title: Pax3Zic1-injected animal cap, stage 12, induced with Dex, replicate 3

description: PZc3; targets_3I.CEL

source_name: Pax3Zic1-injected animal cap_stage 12_induced with Dex


title: Control animal cap, stage 12, replicate 2

status: Public on Dec 28 2013

type: RNA

city: Orsay

first: Anne-Helene

last: Monsoro-Burq

address: Bat 110

department: Université Paris Sud

country: France

institute: Institut Curie

description: pzc2; targets_2N.CEL

hyb_protocol: Hybridization was completed using the standard affymetrix protocol

scan_protocol: Scanning was completed using an Affymetrix Genechip scanner 3000 7G

data_processing: The data was analysed with R (v.2.14.2) and the Bioconductor Biobase (v.2.14.0) affy library (v.1.32.1 package) with default settings.

label: biotin

molecule: total RNA

organism: Xenopus laevis

source_name: Control animal cap_stage 12

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: Xenopus laevis 2-4 cells stage embryos were injected with inducible Pax3-GR+/-Zic1-GR constructs and then grown at 15°C in 1/3 MMR until stage 9

extract_protocol: Total RNA was isolated using the standard trizol protocol and eppendorf phase-lock gel tubes, followed by proteinase K digestion, and Qiagen Rneasy columns

treatment_protocol: Cycloheximide (0,1mg/ml) was then applied to the healed animal caps, from stage 10 to 10.5 (i.e. for 30 min at 23*C), then dexamethasone was added at stage 10.5 to the cycloheximide-containing medium. Explants were rinced and lysed after two additional hours at 23*C, i.e. when sibling embryos reached stage 11.5-12.

tag: tissue

value: Xenopus laevis animal cap explant, stage 12

tag: dex treatment

value: no

tag: pax3 injection

tag: zic1 injection

tag: chx treatment

tag: biological eplicate


title: Pax3Zic1-injected animal cap, stage 12, induced with Dex, replicate 2.2

description: PZc2r2; targets_2U-2.CEL

value: yes


title: Pax3-injected animal cap, stage 12, induced with Dex, replicate 2

description: Pzc2; targets_2Q.CEL

source_name: Pax3-injected animal cap_stage 12_induced with Dex


title: Pax3-injected animal cap, stage 12, treated with Chx, induced with Dex, replicate 3

description: PzC3; targets_3F.CEL

source_name: Pax3-injected animal cap_stage 12_treated with Chx_induced with Dex


title: Pax3-injected animal cap, stage 12, induced with Dex, replicate 3

description: Pzc3; targets_3G.CEL


title: Pax3Zic1-injected animal cap, stage 12, induced with Dex, replicate 2.1

description: PZc2r1; targets_2U-1.CEL


title: Pax3Zic1-injected animal cap, stage 12, induced with Dex, replicate 1

description: PZc1; targets_1I.CEL


title: Pax3Zic1-injected animal cap, stage 12, treated with Chx, induced with Dex, replicate 1

description: PZC1; targets_1H.CEL

source_name: Pax3Zic1-injected animal cap_stage 12_treated with Chx_induced with Dex


title: Pax3-injected animal cap, stage 12, induced with Dex, replicate 1

description: Pzc1; targets_1G.CEL


title: Pax3-injected animal cap, stage 12, treated with Chx, induced with Dex, replicate 1

description: PzC1; targets_1F.CEL


title: pIgR-KO mice antibiotic treated, rep6

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in J-express.

organism: Mus musculus

source_name: Colon intestinal epithelial cells, pIgR-KO, antibiotic

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

extract_protocol: The IECs were resuspended in TRI Reagent® (Ambion Applied Biosystems, Foster City, CA), and stored at -70oC until RNA isolation according to the manufacturer’s instructions.

treatment_protocol: After 17 days of antibiotic treatment, mice were anaesthetized with 150 µl Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanison 10 mg/ml, VetaPharma Ltd) and midazolam (5 mg/ml, B. Braun Meslungen AG) subcutaneously and bled to death by cardiac puncture. Colon was swiftly excised and flushed with 2x 10 ml ice cold PBS (w/o Mg2+ and Ca2+) and kept moist. Mesenteric and adipose tissue was removed from the colon, which was subsequently opened longitudinally, then cut transversally in 5 cm long pieces and incubated 25 min in 25 ml 20 mM EDTA (Sigma-Aldrich, St. Louis, MO) at room temperature on a shaker before being vigorously hand shaken for 5 minutes. The intestinal epithelial cells (IECs) were harvested in a fresh tube, washed twice in ice cold PBS, and resuspended in TRI Reagent® (Ambion Applied Biosystems, Foster City, CA).

tag: strain

value: BALB/c

tag: genotype

value: polymeric Ig receptor (pIgR) knockout

tag: gender

value: male

tag: age

value: 6-10 weeks

value: colon

tag: cell type

value: intestinal epithelial cells

tag: treatment

value: antibiotic


title: Control animal cap, stage 12, replicate 1

description: pzc1; targets_1E.CEL

source_name: Control animal cap, stage 12


title: Pax3-injected animal cap, stage 12, treated with Chx, induced with Dex, replicate 2

description: PzC2; targets_2P.CEL


title: pIgR-KO mice antibiotic treated, rep2


title: pIgR-KO mice antibiotic treated, rep5


title: pIgR-KO mice antibiotic treated, rep3


title: LLC8P/phESC-5

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2; The 'complete_data.txt' contains 5 columns of data per each sample; AVG_Beta, SignalA (nonmethylated), SignalB (methylated), Dectection Pval, Intensity.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: parthenogenetic activated oocytes

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

value: female

tag: health state

value: activated metaphase-2 oocyte

value: parthenogenetic activated oocytes


title: Genome-wide pUPD1

source_name: Leukocytes

value: Beckwith Wiedemann-like

value: Leukocytes


title: Genome-wide mUPD

value: Silver Russell-like


title: pIgR-KO mice antibiotic treated, rep1


title: pIgR-KO mice antibiotic treated, rep4


title: Genome-wide pUPD2


title: Genome-wide pUPD4


title: Genome-wide pUPD3


title: LLC7P/phESC-4


title: LLC9P/phESC-6


title: LLC6P/phESC-3


title: pIgR-KO mice untreated, rep5

source_name: Colon intestinal epithelial cells, pIgR-KO, untreated


title: pIgR-KO mice untreated, rep3


title: SHEF 5

source_name: human embryonic stem cells

value: isolated from blastocyst

value: human embryonic stem cells


title: pIgR-KO mice untreated, rep2


title: SHEF 3


title: SHEF 6


title: pIgR-KO mice untreated, rep6


title: Placenta (PL7)

source_name: Term placenta- fetal side

value: Term Placenta 40.3 weeks

value: Term placenta- fetal side


title: pIgR-KO mice untreated, rep1

value: BALB/c


title: Wild-type mice antibiotic treated, rep4

source_name: Colon intestinal epithelial cells, wild-type, antibiotic

value: wild type


title: Wild-type mice antibiotic treated, rep5

value: male


title: Val 10B

value: isaloted from cleavage embryo


title: Placenta (PL5)

value: Term Placenta 38 weeks


title: Wild-type mice antibiotic treated, rep3

value: 6-10 weeks

value: colon

value: intestinal epithelial cells


title: Sperm 1

source_name: Sperm

value: Health tissue

value: Sperm


title: Placenta (PL3)

value: Term Placenta 39.3 weeks


title: Wild-type mice antibiotic treated, rep2

value: antibiotic


title: Wild-type mice antibiotic treated, rep1


title: Wild-type mice untreated, rep5

source_name: Colon intestinal epithelial cells, wild-type, untreated


title: Sperm 2


title: Wild-type mice untreated, rep4


title: Placenta (PL1)

value: female

value: Term Placenta 40.6 weeks


title: LU134-MAX-shBRG1-3

hyb_protocol: Microarray: SurePrint G3 Human Gene Expression 8x60K v2 Microarray (Agilent microarray design ID 039494)

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent).

data_processing: Images were quantified using Agilent Feature Extraction Software (ver. 10.7)

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis” v.6.6 kit by following manufacturer instructions. Agilent manual G4140-90040 of September 2012. Amplification: by RNA polymerases.

growth_protocol: Cells where growth on RPMI media with 10% FBS, 1% PS

extract_protocol: Total mRNA  where extrated using Trizol Reagent.

treatment_protocol: Not special  additional treatment

tag: cell line

value: Small Cell Lung Cancer (SCLC)


title: THP-1 #3

city: Omaha

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

department: Pharmacology and Experimental Neuroscience

country: USA

institute: University of Nebraska Medical Center

description: Gene expression data from THP-1s not stimulated with PMA

hyb_protocol: Overnight hybridization using the Affymetrix hybridization over at 42oC. 500ng of cDNA was used

scan_protocol: Affymetrix GeneChip Scanner 3000 7G generated the resulting array image

data_processing: RMA normalization followed by Partek Genomic Suite 6.6 analysis

label: Biotin

source_name: THP-1s not stimulated with PMA

label_protocol: Biotin labled using definded Affymetrix protocol

growth_protocol: THP-1 cells were cultured in RPMI media supplemented with 10% FBS, 2.5mM glutamate, and 0.05mM 2-mercaptoethanol.

extract_protocol: trizol

treatment_protocol: THP-1s were differentiated by adding 200nM phorbol myristrate acetate for three days and then resting without PMA for three additional days.

value: Monocytic leukemia


title: LU134-shBRG1


title: Wild-type mice untreated, rep1


title: LU165-MAX


title: PMA Differentiated THP-1 #3

description: Gene expression data from THP-1s stimulated with PMA

source_name: THP-1s stimulated with PMA


title: Androgenetic hydatidiform mole 1

source_name: Hydatidiform mole

value: Hydropic molar tissue

value: Hydatidiform mole


title: PMA Differentiated THP-1 #2


title: LU165-shBRG1


title: pIgR-KO mice untreated, rep4

value: BALB/c

value: polymeric Ig receptor (pIgR) knockout


title: LU134-MAX


title: Muscle

source_name: Muscle

value: Muscle


title: THP-1 #2


title: LU134-MAX-shBRG1-2


title: Wild-type mice untreated, rep2

value: wild type

value: male


title: Wild-type mice untreated, rep3

value: 6-10 weeks

value: colon


title: LU134-MAX-shBRG1-1


title: Pancreas

source_name: Pancreas

value: Health tissue

value: Pancreas


title: H1417-shBRG1


title: Androgenetic hydatidiform mole 3


title: H1417-MAX


title: PMA Differentiated THP-1 #1


title: LU165-Ø


title: THP-1 #1


title: Androgenetic hydatidiform mole 2


title: Brain 1

source_name: Fetal Brain

value: Fetal Brain


title: Liver

source_name: Liver

value: Liver


title: Brain 2

source_name: Adult Brain

value: female

value: Adult Brain


title: anterior neural fold, stage 18, biological replicate 1

source_name: Xenopus laevis anterior neural fold, stage 18

growth_protocol: Xenopus laevis embryos were grown at 15°C in 1/3 MMR until the desired stage

treatment_protocol: Neural border, neural plate, anterior neural fold, and animal cap explants were microdissected and incubated with trizol on ice for 5 minutes.

value: anterior neural fold

tag: Stage


title: Androgenetic hydatidiform mole 4


title: anterior neural fold, stage 18, biological replicate 2


title: neural border, stage 18, biological replicate 1

source_name: Xenopus laevis neural border, stage 18

value: neural border


title: neural border, stage 14, biological replicate 3

source_name: Xenopus laevis neural border, stage 14


title: LU134-Ø

value: Small Cell Lung Cancer (SCLC)


title: DMSO

city: Osaka

first: Kiyoshi

last: Higashi

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

country: Japan

institute: Sumitomo Chemical Co. Ltd.

description: Gene expression data from fibroblasts

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133_Plus_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: fibroblasts exposed to DMSO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, Affymetrix).

