title: inducible_200druganalog_mif_rep3_total

description: total RNA


title: inducible_200druganalog_mif_rep2_total

status: Public on Dec 31 2015

type: RNA

city: Minneaplois

first: Matthew

last: Parker

state: MINNESOTA

address: 420 Delaware St. SE

department: Department of Medicine

country: USA

institute: University of Minnesota

description: total RNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalized using the robust spline normalization (RSN) and log2 transformed in the statistical R package

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: inducible 200 druganalog mif  total

label_protocol: Illumina Total Pre-96 RNA Amp. Kit

extract_protocol: Cells were treated with cycloheximide to immobilize ribosomes on RNA. Total RNA was isolated using Tri Reagent. Polysome-associated RNA was obtained by centrifuging samples on sucrose gradient, fractionating, and isolating using Tri Reagent.

tag: cell line

value: NIH 3T3

tag: cell type

tag: fraction

value: total

tag: dose 4ei-1

tag: dose 4ei-4

tag: mifepristone treatment

value: TRUE

tag: replicate

tag: processing batch


title: HK-2 cells, Aa, ld, t48h, control sample, biological rep 3

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

hyb_protocol: 15 ug fragmented labelled cRNA was hybridized for 16 hours at 45oC to Affymetrix HGU133_Plus 2.0 GeneChips, which were then stained and washed on an Affymetrix Fluidics Station 400.

scan_protocol: Fluorescence was read with an Affymetrix 3000 Scanner.

data_processing: Data was normalized using the gcrma library (version 2.8.1) of Bioconductor.

organism: Homo sapiens

source_name: Human renal proximal tubular epithelial cells, control for Aa, t48h

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

growth_protocol: HK-2 cells were maintained in a 1-1 mixture of DMEM and Ham'sF12 containing 5 mM glucose supplemented with 10 ng/ml human recombinant EGF, 36 ng/ml hydrocortisone, 5 µg/ml bovine insulin, 5 µg/ml human transferrin, 5 ng/ml sodium selenite, 2 mM Glutamax (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy mini kit.

treatment_protocol: Cells were seeded 24 hours before treatment on Greiner 6-well plates at a density of 7x10^5 cells per well with 2mls of medium per well. Cells were treated at ~90% confluency with the required doses for the required timepoints. Control cells were exposed to an appropriate concentration of the control vehicle.

value: immortalized human renal proximal tubular epithelial cells

tag: treatment

value: control

tag: treatment duration

value: 48 hrs


title: inducible_200druganalog_mif_rep2_heavy

description: polysome-associated RNA

source_name: inducible 200 druganalog mif  heavy

value: heavy


title: HK-2 cells, Di, t12h, biological rep 2

source_name: Human renal proximal tubular epithelial cells, treated with Di, t12h

value: Di

value: 12 hrs


title: inducible_10drug_mif_rep3_total

description: total RNA

source_name: inducible 10 drug mif  total


title: inducible_0drug_mif_rep3_total

description: total RNA

source_name: inducible 0 drug mif  total


title: HK-2 cells, Aa, ld, t48h, control sample, biological rep 2


title: inducible_200druganalog_mif_rep1_heavy

description: polysome-associated RNA


title: HK-2 cells, Aa, ld, t48h, control sample, biological rep 1


title: inducible_10drug_mif_rep3_heavy

description: polysome-associated RNA

source_name: inducible 10 drug mif  heavy


title: noninducible_0drug_mif_rep3_heavy

description: polysome-associated RNA

source_name: noninducible 0 drug mif  heavy

value: non-inducible


title: HK-2 cells, Aa, ld, t24h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Aa, t24h

value: 24 hrs


title: HK-2 cells, Aa, ld, t24h, control sample, biological rep 2


title: inducible_10drug_mif_rep2_total

description: total RNA


title: HK-2 cells, Aa, ld, t48h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t48h

value: Aa

tag: treatment dosage

value: low


title: inducible_10drug_mif_rep1_total

description: total RNA


title: inducible_0drug_nomif_rep3_heavy

description: polysome-associated RNA

source_name: inducible 0 drug nomif  heavy

value: FALSE


title: inducible_0drug_nomif_rep2_total

description: total RNA

source_name: inducible 0 drug nomif  total


title: inducible_0drug_nomif_rep3_total

description: total RNA


title: inducible_200drug_mif_rep3_total

description: total RNA

source_name: inducible 200 drug mif  total


title: inducible_200drug_mif_rep2_total

description: total RNA


title: inducible_10drug_mif_rep1_heavy

description: polysome-associated RNA


title: inducible_200drug_mif_rep3_heavy

description: polysome-associated RNA

source_name: inducible 200 drug mif  heavy


title: HK-2 cells, Aa, ld, t24h, control sample, biological rep 1


title: inducible_0drug_mif_rep3_heavy

description: polysome-associated RNA

source_name: inducible 0 drug mif  heavy


title: inducible_100drug_mif_rep3_total

description: total RNA

source_name: inducible 100 drug mif  total


title: inducible_50drug_mif_rep3_heavy

description: polysome-associated RNA

source_name: inducible 50 drug mif  heavy


title: inducible_0drug_nomif_rep2_heavy

description: polysome-associated RNA


title: HK-2 cells, Aa, ld, t48h, biological rep 1


title: HK-2 cells, Aa, ld, t24h, biological rep 2

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t24h


title: inducible_50drug_mif_rep2_total

description: total RNA

source_name: inducible 50 drug mif  total


title: inducible_100drug_mif_rep3_heavy

description: polysome-associated RNA

source_name: inducible 100 drug mif  heavy


title: inducible_0drug_mif_rep2_total

description: total RNA


title: inducible_10drug_mif_rep2_heavy

description: polysome-associated RNA


title: HK-2 cells, Aa, ld, t24h, biological rep 1


title: inducible_50drug_mif_rep2_heavy

description: polysome-associated RNA


title: HK-2 cells, Aa, ld, t48h, biological rep 2


title: HK-2 cells, Aa, ld, t24h, biological rep 3


title: inducible_0drug_nomif_rep1_total

description: total RNA


title: inducible_50drug_mif_rep3_total

description: total RNA


title: inducible_0drug_mif_rep2_heavy

description: polysome-associated RNA


title: HK-2 cells, Aa, hd, t48h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Aa, t48h


