title: 30_degree_4B

description:
Genotypes of spore of KZ30-4B
30-4B

source_name: cell culture of strain KZ30-4B


title: 30_degree_4D

status: Public on Jun 06 2017

type: genomic

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

description:
Genotypes of spore of KZ30-4D
30-4D

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 48 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°.

scan_protocol: We acquired the microarray images with a GenePix 4000B scanner and analyzed the images with the GenePix Pro 6.0 software

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: cell culture of strain KZ30-4D

label_protocol: The DNA was labeled using either Cy3-dUTP (control) or Cy5-dUTP (samples) using Invitrogen Bioprime Array CGH Genome Labeling Module using the kit protocol.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Approximately 55 mg of the pelleted culture was resuspended in 500 ml of a melted agarose solution (0.5% low melt agarose, 100 mM EDTA pH 7.5 at approximately 42°), and then 20 μl of a 25 mg/ml Zymolase solution was added. This cell-agarose mixture was distributed into five plug molds and allowed to solidify. The plugs were then incubated in 700 μl of an EDTA/Tris solution (500 mM EDTA, 10 mM Tris, pH 7.5) overnight at 37°.  The next day, 400 μl of a sarcosyl/proteinase K solution (5% sarcosyl, 5 mg/ml proteinase K, 500 mM EDTA pH 7.5) was added to the tubes containing the plugs, and they were incubated at 50° for five hours to overnight. DNA was isolated from three plugs per strain analyzed using the Fermentas Life Sciences GeneJet Gel Extraction Kit. Following the addition of the “Binding” buffer from the kit, the samples were incubated at room temperature (~25°) until the agarose had melted and were then incubated on ice for 5 minutes. These samples were sonicated using a BioRupter sonicater for two 15-minute sessions of 30-second high pulses, followed by 30 seconds without sonication, resulting in DNA fragments of about 200-300 bp. Following sonication, the samples were treated according to the kit protocol.

treatment_protocol: Yeast cells were collected after culture in YPD medium for 20 hours.

tag: strain

tag: temperature

value: 30 degree

source_name: cell culture of JSC24-2


title: 30_degree_6B

description:
Genotypes of spore of KZ30-6B
30-6B

source_name: cell culture of strain KZ30-6B


title: 30_degree_5D

description:
Genotypes of spore of KZ30-5D
30-5D

source_name: cell culture of strain KZ30-5D


title: 30_degree_7C

description:
Genotypes of spore of KZ30-7C
30-7C

source_name: cell culture of strain KZ30-7C


title: 30_degree_7D

description:
Genotypes of spore of KZ30-7D
30-7D

source_name: cell culture of strain KZ30-7D


title: 30_degree_7A

description:
Genotypes of spore of KZ30-7A
30-7A

source_name: cell culture of strain KZ30-7A


title: 30_degree_3D

description:
Genotypes of spore of KZ30-3D
30-3D

source_name: cell culture of strain KZ30-3D


title: 30_degree_3B

description:
Genotypes of spore of KZ30-3B
30-3B

source_name: cell culture of strain KZ30-3B


title: 30_degree_3C

description:
Genotypes of spore of KZ30-3C
30-3C

source_name: cell culture of strain KZ30-3C


title: 30_degree_3A

description:
Genotypes of spore of KZ30-3A
30-3A

source_name: cell culture of strain KZ30-3A


title: 30_degree_6D

description:
Genotypes of spore of KZ30-6D
30-6D

source_name: cell culture of strain KZ30-6D


title: 30_degree_7B

description:
Genotypes of spore of KZ30-7B
30-7B

source_name: cell culture of strain KZ30-7B


title: 30_degree_5B

description:
Genotypes of spore of KZ30-5B
30-5B

source_name: cell culture of strain KZ30-5B


title: 30_degree_5C

description:
Genotypes of spore of KZ30-5C
30-5C

source_name: cell culture of strain KZ30-5C


title: 30_degree_6C

description:
Genotypes of spore of KZ30-6C
30-6C

source_name: cell culture of strain KZ30-6C


title: 30_degree_6A

description:
Genotypes of spore of KZ30-6A
30-6A

source_name: cell culture of strain KZ30-6A


title: 30_degree_4C

description:
Genotypes of spore of KZ30-4C
30-4C

source_name: cell culture of strain KZ30-4C


title: 30_degree_5A

description:
Genotypes of spore of KZ30-5A
30-5A

source_name: cell culture of strain KZ30-5A

source_name: cell culture of JSC24-2


title: 14_degree_5D

description:
Genotypes of spore of KZ14-5D
14-5D

source_name: cell culture of strain KZ14-5D

value: 14 degree


title: 30_degree_1A

description:
Genotypes of spore of KZ30-1A
30-1A

source_name: cell culture of strain KZ30-1A


title: 30_degree_4A

description:
Genotypes of spore of KZ30-4A
30-4A

source_name: cell culture of strain KZ30-4A


title: 14_degree_4C

description:
Genotypes of spore of KZ14-4C
14-4C

source_name: cell culture of strain KZ14-4C


title: 14_degree_4D

description:
Genotypes of spore of KZ14-4D
14-4D

source_name: cell culture of strain KZ14-4D


title: 30_degree_1D

description:
Genotypes of spore of KZ30-1D
30-1D

source_name: cell culture of strain KZ30-1D


title: 14_degree_3C

description:
Genotypes of spore of KZ14-3C
14-3C

source_name: cell culture of strain KZ14-3C


title: 14_degree_4B

description:
Genotypes of spore of KZ14-4B
14-4B

source_name: cell culture of strain KZ14-4B


title: 30_degree_2C

description:
Genotypes of spore of KZ30-2C
30-2C

source_name: cell culture of strain KZ30-2C


title: 14_degree_2C

description:
Genotypes of spore of KZ14-2C
14-2C

source_name: cell culture of strain KZ14-2C


title: 14_degree_2A

description:
Genotypes of spore of KZ14-2A
14-2A

source_name: cell culture of strain KZ14-2A


title: 30_degree_1C

description:
Genotypes of spore of KZ30-1C
30-1C

source_name: cell culture of strain KZ30-1C


title: 30_degree_2B

description:
Genotypes of spore of KZ30-2B
30-2B

source_name: cell culture of strain KZ30-2B


title: 14_degree_1D

description:
Genotypes of spore of KZ14-1D
14-1D

source_name: cell culture of strain KZ14-1D


title: 30_degree_2A

description:
Genotypes of spore of KZ30-2A
30-2A

source_name: cell culture of strain KZ30-2A


title: 14_degree_2D

description:
Genotypes of spore of KZ14-2D
14-2D

source_name: cell culture of strain KZ14-2D


title: 14_degree_3D

description:
Genotypes of spore of KZ14-3D
14-3D

source_name: cell culture of strain KZ14-3D

source_name: cell culture of JSC24-2


title: 14_degree_3B

description:
Genotypes of spore of KZ14-3B
14-3B

source_name: cell culture of strain KZ14-3B


title: 14_degree_5B

description:
Genotypes of spore of KZ14-5B
14-5B

source_name: cell culture of strain KZ14-5B


title: 14_degree_5C

description:
Genotypes of spore of KZ14-5C
14-5C

source_name: cell culture of strain KZ14-5C


title: 30_degree_2D

description:
Genotypes of spore of KZ30-2D
30-2D

source_name: cell culture of strain KZ30-2D


title: 14_degree_2B

description:
Genotypes of spore of KZ14-2B
14-2B

source_name: cell culture of strain KZ14-2B


title: 14_degree_3A

description:
Genotypes of spore of KZ14-3A
14-3A

source_name: cell culture of strain KZ14-3A


title: 30_degree_1B

description:
Genotypes of spore of KZ30-1B
30-1B

source_name: cell culture of strain KZ30-1B


title: Lung_epithelial_brushing_severe_asthma_SAM5495271

type: RNA

city: South San Francisco

first: David

middle: Fong

last: Choy

state: CA

address: 1 DNA Way

country: USA

institute: Genentech, Inc.

hyb_protocol: 18 hours at 60°C with constant rotation on Agilent WHG

scan_protocol: Agilent scanner according to the manufacturer’s protocol

data_processing: Agilent Feature Extraction Software (v 8.5.1.1); vsn normalization of test and reference channels.