growth_protocol: Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum

extract_protocol: Total RNA were prepared using RNeasy Mini Kit purchased from Qiagen

treatment_protocol: Fibroblasts were treated with 0.1% DMSO, 100 mM HSc025, 2.5ng/ml TGF-beta or 100 mM HSc025 plus 2.5ng/ml TGF-beta for 24 hour

value: dermal fibroblasts


title: 6 h cis-31-treated seedlings vs control: replicate 2

city: Fuchu

first: Naoya

last: Wasano

state: Tokyo

address: Saiwai-cho 3-5-8

institute: Tokyo University of Agriculture & Technology

description: Biological replicate 2 of 2

hyb_protocol: Mixtures of 0.825 µg of Cy3-labeled and Cy5-labeled cRNAs were co-hybridized at 65 °C for 17 h on an Agilent Technologies 4 × 44K Arabidopsis 4 60-mer oligo-microarray.

scan_protocol: The slides were then washed and scanned with an Agilent G2505B Scanner to detect fluorescence intensity.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Data represent the log ratio control/treated. Features flagged in Feature Extraction software as non-uniform (IsFeatNonUnifOL and IsFeatPopnOL field),

organism: Arabidopsis thaliana

source_name: 6 h cis-31-treated seedlings

label_protocol: Two-color spike mix was added to the total RNA, and the RNA was labeled with a Quick Amp Labeling Kit, two-color (Agilent Technologies), according to the manufacturer’s protocol. Fluorescent cRNA was generated from total RNA: 500 ng of RNA was reverse-transcribed with MMLV reverse transcriptase and an oligo(dT) primer containing the T7 promoter, and subsequently transcribed in vitro using T7 RNA polymerase, resulting in Cy3-labeled (control) and Cy5-labeled (cis-CA-treated) cRNAs. The cRNAs were purified through RNeasy Mini Spin columns (Qiagen) and then quantified with a NanoDrop ND-1000 UV-VIS spectrophotometer

growth_protocol: The sterilized seeds were placed on 0.8% agar (Nakalai Tesque, Inc., Kyoto, Japan) with Murashige and Skoog Plant Salt Mixture (Nihon Pharmaceutical Co., Ltd., Tokyo, Japan) and 1% sucrose (Wako Pure Chemical Industries, Osaka, Japan) in a sterilized Petri dish (90-mm diameter). The seeds were held at 4 °C overnight in darkness and then transferred to a growth chamber. Emerging plants were maintained in the growth chamber under a schedule of 16-h light (22 °C) and 8-h dark (20 °C).

extract_protocol: Total RNA extracted using RNeasy following manufacturer's instructions

treatment_protocol: After 14 d in the growth chamber, seedlings were removed from the agar and transferred to 20 ml of deionized water in petri-dish, equilibrated for 1 h at 22 °C. Seedlings were transferred to 20 ml of deionized water containing 20 µM cis-cinnamic acid analogue, and then incubated under light. Plants were collected at 0 (control)and 6 h and immediately frozen in liquid nitrogen, and then stored at –80 °C before analysis.

tag: ecotype

value: Col. 0

value: day 14

value: seedling

source_name: control seedlings


title: HSc025

description: Gene expression data from fibroblasts

source_name: fibroblasts exposed to HSc025


title: Technical Replicate 2

city: Irapuato

first: Jose Luis

last: Hernandez-Flores

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

hyb_protocol: Labelled probes were dried and resuspended in 40 µl of hybridization solution (25% hybridization buffer supplied in the CyScribe kit, 25% nuclease-free water and 50% formamide). The probe was immediately applied onto the array and covered with a cover slip (Hybri-slips, Sigma-Aldrich Co.), and hybridized 16 hours at 45°C in a humid hybridization chamber (Corning Incorporated).  After hybridization, the slides were washed once in solutions 1–4 (wash solution 1: 2% SSC, 0.1% SDS at 45 ºC; wash solution 2: 0.1% SSC, 0.1% SDS; wash solution 3: 0.1% SSC; wash solution 4: 0.01% SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation for 1 min at 1600 r.p.m.

scan_protocol: Slides were scanned with an Axon GenePix® 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels.

data_processing: Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis. Raw data was imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method Robust Multichip Analysis RMA (Irizarry et al., 2003) whereas normalization of the signal intensities within slides was carried out using the printtiploess method (Yang et al., 2002) using the LIMMA package (Smyth and Speed, 2003) (www.bioconductor.org). Normalized data were log2 transformed and then fitted into mixed model ANOVAs (Benjamini and Hochberg, 1995; Wolfinger et al., 2001; Gibson, 2004) using the Mixed procedure. The p-values of the gacA effects were adjusted by the False Discovery Rate method “FDR” (Benjamini and Hochberg, 1995). Estimates of the expression differences were calculated using the mixed model. Based on these statistical analyses, the spots with tests with an FDR value less or equal to 5% and with changes in signal intensity between phTL and wild type strain of 1.5 fold or higher difference were considered as differentially expressed.

organism: Pseudomonas savastanoi pv. phaseolicola

source_name: Pseudomonas syringae pv. phaseolicola wt

label_protocol: aRNA generated by the MessageAmp II-Bacteria Kit (Ambion, AM1790) was labeled accoding to manufacturer's especifications. This kit enables prokaryotic RNA amplification for whole genome expression analysis from bacterial samples. The kit employs an in vitro transcription (IVT)-mediated linear amplification method optimized for use with bacterial RNA. Briefly, 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: P. syringae strains: pv. phaseolicola NPS3121 wild type and phtL- mutant, were grown on M9 minimal medium at 18 ºC.

extract_protocol: Total RNA was isolated using Trizol reagent as recommended by the manufacturer (Invitrogen). A second step of purification was performed using RNeasy MinElute spin columns (Qiagen) to remove contaminating DNA. RNAs were eluted in 50 µl of nuclease-free water (Ambion,, AM9937) and the concentration was determined using the NanoDrop (ND-1000 spectrophotometer) equipment. RNA integrity was checked using the Bioanalyzer 2100 (Agilent, G2938C).

source_name: Pseudomonas syringae pv. phaseolicola PhtL-


title: neural border, stage 14, biological replicate 2


title: neural border, stage 18, biological replicate 2


title: Biological Replicate 3


title: 6 h endo-8-treated seedlings vs control: replicate 1

description: Biological replicate 1 of 2

source_name: 6 h endo-8-treated seedling


title: H1417-Ø


title: TGF-beta

description: Gene expression data from fibroblasts

source_name: fibroblasts exposed to TGF-beta


title: anterior neural fold, stage 18, biological replicate 3


title: 6 h cis-8-treated seedlings vs control: replicate 1

description: Biological replicate 1 of 2

source_name: 6 h cis-8-treated seedling


title: HSc025 plus TGF-beta

description: Gene expression data from fibroblasts

source_name: fibroblasts exposed to HSc025 plus TGF-beta


title: Technical Replicate 3


title: BEC_DP_3

city: Charlottesville

first: Stefan

last: Bekiranov

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry & Molecular Genetics

institute: University of Virginia

description: BEC, DP,biological replicate 3

hyb_protocol: Labeled cRNA was hybridized to GeneChip Mouse Genome 430 2.0 Array chips (Affymetrix) according to the manufacturer's instructions.

scan_protocol: Laser GeneArray scanner

data_processing: The data were analyzed using GCRMA (default settings) to arrive at normalized expression estimates and limma to determine differentially expressed genes within Bioconducotor/R.

source_name: BEC, DP

label_protocol: Total cRNA was biotin-labeled using the Arcturus Turbo Labeling Kit (Life Technologies) according to the manufacturer's instructions.

growth_protocol: C57BL/6 mice were maintained in pathogen-free facilities and procedures were approved by the University of Virginia Animal Care and Use Committee.

extract_protocol: Total RNA was purified using the Arcturus PicoPure RNA Isolation Kit (Life Technologies) according to the manufacturer's instructions and quantified using the NanoDrop 2000 (Thermo Scientific). 20ng of total RNA per sample underwent 2 round of linear amplification using the Arcturus RiboAmp HS Plus Kit (Life Technologies) according to the manufacturer's instructions.

treatment_protocol: 6 week old mice were anesthetized with tribromoethanol, and sacrificed by cervical dislocation. Inguinal, brachial, axillary, cervical, and mesenteric lymph node were harvested and minced with fine dissection scissors. Minced lymph node material was enzymatically digested for 30min in 2%FCS/DMEM media containing 1mg/ml Collagenase IV (Worthington) and 40ug/ml DNAse (Sigma), then 40min with 1mg/ml Collagenase D (Roche) and 40ug/ml DNAse (Sigma) to obtain single cell suspensions. Lymph node stromal cells were negatively selected using CD45 magnetic beads and the MACS system (Miltenyi) according to the manufacturer's instructions, and were >90% pure by flow cytometry. The resulting flow through fraction was then stained with antibodies specific for CD45 (eBioscience), CD31 (eBioscience), and gp38 (hybridoma 8.1.1, gift from Dr. Andrew Farr). DAPI (Sigma) was added as a live/dead discriminatory marker. Lymph node stormal cells were then gated off CD45neg DAPIneg gate and sorted into 4 distinct populations according to their gp38, CD31 expression pattern.

tag: background strain

value: blood endothelial cells

value: Double positive


title: 6 h cis-31-treated seedlings vs control: replicate 1

description: Biological replicate 1 of 2

tag: tissue


title: Biological Replicate 2


title: BEC_DP_2

description: BEC, DP,biological replicate 2


title: 6 h endo-8-treated seedlings vs control: replicate 2

description: Biological replicate 2 of 2


title: Light-touched Rat-blood vs Tickled Rat-blood

city: Tsurumi-ku, Yokohama

first: Katsuyuki

last: Hayashi

state: Kanagawa

address: 1-1-43, Suehiro-cho

department: Business Development

institute: DNA Chip Research Inc

description: Tickled group received stimulation for 4weeks. Stimulation was conducted once per day consisting of two set of four succesive alternating cycles of 15 sec. of resting followed by 15 sse. of stimulation.

hyb_protocol: Equal volumes of Cy5 sample and Cy3 sample were combined, mixed with 2x hybridisation buffer (Agilent Technoloiges) and hybridized to a Whole Rat Genome oligo array (G4131A, Agilent Technologies), for 17 hours at 60°C in an Agilent hybridization oven with

scan_protocol: Scanned on an Agilent G2505B scanner and images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Expression ratios were calculated using Feature Extraction Software (version9.1). GE2-v5_91_0806 was used as a extraction protocol.

organism: Rattus norvegicus

source_name: Light-touched rat

label_protocol: Second strand cDNAs were synthesized from 500ng of total RNA, and non-labeled aminoallyed cRNAs were generated by IVT reactions. cRNAs were labeled with Cy3/Cy5 monoreactive dyes.

extract_protocol: Total RNA was isolated from RNAlater-stabilized hypothalamus using a RNeasy Mini Kit (Qiagen)

value: Peripheral leukocyte

value: adolescent (60 days of age)

value: Wistar

value: male

source_name: Tickled rat


title: BEC_DP_1

description: BEC, DP,biological replicate 1


title: neural plate, stage 12, biological replicate 2

source_name: Xenopus laevis neural plate, stage 12

value: neural plate


title: 6 h cis-8-treated seedlings vs control: replicate 2

description: Biological replicate 2 of 2


title: neural border, stage 14, biological replicate 1


title: S_910

status: Public on Dec 27 2013

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: T

hyb_protocol: Using agitation, array strips were washed for 5 min with bi-distilled water and 5 min with hybridization buffer at room temperature. 10 µl of labeled amplified DNA was mixed with 90 µl of hybridization buffer, then denatured at 95°C during 2 min and subsequently kept on ice. The denatured sample was incubated in the array strip at 50°C for 1 hour. After hybridization, samples were carefully removed from the array strips, then washed 3-times with proprietary buffers (100 µl Washing Buffer I for 5 min at 30°C, 100 µl Washing Buffer II for 5 min at 20°C and 100 µl Washing Buffer III for 5 min at 20°C). To block the reaction, 100 µl of blocking buffer solution (2% of blocking reagent in 6X SSPE/0.005% Triton) was added in each array and incubated 15 min at 30°C with shaking. Then, the blocking solution was removed and 60 µl of HRP streptavidin (100 pg/µl; Poly-HRP streptavidin by Thermo Scientific in 6X SSPE) was added, and the array strips were incubated for 15 min at 30°C. After removal of the conjugation solution, array strips were washed 3-times during 5 min with proprietary buffers. After removal of the washing solution, 50 µl of staining solution (SeramunGrün by Seramun Diagnostica GmbH) was added and incubated for 5 min at 25°C.

