title: GR-KD shRNA_31_H

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: MiRNA expression data from liver of wt mice treated with GR-directed rAAV virus

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol. The miRNA 2.0 Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were imported with the expression console from affymetrix and performed an analysis using the RMA+DABG Workflow (Default settings)

source_name: C57BL/6J liver treated with GR-directed miRNA-rAAV

label_protocol: FlashTag RNA Labeling with Biotin HSR RNA Labeling Kit

growth_protocol: Mice for wt vs db/db miRNA screening were fasted for 24hours and re-fed for 6 hours; Mice in the Neg. Cntrl vs GR-KD screening were sacrificed under fed state

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

treatment_protocol: After the indicated time of re-feeding or virus-treatment, mice were sacrificed where the livers were taken, washed with PBS, and snap-frozen in liquid nitrogen

value: liver

tag: genotype/variation

value: wildtype

tag: shRNA

value: GR-KD shRNA

tag: strain


title: GR-KD shRNA_32_H

status: Public on Oct 15 2014

type: RNA

country: Germany

label: biotin

molecule: total RNA

organism: Mus musculus

tag: tissue


title: NasalMucosa_RSVpositive_SevereDisease_Sample15

city: Lørenskog

first: Christopher

middle: Stephen

last: Inchley

address: Sykehusveien

department: Department of Pediatric and Adolescent Medicine

country: Norway

institute: Akershus University Hospital

description: Nasal mucosal miRNA expression on admission with Respiratory Syncytial Virus infection

hyb_protocol: miRNA Spike-In Kit and miRNA Complete Labeling and Hyb Kit (Agilent), according to manufacturer's instructions

scan_protocol: Arrays were scanned on Agilent G2565BA Microarray Scanner. Data collection and quality assessment were performed using Agilent Feature Extraction Software v8.5

data_processing: The AgiMiRNA package for R was used to normalize data by Quantile normalization. miRNAs were removed if <50% of samples in all experimental groups expressed that miRNA or if < 25% of samples in all experimental groups had expression levels equal to or less than the mean + 1.5 standard deviations of negative control features.

organism: Homo sapiens

source_name: Nasal mucosa

extract_protocol: Brushes were immediately immersed in RNA stabilization reagent RNAlater (Sigma-Aldrich, Saint Louis, Missouri, USA). Epithelial cells were detached from the brushes and stored at -80°C in RNAlater for miRNA analysis. Epithelial cells stored at -80℃ were pelleted before homogenization in QIAzolLysis Reagent (Qiagen, Hilden, Germany). The miRNeasy mini kit (Qiagen) was then used according to the manufacturer’s instructions with additional DNase treatment.

tag: disease state

value: Severe Respiratory Syncytial Virus Disease

tag: age (months)

tag: gender

value: Male


title: NasalMucosa_Healthy_Control_Sample14

description: Nasal mucosal miRNA expression in healthy child without symptoms of respiratory infection

label_protocol: miRNA Spike-In Kit and miRNA Complete Labeling and Hyb Kit (Agilent), according to manufacturer's instructions

value: Healthy Control

value: Female


title: Liver_Metastasis-HM_056_MC

city: Montpellier Cedex 5

first: Pierre

last: Martineau

address: 208 Rue des Apothicaires

department: IRCM

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133B  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with HWS kit.

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

data_processing: Signal intensity for each transcript and detection call (present, absent, or marginal) were determined using MAS 5.0 Software (Affymetrix). Interarray normalization was performed using a set of internal standard genes (normalization set ϩ internal controls) leading to the determination of a scaling factor.

source_name: Tissue samples taken from colorectal cancer patients

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT protocol from 3µg total RNA (3'IVT ExpressTechnical Manual).

extract_protocol: Rneasy kit (Qiagen) for total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Samples were collected before chemotherapy

value: Liver Metastasis

tag: patient number

tag: Sex

tag: age

tag: who performance status

tag: tumor location

value: Left colon

tag: differentiation

value: Moderate

tag: pn

tag: pt

tag: folfiri status

value: NR


title: NasalMucosa_RSVpositive_MildDisease_Sample13

value: Mild Respiratory Syncytial Virus Disease


title: NasalMucosa_RSVpositive_SevereDisease_Sample16


title: GR-KD shRNA_29_H


title: GR-KD shRNA_30_H


title: NasalMucosa_Healthy_Control_Sample12


title: Neg. Cntrl shRNA_28_G

description: MiRNA expression data from liver of wt mice treated with negative control rAAV virus

source_name: C57BL/6J liver treated with Negative control miRNA-rAAV

value: Negative control shRNA


title: Neg. Cntrl shRNA_27_G


title: NasalMucosa_RSVpositive_MildDisease_Sample11


title: NasalMucosa_Healthy_Control_Sample10


title: Neg. Cntrl shRNA_26_G


title: NasalMucosa_RSVpositive_SevereDisease_Sample9


title: Neg. Cntrl shRNA_25_G


title: db/db, refed_24_F

description: MiRNA expression data from liver of refed db/db mice

source_name: BKS.Cg-Dock7m +/+ Leprdb/J, liver

value: db/db


title: Primary_Tumor-CT_244_FP

value: Primary Tumor

value: Transverse colon

value: R


title: Primary_Tumor-CT_227_SS

value: Poor


title: Liver_Metastasis-HM_003_JCP

value: Rectum-sigmoid junction


title: Primary_Tumor-CT_222_PEC


title: NasalMucosa_RSVpositive_MildDisease_Sample8


title: db/db, refed_23_F

value: liver


title: NasalMucosa_RSVpositive_SevereDisease_Sample7

value: Severe Respiratory Syncytial Virus Disease


title: Primary_Tumor-CT_196_TD

value: Well


title: Primary_Tumor-CT_189_JR

value: Male


title: Primary_Tumor-CT_213_RG

value: Female


title: db/db, refed_21_F


title: NasalMucosa_Healthy_Control_Sample5

value: Healthy Control


title: NasalMucosa_RSVpositive_SevereDisease_Sample6


title: Primary_Tumor-CT_149_JGI

value: Left colon


title: wt, refed_11_C

description: MiRNA expression data from liver of refed wt mice

source_name: C57BL/6J, liver

value: wildtype


title: NasalMucosa_RSVpositive_MildDisease_Sample4


title: Primary_Tumor-CT_119_PM

value: NR


title: wt, refed_10_C


title: Primary_Tumor-CT_223_GB

value: Moderate


title: Primary_Tumor-CT_115_CB

value: Right colon


title: db/db, refed_22_F

value: db/db


title: wt, refed_12_C


title: wt, refed_9_C


title: NasalMucosa_RSVpositive_MildDisease_Sample2

value: Mild Respiratory Syncytial Virus Disease


title: NasalMucosa_Healthy_Control_Sample1


title: Primary_Tumor-CT_073_PD

value: Primary Tumor


title: Primary_Tumor-CT_130_YL

value: R


title: Primary_Tumor-CT_061_CM


title: Primary_Tumor-CT_094_AM

value: Poor


title: NasalMucosa_RSVpositive_SevereDisease_Sample3


title: Primary_Tumor-CT_045_JC


title: Primary_Tumor-CT_044_MB


title: Primary_Tumor-CT_059_MT


title: Primary_Tumor-CT_022_JB


title: Primary_Tumor-CT_056_MC


title: Non-dynamic Linear RGD Surface

city: Clayton

first: Eun-ju

last: Lee

state: Victoria

address: Bayview Avenue

country: Australia

institute: Commonwealth Science and Industrial Research Organisation

description: Cells were directly added and incubated on the linear RGD-immobilized surface for 24 hours before harvest.

hyb_protocol: The labeled samples and reference were co-hybridized to Agilent Whole Mouse Genome Microarrays using Agilent microarray hybridization chamber and its protocol.

scan_protocol: Scanned on an Agilent DNA microarray scanner (Agilent Technologies Inc.) and the microarray images generated by the scanner were analyzed using Feature Extraction 9.5.3 software (Agilent Technologies Inc.).

data_processing: Feature Extraction 9.5.3 software was used for background subtraction and Lowess normalization.

source_name: Cells cultured on a linear RGD-immobilized surface

label_protocol: The integrity of the RNA was determined using the 2100 Bioanalyzer RNA Series Ⅱ Kits (Agilent Technologies Inc.). The spike mixes of Two-color RNA Spike-In kit (Agilent Technologies Inc.) were diluted, then added directly to RNA samples prior to amplification and labeling. Total RNA samples (2.0 µg) were amplified using T7 primers to make cRNA. The cRNAs from samples were labeled with Cy5 and the reference cRNA was incorporated with Cy3.

growth_protocol: 3T3-Swiss albino cells were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10 % bovine calf serum. To detach cells from the culture flask, cells were rinsed with phosphate-buffered saline twice and 0.05 % trypsin /0.53 mM EDTA was added. After incubating for 5 minutes, cells were resuspended in serum-free medium and centrifuged at 1000 rpm for 5 minutes to remove trypsin. Cells were resuspended in serum-free medium and added onto each surface for the experiments. When cells were attached onto the surface, the medium was changed to serum media.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: For dynamic surfaces, cells attached on the fibronectin patterns were rinsed in serum-free medium twice. The substrates were chemically treated in presence of cells to immobilize either linear or cyclic RGD for 2 hours, then placed in serum-containing medium and incubated.

tag: cell line

value: 3T3-Swiss albino

tag: cell type

value: Fibroblast

source_name: Cells cultured in a standard tissue culture flask


title: Dynamic Cyclic RGD Surface

description: Cells were incubated on the fibronectin patterned surface for 12 hours, then allowed to interact with immobilzed cyclic RGD for 24 hours before harvest.

source_name: Cells cultured initially on fibronectin pattern then exposed to cyclic RGD


title: [skeletal muscle]-[Lipocalin13 + TSC22D4 shRNA]-[32]

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version5, from SAS. Gene expression profiling was performed using arrays of mogene-2.0-st -type from Affymetrix. A Custom CDF Version 17 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization. Background correction was performed with RMA. Probeset-Summary was performed with Medianpolish.

source_name: LIPO_TSC_KD_skeletal muscle

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

growth_protocol: 12 week old BKS.Cg-Dock7m +/+ Leprdb/J (000642) mice were obtained from Charles River Laboratories (Brussels, Belgium) and maintained on a 12 h light-dark cycle with regular unrestricted diet and free access to water.