molecule: total RNA

organism: Homo sapiens

label_protocol: T7 RNA polymerase single round of linear amplification

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

tag: disease state

value: Severe asthma

tag: tissue

value: Endobronchial Epithelial Brushings

source_name: Pooled human RNA

value: Stratagene Universal Human Reference RNA


title: 14_degree_5A

description:
Genotypes of spore of KZ14-5A
14-5A

source_name: cell culture of strain KZ14-5A


title: Lung_epithelial_brushing_severe_asthma_SAM5495234


title: Lung_epithelial_brushing_severe_asthma_SAM5495243


title: Lung_epithelial_brushing_severe_asthma_SAM5495250


title: Lung_epithelial_brushing_severe_asthma_SAM5495233


title: Lung_epithelial_brushing_severe_asthma_SAM5495217


title: Lung_epithelial_brushing_severe_asthma_SAM5495211


title: 14_degree_4A

description:
Genotypes of spore of KZ14-4A
14-4A

source_name: cell culture of strain KZ14-4A


title: Lung_epithelial_brushing_severe_asthma_SAM5495221


title: Lung_epithelial_brushing_severe_asthma_SAM5495236


title: Lung_epithelial_brushing_severe_asthma_SAM5495260


title: Lung_epithelial_brushing_severe_asthma_SAM5495272


title: 14_degree_1C

description:
Genotypes of spore of KZ14-1C
14-1C

source_name: cell culture of strain KZ14-1C


title: 14_degree_1A

description:
Genotypes of spore of KZ14-1A
14-1A

source_name: cell culture of strain KZ14-1A


title: Lung_epithelial_brushing_severe_asthma_SAM5495226


title: Lung_epithelial_brushing_severe_asthma_SAM5495223


title: Lung_epithelial_brushing_severe_asthma_SAM5495267


title: Lung_epithelial_brushing_severe_asthma_SAM5495219


title: Lung_epithelial_brushing_severe_asthma_SAM5495229


title: Lung_epithelial_brushing_severe_asthma_SAM5495245


title: Lung_epithelial_brushing_severe_asthma_SAM5495255


title: Lung_epithelial_brushing_severe_asthma_SAM5495218


title: Lung_epithelial_brushing_severe_asthma_SAM5495224


title: 14_degree_1B

description:
Genotypes of spore of KZ14-1B
14-1B

source_name: cell culture of strain KZ14-1B


title: Lung_epithelial_brushing_severe_asthma_SAM5495252


title: Lung_epithelial_brushing_severe_asthma_SAM5495247


title: Lung_epithelial_brushing_severe_asthma_SAM5495249


title: Lung_epithelial_brushing_severe_asthma_SAM5495240


title: Lung_epithelial_brushing_severe_asthma_SAM5495266


title: Lung_epithelial_brushing_severe_asthma_SAM5495210


title: Lung_epithelial_brushing_severe_asthma_SAM5495209


title: Lung_epithelial_brushing_severe_asthma_SAM5495222


title: Lung_epithelial_brushing_severe_asthma_SAM5495212


title: Lung_epithelial_brushing_severe_asthma_SAM5495254


title: Lung_epithelial_brushing_severe_asthma_SAM5495259


title: Lung_epithelial_brushing_severe_asthma_SAM5495227


title: Lung_epithelial_brushing_severe_asthma_SAM5495214


title: Lung_epithelial_brushing_severe_asthma_SAM5495216


title: Lung_epithelial_brushing_severe_asthma_SAM5495244


title: Lung_epithelial_brushing_severe_asthma_SAM5495220


title: Lung_epithelial_brushing_severe_asthma_SAM5495235


title: Lung_epithelial_brushing_severe_asthma_SAM5495225


title: Lung_epithelial_brushing_severe_asthma_SAM5495256


title: Lung_epithelial_brushing_severe_asthma_SAM5495270


title: Lung_epithelial_brushing_severe_asthma_SAM5495238


title: Lung_epithelial_brushing_severe_asthma_SAM5495263


title: Lung_epithelial_brushing_severe_asthma_SAM5495265


title: Lung_epithelial_brushing_severe_asthma_SAM5495228


title: Lung_epithelial_brushing_severe_asthma_SAM5495231


title: Lung_epithelial_brushing_severe_asthma_SAM5495239


title: Lung_epithelial_brushing_severe_asthma_SAM5495258


title: Lung_epithelial_brushing_severe_asthma_SAM5495257


title: Lung_epithelial_brushing_severe_asthma_SAM5495242


title: Lung_epithelial_brushing_severe_asthma_SAM5495237


title: Lung_epithelial_brushing_severe_asthma_SAM5495230


title: Lung_epithelial_brushing_severe_asthma_SAM5495251


title: Lung_epithelial_brushing_severe_asthma_SAM5495213


title: Lung_epithelial_brushing_severe_asthma_SAM5495248


title: Lung_epithelial_brushing_severe_asthma_SAM5495262


title: Liver_Mouse_HFCFD_rep8

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description:
A407_H5_Liver_10_WT_HFD
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water (reference diet), replicate 8.

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.0).

label: biotin

organism: Mus musculus

source_name: liver, HFCFD

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Studies were performed using pure-bred male C57BL/6 mice. Mice were individually housed in temperature- and humidity-controlled specific pathogen-free conditions. At the age of 11 wks, mice were fed a high-fat/high-cholesterol/high-fructose diet (HFCFD) providing 10% or 45% energy percent as triglycerides (based on formula D12451 from Research Diets, Inc., manufactured by Research Diet Services, Wijk bij Duurstede, Netherlands). The fat source of this HFCFD was replaced by safflower oil and supplemented with 1% cholesterol (Dishman, Veenendaal, Netherlands). Mice were also provided with 20% fructose water (wt/vol) to promote development of NAFLD. The fiber-enriched diets were identical to the HFCFD (reference) except that corn starch was replaced by 10% (wt/wt) resistant starch (RS) or guar gum (GG). Resistant starch, a retrograded tapioca starch classified as RS type 3 (brand name C* Actistar 11700) and guar gum (brand name Viscogum) were obtained from Cargill R&D Centre Europe (Vilvoorde, Belgium). Diets were given for 18 wks. Mice had ad libitum access to food and water. Samples from only the HFCFD and GG groups were subjected to gene expression profiling.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: After the dietary intervention, mice were anesthetized and livers were removed, snap frozen in liquid nitrogen, and stored at -80°C.

tag: strain/background

tag: gender

value: male

value: liver

tag: diet group

value: high-fat/high-cholesterol diet with 20% fructose in drinking water

tag: age at start of intervention (wk)

tag: age sacrificed (wk)


title: Liver_Mouse_HFCFD_GuarGum_rep7

description:
A407_G9_Liver_45_WT_HFD_GG
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water, but with 10% (w/w) guar gum added, replicate 7.

source_name: liver, HFCFD + GG

value: high-fat/high-cholesterol diet with 20% fructose in drinking water + guar gum


title: M4 PSIP1sh2 treatment rep1

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization within lumi package in R

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

growth_protocol: M4 cells were cultured in DMEM/F12 with 5% Horse serum, at 37oC, 5%CO2.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Stable knock down of PSIP1 was made in M4 using shRNA. Scrambled shRNA was used as control in M4 cells.

tag: cell line

tag: genotype/variation


title: M4 Control rep 2

value: Control


title: M4 Control rep 3


title: Liver_Mouse_HFCFD_GuarGum_rep5

description:
A407_E9_Liver_43_WT_HFD_GG
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water, but with 10% (w/w) guar gum added, replicate 5.


title: Lung_epithelial_brushing_severe_asthma_SAM5495232


title: Liver_Mouse_HFCFD_rep7

description:
A407_G5_Liver_9_WT_HFD
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water (reference diet), replicate 7.


title: Lung_epithelial_brushing_severe_asthma_SAM5495246


title: M4 PSIP1sh2 treatment rep2


title: Liver_Mouse_HFCFD_GuarGum_rep8

description:
A407_H9_Liver_46_WT_HFD_GG
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water, but with 10% (w/w) guar gum added, replicate 8.


title: Liver_Mouse_HFCFD_rep5

description:
A407_E5_Liver_7_WT_HFD
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water (reference diet), replicate 5.


title: Liver_Mouse_HFCFD_GuarGum_rep6

description:
A407_F9_Liver_44_WT_HFD_GG
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water, but with 10% (w/w) guar gum added, replicate 6.


title: Liver_Mouse_HFCFD_GuarGum_rep4

description:
A407_D9_Liver_40_WT_HFD_GG
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water, but with 10% (w/w) guar gum added, replicate 4.


title: M4 PSIP1sh2 treatment rep3


title: T-helper cell population Th17, miRNA, biological replicate 2

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
Th17_miRNA_2
miRNA expression data from T-helper cell population Th17

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary with standard settings (RMA+DABG) of the Affymetrix Expression Console software (v.1.3.0.187)

source_name: Th17 cells derived from CD4 positive spleen lymphocytes

label_protocol: FlashTag Biotin HSR kit (Genisphere)

growth_protocol: Animals per housed under spf conditions

extract_protocol: miRNeasy (Qiagen) including DNase treatment

treatment_protocol: Cells populations were treated as described in the paper. Briefly, isolation of CD4+ lymphocytes from spleens of Balb/c mice were conducted with the mouse CD4+ Isolation Kit II from Miltenyi Biotechnology. 2*105 CD4+ cells were seeded in one well of a 96- well plate. All cells were cultured with RPMI1640 media containing 10% FCS, 1% penicillin/streptomycin and antibodies against CD3 (4µg/ml) and CD28 (30ng/ml) (BioLegend). Th17 cells were additionally cultured with IL-6(20ng/ml), TGFβ (5ng/ml), IL-23 (10ng/ml) (R&D Systems) and an antibody against IFNγ (10µg/ml) (BioLegend). Th2 cells were differentiated with IL-4 (100ng/ml) (R&D Systems) and an antibody against IFNγ (10µg/ml) (BioLegend). Th0 cells serve as a control aand were cultured with solely anti-CD3 and anti-CD28 antibodies. The primary Th cells were cultivated at 37°C and 5% CO2 in a humidified incubator. After 72h the media was exchanged by fresh differentiation media.

value: Balb/c

value: WT

tag: age

value: 10-14 weeks

value: female

tag: t-helper cell source

value: CD4 positive spleen lymphocytes

tag: t-helper populations

value: Th17 cells


title: T-helper cell population Th17, biological replicate 2

description:
Th17_2
Gene expression data from T-helper cell population Th17

scan_protocol: According to the Affymetrix expression protocol

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.3.0.187) including median polish and Sketch-Quantile normalisation

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen)


title: T-helper cell population Th0, miRNA, biological replicate 3

description:
Th0_miRNA_3
miRNA expression data from T-helper cell population Th0, control

source_name: Th0 cells derived from CD4 positive spleen lymphocytes, control

value: Th0 cells


title: T-helper cell population Th17, miRNA, biological replicate 1

description:
Th17_miRNA_1
miRNA expression data from T-helper cell population Th17


title: Liver_Mouse_HFCFD_rep1

description:
A407_A5_Liver_1_WT_HFD
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water (reference diet), replicate 1.


title: T-helper cell population Th0, miRNA, biological replicate 2

description:
Th0_miRNA_2
miRNA expression data from T-helper cell population Th0, control


title: T-helper cell population Th17, miRNA, biological replicate 4

description:
Th17_miRNA_4
miRNA expression data from T-helper cell population Th17


title: Liver_Mouse_HFCFD_rep2

description:
A407_B5_Liver_2_WT_HFD
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water (reference diet), replicate 2.


title: T-helper cell population Th2, biological replicate 1

description:
Th2_1
Gene expression data from T-helper cell population Th2

source_name: Th2 cells derived from CD4 positive spleen lymphocytes

value: Th2 cells


title: Liver_Mouse_HFCFD_GuarGum_rep1

description:
A407_A9_Liver_37_WT_HFD_GG
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water, but with 10% (w/w) guar gum added, replicate 1.


title: T-helper cell population Th2, biological replicate 2

description:
Th2_2
Gene expression data from T-helper cell population Th2


title: T-helper cell population Th17, biological replicate 1

description:
Th17_1
Gene expression data from T-helper cell population Th17


title: Liver_Mouse_HFCFD_GuarGum_rep3

description:
A407_C9_Liver_39_WT_HFD_GG
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water, but with 10% (w/w) guar gum added, replicate 3.


