title: Subject 32, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134842_HUGENE-1_0-ST-V1_HOLO3204-06-10.rma-gene-default-Signal

value: Subject 32


title: 36127.H

status: Public on Jun 15 2015

type: RNA

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

country: Denmark

institute: University of Aarhus

hyb_protocol: The labelled and purified reference samples were mixed and divided into aliquots before combining it with a labelled sample. Each of the 36 labelled samples were co-hybridized with an aliquot of the labelled reference sample and a hybridization blocker containing polydA (Invitrogen Corporation, CA, USA) and Yeast tRNA (Invitrogen Corporation, CA, USA) to 27k pig oligonucleotide microarrays (GEO accession: GPL5972) using a Discovery XT hybridisation station (Ventana Discovery Systems, Tucson, AZ, USA). Chip Prep-2 was transferred from 4 ºC to room temperature 1 hour before use. ChipSpread was prepared by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) followed by incubation at room temperature for 1 hour before use. Labels were printed, trimmed and placed on the slides. The Chip Map reagents (Chip Prep-1, -2 and - 3) were mixed by inversion; the caps were removed and the reagents were placed in the Discovery. The slides were placed in the machine and the run was initiated. The slides were covered with 2.5 mL ChipSpread when the message appeared and the machine used app. 1.5 hours for pre-hybridization of the slides. The Chiphybe80 was mixed and 200 µL were added to the sample (<20 µL) followed by careful mixing. The sample mixtures were heated at 90°C for 3 minutes in a PCR machine carefully mixed by pipetting. The "button" on the machine was pressed to prepare the slides for hybridization. When prompted to, the samples were applied to the slides which were hybridized at 48 ºC for 6 hours. Oil was wiped from the backside of the slides using a clean-room napkin and the slides were placed in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, an equal number of slides were placed in two slide-holders and continued in parallel. The slide-holder was transferred to a HTW filled with RiboWash and washed for 2 min with magnetic stirring at 700 rpm. The HTW was refilled with RiboWash and the wash was repeated. The slide-holder was dipped in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). The slide-holder was then transferred to a HTW filled with 2x SSC and washed for 2 min with magnetic stirring at 700 rpm followed by refill of the HTW with 2x SSC and repetition of the wash. The slide-holder was dipped 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and the holder was left submerged in 0.1x SSC. The slides were transferred to a mBox slide holder placed in a mTub filled with Elga H2O. Arrays were dried by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.27, Molecular Devices) using FeatureType = Irregular Filled and BackgroundSubtraction = MorphologicalClosingFollowedByOpening

data_processing: Statistical analysis was carried out in the R computing environment (version 2.9.0 for Linux) using the package Linear Models for Microarray Analysis (Limma, version 2.18.0) which is part of the Bioconductor project. The log2-transformed median intensity ratios of Alexa-647 to Alexa-555 (not background corrected) were first normalized within-slide using the loess method and subsequently normalized between arrays using the scale method, both as implemented in Limma. The individual spots were weighted by a spot binary weight matrix where spots flagged by GenePix as non-detectable were given a weight of zero and a sum of the spot weights were calculated for each probe across the 27 microarrays in the two groups (high and low skatole). Probes with a sum of 10 or less in either of the two groups were excluded from further analysis together with the control spots. A linear model including array quality weights was fitted to the normalized data set which subsequently was subjected to an empirical Bayes method to determine differentially expressed genes between the samples of high skatole level and samples of low skatole level. The false discovery rate (FDR) was taken into consideration using the method of Benjamini and Hochberg as implemented in Limma and an adjusted P-value below 0.05 was considered significant.

molecule: total RNA

organism: Sus scrofa

label_protocol: Total-RNA was extracted from each sample and DNase treated using RNeasy Maxi Kit (Qiagen) following the enclosed protocols. Quantities were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE, USA) and qualities were examined by the 28S:18S rRNA ratio using the RNA 6000 Nano LabChip Kit on 2100 Bioanalyzer (Agilent Technologies, CA, USA). Alexa Flour-labeled cDNA was synthesized from 20 µg of total-RNA using Superscript Plus Direct cDNA Labeling System (Invitrogen) and purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. "Green" spike-in RNA was added to the common reference samples and "red" spike-in RNA was added to the samples.

growth_protocol: The animals were raised on the same farm under identical conditions.

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen).

tag: breed

value: Danish Landrace

tag: gender

value: boar, uncastrated

tag: weight

value: approx. 80 kg

tag: tissue

value: liver

tag: animal id

tag: skatole level

value: high

value: DLY X Hampshire

value: female

tag: animal

tag: project

value: RN


title: 32125.L

value: low


title: Subject 34, Clean Air

city: San Francisco

first: Mehrdad

last: Arjomandi

state: CA

address: 4150 Clement St, 3A-20

country: USA

institute: UCSF

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134847_HUGENE-1_0-ST-V1_HOLO3404-27-10.rma-gene-default-Signal

hyb_protocol: Hybridization was performed using 5 ug of biotinylated target, which was incubated with GeneChip Human Gene 1.0 ST array at 45 C for 16-20 hours. Following hybridization, non-specifically bound material was removed by washing. Detection of specifically bound target was performed using GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G and raw data was extracted from the scanned images

data_processing: The Data were analyzed with the Affymetrix GeneChip Command Console Software (Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method

label: Biotin

organism: Homo sapiens

source_name: BAL_Clean Air_4hrs

label_protocol: Biotin-labeled target was prepared using 100 ng of total RNA of each sample. cDNA was synthesized using the GeneChip WT Sense Target Labeling and Conttrol Reagents kit. Sense cDNA was fragmented by UDG and APE 1 using the GeneChip WT Terminal Labelling Kit.

growth_protocol: BAL cells were collected via bronchoscopy 20 hours after exposure to clean air, 100 ppb ozone, or 200 ppb ozone.

extract_protocol: RNA was extracted from BAL cells stored in Buffer RLT using the Rneasy kit (Qiagen), and concentration and quality were assessed using the Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: BAL cell pellets were stored in Buffer RLT prior to RNA extraction

tag: subject id

value: Subject 34

tag: ozone exposure (ppb)

tag: cell type

value: bronchoalveolar lavage (BAL) cells


title: Subject 32, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134843_HUGENE-1_0-ST-V1_HOLO3211-05-09.rma-gene-default-Signal

source_name: BAL_200 ppb Ozone_4hrs

value: male


title: Subject 33, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134846_HUGENE-1_0-ST-V1_HOLO3304-11-10.rma-gene-default-Signal

value: Subject 33


title: Glycerol 1 h_rep1

type: mixed

city: Dublin 4

first: Sarah

last: Finn

address: University College Dublin

country: Ireland

institute: Centre for Food Safety

hyb_protocol: 1)Prepared Cy 5 labelled gDNA (6 µl) was added to Cy3 labelled cDNA (18 µl) for a total volume of 24 µl. 2) To each sample, 6µl of blocking solution (Agilent 5188-5973) and 30 µl of :hybridisation buffer (Agilent 5188-6420) were added. 3) Samples were boiled for 2 min at 95oC and centrifuged for 1 min at 13000 rpm. 4) The gasket slide was placed in hybridization chamber rubber and 50 µl of sample placed directly into centre of gasket slide. 5) When all samples were dispensed the array slide was inserted into the hybridisation chamber, sealed and placed in pre-heated hybridisation over (65˚C) at 10 rpm overnight. 6) Slides were removed from chamber washed according to manufacturer’s instructions (http://www.chem.agilent.com/Library/usermanuals/Public/G2534-90004_HybridizationChamber_User.pdf). 7) Array slides were cleaned with inert gas before measurement.

scan_protocol: Scans were carried out using an Agilent DNA Microarray Scanner, Model G2565, at at 5 µm resolution with Green and Red PMT values set to 100 % and an XDR value of 0.1.  Images generated were saved as multi-image .tiff files.

data_processing: Agilent Feature extraction software was used to process the scanned images of the arrays.  The data generated was then analysed using GeneSpring version 7.3 (Agilent Technologies, Santa Clara, California) based on the log ratio of median Cy3/Cy5 signal normalised to the 50th percentile.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

source_name: Salmonella exposed to Glycerol for 1 h

label_protocol: 1)Random priming reactions were set up in 1.5 ml microfuge tubes. Total RNA (10 µg) and 5 µg of random hexamers (Invitrogen, Cat: 48190011) were added to a final volume of 9.4 µl in RNase free water. 2) Samples incubated at 70 ˚C for 5 min and chilled on ice for 10 min. 3) RT reaction mix prepared by using the Stratagene AffinityScript multi-temperature Reverse Transcriptase by adding the following to each tube: 2 µl of 10 X RT buffer; 2 µl of 0.1 M DDT; 0.6 µl of 50 X dNTP’s (25 mM dATP, dGTP, dTTP and 10 mM dCTP[GE Healthcare Lifesciences, Cat: 27-2035-02]); 2 µl of Cy3 dCTP (1 mM stock, GE Healthcare Lifesciences, Cat: PA55321); 4 µl of reverse transcriptase. 4) Samples were vortexed to mix and incubated shaking at 25 ˚C for 10 min. 5) Samples then incubated overnight at 42 ˚C. 6) Freshly prepared 0.1 M NaOH (15 µl) was added and the RNA hydrolysed at 70 ˚C for 10 min. Freshly prepared 0.1 M HCl (15 µl) was added to neutralise the alkali. Samples were placed on ice to cool to room temperature.  7) Qia-quick PCR purification kit (Qiagen, Cat: 28104) was used to remove unincorporated/quenched cy dyes.  Samples eluted into 40 µl RNase free water and dried-down on speed vac to 18 µl.