extract_protocol: gastrocnemius muscle tissue was collected immediately after sacrifice of the animal and snap-frozen. RNA extraction was carried out with a RNeasy RNA-extraction Kit (Qiagen) according to the manufacturers protocols

treatment_protocol: mice were treated with either control (control shRNA), LCN13 (LCN13 shRNA), TSC22D4 (TSC22D4 shRNA), TSC22D4 plus LCN13 (TSC22D4+LCN13 shRNA) shRNA adenovirus at a concentration of 2x(2x109) plaque-forming units (pfu) recombinant virus per treatment group (control group group: 4x109 control shRNA; LCN13 group: 2x109 LCN13 shRNA + 2x109 control shRNA; TSC22D4 group: 2x109 TSC22D4 shRNA + 2x109 control shRNA; TSC22D4+LCN13 group: 2x109 TSC22D4 shRNA + 2x109 LCN13 shRNA)

tag: strain background

value: BKS.Cg-Dock7m +/+ Leprdb/J (000642)

value: 12 weeks

tag: treated with

value: 2x10^9 TSC22D4 shRNA + 2x10^9 LCN13 shRNA

value: skeletal muscle


title: [skeletal muscle]-[Lipocalin13 + TSC22D4 shRNA]-[30]

tag: tissue


title: Primary_Tumor-CT_016_MV

value: Female

value: Well


title: Normal_Colon-CN_227_SS

value: Normal Colon

value: Male

value: Left colon


title: Non-dynamic Cyclic RGD Surface

description: Cells were directly added and incubated on the cyclic RGD-immobilized surface for 24 hours before harvest.

source_name: Cells cultured on a cyclic RGD-immobilized surface


title: [skeletal muscle]-[TSC22D4 shRNA]-[26]

source_name: TSC_KD_skeletal muscle

value: 2x10^9 TSC22D4 shRNA + 2x10^9 control shRNA


title: Normal_Colon-CN_234_YC

value: Caecum

value: Moderate

value: NR


title: Fibronectin Surface

description: Cells were incubated on the fibronectin patterned surface for 24 hours before harvest.

source_name: Cells cultured on fibronectin-coated confined area


title: Normal_Colon-CN_223_GB


title: Normal_Colon-CN_222_PEC


title: Dynamic Linear RGD Surface

description: Cells were incubated on the fibronectin patterned surface for 12 hours, then allowed to interact with immobilzed linear RGD for 24 hours before harvest.

source_name: Cells cultured initially on fibronectin pattern then exposed to linear RGD


title: lps_1

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

country: USA

institute: University of California, San Francisco

hyb_protocol: 600 ng of each Cy3-labeled aaRNA hybridized to a SurePrint G3 Mouse Gene Expression 8x60K microarray (Agilent-028005) as per manufacturer's protocol.

scan_protocol: Arrays were scanned on an Agilent scanner, 3 um resolution, 20-bit tiff.

data_processing: Custom in-house scripts and the Bioconductor Limma package were used for filtering and normalization. Control features and sample features with saturated, non-uniform feature, and non-uniform background flags were removed. Genes present across 70% of arrays were retained, log2 transformed, KNN-imputed, and quantile normalized. Genes determined to be not expressed were filtered out (expressed genes = log2 intensity >= 7 across all samples within a group). Arrays were median centered, followed by median centering of genes.

source_name: LPS-treated mouse, lung neutrophil

label_protocol: 1.5 ug of aRNA coupled to Cy3 in 0.1 M sodium bicarbonate pH 9 buffer and purified over spin columns.

extract_protocol: RNA was isolated from frozen neutrophils (RNAqueous Micro, Life Technologies). Purified RNA was amplified (MessageAmp II, Life Technologies) with minor modifications to manufacturer’s instructions to generate amino-allyl incorporated amplified RNA.

treatment_protocol:
Mice were infected with N. brasiliensis as described. 50 micrograms of LPS was administered to mice intratracheally in 50 microliters of PBS.
Total RNA extraction from FACS-isolated lung neutrophils 2 days after N. brasiliensis infection or LPS treatment.

tag: strain/background

value: BALB/c

tag: genotype/variation

value: wildtype

value: female

value: lung neutrophil

tag: treatment

value: lipopolysaccharide


title: [skeletal muscle]-[TSC22D4 shRNA]-[25]

value: BKS.Cg-Dock7m +/+ Leprdb/J (000642)

value: 12 weeks


title: lps_3

tag: gender


title: nb_3

source_name: Nb-infected mouse, lung neutrophil

value: Nippostrongylus brasiliensis infection


title: Normal_Colon-CN_196_TD

tag: patient number

tag: Sex

value: Female


title: [skeletal muscle]-[TSC22D4 shRNA]-[27]

tag: age

value: skeletal muscle


title: [skeletal muscle]-[Lipocalin13 shRNA]-[22]

source_name: Lipo_KD_skeletal muscle

value: 2x10^9 LCN13 shRNA + 2x10^9 control shRNA


title: [skeletal muscle]-[Lipocalin13 shRNA]-[23]


title: lps_2


title: Normal_Colon-CN_189_JR

value: Normal Colon

value: Male

tag: who performance status

tag: tumor location

value: Well


title: Fetal liver double knockout rep4

city: Philadelphia

first: John

last: Pehrson

state: PA

address: 3800 Spruce Street

institute: University of Pennsylvania

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of the microarray sectors was set as background and subtracted from all features in that sector.

label: Biotin

source_name: Liver, fetus, 18.5 d.p.c, macroH2A1/2 double knockout

label_protocol: Labeled cDNA was prepared from 250 ng of total RNA using the standard procedure of the Ambion WT Expression Kit (Life Technologies)

growth_protocol: Pregnant mice were maintained on a 12 hr day/night cycle with the lights coming on a 8 AM. They were given water and low fat rodent chow Ad libitum. They were killed between 9 and 10 AM.

extract_protocol: Total liver RNA was extracted with Trizol (life technologies) following standard protocol

treatment_protocol: No special treatments.

tag: strain

value: 129/S6 (taconic)

value: Liver

tag: developmental stage

value: 18.5 days post coitum

value: macroH2A1 macroH2A2 double knockout


title: Fetal liver double knockout rep5

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.


title: [skeletal muscle]-[Lipocalin13 shRNA]-[21]


title: Fetal liver double knockout rep3


title: Fetal liver double knockout rep6


title: Normal_Colon-CN_119_PM

value: Left colon

tag: pn

tag: pt

tag: folfiri status

value: NR


title: [skeletal muscle]-[NC shRNA]-[20]

source_name: control_skeletal muscle

tag: strain background

value: 4x10^9 control shRNA


title: [skeletal muscle]-[NC shRNA]-[19]

tag: treated with


title: nb_1

value: BALB/c

value: wildtype

value: female

tag: cell type

value: lung neutrophil


title: Fetal liver double knockout rep2

tag: tissue


title: naïve_2

source_name: Naïve mouse, lung neutrophil

tag: strain/background

tag: genotype/variation

value: naïve


title: nb_2

tag: gender

tag: treatment

value: Nippostrongylus brasiliensis infection


title: [skeletal muscle]-[Lipocalin13 + TSC22D4 shRNA]-[29]

value: BKS.Cg-Dock7m +/+ Leprdb/J (000642)

value: 12 weeks

value: 2x10^9 TSC22D4 shRNA + 2x10^9 LCN13 shRNA

value: skeletal muscle


title: Fetal liver double knockout rep1

value: Male

value: 129/S6 (taconic)


title: Normal_Colon-CN_149_JGI

source_name: Tissue samples taken from colorectal cancer patients

value: Normal Colon

tag: patient number

tag: Sex

tag: differentiation

value: Well

value: R


title: naïve_1


title: [skeletal muscle]-[NC shRNA]-[18]

tag: age


title: [abdominal fat tissue]-[Lipocalin13 + TSC22D4 shRNA]-[13]

source_name: LIPO_TSC_KD_abdominal fat

extract_protocol: abdominal fat tissue was collected immediately after sacrifice of the animal and snap-frozen. RNA extraction was carried out with a RNeasy RNA-extraction Kit (Qiagen) according to the manufacturers protocols

treatment_protocol: mice were treated with either control (control shRNA), LCN13 (LCN13 shRNA), TSC22D4 (TSC22D4 shRNA), TSC22D4 plus LCN13 (TSC22D4+LCN13 shRNA) shRNA adenovirus at a concentration of 2x(2x10^9) plaque-forming units (pfu) recombinant virus per treatment group (control group group: 4x10^9 control shRNA; LCN13 group: 2x10^9 LCN13 shRNA + 2x10^9 control shRNA; TSC22D4 group: 2x10^9 TSC22D4 shRNA + 2x10^9 control shRNA; TSC22D4+LCN13 group: 2x10^9 TSC22D4 shRNA + 2x10^9 LCN13 shRNA)

value: LCN13_TSC22D4 knockdown

value: abdominal fat


title: [abdominal fat tissue]-[Lipocalin13 + TSC22D4 shRNA]-[16]


title: Fetal liver wild-type rep4

source_name: Liver, fetus, 18.5 d.p.c, wild-type

tag: strain

value: Liver

value: 18.5 days post coitum

value: Wild-type


title: Fetal liver wild-type rep5

tag: developmental stage


title: sphere_ndr1-inj_rep2

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: One colour microarray comparison to determine targets of Nodal signaling by overexpression of ndr1 in zebrafish blastulas

hyb_protocol: Labelled cDNA was hybridized to Agilent zebrafish V2 expression microarrays according to manufacturers protocol.

scan_protocol: Microarrays were scanned using a GenePix 4000B scanner with GenePix Pro 6 software.

data_processing: Spot intensities were extracted using GenePix Pro 6 software and median spot intensities were normalized using the qspline algorithm in oneChannelGUI.

label: Alexa Fluor 555

organism: Danio rerio

source_name: Whole sphere stage embryo

label_protocol: Alexa Fluor 555 labelled cDNA was produced from 15µg total RNA using Invitrogen Superscript Plus Direct cDNA labelling system according to manufacturers protocol.

growth_protocol: Embyos were maintained in E3 embryo medium at 28.5 degrees celcius

extract_protocol: 200 embryos were lysed in 1ml Trizol and total RNA extracted according to manufacturers protocol. RNA was then cleaned using QIAGEN Rneasy columns.