title: T-helper cell population Th17, biological replicate 3

description:
Th17_3
Gene expression data from T-helper cell population Th17


title: T-helper cell population Th17, miRNA, biological replicate 3

description:
Th17_miRNA_3
miRNA expression data from T-helper cell population Th17


title: Liver_Mouse_HFCFD_GuarGum_rep2

description:
A407_B9_Liver_38_WT_HFD_GG
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water, but with 10% (w/w) guar gum added, replicate 2.


title: T-helper cell population Th0, miRNA, biological replicate 1

description:
Th0_miRNA_1
miRNA expression data from T-helper cell population Th0, control


title: M4 Control rep 1


title: T-helper cell population Th2, miRNA, biological replicate 3

description:
Th2_miRNA_4
miRNA expression data from T-helper cell population Th2


title: T-helper cell population Th2, miRNA, biological replicate 2

description:
Th2_miRNA_2
miRNA expression data from T-helper cell population Th2


title: T-helper cell population Th0, biological replicate 3

description:
Th0_3
Gene expression data from T-helper cell population Th0, control


title: T-helper cell population Th0, biological replicate 2

description:
Th0_2
Gene expression data from T-helper cell population Th0, control


title: T-helper cell population Th2, biological replicate 3

description:
Th2_4
Gene expression data from T-helper cell population Th2


title: T-helper cell population Th17, biological replicate 4

description:
Th17_4
Gene expression data from T-helper cell population Th17


title: Liver_Mouse_HFCFD_rep4

description:
A407_D5_Liver_4_WT_HFD
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water (reference diet), replicate 4.


title: T-helper cell population Th0, biological replicate 1

description:
Th0_1
Gene expression data from T-helper cell population Th0, control


title: Liver_Mouse_HFCFD_rep6

description:
A407_F5_Liver_8_WT_HFD
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water (reference diet), replicate 6.


title: T-helper cell population Th2, miRNA, biological replicate 1

description:
Th2_miRNA_1
miRNA expression data from T-helper cell population Th2


title: Liver_Mouse_HFCFD_rep3

description:
A407_C5_Liver_3_WT_HFD
Liver from a mouse fed a high-fat, high-cholesterol diet and with 20% fructose in drinking water (reference diet), replicate 3.


title: 0.01nM_E2_4h_Rep2 [US12302349_252800421192_S01_GE1_1105_Oct12_1_4]

status: Public on Jun 05 2017

city: RTP

first: Salil

middle: N

last: Pendse

state: NC

address: 6 Davis Drive

institute: Scitovation

hyb_protocol: Hybridization to Agilent SurePrint G3 human whole genome 8x60K microarray (Agilent) was conducted following manufacturer’s protocol

scan_protocol: Microarrays were scanned with an Agilent DNA microarray scanner

data_processing: Feature Extraction (11.5.1.1 version, Agilent) was used to filter, normalize, and calculate the signal intensity and ratios. Processed data were subjected to GeneSpring (Agilent) analysis.

source_name: MCF-7 Human Breast Cancer Cell Line

label_protocol: 100 ng of total RNA from treated and control cells were converted into cDNA and then into labeled cRNA using Agilent LowInput QuickAmp Labeling Kit (Agilent). The resulting cRNA was labeled with Cy3

growth_protocol: Cells were seeded at a density of 300,000 cells/well in 6-well plates and allowed to grow for 72 hours in complete growth media composed of DMEM-F12 (GIBCO, Life Technologies, Grand Island, NY, USA, no. 11309) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Norcross, GA, USA, no. S11150), nonessential amino acids (GIBCO, Life Technologies, no. 11140), 10μg/mL bovine insulin (Akron Biotech, Boca Raton, FL, USA, no. AK8213) and gentamicin (Invitrogen, Life Technologies, no. 15710) in Bisphenol-A-free culture flasks.

extract_protocol: Total RNA from MCF-7 cells was extracted using TRizol Reagent (Thermofisher no. 10296028) according to manufacturer’s instruction, and purified using RNeasy Mini Kit (Qiagen). Purified RNA was quantified by using NanoDrop ND-1000 spectrophotometer and the quality of RNA was analyzed by using Agilent Bioanalyzer (Agilent)

treatment_protocol: After 72 hours, cells were rinsed with PBS and placed in treatment media composed of DMEM/F12 supplemented with 5% dextran charcoal-stripped fetal bovine serum (DCC, Gemini Bio-products, Sacramento, CA, US, no. 100-119), nonessential amino acids, 6ng/mL bovine insulin and gentamicin (Invitrogen 15710064 as per protocol.) for 48 hours. Cells were then exposed to 17β estradiol (E2, SigmaAldrich, St. Louis, MO, USA, no. E8875) or vehicle control dimethylsulfoxide (DMSO, Sigma Aldrich, no. D8418) in fresh treatment media for 2, 4, 8, and 24 hours.

tag: agent

tag: time point


title: 1nM_E2_8h_Rep1 [US12302349_252800421195_S01_GE1_1105_Oct12_2_4]


title: 0.1nM_E2_2h_Rep2 [US12302349_252800421194_S01_GE1_1105_Oct12_1_4]


title: 0.1nM_E2_8h_Rep3 [US12302349_252800421191_S01_GE1_1105_Oct12_2_3]


title: 0.1nM_E2_4h_Rep1 [US12302349_252800421192_S01_GE1_1105_Oct12_2_2]


title: 0.01nM_E2_4h_Rep1 [US12302349_252800421192_S01_GE1_1105_Oct12_1_3]


title: 0.1nM_E2_8h_Rep2 [US12302349_252800421191_S01_GE1_1105_Oct12_2_2]


title: 0.01nM_E2_8h_Rep2 [US12302349_252800421191_S01_GE1_1105_Oct12_1_2]


title: 0.1nM_E2_2h_Rep3 [US12302349_252800421194_S01_GE1_1105_Oct12_2_1]


title: 0.01nM_E2_8h_Rep3 [US12302349_252800421191_S01_GE1_1105_Oct12_1_3]


title: 0.1nM_E2_4h_Rep2 [US12302349_252800421192_S01_GE1_1105_Oct12_2_3]


title: 0.01nM_E2_8h_Rep1 [US12302349_252800421191_S01_GE1_1105_Oct12_1_1]


title: 0.01nM_E2_4h_Rep3 [US12302349_252800421192_S01_GE1_1105_Oct12_2_1]


title: 0nM_E2_4h_Rep3 [US12302349_252800421194_S01_GE1_1105_Oct12_2_4]


title: 0.01nM_E2_2h_Rep2 [US12302349_252800421194_S01_GE1_1105_Oct12_1_1]


title: 0.01nM_E2_2h_Rep3 [US12302349_252800421194_S01_GE1_1105_Oct12_1_2]


title: 0.01nM_E2_2h_Rep1 [US12302349_252800421193_S01_GE1_1105_Oct12_2_4]


title: 0.1nM_E2_2h_Rep1 [US12302349_252800421194_S01_GE1_1105_Oct12_1_3]


title: 1nM_E2_4h_Rep2 [US12302349_252800421195_S01_GE1_1105_Oct12_1_2]


title: 0nM_E2_8h_Rep3 [US12302349_252800421195_S01_GE1_1105_Oct12_2_3]


title: 1nM_E2_4h_Rep3 [US12302349_252800421195_S01_GE1_1105_Oct12_1_3]


title: 0.1nM_E2_4h_Rep3 [US12302349_252800421192_S01_GE1_1105_Oct12_2_4]


title: 1nM_E2_4h_Rep1 [US12302349_252800421195_S01_GE1_1105_Oct12_1_1]


title: 1nM_E2_8h_Rep2 [US12302349_252800421192_S01_GE1_1105_Oct12_1_1]


title: 0nM_E2_8h_Rep2 [US12302349_252800421195_S01_GE1_1105_Oct12_2_2]


title: 0nM_E2_4h_Rep2 [US12302349_252800421194_S01_GE1_1105_Oct12_2_3]


title: 0.1nM_E2_8h_Rep1 [US12302349_252800421191_S01_GE1_1105_Oct12_2_1]


title: 1nM_E2_8h_Rep3 [US12302349_252800421192_S01_GE1_1105_Oct12_1_2]


title: 0nM_E2_4h_Rep1 [US12302349_252800421194_S01_GE1_1105_Oct12_2_2]


title: 1nM_E2_2h_Rep2 [US12302349_252800421193_S01_GE1_1105_Oct12_2_2]


title: 1nM_E2_2h_Rep1 [US12302349_252800421193_S01_GE1_1105_Oct12_2_1]


title: 1nM_E2_4h_Rep3 [US12302349_252800421119_S02_GE1_1105_Oct12_2_2]


title: 0nM_E2_2h_Rep3 [US12302349_252800421193_S01_GE1_1105_Oct12_1_3]


title: 0nM_E2_2h_Rep1 [US12302349_252800421193_S01_GE1_1105_Oct12_1_1]


title: 0.01nM_E2_4h_Rep2 [US12302349_252800421195_S01_GE1_1105_Oct12_1_4]


title: 0.01nM_E2_4h_Rep1 [US12302349_252800421193_S01_GE1_1105_Oct12_1_4]


title: 0.1nM_E2_4h_Rep1 [US12302349_252800421118_S02_GE1_1105_Oct12_1_2]


title: 1nM_E2_24h_Rep1 [US12302349_252800421117_S03_GE1_1105_Oct12_2_2]


title: 0nM_E2_2h_Rep2 [US12302349_252800421193_S01_GE1_1105_Oct12_1_2]


title: 0.1nM_E2_24h_Rep3 [US12302349_252800421117_S03_GE1_1105_Oct12_1_2]


title: 0.01nM_E2_4h_Rep3 [US12302349_252800421118_S02_GE1_1105_Oct12_1_1]


title: 1nM_E2_4h_Rep1 [US12302349_252800421119_S02_GE1_1105_Oct12_1_4]


title: 0.1nM_E2_4h_Rep3 [US12302349_252800421118_S02_GE1_1105_Oct12_1_4]


title: 0nM_E2_4h_Rep3 [US12302349_252800421119_S02_GE1_1105_Oct12_1_3]


title: 0.01nM_E2_24h_Rep2 [US12302349_252800421117_S03_GE1_1105_Oct12_1_4]


title: 0.1nM_E2_4h_Rep2 [US12302349_252800421118_S02_GE1_1105_Oct12_1_3]


title: 1nM_E2_2h_Rep3 [US12302349_252800421193_S01_GE1_1105_Oct12_2_3]


title: 0.01nM_E2_24h_Rep1 [US12302349_252800421117_S03_GE1_1105_Oct12_1_3]


title: 0nM_E2_4h_Rep2 [US12302349_252800421119_S02_GE1_1105_Oct12_1_2]


title: 1nM_E2_4h_Rep2 [US12302349_252800421191_S01_GE1_1105_Oct12_2_4]


title: 0.01nM_E2_24h_Rep3 [US12302349_252800421117_S03_GE1_1105_Oct12_2_1]


title: 0.1nM_E2_24h_Rep1 [US12302349_252800421118_S02_GE1_1105_Oct12_2_4]


title: 1nM_E2_24h_Rep3 [US12302349_252800421117_S03_GE1_1105_Oct12_2_4]


title: 0.1nM_E2_24h_Rep2 [US12302349_252800421117_S03_GE1_1105_Oct12_1_1]


title: Tumor epithelial component - sample 702

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data from microdissected ovarian tumor epithelial component

hyb_protocol: For each sample, 15 microgram of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array

scan_protocol: GeneChip Scanner 3000 (Affymetrix) was used for array scanning and data collection

data_processing: Microarray data analysis software, GeneSpring V.11.0.2 (Agilent Technologies Inc.) was used to perform the primary data analysis. RMA summerization algorithm was used and baseline transformation to median of all samples were performed.

