title: Bj_H2O2 shock vs. no treatment_Rep3

city: Arlington

first: Woo-Suk

last: Chang

address: 501 S. Nedderman Dr. , Life Science Building 216

institute: University of Texas at Arlington

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined and averaged. Significant genes were selected based on a 1.5-cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: No Treatment

label_protocol: 30 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Five micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot-phenol method

value: USDA 110

tag: treatment type

tag: medium

value: Arabinose-gluconate

source_name: H2O2 shock treatment

tag: treatment concentration

value: 10 mM

tag: treatment time

value: 10 minutes


title: Bj_H2O2 shock vs. no treatment_Rep3_dyeswap

status: Public on Jul 30 2011

type: RNA

state: TX

department: Biology

country: USA

molecule: total RNA

tag: strain


title: Decay Ref mutant t=30

city: Rehovot

first: Ophir

last: Shalem

address: Hertzel

country: Israel

institute: Weizmann Inst.

description: Reference decay profile

data_processing: RMA algorithms using bioconductor software implemented in R for mRNA abundance. For decay experiments data was scaled as described in the materials and methods of the accompanied manuscript. For mRNA abundnce (MA) Fold change: log2 of the intesity value divided by the intensity value at time point zero. For Decay data: the precentage of decrease from time point zero, e.g. 0.4 means 40% of the initial mRNA amount. These data are presented on the Series record.

label: biotin

organism: Saccharomyces cerevisiae

source_name: Decay Ref mutant t=30

label_protocol: cDNA was prepared using poly(T) primers, labeled cRNA was prepared using the GeneChip system according to manufacture instructions.

growth_protocol: cells were grown in YPD to mid log phase in 30 degrees

extract_protocol: Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)

treatment_protocol: At time 0 cells were treated with 0.3mM of H2O2 or 0.1% of MMS for mRNA abundance measurements. For decay experiments cells were treated with 1,10-phenanthroline (100mg/ml) either with (Oxi) or without (Ref) adding H2O2 (0.3mM) 7 minutes before 1,10-phenanthroline.


title: Bj_H2O2 shock vs. no treatment_Rep2_dyeswap


title: MA MMS wt t=180

description: mRNA abundance following treatment of 0.1% of MMS

hyb_protocol: GeneChip system according to manufacture instructions.

source_name: MA MMS wt t=180


title: MA MMS wt t=140

scan_protocol: GeneChip system according to manufacture instructions.

source_name: MA MMS wt t=140


title: MA MMS wt t=120

source_name: MA MMS wt t=120


title: BW25113 wild type treated with nalidixic acid

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from E. coli K-12 wild type treated with 2 ug/mL nalidixic acid for 90 min at 37C in LB.

hyb_protocol: Following Affymetrix protocol.

scan_protocol: After washing and staining, the probe array was scanned using the Affymetrix Genechip scanner GCS3000 7G system and the software GeneChip Operating Software (GCOS).

data_processing: MAS5.0 Expression Analysis Default Setting

label: Biotin

organism: Escherichia coli K-12

source_name: BW25113 treated with nalidixic acid

label_protocol: cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using the Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: After breaking the cells with a bead beater, the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

tag: genotype

value: wild type

tag: treatment

value: nalidixic acid


title: BW25113 wild type untreated

description: RNA extracted from E. coli K-12 wild type after 90 min at 37C in LB (start at OD =0.8).

source_name: BW25113 untreated

growth_protocol: 90 min at 37C in LB.


title: MA MMS wt t=100

source_name: MA MMS wt t=100


title: BW25113 wild type treated with azlocillin

description: RNA extracted from E. coli K-12 wild type treated with 10 ug/mL azlocillin for 90 min at 37 C in LB.

source_name: BW25113 treated with azlocillin

treatment_protocol: 10 ug/mL azlocillin for 90 min at 37C in LB.

value: azlocillin


title: Bj_H2O2 shock vs. no treatment_Rep1_dyeswap


title: Bj_H2O2 prolonged exposure vs. no treatment_Rep2_dyeswap

source_name: H2O2 prolonged exposure treatment

value: arabinose-gluconate

tag: growth condition

value: aerobic

value: entire growth period

value: no-treatment


title: MCF10A-HER2(+) 9days

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

institute: Weizmann Institute of Science

hyb_protocol: According to Affymetrix instructions

scan_protocol: According to Affymetrix instructions

data_processing: Data was normalized by RMA method using Command Console CHP file version 1.

organism: Homo sapiens

source_name: MCF10A-HER2(+) 9days

label_protocol: According to Affymetrix instructions

growth_protocol: Trypsin-treated cells were re-suspended in DME/F12 medium supplemented with 2% horse serum, insulin, cholera toxin and hydrocortisone. Eight-chambered plates (BD Biosciences) were coated with 35 µl MatrigelTM per well. The cells were mixed 1:1 with assay medium containing MatrigelTM (4%) and EGF (20 ng/ml), and 400 µl added to each chamber.

extract_protocol: Cells were lysed and RNA isolated using a Versagene kit (Gentra Systems, Minneapolis).

treatment_protocol: Cells were grown in the absence or presence of EGF.

tag: cell line

tag: genome/variation

value: HER2 overexpression

tag: treatment group

value: untreated

tag: length of treatment (days)


title: Bj_H2O2 prolonged exposure vs. no treatment_Rep3


title: MCF10A-HER2(+) EGF treated 1.5days

source_name: MCF10A-HER2(+) EGF treated 1.5days

value: EGF treated


title: MA MMS wt t=40

source_name: MA MMS wt t=40


title: Bj_H2O2 shock vs. no treatment_Rep2


title: MCF10A-HER2(+) EGF treated 7days

source_name: MCF10A-HER2(+) EGF treated 7days


title: MA MMS wt t=80

source_name: MA MMS wt t=80


title: Bj_H2O2 prolonged exposure vs. no treatment_Rep3_dyeswap


title: MCF10A-HER2(+) EGF treated 3days

source_name: MCF10A-HER2(+) EGF treated 3days


title: MCF10A-HER2(+) EGF treated 9days

source_name: MCF10A-HER2(+) EGF treated 9days


title: MCF10A-HER2(+) 5days

source_name: MCF10A-HER2(+) 5days


title: MA MMS wt t=20

source_name: MA MMS wt t=20


title: MCF10A-HER2(+) 3days

source_name: MCF10A-HER2(+) 3days


title: MCF10A EGF treated 9days

source_name: MCF10A EGF treated 9days


title: Bj_H2O2 prolonged exposure vs. no treatment_Rep2

source_name: No Treatment


title: MCF10A-HER2(+) 7days

source_name: MCF10A-HER2(+) 7days


title: Bj_H2O2 shock vs. no treatment_Rep1

source_name: H2O2 shock treatment


title: MCF10A EGF treated 7days

source_name: MCF10A EGF treated 7days


title: MA oxidative wt t=45

description: mRNA abundance following treatment of 0.3mM of H2O2

source_name: MA oxidative wt t=45


title: MCF10A-HER2(+) 1.5days

source_name: MCF10A-HER2(+) 1.5days


title: MCF10A-HER2(+) EGF treated 5days

source_name: MCF10A-HER2(+) EGF treated 5days


title: Bj_H2O2 prolonged exposure vs. no treatment_Rep1_dyeswap

source_name: H2O2 prolonged exposure treatment


title: MCF10A EGF treated 5days

source_name: MCF10A EGF treated 5days


title: MA oxidative wt t=35

source_name: MA oxidative wt t=35


title: MA oxidative wt t=15

source_name: MA oxidative wt t=15


title: Bj_H2O2 prolonged exposure vs. no treatment_Rep1


title: MA MMS wt t=0

source_name: MA MMS wt t=0


title: MA oxidative wt t=25

source_name: MA oxidative wt t=25


title: MCF10A EGF treated 3days

source_name: MCF10A EGF treated 3days


title: MCF10A 7days

source_name: MCF10A 7days


title: MA oxidative wt t=10

source_name: MA oxidative wt t=10


title: MCF10A EGF treated 1.5days

source_name: MCF10A EGF treated 1.5days


title: wildtype, biological rep3

city: Oshawa

first: Dario

last: Bonetta

state: ON

address: 2000 Simcoe St N

department: Science

country: Canada

institute: Ontario Institute of Technology

description: Gene expression data from seedling

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with 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.

