title: Normal oral tissue_88N

description: normal person


title: Normal oral tissue_84N

status: Public on Sep 01 2011

type: RNA

city: Taoyuan

first: Chien-Hua

last: Peng

address: No. 5, Fu-Hsing ST.

country: Taiwan

institute: Chang Gung Memorial Hospital

description: normal person

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000

data_processing:
Data were processed using Partek software. Gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Normal oral tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total RNA was isolated from tissue using the Qiagen RNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to the manufacturer’s protocol.

treatment_protocol: OSCC tissues were surgical dissected and immediately froze in liquid nitrogen until use

tag: disease state

value: normal


title: cna1_2/FK506_2

city: Durham

first: Ying-Lien

last: Chen

state: NC

address: Dept. of Molecular Genetics and Microbiology, Duke University Medical Center

department: Molecular Genetics and Microbiology

country: USA

institute: Duke University

description:
Biological Replicate 2, wheel 2
cna1 replicate 2 vs FK506 treated replicate 2

hyb_protocol: Standard Agilent protocols for Agilent Custom Oligo Microarray 8x15K G4427A for samples 5-20, and Oligo Microarray 4x44K G2519F for samples 1-4

scan_protocol: Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.  Reported expression values for each gene are median log2 ratios across all probes.

organism: Nakaseomyces glabratus

source_name: cna1 rep 2

label_protocol: Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.

growth_protocol: Strains were grown overnight at 24°C and washed twice by dH2O. Cells were diluted to 0.2 OD/ml in YPD and incubated 3 hr at 24°C. For wild-type, cells in log-phase were then diluted to 0.2 OD/ml (10 ml) in YPD in the presence or absence of FK506 (1 µg/ml) and CaCl2 (0.2 M).  cna1 (YC98), and crz1 (YC182) mutants were diluted to 0.2 OD/ml (10 ml) in YPD. Following 3 hr incubation at 37°C/250 rpm, 10 ml of cultures were immediately poured to dry-ice/ethanol precolded 15 ml methanol (60%) to stop cellular processes and RNase activity. Cells were pelleted at 3000 rpm at -4°C, flash freezed with liquid N2, and stored at -80°C for further total RNA extraction.

extract_protocol: Qiagen Yeast RNA extraction

treatment_protocol: Wild-type CBS138 was treated with FK506 (1 ug/ml) or CaCl2 (0.2 M)

tag: genotype/variation

source_name: FK506 rep 2

value: wild-type

tag: agent


title: FK506_2/crz1_2

description:
Biological Replicate 2, wheel 2
FK506 treated replicate 2 vs crz1 replicate 2

source_name: crz1 rep 2


title: Normal oral tissue_85N

description: normal person


title: crz1_2/CaCl2_2

description:
Biological Replicate 2, wheel 2
crz1 replicate 2 vs CaCl2 treated replicate 2

source_name: CaCl2 rep 2


title: B. subtilis_RNaseY depletion_replicate A_hyb1

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: B. subtilis_RNase Y depletion_first biological replicate

hyb_protocol: 500 ng of Cy5-labeled cDNA and 500 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: B. subtilis GP193_with xylose

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies). The RNA/primer mixture was incubated at 70 °C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare) and 2µl of SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 60 min and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: The B. subtilis strain GP193 expressing the essential gene rny (encoding RNase Y) under a xylose inducible promoter was grown under vigorous agitation at 37 °C in CSE minimal medium (Wacker et al., 2003, Microbiology 149: 3001-3009) in the presence and absence of xylose.

extract_protocol: Total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002, J. Bacteriol. 184: 2500-2520).

treatment_protocol: Cells were harvested immediately after the first detectable change in growth rate of the culture without xylose due to the reduced amounts of RNase Y.

tag: strain

tag: treatment

value: with xylose

source_name: B. subtilis GP193_without xylose

value: no xylose


title: WT_2/crz1_2

description:
Biological Replicate 2, wheel 2
wild-type replicate 2 vs crz1 replicate 2

source_name: wild-type rep 2


title: CaCl2_2/WT_2

description:
Biological Replicate 2, wheel 2
CaCl2 treated replicate 2 vs wild-type replicate 2


title: WT_1/cna1_1

description:
Biological Replicate 1, wheel 1
wild-type treated replicate 1 vs cna1 replicate 1

source_name: wild-type rep 1

source_name: cna1 rep 1


title: Normal oral tissue_81N

description: normal person


title: Normal oral tissue_82N

description: normal person


title: CaCl2_2/FK506_2

description:
Biological Replicate 2, wheel 2
CaCl2 treated replicate 2 vs FK506 treated replicate 2


title: cna1_2/CaCl2_2

description:
Biological Replicate 2, wheel 2
cna1 replicate 2 vs CaCl2 treated replicate 2


title: Normal oral tissue_83N

description: normal person


title: crz1_2/cna1_2

description:
Biological Replicate 2, wheel 2
crz1 replicate 2 vs cna1 replicate 2


title: crz1_1/CaCl2_1

description:
Biological Replicate 1, wheel 1
crz1 replicate 1 vs CaCl2 treated replicate 1

source_name: crz1 rep 1

source_name: CaCl2 rep 1


title: CaCl2_1/WT_1

description:
Biological Replicate 1, wheel 1
CaCl2 treated replicate 1 vs wild-type replicate 1


title: B. subtilis_RNaseY depletion_replicate A_hyb2

description: B. subtilis_RNase Y depletion_first biological replicate_dye swap


title: crz1_1/cna1_1

description:
Biological Replicate 1, wheel 1
crz1 replicate 1 vs cna1 replicate 1


title: cna1_1/CaCl2_1

description:
Biological Replicate 1, wheel 1
cna1 replicate 1 vs CaCl2 treated replicate 1


title: WT_1/crz1_1

description:
Biological Replicate 1, wheel 1
wild-type replicate 1 vs crz1 replicate 1


title: Normal oral tissue_80N

description: normal person


title: CaCl2_1/FK506_1

description:
Biological Replicate 1, wheel 1
CaCl2 treated replicate 1 vs FK506 replicate 1

source_name: FK506 rep 1


title: Normal oral tissue_79N

description: normal person


title: Normal oral tissue_78N

description: normal person


title: FK506_1/WT_1

description:
Biological Replicate 1, wheel 1
FK506 replicate 1 vs wild-type replicate 1


title: Normal oral tissue_72N

description: normal person


title: Normal oral tissue_77N

description: normal person


title: Normal oral tissue_68N

description: normal person


title: Normal oral tissue_65N

description: normal person


title: Tnrc6a(GW182) mutant mouse E9.5 yolk sac rep3

city: BoSTON

first: jining

last: lu

address: 715 Albany street R304

institute: Boston University

description: Gene expression data from yolk sac of Tnrc6a (GW182) mutant mouse

hyb_protocol: Standard Affymetrix protocol

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.

organism: Mus musculus

source_name: yolk sac of E9.5 Tnrc6a(GW128) mutant mouse

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

extract_protocol: Trizol extraction of total RNA of yolk sac disseected from individual embryo was performed according to the manufacturer's instructions.

tag: tissue

value: yolk sac

value: Tnrc6a (GW182) mutant (mixed)

tag: age


title: Normal oral tissue_66N

description: normal person


title: Tnrc6a(GW182) mutant mouse E9.5 yolk sac rep2


title: Normal oral tissue_57N

description: normal person


title: TCF-1-deficient thymocytes

city: duarte

first: ruiqing

last: wang

state: ca

address: 1500 duarte rd

institute: city of hope

description:
Tcf-KO
gene expression data from TCF-1-/- thymocytes

hyb_protocol: Following fragmentation,2.5 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix Mouse Gene ST 1.0 Array.  The arrays were washed and stained in the Affymetrix Fluidics Station 450 using FS450_0007 script.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G and the CEL intensity files were produced by GeneChip Operating Software v. 1.4.

data_processing: Normalized expression values were produced using RMA normalization according the default settings in Partek Genomics Suite

source_name: TCF-1-deficient thymocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100-300ng total RNA (Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay)

growth_protocol: Primary thymocytes were harvested and isolated by using a 40um cell strainer, and resuspended in RPMI 1640 medium

extract_protocol: Qiagen Rneasy Plus according to manufacturer's protocol

value: 8 wks

value: thymocytes


title: β-catenin transgenic thymocytes

description:
b-Cat Tg
gene expression data from β-catenin transgenic thymocytes

source_name: β-catenin transgenic thymocytes

value: β-catenin transgenic

value: 16 wks


title: Tnrc6a(GW182) mutant mouse E9.5 yolk sac rep1


title: Normal oral tissue_56N

description: normal person


title: wild type mouse E9.5 yolk sac rep1

description: Gene expression data from yolk sac of wt mouse

source_name: yolk sac of E9.5 wild type mouse

value: wild type (mixed)


title: Uninduced Id2-HPC, biological replicate 1

city: La Jolla

first: Yin

middle: Chun

last: Lin

state: CA

address: 9500 Gilman Drive

department: Division of Biological Sciences

institute: UCSD

hyb_protocol: The Illumina hybridization protocol was used. 1500 ng of cRNA. Hybridization in HYB buffer for 18-20 hours at 58°C with gentle rocking followed by standard Illumina washes and streptavidin-Cy3 staining.

scan_protocol: Illumina BeadArray Reader was used. Green Channel with a PMT setting of 100%.

data_processing: Illumina Genome Studio Software produced raw data which was normalized using a modified LOESS or quantile normalization.

source_name: Uninduced Id2-HPC cells

label_protocol: The Ambion kit Illumina TotalPrep RNA Amplification Kit produced amplified biotinylated cRNAs by the Eberwine protocol.

growth_protocol: Id2-HPC cells were cultured in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL7, Flt3-ligand, and SCF cytokines on S17 feeder cells in a humidified incubator at 37 degree C with 5% CO2. Id2-HPC expanded cells were depleted of small (<1-5%) numbers of CD19, CD25 and CD11b positive cells by auto-MACS. For myeloid differentiation, cells were cultured for up to 6 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL3, Flt3L, GMCSF and MCSF cytokines and in the presence or absence of 1 ug/mL doxycycline. To promote B-cell differentiation, cells were cultured for up to 10 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL-7 and SCF cytokines on S17 feeder cells in the presence of 1 ug/mL doxycycline. Fresh doxcycline and cytokines were added every two days.

extract_protocol: Total RNA was extracted from 5 Mio cells on RNeasy columns (Qiagen) with on-column DNase digestion following the manufacturer's instructions. RNA quality was assessed on an Agilent 2100 BioAnalyzer.

treatment_protocol: None.

tag: genotype

value: human ID2 transgenic

tag: cell type

value: hematopoietic progenitor cells (HPCs)

tag: hpc induction

value: uninduced


title: Normal oral tissue_63N

description: normal person

source_name: Normal oral tissue


title: Id2-HPC induced under myeloid conditions

description: M

source_name: Id2-HPC cells induced under myeloid conditions

value: myeloid conditions


title: Id2-HPC induced under B-cell conditions for 120 hours, biological replicate 1

source_name: Id2-HPC cells induced under B-cell conditions, 120 hours

value: B-cell conditions

tag: induction duration

value: 120 hrs


title: WT thymocytes

description:
WT
gene expression data from WT thymocytes

source_name: WT thymocytes

value: WT

value: 12 wks


title: wild type mouse E9.5 yolk sac rep3


title: wild type mouse E9.5 yolk sac rep2


title: Normal oral tissue_58N

description: normal person

value: normal


title: myotubes expressing mutant PABPN1-FLAG at level similar to WTA [D7E2]

city: Leiden

first: Seyed Yahya

last: Anvar

address: Einthovenweg 20

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description:
4 days fused myoblasts
D7E2

hyb_protocol: Total RNA was extracted from myotubes using RNA Bee (Amsbio) according to the manufacturer's instructions. RNA integration number (RIN) was determined with RNA 6000 Nano (Agilent Technologies). RNA with RIN >7 were used for subsequent steps. RNA labeling was performed with the Illumina® TotalPrep RNA Amplification kit (Ambion) according to the manufacturer's protocol, and subsequently was hybridized to Illumina Mouse v2 Bead arrays.