scan_protocol: After removal of the staining solution, scanning of the microarrays was performed with the Clondiag Array Mate device (Clondiag GmbH, Germany) following manufacturer's default recommandations.

data_processing: Signal intensities were extracted using IconoClust software (Clondiag GmbH). For each spot, the extinction signal of local background was subtracted from the intensity value. Normalization and analysis were performed using the Partek Genomic Suite 6.4 (Partek, USA). First, array signals were adjusted in order to normalize the quantity of DNA. Each array was normalized against the 8 negative control probes, and then quantile-normalized. Following calibration experiments (not shown), we defined spots with a signal value > 0.35 and a confidence index > 0.75 as positive spots. Differences among the 5 conditions (G, n = 31; Gn, n = 34; N, n = 83; Nn, n = 84; C, n = 443) were sought using ANOVA test, where probes with a fold-change > 2 and a P value< 0.05 were considered as statistically significant.

organism: human oral metagenome

label_protocol: Total gDNA was amplified and biotinylated by duplex PCR using eubacterial universal primers  fD1 (0.4 µM; ccgaattcgtcgacaacAGAGTTTGATCCTGGCTCAG) and rD1 (4 µM; cccgggatccaagcttAAGGAGGTGATCCAGCC). Each 25 µl reaction contained 15 µl of ReadyMix kit (Sigma-Aldrich), 1nM of biotin-16-dUTP and 10 ng of template DNA. Quality control and quantification of PCR products were assessed by using a NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies Inc., USA).

growth_protocol: Gengival fluid from human samples

extract_protocol: Extraction of total genomic DNA (gDNA) was performed with glass beads (Sigma-Aldrich, diameter: 212-300 µm) and DNeasy kit (Qiagen) following the manufacturer’s protocol. Asymmetrical PCR was chosen in order to favor the amplification of the negative strand.

treatment_protocol: Soak in chaotrophic buffer and stocked at -80°C until purification

tag: patient category and number

tag: sample type

value: Control


title: S_909

description: T


title: S_908

description: T


title: S_912

description: T


title: S_911

description: T


title: neural plate, stage 12, biological replicate 1


title: S_907

description: T


title: S_906

description: T


title: S_905

description: T


title: S_904

description: T


title: S_903

description: T


title: animal cap, stage 14, biological replicate 1

source_name: Xenopus laevis animal cap explant, stage 14

value: animal cap explant (epidermis)


title: LEC_CD31_3

description: LEC CD31+, biological replicate 3

source_name: LEC CD31+

value: lymphatic endothelial cells


title: S_902

description: T


title: Control Rat-blood vs Tickled Rat-blood

source_name: No stimulated rat


title: LEC_CD31_2

description: LEC CD31+, biological replicate 2


title: S_901

description: T


title: S_898

description: T


title: S_900

description: T


title: S_899

description: T


title: Control Rat- salivary glands vs Tickled Rat- salivary glands

value: Salivary glands


title: LEC_CD31_1

description: LEC CD31+, biological replicate 1


title: S_897

description: T


title: Control Rat-striatum vs Tickled Rat-striatum

value: Striatum


title: S_894

description: T


title: S_895

description: T


title: S_896

description: T


title: Biological Replicate 1


title: S_892

description: T


title: S_893

description: T


title: S_890

description: T


title: S_891

description: T


title: S_885

description: T


title: S_886

description: T


title: S_887

description: T


title: S_888

description: T


title: S_884

description: T


title: Technical Replicate 1


title: S_889

description: T


title: S_882

description: T


title: S_881

description: T


title: S_880

description: T


title: S_883

description: T


title: S_879

description: T


title: Light-touched Rat-striatum vs Tickled Rat-striatum

description: Both groups received stimulation for 4weeks. Stimulation was conducted once per day consisting of two set of four succesive alternating cycles of 15 sec. of resting followed by 15 sec. of stimulation.


title: S_877

description: T


title: S_875

description: T


title: S_876

description: T


title: S_872

description: H

value: témoin hôpital

value: H


title: S_873

description: H


title: S_871

description: T


title: S_870

description: T


title: S_867

description: T


title: S_868

description: H


title: S_866

description: T


title: S_864

description: T


title: S_869

description: T


title: S_878

description: T


title: S_860

description: T


title: S_856

description: Lesion-side

value: noma 34

value: NOMA


title: S_857

description: T


title: S_858

description: H


title: S_861

description: T


title: S_854

description: Lesion-side

value: noma 33


title: S_863

description: T


title: S_853

description: Healthy-side


title: S_855

description: Healthy-side


title: S_852

description: Lesion-side

value: noma 31


title: S_848

description: Lesion-side

value: noma 25


title: S_850

description: Lesion-side

value: noma 27


title: S_849

description: Healthy-side


title: S_862

description: T


title: S_847

description: Lesion-side

value: noma 22


title: S_845

description: Healthy-side

value: noma 19


title: S_859

description: T


title: S_846

description: Healthy-side


title: S_865

description: T


title: S_843

description: Healthy-side

value: noma 18


title: S_844

description: Lesion-side


title: S_842

description: Healthy-side

value: noma 17


title: S_841

description: Healthy-side

value: NOMA 16


title: S_837

description: Lesion-side

value: noma 11


title: S_835

description: Lesion-side

value: noma 10


title: S_839

description: Healthy-side

value: noma 15


title: S_834

description: Healthy-side

value: noma 8


title: S_836

description: Healthy-side


title: S_833

description: Lesion-side

value: noma 7


title: S_831

description: Lesion-side

value: noma 5


title: S_832

description: Healthy-side

value: noma 6


title: S_840

description: Lesion-side

value: NOMA


title: S_838

description: Lesion-side

value: noma 12


title: Light-touched Rat- salivary glands vs Tickled Rat- salivary glands

value: Salivary glands

value: adolescent (60 days of age)