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 10 day old seedling

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

growth_protocol: Seeds were sown onto 0.5 MS, kept at 4C for 4 days in the dark and transferred to 21C at 200 uE/m/s  for 10 days.

extract_protocol: Trizol method according to manufacterer's instructions.

tag: cultivar

tag: genotype/variation

value: wildtype

tag: tissue

value: whole seedling


title: wildtype, biological rep1

description: Gene expression data from seedling


title: MCF10A 3days

source_name: MCF10A 3days


title: MCF10A 5days

source_name: MCF10A 5days


title: frb1 mutant, biological rep2

description: Gene expression data from seedling

value: frb1 mutant


title: MA oxidative wt t=5

source_name: MA oxidative wt t=5


title: MCF10A 9days

source_name: MCF10A 9days


title: MCF10A 1.5days

source_name: MCF10A 1.5days


title: frb1 mutant, biological rep1

description: Gene expression data from seedling


title: MA oxidative mutant t=45

source_name: MA oxidative mutant t=45


title: MA oxidative wt t=0

source_name: MA oxidative wt t=0


title: frb1 mutant, biological rep3

description: Gene expression data from seedling


title: ESP cells that overexpress Igf2_rep2

city: Seu-gu

first: Jaeku

last: Kang

state: Daejeon

address: 685, Gasuwon-dong

department: Department of Pharmacology

country: South Korea

institute: College of Medicine, Konyang University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. The filtering parameter, 50% sample of total are Detection pval < 0.05, used to derive our reduced data set.

organism: Mus musculus

source_name: genetically modified parthenogenetic mouse embryonic stem cells

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

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

tag: cell type

value: B6D2F1 hybrid mice


title: wildtype, biological rep2

description: Gene expression data from seedling


title: ESP cells with down-regulated H19 gene expression_rep2

description: replicate 2

value: parthenogenetic mouse embryonic stem cells


title: MA oxidative mutant t=35

source_name: MA oxidative mutant t=35


title: MA oxidative mutant t=25

source_name: MA oxidative mutant t=25


title: Partenogenetic mouse embryonic stem cells_rep2

description: replicate 2

source_name: parthenogenetic mouse embryonic stem cells

value: mouse oocytes


title: Normal mouse embryonic stem cells_rep2

description: replicate 2

source_name: mouse embryonic stem cell

value: mouse embryo


title: MA oxidative mutant t=5

source_name: MA oxidative mutant t=5


title: MA oxidative mutant t=10

source_name: MA oxidative mutant t=10


title: MA oxidative mutant t=15

source_name: MA oxidative mutant t=15


title: Normal mouse embryonic stem cells_rep1

description: replicate 1


title: ESP cells with down-regulated H19 gene expression_rep1

description: replicate 1


title: MA oxidative mutant t=0

source_name: MA oxidative mutant t=0


title: Decay Ref mutant t=10

description: Reference decay profile

source_name: Decay Ref mutant t=10


title: Partenogenetic mouse embryonic stem cells_rep1

description: replicate 1


title: NML2010031703

status: Public on Jul 29 2011

city: London

first: Adam

last: Giess

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: MRC Clinical Sciences Centre

hyb_protocol: 5.5μg of cDNA was hybridized per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. The arrays were washed on Affymetrix Fluidics stations using the Affymetrix wash and stain kit and the FS450_0001 protocol

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Quantile normalisation and median centering with Tiling Analysis Software (TAS). P-values adjusted with Benjamini Hochberg method. Signal and P-value statistics were reported in .chp format. *signal.chp and *pvalue.chp files were generated from TAS. *signal.chp contain log2 signal for each probe. *pvalue.chp contain linear pvalues for each probe. [*signal.chp and *pvalue.chp files are provided as Series supplementary file]

source_name: CDC15 Strain at 25°C

label_protocol: 2x20ug of total RNA was reverse transcribed into double stranded cDNA using 1.72ug of Random hexamer6 and 0.05ug OligodT primer and the Invitrogen Superscript kit; the cDNA was cleaned using the Affymetrix cleanup module and 5.5ug of cDNA was fragmented and biotin-labelled using the Affymetrix WT terminal labeling kit.

growth_protocol: Cells were grown o/n in YPD media at 25°C. The day after, cells were transferred to new YPD media at 25 at OD 0.2 for 2 hours. Later, the culture was split into two; one half was grown at 25°C and the other at 37°C for 1.5hours.

extract_protocol: Total RNA was isolated by hot phenol extraction.

treatment_protocol: Cells were collected at 25°C or 37°C as required, washed with PBS and frozen in liquid nitrogen.

tag: growth temperature


title: NML2010031707

source_name: CDC15 Strain at 37°C


title: NML2010031706


title: NML2010031708


title: LDG2009032507

source_name: CDC14 Strain at 37°C


title: NML2010031701


title: LDG2009032504

source_name: CDC14 Strain at 25°C


title: NML2010031702


title: ESP cells that overexpress Igf2_rep1

description: replicate 1


title: NML2010031705


title: LDG2009032506


title: LDG2009032503


title: LDG2009032502


title: NML2010031704


title: LDG2009032505


title: mRNA miR-128 2 (GCRMA)

city: Atlanta

first: Shubin

last: Shahab

state: GA

address: 310 Ferst Drive

institute: Georgia Institute of Technology

description: HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62)  in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.

hyb_protocol: Labeled mRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays in the GeneChip Hybridization oven 640, further processed with the GeneChip Fluidics Station 450 and scanned with the GeneChip Scanner 3000.

scan_protocol: as per manufacturer's protocol using GeneChip Scanner 3000.

data_processing: GCRMA via R Statistical software. False Discovery Rate was calculated using the SAM algorithm, based on Log2 signal values of samples after this preprocessing step.

source_name: HEY ovarian cancer cell, miR-128 mimic treated

label_protocol: mRNAs were converted to double stranded (ds)-cDNA and amplified using Applause 3’-Amp System (NuGen, San Carlos, CA). This cDNA was then biotin labeled and fragmented by using Encode Biotin Module (NuGen)

growth_protocol: Hey cells were cultured in RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10% v/v heat-inactivated fetal calf serum (Invitrogen, Carlsbad, CA), 2 mM L-glutamine (Mediatech), 10 mM HEPES buffer (Mediatech), penicillin (100 U/ml), and streptomycin (100 μg/mL).

extract_protocol: RNA was isolated with Trizol (Invitrogen) and purified with PicoPure RNA Isolation Kit (Arcturus). RNA quality was verified on the Bioanalyzer RNA Pico Chip (Agilent Technologies).

treatment_protocol: Approximately 12h before transfection, these cells (1.5 × 105) were seeded on six-well plates in growth medium and allowed to adhere overnight at 37°C in a 5% CO2 atmosphere. The following day after washing the wells with PBS and replacing the growth medium with Opti-MEM (Invitrogen) cells were transfected with the miRNA [hsa-miR-7 miRIDIAN mimic, miRIDIAN miRNA mimic negative control #1 (miRNC), or has-miR-128 miRIDIAN mimic [(Thermo Fisher Scientific, Lafayette, CO)] using Lipofectamine 2000 transfection agent (Invitrogen) according to the manufacturer's instructions at a final concentration of 25nM. Cells were incubated for four hours, washed with PBS, and then incubated at 37°C and 5% CO2  for 44h (total 48h) after adding fresh growth medium to the wells.

tag: originial tumor type of initial cell

value: Papillary Cystadenocarcinoma of the ovary

value: HEY


title: mRNA miR128NC-1 (GCRMA)

source_name: HEY ovarian cancer cell, negative control miRNA treated


title: mRNA miR128NC-3 (GCRMA)


title: mRNA miR-128 1 (GCRMA)


title: mRNA miR128NC-2 (GCRMA)


title: mRNA miR7NC-3 (GCRMA)


title: mRNA miR7NC-2 (GCRMA)


title: Group 3 P09

city: Hamburg

last: Streichert

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

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Gene expression data from mice infected with L. sigmodontis

hyb_protocol: 10 µg of cDNA were hybridized for 16 hours at 60°C on the corresponding Eppendorf Thermomixer adapter. Washing and staining with IgG anti-biotin gold conjugate and silver  were performed according to the Eppendorf Silverquant protocol using corresponding washing thermomixer adapter from Eppendorf.