scan_protocol: Standard Illumina protocol

data_processing: Microarray measurements were normalized using the quantile method. The quality of the data was assessed by principal component analysis.

source_name: myotubes

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit  AMIL1791

growth_protocol: Myoblasts were seeds to confluence and incubated at fusion conditions for 4 days, followed by RNA extraction

treatment_protocol: No treatments

tag: cell line

value: IM2 myotube culture


title: myotubes expressing mutant PABPN1-FLAG at level similar to WTA [D7E1]

description:
4 days fused myoblasts
D7E1

extract_protocol: RNA Bee (Amsbio) according to the manufacturer's instructions.


title: myotubes expressing mutant PABPN1-FLAG at level similar to WTA [D7E3]

description:
4 days fused myoblasts
D7E3


title: Uninduced Id2-HPC, biological replicate 2


title: myotubes expressing wild type PABPN1-FLAG [DWTA1_D7E]

description:
4 days fused myoblasts
DWTA1

value: wild type PABPN1-FLAG


title: Id2-HPC induced under B-cell conditions for 120 hours, biological replicate 2


title: myotubes expressing wild type PABPN1-FLAG [DWTA2_D7E]

description:
4 days fused myoblasts
DWTA2


title: myotubes expressing wild type PABPN1-FLAG at low level [DWTD3]

description:
4 days fused myoblasts
DWTD3

value: wild type PABPN1-FLAG at low level


title: Normal oral tissue_50N

description: normal person


title: ACC S1

type: genomic

city: Ube

first: Atsunori

last: Oga

state: Yamaguchi

address: Minami-Kogushi 1-1-1

department: Pathology

country: Japan

institute: Yamaguchi University

description: without PCR

hyb_protocol: For hybridization, labeled DNA was mixed with Cot-1 DNA (50 mg, Gibco BRL, Gaithersburg, MD, USA) and ethanol precipitated. The precipitated DNA was dissolved in 40 µl hybridization  mix. The probe mixture was denatured at 75 ◦C for 5 min and incubated at 37 ◦C for 60 min for blocking of repetitive sequences. The arrays were prehybridized with salmon sperm DNA to reduce non-specific back-ground staining. The probe mixture was applied to the array. The arrays were placed in a moist chamber at 37 ◦C for 72 h for hybridization. The array slides were washed twice in 2 × standard saline citrate (2 ×SSC), 50% formamide, pH 7.0, at 45 ◦C. Then the array slides were washed well in phosphate buffer with 0.1% NP-40, pH 8.0, in 2 × SSC at room temperature.

scan_protocol: After hybridization, the slides were scanned on a GenePix 4000A scanner (Axon Instruments, Union City, CA, USA) and the 16-bit TIFF images were captured using GenePix Pro 5.0 software. The fluorescence images were analyzed using a software (MacViewer, Macrogen Inc.) optimized for analysis of the array. The fluorescence spots were defined using the automatic grid feature and adjusted manually.

data_processing:
Then the ratio of the green:red channel of each clone was calculated and all CGH ratios were converted to log base 2 (log2 ratios). The clones with log2 ratios that exceeded ± 0.25 were considered gain and loss of the copy number.
Because the chromosomal region showing high-level gain often contain an important oncogene, the high-level gain was marked and defined a log2 (green/red) ratio >1.0 as an amplification.
In order to define chromosomal regions with DCNAs, the adaptive weights smoothing (AWS) procedure with the gain and loss analysis of DNA (GLAD) algorithm was applied to the ratio data.

molecule: genomic DNA

source_name: ACC case 1 cells

label_protocol: Test DNA and sex-matched reference DNA (Promega, Madison, WI) were labeled with Cy3 and Cy5-dCTP, (Perkin-Elmer Life Science), respectively, with a random primer labelling kit (BioPrime, DNA Labelling System, Invitrogen Co.).

extract_protocol: using a commercial kit, DNeasy Tissue Kit, (Qiagen Co., Hilden, Germany) according to the manufacturer’s instructions

treatment_protocol: no chemotherapy, no radiation therapy

value: adenoid cystic carcinoma (ACC)

tag: case

value: frozen cancer tissue

source_name: human normal cell (reference)

tag: reference provider

value: Promega Co.


title: OSCC tumor_2231T

description: patient with OSCC

source_name: OSCC  specimens

value: tumor


title: Small intestine, proximal part, high fat group, mouse 11

city: Marseille Cedex 5

first: Charles

last: Desmarchelier

address: 27 Boulevard Jean Moulin

department: Nutriments Lipidiques et Prévention des Maladies Métaboliques

country: France

institute: UMR INRA 1260 / INSERM 476 - Universités Aix-Marseille I & II

hyb_protocol: Hybridization of 15µg cRNA was done overnight for 16 hours at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701021, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 3 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701021, revision 5).

data_processing: The quality of the data was analyzed by a Bioconductor and R based method in the Nutrigenomics Organisation NuGO Array Pipeline. Expression levels of probe sets were normalized using GCRMA.

label: Biotin

source_name: Proximal small intestine, scraped off epithelial (mucosal) cells, high fat group

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 15 µg of total RNA. The protocol was conducted using the reagents provided by Affymetrix, following the manufacturer's instructions provided in the eukaryotic section of the Genechip Expression Analysis Technical Manual from Affymetrix (P/N 701021, revision 5).

extract_protocol: Total RNA from the upper and lower small intestine was isolated using Trizol reagent (Invitrogen) until the ethanol precipitation step and further purified using the QIAGEN RNeasy Mini Kit spin columns (QIAGEN GmbH). RNA concentration and purity were measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies).

treatment_protocol:
Conventionally raised eight-week-old male C57BL/6NCrl mice (Charles River Laboratories) were housed individually in a light- and temperature-controlled facility (lights on 7 AM - 7 PM, 22 °C) and had free access to water and food. They were fed a standard laboratory chow (Ssniff GmbH, cat. no. V1534) for two weeks and thereafter divided into two groups with similar mean body weights (n = 12). Mice were then fed group-specific pellet diets (control; high fat) (Ssniff GmbH, cat. no. E15000-04 and E15741-34, respectively). Throughout the feeding trial, body weight, food and water consumption were recorded once per week. Energy intake was corrected for spilled food, collected under metal grids placed below the food containers.
After 12 weeks, mice in a non-fasting state were anesthetized using isoflurane and blood was collected from the retro-orbital sinus. Mice were then killed by cervical dislocation. Tissues were harvested at the same time of the day for both groups to avoid diurnal variability. The small intestine was divided into two equal parts along the longitudinal axis (proximal and distal), mucosa was scraped off, snap-frozen in liquid nitrogen and stored at -80 °C until further processing.

tag: gender

value: male

value: 22 weeks

value: proximal small intestine

value: mucosal

tag: diet

value: high fat


title: myotubes expressing wild type PABPN1-FLAG at low level [DWTD2]

description:
4 days fused myoblasts
DWTD2


title: Small intestine, proximal part, control group, mouse 16

source_name: Proximal small intestine, scraped off epithelial (mucosal) cells, control group

value: control


title: Small intestine, proximal part, high fat group, mouse 17

treatment_protocol:
l 	Conventionally raised eight-week-old male C57BL/6NCrl mice (Charles River Laboratories) were housed individually in a light- and temperature-controlled facility (lights on 7 AM - 7 PM, 22 °C) and had free access to water and food. They were fed a standard laboratory chow (Ssniff GmbH, cat. no. V1534) for two weeks and thereafter divided into two groups with similar mean body weights (n = 12). Mice were then fed group-specific pellet diets (control; high fat) (Ssniff GmbH, cat. no. E15000-04 and E15741-34, respectively). Throughout the feeding trial, body weight, food and water consumption were recorded once per week. Energy intake was corrected for spilled food, collected under metal grids placed below the food containers.
After 12 weeks, mice in a non-fasting state were anesthetized using isoflurane and blood was collected from the retro-orbital sinus. Mice were then killed by cervical dislocation. Tissues were harvested at the same time of the day for both groups to avoid diurnal variability. The small intestine was divided into two equal parts along the longitudinal axis (proximal and distal), mucosa was scraped off, snap-frozen in liquid nitrogen and stored at -80 °C until further processing.


title: Small intestine, proximal part, control group, mouse 13


title: myotubes expressing wild type PABPN1-FLAG [DWTA2_DWTD]

description:
4 days fused myoblasts
DWTA2


title: Normal oral tissue_052CN

description: normal person


title: Small intestine, proximal part, control group, mouse 7


title: pMSG_72h_rep2 (microRNA)

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: miRNA expression after 72h induction

hyb_protocol: Hybridization was perfored  following the instrcution in the Agilent miRNA microarray system protocol (Agilent Technologies, Rockville, MD). Hybridization was performed in +55 ºC for 20 hours. Washing was performed by the Agilent protocol 5 minutes in GE wash buffer 1 and 5 minutes in GE wash buffer 2 (+37ºC). Arrays were dried with a 1 minute spin in a Spectrafuge mini (Labnet, Woodbridge, NJ).

scan_protocol: Default scanning performed with Axon 4200AL for Cy3 and Cy5 using resolution of five micrometer.

data_processing: log2 transformation followed by quantile normalization

source_name: keratinocytes

label_protocol: Total RNA was (100ng) was labeled with Cy3 -pCp following the instructions from the Agilent miRNA microarray system protocol (Agilent Technologies, Rockville, MD).

growth_protocol: HaCaT-E5 and control cells were grown in D-MEM growth medium with 10% FBS and glutamine and antibiotics, and serum-starved 24h before treatment.

extract_protocol: Total RNA was extracted using mirVana miRNA Isolation kit (Ambion, Austin, TX) according to the manufacturer's instructions.

treatment_protocol: E5 expression was induced by 1 mM dexamethasone treatment for different times.

value: skin keratinocyte

value: HaCaT

tag: transfection

value: vector control

tag: time


title: pMSG_72h_rep3 (microRNA)

description: miRNA expression after 72h induction


title: Small intestine, proximal part, control group, mouse 1


title: Small intestine, proximal part, high fat group, mouse 14


title: SARS-CoV-Urbani-day-21-replicate-2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from__SARS-CoV-Urbani-day-21-replicate-2

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip Rhesus Macaque Genome Arrays (Affymetrix) according to manufacturer's recommendations

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Macaca mulatta

label_protocol: Five nanograms of RNA sample from tissue with equivalent viral RNA levels  was processed according to manufacturer's instructions using WT-Ovation™ Pico system RNA Amplification System (Nugen Inc.). Each sample was fragmented and labeled according to manufacturer's instructions for standard format anti-sense (AT) GeneChip arrays (Nugen Inc).

