH18 was expanded to mid-log phase (OD620nm ~ 1.0) in brain heart infusion (BHI) medium at 37°C 250 rpm. Monolayers of Detroit 562 cells in tissue culture plates (6 wells) were washed twice with PBS, after which bacteria were added at a multiplicity of infection of 10:1 (bacteria:cells). Bacteria were also incubated in the infection medium (DMEM with GlutaMAX™-I  with 1% FCS) only.

extract_protocol: Total RNA was isolated using RNeasy columns (Qiagen) for the adherent fraction (n = 4), non-adherent fraction (n =4), and bacteria without Detroit 562 cells (n =3). Contaminating genomic DNA was removed by treatment with Turbo DNase (Ambion). RNA obtained from the adherent fraction was enriched for bacterial RNA using the MICROBEnrich kit (Ambion) according to manufacturer’s instructions.

treatment_protocol: After 1 h adherence, non-adherent bacteria of two wells (6-8 ml) were combined and 2 volumes of RNAprotect Bacteria Reagent (Qiagen) was added. Subsequently, wells were washed 3 times with PBS, 1 ml RNAprotect Bacteria Reagent was added to each well, adherent bacteria were harvested by scraping, and pooled per 2 wells. The bacteria were also incubated in the infection medium without eukaryotic cells and after 1 h, 8 ml RNAprotect Bacteria Reagent was added to 4 ml bacterial suspension. After 5 min incubation at room temperature and harvesting by centrifugation, pellets were stored at -80°C

value: BBH18 wild-type

tag: genbank


title: T-ALL-SNP_#85


title: Non-adherent_biological_repl_3

description:
nAdh3
Gene expression of planktonic (non-adherent) M. catarrhalis BBH18, biological replicate 3


title: Control_biological_repl_2

description:
Control2
Gene expression of M. catarrhalis BBH18 in the infection medium alone, biological replicate 2

source_name: M. catarrhalis BBH18 in infection medium


title: Control_biological_repl_3

description:
Control3
Gene expression of M. catarrhalis BBH18 in the infection medium alone, biological replicate 3


title: Control_biological_repl_1

description:
Control1
Gene expression of M. catarrhalis BBH18 in the infection medium alone, biological replicate 1


title: Non-adherent_biological_repl_4

description:
nAdh4
Gene expression of planktonic (non-adherent) M. catarrhalis BBH18, biological replicate 4


title: T-ALL-SNP_#90


title: Non-adherent_biological_repl_1

description:
nAdh1
Gene expression of planktonic (non-adherent) M. catarrhalis BBH18, biological replicate 1


title: T-ALL-SNP_#89


title: Adherent_biological_repl_4

description:
Adh4
Gene expression of M. catarrhalis BBH18 bound to Detroit 562 pharyngeal epithelial cells, biological replicate 4

source_name: M. catarrhalis bound to Detroit 562


title: Adherent_biological_repl_2

description:
Adh2
Gene expression of M. catarrhalis BBH18 bound to Detroit 562 pharyngeal epithelial cells, biological replicate 2


title: Adherent_biological_repl_3

description:
Adh3
Gene expression of M. catarrhalis BBH18 bound to Detroit 562 pharyngeal epithelial cells, biological replicate 3


title: T-ALL-SNP_#74


title: Adherent_biological_repl_1

description:
Adh1
Gene expression of M. catarrhalis BBH18 bound to Detroit 562 pharyngeal epithelial cells, biological replicate 1


title: T-ALL-SNP_#99


title: T-ALL-SNP_#101


title: T-ALL-SNP_#96


title: T-ALL-SNP_#87


title: T-ALL-SNP_#75


title: T-ALL-SNP_#26


title: T-ALL-SNP_#27


title: T-ALL-SNP_#92


title: T-ALL-SNP_#19


title: T-ALL-SNP_#88


title: T-ALL-SNP_#28


title: T-ALL-SNP_#22


title: T-ALL-SNP_#91

value: T-lineage ALL and early thymic progenitor immunophenotype


title: T-ALL-SNP_#73


title: Cohort2_Striatum_Methylphenidate group_Sample 1

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

hyb_protocol: Hybridization was carried out using Affymetrix GeneChip Rat Genome 230 2.0 oligonucleotide arrays (Affymetrix, Santa Clara,CA, USA). The hybridized probe array was stained and washed with GeneChip hybridization, wash and stain kit using the Fluidics Station 450 (Affymetrix).