value: AB

value: sphere

value: 1nl water containing 50pg ndr1 mRNA


title: [abdominal fat tissue]-[Lipocalin13 + TSC22D4 shRNA]-[14]

value: BKS.Cg-Dock7m +/+ Leprdb/J (000642)


title: Fetal liver wild-type rep6


title: sphere_ndr1-inj_rep3


title: sphere_ndr1-inj_rep1


title: Normal_Colon-CN_059_MT

tag: who performance status

tag: tumor location

value: Left colon

tag: pn


title: Normal_Colon-CN_044_MB

value: Female

tag: pt

tag: folfiri status


title: [abdominal fat tissue]-[TSC22D4 shRNA]-[11]

source_name: TSC_KD_abdominal fat

tag: strain background

value: 12 weeks

tag: treated with

value: 2x10^9 TSC22D4 shRNA + 2x10^9 control shRNA

value: TSC22D4 knockdown


title: Normal_Colon-CN_061_CM

tag: tissue

value: Normal Colon

value: Male

value: Moderate


title: [abdominal fat tissue]-[TSC22D4 shRNA]-[12]

tag: genotype/variation


title: Fetal liver wild-type rep2

tag: gender

value: 129/S6 (taconic)


title: sphere_cont-inj_rep3

tag: treatment

value: 1nl water


title: Normal_Colon-CN_213_RG

tag: patient number

value: NR


title: Normal_Colon-CN_115_CB

tag: Sex

value: Right colon

value: R


title: Normal_Colon-CN_026_SA


title: Normal_Colon-CN_089_NC

value: Transverse colon

tag: differentiation


title: Normal_Colon-CN_073_PD

tag: age

value: Well


title: sphere_cont-inj_rep2

tag: strain

value: AB

value: sphere


title: [abdominal fat tissue]-[TSC22D4 shRNA]-[10]

value: BKS.Cg-Dock7m +/+ Leprdb/J (000642)

value: abdominal fat


title: [abdominal fat tissue]-[Lipocalin13 shRNA]-[5]

source_name: Lipo_KD_abdominal fat

value: 12 weeks

value: 2x10^9 LCN13 shRNA + 2x10^9 control shRNA

value: LCN13 knockdown


title: Normal_Colon-CN_022_JB

value: Normal Colon

value: Female

value: Left colon


title: sphere_cont-inj_rep1

tag: developmental stage


title: [abdominal fat tissue]-[Lipocalin13 shRNA]-[8]


title: Fetal liver wild-type rep3

value: Male

value: 129/S6 (taconic)

value: Liver

value: 18.5 days post coitum

value: Wild-type


title: Fetal liver wild-type rep1


title: [abdominal fat tissue]-[NC shRNA]-[3]

source_name: control_abdominal fat

value: 4x10^9 control shRNA

value: WT


title: heart_OFT_Superior_7

city: Marseille

first: Magali

address: Parc Scientifique de Luminy

department: Aix Marseille Université

institute: Institut de Biologie du Développement de Marseille

description:
Regions from six littermate embryos were combined
UP7

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

scan_protocol: Microarrays were scanned using Affymetrix GeneChip Scanner 3000 (Affymetrix Inc. Santa Clara, CA95051, USA)

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

source_name: Heart, excised superior OFT, pool 7

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

extract_protocol: OFT subdomains of E10.5 embryonic mouse hearts were dissected in cold Rnase free PBS.Pooled samples were homogenized and RNA extracted using Trizol before cleaning using the RNeasy cleanup kit (QIAgen).

value: heart

tag: heart subregion

value: OFT subdomain

value: embryonic E10.5


title: seedlings of 2-week-old RECA1-overexpressing transgenic plants, biological rep1

city: Seoul

first: Hyesung

last: Jeon

address: Shillim-Dong

department: Agricutural Biotechnology

country: South Korea

institute: Seoul National University

description: Gene expression data from 2-week-old RECA1-overexpressing transgenic arabidopsis

hyb_protocol: Following fragmentation, 10ug of cRNA were hybiridized for 16 h at 45˚C on Affymetrix ATH1 genome arrays using and Affymetrix Fluidics Station 450

scan_protocol: Gene Chip were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suit version 5.0 (MAS 5.0) using Affymetrix default analysis setting and Quantile as nomalization method.

organism: Arabidopsis thaliana

source_name: RECA1-overexpressing transgenic plants

label_protocol: Five microgram of total RNA was used to generate double-stranded cDNA using GeneChip one-cycle cDNA synthesis kit (Affymetrix) with T7 promoter-containing oligo(dT)primer. Synthesized cDNA was in vitro transcribed and biotinylated using the GeneChip IVT labelilng kit (Affymetrix).

growth_protocol: Seeds were sterlized and plated on 1/2 MS medium, and then stratified for 4 days before growing in a growth in a growth camber at 23˚C under long day conditions (16 h light and 8 h dark).

extract_protocol: Total RNA was extracted from 2-week-old Arabidopsis seedling using RNeasy mini kit (Qiagen).

treatment_protocol: without any treatments

tag: ecotype

tag: genotype

value: RECA1 overexpression

value: seedlings


title: [abdominal fat tissue]-[Lipocalin13 shRNA]-[6]

value: BKS.Cg-Dock7m +/+ Leprdb/J (000642)

value: 12 weeks

value: 2x10^9 LCN13 shRNA + 2x10^9 control shRNA

value: abdominal fat


title: Normal_Colon-CN_016_MV

value: Normal Colon

value: Female

tag: who performance status

tag: tumor location

value: Left colon

value: Well

tag: pn

tag: pt

value: R


title: heart_OFT_Inferior_7

description:
Regions from six littermate embryos were combined
DOWN7

source_name: Heart, excised inferior OFT, pool 7

tag: tissue


title: seedlings of 2-week-old Col-0, biological rep2

description: Gene expression data from 2-week-old Col-0

source_name: Arabidopsis thaliana ecotype Columbia-0

value: wild type


title: seedlings of 2-week-old RECA1-overexpressing transgenic plants, biological rep2


title: heart_OFT_Inferior_1

description:
Regions from six littermate embryos were combined
DOWN1

source_name: Heart, excised inferior OFT, pool 1


title: heart_OFT_Superior_6

description:
Regions from six littermate embryos were combined
UP6

source_name: Heart, excised superior OFT, pool 6


title: heart_OFT_Superior_1

description:
Regions from six littermate embryos were combined
UP1

source_name: Heart, excised superior OFT, pool 1


title: heart_OFT_Inferior_6

description:
Regions from six littermate embryos were combined
DOWN6

source_name: Heart, excised inferior OFT, pool 6


title: seedlings of 2-week-old Col-0, biological rep1


title: [abdominal fat tissue]-[NC shRNA]-[1]

tag: strain background

tag: treated with

value: 4x10^9 control shRNA

tag: genotype/variation


title: Breast Cancer Sample BC2048

status: Public on Oct 14 2014

city: Frankfurt

first: Thomas

last: Karn

address: Theodor-Stern-Kai 7

description: Gene expression data from primary breast tumors

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133a Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: primary breast cancer tissue

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturers instructions

extract_protocol: RNeasy kit, Qiagen. according to the manufacturer's instructions

treatment_protocol: samples were snap frozen and stored at -80°C

tag: gender

value: female

value: pretreatment excision biopsy

tag: cell type

value: invasive mammary carcinoma


title: Breast Cancer Sample BC2053


title: Breast Cancer Sample BC2345


title: Breast Cancer Sample BC2029


title: [abdominal fat tissue]-[NC shRNA]-[2]

value: WT


title: Breast Cancer Sample BC2025


title: Breast Cancer Sample BC2032


title: Breast Cancer Sample BC1951


title: Breast Cancer Sample BC1954


title: Breast Cancer Sample BC1987


title: Breast Cancer Sample BC1992


title: Breast Cancer Sample BC1943


title: Breast Cancer Sample BC1947


title: Breast Cancer Sample BC1933


title: Breast Cancer Sample BC2027


title: Breast Cancer Sample BC2030


title: Breast Cancer Sample BC1948


title: Breast Cancer Sample BC1927


title: Breast Cancer Sample BC1938


title: Breast Cancer Sample BC1989


title: Breast Cancer Sample BC1939


title: Breast Cancer Sample BC1934


title: Breast Cancer Sample BC1949


title: Breast Cancer Sample BC1930


title: Breast Cancer Sample BC1926


title: Breast Cancer Sample BC1896


title: Breast Cancer Sample BC1897


title: Breast Cancer Sample BC1929


title: Breast Cancer Sample BC1889


title: Breast Cancer Sample BC1892


title: Breast Cancer Sample BC1898


title: Breast Cancer Sample BC1894


title: Breast Cancer Sample BC1895


title: Breast Cancer Sample BC1776


title: Breast Cancer Sample BC1777


title: Breast Cancer Sample BC1888


title: Breast Cancer Sample BC1765


title: Breast Cancer Sample BC1768


title: Breast Cancer Sample BC1904


title: Breast Cancer Sample BC1769


title: Breast Cancer Sample BC1763


title: Breast Cancer Sample BC1748


title: Breast Cancer Sample BC1764


title: Breast Cancer Sample BC1750


title: Breast Cancer Sample BC1775


title: Breast Cancer Sample BC1766


title: Tumor R-163


title: Tumor R-97


title: Tumor R-147


title: Breast Cancer Sample BC1755


title: Tumor R-149


title: Tumor R-47


title: Tumor R-51


title: Tumor R-45


title: Tumor R-151


title: Tumor R-41


title: Breast Cancer Sample BC1732


title: Tumor R-37


title: Tumor R-59


title: Tumor R-38


title: Tumor R-42


title: Tumor R-40


title: Tumor R-39


title: Tumor R-83


title: Tumor R-33


title: Tumor R-35


title: Tumor R-32


title: Tumor R-28


title: Tumor R-36


title: Tumor R-30


title: Tumor R-26


title: Tumor R-25


title: Tumor R-21


title: Tumor R-27


title: Tumor R-29


title: Tumor R-23


title: Tumor R-34


title: Tumor R-18


title: Tumor R-17


title: Tumor R-31


title: Tumor R-19


title: Tumor R-22


title: Tumor R-20


title: Tumor R-24


title: Tumor R-16


title: Tumor R-12


title: Tumor R-13


title: Tumor R-11


title: Tumor R-10


title: Tumor R-15


title: Tumor R-7


title: Tumor R-14


title: Tumor R-9


title: Tumor R-8


title: Tumor R-6


title: Tumor R-5


title: Tumor R-4


title: Tumor R-2


title: Tumor R-3


title: Tumor R-179


title: Tumor R-176


title: Tumor R-172


title: Tumor R-170


title: Tumor R-156


title: Tumor R-166


title: Tumor R-161


title: Tumor R-154


title: Tumor R-174


title: Tumor R-144


title: Tumor R-153


title: Tumor R-1


title: Tumor R-137


title: Tumor R-139


title: Tumor R-134


title: Tumor R-142


title: Tumor R-138


title: Tumor R-132


title: Tumor R-131


title: Tumor R-133


title: Tumor R-128


title: Tumor R-113


title: Tumor R-130


title: Tumor R-114


title: Tumor R-124


title: Tumor R-117


title: Tumor R-109


title: Tumor R-115


title: Tumor R-90


title: Tumor R-94


title: Tumor R-72


title: Tumor R-96


title: Tumor R-104


title: Tumor R-100


title: Tumor R-85


title: Tumor R-79


title: Tumor R-70


title: Tumor R-106


title: Tumor R-80


title: Tumor R-89


title: Tumor R-76


title: Tumor R-58


title: Tumor R-169


title: Tumor R-63


title: Tumor R-71


title: Tumor R-82


title: Tumor R-66


title: Tumor R-57


title: Tumor R-173


title: Tumor R-178


title: Tumor R-171


title: Tumor R-167


title: Heart from a 10 week old adult mouse,Biological Rep2, Technical Rep 2

first: Junhyong

address: 433 S University Avenue

department: Biology

description: Gene expression data from 10 weeks old mouse Heart

hyb_protocol: Without fragmentation, 5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430.2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000and the outpout files analyzed via Affymetrix GeneChip Operating Software (GCOS), v 1.4

data_processing: The expression intensities of the probes were summarized using the upper decile statistic by using Affymetrix RMA 2.0 methods. All the arrays were median centered and scaled by the range of expression values between the 10th and the 90th percentile in each array.

source_name: Heart from a 10 week old adult mouse, Biological Rep4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using a total of  5µg of aRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Hippocampus and heart tissue dissected from 7 days old mouse (C57/BL6).