growth_protocol: All viruses were propagated on Vero E6 cells in Dulbecco's minimal essential medium (DMEM; Invitrogen) supplemented with 10% fetal bovine serum L-Glutamine penicillin (10000 IU/mL) and streptomycin (10000 IU/mL) at 37°C in a humidified CO2 incubator.

extract_protocol: Tissue samples were placed in RNAlater (Qiagen) for 11 days at 4°C. RNAlater was removed and samples were homogenized in 1 ml of Trizol for subsequent RNA extraction. Upon thawing 200 µl chloroform was added vials were vortexed and centrifuged at 16000 x g for 15 min.  RNA containing aqueous phase of 350-550 µl was collected from each sample and passed through Qiashredder column (Qiagen) at 21000 x g for 2 minutes to homogenize any remaining genomic DNA in the aqueous phase.  RNA was purified using RNeasy 96 kit (Qiagen) as described previously except RNA samples were treated with DNase I during extraction

treatment_protocol: Animals were infected with either Urbani GZ02 or HC/SZ/61/03 under anesthesia through a combination of intratracheal (4 ml) and intranasal (0.5 ml per nostril) installation  with a suspension containing 2x106 plaque forming units (pfu) per ml DMEM (total infectious dose = 1x107 pfu) of each of the 3 different SARS-CoV strains. Three animals were mock infected with DMEM only. Animals were anesthetized for challenge clinical examination temperature respiration rate chest radiographs blood draw and swabs of nasal oral and rectal mucosa on days 01247 11 and 14 p.i. Three animals from each infected group and 1 control animal were euthanized and necropsied on days 1 4 and 14 p.i. with collection of clinical specimens.  Experiments were conducted under BSL-3+ conditions and approval for animal experiments was obtained from the institutional Animal Care and Use Committee by certified staff in an Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) approved facility

tag: infection

value: SARS-CoV-Urbani

value: day 21

value: lung


title: myotubes expressing wild type PABPN1-FLAG at low level [DWTD1]

description:
4 days fused myoblasts
DWTD1

value: IM2 myotube culture

tag: genotype/variation

value: wild type PABPN1-FLAG at low level


title: pMSG_48h_rep1 (microRNA)

description: miRNA expression after 48h induction


title: Small intestine, proximal part, high fat group, mouse 8

tag: strain


title: Small intestine, proximal part, control group, mouse 4


title: pMSG_48h_rep2 (microRNA)

description: miRNA expression after 48h induction


title: Small intestine, proximal part, high fat group, mouse 2


title: pMSG_24h_rep3 (microRNA)

description: miRNA expression after 24h induction


title: Small intestine, proximal part, high fat group, mouse 5


title: pMSG_24h_rep2 (microRNA)

description: miRNA expression after 24h induction


title: pMSG_24h_rep1 (microRNA)

description: miRNA expression after 24h induction


title: SARS-CoV-Urbani-day-4-replicate-2

description: Gene expression data from__SARS-CoV-Urbani-day-4-replicate-2

value: day 4


title: SARS-CoV-Urbani-day-4-replicate-1

description: Gene expression data from__SARS-CoV-Urbani-day-4-replicate-1


title: pMSG_72h_rep1 (microRNA)

description: miRNA expression after 72h induction


title: pMSG_0h_rep3 (microRNA)

description: miRNA expression after 0h induction


title: SARS-CoV-Urbani-day-1-replicate-1

description: Gene expression data from__SARS-CoV-Urbani-day-1-replicate-1

value: day 1


title: SARS-CoV-Urbani-day-4-replicate-3

description: Gene expression data from__SARS-CoV-Urbani-day-4-replicate-3


title: myotubes expressing wild type PABPN1-FLAG [DWTA1_DWTD]

description:
4 days fused myoblasts
DWTA1

value: wild type PABPN1-FLAG


title: pMSG_48h_rep3 (microRNA)

description: miRNA expression after 48h induction


title: SARS-CoV-Urbani-day-1-replicate-2

description: Gene expression data from__SARS-CoV-Urbani-day-1-replicate-2


title: Small intestine, proximal part, control group, mouse 10

value: male


title: Normal oral tissue_47N

description: normal person

tag: disease state

value: normal


title: SARS-CoV-Urbani-day-21-replicate-1

description: Gene expression data from__SARS-CoV-Urbani-day-21-replicate-1

tag: tissue


title: SARS-CoV-Urbani-day-1-replicate-3

description: Gene expression data from__SARS-CoV-Urbani-day-1-replicate-3


title: pMSG_0h_rep2 (microRNA)

description: miRNA expression after 0h induction


title: SARS-CoV-Urbani-day-21-replicate-3

description: Gene expression data from__SARS-CoV-Urbani-day-21-replicate-3


title: SARS-CoV-HC/SZ/6103-day-21-replicate-3

description: Gene expression data from__SARS-CoV-HC/SZ/6103-day-21-replicate-3


title: E5_24h_rep2 (microRNA)

description: miRNA expression after 24h induction

value: type 16 E5 oncogene


title: E5_0h_rep2 (microRNA)

description: miRNA expression after 0h induction


title: E5_72h_rep1 (microRNA)

description: miRNA expression after 72h induction


title: E5_48h_rep1 (microRNA)

description: miRNA expression after 48h induction


title: E5_48h_rep2 (microRNA)

description: miRNA expression after 48h induction


title: E5_24h_rep1 (microRNA)

description: miRNA expression after 24h induction


title: E5_72h_rep2 (microRNA)

description: miRNA expression after 72h induction


title: pMSG_0h_rep1 (microRNA)

description: miRNA expression after 0h induction


title: root high N 15 days and transient into low N for 2 hours, biological replicate1

city: Beijing

first: Chuanxiao

last: Xie

address: Zhong-guan-cun South St. No12

department: Institute of Crop Science

country: China

institute: Chinese Academy of Agricultural Sciences

hyb_protocol: 20×Eukaryotic Hybridization Controls (GeneChip○R Eukaryotic Hybridization Control Kit, Affymetrix) were incubated at 65 °C for 5 min. 21.5 μl biotin-labeled RNA was suspended in 78.5 μl hybridization solution containing 2×Hybridization Mix, deionized formamide, DMSO, 20×Eukaryotic Hybridization Controls, 3 nM Control Oligonucleotide B2 and nuclease-free water, which was incubated at 99 °C for 5 min, followed by 45 °C for 5 min. The hybridization was performed at 48 °C for 16 h. The arrays were then washed and stained with GeneChip○R Hybridization Wash and Stain Kit (Affymetrix, Inc.)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The Affymetrix○C miRNA QC Tool software (Affymetrix, Inc.) was used for data summarization, normalization, and quality control. The miRNAs with P<0.05(q<0.001) and fold changes >2.0 or <0.5 were defined as differentially expressed. Three biological replicates were used in all chip hybridization experiments.

organism: Zea mays subsp. mays

source_name: maize root culture at 4mM nitrate for 15 days and move into 0.04mM nitrate culture for 2 hours

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 of Ye478 were sterilized with 10% (v/v) H2O2 for 30 min, washed with distilled water, soaked in saturated CaSO4 for 6 h, and then germinated at 28 °C for 2 d in the dark between two layers of filter paper moistened with saturated CaSO4. Seeds 1-2 cm germ were transferred to coarse silica sand to grow at 28 °C /22 °C during the 14/10 h light / dark cycle. Uniform seedlings with two visible leaves were selected. The residual endosperms of the seedlings were discarded. Plants were planted in a glass beaker. The outside of the glass beakers were covered with a black sheet to ensure that the roots were kept in complete darkness. Glass beakers each containing ten seedlings were maintained in an illumination chamber.

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

treatment_protocol: Two nitrate concentrations were tested: 4 mM, which represented an optimal nitrate condition (high N) and 0.04 mM, which represented low-nitrate availability (low N) with Ca (NO3)2•4H2O used as the nitrate source. Ca was compensated to 2 mM at low N with CaCl2 . The other nutrients in solution were (in mmol L-1): 0.75 K2SO4, 0.1 KCl, 0.25 KH2PO4, 0.65 MgSO4.7H2O, and 0.2 EDTA-Fe, and in μmol L-1, 1.0 MnSO4.H2O, 1.0 ZnSO4.7H2O, 0.1 CuSO4.5H2O, and 0.005 (NH4)6Mo7O24.4H2O. Air was continuously pumped through the solution (pH 6.0) that was changed every 2 days. For identification of chronic nitrate regulated miRNAs, seedlings were sampled at 15 days for RNA extraction. For transient expression pattern of miRNAs from high to low N, the 15-day-old seedlings were transferred from high N to low N conditions for hours.

value: root tips

value: Ye478, an inbred line

tag: age

value: roots around 20 days after germination

tag: treatment

value: 4 mM nitrate for 15 days and then 0.04 mM  nitrate for 2 hours


title: root high N 15 days and transient into low N for 2 hours, biological replicate2

tag: genotype


title: root low N biological replicate1

source_name: maize root at 0.04mM nitrate culture for 15 days

value: 0.04 mM nitrate


title: root high N biological replicate3

source_name: maize root at 4mM nitrate culture for 15 days

value: 4 mM nitrate


title: root high N 15 days and transient into low N for 2 hours, biological replicate3


title: root low N biological replicate3


title: root high N biological replicate1


title: SARS-CoV-HC/SZ/6103-day-1-replicate-2

description: Gene expression data from__SARS-CoV-HC/SZ/6103-day-1-replicate-2


title: SARS-CoV-GZ02-day-21-replicate-3

description: Gene expression data from__SARS-CoV-GZ02-day-21-replicate-3


title: SARS-CoV-HC/SZ/6103-day-4-replicate-2

description: Gene expression data from__SARS-CoV-HC/SZ/6103-day-4-replicate-2


title: SARS-CoV-HC/SZ/6103-day-1-replicate-3

description: Gene expression data from__SARS-CoV-HC/SZ/6103-day-1-replicate-3


title: root high N biological replicate2


title: E5_0h_rep1 (microRNA)

description: miRNA expression after 0h induction

tag: cell type

value: skin keratinocyte

value: HaCaT


title: SARS-CoV-HC/SZ/6103-day-21-replicate-1

description: Gene expression data from__SARS-CoV-HC/SZ/6103-day-21-replicate-1

value: day 21

value: lung


title: SARS-CoV-GZ02-day-21-replicate-2

description: Gene expression data from__SARS-CoV-GZ02-day-21-replicate-2


title: NSPCs grown in EC/NSPC co-cultures (microRNA) rep3

city: Albuquerque

first: Tamara

last: Roitbak

state: NM

address: 2212 Lomas NE

department: Neurosurgery

institute: UNM

description: miRNA expression data from NSPCs grown in EC/NSPC co-cultures

hyb_protocol: Affymetrix GeneChip miRNA Procedure (FluidicsScript 450-0003, Hyb. 48°C)

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

data_processing: Data files were analyzed with  Affymetrix miRNAQCtool using RMA background correction and quartile normalization (signal data as log2)

source_name: Neural stem/progenitor cells isolated from E14 mouse embryonic brain, grown in co-culture with mouse primary brain Endothelial cells (Celprogen)

label_protocol: FlashTag RNA Labeling with Genisphere RNA Labeling Kit

growth_protocol: For cell growth and propagation: NSPCs were grown in serum-free NSPC medium and ECs were grown in EC medium (Celprogen), at 37C, in CO2 incubator

extract_protocol: After 24 hours in transwell co-culture, the ECs and NSPCs were separated and miRNA were isolated using mirVana miRNA  (AB/Ambion) isolation kit. FlashPAGE fractionator (AB/Ambion) was used for rapid PAGE-purification of miRNAs.