scan_protocol: The stained GeneChip probe array was scanned with a GeneChip Scanner 3000+7G (Affymetrix).

data_processing: The signal intensity of the gene expression level was calculated by the Expressin Console Software, Version 1.1 (Affymetrix) based on the MAS 5.0 algorithm.

organism: Rattus norvegicus

source_name: Striatum, Methylphenidate

label_protocol: RNA was converted to cDNA and transcribed into cRNA in the presence of biotinylated ribonucleotides, according to standard Affymetrix protocols (Affymetrix ‘Expression Analysis Technical Manual’, #701021 Rev. 5).

growth_protocol: Male Wistar rats ( 4 weeks old) were obtained from Orient Bio Korea. The animals were housed in an environmentally-controlled animal room (temperature [22 ± 2°C] and humidity- [55 ± 5%], 12 hr/12 hr light/dark [6 AM-6 PM] cycle), in groups (during drug treatment and CPP experiments) and individually thereafter during self-administration tests. All experiments were performed in accordance with the Principles of Laboratory Animal Care (NIH) and the Animal Care and Use Guidelines of Sahmyook University, Korea.

extract_protocol: Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer's instructions.

treatment_protocol: Rats were acclimatized to their housing conditions prior to drug or saline administration. Drug treatment (twice daily, intraperitoneal [i.p.]) commenced when rats were 6 weeks old, and lasted for 7 days. Rats were divided into two groups: (cohort 1) 4 groups of rats (n=12 rats per group) given saline only (1 mg/kg, i.p.,”drug-naive” rats); and (cohort 2): 3 groups of rats given either methamphetamine, amphetamine or methylphenidate (5 mg/kg,i.p., “drug-pretreated”) prior to behavioral assays (Conditioned Place Preference and Self-administration tests).

tag: strain

value: Wistar

tag: pretreatment drug & dose

value: Methylphenidate (5 mg/kg)

tag: cpp conditioning drug and dose

value: 0.25 mg/0.1 ml infusion, methylphenidate

value: Striatum


title: Cohort2_Striatum_Methylphenidate group_Sample 2


title: Cohort2_Striatum_Methamphetamine group_Sample 1

source_name: Striatum, Methamphetamine

value: Methamphetamine (5 mg/kg)

value: 0.1 mg/kg/infusion, Methamphetamine


title: Cohort2_Striatum_Methylphenidate group_Sample 3


title: T-ALL-SNP_#04


title: Cohort2_Striatum_Methamphetamine group_Sample 2


title: Cohort2_Striatum_Methamphetamine group_Sample 3


title: T-ALL-SNP_#8

value: tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement


title: MLL-SNP_#20


title: T-ALL-SNP_#10


title: MLL-SNP_#13


title: T-ALL-SNP_#79


title: Cohort2_Striatum_Amphetamine group_Sample 1

source_name: Striatum, Amphetamine

value: Amphetamine (5 mg/kg)

value: 0.1 mg/kg/infusion, Amphetamine


title: Cohort2_Striatum_Amphetamine group_Sample 3


title: Cohort2_Striatum_Amphetamine group_Sample 2


title: T-ALL-SNP_#80


title: Cohort2_Striatum_Control group_Sample 2

source_name: Striatum, Saline (Control)