extract_protocol: Mouse tissue samples (C57BL/6, Charles River Laboratories, Inc.) were isolated and stored immediately at -80°C. Subsequently, the mRNA was isolated using TRIzol Reagent and MicroFastTrack 2.0 Kit (Invitrogen). The integrity of these mRNA samples was evaluated with an Agilent Technologies 2100 Bioanalyzer and RNA Nano Lab Chip.  mRNA from hippocampal and heart tissue of  10 weeks old male mouse (C57/BL6) was purchased from Zyagen.

value: Heart

value: 10 weeks old male


title: Tumor R-46


title: Tumor R-50


title: Tumor R-159


title: Heart from a 10 week old adult mouse,Biological Rep2, Technical Rep 1

source_name: Heart from a 10 week old adult mouse, Biological Rep3


title: Tumor R-155


title: Tumor R-164


title: Tumor R-157


title: Tumor R-162


title: Tumor R-165


title: Heart from a 10 week old adult mouse, Biological Rep1, Technical Rep 1


title: Tumor R-150


title: Tumor R-152


title: Hippocampus from a 10 week old adult mouse, Biological Rep1, Technical Rep 1

description: Gene expression data from 10 weeks old mouse hippocampus

value: Hippocampus


title: Hippocampus from a 10 week old adult mouse, Biological Rep1, Technical Rep 2

source_name: Hippocampus from a 10 week old adult mouse, Biological Rep2


title: Hippocampus from a 10 week old adult mouse, Biological Rep2, Technical Rep 1

source_name: Hippocampus from a 10 week old adult mouse, Biological Rep3


title: Tumor R-145


title: Tumor R-146


title: Hippocampus from a 10 week old adult mouse, Biological Rep2, Technical Rep 2

source_name: Hippocampus from a 10 week old adult mouse, Biological Rep4


title: Heart from a 10 week old adult mouse, Biological Rep1, Technical Rep 2

source_name: Heart from a 10 week old adult mouse, Biological Rep2


title: Tumor R-148


title: Tumor R-143


title: Heart from a one week old pup mouse, Biological Rep3

description: Gene expression data from 7 days old mouse heart

value: 7 days old pup


title: Heart from a one week old pup mouse, Biological Rep1


title: Heart from a one week old pup mouse, Biological Rep2


title: Tumor R-141


title: Tumor R-123


title: Tumor R-125


title: Tumor R-135


title: Tumor R-122


title: Tumor R-129


title: Hippocampus from a one week old pup mouse, Biological Rep2

description: Gene expression data from 7 days old mouse hippocampus


title: Tumor R-136


title: Hippocampus from a one week old pup mouse, Biological Rep1


title: Tumor R-126


title: Tumor R-121


title: Tumor R-119


title: Tumor R-140


title: C57BL6 mouse, 1 cell body from a neuron, biological rep3

description: Gene expression data from soma dissected from mouse hippocampal neurons

source_name: One single cell body dissected from a mouse hippocampal neuron from primary culture

growth_protocol: Hippocampal primary cultures from mouse E18 (C57BL/6 and Balb/c Charles River Laboratories, Inc.).These dispersed primary cultures allowed single-cell harvesting using glass pipette dissections. One signle cell body (soma) was dissected from one pyramidal neuron.

extract_protocol: All dissected somas samples were assessed through standard aRNA amplification methods. After two rounds of amplification, a final aRNA amplification was performed with the Ambion Illumina TotalPrep RNA Amplification kit with an incubation time of 14 h. The integrity of these aRNA samples was evaluated with an Agilent Technologies 2100 Bioanalyzer and RNA Nano Lab Chip.

value: hippocampal neurons

value: Pyramidal neurons

value: 14 days old primary cultures of neurons from mouse embryos, E18


title: Hippocampus from a one week old pup mouse, Biological Rep3


title: Tumor R-116


title: Tumor R-112


title: Tumor R-107


title: Tumor R-111


title: Tumor R-118


title: C57BL6 mouse, 1 cell body from a neuron, biological rep1


title: Tumor R-108


title: Tumor R-110


title: Tumor R-120


title: C57BL6 mouse, 1 cell body from a neuron, biological rep2


title: C57BL6 mouse, pool of 400 dendrites, biological rep4

description: Gene expression data from dendrites dissected from mouse hippocampal neurons

source_name: Pool of dendrites dissected from primary cuture of hippocampal neurons from mouse embryos

growth_protocol: Hippocampal primary cultures from mouse E18 (C57BL/6 and Balb/c Charles River Laboratories, Inc.).These dispersed primary cultures allowed single-cell harvesting using glass pipette dissections. A pool of 100-400 dendrites were collected across multiple cells.

extract_protocol: All dissected dendrite samples were assessed through standard aRNA amplification methods. After two rounds of amplification, a final aRNA amplification was performed with the Ambion Illumina TotalPrep RNA Amplification kit with an incubation time of 14 h. The integrity of these aRNA samples was evaluated with an Agilent Technologies 2100 Bioanalyzer and RNA Nano Lab Chip.


title: C57BL6 mouse, pool of 400 dendrites, biological rep5


title: C57BL6 mouse, pool of 400 dendrites, biological rep3


title: Tumor R-98


title: Tumor R-102


title: Tumor R-103


title: Tumor R-99


title: Tumor R-93


title: C57BL6 mouse, pool of 200 dendrites, biological rep5


title: Tumor R-88


title: C57BL6 mouse, pool of 200 dendrites, biological rep4


title: C57BL6 mouse, pool of 400 dendrites, biological rep2


title: Tumor R-91


title: C57BL6 mouse, pool of 200 dendrites, biological rep2


title: Tumor R-81


title: Tumor R-84


title: C57BL6 mouse, pool of 200 dendrites, biological rep3


title: Tumor R-105


title: C57BL6 mouse, pool of 100 dendrites, biological rep2


title: Tumor R-74


title: C57BL6 mouse, pool of 100 dendrites, biological rep4


title: C57BL6 mouse, pool of 100 dendrites, biological rep3


title: Tumor R-92


title: C57BL6 mouse, pool of 100 dendrites, biological rep1


title: Tumor R-87


title: Tumor R-73


title: Tumor R-78


title: Tumor R-95


title: Tumor R-67


title: Tumor R-68


title: Tumor R-69


title: BalbC mouse, pool of 400 dendrites, biological rep2

value: Balb/C


title: C57BL6 mouse, pool of 400 dendrites, biological rep1


title: Tumor R-54


title: Tumor R-60


title: Tumor R-56


title: C57BL6 mouse, pool of 200 dendrites, biological rep1


title: Tumor R-75


title: Tumor R-64


title: Tumor R-55


title: Tumor R-61


title: Tumor R-48


title: BalbC mouse, pool of 400 dendrites, biological rep1


title: BalbC mouse, pool of 100 dendrites, biological rep2


title: Tumor R-49


title: BalbC mouse, pool of 200 dendrites, biological rep1


title: Tumor R-44


title: Tumor R-62


title: Tumor R-77


title: Tumor R-52


title: Tumor R-43


title: Tumor R-65


title: C57BL6 mouse cortex, 0.1 pg of mRNA, 4 rounds of aRNA amplification 4C2

description: Gene expression data from adult mouse cortex

hyb_protocol: Without fragmentation, 5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Rat 230.2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Mouse female adult cortex

extract_protocol: Mouse adult female brain’s cortex (C57BL/6, Charles River Laboratories, Inc.) was isolated and stored immediately at -80°C. Subsequently, the mRNA (15µg) was isolated using TRIzol Reagent and MicroFastTrack 2.0 Kit (Invitrogen). diluted to single-cell RNA levels (0.1, 1, and 10 pg) samples were assessed through standard aRNA amplification methods. After two rounds of amplification, a final aRNA amplification was performed with the Ambion Illumina TotalPrep RNA Amplification kit with an incubation time of 14 h. The integrity of these aRNA samples was evaluated with an Agilent Technologies 2100 Bioanalyzer and RNA Nano Lab Chip.

value: Cortex

value: Adult, Female


title: BalbC mouse, pool of 100 dendrites, biological rep1

source_name: Pool of dendrites dissected from hippocampal neurons from primary culture  of from mouse embryos


title: Tumor R-53


title: C57BL6 mouse cortex, 0.1 pg of mRNA, 4 rounds of aRNA amplification 4C3

growth_protocol: Mouse adult female brain’s cortex (C57BL/6, Charles River Laboratories, Inc.) was isolated and stored immediately at -80°C.


title: C57BL6 mouse cortex, 0.1 pg of mRNA, 4 rounds of aRNA amplification 4C1


title: Rice ZH11-ABA8ox3 RNAi-0 h

city: Guangzhou

first: Guohui

last: Zhu

state: Guangdong

address: Wushan Rd, Tianhe

department: College of Life Sciences

country: China

institute: South China Agricultural University

description:
Sample name: Interference_1
Gene expression data from ZH11 ABA8ox3 RNAi normal condition

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: Rice leaf, ABA8ox3 RNAi-0 h

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Rice were grown in a greenhouse at day/night temperature of 28/24℃ with 14-h day and 10-h night periods

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The seedlings sampled at 0 h and 2 h after 20% PEG treatment from WT and OsABA8ox3 RNAi line were used for DNA microarray analysis

value: seedling

value: ZH11, ABA8ox3 RNAi

tag: stress

value: control

tag: time

value: leaf


title: Heart from a 10 week old adult rat, Biological Rep2, Technical Rep 2

description: Gene expression data from 10 weeks old rat Heart

organism: Rattus norvegicus

source_name: Heart from a 10 week old adult rat, Biological Rep4

growth_protocol: Hippocampus and heart tissue dissected from 7 days old rat (Sprague Dawley). These dispersed primary cultures allowed single-cell harvesting using glass pipette dissections. One signle cell body (soma) was dissected from one pyramidal neuron.

extract_protocol: Rat tissue samples ( Sprague Dawley), Charles River Laboratories, Inc.) were isolated and stored immediately at -80°C. Subsequently, the mRNA was isolated using TRIzol Reagent and MicroFastTrack 2.0 Kit (Invitrogen). The integrity of these mRNA samples was evaluated with an Agilent Technologies 2100 Bioanalyzer and RNA Nano Lab Chip. mRNA of Hippocampal and Heart tissue from 10 weeks old male  rat (Sprague Dawley) were purchased from Zyagen.