treatment_protocol: All experimantal samples were grown in growth factor-free NSPC medium (with addition of 10% FBS), for 24 hours, in CO2 incubator at 37C

tag: sample type

value: ECs isolated from the mouse forebrain microvessels and NSPCs from telencephalon of E-14 mouse embryo

value: Primary neural stem/progenitor cells

tag: genetic background


title: root low N biological replicate2


title: SARS-CoV-HC/SZ/6103-day-4-replicate-3

description: Gene expression data from__SARS-CoV-HC/SZ/6103-day-4-replicate-3

value: day 4


title: SARS-CoV-HC/SZ/6103-day-21-replicate-2

description: Gene expression data from__SARS-CoV-HC/SZ/6103-day-21-replicate-2


title: SARS-CoV-HC/SZ/6103-day-1-replicate-1

description: Gene expression data from__SARS-CoV-HC/SZ/6103-day-1-replicate-1

value: day 1


title: SARS-CoV-HC/SZ/6103-day-4-replicate-1

description: Gene expression data from__SARS-CoV-HC/SZ/6103-day-4-replicate-1


title: SARS-CoV-GZ02-day-21-replicate-1

description: Gene expression data from__SARS-CoV-GZ02-day-21-replicate-1


title: NSPCs grown in EC/NSPC co-cultures (microRNA) rep2

value: grown in co-culture with mouse primary brain Endothelial cells (Celprogen)


title: NSPCs grown as monocultures (microRNA) rep3

description: miRNA expression data from NSPCs grown as monoculture

source_name: Neural stem/progenitor cells isolated from E14 mouse embryonic brain, grown as monocultures

value: NSPCs isolated from telencephalon of E-14 mouse embryo

value: grown as monoculture


title: NSPCs grown as monocultures (microRNA) rep2


title: NSPCs grown as monocultures (microRNA) rep1


title: ECs grown as monocultures (microRNA) rep3

description: miRNA expression data from ECs grown as monoculture

source_name: Mouse primary brain endothelial cells (Celprogen, San Diego, CA) grown as monoculture

value: ECs isolated from the mouse forebrain microvessels

value: Primary brain endothelial cells (Celprogen, San Diego, CA, catalog # 11053-07)


title: ECs grown in EC/NSPC co-cultures (microRNA) rep3

description: miRNA expression data from ECs grown in EC/NSPC co-cultures

source_name: Mouse primary brain endothelial cells (Celprogen) grown in  co-culture with neural stem/progenitor cells isolated from E14 mouse embryonic brain


title: ECs grown as monocultures (microRNA) rep1


title: ECs grown as monocultures (microRNA) rep2


title: ECs grown in EC/NSPC co-cultures (microRNA) rep1

value: grown in co-culture with neural stem/progenitor cells isolated from E14 mouse embryonic brain


title: NSPCs grown in EC/NSPC co-cultures (microRNA) rep1


title: ECs grown in EC/NSPC co-cultures (microRNA) rep2


title: SARS-CoV-GZ02-day-4-replicate-3

description: Gene expression data from__SARS-CoV-GZ02-day-4-replicate-3


title: SARS-CoV-GZ02-day-4-replicate-2

description: Gene expression data from__SARS-CoV-GZ02-day-4-replicate-2


title: SARS-CoV-GZ02-day-4-replicate-1

description: Gene expression data from__SARS-CoV-GZ02-day-4-replicate-1


title: SARS-CoV-GZ02-day-1-replicate-2

description: Gene expression data from__SARS-CoV-GZ02-day-1-replicate-2


title: SARS-CoV-GZ02-day-1-replicate-3

description: Gene expression data from__SARS-CoV-GZ02-day-1-replicate-3


title: SARS-CoV-GZ02-day-1-replicate-1

description: Gene expression data from__SARS-CoV-GZ02-day-1-replicate-1


title: SARS-CoV-Control-day-21-replicate-1

description: Gene expression data from__SARS-CoV-Control-day-21-replicate-1


title: kidney at 18 months old

city: Shanghai

first: Qi

last: Wang

address: No. 12 Wulumuqi Middle Road

institute: Huashan hospital, Fudan university,China

description:
KR-18
Gene expression data from kidney at 18-month age.

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

scan_protocol: GeneChips were scanned using the Gene array Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Rattus norvegicus

source_name: Rat kidney, 18 months old

growth_protocol: Sprague-Dawley rats at 4, 10, 18, and 24 months of age were maintained at 37C in 12h dark/light cycle.

treatment_protocol: Rat tissues including hypothalamus, pituitary, adrenal gland, spleen lymphocytes, kidney, liver, and bone were removed as quickly as possible within 10 minutes. Then all samples were rinsed with PBS with 0.7% NaCl, 0.04% Triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

value: Sprague Dawley

value: kidney

value: 18 months


title: kidney at 10 months old

description:
KR-10
Gene expression data from kidney at 10-month age.

source_name: Rat kidney, 10 months old

value: 10 months


title: kidney at 24 months old

description:
KR-OM
Gene expression data from kidney at 24-month age.

source_name: Rat kidney, 24 months old

value: 24 months


title: kidney at 4 months old

description:
KR-4
Gene expression data from kidney at 4-month age.

source_name: Rat kidney, 4 months old

value: 4 months


title: bone at 24 months old

description:
BR-OM
Gene expression data from bone at 24-month age.

source_name: Rat bone, 24 months old

value: bone


title: SARS-CoV-Control-day-4-replicate-1

description: Gene expression data from__SARS-CoV-Control-day-4-replicate-1

value: lung


title: SARS-CoV-Control-day-1-replicate-1

description: Gene expression data from__SARS-CoV-Control-day-1-replicate-1


title: liver at 24 months old

description:
LR-OM
Gene expression data from liver at 24-month age.

source_name: Rat liver, 24 months old

value: liver


title: bone at 4 months old

description:
BR-4
Gene expression data from bone at 4-month age.

source_name: Rat bone, 4 months old


title: no MYCN amplification 1M13

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

country: Canada

institute: The Hospital for Sick Children

description: Tumoral tissue (medulloblastoma)

hyb_protocol: Agilent hybridization protocol following the manufacturer’s instructions.

scan_protocol: Scanned on Agilent Scanner G25505B

data_processing: Array raw data were generated using Feature Extraction 9.1 Software. Normalization of raw signals was performed using vsn (Huber et al., 2002). Feature signals had to fulfill the following criteria to be considered for further analysis: a minimal signal to background ratio ≥ 1.5 in at least one channel; a minimal raw signal of 200; a mean to median spot intensity ≤ the 75% quantile + 3 times the interquartile range of all features on the array; and a feature replicate standard deviation ≤ 0.25 per array. Normalization of raw signals was performed using vsn. Probes with more than 80% missing values across all samples were removed. Based on BLASTing the probes sequence information against the genome, biological annotations were retrieved from EnsEMBL (version 54, NCBI Build 36 of the human genome reference sequence).

source_name: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

label_protocol: Agilent labeling protocol following the manufacturer’s instructions.

extract_protocol: RNA was extracted from biopsy samples using Trizol and RNeasy mini columns following the manufacturer’s instructions.

treatment_protocol: Fresh frozen material was milled in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

value: normal cerebellum

value: f

tag: age [years]

tag: histology

value: classic

tag: ctnnb1 mutation

tag: gli1/2 amplification

tag: myc amplification

tag: mycn amplification

value: medulloblastoma


title: no MYCN amplification 1M22

description: Tumoral tissue (medulloblastoma)

value: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

tag: gender

value: m


title: MYCN amplification 1M28

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M15

description: Tumoral tissue (medulloblastoma)


title: liver at 10 months old

description:
LR-10
Gene expression data from liver at 10-month age.

source_name: Rat liver, 10 months old


title: bone at 10 months old

description:
BR-10
Gene expression data from bone at 10-month age.

source_name: Rat bone, 10 months old


title: liver at 4 months old

description:
LR-4
Gene expression data from liver at 4-month age.

source_name: Rat liver, 4 months old


title: MYCN amplification 1M10

description: Tumoral tissue (medulloblastoma)

value: LCA


title: liver at 18 months old

description:
LR-18
Gene expression data from liver at 18-month age.

source_name: Rat liver, 18 months old


title: bone at 18 months old

description:
BR-18
Gene expression data from bone at 18-month age.

source_name: Rat bone, 18 months old


title: no MYCN amplification 1M20

description: Tumoral tissue (medulloblastoma)

value: desmo


title: no MYCN amplification 1M16

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M1

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M21

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 2M17

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 2M8

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 2M6

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M25

description: Tumoral tissue (medulloblastoma)


title: spleen lymphocyte at 4 months old

description:
C-4
Gene expression data from spleen lymphocyte at 4-month age.

source_name: Rat Spleen lymphocyte, 4 months old

value: Sprague Dawley

value: spleen lymphocyte


title: adrenal at 18 months old

description:
AR-18
Gene expression data from adrenal at 18-month age.

source_name: Rat adrenal, 18 months old

value: adrenal

value: 18 months


title: spleen lymphocyte at 24 months old

description:
C-OM
Gene expression data from spleen lymphocyte at 24-month age.

source_name: Rat Spleen lymphocyte, 24 months old

value: 24 months


title: no MYCN amplification 1M3

description: Tumoral tissue (medulloblastoma)


title: adrenal at 24 months old

description:
AR-OM
Gene expression data from adrenal at 24-month age.

source_name: Rat adrenal, 24 months old


title: no MYCN amplification 2M9

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M2

description: Tumoral tissue (medulloblastoma)


title: adrenal at 4 months old

description:
AR-4
Gene expression data from adrenal at 4-month age.

source_name: Rat adrenal, 4 months old

value: 4 months


title: pituitary at 24 months old

description:
P-OM
Gene expression data from pituitary at 24-month age.

source_name: Rat pituitary, 24 months old

value: pituitary


title: no MYCN amplification 2M20

description: Tumoral tissue (medulloblastoma)


title: spleen lymphocyte at 10 months old

description:
C-10
Gene expression data from spleen lymphocyte at 10-month age.

source_name: Rat Spleen lymphocyte, 10 months old

value: 10 months


title: MYCN amplification 1M24

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M5

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 3M5

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 3M2

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 2M16

description: Tumoral tissue (medulloblastoma)


title: pituitary at 18 months old

description:
P-18
Gene expression data from pituitary at 18-month age.

source_name: Rat pituitary, 18 months old


title: no MYCN amplification 1M17

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 2M15

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 2M11

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M14

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 2M7

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 2M5

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M4

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M33

description: Tumoral tissue (medulloblastoma)


title: spleen lymphocyte at 18 months old

description:
C-18
Gene expression data from spleen lymphocyte at 18-month age.

source_name: Rat Spleen lymphocyte, 18 months old


title: adrenal at 10 months old

description:
AR-10
Gene expression data from adrenal at 10-month age.

source_name: Rat adrenal, 10 months old


title: no MYCN amplification 4M8

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 4M28

description: Tumoral tissue (medulloblastoma)


title: hypothalamus at 24 months old

description:
H-OM
Gene expression data from hypothalamus at 24-month age.