value: saline

value: Saline

value: 0.1 ml/infusion, 0.9% Saline


title: Cohort2_Striatum_Control group_Sample 3


title: Cohort2_Prefrontal Cortex_Methylphenidate group_Sample 3

source_name: Prefrontal Cortex, Methylphenidate

value: Prefrontal Cortex


title: Cohort2_Striatum_Control group_Sample 1


title: Hyperdip47-50-SNP_#38

value: ALL Blast cells

value: B-precursor ALL with low hyperdiploid karyotype


title: MLL-SNP_#21


title: Hypodip-SNP_#06

value: B-precursor ALL with miscellaneous karyotype


title: Cohort2_Prefrontal Cortex_Methylphenidate group_Sample 2


title: Other-SNP_#07


title: Cohort2_Prefrontal Cortex_Methylphenidate group_Sample 1


title: Cohort2_Prefrontal Cortex_Methamphetamine group_Sample 3

source_name: Prefrontal Cortex, Methamphetamine


title: Other-SNP_#102


title: Other-SNP_#110


title: Cohort2_Prefrontal Cortex_Methamphetamine group_Sample 1


title: Cohort2_Prefrontal Cortex_Methamphetamine group_Sample 2


title: Other-SNP_#99


title: Pseudodip-SNP_#11


title: Other-SNP_#122


title: Cohort2_Prefrontal Cortex_Control group_Sample 2

source_name: Prefrontal Cortex, Saline (Control)


title: Pseudodip-SNP_#12


title: Cohort2_Prefrontal Cortex_Amphetamine group_Sample 2

description: Co2_PFC_Amph _2

source_name: Prefrontal Cortex, Amphetamine


title: Detroit_adherent_BBH18_biological_repl_5

hyb_protocol: 2 µg of labeled cDNA was applied to 12x135K pre-designed NimbleGen huamn expression arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).

data_processing:
Raw data was normalized using Arraystar (DNASTAR) software with Quantile RMA normalization.
The 'normalized_data.txt' containining RMA-normalized, averaged gene-level signal intensity (log2-transformed) is available on Series records.

source_name: Detroit 562 cells infected with M. catarrhalis BBH18

label_protocol: Total RNA (5 µg) was labeled according to standard Nimblegen gene expression array protocols.

growth_protocol: Monolayers of Detroit 562 cells in tissue culture plates (6 wells) were washed twice with PBS, after which bacteria were added at a multiplicity of infection of 10:1 (bacteria:cells). Uninfected control cells were incubated with DMEM with GlutaMAX™-I  medium with 1% FCS only.

extract_protocol: After washing, Detroit 562 cells were lysed directly in the tissue culture dish by addition of RLT buffer (Qiagen Benelux B.V.), collected with a rubber policeman, and transferred to a microcentrifuge tube. Subsequently, total RNA was isolated using the RNeasy Mini kit (Qiagen) and DNA was removed by DNase digestion with the DNA-free kit (Ambion).

treatment_protocol: After a 2h incubation period, nonadherent bacteria were removed by three washes with PBS