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 10% Glycerol and incubated statically at 24˚C for 1 h

extract_protocol: 1)Cultures exposed to 10% Glycerol (10 ml) for 24 h were harvested by centrifugation. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions

tag: agent

value: Glycerol

tag: time point

value: 1 h

tag: strain

tag: biological replicate

molecule: genomic DNA

source_name: Reference genomic DNA

label_protocol: 1) Chromosomal DNA (2 µg) added to sterile microfuge tube and brought to 21 µl with RNase free water (Sigma, W4502-1L). 2) 20 µl each of 2.5 X Random primer/reaction buffer mix from the Invitrogen BioPrime® DNA Labelling System (18094011) was added to sample and boiled for 5 min, then put on ice for 5 min. 3) On ice, 5 µl of 10X dNTP mix (10X dNTP mix: 1.2 mM each dATP, dGTP, dTTP; 0.6 mM dCTP; 10 mM Tris pH 8.0; 1 mM EDTA;); 3 µl of Cy5 dCTP (1 mM stock, GE Helathcare Lifesciences, Cat: PA55321); and 1 µl Klenow enzyme from the kit were added. 4) Samples were spun briefly and the reaction mix incubated at 37 ˚C overnight. 5) A Qia-quick PCR purification kit (Qiagen Cat: 28104) was used to remove unincorporated/quenched Cy dyes.  Samples were eluted into 80 µl of RNase free water.  This protocol supplies sufficient labelled DNA for 9 hybridisations.  Samples adjusted to a volume of 50 µl using speed vac.

growth_protocol: Salmonella enterica serovar Typhimurium 4/74 grown to stationary phase at 37˚C

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns).

tag: reference

value: stationary phase at 37˚C


title: 33302.H


title: Subject 31, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134840_HUGENE-1_0-ST-V1_HOLO3104-19-10.rma-gene-default-Signal

value: Subject 31


title: Subject 32, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134841_HUGENE-1_0-ST-V1_HOLO3201-06-10.rma-gene-default-Signal

value: Subject 32


title: 17129.H

value: Danish Landrace

value: boar, uncastrated


title: 32302.L

value: approx. 80 kg

value: liver


title: KCl 6 h_rep3

source_name: Salmonella exposed to KCl for 6 h

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 9.25% KCl and incubated statically at 24˚C for 6 h

extract_protocol: 1)Cultures exposed to 9.25% KCl (10 ml) for 24 h were harvested by centrifugation. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions

value: KCl

value: 6 h


title: KCl 24 h_rep2

source_name: Salmonella exposed to KCl for 24 h

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 9.25% KCl and incubated statically at 24˚C for 24 h


title: Subject 30, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134836_HUGENE-1_0-ST-V1_HOLO3010-10-09.rma-gene-default-Signal

source_name: BAL_100 ppb Ozone_4hrs

value: Subject 30

value: female


title: Subject 31, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134839_HUGENE-1_0-ST-V1_HOLO3102-22-10.rma-gene-default-Signal


title: KCl 24 h_rep1


title: KCl 6 h_rep2


title: Subject 31, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134838_HUGENE-1_0-ST-V1_HOLO3111-15-09.rma-gene-default-Signal


title: KCl 6 h_rep1


title: Subject 28, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134833_HUGENE-1_0-ST-V1_HOLO2812-01-09.rma-gene-default-Signal

value: Subject 28


title: KCl 1 h_rep3

source_name: Salmonella exposed to KCl for 1 h

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 9.25% KCl and incubated statically at 24˚C for 1 h


title: 17126.H

value: high

value: DLY X Hampshire

value: RN


title: 23101.H


title: KCl 24 h_rep3


title: Subject 28, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134834_HUGENE-1_0-ST-V1_HOLO2801-20-10.rma-gene-default-Signal

value: bronchoalveolar lavage (BAL) cells


title: Subject 30, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134835_HUGENE-1_0-ST-V1_HOLO3004-10-10.rma-gene-default-Signal


title: 32338.L

value: low


title: Subject 28, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134832_HUGENE-1_0-ST-V1_HOLO2810-13-09.rma-gene-default-Signal


title: Subject 11, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134828_HUGENE-1_0-ST-V1_HOLO1104-07-09.rma-gene-default-Signal

value: Subject 11

value: male


title: Subject 16, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134831_HUGENE-1_0-ST-V1_HOLO1604-14-09.rma-gene-default-Signal

value: Subject 16


title: Subject 16, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134830_HUGENE-1_0-ST-V1_HOLO1609-03-09.rma-gene-default-Signal


title: Subject 11, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134827_HUGENE-1_0-ST-V1_HOLO1106-23-09.rma-gene-default-Signal


title: 37335.L

value: Danish Landrace


title: 32325.H

value: boar, uncastrated


title: KCl 1 h_rep2

value: 1 h

value: stationary phase at 37˚C


title: Subject 16, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134829_HUGENE-1_0-ST-V1_HOLO1606-04-09.rma-gene-default-Signal


title: 32306.H

value: approx. 80 kg

value: liver


title: Subject 30, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134837_HUGENE-1_0-ST-V1_HOLO3001-09-10.rma-gene-default-Signal

value: Subject 30


title: Subject 11, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134826_HUGENE-1_0-ST-V1_HOLO1102-03-09.rma-gene-default-Signal


title: KCl 1 h_rep1

value: KCl


title: NaCl 24 h_rep3

source_name: Salmonella exposed to NaCl for 24 h

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 6% NaCl and incubated statically at 24˚C for 24 h

extract_protocol: 1)Cultures exposed to 6% NaCl (10 ml) for 24 h were harvested by centrifugation. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions

value: NaCl


title: cutaneous primary melanoma PGEM581

type: genomic

city: Chapel Hill

first: Nathaniel

middle: Allen

last: Slater

state: North Carolina

address: 413 Mary Ellen Jones Building, 116 Manning Drive, CB#7287

department: Dermatology

institute: University of North Carolina School of Medicine

description: FFPE

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Cancer Panel I array using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3, Cy5

source_name: UNM

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from FFPE tumor using a proteinase K digestion protocol

tag: site

value: trunk

tag: sample id

tag: age

value: F

tag: subtype

value: UNCL

tag: breslow thickness

tag: ulceration

value: present

tag: mitoses

tag: mitotic rate

tag: mutation

value: BRAF

value: cutaneous primary melanoma tumor


title: cutaneous primary melanoma PGEM566

description: FFPE

value: HN

tag: gender

value: M

value: WT

tag: tissue


title: Subject 9, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134824_HUGENE-1_0-ST-V1_HOLO906-27-08.rma-gene-default-Signal

tag: subject id

value: Subject 9

value: male

tag: ozone exposure (ppb)

tag: cell type

value: bronchoalveolar lavage (BAL) cells


title: cutaneous primary melanoma PGEM504

description: FFPE

source_name: UNC

value: lower extremity


title: Subject 9, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134825_HUGENE-1_0-ST-V1_HOLO909-24-08.rma-gene-default-Signal


title: Subject 9, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134823_HUGENE-1_0-ST-V1_HOLO907-24-08.rma-gene-default-Signal


title: Subject 3, 100 ppb

description:
Gene expression data from BAL cells after exposure to 100 ppb ozone for 4 hours
EA11012_134821_HUGENE-1_0-ST-V1_HOLO308-20-08.rma-gene-default-Signal

value: Subject 3

value: female


title: NaCl 24 h_rep2

tag: agent

tag: time point

tag: strain

value: stationary phase at 37˚C


title: Subject 3, 200 ppb

description:
Gene expression data from BAL cells after exposure to 200 ppb ozone for 4 hours
EA11012_134822_HUGENE-1_0-ST-V1_HOLO304-10-08.rma-gene-default-Signal


title: 37137.L

tag: breed

value: Danish Landrace

value: boar, uncastrated

tag: weight

value: approx. 80 kg

value: liver

tag: animal id

tag: skatole level

value: low

value: DLY X Hampshire

tag: animal

tag: project

value: RN


title: NaCl 24 h_rep1

value: NaCl

tag: biological replicate

tag: reference


title: NaCl 6 h_rep3

source_name: Salmonella exposed to NaCl for 6 h

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 6% NaCl and incubated statically at 24˚C for 6 h

extract_protocol: 1)Cultures exposed to 6% NaCl (10 ml) for 6 h were harvested by centrifugation. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions

value: 6 h


title: cutaneous primary melanoma PGEM589

description: FFPE

tag: site

value: trunk

tag: sample id

tag: age

value: F

tag: subtype

value: SSM

tag: breslow thickness

tag: ulceration

value: present

tag: mitoses

tag: mitotic rate

tag: mutation

value: WT

value: cutaneous primary melanoma tumor


title: Subject 3, Clean Air

description:
Gene expression data from BAL cells after exposure to clean air for 4 hours
EA11012_134820_HUGENE-1_0-ST-V1_HOLO307-08-08.rma-gene-default-Signal

tag: subject id

value: Subject 3

tag: gender

value: female

tag: ozone exposure (ppb)

tag: cell type

value: bronchoalveolar lavage (BAL) cells


title: 39313.H

tag: breed

value: Danish Landrace

value: boar, uncastrated

tag: weight

tag: tissue

tag: animal id

tag: skatole level

value: high

tag: animal


title: FoxM1 wildtype HSCs, biological rep2

city: CHICAGO

first: Yu

last: Hou

state: Illinois

address: 909 S wolcott AVE. COMRB Rm:5040

department: medicined

institute: university of illinois at chicago

hyb_protocol: Hybridization to Affymetrix MoGene-1_0-st-v1 array was carried out by Core Genomics Facility (CGF) at UIC using standard protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G by Core Genomics Facility (CGF) at UIC using standard protocol.

data_processing: Primary analysis was carried out by Core Genomics Facility (CGF) at UIC using Affymetrix Expression Console software.