label: Biotin

source_name: Microdissected ovarian tumor epithelial component

label_protocol: RNA samples were amplified and labeled using the two-cycle amplification protocol (Affymetrix).

extract_protocol: Frozen sections were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol and stained by 1% methyl green. Air-dried tissue sections were then taken for microdissection using a MD LMD laser microdissecting microscope (Leica). Different types of tissues were dissected and harvested. Total RNA was isolated using the RNeasy Micro kit (Qiagen).

treatment_protocol: Cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). Normal human ovarian surface epithelium (HOSE) specimens were obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.

tag: diagnosis

value: serous ovarian cancer

tag: tissue type

value: epithelial tumor


title: Tumor epithelial component - sample 872


title: WCE (2) spt6-140 TEToff::ARB1 strain 26ºC 8h after Doxicyline

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: Second replica: Whole Cell Extract control for spt6-140 strain on filter V8-L1-14

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

data_processing:
Raw image quantization with background subtracted and Median Absolute Desviation normalization of each duplicate. Elaborated data for GRO were obtained by dividing each individual sample by genomic DNA signal from the same filter. For RPCC IP data were divided by WCE data obtained from the same sample and hybridized on the same filter. For GRO  the value for each gene was corrected by percentage of uridines present in each probe-coding strand. For RPCC and gDNA value for each gene was corrected by percentage of G+C present in each probe.
Value was the result of the local background subtraction to the raw data. In Processed data, we normalized using ArrayStat software (Median Absolute Deviation).

source_name: spt6-140 TEToff::ARB1 at 26ºC

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were permeabilized with 20 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. dCTP labelling of DNA was done by random primming as described in García-Martínez et al. (2004) Mol. Cell 15:303-13.

growth_protocol: Yeast strains grown in YPD al 26ºC to exponential phase and treated with 5 µg/mL Doxicycline for 4 or 8h before GRO or RPCC (RNA pol II Chromatin Immunoprecipitation-Chip hybridization)

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York. Total DNA was extracted from cells or from immunopreciptates as described in Pelechano et al. (2009) Plos Genet. e1000614.

tag: strain/genotype

value: TEToff::ARB1 spt6-140 BY4741 background


title: Tumor epithelial component - sample 765


title: Tumor epithelial component - sample 778


title: 0nM_E2_8h_Rep1 [US12302349_252800421195_S01_GE1_1105_Oct12_2_1]


title: WCE (2) TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: Second replica: Whole Cell Extract control for WT strain on filter V8-L1-12

source_name: wt TEToff::ARB1 at 26ºC

value: TEToff::ARB1 wt BY4741 background


title: Tumor epithelial component - sample 660


title: Tumor epithelial component - sample 486


title: WCE (2) TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: Second replica: Whole Cell Extract control for WT strain on filter V8-L1-11


title: Tumor epithelial component - sample 645


title: 0nM_E2_24h_Rep2 [US12302349_252800421118_S02_GE1_1105_Oct12_2_2]


title: Tumor epithelial component - sample 380


title: WCE (2) spt6-140 TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: Second replica: Whole Cell Extract control for spt6-140 strain on filter V8-L1-13


title: Tumor epithelial component - sample 377


title: 0nM_E2_24h_Rep1 [US12302349_252800421118_S02_GE1_1105_Oct12_2_1]


title: Tumor epithelial component - sample 431


title: WCE (1) TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: First replica: Whole Cell Extract control for WT strain on filter V8-L1-7


title: WCE (1) TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: First replica: Whole Cell Extract control for WT strain on filter V8-L1-8


title: Tumor epithelial component - sample 317


title: Tumor epithelial component - sample 324


title: Human ovarian surface epithelium - sample 2230

description: Gene expression data from microdissected ovarian surface epithelium

source_name: Microdissected ovarian surface epithelium

value: healthy (normal)

value: ovarian surface epithelium


title: WCE (1) spt16-140 TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: First replica: Whole Cell Extract control for spt6-140 strain on filter V8-L1-9


title: Tumor epithelial component - sample 388


title: Tumor epithelial component - sample 412


title: 0nM_E2_24h_Rep3 [US12302349_252800421118_S02_GE1_1105_Oct12_2_3]


title: RNA pol II IP (2) TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: Second replica: 8WG16 Antibody Immunoprecipitation for WT strain on filter V8-L1-11

tag: antibody

value: 8WG16 Antibody


title: WCE (1) spt16-140 TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: First replica: Whole Cell Extract control for spt6-140 strain on filter V8-L1-10


title: Tumor epithelial component - sample 692


title: RNA pol II IP (2) TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: Second replica: 8WG16 Antibody Immunoprecipitation for WT strain on filter V8-L1-12


title: RNA pol II IP (2) spt6-140 TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: Second replica: 8WG16 Antibody Immunoprecipitation for spt6-140 strain on filter V8-L1-14


title: Human ovarian surface epithelium - sample 2064


title: RNA pol II IP (1) spt16-140 TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: First replica: 8WG16 Antibody Immunoprecipitation for spt6-140 strain on filter V8-L1-10


title: GRO (2) spt6-140 TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: Second replica: Run-on labelling for spt6-140 strain on filter V8-L1-13


title: RNA pol II IP (1) TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: First replica: 8WG16 Antibody Immunoprecipitation for WT strain on filter V8-L1-7


title: GRO (2) TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: Second replica: Run-on labelling for WT strain on filter V8-L1-12


title: RNA pol II IP (2) spt6-140 TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: Second replica: 8WG16 Antibody Immunoprecipitation for spt6-140 strain on filter V8-L1-13


title: GRO (1) spt16-140 TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: First replica: Run-on labelling for spt6-140 strain on filter V8-L1-9


title: RNA pol II IP (1) TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: First replica: 8WG16 Antibody Immunoprecipitation for WT strain on filter V8-L1-8


title: GRO (1) TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: First replica: Run-on labelling for WT strain on filter V8-L1-7


title: GRO (2) TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: Second replica: Run-on labelling for WT strain on filter V8-L1-11


title: Human ovarian surface epithelium - sample 2085


title: RNA pol II IP (1) spt16-140 TEToff::ARB1 strain 26ºC 4h after Doxicyline

description: First replica: 8WG16 Antibody Immunoprecipitation for spt6-140 strain on filter V8-L1-9


title: GRO (2) spt6-140 TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: Second replica: Run-on labelling for spt6-140 strain on filter V8-L1-14


title: GRO (1) spt16-140 TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: First replica: Run-on labelling for spt6-140 strain on filter V8-L1-10


title: Tumor epithelial component - sample 389

description: Gene expression data from microdissected ovarian tumor epithelial component


title: Human ovarian surface epithelium - sample 2237

description: Gene expression data from microdissected ovarian surface epithelium


title: normal control_peripheral blood NB2

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

description: miRNA expression healthy volunteer

hyb_protocol: Dried labeled miRNAs were resuspended with 17 μl of nuclease free water and mix with 1 μl of Hyb Spike-In, 4.5 μl of GE Blocking Agent and 22.5 μl of Hi-RPM Hybridisation Buffer. 40 ul of the mixture was hybridised to SurePrint Human miRNA Microarray, release 19.0, 8 X 60K for 20 h at 55°C with rotation. After incubation, the slides were washed according to manufacturer's protocol.

scan_protocol: slides were scanned immediately after washing with Agilent DNA Microarray Scanner  (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software Version 10.7.3.1. Microarray data were analysed using GeneSpring software version 13.0.

source_name: peripheral blood, normal

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNAs using the Agilent miRNA Complete Labeling and Hyb Kit according to manufacturer's recommendation. Labeled cRNAs were purified with MicroBioSpin 6 Column (Bio-Rad)  to wash off unincorporated dyes. Purified labeled RNAs were dried in a vacuum concentrator at low heat.

growth_protocol: cell lines were grow in RPM1640 medium supplemented with 10-15% of FBS in culture flasks at 37°C and 5% CO2 incubator

extract_protocol: Total RNAs were extracted from the samples by using Qiagen miRNeasy mini kit according to manufacturer's protocol.  On-column DNase digestion was performed using Qiagen DNAse I kit. Total RNAs were quantified using a NanoDrop-1000 spectrophotometer and RNA integrity number was assessed with the Agilent 2100 Bioanalyzer.

tag: disease state

value: healthy control

tag: tissue

value: peripheral blood

value: male


title: NPFF-treated macrophages, biol rep 2

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

description: Gene expression data from NPFF-treated cells.

hyb_protocol: Affymetrix GeneChip® Hybridization, Wash, and Stain Kit, 900720

scan_protocol: Hewlett-Packard GeneArray Scanner 3000 7G

data_processing: GeneSpring 13.0 software from Agilent (setting were set for analysis of Affymetrix Expression experiment type; Exon analysis type, and RMA16 summarization algorithm was used.