value: Wistar

value: male


title: S_830

description: Healthy-side

value: NOMA 3


title: S_818

description: Healthy-side

value: gingivite 8

value: Gengivitis


title: S_829

description: Lesion-side

value: noma 2


title: S_822

description: Healthy-side

value: gingivite 15


title: S_826

description: Healthy-side

value: gingivite 18


title: S_825

description: Healthy-side

value: gingivite 17


title: S_816

description: Lesion-side

value: gingivite 6


title: S_828

description: Lesion-side

value: noma 1


title: S_817

description: Healthy-side

value: gingivite 7


title: S_819

description: Lesion-side


title: S_821

description: Lesion-side

value: gingivite 13


title: S_827

description: Lesion-side

value: gingivite 19


title: S_823

description: Healthy-side

value: gingivite 16


title: S_814

description: Lesion-side

value: gingivite 3


title: S_815

description: Lesion-side

value: gingivite 4


title: S_824

description: Lesion-side


title: S_820

description: Lesion-side

value: gingivite 10


title: S_813

description: Lesion-side

value: noma antibio 7

value: N-ATB


title: S_810

description: Healthy-side

value: noma antibio 3


title: S_809

description: Lesion-side

value: noma antibio 2


title: S_808

description: Lesion-side

value: noma antibio 1


title: S_812

description: Healthy-side


title: S_807

description: Healthy-side

value: noma antibio 10


title: S_806

description: T

value: Control


title: S_805

description: T


title: S_804

description: Healthy-side

value: noma antibio 18


title: S_803

description: Healthy-side

value: gingivite 45

value: Gengivitis


title: S_802

description: T


title: S_801

description: T


title: S_800

description: T


title: S_811

description: Lesion-side


title: S_799

description: T


title: S_798

description: T


title: S_793

description: Healthy-side


title: S_797

description: Lesion-side

value: noma 8

value: NOMA


title: S_794

description: Healthy-side

value: noma 5


title: S_790

description: T


title: S_795

description: Lesion-side

value: noma 6


title: S_791

description: T


title: S_796

description: Healthy-side

value: noma 7


title: S_789

description: T


title: S_786

description: Healthy-side


title: S_787

description: Lesion-side


title: S_785

description: T


title: S_788

description: Lesion-side

value: noma 35


title: S_784

description: T


title: S_783

description: T


title: S_782

description: T


title: S_779

description: T


title: S_781

description: T


title: S_792

description: Healthy-side

value: gingivite 3


title: S_778

description: T


title: S_777

description: Healthy-side


title: S_775

description: T


title: S_776

description: Lesion-side

value: gingivite 17


title: S_774

description: Healthy-side

value: noma 31


title: S_780

description: T


title: S_770

description: T


title: S_772

description: T


title: S_771

description: T


title: S_766

description: T


title: S_767

description: T


title: S_769

description: T


title: S_768

description: T


title: S_765

description: T


title: S_758

description: Healthy-side

value: noma 32


title: S_762

description: T


title: S_756

description: Healthy-side

value: noma 30


title: S_759

description: Healthy-side

value: noma 36


title: S_757

description: Lesion-side


title: S_760

description: Lesion-side


title: S_761

description: T


title: S_754

description: Healthy-side

value: noma antibio 5

value: N-ATB


title: S_755

description: Healthy-side

value: noma 29


title: S_753

description: Lesion-side

value: noma antibio 4


title: S_764

description: T

value: Control


title: S_763

description: T


title: S_751

description: T


title: S_773

description: T


title: S_752

description: Healthy-side


title: S_748

description: T


title: S_750

description: T


title: S_747

description: T


title: S_744

description: T


title: S_745

description: T


title: S_746

description: T


title: S_740

description: T


title: S_738

description: T


title: S_734

description: T


title: S_735

description: T


title: S_742

description: T


title: S_737

description: T


title: S_741

description: T


title: S_732

description: T


title: S_729

description: T


title: S_731

description: T


title: S_733

description: T


title: S_739

description: T

value: tém.village-N36 bis


title: S_728

description: T


title: S_727

description: T


title: S_725

description: Lesion-side

value: noma antibio 18


title: S_726

description: T


title: S_723

description: Lesion-side

value: noma antibio 15


title: S_730

description: T


title: S_721

description: Lesion-side

value: Noma 60

value: NOMA


title: S_722

description: Healthy-side


title: S_743

description: T


title: S_724

description: Healthy-side


title: S_720

description: Healthy-side


title: S_736

description: T


title: S_718

description: Healthy-side

value: Noma 58


title: S_719

description: Lesion-side


title: S_874

description: T


title: S_851

description: Lesion-side


title: S_714

description: Healthy-side

value: Noma 56


title: S_717

description: Lesion-side

value: Noma 57


title: S_715

description: Lesion-side


title: S_716

description: Healthy-side


title: S_713

description: Lesion-side

value: ginigivite 67

value: Gengivitis


title: S_709

description: Lesion-side

value: gingivite 68


title: S_712

description: Healthy-side


title: S_706

description: Healthy-side

value: gingivite 62


title: S_702

description: Healthy-side

value: gingivite 49


title: S_701

description: Lesion-side

value: gingivite 45


title: S_698

description: Healthy-side

value: gingivite 44


title: S_707

description: Lesion-side


title: S_705

description: Lesion-side

value: gingivite 57


title: S_694

description: T

value: Control


title: S_696

description: Healthy-side

value: gingivite 37


title: S_697

description: Lesion-side


title: S_695

description: T


title: S_703

description: Lesion-side


title: S_700

description: Healthy-side


title: S_699

description: Lesion-side


title: S_711

description: Lesion-side

value: ginigivite 66


title: S_710

description: Healthy-side


title: S_708

description: Healthy-side


title: S_693

description: T


title: S_704

description: Healthy-side


title: S_690

description: T


title: S_691

description: T


title: S_689

description: T


title: S_686

description: T


title: S_687

description: T


title: S_688

description: T


title: S_681

description: Healthy-side

value: noma 39


title: S_682

description: T

value: tém.village-N36 bis


title: S_684

description: Lesion-side

value: noma 26

value: NOMA


title: S_683

description: Healthy-side

value: noma antibio 1

value: N-ATB


title: S_680

description: T


title: S_677

description: T


title: S_676

description: T


title: S_678

description: T


title: S_692

description: T


title: S_674

description: T


title: S_670

description: T


title: S_675

description: T


title: S_672

description: T


title: S_673

description: T


title: S_671

description: T


title: S_668

description: T


title: S_685

description: T


title: S_667

description: T


title: S_665

description: T


title: S_666

description: Lesion-side


title: S_664

description: T


title: S_663

description: T


title: S_679

description: T


title: S_661

description: T


title: S_660

description: T


title: S_658

description: T


title: S_662

description: T


title: S_654

description: T


title: S_659

description: T


title: S_650

description: T


title: S_652

description: T


title: S_653

description: Healthy-side

value: noma 40


title: S_669

description: T


title: S_657

description: Lesion-side


title: S_651

description: T


title: S_649

description: Lesion-side

value: noma 38


title: S_647

description: T


title: S_646

description: Lesion-side

value: noma antibio 16


title: S_645

description: Healthy-side


title: S_642

description: Lesion-side

value: noma antibio 14


title: S_648

description: Healthy-side


title: S_656

description: T


title: S_655

description: T


title: S_643

description: Lesion-side

value: noma antibio 15


title: S_644

description: T


title: S_637

description: T


title: S_634

description: Lesion-side

value: noma antibio 6


title: S_638

description: Healthy-side

value: noma antibio 13


title: S_641

description: Healthy-side


title: S_635

description: Lesion-side

value: noma antibio 9


title: S_636

description: T

value: Control


title: S_629

description: T


title: S_639

description: Lesion-side


title: S_640

description: T


title: S_630

description: Lesion-side

value: noma antibio 11


title: S_626

description: T


title: S_631

description: Lesion-side

value: noma antibio 12


title: S_627

description: T


title: S_628

description: T


title: S_632

description: Lesion-side

value: noma antibio 5


title: S_625

description: T


title: S_622

description: T


title: S_624

description: T


title: S_620

description: T


title: S_621

description: T


title: S_619

description: T


title: S_618

description: T


title: S_633

description: Healthy-side


title: S_617

description: T


title: S_616

description: T


title: S_615

description: T


title: S_623

description: T


title: S_613

description: T


title: S_610

description: T


title: S_611

description: T


title: S_609

description: T


title: S_612

description: T


title: S_605

description: T


title: S_602

description: T


title: S_606

description: T


title: S_607

description: T


title: S_608

description: T


title: S_604

description: T


title: S_603

description: T


title: S_598

description: T


title: S_600

description: T


title: S_599

description: T


title: S_601

description: T


title: S_592

description: T


title: S_597

description: T


title: S_591

description: T


title: S_614

description: T


title: S_594

description: T


title: S_590

description: T


title: S_596

description: T


title: S_593

description: T


title: S_589

description: T


title: S_588

description: T


title: S_586

description: T


title: S_583

description: T


title: S_584

description: T


title: S_585

description: T


title: S_582

description: T


title: S_749

description: T


title: S_595

description: T


title: S_577

description: Lesion-side

value: noma 21


title: S_578

description: Lesion-side

value: noma 23


title: S_581

description: Healthy-side

value: noma 26

value: NOMA


title: S_570

description: Lesion-side

value: noma 16


title: S_574

description: Healthy-side

value: noma 20


title: S_562

description: T


title: S_563

description: Healthy-side

value: gingivite 9

value: Gengivitis


title: S_571

description: Lesion-side

value: noma 17


title: S_568

description: Healthy-side

value: noma 14


title: S_576

description: Healthy-side


title: S_569

description: Lesion-side


title: S_566

description: Healthy-side

value: noma 13


title: S_579

description: Healthy-side


title: S_567

description: Lesion-side


title: S_575

description: Lesion-side


title: S_572

description: Lesion-side

value: noma 19


title: S_580

description: Healthy-side

value: noma 25


title: S_561

description: T

value: Control


title: S_560

description: T


title: S_559

description: T


title: S_558

description: T


title: S_557

description: T


title: S_573

description: Healthy-side

value: noma 2


title: S_554

description: T


title: S_555

description: T


title: S_565

description: Healthy-side

value: noma 12


title: S_553

description: T


title: S_556

description: T


title: S_564

description: Lesion-side


title: S_587

description: T


title: S_551

description: T


title: S_552

description: T


title: S_546

description: T


title: S_550

description: T


title: S_547

description: T


title: S_544

description: T


title: S_549

description: T


title: S_548

description: T


title: S_538

description: Healthy-side

value: gingivite 5


title: S_541

description: Healthy-side

value: noma 1


title: S_533

description: Lesion-side

value: gingivite 12


title: S_542

description: Healthy-side

value: noma 10


title: S_539

description: Healthy-side

value: gingivite 6


title: S_530

description: Healthy-side

value: gingivite 10


title: S_534

description: Healthy-side

value: gingivite 13


title: S_536

description: Lesion-side

value: gingivite 14


title: S_543

description: Healthy-side

value: NOMA


title: S_531

description: Lesion-side

value: gingivite 11

value: Gengivitis


title: S_535

description: Healthy-side


title: S_526

description: Healthy-side

value: gingivite 53


title: S_529

description: Healthy-side

value: gingivite 1


title: S_528

description: Healthy-side

value: gingivite 54


title: S_527

description: Lesion-side


title: S_524

description: T

value: Control


title: S_540

description: Lesion-side

value: gingivite 7


title: S_537

description: Lesion-side

value: gingivite 15


title: S_545

description: T


title: S_532

description: Healthy-side


title: S_523

description: T


title: S_522

description: Healthy-side

value: noma antibio 20

value: N-ATB


title: S_525

description: Lesion-side


title: S_521

description: Lesion-side


title: S_520

description: T


title: S_514

description: Healthy-side

value: Noma 45


title: S_519

description: T


title: S_513

description: Lesion-side


title: S_517

description: Lesion-side

value: noma antibio 21


title: S_512

description: T


title: S_516

description: T


title: S_510

description: Lesion-side

value: Noma 50


title: S_511

description: T


title: S_502

description: Unknown

value: gingivite 5

value: Unknown


title: S_505

description: Lesion-side

value: noma 41


title: S_506

description: Healthy-side

value: NOMA


title: S_508

description: T


title: S_518

description: Healthy-side


title: S_507

description: T


title: S_503

description: Unknown


title: S_498

description: T


title: S_501

description: T


title: S_504

description: Healthy-side


title: S_509

description: Healthy-side


title: S_497

description: T


title: S_496

description: T


title: S_500

description: T


title: S_499

description: T


title: S_495

description: T


title: S_494

description: T


title: S_515

description: T


title: S_493

description: T


title: S_491

description: T


title: S_492

description: T


title: S_490

description: Unknown

value: noma antibio 12


title: S_486

description: Unknown

value: noma antibio 9


title: S_489

description: Unknown

value: noma antibio 11


title: S_488

description: Unknown

value: noma antibio 10


title: S_487

description: Unknown


title: S_485

description: Unknown

value: noma 35


title: S_483

description: Unknown

value: noma 31


title: S_482

description: Unknown


title: S_481

description: Unknown

value: gingivite 17


title: S_478

description: T

value: Control


title: S_474

description: T


title: S_476

description: Lesion-side

value: noma 24


title: S_473

description: T


title: S_475

description: T


title: S_480

description: Unknown

value: gingivite 11


title: S_479

description: T


title: S_472

description: T


title: S_469

description: Healthy-side

value: noma antibio 1

value: N-ATB


title: S_467

description: T

value: tém.villag- E1


title: S_468

description: T


title: S_471

description: T


title: S_466

description: T


title: S_465

description: T


title: S_470

description: T


title: S_464

description: T


title: S_484

description: Unknown

value: noma 32


title: S_462

description: T


title: S_477

description: T


title: S_461

description: T


title: S_460

description: T


title: S_459

description: T


title: S_458

description: T


title: S_454

description: T


title: S_457

description: T


title: S_455

description: T


title: S_456

description: T


title: S_452

description: T


title: S_451

description: T


title: S_450

description: T


title: S_449

description: T


title: S_442

description: T


title: S_446

description: T


title: S_445

description: Lesion-side

value: Noma 47


title: S_448

description: T


title: S_447

description: T


title: S_443

description: T


title: S_441

description: T

value: tém.village N


title: S_438

description: T


title: S_444

description: T


title: S_437

description: T


title: S_463

description: T


title: S_434

description: T


title: S_436

description: T


title: S_439

description: T


title: S_440

description: Healthy-side

value: gingivite 53

value: Gengivitis


title: S_435

description: T


title: S_453

description: T


title: S_433

description: T


title: S_432

description: T


title: S_430

description: T


title: S_431

description: Healthy-side

value: Noma 44

value: NOMA