value: pharyngeal epithelial cells


title: Detroit_adherent_BBH18_biological_repl_4


title: Detroit_adherent_BBH18_biological_repl_6


title: Cohort2_Prefrontal Cortex_Amphetamine group_Sample 1

description: Co2_PFC_Amph _1

value: Wistar


title: Cohort2_Prefrontal Cortex_Control group_Sample 1


title: Pseudodip-SNP_#07


title: Other-SNP_#140

value: tumor with alteration of ERG


title: Detroit_adherent_BBH18_biological_repl_3


title: Detroit_adherent_BBH18_biological_repl_2


title: Other-SNP_#100


title: Cohort2_Prefrontal Cortex_Amphetamine group_Sample 3

description: Co2_PFC_Amph _3


title: Pseudodip-SNP_#08


title: T-ALL-SNP_#77

value: T-lineage ALL and early thymic progenitor immunophenotype


title: T-ALL-SNP_#71


title: T-ALL-SNP_#25

value: T-lineage ALL


title: Cohort2_Prefrontal Cortex_Control group_Sample 3


title: Pseudodip-SNP_#10


title: Detroit_adherent_BBH18_biological_repl_1


title: Cohort1-Striatum_Methylphenidate ( 5 mg/kg) group_Sample 3

description: Co1-STR_Mph 5_3

treatment_protocol: Rats were acclimatized to their housing conditions prior to drug or saline administration. Drug treatment (twice daily, intraperitoneal [i.p.]) commenced when rats were 6 weeks old, and lasted for 7 days. Rats were divided into two groups: (cohort 1) 4 groups of rats (n=12 rats per group) given saline only (1 mg/kg, i.p.,”drug-naive” rats); and (cohort 2): 3 groups of rats given either methamphetamine, amphetamine or methylphenidate (5 mg/kg,i.p., “drug-pretreated”) prior to behavioral assays (Conditioned Place Preference [CPP] and Self-administration tests). During CPP tests, rats were conditioned with the psychostimulants at one of the following drugs and doses: Saline (Control group), 1.25 and 5 mg/kg, i.p. for stimulant-treated groups.

value: Methylphenidate (5 mg/kg)

value: 0.25 mg/0.1 ml infusion, methylphenidate

value: Striatum


title: Detroit_control_biological_repl_6

source_name: Detroit 562 cells uninfected


title: Detroit_control_biological_repl_5


title: Other-SNP_#113


title: Pseudodip-SNP_#09


title: Detroit_control_biological_repl_4


title: Other-SNP_#159


title: Other-SNP_#112


title: Other-SNP_#125


title: Cohort1-Striatum_Methylphenidate ( 5 mg/kg) group_Sample 2

description: Co1-STR_Mph 5_2


title: Detroit_control_biological_repl_3


title: Other-SNP_#129


title: Cohort1-Striatum_Methylphenidate ( 5 mg/kg) group_Sample 1

description: Co1-STR_Mph 5_1


title: Other-SNP_#147


title: Other-SNP_#126


title: Other-SNP_#141


title: Other-SNP_#101

value: tumor cells obtained at diagnosis in childhood ALL with CRLF2 rearrangement


title: Detroit_control_biological_repl_2


title: Cohort1-Striatum_Methamphetamine ( 5 mg/kg) group_Sample 3

description: Co1-STR_Meth 5_3

value: Methamphetamine (5 mg/kg)

value: 0.1 mg/kg/infusion, Methamphetamine


title: Detroit_control_biological_repl_1


title: Cohort1-Striatum_Methamphetamine (1.25 mg/kg) group_Sample 3

description: Co1-STR_Meth 1.25_3

value: saline

value: Methamphetamine (1.25 mg/kg)


title: Hyperdip47-50-SNP_#12


title: Cohort1-Striatum_Methamphetamine ( 5 mg/kg) group_Sample 1

description: Co1-STR_Meth 5_1


title: Hyperdip47-50-SNP_#07


title: Cohort1-Striatum_Methamphetamine ( 5 mg/kg) group_Sample 2

description: Co1-STR_Meth 5_2


title: Down-SNP_#20


title: Other-SNP_#108


title: Cohort1-Striatum_Methamphetamine (1.25 mg/kg) group_Sample 2

description: Co1-STR_Meth 1.25_2


title: Cohort1-Striatum_Methamphetamine (1.25 mg/kg) group_Sample 1

description: Co1-STR_Meth 1.25_1


title: Cohort1-Striatum_Amphetamine (5 mg/kg) group_Sample 3

description: Co1-STR_Amph 5_3

value: Amphetamine (5 mg/kg)

value: 0.1 mg/kg/infusion, Amphetamine


title: Adipocyte_PU1_rep4

city: Philadelphia

first: Joanna

middle: R

last: DiSpirito

state: PA

address: Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: IDOM

institute: University of Pennsylvania

hyb_protocol: Cy3-labeled cRNA was fragmented at 60 oC for 30 minutes with the following combination 720 ng of Cy3 cRNA, 6 ul of 10X Blocking Agent, 1.2 ul of 25X fragmentation buffer and H2O to 30 ul. The hybridization cocktail was made by mixing 25 ul of fragmented Cy3 cRNA with 25 ul of 2x GEx hybridization buffer HI-RPM. Following the manufacturer's protocol, 45 ul of the cocktail was loaded onto each array of the 8X array/slide. The assembled array was incubated at 65 oC on a rotator at 10 rpm for 17 hours. Array slides were disassembled in GE Wash Buffer 1 at room temperature (RT). They were washed in GE Wash Buffer 1 at RT for 1 minute. They were washed again in GE Wash Buffer 2 at 37 oC for 1 minute. Slides were put in slide holder for scanning.