title: HK-2 cells, Aa, hd, t48h, control sample, biological rep 2


title: inducible_200drug_mif_rep2_heavy

description: polysome-associated RNA


title: inducible_0drug_nomif_rep1_heavy

description: polysome-associated RNA


title: inducible_200drug_mif_rep1_total

description: total RNA


title: inducible_100drug_mif_rep2_heavy

description: polysome-associated RNA


title: HK-2 cells, Aa, hd, t48h, control sample, biological rep 1


title: HK-2 cells, Aa, hd, t24h, control sample, biological rep 3


title: inducible_100drug_mif_rep1_total

description: total RNA


title: inducible_100drug_mif_rep2_total

description: total RNA


title: inducible_200drug_mif_rep1_heavy

description: polysome-associated RNA


title: inducible_50drug_mif_rep1_total

description: total RNA


title: inducible_100drug_mif_rep1_heavy

description: polysome-associated RNA


title: HK-2 cells, Aa, hd, t24h, control sample, biological rep 2


title: HK-2 cells, Aa, hd, t24h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with high dose of Aa, t24h

value: high


title: day7, Repl1

city: Helsinki

first: Zoltan

last: Wiener

address: Haartmaninkatu 8

department: Molecular Cancer Biology Programme

country: Finland

institute: University of Helsinki

data_processing: The data were normalized with the default normalization method for Illumina arrays by Chipster.

source_name: ex vivo intestinal organoid

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

growth_protocol: Intestinal organoids were grown according to Sato et al (Nature, 2009). To select the Apc-mutant organoids, the Wnt-agonist R-Spondin1 was removed 2 days after the addition of tamoxifen for 5 or 18 days.

extract_protocol: Total RNA was extracted by the NucleoSpin RNA II isolation kit (Macherey-Nagel) according to the manufacturer, including DNase treatment. RNA quality was checked by Agilent Bioanalyzer

treatment_protocol: Tamoxifen for 2 days to activate the intestinal stem cell-specific expression of the CreER allele.

tag: strain

tag: age

value: 2-3 months

tag: tissue

value: intestinal organoid

tag: time


title: day20, Repl4


title: HK-2 cells, Aa, hd, t24h, control sample, biological rep 1


title: day7, Repl4


title: HK-2 cells, Aa, hd, t48h, biological rep 2

source_name: Human renal proximal tubular epithelial cells, treated with high dose of Aa, t48h


title: HK-2 cells, Aa, hd, t48h, biological rep 3


title: inducible_0drug_mif_rep1_total

description: total RNA

source_name: inducible 0 drug mif  total

value: NIH 3T3


title: HK-2 cells, Aa, hd, t48h, biological rep 1


title: HK-2 cells, Aa, hd, t24h, biological rep 2


title: day7, Repl3


title: inducible_50drug_mif_rep1_heavy

description: polysome-associated RNA


title: hMSCs treated with Mdm2 knock down and differentiated into osteoblasts (2)

city: Goettingen

first: Magdalena

last: Wienken

address: Justus-von-Liebig-Weg 11

country: Germany

institute: University Medical Center Goettingen

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in the hybridization oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed.

data_processing:
Intensity data were extracted using Agilent's Feature Extraction (FE) software (version 11.5.1.1) including a quality control based on internal controls using Agilent's protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma package 43 of Bioconductor 44.
Specifically for the normalization we used the quantile normalization to make the distribution of probe intensities for each array in a set of arrays the same. This implies that we can give each array the same distribution by taking the mean quantile and substituting it as the value of the data item in the original dataset.    The microarray data analysis consists of the following steps:  1. between-array normalization, 2. global clustering and PCA-analysis, 3. fitting the data to a linear model, 4. detection of differential gene expression and 5. over-representation analysis of differentially expressed genes. Quantile-normalization was applied to the log2-transformed intensity values as a method for between-array normalization, to ensure that the intensities had similar distributions across arrays.

source_name: human mesenchymal stem cells differentiated into osteoblasts

label_protocol: Microarrays were done using the Low RNA Input linear Amplification Kit Plus, One Color protocol (Cat. N°: 5188-5339, 2007; Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5282) following the manufacturer's standard protocol. Global gene expression analysis was applied using the Agilent SurePrint G3 Human GE v2 4x44K Kit, P/N G4845A, (Agilent Microarray Design ID 039494. 200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer's recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

extract_protocol: Total RNA was extracted from cells using TRIzol® (Invitrogen/Life Technologies). mRNA was reverse-transcribed using oligo-dT and random hexameric primers and was quantified via qRT-PCR analysis using SYBR Green (Invitrogen/Life Technologies).

treatment_protocol: The differentiation of human mesenchymal stem cells (hMSCs) was induced according to a previously published protocol (Karpiuk et al., 2012). Briefly, hMSC-Tert cells were cultured in low glucose, phenol red free MEM (Invitrogen, Carlsbad, CA), supplemented with 10% bovine growth serum (BGS; HyClone, USA) and 1X penicillin/streptomycin (Invitrogen). 24 h before differentiation, the first siRNA mediated knockdown (kd) was performed using Lipofectamine RNAiMAX (Invitrogen) and siRNA at final concentrations of 10 nM. Kd was performed twice (the second time 72h after the first kd). For osteoblast differentiation, the growth medium was supplemented with 10 mM β-glycerophosphate, 0.2 mM ascorbate, 10 nM calcitriol, and 100 nM dexamethasone, and changed daily for 7 days. Differentiation was evaluated via semi-quantitative analysis of AP activity

tag: sirna

value: Mdm2 siRNA


title: hMSCs treated with EZH2 knock down and differentiated into osteoblasts (2)

