title: T37 II

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

description:
Lab strain.
The sample carries a strong meiotic drive system.

hyb_protocol: Hybridization was performed by NimbleGen Systems, Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems, Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Aedes aegypti

source_name: testes, T37

label_protocol: Labeling was performed by NimbleGen Systems, Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Larvae for both strains were reared on a suspension of bovine liver powder.
Pupae were used for the RNA preparation.

extract_protocol: Testes were dissected from approximately 350 pupae of each strain. The testis samples were homogenized with plastic pestles in TRIZOL reagent (Invitrogen) after removing the RNAlater reagent. Standard phenol-chloroform extractions were then performed and the RNA was precipitated with isopropanol.

tag: phenotype

value: carries a strong meiotic drive system

value: testes

tag: developmental stage

value: pupae


title: PR/Flt3 CD34+ 1020/4

status: Public on Jul 15 2015

type: RNA

city: San Francisco

first: Scott

last: Kogan

state: CA

address: 513 Parnassus, S-561, Box 0451

department: Laboratory Medicine

country: USA

institute: UCSF

description: Gene Expression after  bone marrow harvest and double sorting of populations by flow cytometry (no culture, reflects in vivo settings)

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction 10.1 software, using median feature pixel intensity.

data_processing: The dataset was quantile normalized (ref: Bolstad et al, 2003) without background subtraction. Differential expression analysis using moderated t statistic with Benjamini–Hochberg false discovery rate (adjusted P value) correction was performed using the limma R/Bioconductor package.

molecule: total RNA

organism: Mus musculus

source_name: Bone Marrow PML/RARa transgenic-transduced

label_protocol: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu and http://www.agilent.com). RNA was amplified (2 rounds) and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol. Labeled cRNA was assessed using the Nanodrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole genome mouse 4x44K arrays.

extract_protocol: For the PML/RARA early promyelocytes samples, bone marrow was harvested. Following gradient centrifugation (Histopaque 1119) and CKIT-enrichment, the cell suspension was stained to isolate the populations by flow cytometry. After two rounds of sorting, cells were sorted into Trizol. Following phenol/chloroform extraction, RNA was purified on PicoPure columns (Life technologies #KIT0204). Quality was assessed on the Bioanalyzer. For the leukemic samples, 8 weeks/old PML/RARA bone marrow was harvested and transduced with a Flt3-ITD-GFP retrovirus, and transplanted back into recipients until disease onset. Leukemias were serially passaged until harvest, by sorting GFP+CKIT+GR1+CD34+ cells onto Trizol, and subsequently treated as described for the preleukemic samples

tag: gender

value: female

tag: age

value: >12 weeks

tag: strain

value: FVB/n


title: lung Prdm11 chall_rep3

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

label: biotin

source_name: lung

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

treatment_protocol: Mice were sensitized by i.p. injection of 10 µg OVA in 2 mg alum in 200 µg PBS. Mice were subsequently challenged three time by inhalative exposure to OVA aerosol (1% in PBS) for 30 min for weeks after i.p. injection as described in Alessandrini et al, 2006, J Allergy Clin Immunol.

tag: Sex

tag: genotype/variation

value: Prdm11 knockout mice

value: 35 weeks

tag: mouse id

tag: treatment


title: lung Prdm11 chall_rep4

description: replicate 4

value: challenged three time by inhalative exposure to OVA aerosol (1% in PBS) for 30 min


title: T37 I

tag: tissue


title: PR/Flt3 CD34+ 1087/5-biol-rep


title: PR/Flt3 CD34+ 1127/4-tech-dupl


title: Early PML/RARA promyelocyte #4-tech-dupl

source_name: Bone Marrow PML/RARa transgenic

value: mix male:female (1:1)

value: 3 weeks 5 days


title: PR/Flt3 CD34+ 1087/5


title: T37 III


title: Red III

description:
Lab strain.
The sample is sensitive to the meiotic drive system.

source_name: testes, RED

value: RED

value: sensitive to the meiotic drive system


title: Red II


title: Red I


title: lung wt chall_rep1

description: replicate 1

value: wild type


title: lung wt chall_rep2

description: replicate 2


title: lung Prdm11_rep2

description: replicate 2

value: 22 weeks


title: lung Prdm11 chall_rep2

description: replicate 2


title: lung wt chall_rep4

description: replicate 4


title: lung wt chall_rep3

description: replicate 3


title: lung Cox4 chall rep4

description: replicate 4

value: Cox4-2 mutant line

value: 17 weeks


title: lung Prdm11 chall_rep1

description: replicate 1


title: lung wt_rep4

description: replicate 4


title: lung Prdm11_rep1

description: replicate 1


title: lung Prdm11_rep3

description: replicate 3


title: lung Cox4 chall rep2

description: replicate 2


title: lung Prdm11_rep4

description: replicate 4


title: lung Cox4 chall rep3

description: replicate 3


title: lung wt chall rep2

description: replicate 2


title: lung wt_rep3

description: replicate 3


title: lung wt chall rep4

description: replicate 4


title: lung wt chall rep3

description: replicate 3


title: lung Cox4 chall rep1

description: replicate 1


title: lung wt_rep2

description: replicate 2


title: lung wt chall rep1

description: replicate 1


title: lung_Cox4 rep1

description: replicate 1


title: lung wt_rep1

description: replicate 1


title: lung wt rep4

description: replicate 4


title: lung_Cox4 rep4

description: replicate 4


title: lung_Cox4 rep2

description: replicate 2


title: neonatal mouse exposed to hyperoxia

city: Fukushima

first: Hayato

last: Go

state: Fukushima

address: Hikarigaoka 1

department: Pediatrics

country: Japan

institute: Fukushima Medical University

description:
neonatal mouse exposed to hyperoxia
SAMPLE 2

data_processing: SDS software (Applied Biosystems) was used to collect data.  Threshold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems). Data were processed using Expression Suite Software(Applied Biosystems).

label: FAM

source_name: day3 lung after 72h hyperoxia

label_protocol: Five ul total RNA per sample was reverse-transcripted using Megaplex primers, sets A and B(Applied Biosystems).  PCR amplification was carried out using TaqMan® PreAmp Master Mix (Applied Biosystems) and Megaplex PreAmp Pool (Applied Biosystmes) containing all the primers for detection by TaqMan® Gene Expression Assays for microarray analysis.PCR amplification was carried out using TaqMan® PreAmp Master Mix (Applied Biosystems) and Megaplex PreAmp Pool (Applied Biosystmes) containing all the primers for detection by TaqMan® Gene Expression Assays for microarray analysis.

extract_protocol: Lung samples were obtained from four groups, day3 neonatal mice control, day3 neonatal mice exposed to hyperoxia, adult mice control, and adult mice exposed to hyperoxia. The mice were anesthetized with an intraperitoneal injection of ketamine hydrochloride and xylazine hydrochloride. After the pulmonary artery was perfused with PBS, the right lung was excised and snap-frozen with liquid nitrogen for protein and RNA analyses.

treatment_protocol: Newborn mice (<12 h old) or adult mice (2 months old) were exposed to room air (RA) or hyperoxia (95%) for 72 h. Hyperoxic exposure was conducted in an A-chamber (BioSpherix, Redfield, NY), which allows for continuous monitoring and regulation of oxygen and carbon dioxide. Ambient carbon dioxide was maintained at <1,500 ppm by adjustment of the chamber's ventilation. The dams were switched every 24 h between room air and hyperoxia to avoid injury.

value: lung


title: adult mouse control

description:
adult mouse control
SAMPLE 3

source_name: 2m lung


title: adult mouse exposed to hyperoxia

description:
adult mouse exposed to hyperoxia
SAMPLE 4

source_name: 2m lung after 72h hyperoxia


title: neonatal mouse control

description:
neonatal mouse control
SAMPLE 1

source_name: day3 lung


title: lung wt rep1

description: replicate 1


title: zpl012

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

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

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

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 using the RMA method batch correction for amplficiation assay followed using the three repeated samples assayed by both methods in STATA/SE 11.  Data provided in the spreadsheet are the corrected data. The Median Absolute Deviation (MAD) was calculated for each probe and then ranked to identify the 1000 most varying genes within the dataset (Following samples not included in calculation: dka040, 042 and 044 as these samples are not tumors; dka012, dka016 and dka049 since these were duplicate samples used for correction). Spotfire was used for two-way unsupervised hierarchical clustering and principal component analyses. Initial unsupervised hierarchical analysis used dka012, dka016 and dka049 and found them to cluster with or near their duplicate, so these were not used in the remainder of the analyses.

label: Biotin (One cycle kit)

source_name: colon tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-Cycle protocol).  Some samples were amplified and labeled using the Affyexpress method. Three samples were amplified by both method to serve as basis for batch correction. Biotinylated cRNA were prepared according to the standard Affymetrix one-Cycle protocol).  Some samples were amplified and labeled using the Affyexpress method. Three samples were amplified by both method to serve as basis for batch correction

extract_protocol: Total RNAs were extracted with Trizol reagent (Invitrogen) according to a supplied RNA isolation protocol.

tag: genotype


title: lung wt rep2

description: replicate 2


title: zpl011


title: zpl006

label: Biotin (Affyexpress)

source_name: colitis


title: zpl008


title: zpl009


title: zpl002


title: lung_Cox4 rep3

description: replicate 3


title: zpl003


title: zpl005


title: zpl010


title: zpl004


title: lung wt rep3

description: replicate 3


title: zpl007


title: zpl001


title: Sample 2, 1h TGFb1 treatment

type: other

city: New York

first: Alessia

last: Deglincerti

state: NY

address: 1230 York Ave

institute: The Rockefeller University

scan_protocol: Plates were imaged with an ArrayScan instrument

data_processing: Images were analyzed using custom software written in MATLAB

label: Smad4-GFP, H2B-RFP

molecule: other

source_name: C2C12 cell culture

label_protocol: GFP-Smad4, H2B-RFP

growth_protocol: C2C12 media

treatment_protocol: TGFb1 (2 ng/ml) for 1 or 6 hours

value: 1h TGFb1

tag: cell line


title: Sample 4, 6h TGFb1 treatment

value: 6h TGFb1


title: Sample 3, 6h TGFb1 treatment


title: Early PML/RARA promyelocyte #4


title: PR/Flt3 CD34+ 1127/4

value: female


title: Early PML/RARA promyelocyte #2


title: n5Fi47_25_methylation

type: genomic

city: Moscow

first: Maria

last: Shutova

state: Russia

address: Gubkina 3

department: Epigenetics

country: Russia

institute: Vavilov Institute of General Genetics, Russian Academy of Sciences

description:
fibroblast-derived iPSC line 47, passage 25
7878191161_R05C02

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2; The file unmethylated_and_methylated_signal.txt contains the raw signals and is available on the series record. Raw data are also available in the idat files.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from fibroblast-derived iPSC line 47, passage 25