label: biotin

organism: Mus musculus

source_name: FoxM1 wildtype Hematopoietic Stem Cells

label_protocol: Biotin labeling was carried out by Core Genomics Facility (CGF) at UIC using GeneChip WT Sense Target Labeling and Control Reagents and standard protocol.

growth_protocol: mouse Hematopoietic Stem Cells sorted from 2-month-old C57BL/6 mice

extract_protocol: Bone marrow  cells were isolated and stained with biotin conjugated lineage marker (Gr1, Ter119, B220, CD19, Rat IgM, IL-7R and CD3), and cell surface marker (Sca-1-PE, C-kit-APC-Cy7, CD48-PE-Cy7, CD150-APC, and streptavidin PE-Cy5), the HSCs (Lin-C-kit+Sca-1+CD150+CD48-) were sorted for microarray analysis. RNA extracted from sorted HSCs with QIAGEN RNeasy Micro Kit, and amplified with Ovation® Pico WTA System V2 before microarray analysis.

tag: strain

value: Hematopoietic Stem Cells

tag: genotype

value: wildtype

tag: age

value: 2-month-old mice


title: FoxM1 mutant HSCs, biological rep2

source_name: FoxM1 mutant Hematopoietic Stem Cells

value: FoxM1 mutant


title: FoxM1 wildtype HSCs, biological rep3


title: cutaneous primary melanoma PGEM573

description: FFPE

tag: site

tag: sample id

tag: subtype

tag: breslow thickness

tag: ulceration

value: BRAF


title: siMPS1_6h_2_(HG-U133A_2).CEL

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

hyb_protocol: The affymetrix cartridges were prehybridized for 10 min at 45C in a prehybridization mix. This is followed by hybridization in a hybridization cocktail (GeneChip Hybridization kit, Affymetrix) at 45C for 16 hours.

scan_protocol: The arrays were scanned using Affymetrix GenChip scanner according to the manufacturer's intructions.The CEL files were automatically generated.

data_processing: The data was processed using MAS5 algorithm

source_name: U251 Glioblastoma cell line

label_protocol: Two hundred fifty nanogram of total RNA was used to generate labled aRNA using GeneChip IVT Express Kit (Affymetrix) according to the manufacture's recommendations

extract_protocol: U251 cells were transfected with 2 pmol siRNA using

tag: timie

value: 6 h

tag: treatment

tag: cell line


title: FoxM1 wildtype HSCs, biological rep1

tag: cell type


title: NaCl 6 h_rep1

tag: agent

value: NaCl

tag: time point

tag: biological replicate

tag: reference

value: stationary phase at 37˚C


title: NaCl 6 h_rep2


title: FoxM1 mutant HSCs, biological rep3


title: cutaneous primary melanoma PGEM561

description: FFPE

value: ext

tag: gender

value: M

value: SSM

value: present

tag: mitoses

tag: mitotic rate

tag: mutation

tag: tissue


title: 19338.H

tag: breed

tag: weight

value: approx. 80 kg

value: liver

tag: animal id

tag: skatole level

value: DLY X Hampshire

value: female

tag: animal

tag: project

value: RN


title: siMPS1_48h_2_(HG-U133A_2).CEL

tag: timie

tag: treatment

tag: cell line


title: cutaneous primary melanoma PGEM003

description: FFPE

tag: site

value: HN

tag: sample id

tag: age

tag: subtype

tag: breslow thickness

tag: ulceration

value: cutaneous primary melanoma tumor


title: FoxM1 mutant HSCs, biological rep1

tag: strain

tag: cell type

value: Hematopoietic Stem Cells

tag: genotype

value: 2-month-old mice


title: NaCl 1 h_rep2

source_name: Salmonella exposed to NaCl for 1 h

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C, were harvested and resuspended in 10 ml of LO medium (10 g/l tryptone, 5 g/l yeast extract) containing 6% NaCl and incubated statically at 24˚C for 1 h

extract_protocol: 1)Cultures exposed to 6% NaCl (10 ml) for 1 h were harvested by centrifugation. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions

tag: agent

tag: time point

value: 1 h

tag: biological replicate

tag: reference


title: cutaneous primary melanoma PGEM011

description: FFPE

tag: gender

tag: mitoses

tag: mitotic rate

tag: mutation

value: BRAF

tag: tissue


title: NaCl 1 h_rep3

value: NaCl


title: cutaneous primary melanoma PGEM503

description: FFPE

tag: site

value: Upper extremity

tag: sample id


title: siMPS1_6h_1_(HG-U133A_2).CEL

tag: timie

value: 6 h

tag: treatment

tag: cell line


title: NaCl 1 h_rep1

tag: strain

value: stationary phase at 37˚C


title: siMPS1_48h_1_(HG-U133A_2).CEL


title: Early stationary phase_rep3

source_name: Early stationary phase inoculum culture

growth_protocol: Salmonella Typhimurium 4/74 grown to early stationary phase in LB, statically at 24˚C

extract_protocol: 1)Early stationary phase culture (10 ml) was harvested by centrifugation. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions


title: siMPS1_24h_2_(HG-U133A_2).CEL


title: TSR group S2

city: Goettingen

first: Jana

last: Husse

address: Am Fassberg 11

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol.

scan_protocol: Scanning was performed according to the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: timed sleep restriction (TSR) mouse

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

growth_protocol: tissue was collected at ZT18

extract_protocol: Trizol extraction

treatment_protocol: TSR mice were sleep restricted for 6 hours every day by gentle handling for 5 consecutive days and killed on the last day at ZT18. Epididymal white adipose tissue was directly frozen in liquid nitrogen and stored at -80°C until RNA extraction was performed.

value: epididymal white adipose tissue

tag: sample collection time

value: ZT18 on the last day of treatment


title: TSR group S3


title: siNeg_6h_2_(HG-U133A_2).CEL

value: siNegative


title: cutaneous primary melanoma PGEM571

description: FFPE

tag: age

value: F

tag: subtype

value: NM

tag: breslow thickness

tag: ulceration

value: present

value: WT


title: cutaneous primary melanoma PGEM017

description: FFPE

value: trunk

value: SSM


title: Early stationary phase_rep2

tag: agent

tag: biological replicate

tag: reference


title: siNeg_6h_1_(HG-U133A_2).CEL


title: Early stationary phase_rep1


title: control group C3

source_name: control mouse


title: siNeg_48h_2_(HG-U133A_2).CEL


title: siMPS1_24h_1_(HG-U133A_2).CEL


title: control group C2


title: control group C1


title: TSR group S1


title: cutaneous primary melanoma PGEM559

description: FFPE

value: HN

tag: gender

value: M

tag: mitoses

tag: mitotic rate

value: cutaneous primary melanoma tumor


title: cutaneous primary melanoma PGEM124

description: FFPE

tag: site

value: LMM

tag: mutation

tag: tissue


title: cutaneous primary melanoma PGEM558

description: FFPE

tag: sample id


title: siNeg_24h_2_(HG-U133A_2).CEL

tag: timie

tag: treatment

tag: cell line


title: hAMC_rep8

city: Pavia

first: Patrizia

last: Danieli

address: viale Golgi, 19

country: Italy

institute: Fondazione IRCCS Policlinico San Matteo

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data processing was performed by in GenomeStudio (Illumina) and subsequently in GeneSpring GX software (Agilent technologies)

source_name: fetal origin

label_protocol: Biotinylated, amplified RNA for hybridization with Illumina arrays was generated with Illumina® TotalPrep™-96 RNA

growth_protocol: hAMC and BM-MSC were cultured in non-coated polystyrene culture dishes (Corning Inc., Corning, NY, USA) in alpha-Minimum Essential Medium (alpha-MEM; EuroClone, Milan, ITALY) supplemented with 10% Fetal Bovine Serum (FBS), 2 mmol/L L-glutamine, 100 U/ml penicillin and 100 mcg/ml streptomycin (all from GIBCO™ Invitrogen, Carlsbad, CA, USA). Fibroblasts were cultured in Dulbecco’s Modified Eagle Medium (DMEM, EuroClone, Milan, ITALY) High Glucose with stable L-glutamine supplemented with 10% of FBS, 1 mM Sodium Pyruvate, MEM non essential Ammino Acids, 100 U/ml penicillin and 100 U/ml streptomycin. Cultures were maintained at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: RNA was extracted with Trizol Reagent according to manufacturer's protocol (Invitrogen)

treatment_protocol: Once the cultures of F-MSC, BM-MSC and fibroblasts were 80% confluent, cells were washed twice in PBS, fed with serum-free medium and incubated for 48 h at 37 °C with an atmosphere of 5% CO2/95% O2 before harvesting for RNA extraction

tag: tissue source

value: amniotic membrane

tag: cell type

value: Mesenchymal stem cells of fetal origin (hAMC)


title: cutaneous primary melanoma PGEM554

description: FFPE

tag: age

tag: subtype

tag: breslow thickness

value: BRAF


title: cutaneous primary melanoma PGEM117

description: FFPE

value: ext

value: ALM

tag: ulceration


title: cutaneous primary melanoma PGEM555

description: FFPE

value: absent


title: Control_6h_1_(HG-U133A_2).CEL

value: 6 h


title: hAMC_rep7


title: hAMC_rep6


title: Control_6h_2_(HG-U133A_2).CEL


title: hAMC_rep5


title: S_Leaf at SD, biological rep2

city: TOKAT

first: KUBILAY

last: YILDIRIM

address: TASLICIFTLIK

department: BIOENGINEERING

country: Turkey

institute: GAZIOSMANPASA UNIVERSITY

description:
Gene exprssion data from Sensitive Black poplar leaves under severe drought condition
BP_S_SD_2

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

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

data_processing: The data were analyzed with Robust Multiarray Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Populus nigra

source_name: leaves at 5% field capacity

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: one year old black poplar seedling were cultivated in pots and subjected to a well-watered period by watering the pots up to field capacity (FC).