value: Sprague-Dawley

tag: age


title: Hippocampus from a 10 week old adult rat, Biological Rep2, Technical Rep 1

description: Gene expression data from 10 weeks old rat hippocampus

source_name: Hippocampus from a 10 week old adult rat, Biological Rep3


title: C57BL6 mouse cortex, 1 pg of mRNA, 4 rounds of aRNA amplification 4B2

tag: strain


title: Rice ZH11-ABA8ox3 RNAi-PEG-2h

description:
Sample name: Interference_2
Gene expression data from ZH11 ABA8ox3 RNAi drought stress for 2h

source_name: Rice leaf, ABA8ox3 RNAi-PEG-2h

tag: developmental stage

value: drought


title: C57BL6 mouse cortex, 10 pg of mRNA, 4 rounds of aRNA amplification 4A3


title: Heart from a one week old pup rat, Biological Rep3

description: Gene expression data from 7 days old rat heart


title: Heart from a 10 week old adult rat, Biological Rep1, Technical Rep 2

source_name: Heart from a 10 week old adult rat, Biological Rep2


title: Heart from a one week old pup rat, Biological Rep2


title: Heart from a 10 week old adult rat, Biological Rep1, Technical Rep 1


title: Heart from a 10 week old adult rat, Biological Rep2, Technical Rep 1

source_name: Heart from a 10 week old adult rat, Biological Rep3


title: C57BL6 mouse cortex, 1 pg of mRNA, 4 rounds of aRNA amplification 4B3


title: Heart from a one week old pup rat, Biological Rep1


title: C57BL6 mouse cortex, 1 pg of mRNA, 4 rounds of aRNA amplification 4B1


title: C57BL6 mouse cortex, 10 pg of mRNA, 4 rounds of aRNA amplification 4A2


title: Hippocampus from a 10 week old adult rat, Biological Rep1, Technical Rep 1


title: Rice ZH11-wild type-PEG-2h

description:
Sample name: Ctrl_2
Gene expression data from ZH11 wild type drought stress for 2h

source_name: Rice leaf, PEG, 2h

value: ZH11, wild type


title: Hippocampus from a 10 week old adult rat, Biological Rep2, Technical Rep 2

source_name: Hippocampus from a 10 week old adult rat, Biological Rep4


title: Hippocampus from a one week old pup rat, Biological Rep3

description: Gene expression data from 7 days old rat hippocampus


title: Hippocampus from a one week old pup rat, Biological Rep1


title: Hippocampus from a one week old pup rat, Biological Rep2


title: C57BL6 mouse cortex, 10 pg of mRNA, 4 rounds of aRNA amplification 4A1


title: C57BL6 mouse cortex, 0.1 pg of mRNA, 2 Rounds of aRNA amplification 2C-3


title: Hippocampus from a 10 week old adult rat, Biological Rep1, Technical Rep 2

source_name: Hippocampus from a 10 week old adult rat, Biological Rep2


title: Sprague Dawley Rat, 1 cell body from a neuron, biological rep2

description: Gene expression data from soma dissected from a single  rat hippocampal neuron

source_name: One single cell body dissected from a rat hippocampal neuron from primary culture

growth_protocol: Hippocampal primary cultures from rat E19 (Sprague-Dawley Charles River Laboratories, Inc.). These dispersed primary cultures allowed single-cell harvesting using glass pipette dissections. One signle cell body (soma) was dissected from one pyramidal neuron.

value: 14 days old primary cultures of neurons from rat embryos, E19


title: Sprague Dawley Rat, 1 cell body from a neuron, biological rep3


title: C57BL6 mouse cortex, 0.1 pg of mRNA, 2 Rounds of aRNA amplification 2C-2


title: C57BL6 mouse cortex, 0.1 pg of mRNA, 2 Rounds of aRNA amplification 2C-1


title: Rat, pool of 400 dendrites, biological rep2

description: Gene expression data from dendrites dissected from rat hippocampal neurons

source_name: Pool of dendrites dissected from rat hippocampal neurons from primary cuture

growth_protocol: Hippocampal primary cultures from rat E19 (Sprague-Dawley Charles River Laboratories, Inc.). These dispersed primary cultures allowed single-cell harvesting using glass pipette dissections. A pool of 100-400 dendrites were collected across multiple cells.

extract_protocol: All dissected dendrites samples were assessed through standard aRNA amplification methods. After two rounds of amplification, a final aRNA amplification was performed with the Ambion Illumina TotalPrep RNA Amplification kit with an incubation time of 14 h. The integrity of these aRNA samples was evaluated with an Agilent Technologies 2100 Bioanalyzer and RNA Nano Lab Chip.


title: C57BL6 mouse cortex, 1 pg of mRNA, 2 Rounds of aRNA amplification 2B-3


title: Rat, pool of 200 dendrites, biological rep2


title: Rat, pool of 400 dendrites, biological rep3


title: Rat, pool of 100 dendrites, biological rep3


title: Sprague Dawley Rat, 1 cell body from a neuron, biological rep1


title: Rat, pool of 200 dendrites, biological rep3


title: Rat, pool of 100 dendrites, biological rep1


title: C57BL6 mouse cortex, 1 pg of mRNA, 2 Rounds of aRNA amplification 2B-2


title: IPF_transplant_rep29

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: IPF lung transplant

hyb_protocol: cRNA was hybridized on Agilent-014850 Whole Human Genome Microarray G4112F.

scan_protocol: Chips were scanned using the Agilent Surescan Microarray Scanner.

data_processing: The data were processed with Agilent Feature Extraction software, version 10.7.3.1, using default settings, including linear and Lowess normalization.

source_name: lung tissue

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

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Samples were not treated experimentally.

tag: disease state

value: idiopathic pulmonary fibrosis

value: lung

tag: diagnosis

value: IPF

tag: source

value: transplant

value: Male

molecule: polyA RNA

source_name: Stratagene Universal Human Reference RNA (catalog number 740000)

tag: sample type


title: C57BL6 mouse cortex, 1 pg of mRNA, 2 Rounds of aRNA amplification 2B-1


title: Rat, pool of 400 dendrites, biological rep1

value: hippocampal neurons

value: Pyramidal neurons


title: C57BL6 mouse cortex, 5ug of bulk mRNA wirh  no aRNA amplification 1A

value: Cortex


title: IPF_biopsy_rep11

description: IPF lung biopsy

value: biopsy

value: Stratagene Universal Human Reference RNA (catalog number 740000)


title: Setd2 knockout mESCs, biological rep3

city: Shanghai

first: Qiuhua

last: Huang

address: 197 ruijin road II

institute: Shanghai Institute of Hematology

description: Gene expression data from Setd2 knockout mESCsbiological rep3.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® mouse genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and use Gene Spring Software 11 to normalize data. The trimmed mean target intensity of each array was set to log2.

source_name: Setd2 knockout mESCs, biological rep3

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: Setd2 wt and ko mESCs were cultured on feeder cells in standard ES medium,then trypsinized ES cells were transferred on gelatin-coated cell culture dish, cultured for half an hour, then supernatant ES cells were collected and transferred to new gelatin-coated cell culture dish for 1 passage to maximumly remove feeder cells,two days later, mESCs were collected for microarray analysis.

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

treatment_protocol: No specific treatment

value: murine embryonic stem cells

tag: genotype

value: knockout


title: C57BL6 mouse cortex, 10 pg of mRNA, 2 Rounds of aRNA amplification 2A

value: Adult, Female


title: IPF_transplant_rep28

description: IPF lung transplant


title: Rat, pool of 100 dendrites, biological rep2

value: Sprague-Dawley


title: Rat, pool of 200 dendrites, biological rep1


title: Setd2 knockout mESCs, biological rep1

description: Gene expression data from Setd2 knockout mESCsbiological rep1.

source_name: Setd2 knockout mESCs, biological rep1


title: IPF_transplant_rep27

description: IPF lung transplant


title: IPF_biopsy_rep10

description: IPF lung biopsy


title: IPF_transplant_rep26

description: IPF lung transplant


title: Setd2 knockout mESCs, biological rep2

description: Gene expression data from Setd2 knockout mESCsbiological rep2.

source_name: Setd2 knockout mESCs, biological rep2


title: control_necropsy_rep7

description: control lung necropsy

value: control

value: necropsy


title: control_necropsy_rep8

description: control lung necropsy


title: Setd2 wild type mESCs, biological rep3

description: Gene expression data from Setd2 wild type mESCsbiological rep3.

source_name: Setd2 wild type mESCs, biological rep3

value: Wild type


title: IPF_transplant_rep25

description: IPF lung transplant

value: idiopathic pulmonary fibrosis

value: Female


title: Setd2 wild type mESCs, biological rep1

description: Gene expression data from Setd2 wild type mESCsbiological rep1.

source_name: Setd2 wild type mESCs, biological rep1


title: IPF_transplant_rep24

description: IPF lung transplant

value: lung

value: IPF


title: IPF_transplant_rep23

description: IPF lung transplant

value: transplant

value: Male


title: Liver HF-Q replicate 10

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. Based on visual inspection three arrays were excluded; there was no homogenous hybridization on these arrays. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: liver tissue, high fat diet supplemented with 0.33 % (w/w) quercetin

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al., (Anal Biochem 2007;363:315-7).

extract_protocol: Total RNA was isolated from liver tissue using RNeasy Mini columns (Qiagen) according to the manufacturer’s instruction, quantified using Nanodrop (IsoGen Life Science) and qualified using Experion Automated Electrophoresis System (BioRad).

treatment_protocol: All mice started with a three week adaptation phase, in which they were fed a normal-fat diet. During the intervention the mice received a high-fat diet without (HF) or with supplementation of 0.33% (w/w) quercetin (HF-Q) for 12 weeks. Animals were fasted for 2-4 hr prior anaestetization and sacrification.

value: male

value: adult

value: liver

source_name: liver, reference pool of all samples


title: control_necropsy_rep6

description: control lung necropsy

value: Stratagene Universal Human Reference RNA (catalog number 740000)


title: Setd2 wild type mESCs, biological rep2

description: Gene expression data from Setd2 wild type mESCsbiological rep2.

source_name: Setd2 wild type mESCs, biological rep2

value: murine embryonic stem cells


title: IPF_transplant_rep22

description: IPF lung transplant


title: IPF_biopsy_rep9

description: IPF lung biopsy

value: biopsy


title: IPF_transplant_rep20

description: IPF lung transplant


title: IPF_transplant_rep21

description: IPF lung transplant


title: Liver HF-Q replicate 08


title: Liver HF-Q replicate 09


title: IPF_transplant_rep19

description: IPF lung transplant


title: IPF_biopsy_rep7

description: IPF lung biopsy


title: Liver HF-Q replicate 05


title: IPF_transplant_rep18

description: IPF lung transplant


title: IPF_transplant_rep16

description: IPF lung transplant


title: IPF_transplant_rep17

description: IPF lung transplant


title: control_necropsy_rep4

description: control lung necropsy


title: Liver HF-Q replicate 06


title: control_necropsy_rep3

description: control lung necropsy


title: control_necropsy_rep2

description: control lung necropsy


title: Liver HF-Q replicate 07


title: IPF_transplant_rep15

description: IPF lung transplant


title: IPF_biopsy_rep6

description: IPF lung biopsy


title: IPF_transplant_rep14

description: IPF lung transplant


title: IPF_transplant_rep12

description: IPF lung transplant


title: 6-IS

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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.