title: S_429

description: Lesion-side

value: Noma 42


title: S_428

description: T


title: S_427

description: T


title: S_426

description: T


title: S_425

description: T


title: S_424

description: T


title: S_423

description: T


title: S_422

description: T


title: S_414

description: T


title: S_420

description: T


title: S_421

description: T


title: S_419

description: T


title: S_417

description: T


title: S_418

description: T


title: S_413

description: T


title: S_410

description: T


title: S_415

description: T


title: S_416

description: T


title: S_411

description: T


title: S_402

description: T


title: S_406

description: T


title: S_407

description: T


title: S_405

description: T


title: S_403

description: T


title: S_404

description: T


title: S_408

description: T


title: S_401

description: T


title: S_395

description: T


title: S_396

description: Lesion-side

value: Noma 55


title: S_397

description: Lesion-side


title: S_394

description: Healthy-side


title: S_412

description: T


title: S_409

description: T


title: S_393

description: T


title: S_399

description: T


title: S_400

description: T


title: S_390

description: T


title: S_398

description: T


title: S_391

description: T


title: S_386

description: Lesion-side

value: Noma 43


title: S_382

description: T


title: S_392

description: T


title: S_384

description: T


title: S_387

description: Healthy-side

value: Noma 59


title: S_385

description: Lesion-side


title: S_383

description: Lesion-side

value: Noma 41


title: S_381

description: T

value: Control


title: S_377

description: Lesion-side


title: S_378

description: Healthy-side

value: Noma 64


title: S_380

description: Healthy-side


title: S_379

description: Lesion-side

value: noma antibio 17


title: S_376

description: T


title: S_375

description: T


title: S_374

description: T


title: S_389

description: Healthy-side


title: S_372

description: T


title: S_371

description: T


title: S_373

description: Lesion-side


title: S_388

description: T


title: S_369

description: T


title: S_368

description: Lesion-side


title: S_367

description: T


title: S_366

description: T


title: S_363

description: Healthy-side


title: S_362

description: Healthy-side


title: S_370

description: T


title: S_358

description: T


title: S_359

description: T


title: S_360

value: Pas de PCR


title: S_365

description: T


title: S_361

description: Healthy-side


title: S_353

description: T


title: S_350

description: T


title: S_357

description: T


title: S_352

description: T


title: S_351

description: T


title: S_355

description: Healthy-side

value: Noma 52


title: S_354

description: T


title: S_364

description: T


title: S_346

description: Lesion-side


title: S_349

description: T


title: S_341

description: T


title: S_343

description: T


title: S_339

description: T


title: S_348

description: T


title: S_345

description: T


title: S_344

description: T


title: S_338

description: T


title: S_347

description: Healthy-side


title: S_340

description: Lesion-side


title: S_356

description: T


title: S_336

description: T


title: S_334

description: T


title: S_335

description: T


title: S_342

description: T


title: S_333

description: T


title: S_330

description: Healthy-side


title: S_332

description: T


title: S_337

description: T


title: S_329

description: T


title: S_326

description: ES

value: noma antibio 20

value: N-ATB


title: S_325

description: T


title: S_328

description: Lesion-side

value: noma antibio 19


title: S_327

description: T


title: S_324

description: T


title: S_323

description: Lesion-side


title: S_321

description: T


title: S_318

description: Healthy-side

value: Noma 62


title: S_313

description: Healthy-side


title: S_322

description: Healthy-side


title: S_310

description: Lesion-side

value: Noma 48


title: S_331

description: T


title: S_314

description: T


title: S_312

description: Healthy-side


title: S_311

description: Lesion-side


title: S_309

description: T


title: S_319

description: T


title: S_316

description: Lesion-side


title: S_315

description: T


title: S_320

description: Healthy-side


title: S_306

description: Lesion-side

value: Noma 46


title: S_307

description: Healthy-side

value: NOMA


title: S_305

description: Lesion-side


title: S_304

description: T


title: S_303

description: Lesion-side

value: Noma 49


title: S_302

description: Healthy-side


title: S_308

description: T


title: S_298

description: Lesion-side

value: Noma 61


title: S_300

description: Healthy-side


title: S_301

description: T


title: S_317

description: Healthy-side


title: S_299

description: Lesion-side

value: Noma 63


title: S_297

description: Lesion-side


title: S_296

description: Lesion-side


title: S_295

description: T


title: S_290

description: Lesion-side


title: S_293

description: T


title: S_292

description: Lesion-side


title: S_285

description: Healthy-side

value: Noma 51


title: S_281

description: T


title: S_282

description: Lesion-side

value: Noma 43


title: S_286

description: T

value: Control


title: S_287

description: Lesion-side


title: S_284

description: Healthy-side


title: S_280

description: T


title: S_283

description: Lesion-side

value: Noma 50


title: S_288

description: T


title: S_278

description: T


title: S_279

description: T


title: S_277

description: Healthy-side

value: Noma 65


title: S_276

description: T


title: S_275

description: T


title: S_291

description: Healthy-side


title: S_294

description: T


title: S_269

description: Healthy-side

value: Noma 41


title: S_266

description: Healthy-side


title: S_273

description: T


title: S_272

description: T


title: S_271

description: T


title: S_270

description: Healthy-side


title: S_289

description: Healthy-side


title: S_268

description: Lesion-side


title: S_267

description: Lesion-side


title: S_263

description: T


title: S_264

description: Healthy-side


title: S_265

description: Lesion-side


title: S_262

description: Lesion-side

value: Noma 52


title: S_258

description: T


title: S_260

description: T


title: S_259

description: Healthy-side

value: Noma 42


title: S_261

description: T


title: S_257

description: Healthy-side

value: Noma 54


title: S_254

description: Lesion-side

value: Noma 47


title: S_274

description: T

value: tém.village-N24 ?


title: S_250

description: Lesion-side


title: S_253

description: T


title: S_255

description: T


title: S_256

description: Lesion-side

value: Noma 44


title: S_251

description: T


title: S_252

description: Healthy-side


title: S_249

description: Healthy-side

value: Noma 53


title: S_246

description: T


title: S_247

description: Lesion-side

value: NOMA


title: S_248

description: T


title: S_244

description: Healthy-side

value: Noma 45


title: S_245

description: T


title: S_243

description: T


title: S_238

description: T


title: S_239

description: T


title: S_240

description: T


title: S_242

description: T


title: S_237

description: T


title: S_236

description: T


title: S_234

description: T


title: S_235

description: T


title: S_233

description: T


title: S_232

value: Ctl nég de la PCR


title: S_230

description: T


title: S_229

description: Healthy-side

value: Noma 49


title: S_228

description: T


title: S_226

description: Lesion-side

value: Noma 64


title: S_220

description: Lesion-side

value: Noma 63


title: S_221

description: T

value: Control


title: S_222

description: T


title: S_225

description: T


title: S_223

description: Healthy-side

value: Noma 48


title: S_224

description: T


title: S_218

description: Lesion-side


title: S_241

description: Lesion-side


title: S_217

description: T


title: S_214

description: Healthy-side

value: gingivite 54

value: Gengivitis


title: S_213

description: T


title: S_211

description: T


title: S_209

description: T


title: S_210

description: Lesion-side


title: S_212

description: Healthy-side


title: S_216

description: Lesion-side


title: S_227

description: Healthy-side

value: noma antibio 17

value: N-ATB


title: S_204

description: T


title: S_203

description: Healthy-side

value: noma antibio 19


title: S_202

description: T


title: S_219

description: Healthy-side


title: S_201

description: T


title: S_198

description: T


title: S_215

description: Lesion-side


title: S_231

description: T


title: S_193

description: T


title: S_199

description: Healthy-side


title: S_191

description: Lesion-side

value: Noma 61


title: S_192

description: T


title: S_196

description: Healthy-side

value: noma antibio 21


title: S_197

description: Healthy-side


title: S_208

description: Healthy-side

value: Noma 42


title: S_200

description: T


title: S_206

description: T


title: S_194

description: Lesion-side


title: S_195

description: Healthy-side


title: S_190

description: T


title: S_205

description: T


title: S_185

description: Lesion-side

value: Noma 59


title: S_188

description: T


title: S_183

description: T


title: S_187

description: Lesion-side


title: S_189

description: Lesion-side


title: S_186

description: T


title: S_182

description: Lesion-side


title: S_184

description: Healthy-side

value: NOMA


title: S_179

description: Healthy-side


title: S_207

description: T


title: S_181

description: T


title: S_178

description: T


title: S_180

description: T


title: S_177

description: Lesion-side

value: noma 9


title: S_175

description: Lesion-side

value: noma 4


title: S_176

description: Healthy-side


title: S_174

description: Healthy-side


title: S_165

description: T


title: S_166

description: T

value: tém.villag- E1


title: S_170

description: Lesion-side

value: gingivite 2


title: S_173

description: Lesion-side

value: noma 3


title: S_167

description: T

value: Control


title: S_172

description: Lesion-side

value: gingivite 5


title: S_163

description: H

value: témoin hôpital

value: H


title: S_171

description: Lesion-side

value: gingivite 1

value: Gengivitis


title: S_168

description: T


title: S_161

description: T


title: S_169

description: Healthy-side


title: S_156

description: T


title: S_157

description: T


title: S_153

description: H

value: témoin hôpital 11


title: S_158

description: T


title: S_159

description: T


title: S_160

description: T


title: S_152

description: H


title: S_154

description: T


title: S_151

description: H


title: S_150

description: H


title: S_147

description: T


title: S_164

description: T


title: S_146

description: Lesion-side

value: noma antibio 7

value: N-ATB


title: S_148

description: T


title: S_149

description: Healthy-side

value: gingivite 11


title: S_145

description: Healthy-side


title: S_155

description: T


title: S_144

description: Healthy-side

value: Noma 47


title: S_136

description: Lesion-side

value: Noma 44

value: NOMA


title: S_140

description: Lesion-side

value: Noma 53


title: S_139

description: T


title: S_162

description: T


title: S_141

description: Healthy-side


title: S_137

description: Healthy-side

value: Noma 52


title: S_143

description: T


title: S_142

description: T


title: S_135

description: Healthy-side

value: Noma 45


title: S_134

description: Lesion-side


title: S_132

description: Lesion-side


title: S_133

description: T


title: S_138

description: T


title: S_131

description: Healthy-side

value: Noma 54


title: S_129

description: Lesion-side

value: Noma 42


title: S_128

description: Lesion-side


title: S_125

description: T

value: Control


title: S_126

description: T


title: S_127

description: T


title: S_123

description: Lesion-side

value: gingivite 18


title: S_124

description: Lesion-side

value: noma 32


title: S_118

description: T


title: S_119

description: T


title: S_121

description: T


title: S_117

description: T


title: S_120

description: T


title: S_130

description: Healthy-side


title: S_113

description: Healthy-side

value: noma 19


title: S_114

description: Healthy-side

value: noma 22


title: S_116

description: T


title: S_112

description: Lesion-side

value: noma 18


title: S_111

description: Healthy-side


title: S_108

description: T


title: S_106

description: Lesion-side

value: gengivite 8

value: Gengivitis


title: S_107

description: T


title: S_104

description: Healthy-side

value: noma 16


title: S_105

description: Healthy-side


title: S_122

description: Healthy-side

value: gingivite 19


title: S_110

description: T


title: S_109

description: Healthy-side

value: noma 17


title: S_99

description: Healthy-side

value: noma 11

value: NOMA


title: S_103

description: Lesion-side

value: noma 15


title: S_102

description: Healthy-side


title: S_95

description: Lesion-side

value: gengivite 6


title: S_100

description: Lesion-side


title: S_101

description: Lesion-side

value: noma 12


title: S_98

description: T


title: S_96

description: Healthy-side

value: gengivite 7


title: S_94

description: Lesion-side

value: gengivite 4


title: S_93

description: Lesion-side

value: gengivite 3


title: S_115

description: Lesion-side


title: S_91

description: Lesion-side

value: noma 10


title: S_90

description: T

value: Control


title: S_89

description: Healthy-side

value: noma 8


title: S_88

description: Lesion-side

value: noma 7


title: S_87

description: Healthy-side

value: noma 6


title: S_86

description: Lesion-side

value: noma 5


title: S_85

description: T


title: S_84

description: Lesion-side

value: noma 2


title: S_82

description: T


title: S_97

description: T


title: S_80

description: T


title: S_83

description: T


title: S_92

description: T


title: S_81

description: Lesion-side

value: noma 1


title: S_79

description: T


title: S_76

description: T


title: S_78

description: T


title: S_74

description: T


title: S_75

description: T


title: S_73

description: Unknown


title: corneal endothelia of young mice Y2

city: Qingdao

first: Ye

last: Wang

address: No. 5 Yan'erdao Road

country: China

institute: Shandong Eye Institute

description: SAMPLE Y2

hyb_protocol: Hybridized on the miRCURY™ LNA Array (v.16.0) following standard Exiqon protocol.

scan_protocol: Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor.
Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.
Study encompasses only those microRNAs specific for mouse, mouse cytomegalovirus, mouse gammaherpesvirus.

source_name: corneal endothelia of young mice

label_protocol: After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY Hy3/Hy5 Power labeling kit

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

value: corneal endothelia

value: BALB/c

value: 10-13 weeks

value: Male


title: corneal endothelia of old mice S1

description: SAMPLE S1

source_name: corneal endothelia of old mice

value: 2 years


title: corneal endothelia of young mice Y3

description: SAMPLE Y3


title: corneal endothelia of old mice S3

description: SAMPLE S3


title: S_72

description: Healthy-side

value: gengivite 17

value: Gengivitis


title: corneal endothelia of young mice Y1

description: SAMPLE Y1


title: S_71

description: Lesion-side

value: gengivite 16


title: S_70

description: Healthy-side


title: S_68

description: T


title: S_67

description: T


title: corneal endothelia of old mice S2

description: SAMPLE S2


title: S_69

description: T


title: S_65

description: Lesion-side

value: noma 33

value: NOMA


title: S_64

description: Healthy-side


title: S_77

description: T

value: Control


title: S_62

description: T


title: S_63

description: Lesion-side

value: noma 31


title: S_58

description: T


title: S_61

description: Healthy-side

value: noma antibio 7

value: N-ATB


title: S_59

description: T


title: S_60

description: Healthy-side


title: S_66

description: Healthy-side

value: gengivite 15


title: S_57

description: T


title: S_56

description: T


title: S_54

description: T


title: S_53

description: T


title: S_52

description: Lesion-side

value: noma 27


title: Luc-Tanoue

city: Sapporo

first: takashi

last: kondo

state: Hokkaido

address: South-1, West-16, Chuo-ku

department: Clinical Laboratory Medicine

institute: Sapporo Medical University

description: Gene expression after 6hr in 0.5Gy-irradiated human blood

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1. (Agilent)

source_name: Peripheral Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN), according to the protocol provided by the manufacturer.