source_name: Rat hypothalamus, 24 months old

value: hypothalamus


title: no MYCN amplification 1M31

description: Tumoral tissue (medulloblastoma)

source_name: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

value: normal cerebellum


title: no MYCN amplification 1M12

description: Tumoral tissue (medulloblastoma)


title: hypothalamus at 10 months old

description:
H-10
Gene expression data from hypothalamus at 10-month age.

source_name: Rat hypothalamus, 10 months old


title: no MYCN amplification 4M58

description: Tumoral tissue (medulloblastoma)

value: f


title: hypothalamus at 18 months old

description:
H-18
Gene expression data from hypothalamus at 18-month age.

source_name: Rat hypothalamus, 18 months old


title: no MYCN amplification 1M32

description: Tumoral tissue (medulloblastoma)

value: classic


title: no MYCN amplification 2M21

description: Tumoral tissue (medulloblastoma)

value: medulloblastoma


title: hypothalamus at 4 months old

description:
H-4
Gene expression data from hypothalamus at 4-month age.

source_name: Rat hypothalamus, 4 months old


title: no MYCN amplification 4M55

description: Tumoral tissue (medulloblastoma)

value: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)


title: no MYCN amplification 1M8

description: Tumoral tissue (medulloblastoma)

value: m


title: pituitary at 10 months old

description:
P-10
Gene expression data from pituitary at 10-month age.

source_name: Rat pituitary, 10 months old


title: no MYCN amplification 2M14

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M9

description: Tumoral tissue (medulloblastoma)


title: no MYCN amplification 1M19

description: Tumoral tissue (medulloblastoma)


title: MYCN amplification 4M43

description: Tumoral tissue (medulloblastoma)


title: Cultured EBF-deficient, biological replicate 2

description:
EBFKO_2
Gene expression of cultured EBF-deficient, biological replicate #2.

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on the microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Expression values were calculated by RMAExpress (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

source_name: EBF-/- pre-pro-B cells

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using the Affymetrix GeneChip Expression 3' amplification kit.

growth_protocol: E2A -/- and EBF -/- cells were cultured in IMDM supplemented with 10% FCS/2% PSG/β-me on S17 feeder cells in the presence of IL-7, Flt3-ligand, and SCF cytokines in a humidified incubator at 37 degree C with 5% CO2.

value: EBF -/-

value: pre-pro-B cells


title: mammary tumor tissue rep5

city: Bethesda

first: Jeffrey

middle: E

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

institute: NCI

description: gene expression data

hyb_protocol: cRNA were hybridized onto GeneChip Mouse Genome 430A 2.0 Array.

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

data_processing: Data were collected using Affymetrix GCOS software and then processed with RMA and quantile normalization using Bioconductor affy package (http://www.bioconductor.org/packages/release/bioc/html/affy.html).

source_name: mammary tumor harvested from C3(1)Tag FVB mouse

label_protocol: Biotinylated cRNA were prepared accorded to standard affymetrix protocol

growth_protocol: Primary tumors were harvested from mouse, flash frozen and prepared for RNA.  M6 and M6C cells were grown in DMEM high glucose with 5% FBS, Na Pyruvate, and Pen/Strep prior to harvest

extract_protocol: Trizol extraction of RNA was performed according to manufacturers protocol

value: FVB

value: primary mammary tissue


title: no MYCN amplification 1M29

description: Tumoral tissue (medulloblastoma)

value: desmo


title: mammary tumor tissue rep3

description: gene expression data


title: mammary tumor tissue rep4

description: gene expression data


title: mammary tumor tissue rep2

description: gene expression data


title: no MYCN amplification 5M7

description: Tumoral tissue (medulloblastoma)


title: Cultured EBF-deficient, biological replicate 1

description:
EBFKO_1
Gene expression of cultured EBF-deficient, biological replicate #1.


title: Cultured E2A-deficient, biological replicate 1

description:
E2AKO_1
Gene expression of cultured E2A-deficient, biological replicate #1.

source_name: E2A-/- pre-pro-B cells


title: no MYCN amplification 5M15

description: Tumoral tissue (medulloblastoma)


title: ras mammary tumor rep 5

description: gene expression data

source_name: mammary tumor harvested from trangenic mouse

value: primary mammary tumor

value: ras


title: no MYCN amplification 5M16

description: Tumoral tissue (medulloblastoma)


title: Uninduced Id2-HPC, biological replicate 1

description:
Id2_HPC_1
Gene expression of uninduced Id2_HPC, biological replicate #1.

source_name: Uninduced Id2-HPC cells

growth_protocol: Id2-HPC cells were cultured in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL7, Flt3-ligand, and SCF cytokines on S17 feeder cells in a humidified incubator at 37 degrees C with 5% CO2. Id2-HPC expanded cells were depleted of small (<1-5%) numbers of CD19-, CD25- and CD11b-positive cells by auto-MACS.

value: human Id2 transgenic

value: hematopoietic progenitor cells (HPCs)


title: Cultured E2A-deficient, biological replicate 2

description:
E2AKO_2
Gene expression of cultured E2A-deficient, biological replicate #2.


title: Uninduced Id2-HPC, biological replicate 2

description:
Id2_HPC_2
Gene expression of uninduced Id2_HPC, biological replicate #2.


title: mammary tumor tissue rep1

description: gene expression data


title: GmSAW, biological rep 2

city: Ramat-Gan

first: Ehud

last: Banin

address: Bldg 206

country: Israel

institute: Bar-Ilan University

description: expression data from cells treated with gentamicin and surface acoustic waves (K29-Gm-NV)

hyb_protocol: Following fragmentation, cDNA obtained from 10 ug of total RNA were hybridized for 16 hr at 50C on GeneChip Pseudomonas Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The feature extraction was performed with GeneSpring GX 10.0.1 software (Agilent). The GCRMA algorithm had been used for probe summarization. The algorithm uses quantile normalization.

organism: Pseudomonas aeruginosa PAO1

source_name: combined treatment surface acoustic waves and gentamicin

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual, Prokaryotic target preparation, Affymetrix).

growth_protocol: A 10 cm fragment from standard Foley catheter was inoculated with stationary phase P. aeruginosa under flow cell conditions in 10% TBS medium supplemented with 2% casamino acids. Biofilm formation was allowed for 48 hours.

extract_protocol: RNA was extracted using Tri-reagent followed RNA-easy kit (Qiagen) purification according to manufacturer's instructions

treatment_protocol: Following specific treatments the biofilm was extracted from the catheter and cells were washed with RNA protect solution followed by RNA extraction

tag: physiological state

value: 48 hour old biofilm

tag: experiment type

value: flow cell

tag: specific treatments

value: 2h exposure to combined gentamicin ans surface acoustic waves


title: ras mammary tumor rep 3

description: gene expression data

tag: tissue


title: SAW, biological rep 2

description: expression data from surface acoustic waves treated cells (K30-Nv4)

source_name: surface acoustic waves (SAW) treated biofilm

value: 2 h exposure to surface acoustic waves generated by a piezo element directly attached to the cathter. The frequency of the vibrations generated on the piezo element is 100 kHz ± 10% and at on/off frequency of 30Hz; the acoustic intensity was 0.4 W/cm2 and amplitude of 2µm. The acoustic energy on the inner surface of the catheter is 0.3 mW/cm2 with amplitude of 0.2 - 2 nm.


title: no MYCN amplification 5M18

description: Tumoral tissue (medulloblastoma)

value: normal cerebellum

value: classic


title: no MYCN amplification 5M5

description: Tumoral tissue (medulloblastoma)

value: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

value: f

value: medulloblastoma


title: SAW, biological rep 1

description: expression data from surface acoustic waves treated cells (J77-NV)


title: ras mammary tumor rep 4

description: gene expression data


title: GmSAW, biological rep 1

description: expression data from cells treated with gentamicin and surface acoustic waves (J78-GM NV)


title: no MYCN amplification 5M6

description: Tumoral tissue (medulloblastoma)

value: m


title: no MYCN amplification 5M10

description: Tumoral tissue (medulloblastoma)


title: NSPCs grown in EC/NSPC co-cultures (mRNA) rep3

description: RNA expression data from NSPCs grown in EC/NSPC co-cultures

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

data_processing: The data were analyzed with RMA and 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 500.

source_name: Neural stem/progenitor cells isolated from E14 mouse embryonic brain, grown in co-culture with mouse primary brain Endothelial cells (Celprogen)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Affymetrix 3' IVT Express labeling kit).

extract_protocol: After 24 hours in transwell co-culture, the ECs and NSPCs were separated and total RNA was isolated using RNeasy Mini Kit (Qiagen)

value: ECs isolated from the mouse forebrain microvessels and NSPCs from telencephalon of E-14 mouse embryo

value: Primary neural stem/progenitor cells


title: ras mammary tumor rep 2

description: gene expression data


title: no MYCN amplification 5M17

description: Tumoral tissue (medulloblastoma)


title: polyoma MT mammary tumor rep 4

description: gene expression data

value: polyoma MT


title: ras mammary tumor rep 1

description: gene expression data

value: primary mammary tumor


title: no MYCN amplification 5M13

description: Tumoral tissue (medulloblastoma)


title: NSPCs grown in EC/NSPC co-cultures (mRNA) rep1

value: grown in co-culture with mouse primary brain Endothelial cells (Celprogen)


title: NSPCs grown in EC/NSPC co-cultures (mRNA) rep2


title: NSPCs grown as monocultures (mRNA) rep3

description: RNA expression data from NSPCs grown as monoculture

source_name: Neural stem/progenitor cells isolated from E14 mouse embryonic brain, grown as monocultures

value: NSPCs isolated from telencephalon of E-14 mouse embryo

value: grown as monoculture


title: Gm, biological rep 1

description: expression data from gentamicin treated cells (J76-GM)

source_name: gentamicin treated biofilm

value: 48 hour old biofilm

value: 2 h exposure to 12.5 µg/ml gentamicin


title: Gm, biological rep 2

description: expression data from gentamicin treated cells (K28-GM)

value: flow cell


title: polyoma MT mammary tumor rep 2

description: gene expression data


title: control, biological rep 2

description: expression data from control cells (K27-control)

source_name: non-treated biofilm


title: NSPCs grown as monocultures (mRNA) rep2


title: ECs grown in EC/NSPC co-cultures (mRNA) rep2

description: RNA expression data from ECs grown in EC/NSPC co-cultures

source_name: Mouse primary brain endothelial cells (Celprogen) grown in  co-culture with neural stem/progenitor cells isolated from E14 mouse embryonic brain

value: Primary brain endothelial cells (Celprogen, San Diego, CA, catalog # 11053-07)


title: no MYCN amplification 5M12

description: Tumoral tissue (medulloblastoma)

source_name: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

value: normal cerebellum


title: control, biological rep 1

description: expression data from control cells (J75-control)


title: polyoma MT mammary tumor rep 3

description: gene expression data


title: ECs grown in EC/NSPC co-cultures (mRNA) rep3

value: grown in co-culture with neural stem/progenitor cells isolated from E14 mouse embryonic brain


title: no MYCN amplification 5M1

description: Tumoral tissue (medulloblastoma)

value: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

value: classic


title: no MYCN amplification 5M14

description: Tumoral tissue (medulloblastoma)

value: f

value: medulloblastoma


title: p53 KO ER pos mammary tumor rep 3

description: gene expression data

value: p53 KO ER pos


title: no MYCN amplification 5M8

description: Tumoral tissue (medulloblastoma)

value: LCA


title: no MYCN amplification 5M4

description: Tumoral tissue (medulloblastoma)

value: m


title: p53 KO ER pos mammary tumor rep 4

description: gene expression data

value: primary mammary tumor


title: no MYCN amplification 5M3

description: Tumoral tissue (medulloblastoma)


title: ECs grown in EC/NSPC co-cultures (mRNA) rep1

value: ECs isolated from the mouse forebrain microvessels and NSPCs from telencephalon of E-14 mouse embryo


title: ECs grown as monocultures (mRNA) rep3

description: RNA expression data from ECs grown as monoculture

source_name: Mouse primary brain endothelial cells (Celprogen, San Diego, CA) grown as monoculture

value: ECs isolated from the mouse forebrain microvessels


title: polyoma MT mammary tumor rep 1

description: gene expression data

value: polyoma MT


title: ECs grown as monocultures (mRNA) rep1

value: grown as monoculture


title: no MYCN amplification 5M9

description: Tumoral tissue (medulloblastoma)


title: p53 KO ER pos mammary tumor rep 1

description: gene expression data


title: p53 KO ER pos mammary tumor rep 2

description: gene expression data


title: CD8+_Tcells_healthy_donor_8

city: Sandwich

first: Ketan

middle: Anilkumar

last: Patel

address: Ramsgate Road

department: WWRD

country: United Kingdom

institute: Pfizer

description: Gene expression data from circulating T cells of healthy donor

hyb_protocol: Hybridized to arrays at 45°C for 16 hr.