data_processing: RMA by software Partek

growth_protocol: Human podocyte cell line culture

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

tag: treatment

value: Indoxyl sulfate

value: Human podocyte cell line


title: IPF_biopsy_rep5

description: IPF lung biopsy

tag: tissue


title: 5-IS


title: Liver HF-Q replicate 03


title: Liver HF-Q replicate 01


title: Liver HF-Q replicate 02


title: IPF_transplant_rep13

description: IPF lung transplant


title: Rice ZH11-wild type-0 h

description:
Sample name: Ctrl_1
Gene expression data from ZH11 wild type normal condition

source_name: Rice leaf, 0h

value: seedling

value: ZH11, wild type

value: control

value: leaf


title: Liver HF-Q replicate 04


title: 4-IS


title: Liver HF replicate 11

source_name: liver tissue, high fat diet


title: IPF_biopsy_rep4

description: IPF lung biopsy

value: idiopathic pulmonary fibrosis

value: Female


title: IPF_transplant_rep10

description: IPF lung transplant

value: lung

value: IPF


title: IPF_transplant_rep11

description: IPF lung transplant

value: transplant

value: Male


title: 2-Control

value: Control


title: IPF_transplant_rep9

description: IPF lung transplant


title: control_necropsy_rep1

description: control lung necropsy

value: necropsy


title: 3-Control


title: Liver HF replicate 09

value: male

value: adult

value: liver


title: IPF_transplant_rep8

description: IPF lung transplant

value: Stratagene Universal Human Reference RNA (catalog number 740000)


title: 1-Control

value: Human podocyte cell line


title: IPF_transplant_rep7

description: IPF lung transplant


title: IPF_transplant_rep6

description: IPF lung transplant


title: Liver HF replicate 06


title: Liver HF replicate 10


title: Arabidopsis thaliana_35S::TCP1_1

city: Osnabrueck

first: Andrea

last: Busch

address: Barbarastrasse 11

department: Botany

institute: University Osnabrueck

description: gene expression in young inflorescence and floral stages altered (in comparison to WT/control) upon ectopic expression of the TCP transcription factor TCP1 from Arabidopsis thaliana

hyb_protocol: The prepared targets were hybridized overnight to Affymetrix Arabidopsis GeneChip ATH1 Genome arrays. Following hybridization, the arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Partek Genomics Suite was used for data anlyses. RMA normalisation, quantile normalisation

source_name: secondary inflorescence

label_protocol: for each sample 1-5 µg was sent to the Integrated Functional Genomics Service at the University of Münster, Germany, which carried out probe preparation, hybridization and statistical analysis of the data  The samples were amplified from 100 ng of total RNA in accordance with the Affymetrix´s protocol, fragmented and end-labeled in accordance with the Affymetrix Labeling protocol (Affymetrix UK Ltd., High Wycombe, UK).

growth_protocol: plants were grown on Einheitserde (type mini tray, Fröndenberg, Germany) in growth chambers (CLF plant climatics) at constant 20°C, 55% humidity and 13 hrs light per day

extract_protocol: inflorescences were flash frozen in liquid nitrogen, total RNA was isolated using NucleoSpin RNA XS kit (Machery and Nagel)

tag: cultivar

value: Columbia

value: secondary inflorescence

value: inflorescences with all flowers before anthesis

tag: transgenic plant

value: transgenic plants that carry AtTCP1 under the control of the CaMV35S-promotor (Busch A, Zachgo S:Control of corolla monosymmetry in the Brassicaceae Iberis amara. PNAS 2007, 104:16714-16719) in the pBAR vector (GenBank:AJ251014)

tag: transgenic generation

value: T2 line


title: Arabidopsis thaliana_35S::TCP1_2


title: Liver HF replicate 07

tag: gender


title: IPF_biopsy_rep3

description: IPF lung biopsy

value: idiopathic pulmonary fibrosis

value: biopsy


title: Arabidopsis thaliana_35S::IaTCP1_2

description: gene expression in young inflorescence and floral stages altered (in comparison to WT/control) upon ectopic and heterologous expression of the TCP transcription factor IaTCP1 from Iberis amara

value: transgenic plants that carry IaTCP1 under the control of the CaMV35S-promotor (Busch A, Zachgo S:Control of corolla monosymmetry in the Brassicaceae Iberis amara. PNAS 2007, 104:16714-16719) in the pBAR vector (GenBank:AJ251014)


title: IPF_transplant_rep5

description: IPF lung transplant

value: lung

value: IPF

value: transplant


title: Liver HF replicate 04


title: Arabidopsis thaliana_35S::CYC_2

description: gene expression in young inflorescence and floral stages altered (in comparison to WT/control) upon ectopic and heterologous expression of the TCP transcription factor CYCLOIDEA from Antirrhinum majus

value: transgenic plants that carry AmCYC under the control of the CaMV35S-promotor (Busch A, Zachgo S:Control of corolla monosymmetry in the Brassicaceae Iberis amara. PNAS 2007, 104:16714-16719) in the pBAR vector (GenBank:AJ251014)


title: Arabidopsis thaliana_35S::IaTCP1_1


title: Liver HF replicate 05

value: male


title: Arabidopsis thaliana_35S::CYC_1


title: Liver HF replicate 08

value: adult


title: Arabidopsis thaliana_control_2

description: gene expression was used as control

value: transgenic plants that carry the empty pBAR vector (GenBank:AJ251014)


title: IPF_biopsy_rep2

description: IPF lung biopsy

value: Male

value: Stratagene Universal Human Reference RNA (catalog number 740000)


title: Arabidopsis thaliana_control_1

description: gene expression was used as control

value: Columbia


title: IPF_transplant_rep4

description: IPF lung transplant


title: IPF_transplant_rep3

description: IPF lung transplant


title: ZM4 (ATCC31821) treated by 220 g/L glucose and 10mM sorbitol for 6 hours rep-3

city: chengdu

first: kun

last: zhang

state: sichuan

address: section 29，Wangjiang Rd.

institute: Sichuan University

description: This sample is of wild-type ZM4. It is the third of three wild-type biological replicates treated by 220 g/L glucose and 10mM sorbitol for 6 hours , each from separate cultures.

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

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

data_processing:
Image signals were transformed into digital signals by NimbleScan 2.6 software and corrected by normalization method of RMA (Robust Multichip Analysis) to remove variations. It’s necessary to note that the group will be filtered if all digital signals of its four types for any gene were below 400 of cutoff. In a comparison analysis, the significant analysis of microarray software (SAM, version 3.02) was performed to identify significantly differentially expressed genes between treated and control groups.
Genes were determined to be significantly differentially expressed with a selection threshold of false discovery rate: FDR <5 % and fold change ≥2 (significant induction) or ≤0.5 (significant repression).

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

source_name: ZM4 (ATCC31821)treated by 220 g/L glucose and 10mM sorbitol for 6 hours rep-3

label_protocol: The purified RNA from each sample was used as the template to generate cDNAs while labeled with Cy3-dUTP (CapitalBio).

growth_protocol: Z. mobilis ZM4 (ATCC31821) was cultured in Rich Media (RM)  at 30°C  for 24-48 hours without shaking.Goodman AE, Rogers PL, Skotnicki ML. Appl Environ Microbiol. 1982, 44(2):496 –498.

extract_protocol: Twelve samples representing four patterns of growth conditions in the exponential phase from ZM4 cultures were harvested by centrifugation and total cellular RNA was isolated using an RNA extraction kit (Kangwei century Biotech Co., Ltd., China).The remaining genomic DNA in the RNA samples was erased by following the manufacturer’s protocol (Takara Biotechnology (Dalian) Co., Ltd.). The RNA quality was evaluated by agarose gel electrophoresis and the ratio of its OD 260 to OD280 by a spectrophotometer, respectively.

treatment_protocol: The fresh cultures were subcultured to the inoculum media with 5% of the inoculation and cultivated for 16 h at 30°C.Then the appropriate amount of glucose and sorbitol was added when the ZM4 reached the midexponential phase. The initial concentrations were nearly 0, 220 g/L of glucose, 220 g/L of glucose and 10mM of sorbitol. The time of taking samples  was set at 6 hrs(0 g/L glucose), 8 hrs(220 g/L of glucose), 12 hrs(220 g/L of glucose and 10 mM of sorbitol), 20 hrs(220 g/L of glucose) after treatment, respectively.

value: wild type


title: Inflorescences_Trp1_rep2

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

institute: shenzhen university

hyb_protocol: Affymetrix ATH1 arrays were hybridized in three biological replicates according to the manufacturer's instructions.

scan_protocol: Standard Affymetrix protocol.

data_processing: The microarray data were analyzed using the R package affy (affy_1.34.0) from Bioconductor. The MAS5 method was used.

source_name: inflorescences, top1a-2 mutant

label_protocol: Standard Affymetrix protocol.

growth_protocol: All plants were grown at 23°C under continuous light.

extract_protocol: RNAs were isolated from wild-type and top1a-2 inflorescences. Inflorescences were ground and extracted with the TRI Reagent (Molecular Research Center). RNA was precipitated by isopropanol and treated with DNaseI (Roche) to eliminate contaminating DNA.

tag: ecotype

value: Landsberg erecta (Ler)

tag: genotype/variation

value: top1a-2 mutant

value: inflorescences


title: Inflorescences_Trp1_rep3


title: Inflorescences_ler_rep3

source_name: inflorescences, wild-type

value: wild-type


title: Liver HF replicate 01

value: liver


title: IPF_biopsy_rep8

description: IPF lung biopsy

value: idiopathic pulmonary fibrosis

value: biopsy

value: Female


title: Liver HF replicate 03


title: Inflorescences_ler_rep2


title: ZM4 (ATCC31821) treated by 220 g/L glucose for 14 hours rep-3

description: This sample is of wild-type ZM4. It is the third of three wild-type biological replicates treated by 220 g/L glucose for 14 hours, each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 220 g/L glucose for 14 hours rep-3


title: ZM4 (ATCC31821) treated by 220 g/L glucose and 10mM sorbitol for 6 hours rep-1

description: This sample is of wild-type ZM4. It is the first of three wild-type biological replicates treated by 220 g/L glucose and 10mM sorbitol for 6 hours , each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 220 g/L glucose and 10mM sorbitol for 6 hours rep-1


title: IPF_transplant_rep2

description: IPF lung transplant

source_name: lung tissue

value: lung

value: IPF

value: transplant

source_name: Stratagene Universal Human Reference RNA (catalog number 740000)


title: Liver HF replicate 02

value: male

value: adult


title: ZM4 (ATCC31821) treated by 220 g/L glucose and 10mM sorbitol for 6 hours rep-2

description: This sample is of wild-type ZM4. It is the second of three wild-type biological replicates treated by 220 g/L glucose and 10mM sorbitol for 6 hours , each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 220 g/L glucose and 10mM sorbitol for 6 hours rep-2


title: IPF_transplant_rep1

description: IPF lung transplant

value: Male


title: shCRABP2-2

city: Cleveland

first: Liraz

last: Levi

state: OH

address: 9500 Euclid Avenue

department: Cellular and Molecular Medicine

institute: Lerner Research Institute; Cleveland Clinic

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw data files were analyzed using Affymetrix Expression Console and Transcriptome Analysis Console. Signal intensities were normalized using Robust Multichip Average Method (RMA).