extract_protocol: Leaves collected at each watering regimes were utilized for total RNA isolation as described in Chang et al. (1993) with minor modifications as described in Le-Provost et al (2007).

treatment_protocol: the pots were weighted and let to transpire until the soil water contents (SWC) of the pots were decreased to %75 field capacity. At this level, the pots were weighted daily and the transpired water was replenished to keep the SWC of the pot at 75% FC for one week. The same procedure was adapted when the SWC of the pots was decreased 50 %, 25 % and 5% of FC. Lastly drought stressed plants were irrigated again to FC for three weeks

value: leaf

value: one year old seedling

tag: genotype

value: Drought Sensitive

tag: water availability regime

value: SD


title: siNeg_24h_1_(HG-U133A_2).CEL

value: siNegative


title: siNeg_48h_1_(HG-U133A_2).CEL


title: S_Leaf at MD, biological rep2

description:
Gene exprssion data from Sensitive Black poplar leaves under moderate drought condition
BP_S_MD_2

source_name: leaves at 25% field capacity

value: MD


title: S_Leaf at PDR, biological rep1

description:
Gene exprssion data from Sensitive Black poplar leaves under post drought rewatering condition
BP_S_PDR_1

source_name: leaves at 100% re_field capacity

value: PDR


title: S_Leaf at PDR, biological rep2

description:
Gene exprssion data from Sensitive Black poplar leaves under post drought rewatering condition
BP_S_PDR_2


title: S_Leaf at SD, biological rep1

description:
Gene exprssion data from Sensitive Black poplar leaves under severe drought condition
BP_S_SD_1


title: hAMC_rep4


title: cutaneous primary melanoma PGEM022

description: FFPE

tag: gender

value: M

value: present

tag: mitoses

value: WT


title: cutaneous primary melanoma PGEM579

description: FFPE

tag: site

value: trunk

value: F

value: UNCL

value: cannot evaluate

tag: mitotic rate

value: cutaneous primary melanoma tumor


title: Control_48h_1_(HG-U133A_2).CEL


title: hAMC_rep3

value: amniotic membrane

value: Mesenchymal stem cells of fetal origin (hAMC)


title: Control_24h_2_(HG-U133A_2).CEL


title: Control_48h_2_(HG-U133A_2).CEL


title: hAMC_rep2


title: cutaneous primary melanoma PGEM574

description: FFPE

value: HN

value: absent

tag: mutation

tag: tissue


title: S_Leaf at MD, biological rep1

description:
Gene exprssion data from Sensitive Black poplar leaves under moderate drought condition
BP_S_MD_1

value: leaf

value: one year old seedling

value: Drought Sensitive


title: cutaneous primary melanoma PGEM570

description: FFPE

tag: sample id

value: BRAF


title: cutaneous primary melanoma PGEM560

description: FFPE


title: BM-MSC_rep10

source_name: adult origin

value: bone-marrow

value: bone-marrow derived mesenchymal stem cells (BM-MSC)


title: Control_24h_1_(HG-U133A_2).CEL

tag: timie

tag: treatment


title: S_Leaf at WWP, biological rep2

description:
Gene exprssion data from Sensitivet Black poplar leaves under well watered condition
BP_S_WWP_2

source_name: leaves at 100% field capacity

value: WWP


title: cutaneous primary melanoma PGEM010

description: FFPE

value: ext

value: SSM

value: present

value: WT


title: hAMC_rep1

tag: tissue source


title: BM-MSC_rep9

tag: cell type


title: S_Leaf at WWP, biological rep1

description:
Gene exprssion data from Sensitive Black poplar leaves under well watered condition
BP_S_WWP_1

tag: age


title: cutaneous primary melanoma PGEM001

description: FFPE

value: F

tag: subtype


title: BM-MSC_rep8


title: RAI2-4A #2

city: Heidelberg

first: Benedikt

last: Brors

address: Im Neuenheimer Feld 280

department: Div. Applied Bioinformatics

institute: German Cancer Research Center (DKFZ)

description: RAI-4A, replicate#2

hyb_protocol: Standard Illumina Hybridisation Protocol, Part #11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide); 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina HumanHT-12 v4 BeadChip.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  Part #11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide).

data_processing: Bead-level data were aggregated by BeadStudio software. Data was normalized by the quantile method in limma.

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Life Technologies) is used to generate single-stranded cRNA from input amounts of 500ng total RNA (Label: Biotin, Cy3-Streptavidin)

growth_protocol: Cells were grown as monolayers according to standard conditions in either DMEM or RPMI supplemented with 10% fetal calf serum (FCS) (PAA) and 2 mM L-glutamine at 37°C in a humidified atmosphere containing 10% CO2 or 5% CO2, respectively.

extract_protocol: RNA was extracted using Nucleospin RNA Kit (Macherey Nagel) according to the manufacturer's instructions.

treatment_protocol: To produce retroviral particles, φNX-ampho packaging cells were transfected with 4 µg of retroviral expression plasmid using Lipofectamine 2000 (Life Technology). For transduction, 500 µl of viral supernatant was added to 50% confluent recipient cultures in 6-well plates containing 1 ml DMEM + 10% FCS. Positive selection was begun 24 h after transduction using 2 µg/ml puromycin containing medium. Cells were subsequently maintained under puromycin selection for 4 days.

tag: cell line

tag: vector

value: RAI2-4A expression


title: R_Leaf at PDR, biological rep2

description:
Gene exprssion data from Resistant Black poplar leaves under post drought rewatering condition
BP_R_PDR_2

tag: genotype

value: Drought Resistant

value: PDR


title: cutaneous primary melanoma PGEM580

description: FFPE

value: trunk

tag: breslow thickness

tag: ulceration

value: cutaneous primary melanoma tumor


title: cutaneous primary melanoma PGEM588

description: FFPE

tag: gender

value: absent

tag: mitoses


title: RAI2-4A #1

description: RAI-4A, replicate#1


title: RAI2-4A #3

description: RAI-4A, replicate#3


title: R_Leaf at PDR, biological rep1

description:
Gene exprssion data from Resistant Black poplar leaves under post drought rewatering condition
BP_R_PDR_1

value: leaf

value: one year old seedling

tag: water availability regime


title: BM-MSC_rep6


title: BM-MSC_rep7


title: R_Leaf at SD, biological rep2

description:
Gene exprssion data from Resistant Black poplar leaves under severe drought condition
BP_R_SD_2

value: SD


title: RAI2 #3

description: RAI2, replicate#3

value: RAI2 expression


title: BM-MSC_rep5

value: bone-marrow

value: bone-marrow derived mesenchymal stem cells (BM-MSC)


title: R_Leaf at SD, biological rep1

description:
Gene exprssion data from Resistant Black poplar leaves under severe drought condition
BP_R_SD_1


title: cutaneous primary melanoma PGEM578

description: FFPE

tag: site

tag: mitotic rate

tag: mutation

value: BRAF


title: RAI2 #1

description: RAI2, replicate#1


title: BM-MSC_rep4


title: BM-MSC_rep3


title: R_Leaf at MD, biological rep1

description:
Gene exprssion data from Resistant Black poplar leaves under moderate drought condition
BP_R_MD_1

tag: tissue

value: MD


title: RAI2 #2

description: RAI2, replicate#2


title: cutaneous primary melanoma PGEM575

description: FFPE

value: ext

tag: sample id

value: SSM

value: present


title: vector #3

description: control, replicate#3

value: control


title: R_Leaf at WWP, biological rep2

description:
Gene exprssion data from Resistant Black poplar leaves under well watered condition
BP_R_WWP_2

value: Drought Resistant

value: WWP


title: vector #2

description: control, replicate#2


title: BM-MSC_rep2

tag: tissue source


title: R_Leaf at MD, biological rep2

description:
Gene exprssion data from Resistant Black poplar leaves under moderate drought condition
BP_R_MD_2


title: R_Leaf at WWP, biological rep1

description:
Gene exprssion data from Resistant Black poplar leaves under well watered condition
BP_R_WWP_1


title: vector #1

description: control, replicate#1


title: clone42

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: 10ug of biotinylated cRNA were hybridized for 16hr at 45C to the array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Microarray data were normalized using robust multi-array average (RMA)

label_protocol: Biotin-labeled cRNA was synthesized, purified and fragmented using GeneChip 3’IVT Express Kit (Affymetrix).

growth_protocol: Immortalized progenitor cells were plated and grown in DMEM/H medium supplemented with 10% FBS.

extract_protocol: RNA was isolated from clonal cell lines using Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer’s instructions.

tag: subject

value: BAT

tag: mature adipocyte ucp1 (measured by luciferase reporter system)


title: cutaneous primary melanoma PGEM562

description: FFPE

value: trunk

tag: age

value: M

tag: subtype

value: WT

value: cutaneous primary melanoma tumor


title: cutaneous primary melanoma PGEM552

description: FFPE

value: absent


title: cutaneous primary melanoma PGEM572

description: FFPE

value: F


title: cutaneous primary melanoma PGEM016

description: FFPE

value: NRAS


title: cutaneous primary melanoma PGEM009

description: FFPE


title: cutaneous primary melanoma PGEM004

description: FFPE


title: cutaneous primary melanoma PGEM557

description: FFPE


title: cutaneous primary melanoma PGEM583

description: FFPE


title: clone40


title: clone39


title: Fibroblast_rep5

source_name: control

tag: cell type

value: dermal fibroblasts


title: Fibroblast_rep3


title: Fibroblast_rep4


title: clone36


title: cutaneous primary melanoma PGEM007

description: FFPE


title: cutaneous primary melanoma PGEM002

description: FFPE

value: BRAF


title: clone37


title: BM-MSC_rep1

value: bone-marrow

value: bone-marrow derived mesenchymal stem cells (BM-MSC)


title: Fibroblast_rep6


title: Seedlings L7 rep.2

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Biology

institute: University of Arkansas at Little Rock

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

scan_protocol: Scanning of the Affymetrix Tomato GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

organism: Solanum lycopersicum

source_name: 17 day old  Seedlings of InsP 5-ptase tansgenic line  tomato

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix 3' IVT Expression Kit as specified in the GeneChip Expression Analysis Technical Manual (http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf )

growth_protocol: Tomato seedlings were germinated on MS medium (Magenta boxes) in growth chambers at 12 h day-light and 12 h dark. After 10 days seedlings were transferred to continous light (50 umol m-2 s-1) for 7 days.