source_name: J774A.1 macrophages

label_protocol: according to Affymetrix protocol (Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, 901524)

growth_protocol: RPMI-1640 with 10% FCS

extract_protocol: TRIZOL, whole RNA extraction, each sample 500 ng RNA

treatment_protocol: control cells: PBS vehicle 18 h, treated cells: NPFF 1 nM in PBS, 18 h

tag: strain

value: Balb/c

tag: treatment

value: NPFF 1 nM in PBS, 18 h


title: multiple myeloma_cell line KMS-12BM

description: Cell line

source_name: cell line, multiple myeloma

value: multiple myeloma


title: Genomic DNA on filter V8-L1-13

description: Random primed genomic DNA on filter V8-L1-13

source_name: BY4741 genomic DNA

value: BY4741 wild type


title: NPFF-treated macrophages, biol rep 3


title: Human ovarian surface epithelium - sample 2061


title: Genomic DNA on filter V8-L1-9

description: Random primed genomic DNA on filter V8-L1-9


title: NPFF-treated macrophages, biol rep 1


title: Genomic DNA on filter V8-L1-11

description: Random primed genomic DNA on filter V8-L1-11


title: Genomic DNA on filter V8-L1-14

description: Random primed genomic DNA on filter V8-L1-14


title: multiple myeloma_cell line MM.1S

description: Cell line


title: normal control_peripheral blood NB3

description: miRNA expression healthy volunteer

tag: gender


title: Genomic DNA on filter V8-L1-12

description: Random primed genomic DNA on filter V8-L1-12


title: multiple myeloma_cell line KMS-28BM

description: Cell line


title: GRO (1) TEToff::ARB1 strain 26ºC 8h after Doxicyline

description: First replica: Run-on labelling for WT strain on filter V8-L1-8


title: Genomic DNA on filter V8-L1-8

description: Random primed genomic DNA on filter V8-L1-8


title: multiple myeloma_cell line KMS-20

description: Cell line


title: Genomic DNA on filter V8-L1-10

description: Random primed genomic DNA on filter V8-L1-10


title: 1nM_E2_24h_Rep2 [US12302349_252800421191_S01_GE1_1105_Oct12_1_4]


title: normal control_peripheral blood NB1

description: miRNA expression healthy volunteer

value: female


title: multiple myeloma_cell line KMS-21BM

description: Cell line


title: Genomic DNA on filter V8-L1-7

description: Random primed genomic DNA on filter V8-L1-7


title: multiple myeloma_cell line IM-9

description: Cell line


title: control (non-treated) macrophages, biol rep 3

description: Gene expression data from control cells.

value: PBS vehicle 18 h


title: multiple myeloma_clinical specimen MM16

description: miRNA expression before treatment, newly diagnosed patient

source_name: bone marrow, multiple myeloma

value: bone marrow aspirates


title: multiple myeloma_cell line RPMI-8226

description: Cell line


title: multiple myeloma_clinical specimen MM15


title: multiple myeloma_clinical specimen MM13


title: multiple myeloma_clinical specimen MM9


title: control (non-treated) macrophages, biol rep 1


title: multiple myeloma_clinical specimen MM17


title: control (non-treated) macrophages, biol rep 2


title: multiple myeloma_cell line U-266

description: Cell line


title: multiple myeloma_clinical specimen MM7


title: multiple myeloma_clinical specimen MM10

description: miRNA expression after treatment, relapsed patient


title: multiple myeloma_clinical specimen MM5


title: multiple myeloma_clinical specimen MM6


title: multiple myeloma_clinical specimen MM11


title: multiple myeloma_clinical specimen MM18


title: multiple myeloma_clinical specimen MM14


title: 0nM_E2_4h_Rep1 [US12302349_252800421119_S02_GE1_1105_Oct12_1_1]


title: multiple myeloma_clinical specimen MM8


title: multiple myeloma_clinical specimen MM4


title: multiple myeloma_clinical specimen MM2


title: multiple myeloma_clinical specimen MM19


title: multiple myeloma_clinical specimen MM12


title: non-MI patient 19

status: Public on Jun 04 2017

city: Bangkok

first: Thidathip

last: Wongsurawat

state: Bangkok

address: 11th Flr, SiMR Bldg.,  Num. 2, Wang Lang Rd., Bangkoknoi, Siriraj hospital

country: Thailand

institute: Mahidol University

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0817 (same sample as non-MI patient 10)

hyb_protocol: Hybridize to the Human Genome U219 Plus 2.0 Array plate (Affymetrix, Santa Clara, USA).

scan_protocol: All the reaction plates were washed, stained and scanned with the Gene Titan Instrument.

data_processing: Samples analyzed with Affymetrix platform were preprocessed using the Raw CEL data sets of all samples were normalized by Robust Multi-array Average (RMA) algorithm using the R package affy.

source_name: aortic sample from stable angina (non-MI)

label_protocol: The cDNA products were further subjected to fragmentation and labelling with Encore Biotin Module (company).

growth_protocol: not applicable

extract_protocol: Total RNA was isolated from VSMCs with Tri Reagent® (Molecular Research Centre) following manufacturer’s protocol and amplified with Ovation FFPE WTA System (NuGEN Technologies).

treatment_protocol: not applicable

tag: individual

value: non-MI patient

tag: Sex

value: Male

tag: race

value: Chinese

tag: cad presentation

value: STABLE

tag: cell type

value: vascular smooth muscle cells (VSMCs)


title: non-MI patient 13

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE10/0193

tag: age

value: Malay

value: UA


title: non-MI patient 16

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE10/0038


title: MI patient 14

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0672

source_name: aortic sample from Unstable angina (MI)

value: MI patient

value: Indian

value: NSTEMI


title: non-MI patient 20

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0831


title: non-MI patient 14

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE10/0275

value: Female


title: non-MI patient 18

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0815


title: MI patient 9

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0452


title: non-MI patient 15

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0388


title: non-MI patient 11

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE10/0100


title: non-MI patient 10

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0817 (same sample as non-MI patient 19)


title: MI patient 8

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0390


title: MI patient 5

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0816


title: MI patient 15

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0691


title: MI patient 13

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0646


title: non-MI patient 17

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0793


title: MI patient 12

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0546


title: MI patient 10

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0482

value: STEMI


title: MI patient 16

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0721


title: non-MI patient 12

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE10/0178


title: MI patient 17

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0725


title: MI patient 7

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0963


title: MI patient 11

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0544


title: MI patient 6

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE10/0095


title: Human ovarian surface epithelium - sample 2008

description: Gene expression data from microdissected ovarian surface epithelium

value: healthy (normal)

value: ovarian surface epithelium


title: non-MI patient 9

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0736


title: non-MI patient 8

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0723

value: Other


title: non-MI patient 7

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0538


title: MI patient 4

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE10/0077


title: MI patient 3

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE12/0779


title: MI patient 1

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE13/1144


title: non-MI patient 5

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0518


title: non-MI patient 2

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0483


title: non-MI patient 4

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0496


title: kidney_transfer control_18°C_replicate1

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

description: Pool of 7 individual RNAs

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA (0.6 µg) in hybridization buffer was hybridized at 65 °C for 17 h to 8×60 K Whole Salmon Genome Oligo Microarrays (AMADID 049158; Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 10.7.3.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Coregonus lavaretus

source_name: kidney transfer control 18 C

label_protocol: Seven individual RNA samples from the same tissue (liver, spleen, kidney) and treatment were pooled. 100 ng of each total RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured.

growth_protocol: Fish were grown in water recirculation tanks at the Institute for Fisheries in Born, Germany.

extract_protocol: Liver, spleen, kidney were sampled. RNeasy Mini Kit (Qiagen, Hilden, Germany) in complement with the RNase-free DNase Set (Qiagen) allowed us to obtain high-quality RNA suitable for microarray hybridizations and Fluidigm assays.

treatment_protocol: Fish (30.3 ± 1.7 cm in length, and 300.6 ± 68.5 g in weight ) were randomly allocated to identical 300-L glass tanks (0.74 m length × 0.58 m width × 0.72 m height), receiving brackish water from the Darss-Zingst Bodden chain (2.5–6 practical salinity units) to the recirculating aquaculture system with an exchange rate of about 0.5 times per hour. Two tanks out of nine tanks were assigned as “temperature reference” tanks and kept at 18 °C for the entire duration of the experiments. Water temperature in two other tanks was elevated from 18 °C to 24 °C by 1 °C every two days, assigned as “gradual stress”. The remaining five tanks served to perform the experiment of “acute stress”. Water temperature in two of these tanks was kept constant at 18 °C for 18 d, but at day 19, whitefish were transferred from these tanks into two 24 °C-warm tanks, where fish was kept for 1 h until sampling. To account for handling procedures, fish were transferred in the same manner into the equally 18 °C-tempered tank (temperature reference). Fish were randomly sampled using hand nets. Anaesthetization of fish with was done using phenoxyethanol prior to tissue sampling.

value: kidney

value: mixed

value: 349 days post hatch


title: non-MI patient 1

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0480

value: non-MI patient

value: Male


title: kidney_acute stress_24°C_replicate1

description: Pool of 7 individual RNAs

source_name: kidney acute stress 24 C


title: multiple myeloma_clinical specimen MM3

description: miRNA expression before treatment, newly diagnosed patient

value: multiple myeloma

value: bone marrow aspirates

value: female


title: kidney_acute stress_24°C_replicate2

description: Pool of 7 individual RNAs


title: non-MI patient 6

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0528

value: Chinese

value: STABLE

value: vascular smooth muscle cells (VSMCs)


title: kidney_gradual stress_24°C_replicate2

description: Pool of 7 individual RNAs

source_name: kidney gradual stress 24 C


title: spleen_transfer control_18°C_replicate2

description: Pool of 7 individual RNAs

source_name: spleen transfer control 18 C

value: spleen


title: kidney_gradual stress_18°C_replicate1

description: Pool of 7 individual RNAs

source_name: kidney gradual stress 18 C


title: MI patient 2

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE10/0294

value: MI patient


title: kidney_transfer control_18°C_replicate2

description: Pool of 7 individual RNAs


title: non-MI patient 3

description:
Gene expression data from laser captured microdissection (LCM) of vascular smooth muscle cells (VSMCs)
AE11/0485


title: kidney_gradual stress_18°C_replicate2

description: Pool of 7 individual RNAs


title: spleen_transfer control_18°C_replicate1

description: Pool of 7 individual RNAs


title: multiple myeloma_clinical specimen MM1


title: spleen_acute stress_24°C_replicate2

description: Pool of 7 individual RNAs

source_name: spleen acute stress 24 C


title: kidney_gradual stress_24°C_replicate1

description: Pool of 7 individual RNAs


title: spleen_gradual stress_24°C_replicate2

description: Pool of 7 individual RNAs

source_name: spleen gradual stress 24 C


title: liver_acute stress_24°C_replicate1

description: Pool of 7 individual RNAs

source_name: liver acute stress 24 C

value: liver


title: spleen_gradual stress_18°C_replicate1

description: Pool of 7 individual RNAs

source_name: spleen gradual stress 18 C


title: spleen_gradual stress_24°C_replicate1

description: Pool of 7 individual RNAs


title: liver_transfer control_18°C_replicate1

description: Pool of 7 individual RNAs

source_name: liver transfer control 18 C


title: spleen_acute stress_24°C_replicate1

description: Pool of 7 individual RNAs


title: liver_gradual stress_18°C_replicate2

description: Pool of 7 individual RNAs

source_name: liver gradual stress 18 C


title: 7705_08_021104

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: hyperplasia 2 (PN1b)

hyb_protocol: cRNA was synthesized and hybridized onto Affymetrix MG_U74Av2Affymetrix U133A chips using recommended procedures for synthesis, hybridization, washing, and staining with streptavidin-phycoerythrin.