source_name: MCF-7 cell overexpressing shCRABP2

label_protocol: not provided

growth_protocol: Cells were maintained in Dulbecco’s Modification of Eagle’s Media (DMEM) containing  4.5 g/L glucose, 4.5 g/L L-glutamine, 10% fetal bovine serum (Life Technologies/Gibco), 100 I.U./mL penicillin, and 100 µg/mL streptomycin.

extract_protocol: RNA was extracted using RNeasy columns (Qiagen).

treatment_protocol: For retinoids deplation, FBS in the media was charcoal-treated. For lentiviral infection, MCF-7 cells were transduced with lentiviruses harboring the indicated shRNAs.  4 days post transduction, cells were harvested and RNA extracted.

tag: cell line

tag: cell type

value: breast cancer


title: control_necropsy_rep5

description: control lung necropsy

value: control

value: necropsy

value: Stratagene Universal Human Reference RNA (catalog number 740000)


title: Inflorescences_Trp1_rep1

value: Landsberg erecta (Ler)

value: top1a-2 mutant


title: ZM4 (ATCC31821) treated by 220 g/L glucose for 14 hours rep-1

description: This sample is of wild-type ZM4. It is the first of three wild-type biological replicates treated by 220 g/L glucose for 14 hours , each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 220 g/L glucose for 14 hours rep-1

value: wild type


title: Inflorescences_ler_rep1

value: wild-type

value: inflorescences


title: shCRABP2-3


title: ZM4 (ATCC31821) treated by 220 g/L glucose for 2 hours rep-3

description: This sample is of wild-type ZM4. It is the third of three wild-type biological replicates treated by 220 g/L glucose for 2 hours , each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 220 g/L glucose for 2 hours rep-3


title: shluc-6

source_name: MCF-7 cell overexpressing shluciferase


title: shCRABP2-1


title: ZM4 (ATCC31821) treated by 220 g/L glucose for 2 hours rep-2

description: This sample is of wild-type ZM4. It is the second of three wild-type biological replicates treated by 220 g/L glucose for 2 hours , each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 220 g/L glucose for 2 hours rep-2


title: ZM4 (ATCC31821) treated by 220 g/L glucose for 2 hours rep-1

description: This sample is of wild-type ZM4. It is the first of three wild-type biological replicates treated by 220 g/L glucose for 2 hours, each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 220 g/L glucose for 2 hours rep-1


title: ZM4 (ATCC31821) treated by 220 g/L glucose for 14 hours rep-2

description: This sample is of wild-type ZM4. It is the second of three wild-type biological replicates treated by 220 g/L glucose for 14 hours , each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 220 g/L glucose for 14 hours rep-2


title: IPF_biopsy_rep1

description: IPF lung biopsy

value: idiopathic pulmonary fibrosis

value: biopsy


title: shl-2 Pool 1, biological rep1

city: Pozuelo de Alarcon

first: Alfonso

last: Mouriz-Villar

state: Madrid

address: Campus de Montegancedo

department: Biotechnology

country: Spain

institute: INIA

description: Gene expression data from seedlings of shl-2-2 mutant plants grown in SD conditions

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (GENECHIP MODEL). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

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

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: seedlings from shl-2-2 mutant plants grown in SD conditions

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip 3' IVT Express Kit).

growth_protocol: Plants were grown for 18 days in solid MS medium and in SD conditions.

extract_protocol: The RNA from complete plants was isolated using EZNA Plant RNA kit from OMEGA bio-tek. RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies

treatment_protocol: No further treatment was applied to the samples before harvesting.

value: seedling

value: Landsberg erecta


title: shl-2 Pool 2, biological rep2


title: ZM4 (ATCC31821) treated by 0 g/L glucose for 0 hours rep-3

description: This sample is of wild-type ZM4. It is the third of three wild-type biological replicates without treat as control, each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 0 g/L glucose for 0 hours rep-3


title: shl-2 Pool 3, biological rep3


title: ZM4 (ATCC31821) treated by 0 g/L glucose for 0 hours rep-1

description: This sample is of wild-type ZM4. It is the first of three wild-type biological replicates without treat as control, each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 0 g/L glucose for 0 hours rep-1


title: ebs Pool 3, biological rep3

description: Gene expression data from seedlings of ebs mutant plants grown in SD conditions

source_name: seedlings from ebs mutant plants grown in SD conditions

value: ebs


title: shHuR-3

source_name: MCF-7 cell overexpressing shHuR


title: shluc-3


title: Ler Pool 3, biological rep3

description: Gene expression data from seedlings of wild type plants grown in SD conditions

source_name: seedlings from wild type plants grown in SD conditions


title: shluc-4


title: shHuR-1


title: ZM4 (ATCC31821) treated by 0 g/L glucose for 0 hours rep-2

description: This sample is of wild-type ZM4. It is the second of three wild-type biological replicates without treat as control, each from separate cultures.

source_name: ZM4 (ATCC31821)treated by 0 g/L glucose for 0 hours rep-2


title: shHuR-2


title: shluc-2


title: Ler Pool 2, biological rep2


title: ebs Pool 1, biological rep1


title: shluc-5


title: ebs Pool 2, biological rep2


title: Ler Pool 1, biological rep1


title: Mdx skeletal muscle, sActRIIB-Fc treatment for 7 weeks rep 4

status: Public on Oct 13 2014

city: Jyväskylä

first: Juha

middle: J

last: Hulmi

address: Rautpohjankatu 8a Viv

department: Biology of Physical Activity

country: Finland

institute: University of Jyväskylä

description: SAMPLE 23

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized with quantiles normalization (including log2-transformation of the data) and data quality was assessed using Chipster software (IT Center for Science, Espoo, Finland)

source_name: Mdx skeletal muscle_sActRIIB-Fc treatment for 7 wks

label_protocol: Biotinylated cRNA were  prepared with Illumina TotalPrep RNA Amplification Kit (Applied Biosystems cat # AMIL1791).

extract_protocol: Gastrocnemius muscle was pulverized and homogenized in liquid nitrogen and exactly 70 mg of muscle powder was weighted into Trizol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA and DNA fractions were extracted according to the manufacturer’s guidelines. The RNA and DNA concentrations were analyzed with Nanodrop ND-1000 (Thermo Fisher Scientific Inc., Waltham MA, USA) in duplicate. The quality of RNA was confirmed by spectrophotometry (OD260/OD280 ratio of 1.9 to 2.0) and agarose gel electrophoresis. Possible DNA still left was further degraded using DNAse according to the manufacturer’s instructions (TURBO DNA-free™ Kit, Applied Biosystems by Life Technologies, USA).

tag: strain

value: Mdx

value: male

tag: age

value: 6-7 weeks

tag: sample group

value: sActRIIB-Fc treatment for 7 weeks

value: gastrocnemius muscle


title: Mdx skeletal muscle, sActRIIB-Fc treatment for 7 weeks rep 5

description: SAMPLE 24


title: Mdx skeletal muscle, sActRIIB-Fc treatment for 7 weeks rep 2

description: SAMPLE 21


title: Mdx skeletal muscle, sActRIIB-Fc treatment for 7 weeks rep 3

description: SAMPLE 22


title: Mdx skeletal muscle, sActRIIB-Fc treatment for 7 weeks rep 1

description: SAMPLE 20


title: Mdx skeletal muscle, PBS treatment for 7 weeks rep 5

description: SAMPLE 19

source_name: Mdx skeletal muscle_PBS treatment for 7 wks

value: PBS treatment for 7 weeks


title: hu antr glands ext0678

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

description: Total gastrectomy

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 2.0 ST arrays.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with affymetrix Powertools (APT) using the rma sketch normalization procedure

source_name: Normal antral glands 2503

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with the Ambion® WT Expression Kit, according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Human gastric organoids were grown in Matrigel (BD Biosciences) and culture medium containing the following components: Advanced Dulbecco’s modified Eagle medium/F12 supplemented with penicillin/streptomycin, 10 mmol/L HEPES, Glutamax, 1xB27 (all from Invitrogen), N-Acetylcysteine 1 mM (Sigma-Aldrich), EGF 50 ng/mL (Invitrogen), Noggin conditioned medium 10%, R-spondin conditioned medium 10%, Wnt conditioned medium 50%, FGF10 200 ng/ml (Peprotech), Gastrin 1 nM (Tocris), TGFbeta-inhibitor 2 µM (A-83-01, Tocris) and Nicotinamide 10 mM (Sigma-Aldrich). After seeding RHOKi 10 µM (Y-27632, Sigma-Aldrich) was added.

extract_protocol: Total RNA from patient samples was purified by using the WT (Ambion, Life Technologies).

treatment_protocol: Organoids were either grown 14 days in full medium or 10 days in full medium and subsequently 4 days without Wnt. On day 14, organoids were either non-injected or microinjected with Helicobacter pylori strain P12 at MOI 50. Cells were lyzed after 2 h.

value: Normal antral glands


title: hu corp org ext0679

description: Total gastrectomy

source_name: Normal corpus organoids 2503

value: Normal corpus organoids


title: Mdx skeletal muscle, PBS treatment for 7 weeks rep 4

description: SAMPLE 18


title: shluc-1

value: breast cancer


title: Mdx skeletal muscle, PBS treatment for 7 weeks rep 3

description: SAMPLE 17


title: Mdx skeletal muscle, PBS treatment for 7 weeks rep 2

description: SAMPLE 16


title: hu antr org ext0676

description: Total gastrectomy

source_name: Normal antral organoids 2504

value: Normal antral organoids


title: hu corp glands ext0677

description: Total gastrectomy

source_name: Normal corpus glands 2503

value: Normal corpus glands


title: hu corp org ext0675

source_name: Normal corpus organoids 2504

tag: condition

value: Total gastrectomy


title: Mdx skeletal muscle, PBS treatment for 7 weeks rep 1

description: SAMPLE 15


title: Wildtype skeletal muscle, no treatment rep 4

description: SAMPLE 14

source_name: Wildtype skeletal muscle_no treatment

value: wild type without treatment (control)


title: hu antr org ext0680

description: Total gastrectomy

source_name: Normal antral organoids 2503


title: Wildtype skeletal muscle, no treatment rep 1

description: SAMPLE 11


title: Wildtype skeletal muscle, no treatment rep 3

description: SAMPLE 13


title: Wildtype skeletal muscle, no treatment rep 2

description: SAMPLE 12


title: hu corp glands ext0673

description: Total gastrectomy

source_name: Normal corpus glands 2504


title: Mdx skeletal muscle, sActRIIB-Fc + running for 7 weeks rep 3

description: SAMPLE 8

source_name: Mdx skeletal muscle_sActRIIB-Fc + running for 7 wks

value: sActRIIB-Fc + running for 7 weeks


title: Mdx skeletal muscle, sActRIIB-Fc + running for 7 weeks rep 5

description: SAMPLE 10


title: HuCorp Wnt HP ext0672

description: Male age 51. Gastric resection.