extract_protocol: After light incubation seedlings were isolated and immediately frozen in liquid nitrogen. The harvested seeds and seedlings  were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen.  Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: No special treatments before harvesting were carried out.

value: 17 day-old seedlings

tag: genotype/variation

value: InsP 5-ptase tansgenic line tomato - Line 7

tag: treatment

value: exposed to continous light for 7 days


title: clone35


title: cutaneous primary melanoma PGEM021

description: FFPE

source_name: UNC

value: HN

value: SC

tag: breslow thickness

tag: ulceration

value: present


title: Seedlings L7 rep.1


title: clone41

value: BAT


title: cutaneous primary melanoma PGEM005

description: FFPE

value: ext

tag: gender

tag: mitoses


title: Fibroblast_rep2


title: clone38


title: Fibroblast_rep1


title: CLL patient 11 cultured with IL-4

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

hyb_protocol: Agilent miRNA Complete Labeling and Hyb and MicroRNA Spike-In kits protocols following the manufacturer's instructions

scan_protocol: Agilent G2565CA scanner, Agilent Scan Control software, scanning at 5µm or at 3µm

data_processing: Agilent Feature Extraction software

source_name: CLL cells cultured for 18 hr with IL-4

growth_protocol: Culture for 18 hr in RPMI-1640 medium supplemented with 10% fetal calf serum

extract_protocol: miRNeasy mini kit (Qiagen) protocol following the manufacturer's instructions

treatment_protocol: 10 ng/ml IL-4 (BD Biosciences) or nothing or IL-4

value: Peripheral blood B lymphocytes

tag: disease state

value: CLL

value: cultured with IL-4


title: Seedlings control rep.1

source_name: 17 day old  Seedlings of wild type tomato

value: Wild type (cv. Micro-Tom)


title: Seedlings control rep.2


title: clone34


title: clone33


title: clone31


title: clone32


title: cutaneous primary melanoma PGEM019

description: FFPE

tag: site

value: trunk

value: M

value: NM

value: absent

tag: mitotic rate

value: cutaneous primary melanoma tumor


title: cutaneous primary melanoma PGEM006

description: FFPE

value: F

tag: mutation

value: NRAS

tag: tissue


title: cutaneous primary melanoma PGEM013

description: FFPE

tag: sample id

value: LMM


title: CLL patient 11 cultured with nothing

source_name: CLL cells cultured for 18 hr with nothing

label_protocol: Agilent miRNA Complete Labeling and Hyb and MicroRNA Spike-In kits protocols following the manufacturer's instructions

value: cultured with nothing


title: cutaneous primary melanoma PGEM569

description: FFPE

source_name: UNM

value: ALM

value: WT


title: cutaneous primary melanoma PGEM014

description: FFPE

value: HN

value: present


title: cutaneous primary melanoma PGEM126

description: FFPE

value: lower extremity

value: BRAF


title: NBC 1 cultured with IL-4

source_name: Normal B cells cultured for 18 hr with IL-4

value: Peripheral blood B lymphocytes

value: cultured with IL-4


title: NBC 1 cultured with nothing

source_name: Normal B cells cultured for 18 hr with nothing


title: cutaneous primary melanoma PGEM556

description: FFPE

value: ext


title: NBC 2 cultured with IL-4


title: clone29

tag: subject

value: BAT


title: clone28

tag: mature adipocyte ucp1 (measured by luciferase reporter system)


title: NBC 3 cultured with IL-4


title: clone26


title: NBC 3 cultured with nothing


title: NBC 2 cultured with nothing


title: clone25


title: clone30


title: CLL patient 16 cultured with IL-4

value: CLL


title: CLL patient 15 cultured with IL-4


title: clone27


title: clone23


title: CLL patient 14 cultured with IL-4


title: clone24


title: CLL patient 13 cultured with IL-4


title: Hypothalamus_WildType_6degC_biorep8

city: Olsztyn

first: Monika

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent Fragmentation Buffer and 2x Agilent Gene Expression Blocking Agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37Â°C Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for G3 Microarray Formats.

data_processing: The scanned images were analyzed with Feature Extraction Software v. 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized among the samples by quantile method. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring GX 12 Software (Agilent).

source_name: Hypothalamus, wild type mouse, 6degC, biological replicate 8

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 spectrophotometer.

extract_protocol: Total RNA from the hypothalamus of 7 Lep-/- and 8 Lep+/+ mice maintained at 24 °C and 8 Lep-/- and 8 Lep+/+ mice maintained at 6 °C was isolated using TRI Reagent and BCP phase separation reagent (Molecular Research Center Inc. Cincinnati, OH, United States). RNA was further purified using the RNAeasy minikit (QIAGEN, Valencia, CA, United States) and stored at -80°C in RNase-free H2O with addition of SUPERase-In (Ambion, Austin, TX, United States) for RNase protection. Quality and quantity of RNA was determined using UV spectrophotometry (Nanodrop). RNA with RNA Integrity number higher than 8.5 (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA) was used for microarray analysis of each individual mouse.

treatment_protocol: Eight week-old wild-type C57BL/6J.Lep+/+ (n=16) and homozygous null C57BL/6J.Lep-/- (n=15) mice of both sexes were individually housed in an environmentally controlled chamber (EHRET GmbH, Emmendingen, Germany). After 3 days of habituation to the chamber environment (24 °C) temperature in the chamber was either maintained at 24 °C or reduced by 3 °C/day to 6 °C at which time mice were kept at 6 °C for additional 2 days (n=7-8/genotype/temperature).

value: hypothalamus

tag: strain

tag: genotype

value: Lep+/+

tag: temperature

value: male

tag: age

value: 9 weeks


title: Hypothalamus_WildType_6degC_biorep7

source_name: Hypothalamus, wild type mouse, 6degC, biological replicate 7

value: female


title: Hypothalamus_WildType_6degC_biorep6

source_name: Hypothalamus, wild type mouse, 6degC, biological replicate 6


title: clone20


title: CLL patient 12 cultured with IL-4

tag: cell type

tag: treatment


title: Hypothalamus_WildType_6degC_biorep5

source_name: Hypothalamus, wild type mouse, 6degC, biological replicate 5


title: CLL patient 8 cultured with IL-4


title: clone21


title: clone19


title: CLL patient 7 cultured with IL-4


title: clone18


title: CLL patient 6 cultured with IL-4


title: Hypothalamus_WildType_6degC_biorep4

source_name: Hypothalamus, wild type mouse, 6degC, biological replicate 4


title: CLL patient 10 cultured with IL-4


title: Hypothalamus_WildType_6degC_biorep2

source_name: Hypothalamus, wild type mouse, 6degC, biological replicate 2


title: clone16


title: CLL patient 9 cultured with IL-4


title: clone15


title: CLL patient 5 cultured with IL-4


title: Hypothalamus_WildType_6degC_biorep1

source_name: Hypothalamus, wild type mouse, 6degC, biological replicate 1


title: Hypothalamus_WildType_24degC_biorep8

source_name: Hypothalamus, wild type mouse, 24degC, biological replicate 8


title: Hypothalamus_WildType_6degC_biorep3

source_name: Hypothalamus, wild type mouse, 6degC, biological replicate 3


title: Hypothalamus_WildType_24degC_biorep7

source_name: Hypothalamus, wild type mouse, 24degC, biological replicate 7


title: clone13


title: clone14


title: Hypothalamus_WildType_24degC_biorep6

source_name: Hypothalamus, wild type mouse, 24degC, biological replicate 6


title: clone12


title: Hypothalamus_WildType_24degC_biorep5

source_name: Hypothalamus, wild type mouse, 24degC, biological replicate 5


title: CLL patient 2 cultured with IL-4

source_name: CLL cells cultured for 18 hr with IL-4


title: CLL patient 4 cultured with IL-4


title: CLL patient 1 cultured with IL-4


title: clone11


title: Hypothalamus_WildType_24degC_biorep4

source_name: Hypothalamus, wild type mouse, 24degC, biological replicate 4


title: Hypothalamus_WildType_24degC_biorep3

source_name: Hypothalamus, wild type mouse, 24degC, biological replicate 3


title: clone9

value: WAT


title: CLL patient 13 cultured with nothing

source_name: CLL cells cultured for 18 hr with nothing

value: cultured with nothing


title: Hypothalamus_WildType_24degC_biorep1

source_name: Hypothalamus, wild type mouse, 24degC, biological replicate 1


title: Hypothalamus_WildType_24degC_biorep2

source_name: Hypothalamus, wild type mouse, 24degC, biological replicate 2


title: clone8


title: CLL patient 12 cultured with nothing


title: Hypothalamus_LepDeficient_6degC_biorep8

source_name: Hypothalamus, Leptin-deficient mouse, 6degC, biological replicate 8

value: Lep-/-


title: CLL patient 16 cultured with nothing


title: clone6


title: clone7


title: CLL patient 14 cultured with nothing


title: clone10


title: CLL patient 15 cultured with nothing


title: CLL patient 10 cultured with nothing


title: Hypothalamus_LepDeficient_6degC_biorep6

source_name: Hypothalamus, Leptin-deficient mouse, 6degC, biological replicate 6


title: Hypothalamus_LepDeficient_6degC_biorep7

source_name: Hypothalamus, Leptin-deficient mouse, 6degC, biological replicate 7


title: Hypothalamus_LepDeficient_6degC_biorep5

source_name: Hypothalamus, Leptin-deficient mouse, 6degC, biological replicate 5


title: clone4


title: CLL patient 9 cultured with nothing


title: CLL patient 8 cultured with nothing


title: CLL patient 7 cultured with nothing


title: clone2


title: CLL patient 5 cultured with nothing


title: CLL patient 6 cultured with nothing


title: Hypothalamus_LepDeficient_6degC_biorep3

source_name: Hypothalamus, Leptin-deficient mouse, 6degC, biological replicate 3


title: CLL patient 4 cultured with nothing


title: Hypothalamus_LepDeficient_6degC_biorep1

source_name: Hypothalamus, Leptin-deficient mouse, 6degC, biological replicate 1


title: Hypothalamus_LepDeficient_6degC_biorep2

source_name: Hypothalamus, Leptin-deficient mouse, 6degC, biological replicate 2


title: clone3


title: Hypothalamus_LepDeficient_6degC_biorep4

source_name: Hypothalamus, Leptin-deficient mouse, 6degC, biological replicate 4


title: Hypothalamus_LepDeficient_24degC_biorep6

source_name: Hypothalamus, Leptin-deficient mouse, 24degC, biological replicate 6