growth_protocol: hMSC-Tert cells were cultured in low glucose, phenol red free MEM (Invitrogen, Carlsbad, CA), supplemented with 10% bovine growth serum (BGS; HyClone, USA) and 1X penicillin/streptomycin (Invitrogen)

value: EZH2 siRNA


title: day7, Repl2


title: inducible_0drug_mif_rep1_heavy

description: polysome-associated RNA

value: TRUE


title: day20, Repl3


title: hMSCs treated with EZH2 knock down and differentiated into osteoblasts (1)


title: day20, Repl2


title: HK-2 cells, CsA, t48h, control sample, biological rep 3, lab 4

source_name: Human renal proximal tubular epithelial cells, control for CsA, t48h

value: immortalized human renal proximal tubular epithelial cells

value: control


title: HK-2 cells, Aa, hd, t24h, biological rep 1


title: hMSCs treated with p53 knock down and differentiated into osteoblasts (2)

value: p53 siRNA


title: hMSCs treated with p53 knock down and differentiated into osteoblasts (1)


title: day20, Repl1


title: hMSCs treated with Mdm2 knock down and differentiated into osteoblasts (1)


title: HK-2 cells, CsA, t48h, control sample, biological rep 2, lab 4

value: 48 hrs


title: HK-2 cells, CsA, t12h, control sample, biological rep 2, lab 4

source_name: Human renal proximal tubular epithelial cells, control for CsA, t12h

value: 12 hrs


title: HK-2 cells, CsA, t48h, biological rep 3, lab 4

source_name: Human renal proximal tubular epithelial cells, treated with CsA, t48h

value: CsA


title: HK-2 cells, CsA, t48h, biological rep 2, lab 4


title: HK-2 cells, CsA, t12h, control sample, biological rep 1, lab 4


title: HK-2 cells, CsA, t48h, control sample, biological rep 1, lab 4


title: hMSCs treated with Mdm2&p53 knock down and differentiated into osteoblasts (2)


title: hMSCs treated with control knock down and differentiated into osteoblasts (1)

value: control siRNA


title: hMSCs treated with control knock down and differentiated into osteoblasts (2)


title: CD8+ 1h IFNb 1h TCR

city: Braunschweig

first: Andrea

last: Kröger

address: Inhoffenstrasse 7

department: Regulation and Differentiation

institute: Helmholtz Centre for Infection Research

hyb_protocol: cRNA fragmentation, hybridization, and washing steps were carried out according to Agilent’s One-Color Microarray-Based Gene Expression Analysis Protocol V5.7 (for details see http://www.agilent.com) except that 300ng of each labeled cRNA sample were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings, namely 100% (default setting) and 5%, to increase the dynamic range of the measurements.

data_processing: Data extraction was performed with the “Feature Extraction Software V9.5.3.1” by using the recommended default extraction protocol file: GE1-v5_95_Feb07.xml. Processed intensity values of the green channel (“gProcessedSignal” or “gPS”) were globally normalized by a linear scaling approach: All gPS values of one sample were multiplied by an array-specific scaling factor. This scaling factor was calculated by dividing a “reference 75th Percentile value” (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray (“Array i” in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i X (1500 / 75th PercentileArray i)  A lower intensity threshold was defined as 1% of the reference 75th Percentile value (= 15). All of those normalized gPS values that fell below this intensity border, were substituted by the respective surrogate value of 15.

label: Alexa Fluor 555

source_name: CD8+ 1h IFNb 1h TCR

label_protocol: Total RNA was used to prepare Alexa Fluor 555-labeled cRNA (Amino Allyl MessageAmp™ II Kit; Ambion) as directed by the company. Prior to the reverse transcription reaction, 1µl of a 1:25000 dilution of Agilent’s One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to 100ng of total RNA for each analyzed sample.

growth_protocol: Splenic CD8+ T cells from OT-I TCR tg mice were purified using Pan T cell isolation kit II and AutoMACS magnetic separation system (Miltenyi Biotec) according to the manufacturer´s instructions. Purity of cells was determined by flow cytometry using anti-CD8α (53-6.7), anti-B220 (RA3-6B2) and anti-CD11c (N418) antibodies (all ebioscience) and ranged between 90–97 %. OT I T cells were cultured in RPMI containing 10% FCS and 5 x 10-5 M 2-ME

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen)

treatment_protocol: For T cell activation, 2 x 106 cells were stimulated with SIINFEKL streptamers. To perform streptamer stimulation, Step-Tactin was incubated with recombinant murine MHC-I-Strep H-2Kb SIINFEKL molecules (1 µg/reaction, IBA) at 4°C for 45 min according to the manufacturer´s instructions.

value: CD8+ T cell

tag: genotype

value: OT-I TCR tg mice

value: 1h IFNb 1h TCR stimulation with SIINFEKL

tag: genetic background


title: CD8+ 6h TCR

source_name: CD8+ 6h TCR

tag: cell type

value: 6h TCR stimulation with SIINFEKL


title: CD8+ 1h IFNb 6h TCR

source_name: CD8+ 1h IFNb 6h TCR

value: 1h IFNb 6h TCR stimulation with SIINFEKL


title: Gastric cancer stem cells_CD44 knockdown

city: Chengdu

first: Xiao-Long

last: Chen

address: No.37 Guo Xue Xiang Street

country: China

institute: West China Hospital

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Gastric cancer stem cells were seperated from primary lesions and cultured in serum free DMEM/F12 medium supplemented with 20 ng/ml EGF and 10 ng/ml b-FGF. Gastric cancer stem cells (Lentivirus) were infected with lentivirus that expressed human CD44-speciﬁc short hairpin RNA (shRNA). Control group of gastric cancer stem cells (Vector group) were only infected with scramble shRNA.

tag: gender

value: male

value: 51 yrs

value: gastric cancer stem cells

tag: infected with

value: lentivirus expressing human CD44-speciﬁc short hairpin RNA (shRNA).