scan_protocol: According to Affymetix protocol.

data_processing: CEL files were processed using dChip (using PM-MM model and quantile normalization).

source_name: hyperplasia 2 (PN1b)

label_protocol: According to Affymetix protocol.

growth_protocol: We employed a transplantable model of preneoplastic progression. Transplantation of p53-null mammary epithelial cells into the cleared mammary fad pads of syngeneic wildtype mice led to the formation of several premalignant lines that histologically and genetically recapitulated the various subtypes of human breast cancer. Two of these lines, PN1a and PN1b, were derived from contralateral outgrowths from the same mouse, and tissue from these outgrowths was serially transplanted for over 10 generations to confirm stability.

extract_protocol: Mammary glands from PN1a (n=5) or PN1b (n=6) lesions at 8 weeks post-transplantation were removed and homogenized in TRIzol reagent (Life Technologies) to fully lyse the tissue. Total RNA was isolated according to the manufacturer’s instructions, followed by Qiagen RNeasy column purification (Qiagen).

tag: sample group

value: hyperplasia 2 (PN1b)

value: Mammary glands from PN1b lesions

value: at 8 weeks post-transplantation


title: liver_gradual stress_24°C_replicate2

description: Pool of 7 individual RNAs

source_name: liver gradual stress 24 C


title: 7701_04_021104

description: hyperplasia 2 (PN1b)

tag: time point


title: liver_acute stress_24°C_replicate2

description: Pool of 7 individual RNAs


title: PN1bB_090303

description: hyperplasia 2 (PN1b)


title: liver_temperature reference_18°C_replicate1

description: Pool of 7 individual RNAs

source_name: liver temperature reference 18 C


title: liver_transfer control_18°C_replicate2

description: Pool of 7 individual RNAs


title: PN1aA_090303

description: hyperplasia I (PN1a)

source_name: hyperplasia I (PN1a)

value: hyperplasia I (PN1a)

value: Mammary glands from PN1a lesions


title: spleen_gradual stress_18°C_replicate2

description: Pool of 7 individual RNAs

value: mixed

value: 349 days post hatch


title: 7675_79__020404

description: hyperplasia 2 (PN1b)


title: PN1aB_090303

description: hyperplasia I (PN1a)


title: TG-18_090303

description: hyperplasia 2 (PN1b)


title: 7670_74_021104

description: hyperplasia 2 (PN1b)


title: PN1aC_090303

description: hyperplasia I (PN1a)


title: 3663_090303

description: hyperplasia I (PN1a)


title: FTC372 - follicular thyroid adenoma

status: Public on Jun 03 2017

city: Gliwice

first: Aleksandra

last: Pfeifer

address: Wybrzeze Armii Krajowej 15

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology

hyb_protocol: Arrays were hybrized with Human Genome U133 2.0 PLUS array (Affymetrix) according protocol recommended in Affymetrix  Gene Expression Analysis Technical Manual 701021 rev5

scan_protocol: Arrays were scanned in GeneArray  3000  scanner  (Affymetrix)  as  recommended  by  the  Affymetrix  Gene Expression Analysis Technical Manual 701021 rev5

data_processing: The quality of the microarray data was analyzed using arrayMvout 1.12.0 library in R 2.14.1/Bioconductor environment. The data were pre-processed with the GCRMA method.

source_name: follicular thyroid adenoma

label_protocol: 7 μL  of  double-stranded  cDNA  were  used for labeling (IVT  Labeling  Kit; Affymetrix).  Labeled  cRNA  was  purified  with  GeneChip  Sample  Cleanup  Module  and  fragmented. The  quality  of  cRNA  was  assessed  with  Bioanalyzer  2000

extract_protocol: Samples (40–150 mg) were ground in liquid nitrogen and homogenized in RLT Buffer (Qiagen) with beta-mercaptoethanol. RNA was extracted using RNeasy Midi Kit (Qiagen) and re-purified with RNeasy Mini Kit (Qiagen), including a digestion step with RNase-free DNase I set (Qiagen)

treatment_protocol: Tumor samples (fresh-frozen material) were derived from patients treated by thyroidectomy.

value: Female

tag: age (years)

tag: class

value: FTA

tag: onco/pdtc

value: NO

tag: ras

tag: diagnosis

value: 2 experts

tag: origin

value: Poland

tag: set

value: Primary


title: 4351_090303

description: hyperplasia I (PN1a)

tag: tissue


title: FTC381 - follicular thyroid adenoma

value: Secondary


title: FTC390 - follicular thyroid adenoma


title: FTC376 - follicular thyroid adenoma


title: FTC083 - follicular thyroid cancer

source_name: follicular thyroid cancer

value: FTC

value: 1 expert

value: Germany


title: FTC453 - follicular thyroid adenoma


title: FTC080 - follicular thyroid cancer

value: Male

value: PDTC


title: FTC082 - follicular thyroid cancer

value: ONCO


title: FTC385 - follicular thyroid adenoma


title: FTC392 - follicular thyroid adenoma


title: FTC077 - follicular thyroid cancer


title: FTC062 - follicular thyroid cancer


title: FTC058 - follicular thyroid adenoma


title: FTC052 - follicular thyroid adenoma


title: FTC060 - follicular thyroid adenoma


title: FTC054 - follicular thyroid adenoma


title: FTC056 - follicular thyroid adenoma


title: FTC066 - follicular thyroid cancer


title: FTC073 - follicular thyroid cancer


title: FTC081 - follicular thyroid cancer


title: FTC075 - follicular thyroid cancer

value: primary


title: FTC072 - follicular thyroid cancer

value: unknown


title: FTC079 - follicular thyroid cancer


title: FTC048 - follicular thyroid adenoma


title: FTC074 - follicular thyroid cancer


title: FTC071 - follicular thyroid cancer


title: FTC078 - follicular thyroid adenoma


title: FTC028 - follicular thyroid cancer


title: FTC036 - follicular thyroid adenoma


title: FTC026 - follicular thyroid adenoma


title: FTC046 - follicular thyroid adenoma


title: FTC040 - follicular thyroid adenoma


title: FTC034 - follicular thyroid cancer

value: 2 experts (lack of concordance)


title: FTC032 - follicular thyroid adenoma


title: FTC038 - follicular thyroid adenoma


title: FTC030 - follicular thyroid cancer


title: FTC018 - follicular thyroid adenoma


title: FTC016 - follicular thyroid cancer


title: FTC005 - follicular thyroid cancer


title: FTC042 - follicular thyroid adenoma


title: liver_gradual stress_24°C_replicate1

description: Pool of 7 individual RNAs

value: liver

tag: gender

value: mixed

value: 349 days post hatch


title: 141106_12IR-01

city: Chiba

first: Atsuko

last: Ishikawa

state: Chiba

address: Anagawa 4-9-1

department: Research Center for Charged Particle Therapy

country: Japan

institute: National Institute of Radiologocal Sciences

hyb_protocol: Following fragmentation, the samples ware hybridized on Mouse Gene 2.0 ST arrays at 45C with rotaion set at 60 RPM for 16 hours using the GeneChip Hybridization Oven 645. The fluidics stations used for washing and staining are the GeneChip Fluidics Station 450.

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

data_processing: The software we use is Affymetrix Expression Console Software. The data ware RMA normalized.

source_name: Control (Saline)

label_protocol: RNAs were labeled with biotin using GeneChip® WT PLUS Reagent Kit in accordance with the manufacturer's instructions (GeneChip® WT PLUS Reagent Kit User Manual).

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

value: Skin

tag: strain

value: BALB/cAJcl

value: male


title: FTC014 - follicular thyroid cancer

tag: Sex

value: Female

value: NO

value: 2 experts


title: FTC015 - follicular thyroid cancer

value: FTC

value: Secondary


title: 141106_12IR-02

source_name: Test (FGF18)


title: FTC012 - follicular thyroid cancer

value: Male

value: Germany

value: Primary


title: MLL-EB1 immortalized murine bone marrow cell line rep1

status: Public on Jun 02 2017

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: test

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

source_name: ME1 leukemia cells

label_protocol: Standard Affymetrix protocol

growth_protocol: All of the cell lines were cultured in RPMI complete medium (1× RPMI 1640, 20% fetal bovine serum, 2 mM L-glutamine, and 100 μM 2-mercaptoethanol) supplemented with IL3 (10 ng/ml).

extract_protocol: Total RNA was extracted with Trizol reagent according to manufacturer's instructions.

value: myeloid leukemia cells


title: FTC044 - follicular thyroid adenoma

value: FTA

value: Poland


title: FTC022 - follicular thyroid adenoma

value: primary


title: FTC006 - follicular thyroid adenoma

value: 1 expert


title: FTC010 - follicular thyroid cancer


title: FTC020 - follicular thyroid cancer


title: FTC013 - follicular thyroid cancer


title: Sorted Gr-1high/Mac-1+ CEBPe-KO

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

description: replicate 1

data_processing: Data were normalized by applying control background correction, log transformation and inter-quantile normalization using the neqc function from the limma bioconductor package.