title: Hypothalamus_LepDeficient_24degC_biorep7

source_name: Hypothalamus, Leptin-deficient mouse, 24degC, biological replicate 7


title: CLL patient 1 cultured with nothing


title: clone1


title: Hypothalamus_LepDeficient_24degC_biorep3

source_name: Hypothalamus, Leptin-deficient mouse, 24degC, biological replicate 3


title: Hypothalamus_LepDeficient_24degC_biorep4

source_name: Hypothalamus, Leptin-deficient mouse, 24degC, biological replicate 4


title: CLL patient 7 before culture

source_name: CLL cells

value: before culture


title: CLL patient 8 before culture


title: CLL patient 5 before culture


title: CLL patient 4 before culture


title: CLL patient 6 before culture


title: CLL patient 2 cultured with nothing


title: Control/Mixture_11

city: Chott-Mariem

first: Mohamed

last: Banni

state: Sousse

address: Route Touristique

department: Life sciences

country: Tunisia

institute: Higher Institut of Agronomy

hyb_protocol: 43°C, 16/20 h, hybridization buffer Northern Max (Ambion). Pre-hybridization for 1h in same conditions.

scan_protocol: Scanned on Chip Reader (Applied biosystems Laboratories) at 5 µm resolution

data_processing: Offset background subtracted, loess normalized. Data obtained from log2 of processed Ch1 signal / processed Ch2 signal. LIMMA software was used

organism: Mytilus galloprovincialis

source_name: Digestive gland tissue, Control individual samples

label_protocol: 15 µg of total RNA were primed with 0.5 µg oligodT(19)VN primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U ReverseAid MuLV H minus  RTase (Fermentas), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP or Cy5-label dCTP

extract_protocol: Total RNA extracted from the digestive gland of a pool made from 4 mussel using Trizol following manufacturer's instructions

tag: agent

value: control

value: digestive gland

source_name: Digestive gland tissue, individual samples exposed to binary mixture

value: binary mixture of TCDD and n-TiO2


title: CLL patient 3 before culture

value: Peripheral blood B lymphocytes


title: CLL patient 2 before culture


title: Hypothalamus_LepDeficient_24degC_biorep1

source_name: Hypothalamus, Leptin-deficient mouse, 24degC, biological replicate 1

tag: gender


title: clone22


title: Control/n-TiO2_8

source_name: Digestive gland tissue, individual samples exposed to n-TiO2


title: Hypothalamus_LepDeficient_24degC_biorep5

source_name: Hypothalamus, Leptin-deficient mouse, 24degC, biological replicate 5


title: Control/Mixture_12


title: Control/Mixture_9


title: Hypothalamus_LepDeficient_24degC_biorep2

source_name: Hypothalamus, Leptin-deficient mouse, 24degC, biological replicate 2


title: Control/n-TiO2_6


title: Control/TCDD_1

source_name: Digestive gland tissue, individual samples exposed to TCDD

value: TCDD


title: Control/n-TiO2_5


title: Control/TCDD_2


title: Control/n-TiO2_7


title: Control/Mixture_10


title: CLL patient 1 before culture


title: Control/TCDD_3


title: Control/TCDD_4


title: 12715491-HTB133-24h

status: Public on Jun 13 2015

city: Calgary

first: Don

last: Morris

address: 1331, 29th Street, NW

department: Oncology

country: Canada

institute: Tom Baker Cancer Centre

description: Cy5/Cy3 part 2 (Reverse)

hyb_protocol: Labeled cDNA was column purified and hybridized into 14 K oligo gene chips (manufactured at the Southern Alberta Microarray Facility), and incubated overnight.

scan_protocol: Following washing and scanning, the signal intensity was quantified and analyzed using “Gene traffic” software.

data_processing: The raw data was collected by QuantArray 3.0. LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Gene traffic software was used for further analysis.

source_name: HTB 133 Breast cancer cell line treated with reovirus for 24 hours

label_protocol: Twenty five micrograms of RNA was reverse transcribed to cDNA by use of a FairPlay microarray labeling kit (Stratagene)and labeled with Cy3 and Cy5 (Amersham) via the dye coupling method.

growth_protocol: MCF7 and HTB133 cells were grown in 6 well plates until 75% confluent.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and quantified.  RNA was then subjected to DNase treatment and the intergrity of the purified RNA was confirmed following gel analysis

treatment_protocol: Cells were infected with reovirus for 12 or 24 hours.

tag: cell line

value: breast cancer

source_name: Un-infected HTB 133


title: 12715490-HTB133-24h

description: Cy3/Cy5 part 2


title: 12715493-HTB133-24h

description: Cy5/Cy3 part 1 (Reverse)


title: 12715513-HTB133-12h

description: Cy5/Cy3 part 2 (Reverse)

source_name: HTB 133 Breast cancer cell line treated with reovirus for 12 hours


title: 12715492-HTB133-24h

description: Cy3/Cy5 part 1


title: 12739676-MCF7-24h

description: Cy5/Cy3 part 2 (Reverse)

source_name: MCF7 Breast cancer cell line treated with reovirus for 24 hours

source_name: Un-infected MCF7


title: 12712912-HTB133-12h

description: Cy3/Cy5 part 1


title: 12739275-MCF7-24h

description: Cy5/Cy3 part 1 (Reverse)


title: 12715512-HTB133-12h

description: Cy3/Cy5 part 2


title: 12739675-MCF7-24h

description: Cy3/Cy5 part 2


title: 12712913-HTB133-12h

description: Cy5/Cy3 part 1 (Reverse)


title: Human thyroid tumor cells 8505C expressing Engr HD (-Dox) TTF1 antagonist

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

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

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

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

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

growth_protocol: Transformed 8505C cells expressing the doxycycline-dependent tTA transactivator from a pEFIN4 construct were selected in the presence of 400µg/mL geneticin (GIBCO) and maintained in culture medium supplemented with 200µg/mL of the agent. The pTRE2hyg-Luc construct (Clontech) was used to select the tTA-expressing 8505C clone displaying the best response to doxycycline withdrawal. For the isolation of the clones transformed with the pTRE2hyg construct driving the conditional expression of EngrHD or EngrHDm, cells were transfected in culture medium supplemented with 200 µg/mL of geneticin and 2 µg/mL of doxycycline (Sigma-Aldrich) and then selected in the presence of 200 µg/mL of both geneticin and hygromycin (HygroGold, InvivoGen) and 2 µg/mL of doxycycline.

extract_protocol: Total RNA was obtained from cells at 80-90 % confluency maintained in the presence or absence of doxycycline for one week using the RNeasy mini kit from Invitrogen.

treatment_protocol: Transformed 8508C cells harbouring the Engr-HD-producing construct were grown in the continuous presence of doxycycline, then cell population was split into two pools and maintained in culture for a further 7 days period, either in the presence or in the absence of the agent.

value: human thyroid tumor cells

tag: transformed with

value: Engr-HD-producing construct

tag: culture

value: absence of doxycycline (expressing Engr-HD)

source_name: Human thyroid tumor cells 8505C_not expressing Engr HD (+Dox)

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


title: Human thyroid tumor cells 8505C expressing Engr HD (-Dox) control protein

source_name: Human thyroid tumor cells 8505 expressing control Engr HDm (-Dox)

value: Engr-HDm-producing construct

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


title: MDA-231_shSOX4#1_rep3.

city: Nijmegen

first: Arthur

middle: J

last: Kuipers

address: PO Box 9101

country: Netherlands

institute: Radboudumc

description: replicate 3

hyb_protocol: according to the Illumina Manual “Direct Hybridization Assay Guide

scan_protocol: Illumina iScan

data_processing: Illumina GenomeStudio v2011.1 Gene Expression Software  Expression software

source_name: MDA-MB-231 breast cancer cells (American Type Culture Collection), transduced with SOX4 shRNA

label_protocol: Illumina HumanHT-12 v4

growth_protocol: Cultured in DMEM supplemented with Glutamax, 10% fetal bovine serum and 1% pen/strep

extract_protocol: RNA was extracted with RNeasy Minikit (Qiagen), followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Transduced with scrambled or SOX4 shRNA

tag: transduced with

value: SOX4 shRNA


title: CD19+ B cells from miR-142  KO mouse #1

city: Duarte

first: Mark

middle: P

last: Boldin

address: 1500 E. Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute of the City of Hope

description: Gene expression data from CD19+ KO B cells

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: Data extracted using Expression Console

source_name: Purified CD19+ B cells

label_protocol: Biotinylated cRNA was prepared using Single-Round RNA Amplification and Biotin Labeling System (Enzo)

extract_protocol: Qiagen miRNeasy kit

treatment_protocol: no treatmeant

tag: mouse strain

value: B cell


title: CD19+ B cells from miR-142  KO mouse #3

tag: tissue


title: CD19+ B cells from WT mouse #1

description: Gene expression data from CD19+ WT B cells


title: 12715489-MCF7-12h

description: Cy5/Cy3 part 2 (Reverse)

source_name: MCF7 Breast cancer cell line treated with reovirus for 12 hours


title: 12739274-MCF7-24h

description: Cy3/Cy5 part 1


title: CD19+ B cells from WT mouse #2


title: MDA-231_shCntrl_rep2.