title: HK-2 cells, CsA, t48h, biological rep 1, lab 4

tag: cell line


title: HK-2 cells, CsA, t12h, control sample, biological rep 3, lab 4


title: CD8+ 7h IFNb

source_name: CD8+ 7h IFNb

value: 7h IFNb


title: HK-2 cells, CsA, t12h, biological rep 1, lab 4

source_name: Human renal proximal tubular epithelial cells, treated with CsA, t12h

value: immortalized human renal proximal tubular epithelial cells


title: HK-2 cells, CsA, t12h, biological rep 2, lab 4


title: HK-2 cells, CsA, t12h, biological rep 3, lab 4


title: Gastric cancer stem cells_control

source_name: Gastric cancer stem cells_control

value: scramble shRNA


title: CD8+ 1h TCR

source_name: CD8+ 1h TCR

value: 1h TCR stimulation with SIINFEKL


title: CD8+ rep2


title: HK-2 cells, CsA, t48h, control sample, biological rep 2, lab 1

value: control

value: 48 hrs


title: RPA12 deleion cells_Synthetic medium_Stationay phase_replicate 1

city: Mysore

first: Ram

last: Rajasekharan

state: Karnataka

address: Mysore

department: Lipid Science Department

country: India

institute: Central Food Technological Research Institute

description: Gene expression data from RPA12 deleion cells_Synthetic medium_Stationay phase

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

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

data_processing: The data were analyzed with Expression Console  using Affymetrix default analysis settings and RMA as normalization method used. The differential gene expression is performed using GeneSpring Software.

organism: Saccharomyces cerevisiae

source_name: Stationay phase

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

growth_protocol: RPA12Δ cells were grown in synthetic medium at 30° C till stationary phase

extract_protocol: Total RNA prepared using Qiagen RNA extraction kit

treatment_protocol: No treatment

value: BY4741- MATa; his3Δ 1; leu2Δ 0; met15Δ 0; ura3Δ 0

value: RPA12 delta


title: HK-2 cells, CsA, t48h, control sample, biological rep 3, lab 1


title: CD8+ 2h IFNb

source_name: CD8+ 2h IFNb

value: CD8+ T cell

value: 2h IFNb


title: Wt KK

description: Wild-type cells

value: wild type


title: CD8+ rep1

value: OT-I TCR tg mice


title: RPA12 deleion cells_Synthetic medium_Stationay phase_replicate 2


title: HK-2 cells, CsA, t12h, control sample, biological rep 3, lab 1

value: 12 hrs


title: HK-2 cells, CsA, t12h, control sample, biological rep 2, lab 1


title: HK-2 cells, CsA, t48h, control sample, biological rep 1, lab 1


title: JHD2 OE-biological rep1

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

description: Gene expression data from S.cerevisiae with JHD2 gene over-expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip Yeast 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Freshly grown yeast cell at OD600= 0.6~0.7

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Over-night mini-culture was transferred to final volume of fresh media to make a start OD600=0.2.  Cells were then grown at 30 degree with shaking for 3~5 hours to reach final OD600 as 0.6~0.7.

extract_protocol: Total RNA were extracted from cells by phenol/ chloroform method and then purified with Geneaid total RNA purification kit.

treatment_protocol: Cells were washed twice w/ TBS (150 mM NaCl, 10 mM Tris pH7.4) and stored at -80 degree until total RNA extraction.

tag: genotype/variation

value: (jhd2∆::KanMx)+(JHD2 O/E),his3-1, leu2-0, lys2-0, ura3-0


title: HK-2 cells, CsA, t12h, biological rep 2, lab 1

value: CsA


title: HK-2 cells, CsA, t12h, control sample, biological rep 1, lab 1


title: JHD2 OE-biological rep2


title: WT-JHD2 OE-biological rep2

description: Gene expression data from WT S.cerevisiae

value: his3∆1 le2∆0 lys2∆0 ura3∆0, TRP+, MET15+, ADE+


title: HK-2 cells, CsA, t12h, biological rep 1, lab 1


title: jhd2 deletion-biological rep2

description: Gene expression data from S.cerevisiae with JHD2 gene deletion

value: his3∆1 le2∆0 lys2∆0 ura3∆0 jhd2::KanMX


title: HK-2 cells, CsA, t48h, biological rep 1, lab 1


title: WT-JHD2 OE-biological rep1


title: HK-2 cells, CsA, t48h, biological rep 3, lab 1


title: jhd2 deletion-biological rep3


title: WT jhd2-biological rep3


title: jhd2 deletion-biological rep1


title: HK-2 cells, CsA, t12h, biological rep 3, lab 1


title: HK-2 cells, CsA, t48h, biological rep 2, lab 1


title: WT jhd2-biological rep1


title: WT-jhd2-biological rep2


title: set1 deletion-biological rep2

description: Gene expression data from S.cerevisiae with SET1 gene deletion

value: set1::KanMx, his3-1, leu2-0, met15-0, ura3-0


title: WT-set1-biological rep2

value: his3∆1 le2∆0 lys2∆0 ura3∆0, TRP+, Met15+, ADE+


title: HK-2 cells, CsA, t48h, control sample, biological rep 2, lab 3

value: immortalized human renal proximal tubular epithelial cells


title: HK-2 cells, CsA, t48h, control sample, biological rep 3, lab 3


title: HK-2 cells, CsA, t24h, control sample, biological rep 3, lab 3

source_name: Human renal proximal tubular epithelial cells, control for CsA, t24h

value: 24 hrs


title: HK-2 cells, CsA, t24h, control sample, biological rep 2, lab 3

value: control


title: HK-2 cells, CsA, t48h, control sample, biological rep 1, lab 3

value: 48 hrs


title: set1 deletion-biological rep1


title: WT-set1-biological rep1


title: HK-2 cells, CsA, t24h, control sample, biological rep 1, lab 3


title: HK-2 cells, CsA, t24h, biological rep 2, lab 3

source_name: Human renal proximal tubular epithelial cells, treated with CsA, t24h