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: Female

tag: cell type

value: iPSCs


title: n5F_2_methylation

description:
n5-derived fibroblasts, three month differentiation
7878191161_R06C01

source_name: genomic DNA from n5-derived fibroblasts

value: fibroblasts


title: n5F_1_methylation

description:
n5-derived fibroblasts, three month differentiation
7878191161_R05C01


title: n5Fi7_25_methylation

description:
fibroblast-derived iPSC line 7, passage 25
7878191161_R06C02

source_name: genomic DNA from fibroblast-derived iPSC line 7, passage 25


title: n5Fi7_6_methylation

description:
fibroblast-derived iPSC line 7, passage 6
7878191161_R03C02

source_name: genomic DNA from fibroblast-derived iPSC line 7, passage 6


title: n5Ni27_1_methylation

description:
neuron-derived iPSC line 27, passage 19
7878191040_R06C01

source_name: genomic DNA from neuron-derived iPSC line 27, passage 19


title: n5_1_methylation

description:
parental hESC line n5, passage 14, containing DOX-inducible lentiviral insertions
7878191161_R03C01

source_name: genomic DNA from hESM01-OSKMN-DOX-n5 line

value: ESCs


title: ES5_66_methylation

description:
hESM01 ESC line, passage 66
7878191161_R01C01

source_name: genomic DNA from hESM01 ESC line, passage 66


title: ES5_75_methylation

description:
hESM01 ESC line, passage 75
7878191161_R02C01

source_name: genomic DNA from hESM01 ESC line, passage 75


title: n5Ri22_2_methylation

description:
rpe-derived iPSC line 22, passage 16
7878191040_R06C02

source_name: genomic DNA from rpe-derived iPSC line 22, passage 16


title: n5R_1_methylation

description:
n5-derived rpe cells, 4 month differentiation
7878191040_R02C02

source_name: genomic DNA from n5-derived retinal pigment epithelium cells

value: retinal pigment epithelium


title: n5Ni29_2_methylation

description:
neuron-derived iPSC line 29, passage 19
7878191040_R05C01

source_name: genomic DNA from neuron-derived iPSC line 29, passage 19


title: n5Fi7_7_methylation

description:
fibroblast-derived iPSC line 7, passage 6
7878191161_R04C02

source_name: genomic DNA from  fibroblast-derived iPSC line 7, passage 7


title: Sample 1, 1h TGFb1 treatment


title: n5N_2_methylation

description:
n5-derived neurons, one month differentiation
7878191040_R03C01

source_name: genomic DNA from neurons derived from n5 ESC line

value: neurons


title: n5Fi47_9_methylation

description:
fibroblast-derived iPSC line 47, passage 9
7878191161_R01C02

source_name: genomic DNA from fibroblast-derived iPSC line 47, passage 9


title: n5Ri14_1_methylation

description:
rpe-derived iPSC line 14, passage 14
7878191040_R04C02

source_name: genomic DNA from rpe-derived iPSC line 14, passage 14


title: n5_2_methylation

description:
parental hESC line n5, passage 14, containing DOX-inducible lentiviral insertions
7878191161_R04C01


title: n5Ni29_1_methylation

description:
neuron-derived iPSC line 29, passage 19
7878191040_R04C01


title: n5Fi47_12_methylation

description:
fibroblast-derived iPSC line 47, passage 12
7878191161_R02C02

source_name: genomic DNA from fibroblast-derived iPSC line 47, passage 12


title: n5Ri22_1_methylation

description:
rpe-derived iPSC line 22, passage 16
7878191040_R05C02


title: n5R_2_methylation

description:
n5-derived rpe cells, 4 month differentiation
7878191040_R03C02


title: pitx2ab MO2

status: Public on Jul 14 2015

city: Boston

first: Gabriel

last: Musso

state: MA

address: 75 Francis St, Thorn 1123

department: Medicine

institute: Harvard Medical School

description: Gene expression data from embryonic zebrafish (56hpf)

hyb_protocol: Samples were processed by the Boston Children’s Hospital Molecular Genetics Core Facility for hybridization and analysis using Affymetrix Zv9 microarray chips.

data_processing: Microarray data were normalized and processed using the Oligo package for the R statistical framework. Following normalization, values for replicates were averaged, and fold-change over control was calculated for each gene in both pitx2ab and tbx5a morphants.

organism: Danio rerio

source_name: Zebrafish embryos, 56hpf by morphology, injected with pitx2ab morpholino at 1-cell stage

label_protocol: Nort provided

growth_protocol: Samples were collected from three independent experiments of MO-injected siblings and uninjected wildtype controls at 56hpf by morphology.

extract_protocol: RNA was isolated using Trizol LS as per manufacturer's protocol.

treatment_protocol: Either control embryos or embryos injected with the indicated morpholino were staged using a dissection microscope and homogenized

value: dechorionated embryo


title: Negative Control 2

scan_protocol: Samples were processed by the Boston Children’s Hospital Molecular Genetics Core Facility for hybridization and analysis using Affymetrix Zv9 microarray chips.

source_name: Zebrafish embryos, 56hpf by morphology


title: pitx2ab MO3


title: PBMCs sample_TR067

city: Atlanta

first: Monica

middle: L.

last: Rojas-Peña

state: GA

address: 310 Ferst Dr.

department: School of Biology

institute: Georgia Institute of Technology

description: Test

data_processing: We subtracted each Ct from 30, setting missing values to 0.  Since small Ct values correspond to high transcript abundance, this subtraction yields values ranging from 0 (no expression) to 30 (very high abundance). And Then mean normalization was perform using JMP genomics software.  The non-normalized data, normalized data and fold-change data are available on the series record. Fold-changes were calculated by dividing the non-normalized test values by the non-normalized control value. Normalization was not performed for the control sample data.

label: EvaGreen

source_name: Peripheral blood mononuclear cells (PBMCs)

label_protocol: The qRT-PCR was completed in three steps. (1) Total whole blood RNA was converted to single stranded cDNA using polyT priming of reverse transcription, (2) the 96 targeted genes were pre-amplified in a single 13-cycle PCR reaction for each sample following conditions outlined in the manufacturer’s protocol, by combining 100 ng cDNA with the pooled primers and EvaGreen Pre-Amp Mastermix (Fluidigm BioMark™), (3) exonuclease step was perform to clean any unincorporated primers  and (4) qPCR reactions were performed for each sample and individual gene on each sample on a 96×96 array with 30 amplification cycles. Average Ct value was calculated at a point in which every reaction is in the exponential phase to ensure accuracy and precision of amplification.

extract_protocol: Whole blood mRNA was extracted using TempusTM Blood RNA Tube isolation kits provided by the manufacturer Applied Biosystems, and the quality was determined based on the Agilent Bioanalyzer 2100 RNA Integrity score (RIN).

tag: time

value: DX

tag: site

value: Buenaventura

tag: individual


title: PBMCs sample_TR045

description: Test


title: Negative Control 1


title: tbx5 MO1

source_name: Zebrafish embryos, 56hpf by morphology, injected with tbx5 morpholino at 1-cell stage


title: atxrn4-3_heat_1

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

institute: RIKEN CSRS

hyb_protocol: 1650 ng of cRNAs were hybridized to an Arabidopsis Agilent custom  microarrays at 65oC for 17 h, using Gene Expression Hybridization kit. After hybridization, the microarrays were washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The microarrays were scanned by Agilent DNA Microarray Scanner (G2539A ver.C).

data_processing: Raw signal less than 0.01 was adjusted to 0.01 and a 75 percentile normalization was performed for each chip according to Agilent’s data analysis protocol.

organism: Arabidopsis thaliana

source_name: Whole plant

label_protocol: 200 ng of total RNA was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Arabidopsis plants were grown in  petri dish (100 x 25 mm) containing Murashige and Skoog (MS, Nihon Seiyaku, Tokyo, Japan) medium, 0.7%(w:v) agar (Nacalai Tesque, inc., Kyoto, Japan), 1% (w:v) sucrose and pH 5.7 as described previously with minor modification (Oono et al. 2003). Growth condition is 16-h-light/8-h-dark (40-80 μmol photons m-2 sec-1, light period: A.M. 5:00 to P.M. 9:00).

extract_protocol: Total RNA was isolated using Invitrogen’s ConcertTM Plant RNA reagent according to  “small scale mRNA isolation” protocol. Total mRNA was quantified using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, USA). The integrity of mRNA was confirmed using Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: Two week-old WT and atxrn4-3 mutant plants were subjected to heat stress (37oC) and non-stress (22oC) treatments for 1 h.

value: whole plants

value: atxrn4-3 mutant

tag: ecotype

value: Columbia

tag: growth stage

value: 2 week-old plants

value: Heat stress (37oC, 1 h)


title: PBMCs sample_TR121

description: Test

value: Cali


title: atxrn4-3_control_3

value: Non-stress (22oC, 1 h)


title: Negative Control 3


title: n5Ni27_2_methylation

description:
neuron-derived iPSC line number 27, passage 10
7878191040_R01C02

source_name: genomic DNA from neuron-derived iPSC line 27, passage 10


title: pitx2ab MO1


title: PBMCs sample_TR095

description: Test


title: n5_3_methylation

description:
parental hESC line n5, passage 14, containing DOX-inducible lentiviral insertions
7878191040_R01C01

source_name: genomic DNA from hESM01-OSKMN-DOX-n5 line


title: WT_heat_2

value: WT


title: WT_heat_1


title: PBMCs sample_TR085

description: Test


title: atxrn4-3_heat_2


title: PBMCs sample_TR049

description: Test

value: PRE


title: n5N_1_methylation

description:
n5-derived neurons, one month differentiation
7878191040_R02C01

value: Female


title: WT_heat_3


title: tbx5 MO3


title: PBMCs sample_TR001

description: Test


title: tbx5 MO2


title: PBMCs sample_TR058

description: Test


title: PBMCs sample_TR078

description: Test


title: atxrn4-3_control_1


title: PBMCs sample_TR129

description: Test


title: atxrn4-3_heat_3


title: atxrn4-3_control_2


title: WT_control_3


title: WT_control_1


title: WT_control_2


title: PBMCs sample_TR012

description: Test


title: PBMCs sample_TR018

description: Test


title: PBMCs sample_TR111

description: Test


title: PBMCs sample_TR115

description: Test


title: PBMCs sample_TR132

description: Test


title: PBMCs sample_TR031

description: Test


title: PBMCs sample_TR036

description: Test


title: PBMCs sample_TR107

description: Test


title: PBMCs sample_TR011

description: Test


title: PBMCs sample_TR070

description: Test


title: PBMCs sample_TR089

description: Test


title: PBMCs sample_TR104

description: Test


title: PBMCs sample_TR010

description: Test


title: PBMCs sample_TR075

description: Test


title: PBMCs sample_TR128

description: Test


title: PBMCs sample_TR084

description: Test


title: PBMCs sample_TR124

description: Test


title: PBMCs sample_TR079

description: Test


title: PBMCs sample_TR105

description: Test


title: PBMCs sample_TR034

description: Test


title: PBMCs sample_TR080

description: Test


title: PBMCs sample_TR072

description: Test


title: PBMCs sample_TR086

description: Test


title: PBMCs sample_TR093

description: Test


title: PBMCs sample_TR040

description: Test


title: PBMCs sample_TR027

description: Test


title: PBMCs sample_TR026

description: Test


title: PBMCs sample_TR131

description: Test


title: PBMCs sample_TR117

description: Test


title: PBMCs sample_TR083

description: Test


title: PBMCs sample_TR024

description: Test


title: PBMCs sample_TR064

description: Test


title: PBMCs sample_TR073

description: Test


title: PBMCs sample_TR113

description: Test


title: PBMCs sample_TR035

description: Test


title: PBMCs sample_TR041

description: Test


title: PBMCs sample_TR048

description: Test


title: PBMCs sample_TR046

description: Test


title: PBMCs sample_TR116

description: Test


title: PBMCs sample_TR062

description: Test


title: PBMCs sample_TR055

description: Test


title: PBMCs sample_TR127

description: Test


title: PBMCs sample_TR077

description: Test


title: PBMCs sample_TR091

description: Test


title: PBMCs sample_TR096

description: Test


title: PBMCs sample_TR106

description: Test


title: PBMCs sample_TR051

description: Test


title: PBMCs sample_TR021

description: Test


title: PBMCs sample_TR126

description: Test


title: PBMCs sample_TR103

description: Test


title: PBMCs sample_TR066

description: Test


title: PBMCs sample_TR110

description: Test


title: PBMCs sample_TR099

description: Test


title: PBMCs sample_TR023

description: Test


title: human myofubes, spironolactone treated, biological rep 2

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

description: Pooled samples from Lonza Human skeletal muscle myoblasts Lot # 0000418971 and 0000424749

hyb_protocol: Labeled cDNA targets were hybridized to Affymetrix GeneChip® Human Transcriptome Array 2.0for 16 h at 45⁰C rotating at 60 rpm.