description: replicate 2

source_name: MDA-MB-231 breast cancer cells (American Type Culture Collection), transduced with scrambled shRNA

value: scrambled shRNA


title: MDA-231_shT7#1_rep2

description: replicate 2

source_name: MDA-MB-231 breast cancer cells (American Type Culture Collection), transduced with TRPM7 shRNA

treatment_protocol: Transduced with scrambled or TRPM7 shRNA

value: TRPM7 shRNA


title: MDA-231_shCntrl_rep3.

description: replicate 3


title: MDA-231_shCntrl_rep1.

description: replicate 1


title: MDA-231_shSOX4#1_rep1.

description: replicate 1


title: MDA-231_shCntrl_rep1

description: replicate 1


title: clone17

value: BAT


title: 12715451-MCF7-12h

description: Cy5/Cy3 part 1 (Reverse)


title: 12715450-MCF7-12h

description: Cy3/Cy5 part 1


title: MDA-231_shSOX4#1_rep2.

description: replicate 2


title: MDA-231_shCntrl_rep2

description: replicate 2


title: 12715488-MCF7-12h

description: Cy3/Cy5 part 2


title: dnaA null rok null Replicate 3

city: Cambridge

first: Alan

middle: D.

last: Grossman

address: 31 Ames Street, 68-530

institute: MIT

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAS192-3

hyb_protocol: Salmon testes DNA and yeast tRNA were added, and each cDNA sample was hybridized to a DNA microarray at 42 °C overnight.

scan_protocol: Scanned on a GenePix 4000B scanner. Images were quantified using GenePix 3.0 (Axon Instruments).

data_processing: Loess normalized and background subtracted using the R statistical software package Linear Models for Microarray Data (LIMMA).

organism: Bacillus subtilis

source_name: CAS192 total RNA

label_protocol: 10 µg of each RNA sample was reverse transcribed using Superscript II reverse transcriptase (Invitrogen), random hexamers, and aminoallyl-dUTP (Ambion). The cDNA was labeled by conjugation to monofunctional Cy3 or Cy5 dyes (Amersham) for reference or experimental samples, respectively.  Each experimental sample was mixed with an aliquot of reference sample.

growth_protocol: 30C in defined minimal medium + 0.1 mM IPTG (to induce expression of DnaA from the LacI-repressible, IPTG-inducible promoter Pspank, which is present in the dnaA+ strains CAL2083 and CAS196)

extract_protocol: Cultures were fixed with an equal volume of -20C methanol.  RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.

value: dnaA null; rok null

tag: replication genotype

value: oriC- oriN+

source_name: Reference RNA

tag: reference type

value: Includes pooled total RNA from B. subtilis cultures grown in defined minimal medium and cultures treated with DNA-damaging agents


title: dnaA null rok null Replicate 2

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAS192-2


title: dnaA null rok null Replicate 1

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAS192-1


title: rok null Replicate 3

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAS196-3

source_name: CAS196 total RNA

value: rok null


title: dnaA null Replicate 2

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAL2074-2

source_name: CAL2074 total RNA

value: dnaA null


title: MDA-231_shT7#1_rep1

description: replicate 1

value: breast cancer


title: rok null Replicate 2

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAS196-2


title: rok null Replicate 1

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAS196-1


title: dnaA null Replicate 1

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAL2074-1


title: dnaA null Replicate 3

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAL2074-3


title: ARR1∆DDK:GR, PAC+dexamethasone, biological replicate 2

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

description:
ARR1_PAC_DX_2
Gene expression data in response to ARR1 in the presence of DELLA proteins

hyb_protocol: Fragmented aRNA  was hybridized to Arabidopsis Genome ATH1 Arrays for 16 hours at 45°C (at 60 rpm) (Affymetrix GeneChip® Hybridization, Wash, and Stain Kit, catalogue number 900720).Arrays were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: Expression estimates were calculated using gcRMA implemented in R with standard settings. Statistical analysis was performed using Z-score transformation, and selecting differential genes with p<0.05.

organism: Arabidopsis thaliana

label_protocol: Arabidopsis RNA samples were processed and biotin labeled for array hybridization using the GeneChip 3’ IVT Express Kit from Affymetrix(Affymetrix, catalogue number 901229)

growth_protocol: Arabidopsis thaliana (Columbia accession) and transgenic line 35S::ARR1∆DDK-GR seeds were sown on MS plates after sterilization. Plants were grown at 22ºC under continuous light (~50 μmol m−2 s−1).

extract_protocol: Total RNA was extracted from the whole tissue of 5-day-old plants with the RNeasy Plant Mini Kit (Qiagen) following manufacturer’s instructions.

treatment_protocol: 5-day-old seedlings were transferred to liquid MS, subsequently treatments were performed by adding the respective chemicals at the following timings and concentrations: 10 μM paclobutrazol or 10 μM paclobutrazol + 50 μM GA3 for 18 hours and 5μM dexamethasone or 5 µM N6-benzyladenine (BA) for 3 hours.

tag: ecotype background

tag: genotype/variation

value: transgenic line 35S::ARR1{delta}DDK-GR

value: 6-day-old seedlings

tag: treated with

value: 10 μM paclobutrazol + 5μM dexamethasone


title: Columbia-0, dexamethasone biological replicate 2

description:
COL_DEX_2
Gene expression data in response to dexamethasone

value: wild type

value: 5μM dexamethasone


title: ARR1∆DDK:GR, PAC+GA3, biological replicate 2

description:
ARR1_PAC_GA_2
Gene expression data in the absence of DELLAs

value: 10 μM paclobutrazol + 50 μM GA3


title: Columbia-0, untreated, biological replicate 2

description:
COL_MOCK_2
Gene expression data in basal conditions

value: none (untreated control)


title: Columbia-0, dexamethasone biological replicate 1

description:
COL_DEX_1
Gene expression data in response to dexamethasone


title: crdS knockout in H. pylori 26695 +NO

city: Sacramento

first: CHIU-LIEN

last: HUNG

address: 4645 2nd Ave

institute: UCDMC

description: deltacrdS +NO

hyb_protocol: standard NimbleGen protocol

scan_protocol: GenePix 4000B,  adjusting the PMT gain for each image as recommended

data_processing: Image analysis was performed with the NimbleScan software (NimbleScan™ 2.3), and feature intensities were exported as .pair files. ArrayStar 2.0 was used for probe summarization and normalization (RMA algorithm, quantile normalization), statistical analysis of differentially expressed genes (Student's t-test with Benjamini-Hochberg false discovery rate correction) and gene ontology analysis.

organism: Helicobacter pylori 26695

source_name: crdS-knockout with NO

label_protocol: Cy3-labeled DNA was performed accoding to the Nimblegen protocol

extract_protocol: RNeasy mini kit (QIAGEN)

treatment_protocol: For NONOate treatment, bacteria grown to logarithmic phase in liquid broth were diluted to 1.2 × 10^9 ml-1 in fresh Brucella broth and incubated with 40 μM NO at 37°C.

value: crdS-knockout

value: nitric-oxide (NO)


title: ARR1∆DDK:GR, PAC+GA3, biological replicate 1

description:
ARR1_PAC_GA_1
Gene expression data in the absence of DELLAs


title: Columbia-0, PAC+benzyladenine, biological replicate 2

description:
COL_PAC_CK_2
Gene expression data in response to cytokinin in the presence of DELLA proteins

value: 10 μM paclobutrazol +  5 µM N6-benzyladenine (BA)


title: Columbia-0, untreated, biological replicate 1

description:
COL_MOCK_1
Gene expression data in basal conditions


title: ARR1∆DDK:GR, PAC+GA3+dexamethasone, biological replicate 2

description:
ARR1_PAC_GA_DX_2
Gene expression data in response to ARR1 in the absence of DELLAs

value: 10 μM paclobutrazol + 50 μM GA3 + 5μM dexamethasone


title: Columbia-0, PAC+GA3+benzyladenine, biological replicate 2

description:
COL_PAC_GA_CK_2
Gene expression data in response to cytokinin in the absence of DELLA proteins

value: 10 μM paclobutrazol + 50 μM GA3 + 5 µM N6-benzyladenine (BA)


title: Control dnaA+ rok+ Replicate 3

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAL2083-3

source_name: CAL2083 total RNA

tag: strain

tag: genotype

value: control

value: oriC- oriN+


title: H. pylori 26695 +NO

description: WT + NO

source_name: with NO treatment


title: crdS knockout in H. pylori 26695 -NO

description: deltacrdS -NO

source_name: crdS-knockout without NO

value: none (control)


title: ARR1∆DDK:GR, PAC+GA3+dexamethasone, biological replicate 1

description:
ARR1_PAC_GA_DX_1
Gene expression data in response to ARR1 in the absence of DELLAs


title: Columbia-0, PAC+benzyladenine, biological replicate 1

description:
COL_PAC_CK_1
Gene expression data in response to cytokinin in the presence of DELLA proteins


title: ARR1∆DDK:GR, PAC+dexamethasone, biological replicate 1

description:
ARR1_PAC_DX_1
Gene expression data in response to ARR1 in the presence of DELLA proteins


title: ARR1∆DDK:GR, PAC, biological replicate 2

description:
ARR1_PAC_2
Gene expression data in the presence of DELLA proteins

value: 10 μM paclobutrazol


title: H. pylori 26695 -NO

description: WT -NO

source_name: without NO


title: Control dnaA+ rok+ Replicate 2

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAL2083-2

value: Includes pooled total RNA from B. subtilis cultures grown in defined minimal medium and cultures treated with DNA-damaging agents


title: Control dnaA+ rok+ Replicate 1

description:
citation for reference RNA: Goranov AI, Breier AM, Merrikh H, Grossman AD. YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress. Mol Microbiol 2009 Oct;74(2):454-66. PMID: 19737352
CAL2083-1


title: ARR1∆DDK:GR, PAC, biological replicate 1

description:
ARR1_PAC_1
Gene expression data in the presence of DELLA proteins

value: transgenic line 35S::ARR1{delta}DDK-GR


title: VH-D7-2

status: Public on Jun 12 2015

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

country: Japan

institute: Japanese Science and Technology Agency

hyb_protocol: Using Agilents Gene Expression Hybridizatoin kit #4 and Gene Expression wash pack #5, Cy3-labeled cRNA preparations were hybridized with rhesus macaque arrays (Agilent Microarray Design Identification Number 015421) for 17 h at 65°C.