scan_protocol: Arrays were scanned with an Affymetrix scanner.

data_processing: All steps of data preprocessing including background correction, normalization and expression set summaries were performed using the RMA algorithm in R/Bioconductor rma package.  Batch effects corrected using the ComBat R package.  Data was filtered to remove probes which had low expression in all arrays (rma signal value of < 4 was removed).  Differential gene regulation was determined by taking the output from a shrinkage t-test ('st' R package), and then computing the p-values and q-values (FDR) using 'fdrtool' R package.

label_protocol: According to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion Europe) eluted in 50 ul RNase-free water (Promega UK) and purity was measured using a BioTek PowerWave XS (SSi Robotics, U.S.A.) spectrophotometer and Agilent Bioanalyser, which showed RIN values > 9.5.

treatment_protocol: Human CD4+ and CD8+ T cell were isolated by negative selection using Miltenyi beads and MACS Vario magnetic cell separation apparatus. T-cell purity was assessed by FACS using anti-CD4-FITC and anti-CD8-PE (Miltenyi) using CellQuest software.

value: male

tag: batch

tag: age (years)

tag: patient id

tag: fev1 (% predicted)

tag: fvc (% predicted)

tag: medication

value: CD8+ T-cells


title: CD8+_Tcells_healthy_donor_6

value: female

tag: cell type


title: MYCN amplification MB569

description: Tumoral tissue (medulloblastoma)

tag: sample type

value: normal cerebellum

tag: age [years]

tag: histology


title: pituitary at 4 months old

description:
P-4
Gene expression data from pituitary at 4-month age.

source_name: Rat pituitary, 4 months old

tag: strain

value: Sprague Dawley

value: pituitary

tag: age

value: 4 months


title: MYCN amplification MB707

description: Tumoral tissue (medulloblastoma)

value: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

tag: gender

tag: ctnnb1 mutation

tag: gli1/2 amplification

tag: myc amplification

tag: mycn amplification


title: MYCN amplification Medullo 198

description: Tumoral tissue (medulloblastoma)

tag: tissue

source_name: Medullo 198

value: f

value: medulloblastoma


title: p53 KO ER neg mammary tumor rep 2

description: gene expression data

tag: genotype

value: p53 KO ER neg


title: p53 KO ER neg mammary tumor rep 3

description: gene expression data


title: CD8+_Tcells_healthy_donor_5

tag: batch

tag: age (years)

tag: patient id


title: Muller 1 Day CNTF, biological rep3

city: Rockville

first: Radu

last: Cojocaru

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

hyb_protocol: Following fragmentation and labelling, 3.75 ug (for MOE 430 2.0) or 3 ug (for Exon 1.0 ST) of cDNA were hybridized at 45C for 18 hours.  GeneChips were washed and scanner in the Affymetrix FS450.

scan_protocol: GeneChips were scanner with an Affymetrix GCS3000 7G

data_processing: The data were analyzed using Partek Genomic Suite.

label_protocol: Biotinylated cDNA were prepared for the MOE 430 2.0arrays using Nugen Ovation RNA Amplification System V2 starting with 5 ng of total RNA.  For the Exon 1.0 ST arrays the Nugen WT-Ovation Pico RNA Amplification System starting with 500 pg total RNA for the Muller glia and 2 ng of total RNA for the microglia prior to strand switching using Nugen WT-Ovation Exon Module

extract_protocol: RNA was extracted using the RNeasy Mini kit (Qiagen, Valencia, CA)

value: Flow sorted Muller glial cells

tag: treatment

value: Ciliary neurotrophic factor

tag: time

value: 1 d


title: Muller 1 Day PBS, biological rep2

tag: cell type

value: PBS


title: CD8+_Tcells_healthy_donor_2

tag: fev1 (% predicted)

tag: fvc (% predicted)

tag: medication


title: ECs grown as monocultures (mRNA) rep2

description: RNA expression data from ECS grown as monoculture

tag: sample type

value: ECs isolated from the mouse forebrain microvessels

value: Primary brain endothelial cells (Celprogen, San Diego, CA, catalog # 11053-07)


title: CD8+_Tcells_healthy_donor_7

tag: gender


title: MYCN amplification MB36

description: Tumoral tissue (medulloblastoma)

value: m

tag: age [years]

tag: histology

value: classic

tag: ctnnb1 mutation


title: Her2/Neu mammary tumor rep 4

description: gene expression data

value: primary mammary tumor


title: Muller 1 Day PBS, biological rep1


title: CD8+_Tcells_healthy_donor_3

value: female

value: CD8+ T-cells


title: Muller 1 Day CNTF, biological rep2


title: Muller 1 Day PBS, biological rep3


title: CD8+_Tcells_healthy_donor_4

value: male


title: Muller 1 Day CNTF, biological rep1


title: CD8+_Tcells_healthy_donor_1


title: p53 KO ER neg mammary tumor rep 1

description: gene expression data


title: MYCN amplification ITCC0338

description: Tumoral tissue (medulloblastoma)

value: normal cerebellum

tag: gli1/2 amplification

tag: myc amplification

tag: mycn amplification


title: Her2/Neu mammary tumor rep 5

description: gene expression data

tag: genotype

tag: tissue


title: CD8+_Tcells_severe_asthmatic_8

description: Gene expression data from circulating T cells of severe asthmatic

tag: batch

tag: age (years)

tag: patient id

value: Prednisolone 5mg od, Aminophylline 225mg bd,Seretide 500 2pbd,doxycycline, Tiotropium


title: MYCN amplification ITCC0343

description: Tumoral tissue (medulloblastoma)

value: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

value: f


title: Her2/Neu mammary tumor rep 3

description: gene expression data


title: SM12

city: Boston

first: Haoqiang

last: Ying

state: MA

address: 44 Binney St.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

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

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

data_processing: The software used was Expression Console from Affimatrix and normalization algorithm used was MAS5.

source_name: KrasG12D PDEC

extract_protocol: Trizol extraction of total RNA followed by Rneasy column cleanup was performed according to the manufacturer's instructions.

tag: strain

value: FVB/C57B6 mixed backgroud

tag: cell type

value: primary KrasG12D pancreatic ductal epithelial cells, P7

tag: genotype/variation

value: Pdx1-Cre;LSL-KrasG12D L/+


title: MYCN amplification MB754

description: Tumoral tissue (medulloblastoma)

value: medulloblastoma


title: CD8+_Tcells_severe_asthmatic_7

tag: fev1 (% predicted)

tag: fvc (% predicted)

tag: medication

value: Prednisolone 10mg od, Insulin S/C,Seretide 500mcg 2pbd, Metformin,Nexium, Flixonase,Tramacet,Calcium,Valsartan,Amitriptyline


title: Her2/Neu mammary tumor rep 2

description: gene expression data


title: LZ11


title: normal mammary tissue rep5

description: gene expression data

source_name: mammary tissue harvested from wild type FVB mouse

value: FVB

value: primary mammary tissue


title: MYCN amplification MB426

description: Tumoral tissue (medulloblastoma)

tag: sample type

tag: gender

tag: age [years]


title: MYCN amplification MB1185

description: Tumoral tissue (medulloblastoma)

value: m

tag: histology

value: LCA

tag: ctnnb1 mutation

tag: gli1/2 amplification


title: MYCN amplification MB151

description: Tumoral tissue (medulloblastoma)

value: classic

tag: myc amplification

tag: mycn amplification


title: NSPCs grown as monocultures (mRNA) rep1

value: NSPCs isolated from telencephalon of E-14 mouse embryo

value: Primary neural stem/progenitor cells

tag: treatment

value: grown as monoculture

tag: genetic background


title: normal mammary tissue rep3

description: gene expression data

tag: tissue


title: LZ10

tag: strain


title: CD8+_Tcells_severe_asthmatic_5

value: female

tag: batch

tag: age (years)

tag: patient id

value: Prednisolone 5mg od,Montelukast 10mg od,Symbicort 400/12 2pbd,Omeprazole 20mg od,Uniphyllin 400mg bd,Bricanyl prn

tag: cell type

value: CD8+ T-cells


title: MYCN amplification ITCC0336

description: Tumoral tissue (medulloblastoma)

value: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

value: normal cerebellum


title: 3036

source_name: KrasG12D Pten L/+ PDEC

value: FVB/C57B6 mixed backgroud

value: primary KrasG12D Pten L/+ pancreatic ductal epithelial cells, P4

tag: genotype/variation

value: Pdx1-Cre;LSL-KrasG12D L/+;Pten L/+


title: MYCN amplification MB1238

description: Tumoral tissue (medulloblastoma)

tag: sample type

value: medulloblastoma


title: CD8+_Tcells_severe_asthmatic_4

tag: gender

tag: fev1 (% predicted)

tag: fvc (% predicted)

tag: medication

value: Prednisolone 10mg od,Spiriva 18mcg od,Methotrexate 12.5mg wkly, Seretode 500 1pbd,Fosamax 70mg once/wk,Folic acid 5mg od,Calchichew,Cocodamol prn


title: normal mammary tissue rep2

description: gene expression data

value: FVB

value: primary mammary tissue


title: CD8+_Tcells_severe_asthmatic_2

value: Prednisolone 8mg - 1mg for 5wks(stopped 30/5/08),seretide 500mcg 1pbd,Singular 10mg bd,Phyllocontin 225mg am 450mg pm,Ventolin prn


title: 2975


title: Her2/Neu mammary tumor rep 1

description: gene expression data

tag: genotype

value: primary mammary tumor


title: MYCN amplification MB1179

description: Tumoral tissue (medulloblastoma)

tag: age [years]

tag: histology

tag: ctnnb1 mutation

tag: gli1/2 amplification

tag: myc amplification


title: CD8+_Tcells_severe_asthmatic_6

value: Prednisolone 10-20mg od,Combivent neb 2-4/day,Cetirizine 10mg od,Terbutaline 500mcg od,Budesonide 400mcg 2pbd, Aminophylline SR 450mg bd, Formoterol 12mcg 2pbd