scan_protocol: The arrays were washed and stained using the Fluidics Station 450 and scanned using the GeneChip Scanner 3000.

data_processing: For gene expression analysis, arrays were normalized using RMA algorithm in Expression Console and comparisons made in Transcriptome Analysis Console (Affymetrix, Santa Clara, CA).

source_name: normal primary human myotubes

label_protocol: 5.5 µg of cDNA was labeled and fragmented using the GeneChip® WT PLUS reagent kit (Affymetrix, Santa Clara, CA) following the manufacturer's instructions.

growth_protocol: grown in skeletal muscle cell growth medium (SkGM-2 bullet kit; Lonza), containing: 1% bovine serum albumin (BSA), 1% fetuin, 1% insulin, 0.1% human epidermal growth factor (hEGF), 0.1% dexamethasone and 0.1% gentamicin/amphotericin B (GA) and cultured at 37⁰C in 5% CO2.  When cells reached ~80% confluence, they were serum restricted in differentiation media (DMEM supplemented with 2% horse serum (Invitrogen) and 100 U/mL penicillin-streptomycin) for 5 days.

extract_protocol: RNA was isolated using TRIzol reagent (Life Technologies), according to manufacturer’s instructions. RNA concentration was determined spectrophotometrically using a Nanodrop ND-100 (Nanodrop Technologies).  Samples were DNAse treated using RQ1 DNAse (Promega) for 30 minutes at 37⁰C, reaction was stopped with a 25:24:1 phenol: chloroform: isoamyl alcohol mixture (Malinckrodt, Fischer, Sigma) and centrifuged 5 minutes (14,000 x g; room temperature).  A chloroform phase separation was performed; the aqueous layer was removed and ethanol (Fisher) precipitated.  The pellet was washed (75% ethanol), centrifuged (14,000 x g, 10 minutes, 4⁰C), air dried (5 minutes) and re-suspended in autoclaved millipore filtered water.  DNAse treated RNA concentration was determined spectrophotometrically and samples were stored at -80⁰C.  Samples for microarray analysis were further purified using the RNeasy mini kit (Qiagen) RNA cleanup protocol and final RNA concentrations were determined. RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  A 100 ng aliquot of total mRNA was linearly amplified.

treatment_protocol: Myotubes were treated for 48 hours with aldosterone (10 µM) or spironolactone (10 µM) (purchased from Sigma and dissolved in 100% ethanol unless specified otherwise).  Drugs were added directly to existing differentiation media.

value: male

tag: agent

value: spironolactone


title: human myofubes, untreated/vehicle-treated, biological rep 1

description: Pooled samples from Lonza Human skeletal muscle myoblasts Lot # 0000418971 and 0000424751

value: untreated/vehicle


title: human myofubes, untreated/vehicle-treated, biological rep 2

description: Pooled samples from Lonza Human skeletal muscle myoblasts Lot # 0000418971 and 0000424752


title: PBMCs sample_TR114

description: Test


title: PBMCs sample_TR081

description: Test


title: WE68 cell line [miRNA]

city: Yufu

first: Masanori

last: Kawano

address: 1-1 Idaigaoka, Hasama-machi

institute: Oita University

description: Gene expression data from human Ewing's sarcoma cell line

hyb_protocol: The double-strand cDNA was used as a template for in vitro transcription to generate biotin-labeled cRNA. After fragmentation, 12.5 ug of cRNA was hybridized to the GeneChip array for 16 hr.

scan_protocol: The GeneChips were washed and stained using the GeneChip Fluidics Station 450 (Affymetrix) and then scanned with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The microarray numerical values were analyzed using the GeneSpring GX 11.0 software, according to the RMA16 Algorithm: quantile normalization, filter by flags (detected), filter by expression on the normalized data (20.0–100.0th percentile).

source_name: Human Ewing's sarcoma Cell Line

label_protocol: Biotinylated cRNA was synthesized from total RNA using the Affymetrix 3` IVT Express Kit according to manufacturer’s protocols.

growth_protocol: Ewing's sarcoma cells were cultured in a high-glucose medium, DMEM supplemented with 10% FBS and 1% penicillin and streptomycin.

extract_protocol: Total RNA was extracted with the TRizol reagent and cDNA was synthesized according to the manufacturer's protocol.

treatment_protocol: Cultured Cells are removed by treatment with Trypsin-EDTA　when they reach to 70–80% confluence.

value: Mesenchymal cells


title: PBMCs sample_TR003

description: Test


title: hMSC cell line [miRNA]

description: Gene expression data from human mesenchymal stem cell line

source_name: Human Mesenchymal Stem Cell Line

value: hMSC


title: SCCH cell line [miRNA]

value: SCCH


title: RDES cell line [miRNA]

value: RDES


title: human myofubes, untreated/vehicle-treated, biological rep 3

description: Pooled samples from Lonza Human skeletal muscle myoblasts Lot # 0000418971 and 0000424753


title: PBMCs sample_TR052

description: Test


title: SKNMC cell line [miRNA]

value: SKNMC


title: human myofubes, spironolactone treated, biological rep 3

description: Pooled samples from Lonza Human skeletal muscle myoblasts Lot # 0000418971 and 0000424750


title: PBMCs sample_TR112

description: Test

value: Buenaventura


title: SKES1 cell line [miRNA]


title: PBMCs sample_TR090

description: Test


title: human myofubes, aldosterone treated, biological rep 3

description: Pooled samples from Lonza Human skeletal muscle myoblasts Lot # 0000418971 and 0000424747

value: aldosterone


title: PBMCs sample_TR068

description: Test


title: PBMCs sample_TR125

description: Test

value: DX


title: PBMCs sample_TR004

description: Test


title: PBMCs sample_TR029

description: Test


title: PBMCs sample_TR038

description: Test


title: human myofubes, aldosterone treated, biological rep 2

description: Pooled samples from Lonza Human skeletal muscle myoblasts Lot # 0000418971 and 0000424746


title: PBMCs sample_TR122

description: Test


title: CONTROL siRNA_C2

city: Montreal

first: John

middle: H

last: White

state: Quebec

address: Room 1109, McIntyre Medical Buiding, 3655 Prom Sir William Osler

department: Physiology

country: Canada

institute: McGill University

description: Microarray done in The McGill University and Génome Québec Innovation Centreand

hyb_protocol: The fragmented and labeled DNA target was hybridized on Human Gene 2.0 ST arrays (Affymetrix) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix).

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).

data_processing: The Robust Multi-array Average (RMA) was applied.

source_name: CONTROL siRNA

label_protocol: Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).  Sense-strand cDNA was synthesized from 250ng of total RNA using the Affymetrix GeneChip® WT PLUS Reagent Kit according to the manufacturer’s instructions. The cDNA was fragmented and labeled with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix).

growth_protocol: RMPI 1640 + 10% FBS NOT-HI

extract_protocol: RNeasy Plus Mini Kit - QIAGEN

treatment_protocol: SIGNAGENE PEPMUTE reagent protocol

value: monocytic cell line THP-1

tag: protocol

value: control


title: PBMCs sample_TR057

description: Test

value: Cali


title: AHR KNOCKDOWN BY AHR siRNA_A3

source_name: AHR KNOCKDOWN BY AHR siRNA

value: AHR KD


title: CONTROL siRNA_C3


title: PBMCs sample_TR098

description: Test


title: PBMCs sample_TR033

description: Test


title: PBMCs sample_TR022

description: Test

value: PRE


title: CONTROL siRNA_C1


title: human myofubes, aldosterone treated, biological rep 1

description: Pooled samples from Lonza Human skeletal muscle myoblasts Lot # 0000418971 and 0000424745


title: PBMCs sample_TR007

description: Test


title: human myofubes, spironolactone treated, biological rep 1

description: Pooled samples from Lonza Human skeletal muscle myoblasts Lot # 0000418971 and 0000424748


title: PBMCs sample_TR005

description: Test


title: CONTROL siRNA_C4


title: PBMCs Control

description: Control

source_name: Human Normal Tissues from Biochain

value: Control


title: AHR KNOCKDOWN BY AHR siRNA_A4


title: PBMCs sample_TR015

description: Test


title: AHR KNOCKDOWN BY AHR siRNA_A1


title: PBMCs sample_TR019

description: Test


title: FS22 T21

city: Madrid

first: José Ramón

middle: Lamas

last: Lamas

state: MADRID

address: Calle Profesor Martín Lagos s/n. Hospital Clínico san Carlos

department: Rheumatology

country: Spain

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC)

description:
MSCs at day 21 of osteogenic differentiation
SAMPLE 24

data_processing:
After run completion, Ct values were calculated using the SDS 2.4 software (Applied Biosystems) and data were analyzed using the StatMiner® software (Integromics)
Start Activity 1 file(s) uploaded This is the number of files successfully uploaded in this project.
Start Activity Undetermined values replaced by 40.00 This is the value used for replacing undetermined Ct values.
Start Activity Number of experimental factors: 4 Experiment design has one or more experimental factors columns added.
Start Activity 1 plate(s) uploaded This is the number of plates successfully uploaded in this project.
Start Activity 24 sample(s) uploaded This is the number of unique samples successfully uploaded in this project.
Start Activity 46 detector(s) uploaded This is the number of unique detectors from the different samples successfully uploaded in this project.
Start Activity 2304 measurement(s) uploaded This is the number of wells with a valid Ct successfully uploaded in this project.
Start Activity 384 well(s) uploaded This is the number of wells successfully uploaded in this project.
Start Activity Type of experiment: Real-Time qPCR Unless you are using AB miRNA assay version 1.0 cards, 'Type of experiment' should be set as 'Real-Time qPCR'.
Start Activity 162 undetermined well(s) (replaced by Ct 40) Wells with Undetermined Ct are replaced by a high Ct value that can be filter out as not detected during the analysis.
Start Activity 0 empty well(s) Wells with empty Ct found. RealTime StatMiner® will try to impute empty Ct using the biological replicates.
Start Activity Main experimental factor: NewExperimentFactor1.1. One of the experimental factors (or a combination of them) must be selected to perform differential expression studies.
Start Exception Experimental factor name NewExperimentFactor1(1) is R-incompatible (renamed as NewExperimentFactor1.1.) The label of the experimental factor has incompatible characters that will be automaticall renamed.
Qualify Activity 3 well(s) flagged as outlier(s) using Grubbs test Technical replicates were flagged and automatically removed.
Qualify Exception Sample CX18.T0 flagged as outlier (6.78 flags) using MAD test This sample is poorly correlated with its biological replicates. Select biological replicates automatic removal from Project Options tool to automatically discard it.
Qualify Exception Sample CX17.T10 flagged as outlier (7.51 flags) using MAD test This sample is poorly correlated with its biological replicates. Select biological replicates automatic removal from Project Options tool to automatically discard it.
Qualify Exception Sample CX18.T21 flagged as outlier (5.75 flags) using MAD test This sample is poorly correlated with its biological replicates. Select biological replicates automatic removal from Project Options tool to automatically discard it.
Qualify Exception Sample FS15.T0 flagged as outlier (3.48 flags) using MAD test This sample is poorly correlated with its biological replicates. Select biological replicates automatic removal from Project Options tool to automatically discard it.
Filter Activity 2 detector(s) have a Ct value equal to or higher than 38 in at least 3 samples in group control.T0 Detectors with high Ct values were flagged as not amplified.
Filter Activity 1 detector(s) have a Ct value equal to or higher than 38 in at least 3 samples in group control.T10 Detectors with high Ct values were flagged as not amplified.
Filter Activity 3 detector(s) have a Ct value equal to or higher than 38 in at least 3 samples in group control.T21 Detectors with high Ct values were flagged as not amplified.
Filter Activity 3 detector(s) have a Ct value equal to or higher than 38 in at least 4 samples in group case.T0 Detectors with high Ct values were flagged as not amplified.
Filter Activity 2 detector(s) have a Ct value equal to or higher than 38 in at least 4 samples in group case.T10 Detectors with high Ct values were flagged as not amplified.
Filter Activity 3 detector(s) have a Ct value equal to or higher than 38 in at least 4 samples in group case.T21 Detectors with high Ct values were flagged as not amplified.
Normalize Activity 6 candidate endogenous control(s) analyzed using Genorm RealTime StatMiner® has automatically evaluated the optimal endogenous controls.
Normalize Activity Project normalized using hsa-miR-103a-3p, hsa-miR-191-5p, hsa-miR-30c-5p, SNORD49A This is the list of endogenous controls selected to normalize the Ct values.
Differential expression Activity Differential expression using the Parametric test (Limma) This statistical test was used in the differential expression study.
Differential expression Activity Benjamini-Hochberg False Discovery Rate p-value adjustment This method corrected the p-value used in the differential expression study statistical test
Differential expression Activity Adjusted p-value cut-off 0.05 P-value cut-off for statistically significant results was set.
Differential expression Activity Differential expression of case.T0 using control.T0 as background This pair of samples was used in the differential expression experiment.
Differential expression Activity Differential expression of case.T10 using control.T10 as background This pair of samples was used in the differential expression experiment.
Differential expression Activity Differential expression of case.T21 using control.T21 as background This pair of samples was used in the differential expression experiment.
Differential expression Activity Differential expression of case.T10,case.T21 using case.T0 as background This pair of samples was used in the differential expression experiment.
Differential expression Activity Differential expression of case.T21 using control.T10 as background This pair of samples was used in the differential expression experiment.
Differential expression Activity Differential expression of case.T21 using case.T10 as background This pair of samples was used in the differential expression experiment.