title: HK-2 cells, CsA, t12h, control sample, biological rep 3, lab 3


title: HK-2 cells, CsA, t12h, biological rep 2, lab 3


title: HK-2 cells, CdCl, t48h, control sample, biological rep 2

source_name: Human renal proximal tubular epithelial cells, control for CdCl, t48h


title: HK-2 cells, CsA, t24h, biological rep 1, lab 3


title: HK-2 cells, CsA, t12h, biological rep 3, lab 3


title: HK-2 cells, CsA, t48h, biological rep 2, lab 3


title: HK-2 cells, CsA, t12h, control sample, biological rep 2, lab 3


title: HK-2 cells, CdCl, t48h, control sample, biological rep 3


title: HK-2 cells, CsA, t48h, biological rep 1, lab 3


title: HK-2 cells, CsA, t12h, control sample, biological rep 1, lab 3


title: HK-2 cells, CdCl, t12h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for CdCl, t12h


title: HK-2 cells, CdCl, t12h, control sample, biological rep 1


title: HK-2 cells, CsA, t48h, biological rep 3, lab 3


title: HK-2 cells, CsA, t24h, biological rep 3, lab 3


title: HK-2 cells, CdCl, t12h, control sample, biological rep 2


title: HK-2 cells, CsA, t12h, biological rep 1, lab 3


title: HK-2 cells, CdCl, t48h, control sample, biological rep 1


title: hMSCs treated with Mdm2&p53 knock down and differentiated into osteoblasts (1)

source_name: human mesenchymal stem cells differentiated into osteoblasts


title: HK-2 cells, CdCl, t48h, biological rep 2

source_name: Human renal proximal tubular epithelial cells, treated with CdCl, t48h

value: CdCl


title: HK-2 cells, CdCl, t48h, biological rep 3


title: GRO src1 YPD

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: nascent Transcriptional Rate: Processed data of Genomic Run On triplicate experiment, Median Absolut Deviation normalized.

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 triplicate.

source_name: src1Δ cells grown in YPD to exponential phase

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.

growth_protocol: Exponential growth in YPD at 28ºC.

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.

value: src1Δ deletion mutant background BY4741


title: cDNA pub1 YPD

description: mRNA Amount: Processed data of cDNA triplicate experiment, [mRNA/cell volume] adjusted and Median Absolut Deviation normalized.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt’s, 0.5% SDS and 100 µg herring sperm DNA/ml. 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 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2X SSC, 0.1% SDS.

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. 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 or re-scanned with the Phosphorimager.

source_name: pub1Δ cells grown in YPD to exponential phase

label_protocol: In vivo labeling by run-on (GRO) using 33P-UTP.Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were washed in cold water and the cell pellet was resuspended in 900 µl of sterile cold water (final volume 950 µl). Then, the cell suspension was transferred to a fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells were incubated for 20 minutes on ice. After the permeabilization step, cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 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). Cells were maintained on ice at all times. The final volume was adjusted to 300 µl with distilled water and 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. In cDNA labeling, about 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 µL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

growth_protocol: Exponential growth in YPD or YPGal at 28ºC.

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

value: pub1Δ deletion mutant background W303

tag: media

value: YPD


title: osnox2 mutant under drought stress condition, biological rep3

city: Yangling

first: Kunming

state: Shaanxi

address: Xinong Road 22#

department: College of Life Sciences

institute: Northwest A&F University

description: Gene expression data from leaves

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip rice genome arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (P/N 00-00212, Affymetrix)

data_processing:
The data were read with Command Console Software 3.1 (Affymetrix) and normalized using GeneSpring Software 11.0 (Agilent) and the MAS5.0 algorithm.
Data quality was assessed and statistical analysis was performed as described in the Affymetrix GeneChip Expression Analysis and Statistical Algorithms Description Documents. The data were analyzed using Student’s t-test.

organism: Oryza sativa

source_name: The youngest fully expanded leaves from 2.5-month-old osnox2 plants under drought stress condition

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

growth_protocol: After germination, rice seeds were transferred into a tray and watered daily with Hoagland’s nutrient solution. After 2 weeks, when the fourth leaf of each seedling had fully expanded, every four seedlings was transferred into a plastic pot, which were each filled with 12.5 kg of soil from a paddy field and cultivated in a greenhouse with a day/night temperature cycle of 36 ◦C/28 ◦C, light intensity of 800 μmol m-1 s-1, 16 h day/8 h dark, and 60%–65% relative humidity. The seedlings were watered at 2–3 d intervals to keep the soil submerged in water until the drought treatments were applied.

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

treatment_protocol: For drought treatment, pairs of 10-week-old osnox2 and WT plants were each grown in the same pot to ensure an identical water-stress condition. The youngest fully expanded leaf from each osnox2 and WT plant was harvested 0 and 15 days after the commencement of the drought treatment. At these two time points, the soil moisture percentages were 47.3 ± 1.9% and 8.5 ± 2.1%, respectively.

value: drought

value: fresh leaves

value: osnox2 T-DNA insertion mutant


title: HK-2 cells, CdCl, t12h, biological rep 1

source_name: Human renal proximal tubular epithelial cells, treated with CdCl, t12h

value: 12 hrs


title: GRO wt-SRC1 YPD

source_name: Wild type cells grown in YPD to exponential phase.

value: BY4741 wild type


title: osnox2 mutant under drought stress condition, biological rep2

description: Gene expression data from leaves


title: osnox2 mutant under normal growth condition, biological rep2

description: Gene expression data from leaves

source_name: The youngest fully expanded leaves from 2.5-month-old osnox2 plants under normal growth condition


title: c_M_08 (GEP)