title: CD8+_Tcells_severe_asthmatic_3

value: male

value: prednisolone 15mg od,Seretide 500mcg 2pbd,Montelukast 10mg nocte,Ventolin prn,Phyllocontin 450mg bd,Flixonase od


title: normal mammary tissue rep4

description: gene expression data

tag: strain

tag: tissue


title: normal mammary tissue rep1

description: gene expression data


title: 3030


title: 2880


title: CD8+_Tcells_non_severe_asthmatic_4

description: Gene expression data from circulating T cells of non severe asthmatic

value: female

tag: batch

tag: age (years)

value: Salbutamol


title: 2826

tag: cell type


title: CD8+_Tcells_severe_asthmatic_1

tag: patient id

value: Flixotide 500mcg 2pbd,Oxis 12 1pbd,Loratadine 1 tab od,Beconase 2pbd

value: CD8+ T-cells


title: Cerebral cortex_wt male_4 week

city: Taipei

first: Yi-Ming

middle: Arthur

last: Chen

state: Taiwan

address: 155, Li-Noun St., Sec. 2

department: AIDS Prevention and Research Center

institute: National Yang-Ming University

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Cerebral cortex from 3 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

value: wild-type

tag: age

value: 4 weeks

value: Cerebral cortex


title: CD8+_Tcells_non_severe_asthmatic_2

tag: gender

value: flixotide


title: MYCN amplification MB70

description: Tumoral tissue (medulloblastoma)

tag: sample type

value: normal cerebellum (pool of 24 donors; Clontech, LOT No.6060073)

value: normal cerebellum

value: f

value: classic

tag: mycn amplification

value: medulloblastoma


title: cmyc mammary tumor rep 3

description: gene expression data

source_name: mammary tumor harvested from trangenic mouse

value: cmyc

value: primary mammary tumor


title: cmyc mammary tumor rep 2

description: gene expression data


title: cmyc mammary tumor rep 1

description: gene expression data


title: CD8+_Tcells_non_severe_asthmatic_1

value: male

tag: fev1 (% predicted)

tag: fvc (% predicted)

tag: medication

value: Becotide, Ventolin


title: MYCN amplification MB1218

description: Tumoral tissue (medulloblastoma)

tag: age [years]

tag: histology

value: LCA


title: MYCN amplification MB835

description: Tumoral tissue (medulloblastoma)

value: m

tag: ctnnb1 mutation

tag: gli1/2 amplification


title: cmyc mammary tumor rep 4

description: gene expression data

tag: genotype


title: MYCN amplification MB1165

description: Tumoral tissue (medulloblastoma)

tag: tissue

tag: myc amplification


title: OvacD8-1

description: Gene Expression Data

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing:
GeneSpring GX was used for RMA normalization with pm probes and validated with R against bgversion=2. This PM based method involves three steps:
1. Background Correction: This step is based on the distribution of PM values amongst probes on an Affymetrix array.
2. Normalization: It uses Quantile normalization.
3. Probe summarization: It involves summarising the log(PM) after background correction of probes which is followed by estimation of expression values using robust procedure called Median Polish.

source_name: T cell clone

label_protocol: Ovation RNA Amplification System V2 (Nugen)

growth_protocol: cell lines were grown in the presence of their respective antigen and antigen-presenting cells in the complete media supplemented with IL-2

extract_protocol: Rneasy Mini kit (Qiagen)

value: OT-1 CD8aa+TCRab+ T cells


title: CD4+_Tcells_severe_asthmatic_8

value: female

tag: batch

tag: age (years)

value: Prednisolone 5mg od, Aminophylline 225mg bd,Seretide 500 2pbd,doxycycline, Tiotropium

value: CD4+ T-cells


title: OvacD8-2

description: Gene Expression Data

tag: cell type


title: brca ko p53 WT tumor rep 4

description: gene expression data

value: brca ko p53 WT


title: CD4+_Tcells_severe_asthmatic_7

tag: patient id

value: Prednisolone 10mg od, Insulin S/C,Seretide 500mcg 2pbd, Metformin,Nexium, Flixonase,Tramacet,Calcium,Valsartan,Amitriptyline


title: Patient 8

city: Paris

first: Edi

last: Prifti

state: IDF

address: 15, rue de l'école de Médecine

institute: INSERM UMRS-U872

description: Biological replicate 8 of 8. Adipose tissue dSAT vs. sSAT.

hyb_protocol: Standard Agilent hybridization protocol.

scan_protocol: Standard Agilent scanning protocol.

data_processing: The data were normalized using quantile normalization with the limma-package in the R statistical language.

source_name: adipose tissue dSAT

label_protocol: Cy5- and Cy3-labeled cRNA were prepared with the Agilent Quick Amp Labeling Kit for arrays.

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

value: deep subcutaneous adipose tissue (dSAT)

source_name: adipose tissue sSAT

value: superficial subcutaneous adipose tissue (sSAT)


title: OvacD8-3

description: Gene Expression Data


title: Patient 6

description: Biological replicate 6 of 8. Adipose tissue dSAT vs. sSAT.


title: brca ko p53 WT tumor rep 5

description: gene expression data


title: brca ko p53 Wt tumor  rep 3

description: gene expression data


title: CD4+_Tcells_severe_asthmatic_6

tag: gender

value: Prednisolone 10-20mg od,Combivent neb 2-4/day,Cetirizine 10mg od,Terbutaline 500mcg od,Budesonide 400mcg 2pbd, Aminophylline SR 450mg bd, Formoterol 12mcg 2pbd


title: Patient 7

description: Biological replicate 7 of 8. Adipose tissue dSAT vs. sSAT.


title: CD8+_Tcells_non_severe_asthmatic_3

value: CD8+ T-cells


title: Cerebral cortex_KO male_4 week

tag: strain

value: wild-type

tag: age

value: 4 weeks

value: Cerebral cortex


title: 2D11-2

description: Gene Expression Data

value: CD8aa Tregs


title: brca ko p53 WT tumor rep 2

description: gene expression data

value: primary mammary tumor


title: 2D11-4

description: Gene Expression Data


title: brca ko p53 WT tumor rep 1

description: gene expression data


title: CD4+_Tcells_severe_asthmatic_4

tag: fev1 (% predicted)

value: Prednisolone 10mg od,Spiriva 18mcg od,Methotrexate 12.5mg wkly, Seretode 500 1pbd,Fosamax 70mg once/wk,Folic acid 5mg od,Calchichew,Cocodamol prn


title: Patient 5

description: Biological replicate 5 of 8. Adipose tissue dSAT vs. sSAT.


title: Zm_Sr5_15_2_Mock4weeks_II

city: Giza

first: Hassan

middle: Abdelalim

last: Ghareeb

address: El Buhouth Str., Dokki

department: Department of Plant Biotechnology

country: Egypt

institute: National Research Centre

hyb_protocol: Array hybridization, washing and staining was performed according to the Midi_Euk2V3 protocols using GeneChip Fluidics Station 400

scan_protocol: arrays were scanned with Affymetrix GSC3000 scanner (Affymetrix)

data_processing: The microarray fluorescence signals were processed using the GCOS v1.4 software package (Affymetrix). The software was used to produce presence-absence calls and to normalize the signal intensities from each array with scaling the target signal to 300 and using default parameters

organism: Zea mays

source_name: ears < 2 cm, 4 weeks post inoculation with S. reilianum strains 5-1 X 5-1, elongated ears with kernels

label_protocol: cRNA labeling and cRNA fragmentation and labeling were performed according to the manual of the GeneChip IVT Labeling Kit (Affymetrix)

extract_protocol: Ears (>2 cm in length) from 20 plants at 4 weeks post inoculation (wpi) were collected from healthy or S. reilianum-infected plants. Of infected ears, those displaying clear vegetative structures were excluded and only ears showing elongation of spikelets were collected. RNA from three independent experiments was extracted with Trizol (Invitrogen, Karlsruhe, Germany). DNAse treatment was performed using RNase-Free DNase Set (Qiagen; Hilden; Germany), and RNA was purified with RNeasy Plant Mini Kit (Qiagen; Hilden; Germany). The RNA quality was verified using a Bioanalyzer 2100 (Agilent, Böblingen, Germany), and the RNA purity and concentration were assessed with NanoDrop ND-1000 (Thermo Fisher Scientific, Schwerte, Germany).

value: ears < 2 cm, elongated ears with kernels

tag: time

value: 4 weaks post inoculation

tag: infection status

value: mock


title: Zm_Sr5_15_2_Mock4weeks_III


title: M6C cell line rep3

description: gene expression data

source_name: metastatic mammary tumor cell line

tag: cell line

value: tissue culture cells


title: Patient 3

description: Biological replicate 3 of 8. Adipose tissue dSAT vs. sSAT.


title: M6C cell line rep4

description: gene expression data


title: CD4+_Tcells_severe_asthmatic_2

value: female

tag: fvc (% predicted)

tag: medication

value: Prednisolone 8mg - 1mg for 5wks(stopped 30/5/08),seretide 500mcg 1pbd,Singular 10mg bd,Phyllocontin 225mg am 450mg pm,Ventolin prn

value: CD4+ T-cells


title: 2D11-1

description: Gene Expression Data


title: CD4+_Tcells_severe_asthmatic_3

value: male

value: prednisolone 15mg od,Seretide 500mcg 2pbd,Montelukast 10mg nocte,Ventolin prn,Phyllocontin 450mg bd,Flixonase od


title: Zm_Sr5_15_2_Mock4weeks_I


title: CD4+_Tcells_severe_asthmatic_5

value: Prednisolone 5mg od,Montelukast 10mg od,Symbicort 400/12 2pbd,Omeprazole 20mg od,Uniphyllin 400mg bd,Bricanyl prn


title: CD4+_Tcells_severe_asthmatic_1

value: Flixotide 500mcg 2pbd,Oxis 12 1pbd,Loratadine 1 tab od,Beconase 2pbd


title: Zm_Sr5_15_2_Leafy ears4weeks_III

value: S. reilianum strains 5-1 X 5-1


title: Patient 1

description: Biological replicate 1 of 8. Adipose tissue dSAT vs. sSAT.

value: deep subcutaneous adipose tissue (dSAT)

value: superficial subcutaneous adipose tissue (sSAT)


title: M6C cell line rep2

description: gene expression data


title: Zm_Sr5_15_2_Leafy ears4weeks_II


title: Patient 2

description: Biological replicate 2 of 8. Adipose tissue dSAT vs. sSAT.


title: M6C cell line rep1

description: gene expression data


title: CD4+_Tcells_healthy_donor_6


title: M6 cell line rep1

description: gene expression data

source_name: mammary tumor cell line


title: CD4+_Tcells_healthy_donor_8


title: normal-6

city: Beppu

first: Koshi

last: Mimori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

institute: Kyushu university

hyb_protocol: Hybridization was carried out using the conditions specified in the Agilent Human Whole Genome Expression system.

scan_protocol: Fluorescence intensities were determined with an Agilent DNA Microarray Scanner.

data_processing: Expression levels were quantified by G2567AA Feature Extraction Software Version A.7.5.1 (Agilent Technologies), which used the  LOWESS (locally weighted linear regression curve fit) normalization method. Further analyses were performed using GeneSpring version 7.3.