scan_protocol: slides were scanned on the Eppendorf Silverquant scanner at 12 µm using the Silverquant Scan Software version 2.0

data_processing: Data were processed with the Silverquant Analysis software using internal controlls and housekeeping genes on the array for normalization.

source_name: C57Bl/6 mouse PLECs

label_protocol: Biotinylated cDNA were prepared according to the Eppendorf DualChip extended Manual for Silverquant Detection version 3.0 from 5 ug total RNA

growth_protocol: Wt B6, gzmAxB, gzmA and gzmB ko mice on the resistant B6 background were provided from the Max-Planck-Institute for Immunobiology Freiburg, Germany (Prof. Markus Simon), and briefly kept at the BNI animal facilities under specific pathogen free conditions in microisolator cages until infected with L. sigmodontis and killed for the isolation of PLECS for the microarray. The natural infections of the mice with L. sigmodontis was performed using infectious mites kept at the BNI.

extract_protocol: Total RNA was isolated from 1x106 PLECs/mouse/group homogenized in 350 μl RA1 buffer using the NucleoSpin RNA II Kit  (Macherey-Nagel,Berlin, Germany), kept at –20°C and processed after thawing according to the manufacturer’s protocol.   PLECs/mouse/group

treatment_protocol: No treatment of mice or cells. Isolation of PLECs by washing pleural cavity with cold, sterile PBS. Centrifugation and washing of cells twice with PBS. Total RNA was isolated from 1x106 PLECs/mouse/group, homogenized in 350 ml RA1 buffer using the NucleoSpin® RNA II Kit (Macherey-Nagel, Berlin, Germany), kept at –20°C and processed after thawing according to the manufacturer’s protocol. RNA quality was checked with a Bioanalyzer (Agilent Technologies).

tag: mouse group

value: Granzyme A knock out

source_name: C57Bl/6 mouse spleen

value: normal spleen tissue


title: Group 3 P08


title: mRNA miR7NC-1 (GCRMA)


title: Group 3 P07


title: Group 2 P06

value: Wild type


title: Clint-Sf1-4-011411

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description: P28 testes wt, Sf1 Sertoli cell Dmrt1 KO, biological rep4.

hyb_protocol: 10 µg of purified, fragmented labeled cRNA was hybridized to Affymetrix 430 2.0 microarrays in the Affymetrix 640 hybridization oven according to the manufacturer's instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004).

scan_protocol: Scanning was performed using an Affymetrix GC3000 G7 scanner.

data_processing: CEL files were normalized using the GC-RMA algorithm as implemented in the Genedata Expressionist Analyst Package.

source_name: P28 testes Sf1 Cre

label_protocol: Labeling was performed by using 5.5 µg of total RNA according to the manufacturer's instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004) with the Affymetrix IVT amplification and labeling kit.

growth_protocol: Testes were dissected from male P28 (4-week-old) mice.

extract_protocol: Total RNA was isolated from testes using TRIzol reagent (Invitrogen #15596-026).

tag: background strain

value: mixed (C57BL6/6J and 129)

value: Dmrt1 flox/flox with SF1-cre

tag: gender

value: male

value: testis

tag: age

value: postnatal day 28 (P28)


title: mRNA miR-128-2 (plier)

data_processing: PLIER via Affymetrix Expression Console (TM) Software Version 1.1. Fold change was calculated based on the log2 difference of average log2 signal values of samples calculated after this preprocessing step.


title: mRNA miR7NC-3 (plier)


title: mRNA miR-7 2 (GCRMA)

source_name: HEY ovarian cancer cell, miR-7 mimic treated


title: mRNA miR128NC-3 (plier)


title: mRNA miR7NC-1 (plier)


title: Clint-Dhh-2-011411

description: P28 testes wt, Dhh Sertoli cell Dmrt1 KO, biological rep2.

source_name: P28 testes Dhh Cre

tag: genotype

value: Dmrt1 flox/flox with Dhh-cre


title: Clint-Sf1-2-011411

description: P28 testes wt, Sf1 Sertoli cell Dmrt1 KO, biological rep2.


title: mRNA miR128NC-1 (plier)


title: mRNA miR7NC-2 (plier)


title: mRNA miR-7 3 (GCRMA)


title: Clint-Sf1-3-011411

description: P28 testes wt, Sf1 Sertoli cell Dmrt1 KO, biological rep3.


title: Clint-Sf1-1-011411

description: P28 testes wt, Sf1 Sertoli cell Dmrt1 KO, biological rep1.


title: Group 2 P05

tag: strain


title: mRNA miR-128 1 (plier)


title: mRNA miR-7 1 (GCRMA)


title: mRNA miR128NC-2 (plier)


title: Clint-Dhh-1-011411

description: P28 testes wt, Dhh Sertoli cell Dmrt1 KO, biological rep1.


title: Group 2 P04


title: Group 1 P01

value: Granzyme AxB knock out


title: Group 1 P02


title: Group 1 P03


title: mRNA miR-7 1 (plier)


title: hAMSC_non-induced_2 weeks_rep3

city: Graz

first: Julia

last: König

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology and Embryology

country: Austria

institute: Medical University of Graz

description:
Gene expression data from non-induced hAMSC of placenta no. 3
non-induced hAMSC_3

hyb_protocol: GeneChip® Expression Wash, Stain and Scan; For Cartridge Arrays (FS450_0007)

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC_3_1_1.)

data_processing:
Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.4): RMA  (background correction, quantile normalization accross all chips in the experiment,  log2 transformation, median polish summarization); paired t-test

source_name: hAMSC, non-induced hAMSC, 2 weeks

label_protocol: GeneChip® Whole Transcript (WT) Sense Target Labeling Assay

growth_protocol: Human term placentas of normal pregnancies (range 38 to 42 weeks) were obtained after spontaneous delivery or caesarean section with informed consent. Approval of the Ethical Committee of the Medical University of Graz was granted (No. 21-079 ex 09/10). Isolation of amnion-derived mesenchymal stromal cells (hAMSC) was performed according to the protocol of Soncini et al. (J Tissue Eng Regen Med. 2007;1:296-305.). The amnion was manually separated from the chorion and washed with sterile 0.9% saline (Fresenius Kabi, Bad Homburg, Germany) supplemented with 150 IU/ml penicillin, 150 µg/ml streptomycin (both from PAA Laboratories, Pasching, Austria) and 0.4 µg/ml amphotericin B (Gibco, Invitrogen, Paisley, UK). The amnion was cut into small pieces and incubated in 2.5 U/ml dispase (BD Biosciences, Bedford, USA) at 37°C for 9 min. Subsequently, the amnion was transferred to DMEM low glucose (Gibco, Invitrogen) supplemented with 15% FBS Gold (Gibco, Invitrogen), 100 IU/ml penicillin and 100 µg/ml streptomycin for 10 min. Next, the amnion was incubated with 1.0 mg/ml Collagenase A and 0.01 mg/ml DNase (both from Roche, Penzberg, Germany) for 2 h. After centrifugation for 3 min at 150 x g, the supernatant was poured over a 100 µm cell strainer (BD Biosciences) and centrifuged for 10 min at 300 x g. The cell pellet was washed in PBS (Gibco, Invitrogen) and resuspended in either DMEM supplemented with 15% FBS, 100 IU/ml penicillin and 100 µg/ml streptomycin (non-induced hAMSC) or EGM-2 (Lonza, Walkersville, USA) for endothelial induction (induced hAMSC).