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

description:
MLBCL
MS_M_M08

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing:
The raw ‘.CEL’ files were converted into probeset-specific expression values using Affymetrix’ MAS5 summarization method as implemented in the BioConductor package ‘simpleaffy’ (Gentleman et al., 2004). All samples were scaled to have a mean expression level of 100.
The file lymphoma2009.nugen.rma.GSmed contains expression values for all probes of the U133plus2 chip across all samples hybridized with this chip. Furthermore, we generated a combined lymphoma.combined.nugen.rma.GS file, which contain gene-centered expression values for all genes assessed by both chips (U133A and U133plus2 chips). Since the expression profiles originated from two separate batches profiled at different times and on different chips (the first batch was profiled on U133A chip, and the 2nd batch was profiled on the U133plus2 chip), we further normalized the data carrying out a gene-specific normalization, whereby the mean and standard deviation of a gene in the 2nd batch were set to the mean and standard deviation of the corresponding gene in the 1st batch. In particular, for each profile j in batch 2, the expression of gene i was transformed as follows:  g'ij=gij-?i(2)si(2)* si(1)+?i(1), where ?i(b) and si(b) denote the mean and standard deviation of gene i in batch b=1,2.

source_name: MLBCL

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

growth_protocol: 10-20 x 20 um sections from snap-frozen tumor specimens from newly diasnosted previously untreated samples were directly transferred to Trizol.

extract_protocol: For total RNA, cells were homogenized in Trizol and RNA was extracted according to standard protocols. RNA amplification was done with Nugen kit as described in detail in the associated manuscript.

tag: disease state

value: primary MLBCL


title: osnox2 mutant under drought stress condition, biological rep1

description: Gene expression data from leaves

tag: treatment


title: cDNA ngr1 YPD

source_name: ngr1Δ cells grown in YPD to exponential phase

value: ngr1Δ deletion mutant background W303


title: HK-2 cells, CdCl, t48h, biological rep 1

tag: treatment duration


title: cDNA pub1 YPGal

source_name: pub1Δ cells grown in YPGal to exponential phase

value: YPGal


title: cDNA wt YPD

value: W303 wild type


title: c_M_09 (GEP)

description:
MLBCL
MS_M_M09


title: osnox2 mutant under normal growth condition, biological rep1

description: Gene expression data from leaves


title: osnox2 mutant under normal growth condition, biological rep3

description: Gene expression data from leaves


title: c_M_06 (GEP)

description:
MLBCL
MS_M_M06


title: c_M_02 (GEP)

description:
MLBCL
MS_M_M02


title: c_M_07 (GEP)

description:
MLBCL
MS_M_M07


title: GRO nrg1 YPD


title: c_M_05 (GEP)

description:
MLBCL
MS_M_M05


title: c_M_03 (GEP)

description:
MLBCL
MS_M_M03


title: c_M_01 (GEP)

description:
MLBCL
MS_M_M01


title: c_M_04 (GEP)

description:
MLBCL
MS_M_M04


title: 180U/D-motility pair-rep2

city: Beijing

first: Zhihua

last: Liu

address: No.17, Panjiayuannanli, Chaoyang District

department: Cancer Institute & Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: Cy3 labelled samples were A while Cy5 labelled samples were B. 30U1 and 30D1,30U2 and 30D2, 180U1 and 180D1, 180U2 and 180D2 were four pairs of subpopulations derived from simultaneously selected four independent parental populations, respectively.

scan_protocol: This procedure was completed by LC Sciences using Axon GenePix 4000B Microarray Scanner.

data_processing: Data was analyzed by professionals in LC Sciences using ArrayPro software. Global Normalization was used to process raw data. Data in processed data files are log2 Cy5/Cy3.

source_name: 180D2-strong motility subpopulation

label_protocol: This procedure was completed by LC Sciences. Notably, RNA for expression array and microRNA array was from the extracted samples.

growth_protocol: Harvested 30U/D and 180U/D subpopulations were grown to about 80% confluence under standard cell culture condition and each subpopulation with the same passages (2 passages after the harvest) was used in the following RNA extraction.

extract_protocol: The frozen samples with dry ice were sent to LC Sciences (Texas, USA) and all of the following procedures were carried out by professionals in LC Sciences. We received RNA QC report analyzed by Agilent 2100 Bioanalyzer.

treatment_protocol: Approximately 80% confluent target cells maintained in 10-cm dishes were washed twice using pre-cooled PBS. Then 6 ml Trizol (Invitrogen) were added to lyse cells thoroughly. Finally, we transferred the lysed cells into 1.5 ml  RNase-free tubes and stored them in -80 degree fridge immediately.

tag: origin cell line

value: esophageal squamous cell carcinoma cell line KYSE-180

tag: morphology

value: Epithelial

tag: primary tumor

value: well differentiated, a3 (Invasion depth)

tag: passage

source_name: 180U2-weak motility subpopulation


title: old_c470 (GEP)

description:
DLBCL
MS_D_470

source_name: DLBCL

value: primary DLBCL


title: GRO (1) pub1 YPGal

tag: strain


title: old_c506 (GEP)

description:
DLBCL
MS_D_506


title: GRO wt YPD


title: 180U/D-motility pair-rep1

hyb_protocol: This procedure was completed by LC Sciences.

source_name: 180U1-weak motility subpopulation

source_name: 180D1-strong motility subpopulation


title: 30U/D-motility pair-rep2

source_name: 30D2-strong motility subpopulation

value: esophageal squamous cell carcinoma cell line KYSE-30

source_name: 30U2-weak motility subpopulation


title: old_c460 (GEP)

description:
DLBCL
MS_D_460


title: GRO pub1 YPD


title: 30U/D-motility pair-rep1

source_name: 30U1-weak motility subpopulation

source_name: 30D1-strong motility subpopulation


title: old_c438 (GEP)

description:
DLBCL
MS_D_438


title: PTC - BRAF(+) - NIS357

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

hyb_protocol: Following fragmentation, 16 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: Data was acquired using GeneChip Command Console Software 1.1 (Affymetrix). The preprocessing was performed by Robust Multi-Array expression measure using sequence information (GCRMA, R/Bioconducor)

source_name: PTC, BRAF(+)

label_protocol: Total RNA (5 ug) was used for synthesis of double stranded cDNA and aRNA labeling according to manufacturer's instructions (GeneChip 3' IVT Express Kit, Affymetrix).