scan_protocol: Immediately after washing, Feature Extraction Software, version 7 (Agilent Technologies) was used for image analysis and data extraction.

data_processing: Per chip and per gene normalization was performed using the LIMMA package in R.

source_name: Lung

label_protocol: Using the Quick Amp Labeling Kit, T7 RNA polymerase was used to simultaneously amplify target material and incorporate cyanine 3-labeled CTP to prepare Cy3-labeled cRNA.

extract_protocol: From the homogenized lung tissues, total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s instructions.

treatment_protocol: Mouse lung tissues were placed in RNALater (Ambion, CA), an RNA stabilization reagent and stored at -80°C. All tissues were thawed together and homogenized for 2 minutes at 30 Hz using a TissueLyser (Qiagen, Hilden, Germany) as per the manufacturer’s instructions.

value: lung

tag: animal number

tag: influenza strain

tag: hours post infection

tag: titer (pfu/g)


title: VH-D7-1


title: VL-D7-1


title: VL-D7-2


title: VH-D5-3


title: VL-D5-1


title: VH-D5-2


title: VH-D5-1


title: VH-D7-3


title: VH-9-1


title: VL-9-2


title: VH-9-2


title: VL-D5-3


title: VH-9-3


title: VL-9-1


title: VH-72-3


title: VL-72-3


title: VL-72-2


title: VH-72-1


title: VL-D7-3


title: VL-9-3


title: crdR

description: CrdR

hyb_protocol: Hybridization System and array washes were performed as recommended by NimbleGene

data_processing: Image analysis was performed with the NimbleScan software (NimbleScan™ 2.3), and feature intensities were exported as .pair files. SignalMap 1.9 was used for probe summarization and normalization (RMA algorithm, quantile normalization), statistical analysis of differentially expressed genes (Student's t-test with Benjamini-Hochberg false discovery rate correction) and gene ontology analysis.

source_name: CrdR

label_protocol: The labeling of Cy5-CrdR-IP samples and Cy3-genomic DNA are according to Nimblegen.

extract_protocol: phenol/choloroform

treatment_protocol: H. pylori 26695 genomic DNA was shared by sonicator. Fragments must be between 100 to 1000 bp, with average length of 400 to 500 bp. The recombinant CrdR protein was phoshporylated in virto in a buffer containing 20 mM Tris (pH8.0), and 50 mM acetylphophate (Sigma-Aldrich) for 30 min at room temperature. The recombinant CrdR-phoshporylated protein 80 μg was incubated with 2 μg DNA-sheared for 0.5 hr at room temperature. Incubate 800 μl chromatin solutions with 10 μl primary antibody anti-His (Santa Cruz Biotechnologies) against the protein G beads (Millipore) on end-over-end rotator overnight at 4°C. Microcentrifuge beads 5 min at 3000 rpm at 4°C. Resuspend beads for 3 min each with 800 μl wash buffer, for 6 times. Add 50 μl elution buffer (10 mM Tris (pH 8.0), 1 mM EDTA, 1% SDS) to each tube. Vortex briefly to resuspend the beads and incubate at 65°C for 10 min, and vortex briefly every 2 min during incubation. Add 150 ml Proteinase K Mix (1 × TE, 10 mg/ml Glycogen, 20 mg/ml Proteinase K). Mix by gentle vortexing and incubate for 2 hr at 37°C. Extract with 300 ml phenol: chloroform: iso-propanol (25:24:1), and retain the aqueous phase. To each tube add 13 μl of 5 M NaCl (200 mM NaCl final). Add 700 μl 100% ethanol and vortex to mix. Incubate at -80°C for 30 min. After centrifugation of 14000 rpm for 15 min at 4°C, remove supernatant and wash pellet with 500 μl 70% ethanol and vortex to mix. Centrifuge 14000 rpm for 15 min at 4°C, decant supernatant, and air dry the pellet. Resuspend the pellet in 100 μl.

tag: sample type


title: VL-D5-2


title: control

description: H. pylori 26695

source_name: H. pylori 26695

value: Cy3-genomic DNA


title: CD19+ B cells from miR-142  KO mouse #2

description: Gene expression data from CD19+ KO B cells

value: B cell


title: VL-72-1


title: CD19+ B cells from WT mouse #3

description: Gene expression data from CD19+ WT B cells


title: VH-6-2


title: VH-72-2


title: VH-6-3


title: VL-60-3


title: VL-60-2


title: VH-60-1


title: VL-6-2


title: VH-6-1


title: VL-6-1


title: VL-6-3


title: VL-60-1


title: VL-48-3


title: VH-60-3


title: VH-60-2


title: VL-48-2


title: VL-3-2


title: VH-48-3


title: VL-3-1


title: VH-3-2


title: VH-3-3


title: VL-3-3


title: VH-48-2


title: VH-48-1


title: Columbia-0, PAC+GA3+benzyladenine, biological replicate 1

description:
COL_PAC_GA_CK_1
Gene expression data in response to cytokinin in the absence of DELLA proteins

value: wild type

value: 6-day-old seedlings


title: VL-48-1


title: VH-36-3


title: VH-36-2


title: VL-36-3


title: VL-30-3


title: VH-24-3


title: VL-36-1


title: VH-18-3


title: VH-18-2


title: VH-30-3


title: VH-24-2


title: VL-30-2


title: VL-24-3


title: VL-30-1


title: VH-12-3


title: VL-24-1


title: VH-36-1


title: VH-30-2


title: VH-12-2


title: VL-18-3


title: VH-30-1


title: VH-18-1


title: VL-12-2


title: VH-24-1


title: VL-18-1


title: VH-12-1


title: VL-18-2


title: VL-36-2


title: VL-12-3


title: VL-24-2


title: VL-12-1


title: VH-0-3


title: VL-0-2


title: Embryonal rhabdomyosarcoma in a Costello syndrome patient

city: Goettingen

first: Jan

last: Menke

address: Robert-Koch-Strasse 40

institute: University Hospital Goettingen

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array (Affymetrix GeneChip Hybridization Oven 645) according to the manufacturer's instructions.

scan_protocol: The array was then washed using Affymetrix GeneChip fluidics station 450, and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip Command Console Software. For confirmation, two Cytoscan HD arrays were performed for the tumor which gave similar results. Their raw DAT files were aligned and averaged by a proprietary C++ program (Microsoft, USA) for further analysis. CEL and CYCHP files were generated from the averaged DAT file using Chromosome Analysis Suite 1.2.2 from Affymetrix.
Allele peak data and SNP copy numbers were analyzed. The standard bi-allelic genotype calls (AA, AB, BB) do not apply in the tumor's trisomies. The quality metric "MAPD < 25" was fulfilled. According to the manufacturer the quality metrics "SNPQC" and "Waviness SD" do not apply in this solid tumor (http://media.affymetrix.com/support/help/faqs/cytoscan/cytoscan.pdf).

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from a fresh-frozen tumor sample using the Quiagen Gentra Puregene Kit, as recommended by the Affymetrix CytoScan Assay user manual. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: tumor

tag: disease state


title: VH-0-2


title: VL-0-1


title: VH-0-1


title: C-D5-3

value: SOIV


title: C-D7-3


title: C-D7-2


title: C-D5-2


title: C-D5-1


title: C-D7-1


title: C-9-1


title: C-9-3


title: C-9-2


title: C-60-1


title: C-48-3


title: C-72-3


title: C-6-3


title: C-3-2


title: C-6-2


title: C-6-1


title: C-72-2


title: C-60-3


title: VL-0-3


title: C-60-2


title: C-48-2


title: C-72-1


title: C-48-1


title: C-3-1


title: C-3-3


title: C-36-1


title: C-30-3


title: C-30-1


title: C-24-3


title: C-36-3


title: C-18-2


title: C-24-2


title: C-30-2


title: C-0-1


title: C-12-1


title: C-24-1


title: C-18-3


title: C-12-2


title: C-18-1


title: C-0-3


title: M-D7-1

value: Mock


title: M-D5-1


title: C-0-2


title: C-12-3


title: M-D7-3


title: C-36-2


title: M-D7-2


title: M-D5-2


title: M-72-2


title: M-D5-3


title: M-9-3


title: M-72-3


title: M-6-3


title: M-72-1


title: M-9-1


title: M-9-2


title: M-60-3


title: M-6-2


title: M-60-1


title: M-60-2


title: M-48-2


title: M-6-1


title: M-36-3


title: M-3-3


title: M-48-3