label: SYBR® Green

source_name: Bone Marrow MSCs

growth_protocol: MSCs were obtained from bone marrow aspirates and after isolation by plastric adhaerence and expansion MSCs were characterized by flow cytometry and lineage multipotential  Phenotypic characterization of isolated MSCs was performed by flow citometry in a Gallios flow cytometer (Beckman Coulter). Cells recovered at the third passage were washed with PBS prior incubation during 30 minutes at 4ºC with specific phycoerythrin conjugated antibodies and their isotype matched antibodies (all from Miltenyi Biotech). Expression of CD105, CD73 and CD90, and lack of expression of CD45, CD34, and CD14 were the minimal criteria required prior to evaluation of their differentiation potential towards chondrogenic, adipogenic and osteogenic lineages, assessed by histochemical stainings.

extract_protocol: For miRNA RT-PCR, total RNA was isolated with miRCURY isolation kit (Exiqon) and cDNA Synthesis was carried out using 10 ng of RNA and the Universal cDNA synthesis kit II (Exiqon). Following reverse transcription, cDNAs were 1:100 diluted and loaded onto the real time PCR plates using a 1:1 mixture of Exilent SYBR Green master mix 2x (Exiqon). Real Time PCR reactions were performed in a 7900HT Fast Real time PCR System (Applied Biosystems) under the following conditions: 95˚C 10min, 45 cycles of 95 ˚C 10s and 60 ˚C 1min.

treatment_protocol: Osteogenic differentiation cultures were performed in 24-well tissue culture plates at a seeding density of (30,000 cells/cm2) using commercial culture media with supplements according to manufacturer instructions (Promocell Cat# C-28013)

value: Bone Marrow MSCs

tag: differentiation

value: day 21 of osteogenic differentiation

tag: group

value: Non OA Fracture


title: Abamectin resistant strain-2

city: Beibei

first: Zhifeng

last: Xu

state: Chongqing

address: Tiansheng street 2#

country: China

institute: Southwest University

description: Gene expression after Abamectin treatment-2

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Tetranychus cinnabarinus

source_name: Abamectin treatment

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The laboratory CSM population was derived by transferring the CSMs growing on cowpea (Vigna sesquipedalis Koern) leaves from the field of Beibei District, Chongqing municipality, China to fresh potted cowpea leaves in the lab, and had been raised in artificial climate chamber for 14 years without any insecticide. The rearing conditions were: 26 ±1℃ temperature, 35% to 55% humidity, and 14:10 (L: D) photoperiod.

extract_protocol: Total RNA was extracted from 3-day-adult-mites using the RNeasy plus Micro Kit kit (Qiagen, Hilden, Germany). Genomic DNAs were removed using a genomic DNA elimination column supplied with the kit.

treatment_protocol: The Susceptible strain (SS) (from Beibei District, Chongqing mulicipality, China in 1998), susceptible to all pesticides. The Fenpropathrin resistant strain (FeR, the resistance radio was about 100-fold). AbR, the resistant strain generated from selection with abamectin on the SS strain, the resistance radio is up to 30-fold. The cyflumetofen resistant strain (CyR, the resistance radio was about 9-fold).

tag: strain resistance

value: abamectin

value: full body

tag: gender

value: Female

tag: developmental stage

value: adult

tag: age

value: 3 day old


title: FS22 T10

description:
MSCs at day 10 of osteogenic differentiation
SAMPLE 23

tag: tissue

value: day 10 of osteogenic differentiation


title: Cyflumetofen resistant strain-1

description: Gene expression after Cyflumetofen treatment-1

source_name: Cyflumetofen treatment

value: cyflumetofen


title: Cyflumetofen resistant strain-2

description: Gene expression afterCyflumetofen treatment-2


title: FS17 T21

description:
MSCs at day 21 of osteogenic differentiation
SAMPLE 21


title: FS22 T0

description:
MSCs at day 0 of osteogenic differentiation
SAMPLE 22

value: day 0 of osteogenic differentiation


title: Abamectin resistant strain-1

description: Gene expression after Abamectin treatment-1


title: Fenpropathrin resistant strain-2

description: Gene expression after Fenpropathrin treatment-2

source_name: Fenpropathrin treatment

value: fenpropathrin


title: Susceptible strain-1

description: Gene expression of original sample-1

source_name: original

value: susceptible


title: FS17 T10

description:
MSCs at day 10 of osteogenic differentiation
SAMPLE 20


title: FS17 T0

description:
MSCs at day 0 of osteogenic differentiation
SAMPLE 19


title: CX25 T0

description:
MSCs at day 0 of osteogenic differentiation
SAMPLE 13

value: Coxarthrosis


title: CX25 T21

description:
MSCs at day 21 of osteogenic differentiation
SAMPLE 15


title: FS15 T0

description:
MSCs at day 0 of osteogenic differentiation
SAMPLE 16


title: CS25 T10

description:
MSCs at day 10 of osteogenic differentiation
SAMPLE 14


title: CX19 T10

description:
MSCs at day 10 of osteogenic differentiation
SAMPLE 11


title: CX19 T0

description:
MSCs at day 0 of osteogenic differentiation
SAMPLE 10


title: FS15 T10

description:
MSCs at day 10 of osteogenic differentiation
SAMPLE 17


title: CX19 T21

description:
MSCs at day 21 of osteogenic differentiation
SAMPLE 12


title: FS15 T21

description:
MSCs at day 21 of osteogenic differentiation
SAMPLE 18


title: Susceptible strain-2

description: Gene expression of original sample-2


title: SAMPLE_170 MNC

city: Adelaide

first: Richard

last: D'Andrea

address: P4-40, City East Campus

country: Australia

institute: University of South Australia

hyb_protocol: as per manufacturer's instructions

scan_protocol: as per manufacturer's instructions

data_processing: Background correction using the negative control probes to estimate the parameters of a Robust Multi Array Average (RMA) like model.  Background corrected data was then log2-transformed and data normalised using Robust Spline Normalization.  Detection above background (DABG) was also performed to select for probes with sufficiently adequate p value.

source_name: Bone Marrow Mononuclear Cells

label_protocol: as per manufacturer's instructions

extract_protocol: RNA isolated using a Qiagen Rneasy Micro Kit as per manufacturer's instructions

value: Bone Marrow Mononuclear Cells

tag: source*

value: Adelaide

value: Unknown

tag: fab

value: MNC

tag: exome capture id

tag: fa/brca-hrr network mutants


title: PBMCs sample_TR076

description: Test

source_name: Peripheral blood mononuclear cells (PBMCs)

tag: time

tag: site

value: Buenaventura


title: SAMPLE_164 AML

source_name: Bone Marrow

value: Bone Marrow

value: F


title: CX18 T21

description:
MSCs at day 21 of osteogenic differentiation
SAMPLE 9

value: Bone Marrow MSCs

value: day 21 of osteogenic differentiation


title: AhNF-YC OE normal conditions

city: Irapuato

first: John P

last: Délano-Frier

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Biotechnology and Biochemistry

country: Mexico

institute: CINVESTAV Irapuato

description: Plants were subjected to normal growth conditions

hyb_protocol: For pre-hybridization, the slide was re-hydrated with water vapor at 60ºC and fixed with two cycles of UV ligth. Then, the slide was submerged in boiling water for two minutes (92ºC) and washed with 95% ethanol for one minute. After that, the oligo array was prepared for hybridization in a buffer solution 5X SSC, 0.1% SDS and 1% BSA for one hour at 41ºC. Finally, the array was washed and dried for hybridization. Equal quantities of labeled cDNA were hybridized to the Arabidopsis array using hybridization solution UniHyb (TeleChem International INC) for 14 hr at 42ºC.

scan_protocol: Scanned on an ScanArray 4000 scanner with ScanArray 4000 software from Packard BioChips.

data_processing: The analysis of the microarray data: background correction, Lowess normalization, intensity filter and selection of differentially expressed genes, was performed with the software genArise (http://www.ifc.unam.mx/genarise/). The identification of differentially expressed genes was done by the calculation of a Z score using a sliding-window approach, where the algorithm calculates the mean and standard deviation (SD) within a window surrounding each data point to define a Z score, where Z is the number of SD a data point is from the window mean. To obtain the Z score, the next formula was applied, zi = (Ri - mean(R))/sd(R), where zi is the Z score for a given data point, Ri is the log ratio of signal intensity for each element, mean(R) and sd(R) are the mean and SD of the log ration of signal intensity of the surrounding window. Only the elements with an absolute Z score greater than 2 were considered differentially expressed (|Zscore| > 2) (Cheteleadle et al., 2003).

source_name: Rosette leaves, 5-week old Wt plants_normal_growth

label_protocol: Total RNA were used for cDNA synthesis incorporating Alexa555 or Alexa647 making use of First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was tested by measuring the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: Arabidospis plants were grown in controlled conditions of light (photosynthetic photon flux density (PPFD) of ≈ 200 µmol m-2 s-1), photoperiod (16 h light/ 8 h dark) and temperature (22 ± 1°C).

extract_protocol: Total RNA was extracted from 100–200 mg of frozen rosette tissue with the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions, with modifications. These consisted of the addition of a salt solution (sodium citrate 0.8 M + 1.2 M NaCl) during precipitation in a 1:1 v/v ratio with isopropanol and further purification with LiCl (8 M) for one hour at 4°C. All RNA samples were analyzed by formaldehyde agarose gel electrophoresis and visual inspection of the ribosomal RNA bands upon ethidium bromide staining.

treatment_protocol: In specified cases, plants were subjected to 5 days of water stress. Tissue was collected at day 5 and 24 hrs later after the reestablishment of normal watering.