tag: phenotyp

value: B-ALL line

value: Tanoue


title: RNA_HVH_sample227 [HumanHT-12 V4.0]

city: Seattle

first: Daniel

middle: A

last: Enquobahrie

state: Washington

address: 1730 Minor Avenue

department: Cardiovascular Health Research Unit

institute: University of Washington

hyb_protocol: Total RNA was hybridized onto Illumina HumanHT-12v4 Beadchip arrays (Illumina, San Diego, CA)

scan_protocol: Scanned images of the array chips were imported into Illumina’s GenomeStudio Gene Expression Module

data_processing: quantile normalization using R version 2.15.2 and the package "aroma.light".  Normalized results were then log2 transformed.

label_protocol: Total RNA labeled with biotin using Illumina® TotalPrep™-96 RNA Amplification Kit (Life Technologies Corp., Carlsbad, CA)

extract_protocol: Total RNA was extracted using PAXgene Blood RNA Kit (QIAGEN Inc., Valencia, CA)

tag: age (yrs)

value: male

value: blood


title: RNA_HVH_sample226 [HumanHT-12 V4.0]

value: female


title: RNA_HVH_sample220 [HumanHT-12 V4.0]


title: SW480, Luc vs. SW480, siRNA_beta-catenin-1

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

description: Integrative ChIP-seq/microarray analysis identifies a beta-catenin target signature enriched in intestinal stem cells and colon cancer. Kazuhide Watanabe, Jacob Biesinger, Michael L. Salmans, Brian S. Roberts, William T. Arthur, Michele Cleary, Bogi Andersen, Xiaohui Xie and Xing Dai. PLOS ONE 2014.  SW480 cells were transfected with control and beta-catenin siRNAs.  Twenty-four hours after transfection, RNA was extracted from the cells using the RNeasy kit (Qiagen, Valencia, CA) and genome-wide cDNA microarray expression analysis was performed.   The data reported here are the microarray data as processed by the standard Rosetta Resolver(R) ratio method for Agilent microarrays.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: conditions

value: SW480, Luc

value: SW480, siRNA_beta-catenin-1


title: RNA_HVH_sample216 [HumanHT-12 V4.0]


title: SW480, Luc vs. SW480, siRNA_beta-catenin-2

value: SW480, siRNA_beta-catenin-2


title: RNA_HVH_sample224 [HumanHT-12 V4.0]


title: RNA_HVH_sample225 [HumanHT-12 V4.0]


title: RNA_HVH_sample217 [HumanHT-12 V4.0]


title: Tanoue-F4

description: Gene expression after 6hr in 0Gy-irradiated human blood

value: highly invasive B-ALL line


title: RNA_HVH_sample223 [HumanHT-12 V4.0]


title: RNA_HVH_sample221 [HumanHT-12 V4.0]


title: RNA_HVH_sample222 [HumanHT-12 V4.0]


title: S_55

description: T


title: RNA_HVH_sample228 [HumanHT-12 V4.0]


title: S_51

description: Healthy-side


title: RNA_HVH_sample218 [HumanHT-12 V4.0]


title: RNA_HVH_sample219 [HumanHT-12 V4.0]


title: S_49

description: T


title: S_50

description: Healthy-side

value: noma 3


title: RNA_HVH_sample215 [HumanHT-12 V4.0]


title: S_48

description: T


title: S_46

description: T


title: RNA_HVH_sample214 [HumanHT-12 V4.0]


title: S_45

description: T


title: S_43

description: T


title: S_41

description: T


title: S_42

description: Lesion-side

value: noma antibio 1


title: S_44

description: T

value: Control


title: S_47

description: T


title: S_37

description: Lesion-side

value: noma antibio 3


title: S_38

description: T


title: S_39

description: T


title: S_36

description: Healthy-side


title: RNA_HVH_sample211 [HumanHT-12 V4.0]


title: RNA_HVH_sample209 [HumanHT-12 V4.0]


title: S_35

description: Lesion-side

value: noma antibio 2


title: RNA_HVH_sample206 [HumanHT-12 V4.0]


title: RNA_HVH_sample201 [HumanHT-12 V4.0]


title: RNA_HVH_sample213 [HumanHT-12 V4.0]


title: RNA_HVH_sample205 [HumanHT-12 V4.0]


title: RNA_HVH_sample207 [HumanHT-12 V4.0]


title: S_40

description: T


title: RNA_HVH_sample208 [HumanHT-12 V4.0]


title: RNA_HVH_sample204 [HumanHT-12 V4.0]


title: RNA_HVH_sample212 [HumanHT-12 V4.0]


title: RNA_HVH_sample210 [HumanHT-12 V4.0]


title: S_34

description: T


title: RNA_HVH_sample200 [HumanHT-12 V4.0]


title: RNA_HVH_sample202 [HumanHT-12 V4.0]


title: S_32

description: T


title: S_30

description: T


title: RNA_HVH_sample203 [HumanHT-12 V4.0]


title: S_33

description: T


title: S_31

description: T


title: RNA_HVH_sample199 [HumanHT-12 V4.0]


title: S_28

description: H

value: témoin hôpital

value: H


title: S_29

description: H


title: S_27

description: T


title: S_26

description: T


title: RNA_HVH_sample198 [HumanHT-12 V4.0]


title: RNA_HVH_sample196 [HumanHT-12 V4.0]


title: RNA_HVH_sample194 [HumanHT-12 V4.0]


title: S_20

description: T


title: S_25

description: T


title: S_19

description: T


title: S_21

description: T


title: S_24

description: T


title: S_23

description: T


title: RNA_HVH_sample195 [HumanHT-12 V4.0]


title: S_18

description: T


title: RNA_HVH_sample197 [HumanHT-12 V4.0]


title: RNA_HVH_sample188 [HumanHT-12 V4.0]


title: RNA_HVH_sample193 [HumanHT-12 V4.0]


title: RNA_HVH_sample192 [HumanHT-12 V4.0]


title: S_16

description: T


title: RNA_HVH_sample190 [HumanHT-12 V4.0]


title: RNA_HVH_sample189 [HumanHT-12 V4.0]


title: RNA_HVH_sample187 [HumanHT-12 V4.0]


title: RNA_HVH_sample181 [HumanHT-12 V4.0]


title: RNA_HVH_sample191 [HumanHT-12 V4.0]


title: S_22

description: T


title: RNA_HVH_sample185 [HumanHT-12 V4.0]


title: RNA_HVH_sample182 [HumanHT-12 V4.0]


title: RNA_HVH_sample184 [HumanHT-12 V4.0]


title: RNA_HVH_sample186 [HumanHT-12 V4.0]


title: RNA_HVH_sample180 [HumanHT-12 V4.0]


title: RNA_HVH_sample178 [HumanHT-12 V4.0]


title: S_15

description: T


title: RNA_HVH_sample179 [HumanHT-12 V4.0]


title: S_14

description: T


title: S_13

description: Lesion-side

value: gingivite 10

value: Gengivitis


title: S_10

description: T


title: S_11

description: Lesion-side

value: gingivite 13


title: S_12

description: Lesion-side

value: noma 25

value: NOMA


title: S_9

description: Unknown

value: CTL


title: S_6

description: Healthy-side

value: gingivite 18


title: S_5

description: Healthy-side

value: noma 35


title: S_8

description: Lesion-side

value: gingivite 19


title: S_7

description: Unknown


title: RNA_HVH_sample183 [HumanHT-12 V4.0]

value: female

value: blood


title: RNA_HVH_sample175 [HumanHT-12 V4.0]

value: male


title: S_3

description: Healthy-side

value: noma 34


title: RNA_HVH_sample169 [HumanHT-12 V4.0]


title: RNA_HVH_sample170 [HumanHT-12 V4.0]


title: RNA_HVH_sample174 [HumanHT-12 V4.0]


title: S_2

description: T

value: Control


title: S_4

description: Lesion-side


title: RNA_HVH_sample176 [HumanHT-12 V4.0]


title: RNA_HVH_sample167 [HumanHT-12 V4.0]


title: RNA_HVH_sample173 [HumanHT-12 V4.0]


title: RNA_HVH_sample165 [HumanHT-12 V4.0]


title: RNA_HVH_sample177 [HumanHT-12 V4.0]


title: S_1

description: Lesion-side

value: noma 29


title: RNA_HVH_sample172 [HumanHT-12 V4.0]


title: RNA_HVH_sample168 [HumanHT-12 V4.0]


title: RNA_HVH_sample171 [HumanHT-12 V4.0]


title: RNA_HVH_sample166 [HumanHT-12 V4.0]


title: RNA_HVH_sample164 [HumanHT-12 V4.0]


title: RNA_HVH_sample162 [HumanHT-12 V4.0]


title: RNA_HVH_sample163 [HumanHT-12 V4.0]


title: RNA_HVH_sample121 [HumanHT-12 V3.0]

hyb_protocol: Total RNA was hybridized onto Illumina HumanHT-12v3 Beadchip arrays (Illumina, San Diego, CA)


title: RNA_HVH_sample161 [HumanHT-12 V4.0]


title: RNA_HVH_sample119 [HumanHT-12 V3.0]


title: RNA_HVH_sample120 [HumanHT-12 V3.0]


title: RNA_HVH_sample158 [HumanHT-12 V4.0]


title: RNA_HVH_sample155 [HumanHT-12 V4.0]


title: RNA_HVH_sample157 [HumanHT-12 V4.0]


title: RNA_HVH_sample160 [HumanHT-12 V4.0]


title: RNA_HVH_sample114 [HumanHT-12 V3.0]


title: RNA_HVH_sample117 [HumanHT-12 V3.0]


title: RNA_HVH_sample118 [HumanHT-12 V3.0]


title: RNA_HVH_sample115 [HumanHT-12 V3.0]


title: RNA_HVH_sample122 [HumanHT-12 V3.0]


title: RNA_HVH_sample159 [HumanHT-12 V4.0]


title: RNA_HVH_sample156 [HumanHT-12 V4.0]


title: RNA_HVH_sample154 [HumanHT-12 V4.0]


title: RNA_HVH_sample111 [HumanHT-12 V3.0]


title: RNA_HVH_sample151 [HumanHT-12 V4.0]


title: RNA_HVH_sample152 [HumanHT-12 V4.0]


title: RNA_HVH_sample113 [HumanHT-12 V3.0]


title: RNA_HVH_sample110 [HumanHT-12 V3.0]


title: S_17

description: H


title: RNA_HVH_sample153 [HumanHT-12 V4.0]


title: RNA_HVH_sample149 [HumanHT-12 V4.0]


title: RNA_HVH_sample150 [HumanHT-12 V4.0]


title: RNA_HVH_sample112 [HumanHT-12 V3.0]


title: RNA_HVH_sample109 [HumanHT-12 V3.0]


title: RNA_HVH_sample116 [HumanHT-12 V3.0]


title: RNA_HVH_sample146 [HumanHT-12 V4.0]


title: RNA_HVH_sample148 [HumanHT-12 V4.0]


title: RNA_HVH_sample147 [HumanHT-12 V4.0]


title: RNA_HVH_sample144 [HumanHT-12 V4.0]


title: RNA_HVH_sample105 [HumanHT-12 V3.0]


title: RNA_HVH_sample140 [HumanHT-12 V4.0]


title: RNA_HVH_sample107 [HumanHT-12 V3.0]


title: RNA_HVH_sample101 [HumanHT-12 V3.0]


title: RNA_HVH_sample108 [HumanHT-12 V3.0]


title: RNA_HVH_sample142 [HumanHT-12 V4.0]


title: RNA_HVH_sample103 [HumanHT-12 V3.0]


title: RNA_HVH_sample145 [HumanHT-12 V4.0]


title: RNA_HVH_sample141 [HumanHT-12 V4.0]


title: RNA_HVH_sample139 [HumanHT-12 V4.0]


title: RNA_HVH_sample99 [HumanHT-12 V3.0]


title: RNA_HVH_sample98 [HumanHT-12 V3.0]


title: RNA_HVH_sample104 [HumanHT-12 V3.0]


title: RNA_HVH_sample138 [HumanHT-12 V4.0]