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany). The integrity of each RNA sample was determined using an Agilent 2100 Bioanalyzer (Agilent, Foster City, CA, USA) and only RNA samples with integrity values of 9.5-10 were used for hybridization.

treatment_protocol: Aliquots of hAMSC isolated from three different placenta  were cultured either in DMEM + 15% FCS (non-induced hAMSC1, 2, 3) or EGM-2 (endothelial-induced hAMSC 1, 2, 3) on gelatin-coated culture flasks until cells reached 90% confluence (about 5-8 d). Then cells were reseeded and cultured in the respective media for 14 d before RNA isolation.

tag: term placenta

value: amnionic membrane

value: human amniotic mesenchymal stromal cells  (hAMSC)

tag: culture conditions

value: control


title: mRNA miRNC-3 (MAS5)

data_processing: MAS 5.0 via Affymetrix Expression Console (TM) Software Version 1.1. Present/Absent/Marginal calls were based on analysis at this preprocessing step.

tag: cell line


title: mRNA miR-7 3 (plier)


title: hAMSC_non-induced_2 weeks_rep2

description:
Gene expression data from non-induced hAMSC of placenta no. 2
non-induced hAMSC_2


title: mRNA miR-7 2 (plier)


title: hAMSC_endothelial-induced_2 weeks_rep1

description:
Gene expression data from endothelial-induced hAMSC of placenta no. 1
induced hAMSC_1

source_name: hAMSC, endothelial-induced hAMSC, 2 weeks

value: endothelial cell medium EGM-2


title: hAMSC_endothelial-induced_2 weeks_rep3

description:
Gene expression data from endothelial-induced hAMSC of placenta no. 3
induced hAMSC_3


title: Native articular cartilage

description: Gene expression data from native articular cartilage

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

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

data_processing: The data were analyzed with Affymetrix GCOS 1.4. Target value scaling, with a target value set to 400, was used as normalization method.

organism: Sus scrofa

source_name: Articular cartilage

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Primary chondrocytes were isolated from articular and growth plate cartilage by using collagenase solution and cultivatted with DMEM/Ham's F12 supplemented with FBS and antibiotics. Chondrocytes were cultured at 37°C under an atmosphere of 5% oxygen and 5% carbon dioxide.

extract_protocol: Trizol extraction of total RNA followed by further purification using RNAeasy Mini Kit was performed according to the manufacturer's instructions.

treatment_protocol: Normal cell culture conditions with no supplements.

value: articular cartilage

value: primary cells


title: Cell culture of isolated chondrocytes from articular cartilage, day 10 of differentiation

description: Gene expression date from isolated and cultivated chorndrocytes from articular cartilage

source_name: Chondrocytes from articular cartilage

value: chondrocytes


title: Clint-Cont-1-011411

description: P28 testes Control, biological rep1.

source_name: P28 testes

value: Dmrt1 flox/flox with no Cre


title: MDA-MB-231A Non-Permissive

city: Halifax

first: Christopher

middle: Donald

last: Richardson

state: Nova Scotia

address: 5850 College St. Tupper 7th Floor 7C

department: Microbiology & Immunology

institute: Dalhousie University

description:
Cells grown to confluence in Dulbecco's 10% FCS
MDA-MB-231A

hyb_protocol: FS450_0007 protocol for hybridization and washing. 5.5 ug cDNA used.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing:
program-name = Expression Console
affymetrix-algorithm-name = rma-gene-default.

source_name: Breast adenocarcinoma cells from ATCC

label_protocol: Samples were prepared and labeled with the Affymetrix IVT kit at the Microarray Facility(Centre for Applied Genomics) Toronto Hospital for Sick Children. Biotin end-labeled fragments. Streptavidin PE detection.

growth_protocol: Confluent permissive and non-permissive cell lines were grown in Dulbecco's medium containing 10% fetal calf serum in T-75cm2 culture flasks..

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy kit. 250ug RNA used.

treatment_protocol: Cells were grown to confluency in Dulbecco's medium containing 10% fetal calf serum.

value: adenocarcinoma cell line MDA-MB-231

tag: adenocarcinoma type

value: Breast adenocarcinoma

tag: adenocarcinoma permissiveness

value: Non-permissive to measles virus


title: Cell culture of isolated chondrocytes from articular cartilage, day 20 of differentiation


title: hAMSC_endothelial-induced_2 weeks_rep2

description:
Gene expression data from endothelial-induced hAMSC of placenta no. 2
induced hAMSC_2


title: A549B Non-permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
A549B

source_name: Lung adenocarcinoma cells from ATCC

value: adenocarcinoma cell line A549

value: Lung adenocarcinoma


title: mRNA miRNC-1 (MAS5)

description: HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62)  in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.

value: Papillary Cystadenocarcinoma of the ovary

value: HEY


title: mRNA miRNC-2 (MAS5)


title: Cell culture of isolated chondrocytes from growth plate cartilage, day 10 of differentiation

description: Gene expression date from isolated and cultivated chorndrocytes from growth plate cartilage

source_name: Chondrocytes from growth plate

value: growth plate cartilage


title: NCI-H125 Permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
NCI-H125

value: adenocarcinoma cell line NCI-H125

value: Permissive to measles virus


title: MDA-MB-231B Non-Permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
MDA-MB-231B


title: MDA-MB-231C Non-Permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
MDA-MB-231C


title: A549A Non-permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
A549A


title: mRNA miR-128 1 (MAS5)


title: mRNA miR-128-2 (MAS5)


title: Native growth plate cartilage

description: Gene expression data from native growth plate cartilage

source_name: Growth plate cartilage


title: hAMSC_non-induced_2 weeks_rep1

description:
Gene expression data from non-induced hAMSC of placenta no. 1
non-induced hAMSC_1

value: amnionic membrane

value: human amniotic mesenchymal stromal cells  (hAMSC)


title: mRNA miR-7 3 (MAS5)


title: T47D Permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
T47D

value: adenocarcinoma cell line T47D


title: Clint-Cont-2-011411

description: P28 testes Control, biological rep2.

value: mixed (C57BL6/6J and 129)

value: male

value: testis

value: postnatal day 28 (P28)


title: MCF Permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
MCF7

value: adenocarcinoma cell line MCF7


title: NCI-H358 Permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
NCI-H358

value: adenocarcinoma cell line NCI-H358


title: MDA-MB-468 Permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
MDA-MB-468

value: adenocarcinoma cell line MDA-MB-468

value: Breast adenocarcinoma


title: MGH24 Permissive

description:
Cells grown to confluence in Dulbecco's 10% FCS
MGH24

value: adenocarcinoma cell line MGH24

value: Lung adenocarcinoma


title: Wild-type, biological rep 1

city: Ann Arbor

last: Alteri

state: MI

address: 5641 MS II 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

hyb_protocol: Standard Affymetrix protocol using Affymetrix E. coli Genome 2.0 GeneChips.

scan_protocol: Standard Affymetrix protocol.

data_processing: Expression values for each gene using a robust multi-array average (RMA).  A principal components analysis (PCA) was fit onto the expression values to determine that the replicated samples grouped together, and a linear model designed specifically for microarray analysis was fit to the data to compute the contrast of interest and filter out probesets with a variance < 0.05.  Probesets were adjusted for multiple comparisons using a false discovery rate (FDR) of 0.05.  Expression levels with a fold-change >2.0 and an adjusted P-value <0.05 from three independent replicates of each strain were compared by using the Affymetrix and Limma packages of Bioconductor implemented in the R statistical environment.

organism: Escherichia coli CFT073

source_name: Wild-type

label_protocol: RNA was labeled according to Affymetrix recommendations.

growth_protocol: Bacteria were cultured in Lysogeny broth (LB) medium at 37°C with aeration to an OD of 0.8.

extract_protocol: For the extraction of total RNA, 1 ml of bacteria culture was added to 0.125 ml of ice cold phenol-ethanol stop solution (5% phenol in ethanol), and the bacteria were collected by centrifugation.  Cells were lysed and RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer’s recommended protocol.

value: wild-type

tag: growth phase

value: logarithmic


title: Mutant, biological rep 3

source_name: Mutant

value: phoP deletion mutant


title: miRNA OSE 440

description: Ovarian surface epithelia brushing from ovaries described by pathology as within normal limits.

data_processing: MAS 5.0 via Affymetrix Expression Console (TM) Software Version 1.1

source_name: Ovarian Surface Epithelia

label_protocol: Affymetrix IVT Labeling Kit

treatment_protocol: Normal ovarian surface epithelial (OSE) cells were collected from ovaries at time of surgery using a Cytobrush Â® Plus (Medscand) and immediately stabilized in RNAlater (Ambion) and stored at â€“20 degrees C.

tag: tumor stage/grade

tag: age at surgery


title: mRNA CEPI 588

description: Serous ovarian tumor tissues were placed in cryotubes and immediately (<1 minute) frozen in liquid nitrogen following resection.