tag: ecotype

tag: genotype

value: wildtype

value: rosette leaves

value: 5-week old

source_name: Rosette leaves, 5-week old transgenic plants_normal_growth

value: Transgenic AhNF-YC-OE


title: SAMPLE_168 AML

value: ALLG

value: Y


title: CX18 T10

description:
MSCs at day 10 of osteogenic differentiation
SAMPLE 8

value: day 10 of osteogenic differentiation


title: SAMPLE_157 CML

value: CML


title: CX18 T0

description:
MSCs at day 0 of osteogenic differentiation
SAMPLE 7

value: day 0 of osteogenic differentiation

value: Coxarthrosis


title: AhNF-YC OE recovery

description: Plant leaves were collected 24 hrs after normal watering was reestablished in water-stressed plants

source_name: Rosette leaves, 5-week old Wt plants_recovery

treatment_protocol: In specified cases, plants were subjected to either 5 days or 8 days of water stress. Tissue was collected at day 5 and 24 hrs later after the reestablishment of normal watering to 8-day water stressed plants.

source_name: Rosette leaves, 5-week old transgenic plants_recovery


title: AhNF-YC OE water stress

description: Tissue was collected after plants were subjected to 5 days of water stress

source_name: Rosette leaves, 5-week old Wt plants_5days_water_stress

source_name: Rosette leaves, 5-week old transgenic plants_5days_water_stress


title: SAMPLE_155 AML

value: Adelaide

value: Unknown


title: SAMPLE_140 AML

value: M


title: SAMPLE_147 AML

value: Bone Marrow

value: N


title: SAMPLE_133 AML

value: F


title: SAMPLE_131 AML


title: CX17 T21

description:
MSCs at day 21 of osteogenic differentiation
SAMPLE 6

value: Bone Marrow MSCs

value: day 21 of osteogenic differentiation


title: SAMPLE_129 AML


title: SAMPLE_139 MNC

value: Bone Marrow Mononuclear Cells

value: MNC


title: SAMPLE_126 AML

value: Misc


title: SAMPLE_107 MNC


title: CX17 T0

description:
MSCs at day 0 of osteogenic differentiation
SAMPLE 4


title: SAMPLE_125 AML


title: SAMPLE_119 AML

value: ALLG


title: CX1 T21

description:
MSCs at day 21 of osteogenic differentiation
SAMPLE 3


title: SAMPLE_105 AML

value: Y


title: SAMPLE_84 AML


title: SAMPLE_98 AML


title: SAMPLE_77 AML


title: SAMPLE_91 AML


title: CX1 T10

description:
MSCs at day 10 of osteogenic differentiation
SAMPLE 2

value: day 10 of osteogenic differentiation


title: hMSC cell line [mRNA]

description: Gene expression data from human mesenchymal stem cell line

data_processing: The microarray numerical values were analyzed using the GeneSpring GX 11.0 software, according to the RAM16 Algorithm: quantile normalization, filter by flags (detected), filter by expression on the normalized data (20.0–100.0th percentile).

source_name: Human Mesenchyamal Stem Cell Line

tag: cell line

value: hMSC

tag: cell type

value: Mesenchymal cells


title: CX1 T0

description:
MSCs at day 0 of osteogenic differentiation
SAMPLE 1

tag: differentiation

value: day 0 of osteogenic differentiation

value: Coxarthrosis


title: CX17 T10

description:
MSCs at day 10 of osteogenic differentiation
SAMPLE 5

tag: group


title: PBMCs sample_TR013

description: Test

value: Cali

tag: individual


title: SAMPLE_63 AML

tag: gender

value: M


title: SAMPLE_70 AML

value: Bone Marrow


title: SAMPLE_59 MNC

value: Adelaide

value: Unknown


title: SAMPLE_123 MNC


title: SAMPLE_112 AML

value: N


title: SCCH cell line [mRNA]

description: Gene expression data from human Ewing's sarcoma cell line

source_name: Human Ewing's sarcoma Cell Line

value: SCCH


title: SAMPLE_56 AML

value: F


title: SAMPLE_49 AML


title: SAMPLE_43 MNC

value: Bone Marrow Mononuclear Cells

value: MNC


title: WE68 cell line [mRNA]


title: SKNMC cell line [mRNA]

value: SKNMC


title: SAMPLE_92 MNC


title: SAMPLE_42 AML

value: ALLG


title: SAMPLE_35 AML


title: SAMPLE_75 MNC


title: SAMPLE_29 AML

value: Misc

value: Y


title: SAMPLE_22 AML


title: SAMPLE_15 AML


title: RDES cell line [mRNA]

value: RDES

value: Mesenchymal cells


title: SKES1 cell line [mRNA]


title: SAMPLE_8 AML


title: AHR KNOCKDOWN BY AHR siRNA_A2

description: Microarray done in The McGill University and Génome Québec Innovation Centreand

source_name: AHR KNOCKDOWN BY AHR siRNA

value: monocytic cell line THP-1

tag: protocol

value: AHR KD


title: SAMPLE_1 AML

value: M


title: SAMPLE_11 MNC


title: Normal 0J

city: Kobe

first: Seiji

last: Takeuchi

address: Kusunoki-cho 7-5-1, Chuou-ku

institute: Kobe University

description: Gene expression data from human primary fibroblast from a healthy person

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained under the control of Affymetrix GeneChip Command Console Software (AGCC)

scan_protocol: GeneChips were scanned using the Laser scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using expression console software.

source_name: Human primary fibroblast from a healthy person

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using GeneChip 3' IVT Express Kit.

growth_protocol: Primary fibroblast cells were grown in DMEM medium supplemented with fatal bovine serum in the 5% CO2  incubator at 37 degree.

extract_protocol: Cell collections were lysed with TrizolTM (Ambion)  solution. Total RNA were purified according to the attached protocol. The quality of total RNA were confirmed using Agilent 2100 Bioanalyzer.

treatment_protocol: Primary fibroblasts were irradiated with germicidal lamp (Toshiba) as a 0.5J/m2 or 5J/m2 in the growing phase. At 4hr or 12hr time point after UV exposure, cells were harvested with cell scraper.

tag: diagnosis

value: healthy

value: primary fibroblast from skin


title: Normal 0.5J 12hr

description: Gene expression data from human primary fibroblast from a healthy person at 12hr after UVC irradiation (0.5 J/m2)

source_name: Human primary fibroblast from a healthy person at 12hr after UVC irradiation (0.5 J/m2)

tag: tissue


title: SAMPLE_179 AML

value: Bone Marrow

tag: source*

value: Adelaide

value: Unknown


title: SAMPLE_172 CD34

source_name: CD34+ Cells

value: CD34+ Cells

tag: fab


title: SAMPLE_161 AML

tag: exome capture id


title: XPA 0.5J 4hr

description: Gene expression data from human primary fibroblast from a XP-A patient at 4hr after UVC irradiation (0.5 J/m2)

source_name: Human primary fibroblast from a XP-A patient at 4hr after UVC irradiation (0.5 J/m2)

value: Xeroderma pigmentosum type A (XPA)


title: Normal 5J 12hr

description: Gene expression data from human primary fibroblast froma healthy person at 12hr after UVC irradiation (5 J/m2)

source_name: Human primary fibroblast froma healthy person at 12hr after UVC irradiation (5 J/m2)


title: XPV 0J

description: Gene expression data from human primary fibroblast from a XP-V patient

source_name: Human primary fibroblast from a XP-V patient

value: Xeroderma pigmentosum variant (XPV)


title: Fenpropathrin resistant strain-1

description: Gene expression after Fenpropathrin treatment-1

source_name: Fenpropathrin treatment

tag: strain resistance

value: fenpropathrin

value: full body

value: Female

tag: developmental stage

value: adult

tag: age

value: 3 day old


title: SAMPLE_166 AML

source_name: Bone Marrow

value: F

tag: fa/brca-hrr network mutants

value: Y


title: SAMPLE_177 AML


title: SAMPLE_178 AML


title: Normal 5J 4hr

description: Gene expression data from human primary fibroblast from a healthy person at 4hr after UVC irradiation (5 J/m2)

source_name: Human primary fibroblast from a healthy person at 4hr after UVC irradiation (5 J/m2)


title: XPV 5J 12hr

description: Gene expression data from human primary fibroblast from a XP-V patient at 12hr after UVC irradiation (5 J/m2)

source_name: Human primary fibroblast from a XP-V patient at 12hr after UVC irradiation (5 J/m2)


title: SAMPLE_169 CD34


title: Normal 0.5J 4hr

description: Gene expression data from human primary fibroblast from a healthy person at 4hr after UVC irradiation (0.5 J/m2)

source_name: Human primary fibroblast from a healthy person at 4hr after UVC irradiation (0.5 J/m2)


title: SAMPLE_171 CD34


title: SAMPLE_162 AML


title: XPA 0J

description: Gene expression data from human primary fibroblast from a XP-A patient

source_name: Human primary fibroblast from a XP-A patient


title: SAMPLE_176 AML


title: SAMPLE_163 AML


title: SAMPLE_174 AML


title: SAMPLE_160 AML


title: XPA 0.5J 12hr

description: Gene expression data from human primary fibroblast from a XP-A patient at 12hr after UVC irradiation (0.5 J/m2)

source_name: Human primary fibroblast from a XP-A patient at 12hr after UVC irradiation (0.5 J/m2)


title: SAMPLE_142 AML


title: SAMPLE_158 AML

value: Misc


title: XPV 5J 4hr

description: Gene expression data from human primary fibroblast from a XP-V patient at 4hr after UVC irradiation (5 J/m2)

source_name: Human primary fibroblast from a XP-V patient at 4hr after UVC irradiation (5 J/m2)


title: SAMPLE_159 AML


title: H2171, 552A for 4 days, rep 1

city: Collegeville

last: Soong

state: PA

address: 1250 S Collegeville Rd

institute: GlaxoSmithKline

description: Gene expression from H2171 cells treated with 552A for 4 days

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: microarray data was processed, normalized, and analyzed using the R Bioconductor package.