source_name: Normal corpus 2407

value: Normal corpus

value: Normal corpus Esophageal resection

value: organoids as in 2 but infected as in 3


title: UPSC-3.MRE

status: Public on Oct 12 2014

type: SRA

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

library_source: genomic

data_processing:
Sequencing reads were aligned to the hg19 (GRCh37) genome build with Bowtie.
For MeDIP-seq, redundant reads were discarded.
For MRE-seq, reads were filtered by MRE recognization site in genome.
Bed files were transformed to bigWig format.
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: Uterine endometrial cancer, UPSC, MRE

extract_protocol:
For MRE, DNA was isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA). Three parallel digests were performed (HpaII, AciI and Hin6I; Fermentas), each with 1μg of DNA. Five units of enzyme per microgram DNA were added and incubated at 37 °C in Fermentas Tango buffer for 3 h. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose TBE gel. A 100-300 bp gel slice was excised using a sterile scalpel and gel-purified using Qiagen QIAquick columns, eluting in 30 µl of Qiagen EB buffer.
Library construction was performed using the Illumina Genomic DNA Sample Kit (Illumina) with single-end adapters, following the manufacturer's instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the Klenow DNA polymerase was diluted 1:5 in water and 1 ul used per reaction. For single-end oligo adaptor ligation, adapters were diluted 1:10 in water and 1 ul used per reaction. Fifteen cycles of PCR were performed using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520bp) was performed by electrophoresis in DNA was eluted in 36 ul EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.

value: uterine endometrial cancer

tag: endometrial cancer type

value: uterine papillary serous carcinoma (UPSC)

tag: tumor grade


title: HuCorp Wnt HP ext0668

description: Female age 41. Gastric resection.

source_name: Normal corpus 2610

value: female


title: HuCorp Wnt NI ext0671

description: Male age 51. Gastric resection.

value: male

value: organoids as in 1 but differentiated for 4 days in differentiation condition ENR_FGNiTi (pit'type organoids) - 2


title: Mdx skeletal muscle, sActRIIB-Fc + running for 7 weeks rep 1

description: SAMPLE 6

value: Mdx

value: 6-7 weeks

value: gastrocnemius muscle


title: HuCorp noWnt NI ext0669

description: Male age 51. Gastric resection.

value: organoids in expansion condition ENRWFGNiTi (gland-type organoids) - 1


title: UPSC-2.MRE


title: Mdx skeletal muscle, PBS+running for 7 weeks rep 4

description: SAMPLE 4

source_name: Mdx skeletal muscle_PBS+running for 7 wks

value: PBS+running for 7 weeks


title: HuCorp Wnt NI ext0667

description: Female age 41. Gastric resection.


title: Mdx skeletal muscle, sActRIIB-Fc + running for 7 weeks rep 4

description: SAMPLE 9


title: HuCorp noWnt NI ext0665

description: Female age 41. Gastric resection.


title: Mdx skeletal muscle, sActRIIB-Fc + running for 7 weeks rep 2

description: SAMPLE 7


title: HuCorp Wnt HP ext0664

description: Female age 64. Esophageal resection.

source_name: Normal corpus 2510


title: HuCorp noWnt HP ext0670

description: Male age 51. Gastric resection.

value: organoids as in 1 but infected with Helicobacter pylori strain P12 MOI 50 for 2 h  - 3


title: UPSC-3.MeDIP

source_name: Uterine endometrial cancer, UPSC, MeDIP

extract_protocol:
For MeDIP, 5-15 μg DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA) was sonicated to ~100-500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 2-5 μg of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg ml-1, Eurogentec, catalog no. BI-MECY-0100). For this, DNA was heat-denatured at 95 °C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μl primary antibody per microgram of DNA overnight at 4 °C with rocking agitation in 500 μl immunoprecipitation buffer (10 mM sodium phosphate buffer, pH 7.0, 140 mM NaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 4 μl of rabbit anti-mouse IgG secondary antibody (2.5 mg ml-1, Jackson Immunoresearch, catalog no. 315-005-008) and 100 μl Protein A/G beads (Pierce Biotechnology, catalog no. PI20421) were added and incubated for an additional 2 h at 4 °C with agitation. After immunoprecipitation, a total of six immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg ml-1proteinase K for 2 h at 55 °C and then allowed to cool to room temperature. MeDIP and supernatant DNA were purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen).
Fifteen cycles of PCR were performed on 5 ul of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520bp) was performed by electrophoresis in DNA was eluted in 36 ul EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.


title: EAC-1.MRE

source_name: Uterine endometrial cancer, EAC, MRE

value: endometrioid adenocarcinoma (EAC)


title: UPSC-2.MeDIP


title: EAC-3.MRE


title: EAC-2.MRE


title: UPSC-1.MRE


title: UPSC-1.MeDIP


title: EAC-3.MeDIP

source_name: Uterine endometrial cancer, EAC, MeDIP


title: EAC-2.MeDIP


title: HuCorp Wnt NI ext0663

description: Female age 64. Esophageal resection.


title: Mdx skeletal muscle, PBS+running for 7 weeks rep 2

description: SAMPLE 2


title: Mdx skeletal muscle, PBS+running for 7 weeks rep 3

description: SAMPLE 3


title: HuCorp noWnt NI ext0661

description: Female age 64. Esophageal resection.


title: EAC-1.MeDIP


title: Mdx skeletal muscle, PBS+running for 7 weeks rep 1

description: SAMPLE 1


title: HuCorp noWnt HP ext0666

description: Female age 41. Gastric resection.


title: HuCorp noWnt HP ext0662

description: Female age 64. Esophageal resection.


title: Mdx skeletal muscle, PBS+running for 7 weeks rep 5

description: SAMPLE 5


title: Male_liver_tamoxifen_420ppm_12weeks_rep2

status: Public on Oct 11 2014

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

description: Gene expression in the livers of male WSB/EiJ mice treated with 420 p.p.m. tamoxifen for 12 weeks

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Oligo Microarrays (G4858A-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

source_name: Male, liver, tamoxifen, 420ppm, 12weeks, replicate 2

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

extract_protocol: Total RNA was extracted from liver tissue using RNeasy Mini kits (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were allocated randomly to receive either NIH-31 diet containing 420 p.p.m. tamoxifen (Dyets, Bethlehem, PA) or control NIH-31 diet. Experimental and control mice were euthanized by exsanguination following deep isoflurane anesthesia 12 weeks after diet initiation. The liver was snap-frozen immediately in liquid nitrogen and stored at −80 °C for subsequent analyses.

value: WSB/EiJ

value: liver

value: Male

value: 18 weeks


title: Male_liver_control_rep1

description: Gene expression in the livers of control male WSB/EiJ mice

source_name: Male, liver, control, replicate 1


title: Female_liver_control_rep3

description: Gene expression in the livers of control female WSB/EiJ mice

source_name: Female, liver, control, replicate 3

value: Female


title: Female_liver_tamoxifen_420ppm_12weeks_rep2

description: Gene expression in the livers of female WSB/EiJ mice treated with 420 p.p.m. tamoxifen for 12 weeks

source_name: Female, liver, tamoxifen, 420ppm, 12weeks, replicate 2


title: Male_liver_tamoxifen_420ppm_12weeks_rep3

source_name: Male, liver, tamoxifen, 420ppm, 12weeks, replicate 3


title: Female_liver_tamoxifen_420ppm_12weeks_rep4

source_name: Female, liver, tamoxifen, 420ppm, 12weeks, replicate 4


title: Female_liver_tamoxifen_420ppm_12weeks_rep3

source_name: Female, liver, tamoxifen, 420ppm, 12weeks, replicate 3


title: Male_liver_control_rep4

source_name: Male, liver, control, replicate 4


title: Female_liver_control_rep1

source_name: Female, liver, control, replicate 1


title: Female_liver_control_rep4

source_name: Female, liver, control, replicate 4


title: Male_liver_tamoxifen_420ppm_12weeks_rep4

source_name: Male, liver, tamoxifen, 420ppm, 12weeks, replicate 4


title: Male_liver_tamoxifen_420ppm_12weeks_rep1

source_name: Male, liver, tamoxifen, 420ppm, 12weeks, replicate 1


title: Male_liver_control_rep2

source_name: Male, liver, control, replicate 2


title: Male_liver_control_rep3

source_name: Male, liver, control, replicate 3


title: SZ28

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

hyb_protocol: Agilent Technologies' manufacturer procedures.

scan_protocol: Slides were scanned with the Agilent Bundle Microarray Scanner System (Agilent Technologies) and data were processed using the Feature Extraction 10.7.3.1 software (Agilent Technologies).

data_processing: Among the 45,015 spots present in each array, only those with none flag for quality control (i.e., low intensity, saturation, controls, etc.) were selected for analysis. For analysis of replicate spots, the average intensity after background correction was calculated, normalization was performed using locally weighted linear regression (LOWESS) with α=0.2 within slides using the R software version 2.11.1 (R Development Core Team, 2010) and Linear Models for Microarray (LIMMA) from Bioconductor.

source_name: frontal cortex, schizophrenia

growth_protocol: Frozen tissue.

extract_protocol:
Total RNA was isolated using TRIzol (Sigma) according to the manufacturer's instructions.
RNA concentration was determined by spectrophotometry (NanoDrop, Thermo Scientific, US), and integrity was assessed using the 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

value: brain (frontal cortex)

tag: disease state

value: schizophrenia

value: 52 yr

tag: population

value: white

tag: dsm-iv

tag: age of onset

value: 28 yr

source_name: Reference

tag: sample type

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: SZ16

label_protocol: Agilent Technologies' manufacturer procedures.

tag: tissue

value: 45 yr

value: 34 yr


title: Female_liver_tamoxifen_420ppm_12weeks_rep1

source_name: Female, liver, tamoxifen, 420ppm, 12weeks, replicate 1

tag: gender


title: SZ20

value: 43 yr

value: 25 yr


title: SZ17

value: 51 yr

value: 23 yr


title: SZ25

value: 41 yr

value: 20 yr


title: SZ19

value: 15 yr


title: SZ26

value: 42 yr

value: 18 yr


title: SZ15

value: brain (frontal cortex)

value: 53 yr


title: SZ27

value: schizophrenia

value: 29 yr


title: SZ22

value: 52 yr

value: white

value: 19 yr


title: Female_liver_control_rep2

source_name: Female, liver, control, replicate 2

value: WSB/EiJ

value: liver

value: Female

value: 18 weeks


title: SZ21

value: 46 yr

value: 22 yr

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: SZ23

value: 44 yr


title: SZ18


title: SZ24

value: 50 yr

value: 31 yr


title: SZ14

value: brain (frontal cortex)

value: 36 yr

value: 33 yr


title: SZ13

value: schizophrenia

value: 47 yr

value: 20 yr


title: SZ11

value: 43 yr

value: white

value: 18 yr


title: SZ12

value: 35 yr

value: 14 yr


title: SZ10

value: 19 yr


title: SZ8

value: 9 yr


title: SZ7

value: 32 yr

value: 29 yr

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: SZ9

value: 39 yr

value: 17 yr


title: CON21

source_name: frontal cortex, healthy control

value: brain (frontal cortex)

value: healthy control


title: CON28

value: 51 yr


title: CON23

value: 44 yr


title: CON24

value: 49 yr