source_name: Sorted Gr-1high/Mac cells

growth_protocol: sorted primary C57BL/6 (WT and CEBPe KO) bone marrow cells without culture

extract_protocol: Rneasy Kit (Qiagen)

tag: genotype

value: CEBPe KO

value: Sorted primary Gr-1high/Mac-1+ bone marrow cells


title: MLL-EB1 immortalized murine bone marrow cell line rep2

description: test

source_name: ME2G leukemia cells


title: Sorted Gr-1high/Mac-1+ WT

description: replicate 1

value: wild type


title: FTC002 - follicular thyroid cancer


title: Sorted Gr-1intermediate/Mac-1+ WT replicate 1

description: replicate 1

source_name: Sorted Gr-1intermediate/Mac-1+ cells

value: Sorted primary Gr-1 intermediate/Mac-1+ bone marrow cells


title: Sorted Gr-1intermediate/Mac-1+ CEBPe-KO replicate 2

description: replicate 2


title: Sorted Gr-1intermediate/Mac-1+ WT replicate 2

description: replicate 2


title: Sorted Gr-1intermediate/Mac-1+ CEBPe-KO replicate 1

description: replicate 1


title: MLL-AF10(OM-LZ) immortalized murine bone marrow cell line

description: Control

source_name: 12G leukemia cells


title: Hep3B TuD rep2

status: Public on Jun 01 2017

city: San Diego

first: Vivek

last: Kaimal

address: 10614 Science Center Dr.

department: Bioinformatics

institute: Regulus Therapeutics

description:
Gene expression data from Hep3B HCC cell line expressing miR-17 TuD
TUD72HR_PLUSDOXREP2

hyb_protocol: Fragmented, biotin-labeled cRNA was hybridized to the Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays overnight at 45°C for 16 to 18 hours according to the manufacturer’s recommendations

scan_protocol: Stain, wash (GeneChip Fluidics Station 450, EukGE-WS2v5_450 script) and scan (GCS 3000 7G with the GeneChip® AutoLoader) were performed according to the manufacturer’s recommendations

data_processing: Microarray data were GC Robust Multiarray Average (GCRMA) normalized using R and the bioconductor.org package gcrma

source_name: Hep3B HCC cell line, miR-17 TuD

label_protocol: Starting with 1.0 ug total RNA, amplified biotin-labeled cRNA targets were produced using the Enzo Target Labeling method

growth_protocol: Hep3B HCC cells were grown in ATCC-formulated Eagle's Minimum Essential Medium supplemented with 10% fetal bovine serum

extract_protocol: Total RNA were prepared from cells using the mRNA isolation RNeasy Mini kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Hep3B HCC cells were incubated with viral particles encoding miR-17 or NC TuD (Sigma-Aldrich) at multiplicity of infection 5 in medium with 10.0 μg/mL polybrene at 37°C for 48 hours, Cells were then selected by culturing in medium supplemented with 1.0 μg/mL puromycin (Life Technologies). After 2 weeks in culture, puromycin-resistant colonies were pooled to establish stable cell lines.

tag: cell line

value: Hep3B HCC cell line

tag: expressing

value: miR-17 TuD


title: Hep3B NC TuD rep2

description:
Gene expression data from Hep3B HCC cell line expressing NC TuD
TUD72HR_NODOXREP2

source_name: Hep3B HCC cell line, NC TuD

value: NC TuD


title: Hep3B NC TuD rep3

description:
Gene expression data from Hep3B HCC cell line expressing NC TuD
TUD72HR_NODOXREP3


title: MM.1S_shDNMT1#1, replicate1

city: Tokushima

first: Takeshi

last: Harada

state: Tokushima

address: 3-18-15 Kuramoto-cho

department: Hematology, Endocrinology and Metabolism

institute: Tokushima University Graduate School of Biomedical Sciences

description: Gene expression data from MM.1S transduced with shDNMT1#1

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured according to the manufacturer's instructions.

data_processing: The data were analyzed with Bioconductor packages in R (3.3.1). Data were normalized using robust multi-array average (RMA) and differentially expressed genes were identified using Bayes empirical method=X.

source_name: MM.1S transduced with shDNMT1#1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1mg of total RNA

growth_protocol: MM.1S cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol: After 48 hours of infection, total RNA was extracted using RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: MM.1S cells were transduced with shRNA by lentivirus.


title: Hep3B TuD rep3

description:
Gene expression data from Hep3B HCC cell line expressing miR-17 TuD
TUD72HR_PLUSDOXREP3


title: MM.1S_shDNMT1#2, replicate2

description: Gene expression data from MM.1S transduced with shDNMT1#2

source_name: MM.1S transduced with shDNMT1#2


title: MM.1S_shDNMT1#2, replicate1


title: Hep3B NC TuD rep1

description:
Gene expression data from Hep3B HCC cell line expressing NC TuD
TUD72HR_NODOXREP1


title: MM.1S_shDNMT1#1, replicate2


title: MM.1S_shHDAC3#1, replicate2

description: Gene expression data from MM.1S transduced with shHDAC3#1

source_name: MM.1S transduced with shHDAC3#1


title: MM.1S_shHDAC3#1, replicate1


title: Hep3B TuD rep1

description:
Gene expression data from Hep3B HCC cell line expressing miR-17 TuD
TUD72HR_PLUSDOXREP1


title: MM.1S_shHDAC3#2, replicate1

description: Gene expression data from MM.1S transduced with shHDAC3#2

source_name: MM.1S transduced with shHDAC3#2


title: GE_Sample32_Timepoint2

city: Indianapolis

first: Brian

last: Walker

state: IN

address: 980 W Walnut St

department: Medicine

institute: Indiana University

hyb_protocol: Affymetrix

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix GCOS 1.3 / MAS5

source_name: MM patient_Timepoint2

label_protocol: IVT

extract_protocol: Rneasy (Qiagen)

tag: subject status

value: multiple myeloma patient

value: male

tag: Stage

value: Relapse

value: Bone Marrow


title: FTC024 - follicular thyroid cancer

value: Female

value: FTC

value: NO

value: 2 experts

value: Primary


title: GE_Sample33_Timepoint1

source_name: MM patient_Timepoint1

value: Presentation


title: MM.1S_shHDAC3#2, replicate2


title: FTC004 - follicular thyroid cancer

value: primary

value: Germany

value: Secondary


title: GE_Sample31_Timepoint1


title: MM.1S_shLuc, replicate2

description: Gene expression data from MM.1S transduced with shLuc (control of shHDAC3)

source_name: MM.1S transduced with shLuc


title: MM.1S_shLuc, replicate1


title: GE_Sample33_Timepoint2


title: GE_Sample29_Timepoint2


title: GE_Sample31_Timepoint2


title: GE_Sample30_Timepoint2


title: GE_Sample28_Timepoint1

value: female


title: GE_Sample29_Timepoint1


title: GE_Sample26_Timepoint2


title: GE_Sample26_Timepoint1


title: GE_Sample30_Timepoint1


title: GE_Sample28_Timepoint2


title: GE_Sample27_Timepoint1


title: GE_Sample32_Timepoint1


title: GE_Sample27_Timepoint2


title: GE_Sample23_Timepoint1


title: GE_Sample20_Timepoint2


title: GE_Sample21_Timepoint1


title: GE_Sample25_Timepoint1


title: GE_Sample21_Timepoint2


title: GE_Sample19_Timepoint2


title: GE_Sample24_Timepoint2


title: GE_Sample22_Timepoint2


title: GE_Sample24_Timepoint1


title: GE_Sample17_Timepoint2


title: GE_Sample20_Timepoint1


title: GE_Sample18_Timepoint1


title: GE_Sample18_Timepoint2


title: GE_Sample23_Timepoint2


title: GE_Sample25_Timepoint2


title: GE_Sample22_Timepoint1


title: GE_Sample17_Timepoint1


title: GE_Sample16_Timepoint2


title: GE_Sample12_Timepoint2


title: GE_Sample19_Timepoint1


title: GE_Sample15_Timepoint2


title: GE_Sample16_Timepoint1


title: GE_Sample12_Timepoint1


title: GE_Sample10_Timepoint2


title: GE_Sample13_Timepoint1


title: GE_Sample10_Timepoint1


title: GE_Sample11_Timepoint1


title: GE_Sample13_Timepoint2


title: GE_Sample14_Timepoint2


title: GE_Sample15_Timepoint1


title: GE_Sample11_Timepoint2


title: GE_Sample6_Timepoint2


title: GE_Sample14_Timepoint1


title: GE_Sample7_Timepoint2


title: GE_Sample9_Timepoint2


title: GE_Sample9_Timepoint1


title: GE_Sample6_Timepoint1


title: GE_Sample4_Timepoint2


title: GE_Sample5_Timepoint1


title: GE_Sample8_Timepoint2


title: GE_Sample8_Timepoint1


title: GE_Sample2_Timepoint2


title: GE_Sample3_Timepoint1


title: GE_Sample7_Timepoint1


title: GE_Sample5_Timepoint2


title: GE_Sample4_Timepoint1


title: PL 2 8% TREAT

city: London

first: Obed

last: Brew

address: St Mary's Road

country: United Kingdom

institute: University of West London

description:
Gene expression data from term placental explant cultured in 8% oxygen for 6 days, treated with histamine.
S0365F048

hyb_protocol: The resultant fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines for hybridisation onto Affymetrix GeneChip® arrays, and hybridised for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.

scan_protocol: Following hybridisation, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script, before being inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Robust Multi-array Average (RMA) algorithm. A background correction on the PM data (Perfect Match) was performed, then applied log2 transformation and a quantile normalization and followed by summarization of the probe set information using Tukey’s median polish algorithm

source_name: Term (weeks 38 -40) placental explant from normal singleton pregnancies delivery by Elective Caesarean Sections

label_protocol: cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2. The enzymatically and chemically fragmented product (50-100 nt) was labelled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

growth_protocol: Placental micro explants  (<50 mg wet weight) were each placed on a mesh support in a 12-well culture plate containing 15mm diameter Netwell inserts with 74µm polyester mesh bottoms attached to polystyrene inserts, and cultured at 37°C in Standard medium made of RPMI 1640 medium, (containing 25mM HEPES for buffering against changes in pH), supplemented with 10% fetal calf serum, 10ml/L insulin transferrin selenium (ITS), 2mM L-glutamine, penicillin (100 IU/ml) and streptomycin (100 µg/ml)