extract_protocol: The RNA was extracted from frozen sections of thyroids of patients operated in MSC Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Poland. The extraxtion was performed with the RNeasy Micro Kit (Qiagen GmbH, Hilden, Niemcy) according to the protocol. The quantity and quality of RNA were analyzed with NanoDrop ND-1000 and Bioanalyzer 2100 (Agilent Technologies) respectively.

tag: type of thyroid tissue

value: papillary thyroid carcinoma

tag: braf/ret/ras status; braf(+)- v600e mutation presence; ret(+)- ret rearrangement presence, ras(+) - ras mutation presence

value: BRAF(+)

tag: Sex

value: female

tag: age (years)


title: PTC - BRAF(+) - NIS377

value: male


title: OCS_day5_4

city: Farmington

first: Anne

middle: M

last: Delany

state: CT

address: 263 Farmington Ave

department: Molecular Medicine

institute: UConn Health Center

description: miRNA expression in bone marrow-derived osteoclast cultures after 5 days of differentiation with M-CSF and RANKL

hyb_protocol: According to the manufacture's instructions, using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies), labeled RNA was hybridized for 20 hours onto a mouse miRNA Microarray, Release 15.0, 8x15K (Agilent Technologies).

scan_protocol: Slides were washed and scanned at 5 µm resolution using an Agilent SureScan Microarray Scanner (Agilent Technologies).

data_processing:
Image processing was completed using Feature Extraction Software (Agilent Technologies).
Microarray data were normalized and analyzed using the GeneSpring GX software (Technology 29152_v.17_0, Agilent Technologies). Quantile normalization was performed on the signal intensities. Data are represented in log2 scale.

source_name: OSC_M-CSF + RANKL_day5

label_protocol: According to the manufacture's instructions, Cyanine-3 (Cy3) labeled RNA was prepared from 200 ng total RNA using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted using the miRNeasy Mini kit (Qiagen, Valencia, CA). On-column DNase digestion and an additional treatment with RQ1 DNase (Promega, Madison, WI) were perfomed to reduce genomic DNA contamination. RNA concentration and purity were assessed by spectrophotometric analysis. The quality of small RNAs in each sample was determined using the 2100 Bioanalyzer assay (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Bone marrow was isolated from mouse long bone. MACS sorting was used to deplete B220/CD45R+ and CD3+ B and T lymphocyes, enriching for the osteoclast precursor population. Osteoclast precursors were cultured in α-MEM supplemented with 10% fetal bovine serum, in the presence of 30 ng/ml each of recombinant M-CSF (macrophage colony-stimulating factor) and RANKL (receptor activator of NFκB ligand) for 1, 3, and 5 days.

tag: gender

tag: age

value: 6-8 weeks old

tag: tissue

value: bone marrow

tag: tissue subtype

value: bone marrow-derived osteoclast precursors

tag: cultured with

value: 30 ng/ml M-CSF and RANKL for 5 days


title: OCS_day5_3


title: PTC - BRAF(+) - NIS356


title: OCS_day5_1


title: OCS_day5_2


title: PTC - BRAF(+) - NIS350


title: PTC - BRAF(+) - NIS340


title: PTC - BRAF(+) - NIS344


title: OCS_day3_4

description: miRNA expression in bone marrow-derived osteoclast cultures after 3 days of differentiation with M-CSF and RANKL

source_name: OSC_M-CSF + RANKL_day3

value: 30 ng/ml M-CSF and RANKL for 3 days


title: PTC - BRAF(+) - NIS346


title: PTC - BRAF(+) - NIS331


title: PTC - RET(+) - NIS329

source_name: PTC, RET(+)

value: RET(+)


title: OCS_day3_3


title: PTC - RAS(+) - NIS342

source_name: PTC, RAS(+)

value: RAS(+)


title: normal thyroid - NIS281

source_name: normal thyroid

value: normal thyroid


title: PTC - RET(+) - NIS321


title: PTC - BRAF(+) - NIS341


title: PTC - BRAF(+) - NIS319


title: PTC - BRAF(+) - NIS349


title: PTC - BRAF(+) - NIS233


title: normal thyroid - NIS224


title: PTC - BRAF(+) - NIS327


title: PTC - RET(+) - NIS162


title: normal thyroid - NIS161


title: PTC - RET(+) - NIS159


title: OCS_day3_2


title: normal thyroid - NIS158


title: normal thyroid - NIS153


title: OCS_day3_1


title: OCS_day1_4

description: miRNA expression in bone marrow-derived osteoclast cultures after 1 day of differentiation with M-CSF and RANKL

source_name: OSC_M-CSF + RANKL_day1

value: 30 ng/ml M-CSF and RANKL for 1 day


title: OCS_day1_3


title: OCS_day1_2


title: OCS_day1_1


title: PTC - RET(+) - NIS146


title: normal thyroid - NIS144


title: PTC - RET(+) - NIS152


title: normal thyroid - NIS138


title: normal thyroid - NIS150


title: PTC - BRAF(+) - NIS378


title: PTC - BRAF(+) - NIS140


title: normal thyroid - NIS232


title: normal thyroid - NIS141


title: PTC - RET(+) - NIS137


title: normal thyroid - NIS209


title: normal thyroid - NIS139


title: PTC - BRAF(+) - NIS135


title: normal thyroid - NIS163


title: PTC - RET(+) - NIS133


title: normal thyroid - NIS134


title: PTC - BRAF(+) - NIS370


title: normal thyroid - NIS132


title: normal thyroid - NIS119


title: normal thyroid - NIS112


title: normal thyroid - NIS136


title: HK-2 cells, CdCl, t12h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with CdCl, t12h

tag: cell line

tag: cell type

value: immortalized human renal proximal tubular epithelial cells

value: CdCl

value: 12 hrs


title: cardiac muscle P30 knockout repl.6

city: Lleida

first: Daniel

last: Sanchis

address: Av. Rovira Roure, 80

department: Basic Medical Sciences

institute: IRBLLEIDA - University of LLeida

hyb_protocol: Approximately 3μg of fragmented and labeled ssDNA was hybridzed per array using the Affymetrix hybridization guides. Arrays were hybridized for 17 h in GeneTitan Affymetrix platform