label_protocol: standard Affymetrix protocol

growth_protocol: RPMI, 10% FBS

extract_protocol: Total RNA was extracted, labeled according to standard Affymetrix procedures and hybridized on GeneChip HGU133 Plus 2.0 slides

treatment_protocol: DMSO or 1uM GSK2879552

tag: passages

value: multiple

tag: treatment

value: 552A for 4 days


title: SAMPLE_143 AML

value: M


title: SAMPLE_145 AML

value: Bone Marrow


title: SAMPLE_146 AML

value: Adelaide


title: SAMPLE_154 AML


title: H1417, DMSO for 4 days, rep 1

description: Gene expression from H1417 cells treated with DMSO for 4 days

tag: cell line

value: DMSO for 4 days


title: SAMPLE_175 AML


title: SAMPLE_144 AML

value: Unknown


title: SAMPLE_135 AML


title: H1417, DMSO for 4 days, rep 2

source_name: H1417 cells treated with DMSO for 4 days


title: SAMPLE_136 CML

value: CML


title: SAMPLE_137 AML


title: SAMPLE_138 AML


title: H2171, 552A for 4 days, rep 2

source_name: H2171 cells treated with 552A for 4 days


title: SAMPLE_165 AML

value: N


title: SAMPLE_148 CD34

value: CD34+ Cells


title: SAMPLE_156 AML


title: SAMPLE_151 AML


title: SAMPLE_149 AML


title: SAMPLE_128 AML


title: SAMPLE_152 AML


title: SAMPLE_153 AML


title: SAMPLE_141 AML


title: H1417, 552A for 4 days, rep 2

description: Gene expression from H1417 cells treated with 552A for 4 days


title: SAMPLE_132 AML


title: SAMPLE_150 AML


title: SAMPLE_127 AML


title: SAMPLE_130 AML


title: SAMPLE_134 AML


title: H2171, DMSO for 4 days, rep 2

description: Gene expression from H2171 cells treated with DMSO for 4 days


title: H1417, 552A for 4 days, rep 1

source_name: H1417 cells treated with 552A for 4 days


title: H69, DMSO for 4 days, rep 2

description: Gene expression from H69 cells treated with DMSO for 4 days

source_name: H69 cells treated with DMSO for 4 days


title: SAMPLE_122 CML


title: COLO668, 552A for 4 days, rep 2

description: Gene expression from COLO668 cells treated with 552A for 4 days


title: H69, DMSO for 4 days, rep 1


title: H2171, DMSO for 4 days, rep 1

source_name: H2171 cells treated with DMSO for 4 days


title: H69, 552A for 4 days, rep 1

description: Gene expression from H69 cells treated with 552A for 4 days

source_name: H69 cells treated with 552A for 4 days


title: SAMPLE_121 AML


title: COLO668, DMSO for 4 days, rep 2

description: Gene expression from COLO668 cells treated with DMSO for 4 days


title: SAMPLE_116 CML


title: SAMPLE_117 AML


title: SAMPLE_118 AML


title: H69, 552A for 4 days, rep 2


title: SAMPLE_115 CD34

source_name: CD34+ Cells


title: SAMPLE_120 AML


title: NCI-H446, DMSO for 4 days, rep 3

description: Gene expression from NCI-H446 cells treated with DMSO for 4 days


title: SAMPLE_114 AML


title: NCI-H446, DMSO for 4 days, rep 2

source_name: NCI-H446 cells treated with DMSO for 4 days


title: NCI-H446, DMSO for 7 days, rep 2

description: Gene expression from NCI-H446 cells treated with DMSO for 7 days

value: DMSO for 7 days


title: SAMPLE_113 AML


title: NCI-H446, 552A for 7 days, rep 2

description: Gene expression from NCI-H446 cells treated with 552A for 7 days

value: 552A for 7 days


title: SAMPLE_111 AML


title: COLO668, DMSO for 7 days, rep 2

description: Gene expression from COLO668 cells treated with DMSO for 7 days


title: SAMPLE_106 AML


title: SAMPLE_110 AML


title: SAMPLE_104 AML


title: NCI-H146, DMSO for 2 days, rep 2

description: Gene expression from NCI-H146 cells treated with DMSO for 2 days

value: DMSO for 2 days


title: SAMPLE_103 AML


title: SAMPLE_109 CML


title: SHP-77, 552A for 7 days, rep 4

description: Gene expression from SHP-77 cells treated with 552A for 7 days


title: SHP-77, 552A for 7 days, rep 2

source_name: SHP-77 cells treated with 552A for 7 days


title: SAMPLE_99 CD34


title: SAMPLE_100 AML


title: SHP-77, 552A for 7 days, rep 1


title: SAMPLE_102 AML


title: NCI-H446, 552A for 7 days, rep 1

source_name: NCI-H446 cells treated with 552A for 7 days


title: SAMPLE_94 AML

source_name: Bone Marrow


title: SAMPLE_97 AML


title: SAMPLE_95 AML


title: SHP-77, DMSO for 7 days, rep 2

description: Gene expression from SHP-77 cells treated with DMSO for 7 days


title: SHP-77, 552A for 7 days, rep 3


title: SAMPLE_101 AML


title: SAMPLE_96 AML


title: NCI-H446, DMSO for 7 days, rep 1

source_name: NCI-H446 cells treated with DMSO for 7 days


title: SAMPLE_93 AML


title: SAMPLE_87 AML


title: SAMPLE_88 AML


title: SAMPLE_82 AML


title: NCI-H446, 552A for 2 days, rep 2

description: Gene expression from NCI-H446 cells treated with 552A for 2 days

value: 552A for 2 days


title: 10C patient

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Data was processed and normalized using GenomeStudio V2011.1

source_name: SCLC patient tumor

label_protocol: standard Illumina protocol

growth_protocol: cell lines: RPMI with 10%FBS

extract_protocol: All the procedure of bisulfite conversion, amplification, labeling and hybridization was performed following the protocol provided by Illumina

treatment_protocol: No treatment

value: SCLC patient tumor


title: NCI-H446, DMSO for 4 days, rep 1


title: NCI-H446, 552A for 4 days, rep 1

description: Gene expression from NCI-H446 cells treated with 552A for 4 days


title: NCI-H446, 552A for 4 days, rep 2

source_name: NCI-H446 cells treated with 552A for 4 days


title: NCI-H446, DMSO for 2 days, rep 2

description: Gene expression from NCI-H446 cells treated with DMSO for 2 days


title: 08C patient


title: 11C patient


title: SAMPLE_85 AML

value: F


title: NCI-H446, DMSO for 2 days, rep 1

source_name: NCI-H446 cells treated with DMSO for 2 days


title: 09C patient


title: SAMPLE_89 AML


title: NCI-H446, 552A for 2 days, rep 1

source_name: NCI-H446 cells treated with 552A for 2 days


title: SAMPLE_124 AML


title: SAMPLE_80 AML


title: 07C patient


title: 05C patient


title: 04C patient


title: SAMPLE_79 AML

value: Y


title: NCI-H146, 552A for 7 days, rep 1

description: Gene expression from NCI-H146 cells treated with 552A for 7 days

value: multiple


title: SAMPLE_78 AML


title: 03C patient


title: NCI-H146, 552A for 4 days, rep 2

description: Gene expression from NCI-H146 cells treated with 552A for 4 days

value: 552A for 4 days


title: NCI-H146, 552A for 7 days, rep 2

source_name: NCI-H146 cells treated with 552A for 7 days


title: SAMPLE_76 AML


title: NCI-H146, DMSO for 7 days, rep 2

description: Gene expression from NCI-H146 cells treated with DMSO for 7 days


title: NCI-H146, DMSO for 7 days, rep 1

source_name: NCI-H146 cells treated with DMSO for 7 days


title: NCI-H146, 552A for 4 days, rep 1

source_name: NCI-H146 cells treated with 552A for 4 days


title: 02C patient


title: SAMPLE_72 AML


title: SAMPLE_74 AML

value: M


title: NCI-H146, DMSO for 4 days, rep 2

description: Gene expression from NCI-H146 cells treated with DMSO for 4 days


title: SAMPLE_73 AML

value: Bone Marrow


title: 06C patient


title: NCI-H82

source_name: SCLC cell line


title: NCI-H146, DMSO for 4 days, rep 1

source_name: NCI-H146 cells treated with DMSO for 4 days


title: SAMPLE_71 AML

value: Adelaide


title: SAMPLE_69 AML


title: NCI-H146, 552A for 2 days, rep 1

description: Gene expression from NCI-H146 cells treated with 552A for 2 days


title: SAMPLE_66 AML


title: SHP77


title: NCI-H146, 552A for 2 days, rep 2

source_name: NCI-H146 cells treated with 552A for 2 days


title: SAMPLE_65 AML


title: SAMPLE_68 AML


title: NCI-H146, DMSO for 2 days, rep 1

source_name: NCI-H146 cells treated with DMSO for 2 days


title: COLO668, 552A for 7 days, rep 1

description: Gene expression from COLO668 cells treated with 552A for 7 days


title: 01C patient


title: SAMPLE_64 AML


title: COLO668, 552A for 7 days, rep 2

source_name: COLO668 cells treated with 552A for 7 days


title: SCLC3


title: NCI-H526


title: SAMPLE_62 AML


title: NCI-H446


title: NCI-H524


title: SAMPLE_61 AML


title: NCI-H510


title: COLO668, 552A for 4 days, rep 1

description: Gene expression from COLO668 cells treated with 552A for 4 days


title: NCI-H69


title: SAMPLE_57 AML


title: COLO668, DMSO for 7 days, rep 1

source_name: COLO668 cells treated with DMSO for 7 days


title: COLO668, DMSO for 4 days, rep 1

description: Gene expression from COLO668 cells treated with DMSO for 4 days

value: DMSO for 4 days


title: SAMPLE_54 AML


title: SAMPLE_55 AML


title: COLO668, 552A for 2 days, rep 2

description: Gene expression from COLO668 cells treated with 552A for 2 days


title: NCI-H1092


title: COLO668, DMSO for 2 days, rep 1

description: Gene expression from COLO668 cells treated with DMSO for 2 days


title: SAMPLE_58 AML


title: COLO668, 552A for 2 days, rep 1

source_name: COLO668 cells treated with 552A for 2 days


title: COLO668, DMSO for 2 days, rep 2

source_name: COLO668 cells treated with DMSO for 2 days


title: NCI-H2171


title: NCI-H1930


title: SAMPLE_53 AML

source_name: Bone Marrow


title: SAMPLE_52 AML


title: NCI-H510, 552A for 7 days, rep 1

description: Gene expression from NCI-H510 cells treated with 552A for 7 days


title: SAMPLE_60 AML

value: Unknown


title: SAMPLE_51 CD34

source_name: CD34+ Cells


title: NCI-H510, DMSO for 7 days, rep 2

description: Gene expression from NCI-H510 cells treated with DMSO for 7 days


title: LX88x PDX

source_name: SCLC patient derived xenograft

value: SCLC patient derived xenograft


title: NCI-H510, 552A for 7 days, rep 2

source_name: NCI-H510 cells treated with 552A for 7 days


title: SAMPLE_48 AML

value: N


title: NCI-H187


title: NCI-H2081


title: NCI-H510, DMSO for 7 days, rep 1

source_name: NCI-H510 cells treated with DMSO for 7 days


title: NCI-H1048


title: SAMPLE_47 AML


title: NCI-H510, 552A for 4 days, rep 2

description: Gene expression from NCI-H510 cells treated with 552A for 4 days


title: SAMPLE_50 AML


title: LX48x PDX


title: NCI-H510, 552A for 4 days, rep 1

source_name: NCI-H510 cells treated with 552A for 4 days


title: NCI-H510, DMSO for 4 days, rep 1

description: Gene expression from NCI-H510 cells treated with DMSO for 4 days


title: SAMPLE_46 AML


title: LX47x PDX


title: LX36x PDX


title: LX33x PDX


title: LX22x PDX


title: SAMPLE_45 AML


title: LX44 PDX


title: NCI-H510, 552A for 2 days, rep 1

description: Gene expression from NCI-H510 cells treated with 552A for 2 days


title: LX108x PDX


title: LX110x PDX


title: SAMPLE_40 AML


title: LX102x PDX


title: SAMPLE_41 AML


title: H1417


title: LX101x PDX


title: SAMPLE_32 AML


title: NCI-H510, DMSO for 2 days, rep 2

description: Gene expression from NCI-H510 cells treated with DMSO for 2 days


title: NCI-H510, 552A for 2 days, rep 2

source_name: NCI-H510 cells treated with 552A for 2 days


title: SAMPLE_38 AML


title: SAMPLE_39 AML


title: NCI-H526, DMSO for 7 days, rep 1

description: Gene expression from NCI-H526 cells treated with DMSO for 7 days


title: NCI-H510, DMSO for 2 days, rep 1

source_name: NCI-H510 cells treated with DMSO for 2 days


title: SAMPLE_34 AML

value: Misc


title: SAMPLE_37 AML


title: NCI-H510, DMSO for 4 days, rep 2

source_name: NCI-H510 cells treated with DMSO for 4 days


title: SAMPLE_33 AML


title: NCI-H526, 552A for 7 days, rep 2

description: Gene expression from NCI-H526 cells treated with 552A for 7 days


title: NCI-H526, DMSO for 7 days, rep 2

source_name: NCI-H526 cells treated with DMSO for 7 days

value: DMSO for 7 days


title: SAMPLE_44 AML


title: H2029

source_name: SCLC cell line


title: NCI-H526, 552A for 7 days, rep 1

source_name: NCI-H526 cells treated with 552A for 7 days

value: 552A for 7 days


title: DMS53


title: NCI-H526, 552A for 4 days, rep 2

description: Gene expression from NCI-H526 cells treated with 552A for 4 days


title: SAMPLE_31 AML


title: NCI-H526, 552A for 4 days, rep 1

source_name: NCI-H526 cells treated with 552A for 4 days


title: NCI-H526, DMSO for 4 days, rep 2

description: Gene expression from NCI-H526 cells treated with DMSO for 4 days


title: NCI-H526, DMSO for 4 days, rep 1

source_name: NCI-H526 cells treated with DMSO for 4 days


title: SAMPLE_21 AML


title: DMS114


title: SAMPLE_24 AML


title: SAMPLE_26 AML


title: murcb s983/s983 3

city: Bad Nauheim

first: Michael

middle: Patrick

last: Housley

state: Hessen

address: Ludwigstr. 43

department: Developmental Genetics

institute: Max Planck Institute

description: murcb-s983 3

hyb_protocol: standard Agilent protocol

scan_protocol: The arrays were imaged using a SureScan Microarray Scanner and Agilent’s Feature Extraction software version 11 was used to read and process the TIFF images.