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

treatment_protocol: Micro explants were treated 8% oxygen (8% oxygen, 5% CO2) or 20% oxygen (95% air; 5% CO2) at the liquid-gas interface. All tissues were incubated at 37°C in standard media for 5 days, followed by a final media change on day 5, with basic only or media containing 100nM histamine in the presence of aminoguanidine (10-4 M final concentration), and incubated for further 24 hours.

value: placenta

tag: treatment

value: Placental Explant in 8% Oxygen, Treated with Histamine


title: PL 4 20% TREAT

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days, treated with histamine.
S0365F036

value: Placental Explant in 20% Oxygen, Treated with Histamine


title: PL 5 8% TREAT

description:
Gene expression data from term placental explant cultured in 8% oxygen for 6 days, treated with histamine.
S0365F041


title: GE_Sample2_Timepoint1

value: multiple myeloma patient


title: PL 4 8% TREAT

description:
Gene expression data from term placental explant cultured in 8% oxygen for 6 days, treated with histamine.
S0365F042


title: PL 5 20% TREAT

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days, treated with histamine.
S0365F046


title: GE_Sample1_Timepoint1

value: male


title: GE_Sample3_Timepoint2

value: Relapse


title: PL 4 20% C

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days.
S0365F037

value: Placental Explant in 20% Oxygen_Control


title: PL 6 8% TREAT

description:
Gene expression data from term placental explant cultured in 8% oxygen for 6 days, treated with histamine.
S0365F038


title: PL 3 20% TREAT

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days, treated with histamine.
S0365F043


title: PL 6 20% TREAT

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days, treated with histamine.
S0365F044


title: PL 5 20% C

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days.
S0365F034


title: PL 1 20% C

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days.
S0365F039


title: PL 2 20% C

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days.
S0365F040


title: GE_Sample1_Timepoint2

value: Bone Marrow


title: PL 5 8% C

description:
Gene expression data from term placental explant cultured in 8% oxygen for 6 days.
S0365F032

value: Placental Explant in 8% Oxygen_Control


title: PL 4 8% C

description:
Gene expression data from term placental explant cultured in 8% oxygen for 6 days.
S0365F035


title: PL 3 8% TREAT

description:
Gene expression data from term placental explant cultured in 8% oxygen for 6 days, treated with histamine.
S0365F033


title: PL 2 20% TREAT

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days, treated with histamine.
S0365F030

value: Placental Explant in 20% Oxygen ,Treated with Histamine


title: PL 2 8% C

description:
Gene expression data from term placental explant cultured in 8% oxygen for 6 days.
S0365F027


title: PL 1 8% C

description:
Gene expression data from term placental explant cultured in 8% oxygen for 6 days.
S0365F028


title: PL 1 20% TREAT

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days, treated with histamine.
S0365F029


title: PL 6 20% C

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days.
S0365F031


title: PL 3 20% C

description:
Gene expression data from term placental explant cultured in 20% oxygen for 6 days.
S0365F026


title: Con si

city: Los Angeles

first: Jiong

last: Li

state: CA - California

department: School of Dentistry

institute: UCLA

description: gene expression of HCT116 cells

hyb_protocol: cRNA were hybridized for 16 hr at 45C on Human U133plus2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix Microarray Scanner.

data_processing: Data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

source_name: Human colon cancer HCT116 cells_control

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol from 0.5ug total RNA

growth_protocol: DMEM with 10% FBS, 37 degree with 5% CO2 culture for 2 days in 10cm dish

extract_protocol: total RNA was extracted using Qiagen RNA extraction kit

treatment_protocol: siRNA treatment followed by Invitrogen RNAimax protocol

tag: cell type

value: human colon cancer cell line


title: AB-1 si

description: gene expression of HCT116 after JMJD1A and JMJD1B depletion

source_name: Human colon cancer HCT116 cells_siJMJD1A_siJMJD1B


title: WAT - after bariatric surgery - rep15

city: Stockholm

first: Niklas

last: Mejhert

address: Hälsovägen 7

country: Sweden

institute: Karolinska Institutet

description: Gene expression profiling based on human abdominal subcutaneous white adipose tissue obtained by needle aspiration

hyb_protocol: Biotinylated RNA was hybridized to Gene 1.1 ST Arrays, and then washed, stained and scanned using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: Standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Results were processed using the RMA method

source_name: Abdominal subcutaneous WAT

label_protocol: Total RNA was amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

growth_protocol: Human abdominal subcutaneous white adipose tissue

extract_protocol: Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany)  according to the instructions provided by the manufacturer

treatment_protocol: Tissues were obtained by needle aspiration under local anasthesia

value: Abdominal subcutaneous white adipose (WAT)

value: Female

tag: obesity status

value: after bariatric surgery


title: WAT - before bariatric surgery - rep15

value: before bariatric surgery


title: WAT - after bariatric surgery - rep16


title: WAT - before bariatric surgery - rep14


title: WAT - never-obese control - rep14

value: never-obese


title: WAT - after bariatric surgery - rep12


title: WAT - never-obese control - rep12


title: WAT - never-obese control - rep16


title: WAT - after bariatric surgery - rep14


title: WAT - before bariatric surgery - rep16


title: WAT - never-obese control - rep13


title: WAT - before bariatric surgery - rep13


title: WAT - before bariatric surgery - rep12


title: WAT - never-obese control - rep15


title: WAT - after bariatric surgery - rep13


title: WAT - never-obese control - rep10


title: WAT - after bariatric surgery - rep11


title: WAT - never-obese control - rep8


title: WAT - before bariatric surgery - rep10


title: WAT - never-obese control - rep7


title: WAT - before bariatric surgery - rep11


title: WAT - after bariatric surgery - rep8


title: WAT - before bariatric surgery - rep9


title: WAT - before bariatric surgery - rep8


title: WAT - after bariatric surgery - rep10


title: WAT - never-obese control - rep9


title: WAT - before bariatric surgery - rep7


title: WAT - never-obese control - rep11


title: WAT - after bariatric surgery - rep7


title: WAT - after bariatric surgery - rep9


title: WAT - before bariatric surgery - rep6


title: WAT - never-obese control - rep5


title: WAT - never-obese control - rep6


title: WAT - after bariatric surgery - rep4


title: WAT - never-obese control - rep4


title: WAT - before bariatric surgery - rep5


title: WAT - never-obese control - rep3


title: WAT - after bariatric surgery - rep6


title: WAT - after bariatric surgery - rep5


title: WAT - after bariatric surgery - rep2


title: WAT - before bariatric surgery - rep2


title: WAT - after bariatric surgery - rep3


title: WAT - before bariatric surgery - rep4


title: WAT - before bariatric surgery - rep1


title: WAT - never-obese control - rep1


title: WAT - before bariatric surgery - rep3


title: WAT - never-obese control - rep2


title: WAT - after bariatric surgery - rep1


title: 61H

city: Donostia

first: Borja

last: Calvo

state: Gipuzkoa

address: Paseo Manuel de Lardizabal, 1

department: Computer Science and Artificial Intelligence

institute: University of the Basque Country

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

data_processing: Normalization and background correction using lumi package available at Bioconductor

label: Cy5 and Cy3

source_name: Hippocampus

label_protocol: Standard as recommended by illumina

extract_protocol: genomic DNA was extracted and purified  using the QIAamp DNA Investigator Kit (Qiagen) according to standard instructions

value: Hippocampus

tag: individual


title: 71H

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

value: Male


title: 61C

source_name: Cortex

value: Cortex


title: 71C


title: 9bisS

source_name: Blood

value: Blood


title: 61S


title: ZNR006S


title: NOR015L

source_name: PBMC

value: PBMC


title: 11S


title: 60H


title: 60C


title: 11L


title: 71S


title: ZNR006L


title: 9bisL


title: 47S


title: 2S


title: 2H


title: 10L


title: 60S


title: 9H


title: 10S


title: NOR015S


title: 47C


title: 9S


title: 47H


title: 203S


title: 4S


title: 204L


title: 64H


title: 7H


title: 203L


title: 4H


title: 7C


title: 8S


title: 64C


title: 57H


title: Tumor telmisartan treated 1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: tumor telmisartan

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Tumor (mouse): Each mouse was inoculated with OE19 cells (5×106cells/animal) subcutaneously on the flank regions of the mouse.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: Tumor: The telmisartan-treated group was injected 5 times a week intraperitoneally (i.p.) at 50μg/body per day for 22 days.

value: tumor

tag: disease type

value: esophageal adenocarcinoma

value: telmisartan


title: 7S


title: Tumor control 7

source_name: tumor control

value: control


title: 204S


title: 2C


title: 9C


title: 4C


title: Tumor control 8


title: 57C


title: Tumor telmisartan treated 4


title: 57S


title: 64S


title: Tumor telmisartan treated 5


title: Tumor telmisartan treated 2


title: Tumor telmisartan treated 3


title: Tumor control 5


title: Tumor control 6


title: Tumor control 2


title: Tumor telmisartan treated 6


title: Tumor control 4


title: Tumor telmisartan treated 8


title: Tumor control 3


title: Cell line control 6

source_name: cell line control

growth_protocol: cell line: OE19 cells were grown in RPM I 1640 supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 at 37°C.

treatment_protocol: cell line: OE19 cells were treated with 100μM telmisartan or without telmisartan for 48 h.


title: Cell line control 7


title: Cell line control 2


title: Cell line control 3


title: Cell line control 5


title: Cell line control 8


title: Cell line control 4


title: Cell line telmisartan treated 6

source_name: cell line telmisartan

value: 100μM telmisartan


title: Cell line telmisartan treated 7


title: Cell line telmisartan treated 3


title: Cell line telmisartan treated 4


title: Tumor control 1


title: Cell line telmisartan treated 5


title: Cell line telmisartan treated 8


title: Cell line control 1


title: 8L


title: Cell line telmisartan treated 2


title: Cell line telmisartan treated 1


title: Tumor telmisartan treated 7


title: Irf4ko-CD4+T cells-Day2-rep

city: Houston

first: wenhao

last: chen

address: 6670 Bertner Street, R7-216

institute: Houston Methodist Research Institute

description: Gene expression of activated Irf4-/- CD4+ T cells at day2

hyb_protocol: 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE v2 8x60K Microarray (074809) 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 Technologies Scanner(G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100_jul11 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Irf4-/-,spleen,activated CD4+ T cells,Day2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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 with RNeasy mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: CD4+ T cells was cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 50 uM 2-ME. The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Spleen

value: male

value: CD4+ T cells

tag: background strain


title: Irf4ko-CD4+T cells-Day2