source_name: Laser Capture Microdissected Serous Ovarian Cancer Epithelia

label_protocol: Total RNA from the above extractions was processed using the RiboAmp OA or HS kit (Arcturus) in conjunction with the IVT Labeling Kit from Affymetrix, to produce an amplified, biotin-labeled mRNA suitable for hybridizing to GeneChip Probe Arrays (Affymetrix).

treatment_protocol: Following pathological verification, a serous papillary epithelial cancer sample was embedded in cryomatrix (Shandon).  Seven micron frozen sections were cut and attached to uncharged microscope slides for each sample.  Immediately following dehydration and staining (HistoGene, LCM Frozen Section Staining Kit, Arcturus), slides were processed in an Autopixâ€˜ instrument (Arcturus) for laser capture microdissection (LCM) of cells to CapSure Macro LCM Caps.  Approximately 30,000 epithelia were collected from each cancer sample.


title: mRNA miR-7 2 (MAS5)

value: Papillary Cystadenocarcinoma of the ovary

value: HEY


title: miRNA OSE 470


title: mRNA miR-7 1 (MAS5)


title: Cell culture of isolated chondrocytes from growth plate cartilage, day 20 of differentiation

tag: tissue

value: growth plate cartilage

tag: cell type

value: chondrocytes


title: 300 ng_big array_5

status: Public on Jul 28 2011

type: genomic

city: Vienna

first: Doris

last: Steger

state: Vienna

address: Althanstrasse 14

department: Department of Microbial Ecology

institute: University of Vienna

description: Hybridization of 300 ng labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 18 hours

hyb_protocol: Labeled RNA was added to hybridization buffer (6X saline-sodium citrate (SSC) buffer, 10% Denhardt’s reagent, 0.1% sodium dodecyl sulfate (SDS), 15% formamide) and incubated at 65°C for 5-15 min. Microarrays were sealed with the HybriWell Hybridization Sealing System (HBW2222-FL, Grace BioLabs), which have a well depth of 0.25 mm. Static microarray hybridizations, i.e.without active mixing of the hybridization solution,were performedin a custom-made hybridization chamber at 42°C for 18 h, except for experiments testing the effect of hybridization time. After hybridization, microarrays were washed by shaking at RT for 5 min sequentially in a 2X SSC, 0.1% SDS buffer and a 0.1X SSC buffer, followed by 20 s in ice-cold MQ water. Slides were dried by centrifugation (3 min, 300 x g) and stored in the dark at RT until scanning on the same day.

scan_protocol: Fluorescence images were recorded by scanning the slides at 10-μm resolution with a GenePix Personal 4100A array scanner (Axon Instruments, Molecular Devices Corporation, Sunnyvale, CA, USA). Each pixel line of the selected area was scanned three times and the obtained signals were averaged to generate the fluorescence image. Gain of the photo multiplier tube was adjusted to record images with signal intensities just below the saturation level. Scanned images were saved as multilayer tiff images and analyzed with the GenePix Pro 6.0 software (Axon Instruments). Low quality hybridizations were repeated.

data_processing: Scanned images were analyzed with GenePix Pro 6.0 software (Axon Instruments) and signal intensity surface plots of microarrays were generated using ImageJ with the Interactive 3D Surface Plot plug-in. Signal intensities were analyzed according to the spot position, and mean relative signal intensities for each spot position were either compared directly or in some cases normalized to either the maximum or minimum mean signal intensity to facilitate comparison. Poor quality spots were removed from the analysis . Statistical testing was performed with the Student’s t-test using Microsoft Excel.

molecule: genomic DNA

organism: Pseudodesulfovibrio halophilus

source_name: D. halophilus 16S rRNA gene, clone

label_protocol: A 1.5 kB-fragment of the 16S rRNA gene of Desulfovibrio halophilus (DSM 5663) was amplified using the PCR primer set 616V-630R. The 616V primer contained a T3 promoter site tag at the 5’ end to allow T3 RNA polymerase-based reverse transcription labeling of PCR products. The target was labeled via an in vitro transcription reaction and template DNA was digested. RNA concentration and dye incorporation rates were measured spectrophotometrically, and labeled 16S rRNA was fragmented via incubation with 10 mM ZnCl2 at 60°C for 30 min and was then stored in the dark at -20 °C.

extract_protocol: Plasmids were used as template. Plasmid DNA was extracted using the Qiaprep Spin Miniprep Kit (QIAgen, Hilden, Germany) according to manufacturer instructions.

tag: amount of labeled rna used for hybridization

tag: hybridization time

value: 18 hours

tag: assayed gene

value: 16S rRNA gene


title: 300 ng_big array_4


title: Wild-type, biological rep 3


title: Wild-type, biological rep 2


title: SAEC 10% Serum

description:
Cells grown 24 hrs
SAEC+FCS

source_name: SAEC Lonza

growth_protocol: Confluent SAEC were purchased in 6 well culture plates from Lonza Pharmaceutical (Walkersville, MD) and cultured 24hr at 37 degrees in 5% CO2 incubator.

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy kit. 250ug used.

treatment_protocol: Half the cells (3 wells) were grown in serum free media (SAGF), the other half were grown in Dulbeccos MEM containing 10% fetal calf serum.

value: Primary smooth airway epithelial cells (SAEC)

tag: agent

value: FSC

tag: saec permissiveness

value: permissive to measles virus


title: SAEC Serum Free Media

description:
Cells grown 24 hrs
SAEC-FCS

value: no FSC

value: non-permissive to measles virus


title: miRNA OSE 437


title: miRNA OSE 475


title: Mutant, biological rep 1

tag: genotype


title: mRNA OSE 434


title: mRNA CEPI 551


title: mRNA CEPI 489


title: 300 ng_big array_2

tag: strain


title: 300 ng_big array_3


title: Mutant, biological rep 2


title: 300 ng_big array_1


title: Normoxic NSCLC fragments patient #1210

first: Katharina

last: Leithner

address: Auenbruggerplatz 20

department: Department of Internal Medicine, Division of Pulmonology

description: Gene expression data from NSCLC fragments cultured ex-vivo in ambient oxygen for three days

hyb_protocol: GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

data_processing:
Gene expression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.4): RMA  (background correction, quantile normalization accross all chips in the experiment, log2 transformation, median polish summarization)

source_name: Ex-vivo cultured tumor fragments from patient #1210

label_protocol: GeneChip® Whole Transcript (WT) Sense Target Labeling Assay; Kits : WT cDNA Synthesis and Amplification Kit 30 rxn, (Cat No. 900673); WT Terminal Labeling Kit 30rxn (Cat No. 900671)

growth_protocol: Dissection of fresh NSCLC tissue into fragments app. 1mmx1mmx1mm, culture in DMEM/F12 growth medium containing 10% FCS and antibiotics in petridishes

extract_protocol: RNA isolation with Qiagen Mini kit according to manufacturer

treatment_protocol: Immediately after dissection treatment in hypoxia (1% oxygen) or normoxia (ambient oxygen) for three days

value: Non-small cell lung cancer (NSCLC)

tag: histology

value: Adenocarcinoma

tag: treatment

value: Normoxia


title: Normoxic NSCLC fragments patient #1209

source_name: Ex-vivo cultured tumor fragments from patient #1209

value: Squamous cell carcinoma


title: Hypoxic NSCLC fragments patient #3609

description: Gene expression data from NSCLC fragments cultured ex-vivo in hypoxia (1% oxygen) for three days

source_name: Ex-vivo cultured tumor fragments from patient #3609

value: Hypoxia


title: Normoxic NSCLC fragments patient #2909

source_name: Ex-vivo cultured tumor fragments from patient #2909


title: Hypoxic NSCLC fragments patient #2909


title: Normoxic NSCLC fragments patient #1010

source_name: Ex-vivo cultured tumor fragments from patient #1010


title: Normoxic NSCLC fragments patient #1309

source_name: Ex-vivo cultured tumor fragments from patient #1309


title: Normoxic NSCLC fragments patient #1310

source_name: Ex-vivo cultured tumor fragments from patient #1310

value: Squamous cell carcinoma/large cell carcinoma


title: Normoxic NSCLC fragments patient #1409

source_name: Ex-vivo cultured tumor fragments from patient #1409


title: Normoxic NSCLC fragments patient #3209

source_name: Ex-vivo cultured tumor fragments from patient #3209


title: Hypoxic NSCLC fragments patient #1010


title: Hypoxic NSCLC fragments patient #1409


title: Normoxic NSCLC fragments patient #1410

source_name: Ex-vivo cultured tumor fragments from patient #1410


title: Hypoxic NSCLC fragments patient #1310


title: Hypoxic NSCLC fragments patient #1410


title: Normoxic NSCLC fragments patient #3609


title: Hypoxic NSCLC fragments patient #1210


title: uninfected primary RPE, biological replicate 4

city: Sydney

first: Luis

last: Munoz-Erazo

state: NSW

address: Room 260, Blackburn building D06

department: Department of Pathology

country: Australia

institute: University of Sydney

description: Gene expression data from uninfected cells

hyb_protocol: Following fragmentation,  cRNA was hybridized onto Human Exon 1.0 ST chips for 16h. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000