scan_protocol: Slides were scanned using Agilent SureScan at 3 um following manufacturer's instruction. Raw data were extracted using Agilent Feature Extraction software.

data_processing: Data was quantile normalized in R with the limma package's function normalizeBetweenArray. FDRs were calculated using the SAMR package.

source_name: 3T3-L1 adipocyte, day 10, adeno-PU1 72hrs

label_protocol: One-color RNA spike-in was diluted at 1:7500 in Dilution Buffer (Agilent, Cat # 5188-5282). T7 promoter primer from Low Input Quick Amp Labeling Kit one-color (Agilent 5190-2305) was diluted at 0.8 ul of T7 primer plus 1 ul of H2O. The reaction mixture was made by combining 2 ul of diluted spike-in, 1.5 ul of RNA (100 ng/ul) and 1.8 ul of diluted T7 primer. The rest of labeling and purification were done according to the manufacturer's protocol for Cy3 one-color labeling.

growth_protocol: 3T3-L1 pre-adipocytes were maintained in DMEM (Hi glucose) + 10% FBS + 1% PennStrep. For differentiation, cells were grown to confluence and media was changed (day -2). Two days later (day 0), a DMI cocktail was added consisting of 1uM dexamethasone, 0.5mM 3-isobutyl-1-methylxanthine and 10ug/mL insulin. On day 2, media was changed to maintenance media + 10ug/mL insulin. On day 4, media was changed to maintenance media. By day 7, differentiation to mature adipocytes was considered complete and cells were infected with adenovirus.

extract_protocol: Total RNA was isolated from adipocytes using TRIzol (Invitrogen) followed by purification with the RNeasy mini kit (Qiagen).

treatment_protocol: For adipocyte infections, purified adenoviruses were incubated in low-serum media (maintenance media with 0.5% FBS) containing 0.5μg/mL poly-L-lysine for two hours at 25C. Adipocytes were washed once with PBS then incubated with adenovirus (5mL of diluted virus per 10cm dish). After four hours, additional low-serum media was added (5mL per 10cm dish). After 16 hours, low serum media was replaced with growth media and cells were incubated under standard conditions until harvest (24-72 hours post-infection).

value: adipocytes

tag: treatment


title: Adipocyte_PU1_rep3


title: Adipocyte_PU1_rep2


title: Down-SNP_#21

value: ALL Blast cells


title: Pseudodip-SNP_#04


title: Other-SNP_#127


title: Ba_1_Soil_rep_2

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

description: data used for Supplementary Table S6

hyb_protocol: DNA was hybridized to the census array using the NimbleGen hybridization kit.  Samples were allowed to hybridize for 17 hours and washed using the NimbleGen Wash Buffer Kit (Roche).

scan_protocol: Microarrays were scanned on an Axon GenePix 4000B 5 µm scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Data was analyzed using NimbleScan software and custom software developed at Lawrence Livermore National Laboratory, CA, USA and  described in 'Gardner et al. A Micobial Detection Array (MDA) for Viral and Bacterial Detection. BMC Genomics 2010 Nov 25;11:668'. Additional stringency criteria were applied to exclude bacterial sequences and viruses having fewer than 20% of probes detected out of those expected. Probes were classified as detected if the intensity exceeded a threshold equal to the 99th percentile of intensities for negative control probes.

organism: Bacillus anthracis str. Ames

source_name: Soil sample spiked with B. anthracis DNA

label_protocol: B. anthracis-spiked samples were amplified using the REPLI-g Midi Kit (Qiagen, Gaithersburg, MD), intended to provide uniform whole genome amplification.  This kit was used according to the manufacturer’s instructions, allowing samples to amplify for 16 hours at 30°C. Amplified samples were purified using the Qiaquick PCR Purification Kit (Qiagen), and yielded 17.0 ± 1.8 µg amplified DNA for each sample. Amplified environmental DNA spiked with B. anthracis Ames genomic DNA was fluorescently labeled using the NimbleGen One-Color DNA Labeling Kit (Roche) according to the manufacturer’s recommended protocols.