title: RNA_HVH_sample106 [HumanHT-12 V3.0]


title: RNA_HVH_sample102 [HumanHT-12 V3.0]


title: RNA_HVH_sample100 [HumanHT-12 V3.0]


title: RNA_HVH_sample96 [HumanHT-12 V3.0]


title: RNA_HVH_sample91 [HumanHT-12 V3.0]


title: RNA_HVH_sample95 [HumanHT-12 V3.0]


title: RNA_HVH_sample88 [HumanHT-12 V3.0]


title: RNA_HVH_sample86 [HumanHT-12 V3.0]


title: RNA_HVH_sample130 [HumanHT-12 V4.0]


title: RNA_HVH_sample136 [HumanHT-12 V4.0]


title: RNA_HVH_sample129 [HumanHT-12 V4.0]


title: RNA_HVH_sample85 [HumanHT-12 V3.0]


title: RNA_HVH_sample143 [HumanHT-12 V4.0]


title: RNA_HVH_sample128 [HumanHT-12 V4.0]


title: RNA_HVH_sample131 [HumanHT-12 V4.0]


title: RNA_HVH_sample89 [HumanHT-12 V3.0]


title: RNA_HVH_sample87 [HumanHT-12 V3.0]


title: RNA_HVH_sample97 [HumanHT-12 V3.0]


title: RNA_HVH_sample90 [HumanHT-12 V3.0]


title: RNA_HVH_sample134 [HumanHT-12 V4.0]


title: RNA_HVH_sample126 [HumanHT-12 V4.0]


title: RNA_HVH_sample124 [HumanHT-12 V4.0]


title: RNA_HVH_sample125 [HumanHT-12 V4.0]


title: RNA_HVH_sample137 [HumanHT-12 V4.0]


title: RNA_HVH_sample132 [HumanHT-12 V4.0]


title: RNA_HVH_sample84 [HumanHT-12 V3.0]


title: RNA_HVH_sample123 [HumanHT-12 V4.0]


title: RNA_HVH_sample83 [HumanHT-12 V3.0]


title: RNA_HVH_sample122 [HumanHT-12 V4.0]


title: RNA_HVH_sample118 [HumanHT-12 V4.0]


title: RNA_HVH_sample116 [HumanHT-12 V4.0]


title: RNA_HVH_sample81 [HumanHT-12 V3.0]


title: RNA_HVH_sample120 [HumanHT-12 V4.0]


title: RNA_HVH_sample76 [HumanHT-12 V3.0]


title: RNA_HVH_sample117 [HumanHT-12 V4.0]


title: RNA_HVH_sample78 [HumanHT-12 V3.0]


title: RNA_HVH_sample121 [HumanHT-12 V4.0]


title: RNA_HVH_sample79 [HumanHT-12 V3.0]


title: RNA_HVH_sample77 [HumanHT-12 V3.0]


title: RNA_HVH_sample82 [HumanHT-12 V3.0]


title: RNA_HVH_sample74 [HumanHT-12 V3.0]


title: RNA_HVH_sample75 [HumanHT-12 V3.0]


title: RNA_HVH_sample119 [HumanHT-12 V4.0]


title: RNA_HVH_sample114 [HumanHT-12 V4.0]


title: RNA_HVH_sample133 [HumanHT-12 V4.0]


title: RNA_HVH_sample112 [HumanHT-12 V4.0]


title: RNA_HVH_sample80 [HumanHT-12 V3.0]


title: RNA_HVH_sample93 [HumanHT-12 V3.0]


title: RNA_HVH_sample111 [HumanHT-12 V4.0]


title: RNA_HVH_sample73 [HumanHT-12 V3.0]


title: RNA_HVH_sample71 [HumanHT-12 V3.0]


title: RNA_HVH_sample72 [HumanHT-12 V3.0]


title: RNA_HVH_sample113 [HumanHT-12 V4.0]


title: RNA_HVH_sample68 [HumanHT-12 V3.0]


title: RNA_HVH_sample110 [HumanHT-12 V4.0]


title: RNA_HVH_sample66 [HumanHT-12 V3.0]


title: RNA_HVH_sample109 [HumanHT-12 V4.0]


title: RNA_HVH_sample107 [HumanHT-12 V4.0]


title: RNA_HVH_sample105 [HumanHT-12 V4.0]


title: RNA_HVH_sample106 [HumanHT-12 V4.0]


title: RNA_HVH_sample65 [HumanHT-12 V3.0]


title: RNA_HVH_sample127 [HumanHT-12 V4.0]


title: RNA_HVH_sample94 [HumanHT-12 V3.0]


title: RNA_HVH_sample135 [HumanHT-12 V4.0]


title: RNA_HVH_sample69 [HumanHT-12 V3.0]


title: RNA_HVH_sample70 [HumanHT-12 V3.0]


title: RNA_HVH_sample64 [HumanHT-12 V3.0]


title: RNA_HVH_sample108 [HumanHT-12 V4.0]


title: RNA_HVH_sample102 [HumanHT-12 V4.0]


title: RNA_HVH_sample63 [HumanHT-12 V3.0]


title: RNA_HVH_sample92 [HumanHT-12 V3.0]


title: RNA_HVH_sample104 [HumanHT-12 V4.0]


title: RNA_HVH_sample103 [HumanHT-12 V4.0]


title: RNA_HVH_sample60 [HumanHT-12 V3.0]


title: RNA_HVH_sample101 [HumanHT-12 V4.0]


title: RNA_HVH_sample62 [HumanHT-12 V3.0]


title: RNA_HVH_sample100 [HumanHT-12 V4.0]


title: RNA_HVH_sample59 [HumanHT-12 V3.0]


title: RNA_HVH_sample98 [HumanHT-12 V4.0]


title: RNA_HVH_sample99 [HumanHT-12 V4.0]


title: RNA_HVH_sample56 [HumanHT-12 V3.0]


title: RNA_HVH_sample96 [HumanHT-12 V4.0]


title: RNA_HVH_sample97 [HumanHT-12 V4.0]


title: RNA_HVH_sample95 [HumanHT-12 V4.0]


title: RNA_HVH_sample55 [HumanHT-12 V3.0]


title: RNA_HVH_sample91 [HumanHT-12 V4.0]


title: RNA_HVH_sample115 [HumanHT-12 V4.0]


title: RNA_HVH_sample93 [HumanHT-12 V4.0]


title: RNA_HVH_sample61 [HumanHT-12 V3.0]


title: RNA_HVH_sample51 [HumanHT-12 V3.0]


title: RNA_HVH_sample92 [HumanHT-12 V4.0]


title: RNA_HVH_sample54 [HumanHT-12 V3.0]


title: RNA_HVH_sample52 [HumanHT-12 V3.0]


title: RNA_HVH_sample90 [HumanHT-12 V4.0]


title: RNA_HVH_sample94 [HumanHT-12 V4.0]


title: RNA_HVH_sample87 [HumanHT-12 V4.0]


title: RNA_HVH_sample48 [HumanHT-12 V3.0]


title: RNA_HVH_sample89 [HumanHT-12 V4.0]


title: RNA_HVH_sample57 [HumanHT-12 V3.0]


title: RNA_HVH_sample86 [HumanHT-12 V4.0]


title: RNA_HVH_sample53 [HumanHT-12 V3.0]


title: RNA_HVH_sample84 [HumanHT-12 V4.0]


title: RNA_HVH_sample88 [HumanHT-12 V4.0]


title: RNA_HVH_sample85 [HumanHT-12 V4.0]


title: RNA_HVH_sample46 [HumanHT-12 V3.0]


title: RNA_HVH_sample47 [HumanHT-12 V3.0]


title: RNA_HVH_sample83 [HumanHT-12 V4.0]


title: RNA_HVH_sample67 [HumanHT-12 V3.0]


title: RNA_HVH_sample81 [HumanHT-12 V4.0]


title: RNA_HVH_sample82 [HumanHT-12 V4.0]


title: RNA_HVH_sample49 [HumanHT-12 V3.0]


title: RNA_HVH_sample50 [HumanHT-12 V3.0]


title: RNA_HVH_sample78 [HumanHT-12 V4.0]


title: RNA_HVH_sample44 [HumanHT-12 V3.0]


title: RNA_HVH_sample79 [HumanHT-12 V4.0]


title: RNA_HVH_sample40 [HumanHT-12 V3.0]


title: RNA_HVH_sample76 [HumanHT-12 V4.0]


title: RNA_HVH_sample38 [HumanHT-12 V3.0]


title: RNA_HVH_sample41 [HumanHT-12 V3.0]


title: RNA_HVH_sample77 [HumanHT-12 V4.0]


title: RNA_HVH_sample35 [HumanHT-12 V3.0]


title: RNA_HVH_sample36 [HumanHT-12 V3.0]


title: RNA_HVH_sample33 [HumanHT-12 V3.0]


title: RNA_HVH_sample73 [HumanHT-12 V4.0]


title: RNA_HVH_sample74 [HumanHT-12 V4.0]


title: RNA_HVH_sample72 [HumanHT-12 V4.0]


title: RNA_HVH_sample34 [HumanHT-12 V3.0]


title: RNA_HVH_sample42 [HumanHT-12 V3.0]


title: RNA_HVH_sample69 [HumanHT-12 V4.0]


title: RNA_HVH_sample37 [HumanHT-12 V3.0]


title: RNA_HVH_sample75 [HumanHT-12 V4.0]


title: RNA_HVH_sample71 [HumanHT-12 V4.0]


title: RNA_HVH_sample29 [HumanHT-12 V3.0]


title: RNA_HVH_sample31 [HumanHT-12 V3.0]


title: RNA_HVH_sample28 [HumanHT-12 V3.0]


title: RNA_HVH_sample32 [HumanHT-12 V3.0]


title: RNA_HVH_sample27 [HumanHT-12 V3.0]


title: RNA_HVH_sample70 [HumanHT-12 V4.0]


title: RNA_HVH_sample30 [HumanHT-12 V3.0]


title: RNA_HVH_sample68 [HumanHT-12 V4.0]


title: RNA_HVH_sample66 [HumanHT-12 V4.0]


title: RNA_HVH_sample80 [HumanHT-12 V4.0]


title: RNA_HVH_sample65 [HumanHT-12 V4.0]


title: RNA_HVH_sample26 [HumanHT-12 V3.0]


title: RNA_HVH_sample25 [HumanHT-12 V3.0]


title: RNA_HVH_sample24 [HumanHT-12 V3.0]


title: RNA_HVH_sample58 [HumanHT-12 V3.0]


title: RNA_HVH_sample23 [HumanHT-12 V3.0]


title: RNA_HVH_sample21 [HumanHT-12 V3.0]


title: RNA_HVH_sample61 [HumanHT-12 V4.0]


title: RNA_HVH_sample60 [HumanHT-12 V4.0]


title: RNA_HVH_sample67 [HumanHT-12 V4.0]


title: RNA_HVH_sample20 [HumanHT-12 V3.0]


title: RNA_HVH_sample63 [HumanHT-12 V4.0]


title: RNA_HVH_sample64 [HumanHT-12 V4.0]


title: RNA_HVH_sample22 [HumanHT-12 V3.0]


title: RNA_HVH_sample39 [HumanHT-12 V3.0]


title: RNA_HVH_sample62 [HumanHT-12 V4.0]


title: RNA_HVH_sample19 [HumanHT-12 V3.0]


title: RNA_HVH_sample18 [HumanHT-12 V3.0]


title: RNA_HVH_sample59 [HumanHT-12 V4.0]


title: RNA_HVH_sample55 [HumanHT-12 V4.0]


title: RNA_HVH_sample15 [HumanHT-12 V3.0]


title: RNA_HVH_sample58 [HumanHT-12 V4.0]


title: RNA_HVH_sample57 [HumanHT-12 V4.0]


title: RNA_HVH_sample17 [HumanHT-12 V3.0]


title: RNA_HVH_sample13 [HumanHT-12 V3.0]


title: RNA_HVH_sample56 [HumanHT-12 V4.0]