data_processing: Data was analysed with the GeneSping Gx11 program using RMA function

source_name: uninfected hRPE cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary cells were extracted from cadaveric eyes and ARPE19 cells were obtained from the ATCC. Cells were then grown at 30ºC with 5% CO2 in DMEM + 10%FCS

extract_protocol: After 24h post infection, cells were lysed with Trizol and RNA was extracted using Rneasy kit (Qiagen)

treatment_protocol: Cells were infected with 1 plaque forming unit per cell of West Nile Virus

value: hRPE

tag: disease state

value: uninfected

tag: gender

value: male


title: uninfected primary RPE, biological replicate 3


title: Hypoxic NSCLC fragments patient #1209


title: infected primary RPE, biological replicate 4

description: Gene expression data from infected cells

source_name: hRPE cells 24h post-infection with WNV

value: 24h post-infection with WNV


title: Slide 176559

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

description:
B cereus pATK31 vs pLM5 replicate 2
Net{A} is the raw signal of channel A minus the local corner background signal of channel A and is channel 1 in the sample
Net{B} is the raw signal of channel B minus the local corner background signal of channel B and is channel 2 in the sample

hyb_protocol: The protocol was performed as described in Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215

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

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Bacillus cereus

source_name: Bacillus cereus carrying empty plasmid (pLM5)

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

growth_protocol: Cultures growth in minimal medium supplemented with chloramphenicol

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

treatment_protocol: Samples were induced at the exponential-growth phase (OD600=0,75) with IPTG to a final concentration of 1mM

tag: plasmid

source_name: Bacillus cereus with induced ComK1 (pATK31


title: Slide 176781

description:
Bacillus cereus pNWcomKBsu vs pNW33N replicate 3
Net{A} is the raw signal of channel A minus the local corner background signal of channel A and is channel 1 in the sample
Net{B} is the raw signal of channel B minus the local corner background signal of channel B and is channel 2 in the sample

source_name: Bacillus cereus carrying empty plasmid (pNW33N)

source_name: Bacillus cereus with overexpressed ComK (pNWcomKBsu)

value: pNWcomKBsu


title: infected ARPE19 cell line

tag: cell line


title: Hypoxic NSCLC fragments patient #3209


title: uninfected ARPE19 cell line


title: infected primary RPE, biological replicate 3


title: Slide 176560

description:
B cereus pATK31 vs pLM5 replicate 3
Net{A} is the raw signal of channel A minus the local corner background signal of channel A and is channel 1 in the sample
Net{B} is the raw signal of channel B minus the local corner background signal of channel B and is channel 2 in the sample


title: Slide 176796

description:
B cereus pATK32 vs pLM5 replicate 1
Net{A} is the raw signal of channel A minus the local corner background signal of channel A and is channel 1 in the sample
Net{B} is the raw signal of channel B minus the local corner background signal of channel B and is channel 2 in the sample

source_name: Bacillus cereus with induced ComK2 (pATK32)


title: Slide 176779

description:
Bacillus cereus pNWcomKBsu vs pNW33N replicate 2
Net{A} is the raw signal of channel A minus the local corner background signal of channel A and is channel 1 in the sample
Net{B} is the raw signal of channel B minus the local corner background signal of channel B and is channel 2 in the sample


title: infected primary RPE, biological replicate 2


title: Slide 176555

description:
B cereus  pATK31 vs pLM5 replicate 1
Net{A} is the raw signal of channel A minus the local corner background signal of channel A and is channel 1 in the sample
Net{B} is the raw signal of channel B minus the local corner background signal of channel B and is channel 2 in the sample


title: Hypoxic NSCLC fragments patient #1309


title: Slide 176777

description:
Bacillus cereus pNWcomKBsu vs pNW33N replicate 1
Net{A} is the raw signal of channel A minus the local corner background signal of channel A and is channel 1 in the sample
Net{B} is the raw signal of channel B minus the local corner background signal of channel B and is channel 2 in the sample


title: Slide 176798

description:
B cereus pATK32 vs pLM5 replicate 3
Net{A} is the raw signal of channel A minus the local corner background signal of channel A and is channel 1 in the sample
Net{B} is the raw signal of channel B minus the local corner background signal of channel B and is channel 2 in the sample


title: uninfected primary RPE, biological replicate 2


title: infected primary RPE, biological replicate 1


title: GABPalpha-deficient HSCs rep1

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

description: GABPa(FL/-) Flt3(-) LSK-1

hyb_protocol: 2.5 ug of labeld cDNA were hybridized  on mouse GENE 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 complete with a 7G upgrade.

data_processing:
The data were analyzed with Partek GS v 6.4 using default RMA  as normalization method.
MoGene-1_0-v1.r4.pgf
MoGene-1_0-v1.r4.mps

source_name: GABPalpha-deficient HSCs

label_protocol: Biotinylated cDNA were prepared using NuGEN WT-Ovation PicoRNA amplification system, starting from 800 pg to 50 ng of total RNA.

growth_protocol: Mx1Cre-GABPa(FL/+) and Mx1Cre-GABPa(FL/-) mice were treated with pIpC to induce inactivation of GABPalpha in bone marrow cells. Four days after last treatment of pIpC, the bone marrow cells were isolated.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by further purification on RNeasy columns.

treatment_protocol: Flt3(-) LSK cells from bone marrow were sorted directly into Trizol LS reagent.

value: C57/BL6 backcross for 4 generations

value: isolated from bone marrow

tag: age

value: 6-8 weeks

value: Flt3(-) LSK

tag: genotype/variation


title: control HSCs rep2

description: GABPa(FL/+) Flt3(-) LSK-2

source_name: control HSCs

tag: tissue


title: control HSCs rep1

description: GABPa(FL/+) Flt3(-) LSK-1

tag: cell type


title: GABPalpha-deficient HSCs rep2

description: GABPa(FL/-) Flt3(-) LSK-2


title: uninfected primary RPE, biological replicate 1


title: Chinese hamster ovary (CHO) cell culture_291

city: Dublin

first: Colin

last: Clarke

address: Collin's Av.

department: NICB

country: Ireland

institute: Dublin City University

description: CHO gene expression data

hyb_protocol: A pre-qualified standard curve reagent consisting of fragmented biotinylated cRNA (Hill AA, Brown EL, Whitley MZ, Tucker-Kellogg G, Hunter CP, Slonim DK. 2001. Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls. Genome Biology 2, 12, Research 0055.1-0055.13) was included in all hybridization reactions. Hybridisation solution (1 mol/L NaCl, 20 mmol/L EDTA, 100 mmol/L 2-(N-morpholino)ethanesulfonic acid, and 0.01% Tween 20) was used to pre-hybridise custom WyeHamster2a oligonucleotide microarrays for 10 min at 45oC and 60 rpm. The prehybridisation solution was removed and replaced with 200 ul hybridisation solution containing 0.025 ug/ul fragmented cRNA. The arrays were hybridised for 16 hrs at 45oC and 60 rpm in a Hybridization Oven 640 (Affymetrix). Arrays were subsequently washed and stained with streptavidin-phycoerythrin solution (2 mg/ml acetylated BSA and 10 ug/ml streptavidin R-phycoerythrin; Molecular Probes) in a Fluidics Station 450 (Affymetrix) as per manufacturer's instructions.

scan_protocol: WyeHamster2a arrays were scanned on an GCS GeneChip GeneArray scanner (Affymetrix) as per manufacturer's instructions.