extract_protocol: DNA was extracted from soil using the UltraClean Soil DNA Isolation Kit (MoBio, Carlsbad, CA) using the manufacturer’s alternative protocol for maximum yield.  Following extraction, 1 ng of each extracted DNA was used in a real-time PCR assay to test for inhibition.  All samples showed a high level of PCR inhibition and were reprocessed starting from Step 12 of the MoBio alternative protocol, intended to remove excess humic acid. For aerosol samples, primary sampling filters were obtained from BioWatch aerosol collection units (collected April 2009) from the National Capital Region Laboratory.  Filters were added to 30 mL 100 mM phosphate buffer (pH 7.4) containing 0.05% (v/v) Tween 80 and vortexed for 30 seconds followed by incubation on a rocking shaker for 15 minutes.  This agitation procedure was repeated three times.  The filters were removed from the tube and the remaining solution centrifuged at 3200 x g for 30 minutes at 4oC.  Following centrifugation, the supernatant was removed and discarded.  DNA purification was subsequently performed using the UltraClean Soil DNA Isolation Kit (MoBio).  DNA concentrations were measured using a Qubit fluorometer (Life Technologies, Grand Island, NY).

treatment_protocol: B. anthracis Ames DNA was acquired from the LLNL select agent laboratory and confirmed to be free of viable cells or spores by plating of 1/10 the total DNA volume on blood agar plates followed by incubation at 37°C for 72 hours.  DNA concentration was determined by measurement using a Qubit fluorometer and the number of femtograms/genome equivalent was determined based on GenBank chromosomal and plasmid genome sizes.  B. anthracis genomic DNA was added to nucleic acid extracted from the two environmental sources in six amounts (1, 10, 100, 1000, 10000, and 100000 genomic equivalents of B. anthracis DNA).  B. anthracis DNA was mixed with 100 pg of DNA extracted from aerosol filters or 1 ng DNA extracted from the combined Oakland and San Francisco soil extracts.

tag: ba copies

tag: background

value: Soil

tag: rep


title: Other-SNP_#152

source_name: ALL Blast cells, MspI representation of genomic DNA

tag: cell type


title: Hyperdip47-50-SNP_#02

tag: all blast cells from

source_name: ALL Blast cells, HpaII representation of genomic DNA


title: Adipocyte_PU1_rep1

tag: cell line


title: Hyperdip47-50-SNP_#15


title: Cohort1-Striatum_Amphetamine (1.25 mg/kg) group_Sample 2

description: Co1-STR_Amph 1.25_2

value: Wistar

value: Amphetamine (1.25 mg/kg)

tag: tissue


title: Ba_1_Soil_rep_1

description: data used for Supplementary Table S6


title: Cohort1-Striatum_Amphetamine (5 mg/kg) group_Sample 1

description: Co1-STR_Amph 5_1


title: Cohort1-Striatum_Amphetamine (5 mg/kg) group_Sample 2

description: Co1-STR_Amph 5_2


title: Cohort1-Striatum_Amphetamine (1.25 mg/kg) group_Sample 3

description: Co1-STR_Amph 1.25_3


title: Adipocyte_LACZ_rep3

source_name: 3T3-L1 adipocyte, day 10, adeno-LACZ 72hrs

value: adeno-LACZ


title: Adipocyte_LACZ_rep2


title: Ba_1_Aerosol_rep_2

description: data used for Supplementary Table S6

source_name: Aerosol filter sample spiked with B. anthracis DNA

value: Aerosol


title: Adipocyte_LACZ_rep4


title: Ba_1_Aerosol_rep_1

description: data used for Supplementary Table S6


title: Adipocyte_LACZ_rep1


title: Cohort1-Striatum_Amphetamine (1.25 mg/kg) group_Sample 1

description: Co1-STR_Amph 1.25_1


title: Hyperdip47-50-SNP_#14


title: BCR-ABL-SNP_#06

value: tumor cells obtained at diagnosis in childhood ALL with BCR-ABL1 rearrangement