data_processing: Data were normalized by using the ranked median quantiles

source_name: Cavin4/Murcb deficient mutant_lavae trunk

label_protocol: standard Agilent protocol

growth_protocol: Standard egg water, 28 degrees C, 40 larvae per dish, 72 hpf

extract_protocol: Individual larvae were dissected to separate the heads from the trunks. The heads were used for genotyping and the trunk was lysed in Trizol. After genotyping, homozygous mutants and heterzygous murcb samples were combined and RNA was extracted. Aqueous phase RNA was purified over a column.

tag: genotype/variation

value: Cavin4/Murcb deficient mutant

value: 72 hpf

value: zebrafish larvae trunk


title: DMS 153

value: DMS 153


title: COLO668


title: SAMPLE_25 AML

value: F

value: Y


title: SAMPLE_28 AML


title: murcb s983/+ 2

description: wt 2

source_name: heterozygous_lavae trunk

value: heterozygous


title: NCI-H526, DMSO for 2 days, rep 2

description: Gene expression from NCI-H526 cells treated with DMSO for 2 days

value: multiple

value: DMSO for 2 days


title: murcb s983/s983 1

description: murcb-s983 1


title: NCI-H526, 552A for 2 days, rep 3

description: Gene expression from NCI-H526 cells treated with 552A for 2 days

value: 552A for 2 days


title: NCI-H526, 552A for 2 days, rep 1

source_name: NCI-H526 cells treated with 552A for 2 days


title: NCI-H526, 552A for 2 days, rep 2


title: murcb s983/+ 1

description: wt 1


title: SHP-77, DMSO for 7 days, rep 1

description: Gene expression from SHP-77 cells treated with DMSO for 7 days


title: murcb s983/+ 3

description: wt 3


title: murcb s983/s983 2

description: murcb-s983 2


title: SAMPLE_20 AML

source_name: Bone Marrow

value: Bone Marrow

value: Adelaide

value: M


title: SAMPLE_19 CD34

source_name: CD34+ Cells

value: CD34+ Cells

value: Unknown


title: SAMPLE_30 AML


title: SAMPLE_23 AML


title: NCI-H526, DMSO for 2 days, rep 1

source_name: NCI-H526 cells treated with DMSO for 2 days


title: SAMPLE_17 AML


title: brs1-1D#3

city: Lanzhou

first: Tao

last: Shi

state: Gansu

address: 222 South Tianshui Road

department: School of Life Sciences

institute: Lanzhou University

description: Gene expression of bri1-5/brs1-1D, repeat 1

hyb_protocol: 20 ug of biotin labeled cRNA were hybridized with Arabidopsis ATH1 genome array, according to the Affymetrix manufacturer's instruction.

scan_protocol: Scanning of Arrays by Agilent GeneArray Scanner.

data_processing: The data were analyzed with EXPANDAR 6.0 and gc-RMA normalization method.

source_name: bri1-5/brs1-1D light-grown 5-days seedling

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

growth_protocol: Seedlings were grown on solid MS medium with 1% sucrose in the light for 5 days.

extract_protocol: Total RNA was extracted with RNeasy (QIAGEN)

treatment_protocol: The 5-days light-grown seedlings were frozen in liquid nitrogen

tag: genotype

tag: genetic background

value: WS2 ecotype

value: whole seedling


title: SHP-77, DMSO for 4 days, rep 2

description: Gene expression from SHP-77 cells treated with DMSO for 4 days

value: DMSO for 4 days


title: SHP-77, 552A for 4 days, rep 2

description: Gene expression from SHP-77 cells treated with 552A for 4 days

value: 552A for 4 days


title: SHP-77, 552A for 4 days, rep 1

source_name: SHP-77 cells treated with 552A for 4 days


title: SAMPLE_16 AML

tag: gender

value: N


title: SAMPLE_14 AML


title: SHP-77, DMSO for 4 days, rep 1

source_name: SHP-77 cells treated with DMSO for 4 days


title: bak1-1D#2

description: Gene expression of bri1-5/bak1-1D, repeat 1

source_name: bri1-5/bak1-1D light-grown 5-days seedling


title: brs1-1D#1


title: SHP-77, 552A for 2 days, rep 1

description: Gene expression from SHP-77 cells treated with 552A for 2 days


title: SHP-77, 552A for 2 days, rep 2

source_name: SHP-77 cells treated with 552A for 2 days


title: bak1-1D#3


title: bak1-1D#1


title: bri1-1D#2

description: Gene expression of bri1-5/bri1-1D, repeat 2

source_name: bri1-5/bri1-1D light-grown 5-days seedling


title: bri1-1D#3

description: Gene expression of bri1-5/bri1-1D, repeat 3


title: SAMPLE_9 AML


title: SHP-77, DMSO for 2 days, rep 1

description: Gene expression from SHP-77 cells treated with DMSO for 2 days


title: SAMPLE_13 AML


title: SAMPLE_12 AML


title: SAMPLE_10 AML


title: bri1-1D#1

description: Gene expression of bri1-5/bri1-1D, repeat 1


title: A549_Sulforaphene_24h_rep2

city: Beijing

first: Zhou

last: Mo

address: North Third Ring Road No. 15

institute: Beijing University of Chemical Technology

description: male, epithelial, lung, Carcinoma, 61 years old, Caucasian

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Wheat Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were normalized using Robust Multi-array Average(RMA) .

source_name: ATCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Volumes used in this protocol are for 75 cm2 flask; proportionally reduce or increase amount of dissociation medium for culture vessels of other sizes.  Remove and discard culture medium.  Briefly rinse the cell layer with 0.25% (w/v) Trypsin- 0.53 mM EDTA solution to remove all traces of serum that contains trypsin inhibitor.  Add 2.0 to 3.0 mL of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 5 to 15 minutes).  Note: To avoid clumping do not agitate the cells by hitting or shaking the flask while waiting for the cells to detach. Cells that are difficult to detach may be placed at 37°C to facilitate dispersal.  Add 6.0 to 8.0 mL of complete growth medium and aspirate cells by gently pipetting.  Add appropriate aliquots of the cell suspension to new culture vessels.  Cultures can be established between 2 x 103 and 1 x 104 viable cells/cm2. Do not exceed 7 x 104 cels/cm2.  Incubate cultures at 37°C.  Interval: Maintain cultures at a cell concentration between 6 X 103 and 6 X 104 cell/cm2.  Subcultivation Ratio: A subcultivation ratio of 1:3 to 1:8 is recommended  Medium Renewal: 2 to 3 times per week

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

treatment_protocol: Cells were treated with steriled water or 30μmol/L Sulforaphene for 24 hours.

value: Sulforaphene


title: bri1-5#3

description: Gene expression of bri1-5, repeat 3

source_name: bri1-5 light-grown 5-days seedling


title: brs1-1D#2


title: SAMPLE_6 AML

value: F


title: bri1-5#2

description: Gene expression of bri1-5, repeat 2


title: WS2#3

description: Gene expression of WS2, repeat 3

source_name: WS2 light-grown 5-days seedling

value: wild type


title: SHP-77, DMSO for 2 days, rep 2

first: David

source_name: SHP-77 cells treated with DMSO for 2 days


title: SAMPLE_7 AML

value: Y


title: SAMPLE_5 AML


title: SAMPLE_3 CD34


title: A549_Control_24h_rep2

description: male, epithelial, lung, Carcinoma, 60 years old, Caucasian

value: control


title: SAMPLE_2 AML


title: WS2#1

description: Gene expression of WS2, repeat 1


title: bri1-5#1

description: Gene expression of bri1-5, repeat 1


title: A549_Control_24h_rep1

description: male, epithelial, lung, Carcinoma, 58 years old, Caucasian


title: WS2#2

description: Gene expression of WS2, repeat 2


title: eWAT-WT_EX WAT_1966_EX_9343563040

city: Lausanne

first: Marie

last: Boutant

address: EPFL Innovation Park, Bâtiment G

country: Switzerland

institute: Nestle Institute of Health Sciences

description: WT (C57/Bl6) mice fed ad libitum on low fat diet and submitted to exercise training (running wheel cage) during 10 weeks

hyb_protocol: Hybridization on MouseRef-8 v2.0 Expression BeadChips

data_processing: Raw microarray data were QCed and extracted using the Illumina genome studio software, and then analyzed using Partek GS software

source_name: epididymal white adipose tissue-WT-EX mice

label_protocol: RNA samples were prepared using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: Mice were fed with a low fat diet and submitt to different challenge (ad libitum feeding, caloric restriction or exercise training)

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

treatment_protocol: animals were sacrificed at 8 a.m. after a 12 hr fast. Tissues were collected upon sacrifice and flash-frozen in liquid nitrogen

value: male

value: EX mice


title: eWAT-WT_EX WAT_1975_EX_9377360021


title: eWAT-WT_EX WAT_1976_EX_9377360017


title: BAT-WT_EX BAT_1976_EX_9377360017

source_name: Brown adipose tissue-WT-EX mice


title: eWAT-WT_EX WAT_1971_EX_9377360015


title: BAT-WT_EX BAT_1966_EX_9343563040


title: BAT-WT_EX BAT_1969_EX_9377360015


title: BAT-WT_EX BAT_1970_EX_9377360021


title: muscle-WT_EX muscle_1970_EX_9377360015

source_name: skeletal muscle-WT-EX mice


title: eWAT-WT_EX WAT_1972_EX_9343563037


title: eWAT-WT_EX WAT_1974_EX_9377360013


title: BAT-WT_EX BAT_1972_EX_9343563037


title: muscle-WT_EX muscle_1972_EX_9377360021


title: Liver-WT_EX liver_1974_EX_9377360021

source_name: Liver-WT-EX mice


title: muscle-WT_EX muscle_1976_EX_9377360013


title: muscle-WT_EX muscle_1974_EX_9343563037


title: BAT-WT_EX BAT_1974_EX_9377360013


title: SAMPLE_4 AML

source_name: Bone Marrow

value: Bone Marrow


title: Liver-WT_EX liver_1972_EX_9377360015


title: A549_Sulforaphene_24h_rep1

description: male, epithelial, lung, Carcinoma, 59 years old, Caucasian


title: Liver-WT_EX liver_1970_EX_9343563040


title: muscle-WT_EX muscle_1969_EX_9343563040


title: muscle-WT_EX muscle_1966_EX_9377360014


title: Liver-WT_EX liver_1976_EX_9343563037


title: TC-2

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

institute: Kyoto University Graduate School of Pharmaceutical Sciences

hyb_protocol: The labeled cDNA were then hybridized on Affimetrix gene chip and stained.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner.