data_processing: All microarray data were pre-processed using the RMA algorithm

organism: Cricetulus griseus

source_name: Cell lysate

label_protocol: 5 ug of Total RNA from each sample underwent cDNA synthesis, followed by cleanup and overnight IVT amplification, labeling and subsequent cleanup using the GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents (#900493, Affymetrix) according to manufacturer's instructions (http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

growth_protocol: All samples were from production cell lines and were grown in replicate suspension cultures using proprietary chemically-defined culture media at both shake flask and benchtop bioreactor scale. Cultures were maintained at 37oC (Pre-temperature shift (Ts) or at either 31oC or 29.5oC (Post-Ts).

extract_protocol: Total RNA was isolated using the RNeasy kit according to the manufacturer's instructions. RNA quantity and purity were assessed at 260 nm and 280 nm using a Nanodrop (Labtech Int.) and Spectramax Spectrophotometer (Molecular Devices). A Bioanalyser 2100 (Agilent Technologies) was used to qualitatively assess RNA after isolation, biotin-labeling and fragmentation.

treatment_protocol: Samples were taken down at discrete time (day) intervals that ranged between 3-14 days of culture. Typically, cell pellets of 5x10^6 cells were lysed in 1ml RLT lysis buffer containing beta-mercaptethanol (RNeasy Mini Prep kit, Qiagen), and stored at -80oC until required.

tag: growth rate

tag: temperature

tag: qammonia

tag: qlactate

tag: cell viability

tag: seeding density

tag: cell density

tag: titre

tag: qproductivity


title: Chinese hamster ovary (CHO) cell culture_292

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_287

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_288

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_294

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_289

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_293

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_295

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_290

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_279

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_283

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_286

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_276

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_277

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_278

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_280

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_282

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_281

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_275

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_284

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_285

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_273

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_270

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_269

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_274

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_272

description: CHO gene expression data


title: DNA replication origins in drosophila Kc G2/M arrested cells

type: mixed

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

description: two independent samples

hyb_protocol: Performed according to NimbleGen protocols

data_processing:
Experimental (Cy5) and control (Cy3) signal intensities quantified and provided by Nimblegen were converted into log2 ratios (log2 (Cy5/Cy3)). The Lowess normalization method was applied to eliminate intensity-dependent variations in dye bias (Yang et al. 2002). A sliding median window with a length of 5 oligonucleotide probes was used to smooth the signal. Mode (m) and s (median absolute deviation) of normalized log2 ratios were computed. Assuming that the normal distribution (specified by m and s) covered the entire background noise (non-significant signals),
for each probe, one p-value was computed by applying the false discovery rate (FDR) correction (Benjamin and Hochberg 1995). One biological independent samples for Drosophila Kc G2/M arrested cells were used. Normalized log2 ratios of replicate samples were combined by averaging the values at the corresponding genomic positions and the corrected p-values were combined using a Chi-Square distribution (Fisher 1932). Thus, one probe was denoted as significant if the combined p-value was lower than 5% (level of significance).

molecule: other

organism: Drosophila melanogaster

source_name: Kc cells nascent strands on G2-M arrested cells

extract_protocol:
Nascent strand (NS) preparation
DNA purification
Dividing cells (2.5-5 ×108) were washed in PBS, harvested and lysed in 15 ml DNAzol (Invitrogen) at room temperature (RT) for 5 min. Samples were digested with 200 μg/ml proteinase K at 37°C for 2 hours. We found that combining the proteinase K treatment with DNAzol significantly improved the yield of NS. Insoluble material was discarded by centrifugation at 3000 g at 4°C for 15 min and genomic DNA was precipitated with 15 ml 100% ethanol at RT for 5 min. DNA was transferred to a new tube and washed with 5 ml 70% ethanol at RT for 5 min and air-dried. DNA was resuspended in 2 ml TEN20 (10 mM Tris-Cl pH 7.9, 2 mM EDTA, 20 mM NaCl, 0.1% SDS, 1000 U RNasin) at 70°C, boiled for 10-15 min and chilled on ice.
NS purification by sucrose gradient
1 ml of denatured genomic DNA was loaded onto a 30 ml neutral 5 to 30% sucrose gradient prepared in TEN300 (10 mM Tris pH 7.9, 2mM EDTA, 300 mM NaCl) and centrifuged in a Beckman SW28 rotor at 24000 RPM, 4°C, for 20 h. 1 ml fractions were withdrawn from the top of the gradient using a wide-bore pipette tip. 50 μl of each fraction was run with appropriate size markers on a 2% alkaline agarose gel at 40-50 volts, overnight at 4°C. The gel was neutralized with 1x TBE and stained with Gel Red (Interchim). Fractions corresponding to 0.5-2.5 kb were pooled and precipitated with 2.5 volumes ethanol at -80°C for 15 min. Pellets were washed with 1 ml 70% ethanol and suspended in 20 μl water with 100 U RNasin (NEB).
Lambda exonuclease treatment
After addition of 2 μl T4 polynucleotide kinase (PNK) 10X buffer (NEB), fractions were boiled for 5 min and chilled on ice. Phosphorylation with T4 PNK was performed in 1X PNK buffer containing 0.2 U/μl PNK in a volume of 100 μl at 37°C for 1 hour. After heat inactivation at 75°C for 15 min, DNA was precipitated with 2.5 volumes ethanol-0.3 M sodium acetate (Na-acetate) at -80°C for 15 min. Pellets were washed with 1 ml 70% ethanol and suspended in 50 μl water with 100 U RNasin. Digestion with 100 U lambda exonuclease was in exo buffer (67 mM Glycine-KOH pH 9.4, 2.5 mM MgCl2, 50 μg/ml BSA) in 100 μl total volume at 37°C overnight. We found that the quality of the lambda exonuclease is crucial, and deserves to be always tested before use. For the experiments described here, we used a custom-made preparation by Fermentas (20U/μl). NS were extracted once with phenol/chloroform/isoamylalcohol and once with chloroform/isoamylalcohol, then precipitated with 2.5 volumes ethanol-0.3M Na-acetate at -80°C for 15 min. Pellets were washed with 1 ml 70% ethanol and suspended in 20 μl water. NS were subjected to one or two further cycles of T4 PNK phosphorylation and exonuclease digestion. We observed that the second round of exonuclease treatment significantly improves the NS preparation. Aliquots of digested and undigested DNA were run on a 2% agarose gel to confirm the efficiency of the exonuclease treatment. Finally, NS were purified using the CyScribe GFX Purification Kit (GE Healthcare) and eluted in 60 μl water.

value: Kc cells

value: embryonic cells

source_name: Genomic DNA

extract_protocol: Genomic DNA were extracted using DNAzol (Invitrogen)


title: Chinese hamster ovary (CHO) cell culture_271

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_266

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_268

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_265

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_267

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_252

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_251

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_254

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_258

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_263

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_264

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_257

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_256

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_262

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_261

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_250

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_260

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_249

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_253

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_255

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_247

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_259

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_246

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_242

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_245

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_243

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_244

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_248

description: CHO gene expression data


title: DNA replication origins in drosophila Kc cells genome

description: two independent samples

scan_protocol: Performed according to NimbleGen protocols

data_processing:
Experimental (Cy5) and control (Cy3) signal intensities quantified and provided by Nimblegen were converted into log2 ratios (log2 (Cy5/Cy3)). The Lowess normalization method was applied to eliminate intensity-dependent variations in dye bias (Yang et al. 2002). A sliding median window with a length of 5 oligonucleotide probes was used to smooth the signal. Mode (m) and s (median absolute deviation) of normalized log2 ratios were computed. Assuming that the normal distribution (specified by m and s) covered the entire background noise (non-significant signals),
for each probe, one p-value was computed by applying the false discovery rate (FDR) correction (Benjamin and Hochberg 1995). Two biological independent samples for Drosophila Kc cells were used. Normalized log2 ratios of replicate samples were combined by averaging the values at the corresponding genomic positions and the corrected p-values were combined using a Chi-Square distribution (Fisher 1932). Thus, one probe was denoted as significant if the combined p-value was lower than 5% (level of significance).