source_name: normal epithelium

label_protocol: Cyanine (Cy)-labeled cRNA was prepared using T7 linear amplification as described in the Agilent Low RNA Input Fluorescent Linear Amplification Kit Manual  (Agilent Technologies).

extract_protocol: Total RNA was extracted with QIAGEN RNeasy minElute Spin Column (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocols.

treatment_protocol: Laser micro-dissection


title: Patient 4

description: Biological replicate 4 of 8. Adipose tissue dSAT vs. sSAT.


title: CD4+_Tcells_non_severe_asthmatic_4

value: Salbutamol


title: normal-9


title: CD4+_Tcells_healthy_donor_1


title: CD4+_Tcells_healthy_donor_5


title: CD4+_Tcells_healthy_donor_3


title: M6 cell line rep3

description: gene expression data


title: Id2-HPC induced under B-cell conditions for 120 hours

city: La Jolla

first: Yin

last: Lin

address: 9500 Gilman Drive

institute: UCSD

hyb_protocol: The Illumina hybridization protocol was used. 1500 ng of cRNA. Hybridization in HYB buffer for 18-20 hours at 58°C with gentle rocking followed by standard Illumina washes and streptavidin-Cy3 staining.

scan_protocol: Illumina BeadArray Reader was used. Green Channel with a PMT setting of 100%.

data_processing: Illumina Genome Studio Software produced raw data which was normalized using a modified LOESS or quantile normalization.

source_name: Id2-HPC cells induced under B-cell conditions, 120 hours

label_protocol: The Ambion kit Illumina TotalPrep RNA Amplification Kit produced amplified biotinylated cRNAs by the Eberwine protocol.

extract_protocol: Total RNA was extracted from 5 Mio cells on RNeasy columns (Qiagen) with on-column DNase digestion following the manufacturer's instructions. RNA quality was assessed on an Agilent 2100 BioAnalyzer.

value: human ID2 transgenic

value: hematopoietic progenitor cells (HPCs)

tag: hpc induction

value: B-cell conditions

tag: induction duration

value: 120 hrs


title: Id2-HPC induced under B-cell conditions for 72 hours

source_name: Id2-HPC cells induced under B-cell conditions, 72 hours

tag: genotype

value: 72 hrs


title: normal-7


title: Id2-HPC induced under B-cell conditions for 12 hours, biological replicate 2

source_name: Id2-HPC cells induced under B-cell conditions, 12 hours

value: 12 hrs


title: Id2-HPC induced under B-cell conditions for 24 hours, biological replicate 2

source_name: Id2-HPC cells induced under B-cell conditions, 24 hours

value: 24 hrs


title: CD4+_Tcells_non_severe_asthmatic_3

value: Becotide, Ventolin


title: CD4+_Tcells_healthy_donor_4

value: CD4+ T-cells


title: Id2-HPC induced under B-cell conditions for 240 hours

source_name: Id2-HPC cells induced under B-cell conditions, 240 hours

value: 240 hrs


title: M6 cell line rep2

description: gene expression data

tag: tissue

value: tissue culture cells


title: Id2-HPC induced under B-cell conditions for 48 hours

source_name: Id2-HPC cells induced under B-cell conditions, 48 hours

value: 48 hrs


title: CD4+_Tcells_healthy_donor_2

value: female

tag: batch


title: Id2-HPC induced under B-cell conditions for 12 hours, biological replicate 1


title: Id2-HPC induced under B-cell conditions for 6 hours, biological replicate 2

source_name: Id2-HPC cells induced under B-cell conditions, 6 hours

value: 6 hrs


title: Id2-HPC induced under B-cell conditions for 24 hours, biological replicate 1


title: CD4+_Tcells_healthy_donor_7

tag: age (years)


title: Id2-HPC induced under B-cell conditions for 6 hours, biological replicate 1

tag: cell type


title: normal-8


title: Zm_Sr5_15_2_Leafy ears4weeks_I

value: ears < 2 cm, elongated ears with kernels

value: 4 weaks post inoculation

value: S. reilianum strains 5-1 X 5-1


title: 30wk old Deaf1-KO-Replicate 2

city: Stanford

first: Linda

last: Yip

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

description:
30w-2
Biological replicate of gene expression in the PLN of 30wk old Deaf1-KO vs.littermate controls

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software (version 10.5.1.1)

data_processing: Lowess normalization was performed using the feature extraction software version 10.5.1.1.  Then this data was processed with Genespring 11.5 to generate the normalized log(2) ratio of the test (cy5-labeled)/reference(cy3-labelled) intensity values.

source_name: Pancreatic Lymph Node

label_protocol: 1 ug of total RNA was labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: Deaf1-KO and wild-type littermate control mice were bred at the Stanford School of Medicine Animal facility.  All mice were maintained under pathogen-free conditions according to institutional guidelines under approved protocols in the Stanford Medical Center’s Department of Comparative Medicine.  Mice were genotyped before use.

extract_protocol: Total RNA was extracted using Trizol Reagent combined with the Qiagen Rneasy Mini Kit.

treatment_protocol: pancreatic lymph node tissues were extracted from mice and homogenized in Trizol Reagent.

value: BALB/c

value: Pancreatic Lymph Node

value: 30 week old

tag: genotype/variation

value: Deaf1-Knock out

source_name: Pancreatic Lymph Node (pool of 3 individuals)

value: Wild type


title: 12wk old Deaf1-KO-Replicate 2

description:
12w-2
Biological replicate of gene expression in the PLN of 12wk old Deaf1-KO vs.littermate controls

value: 12 week old


title: 4wk old Deaf1-KO-Replicate 1

description:
4w-1
Biological replicate of gene expression in the PLN of 4wk old Deaf1-KO vs.littermate controls

value: 4 week old

source_name: Pancreatic Lymph Node (pool of 2 individuals)


title: 30wk old Deaf1-KO-Replicate 3

description:
30w-3
Biological replicate of gene expression in the PLN of 30wk old Deaf1-KO vs.littermate controls


title: CD4+_Tcells_non_severe_asthmatic_1

tag: gender

value: male

tag: patient id

value: Becotide, Ventolin


title: CD4+_Tcells_non_severe_asthmatic_2

value: flixotide

value: CD4+ T-cells


title: 12wk old Deaf1-KO-Replicate 3

description:
12w-3
Biological replicate of gene expression in the PLN of 12wk old Deaf1-KO vs.littermate controls

tag: strain

tag: age


title: Heavy fractions

description: Differential gene expression in heavy polysome fractions

source_name: cultured lymph node stromal cells

label_protocol: 200 ng of total RNA was labeled RNAusing the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: Cultured lymph node stromal cells (LNSCs) were grown in 10 cm culture dishes in DMEM containing 10% FCS until ~80% confluent.

extract_protocol: Total RNA was extracted by acid phenol/chloroform extraction following incubation with 250 μg/ml proteinase K (NEB) and 0.5% SDS at 37ºC for 30 min.  Extracted RNA was precipitated overnight at -20ºC with glycogen (Roche), 300 mM sodium acetate (pH5), and 3 volumes of ethanol.  RNA pellets were washed in 75% ethanol and reconstituted in nuclease free water.

treatment_protocol: Cells were transfected with 400 pmol of control or Eif4g3 siRNA in a volume of 10 ml media using Lipofectamine 2000. Media was changed at 24h after transfection, and cells were harvested at 48 h.

tag: transfection

value: Eif4g3-siRNA treated

tag: polysome fraction

value: Heavy fractions

value: Control-siRNA treated


title: 30wk old Deaf1-KO-Replicate 1

description:
30w-1
Biological replicate of gene expression in the PLN of 30wk old Deaf1-KO vs.littermate controls


title: 12wk old Deaf1-KO-Replicate 1

description:
12w-1
Biological replicate of gene expression in the PLN of 12wk old Deaf1-KO vs.littermate controls


title: 4wk old Deaf1-KO-Replicate 2

description:
4w-2
Biological replicate of gene expression in the PLN of 4wk old Deaf1-KO vs.littermate controls


title: Uninduced Id2-HPC, biological replicate B

source_name: Uninduced Id2-HPC cells

value: human ID2 transgenic

value: hematopoietic progenitor cells (HPCs)

value: uninduced


title: Uninduced Id2-HPC, biological replicate A


title: Light fractions

description: Differential gene expression in light polysome fractions

value: BALB/c

value: Cultured lymph node stromal cells (LNSCs)

value: Light fractions


title: washed-out for 48h after an initial 48 h treatment with 1 micromolar Ro3303544: replicate 2

city: Tokyo

first: francois

middle: frederic

last: renault-mihara

address: 35 Shinanomachi, Shinjuku-ku

department: Physiology

institute: Keio University School of Medicine

description: Gene expression after 48h wash-out (after an initial treatment with 1 µM Ro3303544)

hyb_protocol: Cy3-labeled cRNA (1000 ng) was hybridized to an Agilent Whole Mouse Gene Expression Microarray (#14868), as per the manufacturer’s protocol.

scan_protocol: Slides were scanned using the Agilent dual-laser DNA microarray scanner (G2565CA).

data_processing:
The data were extracted by the Agilent Feature Extraction software version 10.1. Normalization for each plot was performed as recommended by Agilent: Values below 0.01 were set to 0.01. Each measurement was divided by the 50.0th percentile of all measurements in that sample. Data were analyzed using Genespring GX software (Tomy Digital Biotechnologies).
Genes that were up- or down-regulated more than twofold were identified. Statistical comparisons between the control and Ro3303544 groups, or between the control and wash-out groups were performed using an unpaired t-test (unequal variances), and the threshold for statistical significance was set at p ≤0.05.

source_name: cortico-striatal astrocytes in primary culture

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared using the QuickAmp labeling kit (Agilent), according to the manufacturer’s instructions.

growth_protocol: Astrocytes in primary cultures were prepared as previously described (Araujo et al., 1993). Briefly, striatal and cortical cells from 1-day postnatal wild-type C57BL/6J mice were dissociated and plated on culture dishes coated with poly-L-ornithine (1.5 g/ml; MW 40,000, Sigma) in defined MEM-F12 medium consisting of a 1:1 mixture of MEM and F-12 nutrient (Invitrogen) supplemented with glucose (33 mM), L-glutamine (2 mM), sodium bicarbonate (3 mM), HEPES (pH 7.4, 5 mM), penicillin (50 IU/ml), streptomycin (5 g/ml) (all from Invitrogen), and 10% heat-inactivated fetal bovine serum (Nichirei Biosciences, Japan). The culture medium was changed every 3 days. When the cells were almost confluent, at around day 7, they were treated with 5 M cytosine arabinoside for 2 days, to deplete the contaminating microglial cells. Further stringent washes with PBS were performed to obtain high-purity cultures of astrocytes (less than 1% Iba1-positive contaminating microglial cells at 12 days in culture).

extract_protocol: Total RNA was isolated from astrocytes in primary culture upon the indicated treatments using Trizol®, following the manufacturer’s protocol, and further purified with the RNeasy mini kit (Qiagen). Two replicates were run per condition. RNA was quantified using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies), and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The RNA had an A260/280 ratio ≥ 2, and the RNA Integrity Number was ≥ 6.5.

treatment_protocol: After 13 days in vitro, cells were treated for 48 h with either 1 µM Ro3303544 (dissolved in growth medium), or an equivalent final concentration of DMSO, or treated for 48h with 1 µM Ro3303544 and wash-out for two additional days in growth medium.

value: wild-type

value: 1-day postnatal

tag: condition