data_processing: The data were analyzed with R software. The MAS 5.0 normalization were performed using the justMAS function in the simpleaffy package from Bioconductor.

organism: Rattus norvegicus

source_name: GBM nephritis tricaprylin treated

label_protocol: cDNA labeling was performed according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cDNA.

value: whole kidney

tag: cell type

value: anti-glomerular basement membrane nephritis (anti-GBM)


title: Liver-WT_EX liver_1966_EX_9377360018


title: TC-3


title: Liver-WT_EX liver_1969_EX_9377360014


title: eWAT-WT_CR WAT_2245_CR_9377360017

description: WT (C57/Bl6) mice on caloric restriction (EODF) for 3 months

source_name: epididymal white adipose tissue-WT-CR mice

value: eWAT-WT-CR

value: CR mice


title: eWAT-WT_CR WAT_2242_CR_9377360013


title: E-3

source_name: GBM nephritis emodin treated


title: TC-1


title: eWAT-WT_CR WAT_2241_CR_9343563037


title: eWAT-WT_CR WAT_2239_CR_9377360021


title: GBM-2

source_name: GBM nephritis


title: BAT-WT_CR BAT_2245_CR_9377360017

source_name: Brown adipose tissue-WT-CR mice

value: BAT-WT-CR


title: BAT-WT_CR BAT_2242_CR_9377360013


title: eWAT-WT_CR WAT_2230_CR_9377360018


title: eWAT-WT_CR WAT_2236_CR_9377360015


title: E-2


title: GBM-1


title: C-1

source_name: Control

value: Normal (control)


title: GBM-3


title: BAT-WT_CR BAT_2230_CR_9377360018


title: E-1


title: EWAT lard germ free mouse 6

city: Gothenbrug

first: Robert

last: Caesar

address: Gothenburg University

department: Wallenberg Laboratory

country: Sweden

institute: Gothenburg University

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: The samples were scanned using the GeneChip® Scanner 3000 7G according to the manufacturer’s manual (PN 702731 Rev 3, Affymetrix).

data_processing: The raw data were normalized using the robust multi-array average method (Li and Wong, 2001). Differential expression of microarray data was evaluated by Student's t-test followed by correction for false discovery rate. Analysis of interaction, using colonization status and diet as independent variables, was evaluated by two-way analysis of interaction followed by correction for false discovery rate.

source_name: epidiymal WAT, germ free mouse fed lard

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression Kit (P/N 4425209 Rev C 09/2009) and Affymetrix GeneChip® WT Terminal

growth_protocol: Mice were fed high fat diet for 11 weeks

extract_protocol: RNA was isolated usinr Rneasy Lipid Tissue Mini kit (Qiagen)

treatment_protocol: Mice were fasted for 4 hours before sac

tag: strain

value: 11 weeks of age

value: wildtype

value: EWAT

tag: bacterial status

value: germ-free

tag: diet

value: lard


title: C-2

tag: tissue


title: BAT-WT_CR BAT_2236_CR_9377360015


title: EWAT lard germ free mouse 4


title: BAT-WT_CR BAT_2241_CR_9343563037


title: EWAT lard germ free mouse 5


title: EWAT lard germ free mouse 2


title: BAT-WT_CR BAT_2239_CR_9377360021


title: C-3


title: muscle-WT_CR muscle_2245_CR_9377360013

source_name: skeletal muscle-WT-CR mice

value: muscle-WT-CR


title: muscle-WT_CR muscle_2242_CR_9343563037


title: muscle-WT_CR muscle_2241_CR_9377360021


title: muscle-WT_CR muscle_2230_CR_9374592017


title: EWAT lard germ free mouse 3


title: muscle-WT_CR muscle_2236_CR_9343563040


title: EWAT lard conventional mouse 6

source_name: epidiymal WAT, conventional mouse fed lard

value: conventional


title: EWAT lard germ free mouse 1


title: Liver-WT_CR liver_2245_CR_9343563037

source_name: Liver-WT-CR mice

value: Liver-WT-CR


title: Liver-WT_CR liver_2241_CR_9377360015

value: male


title: EWAT lard conventional mouse 2


title: Liver-WT_CR liver_2239_CR_9343563040


title: EWAT lard conventional mouse 4


title: EWAT fish oil germ free mouse 5

source_name: epidiymal WAT, germ free mouse fed fish oil

value: fish oil


title: Liver-WT_CR liver_2242_CR_9377360021


title: EWAT lard conventional mouse 5


title: EWAT lard conventional mouse 3


title: muscle-WT_CR muscle_2239_CR_9377360015


title: EWAT fish oil germ free mouse 6


title: EWAT fish oil germ free mouse 4


title: Liver-WT_CR liver_2236_CR_9377360014


title: EWAT lard conventional mouse 1


title: EWAT fish oil germ free mouse 2


title: eWAT_WT WAT_1960_WT_9377360018

description: WT (C57/Bl6) mice fed ad libitum on low fat diet

source_name: epididymal white adipose tissue-WT mice

value: eWAT-WT

value: WT mice


title: eWAT_WT WAT_2228_WT_9377360014


title: Liver-WT_CR liver_2230_CR_9374592010


title: BAT_WT BAT_2232_WT_9343563040

source_name: Brown adipose tissue-WT mice

value: BAT-WT


title: EWAT fish oil conventional mouse 6

source_name: epidiymal WAT, conventional mouse fed fish oil


title: EWAT fish oil germ free mouse 3


title: eWAT_WT WAT_2232_WT_9343563040


title: EWAT fish oil germ free mouse 1


title: BAT_WT BAT_2231_WT_9377360014


title: eWAT_WT WAT_2226_WT_9374592017


title: EWAT fish oil conventional mouse 3


title: EWAT fish oil conventional mouse 2


title: eWAT_WT WAT_1961_WT_9377360014


title: EWAT fish oil conventional mouse 1


title: eWAT_WT WAT_1959_WT_9374592017


title: muscle_WT muscle_1961_WT_9377360017

source_name: skeletal muscle-WT mice

value: muscle-WT


title: BAT_WT BAT_1961_WT_9377360014


title: BAT_WT BAT_2226_WT_9374592017


title: muscle_WT muscle_2232_WT_9377360014


title: EWAT fish oil conventional mouse 4


title: BAT_WT BAT_1960_WT_9377360018


title: Obese 80% Hepatectomy Rep 3

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Obese 80% Hepatectomy

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

value: 12 weeks

value: Liver


title: Obese 80% Hepatectomy Rep 4


title: Lean 80% Hepatectomy Rep 3

source_name: Lean 80% Hepatectomy


title: BAT_WT BAT_1959_WT_9374592017


title: Lean 80% Hepatectomy Rep 2


title: Obese 70% Hepatectomy Rep 4

source_name: Obese 70% Hepatectomy


title: Liver_WT liver_1960_WT_9377360017

source_name: Liver-WT mice

value: Liver-WT


title: EWAT fish oil conventional mouse 5

value: 11 weeks of age


title: Obese 80% Hepatectomy Rep 2


title: muscle_WT muscle_1960_WT_9377360018


title: Obese 80% Hepatectomy Rep 1


title: Liver_WT liver_2231_WT_9374592017


title: Lean 80% Hepatectomy Rep 4


title: muscle_WT muscle_1959_WT_9374592017


title: Obese 70% Hepatectomy Rep 3


title: Lean 80% Hepatectomy Rep 1


title: Obese 70% Hepatectomy Rep 2


title: muscle_WT muscle_2231_WT_9377360018


title: Liver_WT liver_1959_WT_9374592010


title: Lean 70% Hepatectomy Rep 2

source_name: Lean 70% Hepatectomy


title: Lean 70% Hepatectomy Rep 4


title: Liver_WT liver_1961_WT_9374592017


title: Obese Sham Rep 4

source_name: Obese Sham surgery


title: Liver_WT liver_2226_WT_9374592003


title: eWAT_Tg WAT_1954_SiRT1_9374592003

description: SIRT1Tg/Tg mice fed ad libitum on low fat diet

source_name: epididymal white adipose tissue-SIRT1Tg/Tg mice

value: eWAT-Tg

value: SIRT1Tg/Tg mice


title: Liver_WT liver_2232_WT_9377360018


title: Lean 70% Hepatectomy Rep 3


title: Obese 70% Hepatectomy Rep 1


title: eWAT_Tg WAT_2222_SiRT1_9374592003


title: Obese Sham Rep 2


title: Lean 70% Hepatectomy Rep 1


title: eWAT_Tg WAT_1955_SiRT1_9374592010


title: ExVivoBlood_periostin_rep7

city: Sendai

first: Masayuki

last: Asano

state: Miyagi

address: Seiryo-machi 1-1, Aoba-ku

department: Department of Dermatology

institute: Tohoku University Graduate School of Medicine

description: Gene expression with periostin treatment

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20100115) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peripheral Blood, periostin, replicate 7

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

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: CD14+ cells were isolated from the peripheral blood mononuclear cells of healthy donors using magnetic-activated cell sorting beads (CD14 microbeads, Miltenyi Biotec, CA) according to the manufacturer’s protocol. CD14+ monocytes (2 x 105 /ml) were cultured in complete medium containing 100 ng/ml of recombinant human M-CSF for 5 days. On the fifth day, the monocyte-derived M2 macrophages (M2MF) were treated with or without periostin (100 ng/ml) for 6 hours.

value: whole blood

tag: agent

value: 100 ng/ml periostin

value: monocyte-derived M2 macrophages


title: Lean Sham Rep 3

source_name: Lean Sham surgery


title: Lean Sham Rep 2


title: BAT_Tg BAT_2223_SiRT1_9374592010

source_name: Brown adipose tissue-SIRT1Tg/Tg mice

value: BAT-Tg


title: Obese Sham Rep 3


title: Lean Sham Rep 4


title: eWAT_Tg WAT_1953_SiRT1_9374592008


title: ExVivoBlood_periostin_rep8

source_name: Peripheral Blood, periostin, replicate 8

value: female


title: muscle_WT muscle_2226_WT_9374592010

value: male


title: Lean Sham Rep 1


title: muscle_Tg muscle_2223_SiRT1_9374592003

source_name: skeletal muscle-SIRT1Tg/Tg mice

value: muscle-Tg


title: BAT_Tg BAT_2207_SiRT1_9374592008


title: BAT_Tg BAT_1953_SiRT1_9374592008


title: ExVivoBlood_control_rep7

description: Gene expression without periostin treatment

source_name: Peripheral Blood, control, replicate 7


title: eWAT_Tg WAT_2207_SiRT1_9374592008


title: Obese Sham Rep 1


title: BAT_Tg BAT_1955_SiRT1_9374592010


title: ExVivoBlood_periostin_rep6

source_name: Peripheral Blood, periostin, replicate 6


title: muscle_Tg muscle_2207_SiRT1_9377360017


title: ExVivoBlood_control_rep8

source_name: Peripheral Blood, control, replicate 8


title: BAT_Tg BAT_2222_SiRT1_9374592003


title: muscle_Tg muscle_2222_SiRT1_9374592008


title: ExVivoBlood_control_rep6

source_name: Peripheral Blood, control, replicate 6


title: BAT_Tg BAT_1954_SiRT1_9374592003


title: ExVivoBlood_control_rep5

source_name: Peripheral Blood, control, replicate 5


title: ExVivoBlood_periostin_rep5

source_name: Peripheral Blood, periostin, replicate 5


title: eWAT_Tg WAT_2223_SiRT1_9374592010