source_name: Kc cells nascent strands


title: Chinese hamster ovary (CHO) cell culture_240

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_241

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_238

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_239

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_237

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_231

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_236

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_235

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_229

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_233

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_232

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_226

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_230

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_234

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_228

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_227

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_220

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_219

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_221

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_215

description: CHO gene expression data


title: Slide 176797

description:
B cereus pATK32 vs pLM5  replicate 2
Net{A} is the raw signal of channel A minus the local corner background signal of channel A and is channel 1 in the sample
Net{B} is the raw signal of channel B minus the local corner background signal of channel B and is channel 2 in the sample


title: Chinese hamster ovary (CHO) cell culture_225

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_214

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_217

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_216

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_224

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_213

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_223

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_222

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_212

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_211

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_218

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_204

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_203

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_201

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_202

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_210

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_198

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_199

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_197

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_208

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_207

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_209

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_205

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_206

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_195

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_200

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_196

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_193

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_194

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_184

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_186

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_185

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_188

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_191

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_192

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_190

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_187

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_183

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_182

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_189

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_180

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_181

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_179

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_167

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_166

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_165

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_175

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_174

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_178

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_168

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_173

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_172

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_171

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_169

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_170

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_177

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_176

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_163

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_164

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_160

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_161

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_162

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_156

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_155

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_159

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_151

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_154

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_157

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_150

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_153

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_152

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_158

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_137

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_141

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_147

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_136

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_135

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_134

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_149

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_140

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_146

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_148

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_143

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_144

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_138

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_145

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_142

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_133

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_139

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_130

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_132

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_131

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_129

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_120

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_121

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_122

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_126

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_128

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_127

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_124

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_125

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_123

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_119

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_112

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_109

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_111

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_101

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_114

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_100

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_117

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_113

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_110

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_102

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_118

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_116

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_103

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_106

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_108

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_107

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_104

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_105

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_115

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_98

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_99

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_97

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_93

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_94

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_92

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_96

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_88

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_87

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_84

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_85

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_83

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_86

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_82

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_80

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_81

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_89

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_77

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_72

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_78

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_76

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_70

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_79

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_74

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_75

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_68

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_91

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_71

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_73

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_61

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_67

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_69

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_65

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_59

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_58

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_60

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_51

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_62

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_63

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_57

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_56

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_54

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_53

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_64

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_66

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_55

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_49

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_44

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_46

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_47

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_48

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_45

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_50

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_52

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_43

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_42

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_35

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_38

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_37

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_39

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_41

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_40

description: CHO gene expression data


title: Colon 2x amplified EH81R11

city: Kamakura

first: Hiroko

last: Sudo

state: Kanagawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

country: Japan

institute: Toray Industries, Inc.

description: Used in Fig. 4

hyb_protocol: Hybridized for 16 h at 42 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.. The labeled samples were individually hybridized onto DNA chip surface, and incubated at 42 ℃ for 16 hours.

scan_protocol: ScanArray Lite (Perkin Elmer) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments). Washed and dried DNA chip in an ozone-removed environment was scanned using a ProScanArray™ microarray scanner. The obtained microarray images were analyzed using the Genepix Pro™ 4.0 software.

data_processing:
F635 Median column as Red signal. The raw data of each spot was globally normalized by adjusting the median signal intensity for each DNA chip. To be equal.
The median values of the foreground signal minus the local background were represented as feature intensities. All data obtained from microarray experiments were normalized by a quantile normalization method, and filtered.

source_name: Human colon RNA

label_protocol:
Biotinylated UTP was incorporated into cDNA during reverse transcription. After hybridization, the microarrays were post-labled using nucleic acid dendrimers attached with Oyster650 dye (Genisphere).
For each patient, 500 ng of total RNA derived from tumor and non-tumor samples were labeled using miRCURY LNA™ microRNA Power Labeling Kits Hy5

extract_protocol: Tumor and non-tumor tissues were obtained and frozen in liquid nitrogen immediately after hepatic resection, and stored in liquid nitrogen until RNA extraction. Total RNA samples were extracted by a phenol-chloroform RNA extraction method.

tag: method

value: Colon 2x amplified

value: Colon

value: 68 yr

value: female

tag: ethnicity

value: caucasian

tag: sample type

value: 68 yo caucasian female


title: Colon non-amplified EH86G21

description: Used in Fig. 4

value: Colon non-amplified

tag: gender


title: Chinese hamster ovary (CHO) cell culture_33

description: CHO gene expression data


title: Human Alzheimer brain non-amplified EH92B10

description: Used in Fig. 5 and Table 2

source_name: Human Alzheimer brain RNA

value: Human Alzheimer brain non-amplified

value: Brain from Alzheihmer patient

tag: age

value: 87 yr

value: 87 yo male Alzheimer patient


title: Chinese hamster ovary (CHO) cell culture_34

description: CHO gene expression data


title: Human Alzheimer brain 1x amplified EH92B14

description: Used in Fig. 5 and Table 2

value: Human Alzheimer brain 1x amplified


title: Colon 1x amplified h25k#5608

description: Used in Fig. 4

value: Colon 1x amplified


title: Human Alzheimer brain non-amplified EH92B12

description: Used in Fig. 5 and Table 2


title: Breast 2x amplified EH81R06

description: Used in Fig. 4

source_name: Hunan breast RNA

value: Breast 2x amplified

value: Breast

value: 27 yr

value: 27 yo caucasian female


title: Human brain reference RNA 1x amplified h25k#5627

description: Used in Fig. 4 and 5

source_name: human brain reference RNA

value: Human brain reference RNA 1x amplified

value: Brain at several regions

value: Pooled from multiple donors


title: Human Alzheimer brain 1x amplified EH92T04

description: Used in Fig. 5 and Table 2


title: Chinese hamster ovary (CHO) cell culture_36

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_32

description: CHO gene expression data


title: Breast non-amplified EH86G20

description: Used in Fig. 4

value: Breast non-amplified

value: female


title: Human brain reference RNA 1x amplified h25k#5624

description: Used in Fig. 4 and 5


title: Human brain reference RNA non-amplified EH86H04

description: Used in Fig. 4 and 5

value: Human brain reference RNA non-amplified


title: Breast 1x amplified h25k#5619

description: Used in Fig. 4

value: Breast 1x amplified

value: caucasian


title: Chinese hamster ovary (CHO) cell culture_31

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_30

description: CHO gene expression data


title: Human brain reference RNA 2x amplified EH81R14

description: Used in Fig. 4

value: Human brain reference RNA 2x amplified


title: Universal human reference RNA 2x amplified EH81R09

description: Used in Fig. 4

source_name: Universal human reference RNA

value: Mixture of ten human cell lines


title: Chinese hamster ovary (CHO) cell culture_28

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_27

description: CHO gene expression data


title: Human brain reference RNA non-amplified EH86H03

description: Used in Fig. 4 and 5


title: Chinese hamster ovary (CHO) cell culture_24

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_22

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_29

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_26

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_25

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_23

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_19

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_20

description: CHO gene expression data


title: Universal human reference RNA 1x amplified EH8XP16

description: Used in Fig. 1 and 2


title: Universal human reference RNA 1x amplified EH8XW05

description: Used in Fig. 2


title: Universal human reference RNA non-amplified EH86H01

description: Used in Fig. 4


title: Universal human reference RNA 2x amplified EH92B01

description: Used in Fig. 2


title: Universal human reference RNA 1x amplified EH8XP22

description: Used in Fig. 1 and 2


title: Universal human reference RNA 2x amplified EH92A21

description: Used in Fig. 1 and 2


title: Universal human reference RNA 1x amplified h25k#5636

description: Used in Fig. 4


title: Universal human reference RNA 1x amplified EH8XM22

description: Used in Fig. 2


title: Universal human reference RNA 1x amplified EH8XW04

description: Used in Fig. 2


title: Chinese hamster ovary (CHO) cell culture_17

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_16

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_18

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_95

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_90

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_14

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_15

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_21

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_11

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_12

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_13

description: CHO gene expression data


title: Universal human reference RNA non-amplified EM8XT06

description: Used in Fig. 2


title: Universal human reference RNA non-amplified EM8XT12

description: Used in Fig. 2


title: Chinese hamster ovary (CHO) cell culture_10

description: CHO gene expression data


title: Universal human reference RNA non-amplified EM8XT11

description: Used in Fig. 2


title: Chinese hamster ovary (CHO) cell culture_7

description: CHO gene expression data