title: RNA_HVH_sample11 [HumanHT-12 V3.0]


title: RNA_HVH_sample16 [HumanHT-12 V3.0]


title: RNA_HVH_sample54 [HumanHT-12 V4.0]


title: RNA_HVH_sample45 [HumanHT-12 V3.0]


title: RNA_HVH_sample53 [HumanHT-12 V4.0]


title: RNA_HVH_sample12 [HumanHT-12 V3.0]


title: RNA_HVH_sample10 [HumanHT-12 V3.0]


title: RNA_HVH_sample52 [HumanHT-12 V4.0]


title: RNA_HVH_sample50 [HumanHT-12 V4.0]


title: RNA_HVH_sample46 [HumanHT-12 V4.0]


title: RNA_HVH_sample8 [HumanHT-12 V3.0]


title: RNA_HVH_sample7 [HumanHT-12 V3.0]


title: RNA_HVH_sample43 [HumanHT-12 V3.0]


title: RNA_HVH_sample14 [HumanHT-12 V3.0]


title: RNA_HVH_sample9 [HumanHT-12 V3.0]


title: RNA_HVH_sample6 [HumanHT-12 V3.0]


title: RNA_HVH_sample49 [HumanHT-12 V4.0]


title: RNA_HVH_sample48 [HumanHT-12 V4.0]


title: RNA_HVH_sample51 [HumanHT-12 V4.0]


title: RNA_HVH_sample47 [HumanHT-12 V4.0]


title: RNA_HVH_sample44 [HumanHT-12 V4.0]


title: RNA_HVH_sample3 [HumanHT-12 V3.0]


title: RNA_HVH_sample5 [HumanHT-12 V3.0]


title: RNA_HVH_sample40 [HumanHT-12 V4.0]


title: RNA_HVH_sample43 [HumanHT-12 V4.0]


title: RNA_HVH_sample4 [HumanHT-12 V3.0]


title: RNA_HVH_sample38 [HumanHT-12 V4.0]


title: RNA_HVH_sample1 [HumanHT-12 V3.0]


title: RNA_HVH_sample45 [HumanHT-12 V4.0]


title: RNA_HVH_sample41 [HumanHT-12 V4.0]


title: RNA_HVH_sample35 [HumanHT-12 V4.0]


title: RNA_HVH_sample34 [HumanHT-12 V4.0]


title: MCF7, siRNA containing a scramble sequence, 96hr transfection, biological rep3

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St

department: Medicine

institute: Indiana University

description: Gene expression profiling of MCF7 after 96hr incubation with siRNA tranfection mix (RNAi+ Lypofectamine RNAiMAX Reagent)

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on the Affymetrix HG-U133 Plus2.0 GeneChip according to the protocols provided by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.

source_name: MCF7 cells after transfection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)..The cDNA was prepared from 1 µg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: MCF7 cells were growth in Dulbecco’s Modified Eagle Medium supplemented with 10%FBS, under humidified 37°C incubator at 5% CO2.

extract_protocol: siRNA-MSG transfected MCF7 cells were collected at 48 h and 96 h using TRIzol Reagent method (Invitrogen). RNA was extracted using RNeasy® miny Kit (Qiagen, Valencia, CA) and DNase I (Qiagen) following the manufacturer’s instructions.  The RNA concentration was assessed using the Nanodrop ND-1000 spectrophotometer (ThermoScientific, Wilmington, DE). RNA quality was measured by calculating the RNA integrity number on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). To assess the MSG-knockdown efficiency in each sample, real-time quantitative RT-PCR (qRT-PCR) analysis was performed.

treatment_protocol: MCF7 cells were transfection with small RNA interference (siRNA; Qiagen) using LipofectamineTM RNAiMax (Invitrogen) according to the manufacturer’s protocol. Briefly, 30 nM siRNAs and 30 µl Lipofectamine RNAiMax were diluted in 2 ml Opti-MEM I Medium and added to 100mm-plate. After 20 min incubation at room temperature, either 1x106 (end time point: 96 h) or 2x106 (end time point: 48 h) cells were diluted in 9 ml DMEM, added to the dishes and incubated for either 48 h or 96 h at 37°C.

tag: tissue of origin

value: breast tumor cell line

tag: sirna transfection time

value: Cells were collected 96hr after siRNA transfection

value: siRNA containing a scramble sequence

tag: time

value: 96hr transfection


title: MCF7, wild type, biological rep2

description: Gene expression profiling of MCF7 cells

value: Cells were collected after 96hr of culture

value: untreated

value: control


title: RNA_HVH_sample36 [HumanHT-12 V4.0]

tag: gender


title: RNA_HVH_sample42 [HumanHT-12 V4.0]


title: RNA_HVH_sample31 [HumanHT-12 V4.0]


title: RNA_HVH_sample33 [HumanHT-12 V4.0]


title: RNA_HVH_sample39 [HumanHT-12 V4.0]


title: MCF7, siRNA containing a scramble sequence, 96hr transfection, biological rep2


title: MCF7, siRNA containing a scramble sequence, 96hr transfection, biological rep1


title: MCF7, siRNA containing a scramble sequence, 48hr transfection, biological rep3

description: Gene expression profiling of MCF7 after 48hr incubation with siRNA tranfection mix (RNAi+ Lypofectamine RNAiMAX Reagent)

value: Cells were collected 48hr after siRNA transfection

value: 48hr transfection


title: RNA_HVH_sample2 [HumanHT-12 V3.0]


title: RNA_HVH_sample37 [HumanHT-12 V4.0]


title: RNA_HVH_sample30 [HumanHT-12 V4.0]


title: MCF7, siRNA containing a scramble sequence, 48hr transfection, biological rep1


title: MCF7, wild type, biological rep1

description: Gene expression profiling of MCF7 cells


title: RNA_HVH_sample32 [HumanHT-12 V4.0]


title: MCF7, siRNA containing a scramble sequence, 48hr transfection, biological rep2


title: RNA_HVH_sample26 [HumanHT-12 V4.0]


title: RNA_HVH_sample28 [HumanHT-12 V4.0]


title: RNA_HVH_sample29 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting BRMS1, 48hr transfection, biological rep2

value: siRNA targeting BRMS1


title: MCF7, siRNA targeting RRM1, 96hr transfection, biological rep2

value: siRNA targeting RRM1


title: RNA_HVH_sample22 [HumanHT-12 V4.0]

value: female


title: MCF7, siRNA targeting BRMS1, 96hr transfection, biological rep2


title: RNA_HVH_sample21 [HumanHT-12 V4.0]

value: blood


title: MCF7, siRNA targeting BRMS1, 48hr transfection, biological rep1


title: RNA_HVH_sample24 [HumanHT-12 V4.0]


title: RNA_HVH_sample27 [HumanHT-12 V4.0]

value: male


title: MCF7, siRNA targeting KISS1, 48hr transfection, biological rep1

value: siRNA targeting KISS1


title: RNA_HVH_sample25 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting RRM1, 48hr transfection, biological rep1


title: RNA_HVH_sample19 [HumanHT-12 V4.0]


title: RNA_HVH_sample20 [HumanHT-12 V4.0]


title: RNA_HVH_sample17 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting BRMS1, 96hr transfection, biological rep1


title: MCF7, siRNA targeting PEBP1, 96hr transfection, biological rep2

value: siRNA targeting PEBP1


title: RNA_HVH_sample18 [HumanHT-12 V4.0]


title: RNA_HVH_sample16 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting PEBP1, 48hr transfection, biological rep2


title: MCF7, siRNA targeting RRM1, 96hr transfection, biological rep1


title: MCF7, siRNA targeting PEBP1, 96hr transfection, biological rep1


title: RNA_HVH_sample14 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting DRG1, 48hr transfection, biological rep2

value: siRNA targeting DRG1


title: RNA_HVH_sample15 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting DRG1, 48hr transfection, biological rep1

value: breast tumor cell line


title: MCF7, siRNA targeting CD44, 96hr transfection, biological rep1

value: Cells were collected 96hr after siRNA transfection

value: siRNA targeting CD44


title: MCF7, siRNA targeting CD44, 48hr transfection, biological rep1


title: MCF7, siRNA targeting AKAP12, 96hr transfection, biological rep2

value: siRNA targeting AKAP12

value: 96hr transfection


title: RNA_HVH_sample12 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting KISS1, 48hr transfection, biological rep2


title: MCF7, siRNA targeting DRG1, 96hr transfection, biological rep2


title: RNA_HVH_sample9 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting PEBP1, 48hr transfection, biological rep1


title: MCF7, siRNA targeting ARGHDIB, 96hr transfection, biological rep2

value: siRNA targeting ARGHDIB


title: RNA_HVH_sample13 [HumanHT-12 V4.0]


title: RNA_HVH_sample8 [HumanHT-12 V4.0]


title: RNA_HVH_sample7 [HumanHT-12 V4.0]


title: RNA_HVH_sample10 [HumanHT-12 V4.0]


title: RNA_HVH_sample11 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting AKAP12, 96hr transfection, biological rep1


title: RNA_HVH_sample6 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting ARGHDIB, 48hr transfection, biological rep2


title: MCF7, siRNA targeting DRG1, 96hr transfection, biological rep1


title: RNA_HVH_sample5 [HumanHT-12 V4.0]


title: RNA_HVH_sample4 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting MAPK14, 48hr transfection, biological rep2

value: siRNA targeting MAPK14


title: MCF7, siRNA targeting MAPK14, 96hr transfection, biological rep2


title: MCF7, wild type, biological rep3

description: Gene expression profiling of MCF7 cells

value: Cells were collected after 96hr of culture

value: untreated

value: control


title: MCF7, siRNA targeting ARGHDIB, 96hr transfection, biological rep1


title: MCF7, siRNA targeting MAPK14, 96hr transfection, biological rep1


title: RNA_HVH_sample2 [HumanHT-12 V4.0]


title: RNA_HVH_sample1 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting ARGHDIB, 48hr transfection, biological rep1

value: Cells were collected 48hr after siRNA transfection

value: 48hr transfection


title: RNA_HVH_sample23 [HumanHT-12 V4.0]

value: female

value: blood


title: MCF7, siRNA targeting MAP2K7, 96hr transfection, biological rep2

value: siRNA targeting MAP2K7


title: MCF7, siRNA targeting MAPK14, 48hr transfection, biological rep1


title: MCF7, siRNA targeting MAP2K7, 96hr transfection, biological rep1


title: LREX' (23)

city: New York

first: Vivek

middle: Kumar

last: Arora

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

source_name: LREX' Mouse Xenograft

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

extract_protocol: Total RNA was harvested from xenografts with Triazole and then further purified using the RNAeasy (Qiagen) Kit.

value: LREX'

value: prostate cancer

value: Enzalutamide


title: RNA_HVH_sample3 [HumanHT-12 V4.0]


title: MCF7, siRNA targeting MAP2K6, 96hr transfection, biological rep1

value: breast tumor cell line

value: Cells were collected 96hr after siRNA transfection

value: siRNA targeting MAP2K6


title: LREX' (11)


title: LREX' (24)


title: LREX' (21)


title: MCF7, siRNA targeting MAP2K6, 48hr transfection, biological rep2


title: Con B (14)

source_name: LnCaP/AR Mouse Xenograft

value: LnCaP/AR

value: Vehicle


title: MCF7, siRNA targeting MAP2K7, 48hr transfection, biological rep1


title: LREX' (22)


title: MCF7, siRNA targeting MAP2K6, 96hr transfection, biological rep2

value: 96hr transfection


title: MCF7, siRNA targeting GSN, 96hr transfection, biological rep2

value: siRNA targeting GSN


title: Con B (16)


title: Con B (15)


title: MCF7, siRNA targeting MAP2K7, 48hr transfection, biological rep2


title: MCF7, siRNA targeting GSN, 96hr transfection, biological rep1


title: MCF7, siRNA targeting MAP2K6, 48hr transfection, biological rep1


title: MCF7, siRNA targeting RRM1, 48hr transfection, biological rep2

value: siRNA targeting RRM1


title: LREX' (12)