title: Ba_10_Soil_rep_2

description: data used for Supplementary Table S6


title: BCR-ABL-SNP_#02


title: Cohort1-Striatum_Control group_Sample 5

value: Saline

value: 0.1 ml/infusion, 0.9% Saline


title: Ba_10_Aerosol_rep_2

description: data used for Supplementary Table S6


title: Cohort1-Striatum_Control group_Sample 3

value: Striatum


title: BCR-ABL-SNP_#07


title: Cohort1-Striatum_Control group_Sample 4


title: BCR-ABL-SNP_#03


title: BCR-ABL-SNP_#04


title: Ba_10_Soil_rep_1

description: data used for Supplementary Table S6


title: Ba_10_Aerosol_rep_1

description: data used for Supplementary Table S6


title: BCR-ABL-SNP_#08


title: Ba_100_Soil_rep_1

description: data used for Supplementary Table S6


title: Ba_100_Soil_rep_2

description: data used for Supplementary Table S6


title: Ba_100_Aerosol_rep_2

description: data used for Supplementary Table S6


title: BCR-ABL-SNP_#14


title: BCR-ABL-SNP_#13


title: Cohort1-Striatum_Control group_Sample 2


title: Cohort1-Prefrontal Cortex_Methylphenidate ( 5 mg/kg) group_Sample 2

description: Co1-PFC_Mph 5_2

value: Methylphenidate (5 mg/kg)

value: 0.25 mg/0.1 ml infusion, methylphenidate

value: Prefrontal Cortex


title: Cohort1-Prefrontal Cortex_Methylphenidate ( 5 mg/kg) group_Sample 3

description: Co1-PFC_Mph 5_3

value: saline


title: Ba_1000_Soil_rep_2

description: data used for Supplementary Table S6


title: Cohort1-Prefrontal Cortex_Methylphenidate ( 5 mg/kg) group_Sample 1

description: Co1-PFC_Mph 5_1


title: Cohort1-Striatum_Control group_Sample 1


title: Ba_100_Aerosol_rep_1

description: data used for Supplementary Table S6


title: Ba_1000_Soil_rep_1

description: data used for Supplementary Table S6


title: Cohort1-Prefrontal Cortex_Methamphetamine ( 5 mg/kg) group_Sample 2

description: Co1-PFC_Meth 5_2

value: Methamphetamine (5 mg/kg)

value: 0.1 mg/kg/infusion, Methamphetamine


title: Cohort1-Prefrontal Cortex_Methamphetamine ( 5 mg/kg) group_Sample 1

description: Co1-PFC_Meth 5_1


title: BCR-ABL-SNP_#18


title: Cohort1-Prefrontal Cortex_Methamphetamine ( 5 mg/kg) group_Sample 3

description: Co1-PFC_Meth 5_3


title: Ba_1000_Aerosol_rep_2

description: data used for Supplementary Table S6


title: Ba_1000_Aerosol_rep_1

description: data used for Supplementary Table S6


title: Cohort1-Prefrontal Cortex_Amphetamine (5 mg/kg) group_Sample 3

description: Co1-PFC_Amph 5_3

value: Amphetamine (5 mg/kg)

value: 0.1 mg/kg/infusion, Amphetamine


title: BCR-ABL-SNP_#16

value: ALL Blast cells


title: BCR-ABL-SNP_#11


title: BCR-ABL-SNP_#10


title: BCR-ABL-SNP_#20


title: Cohort1-Prefrontal Cortex_Methamphetamine (1.25 mg/kg) group_Sample 2

description: Co1-PFC_Meth 1.25_2

value: Wistar

value: Methamphetamine (1.25 mg/kg)


title: Ba_10000_Soil_rep_1

description: data used for Supplementary Table S6

value: Soil


title: Ba_10000_Soil_rep_2

description: data used for Supplementary Table S6


title: Cohort1-Prefrontal Cortex_Methamphetamine (1.25 mg/kg) group_Sample 1

description: Co1-PFC_Meth 1.25_1