scan_protocol: Arrays were scanned on GeneTitan Affymetrix platform

data_processing:
Data were processed using the limma (v3.14) and oligo (v1.22) packages in the R (v2.15) environment. Probeset level expression was derived using Robust Multi-array Average normalization. Non-specific filtering of 50% less intense and variable data was applied. Data were limited to core probe set only, and summarized at the gene expression level.
probe group file: MoGene-1_1-st-v1.r4.pgf
meta-probeset file: MoGene-1_1-st-v1.r4.mps

source_name: heart, 1-month-old,KO

label_protocol: Samples 5μg of ssDNA were fragmented and labeled using the Terminal Labeling kit  (Affymetrix) following protocol guides.Approximately 3μg of fragmented and labeled ssDNA was hybridzed per array using the Samples 5μg of ssDNA were fragmented and labeled using the Terminal Labeling kit (Affymetrix) following protocol guides.

growth_protocol: mouse ventricular muscle dissected from P1-2 and P30 mice

extract_protocol: hearts were scised, minced and washed in ice-cold buffered saline and inmediatly frozen. Kept at -80ºC until RNA extraction

treatment_protocol: not applicable

value: cardiac muscle

value: 1 month-old

tag: genotype/variation

value: knockout


title: HK-2 cells, CdCl, t12h, biological rep 2

tag: treatment

tag: treatment duration


title: cardiac muscle P30 knockout repl.4


title: cardiac muscle P30 knockout repl.5


title: cardiac muscle P30 wt repl.5

source_name: heart,1-month-old,wild type

value: wild type


title: PTC - BRAF(+) - NIS131

value: papillary thyroid carcinoma

value: BRAF(+)

value: female


title: cardiac muscle P30 knockout repl.2


title: cardiac muscle P30 knockout repl.3


title: cardiac muscle P30 wt repl.4


title: cardiac muscle newborn knockout repl.5

source_name: heart, neonate,KO

value: newborn


title: cardiac muscle newborn wild type repl.3

source_name: heart, neonate,wild type


title: cardiac muscle newborn knockout repl.2


title: cardiac muscle newborn knockout repl.4


title: cardiac muscle P30 wt repl.3


title: cardiac muscle P30 wt repl.2


title: cardiac muscle newborn wild type repl.4


title: cardiac muscle newborn wild type repl.2


title: CTY018 [V1]

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

hyb_protocol: High quality RNA was reverse transcribed and hybridized on the Illumina HumanHT12 V4 Expression BeadChip

data_processing: quantile normalisation using Bioconductor

source_name: PBMC

extract_protocol: Total cellular RNA was extracted from PBMC using RNeasy columns kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Blood samples were collected in EDTA tubes.

tag: donor

value: PBMCs


title: cardiac muscle newborn knockout repl.1


title: cardiac muscle P30 wt repl.6


title: cardiac muscle newborn knockout repl.6


title: cardiac muscle P30 knockout repl.1


title: cardiac muscle newborn wild type repl.5


title: cardiac muscle newborn wild type repl.6


title: CTY019 [V2]


title: cardiac muscle newborn wild type repl.1


title: CTY017 [V2]


title: CTY014 [V1]


title: cardiac muscle newborn knockout repl.3


title: CTY016 [V1]


title: CTY012 [V1]


title: CTY013 [V2]


title: Pig 1502

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

hyb_protocol: Fluidics station FS450

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: rma normalisation with apt-probeset-summarize from Affymetrix apt suite, filtered for genes with dabg <=0.05 for at least 2 members of at least one experimental group.dabg values were obtained from apt-probeset-summarize.

organism: Sus scrofa

source_name: skeletal muscle (biceps brachii)_placebo-treated

label_protocol: NuGen Applause WT-Amp ST System

growth_protocol: Determination of skeletal muscle samples from Musculus biceps brachii of liraglutide- and placebo-treated pigs

extract_protocol: Trizol

treatment_protocol: 0.6-1.8 mg liraglutide or placebo per day was injected subcutaneously for 90 days

value: skeletal muscle

value: placebo-treated pigs

value: 5 months


title: HME3-ZEB1-RAS D90

type: genomic

city: Lyon

last: Wierinckx

state: select a state

address: 8, av Rockefeller

country: France

institute: University Lyon1

hyb_protocol: Agilent oligonucleotide array-based CGH for genomic DNA analysis protocol

scan_protocol: The Arrays were scanned using the SureScan Microarray scanner and the Agilent Microarray Scan Control software

data_processing: files were processed using Feature Extraction software  (Agilent)

molecule: genomic DNA

source_name: mammary cells

label_protocol: ULS array-CGH labeling kit

growth_protocol: Primary human mammary epithelial cells (HMECs) immortalized by-hTert, called HME, were cultured in 1:1 Dulbecco’s Modified Eagle’s Medium (DMEM)/HAMF12 medium (Invitrogen) complemented with 10% FBS (Cambrex), 100 U/ml penicillin-streptomycin (Invitrogen), 2 mM L glutamine (Invitrogen), 10 ng/ml human epidermal growth factor (EGF) (PromoCell), 0.5 mg/ml hydrocortisone (Sigma) and 10 mg/ml insulin (Actrapid).

extract_protocol: Phenol chloroform Alcool isoamylic technology

value: HMEC hTERT immortalized cell line ectopically expressing HRasG12V and ZEB1

tag: retrovirus expression

value: expressed Zeb1 and HRasG12V

tag: state

value: transformed

value: pool normal lymphocytes


title: CTY015 [V2]

scan_protocol: Standard Illumina scanning protocol


title: CTY011 [V2]


title: Pig 1505


title: HCC95-LZTFL1-GFP

city: Dallas

first: Zhi-Ping

state: TX

address: 5323 Harry Hines Boulevard

department: Internal Medicine

institute: University of Texas Southwestern Medical Center at Dallas

description:
SAMPLE 3
replicate 1

hyb_protocol: according to the Illumina Manual “Direct Hybridization Assay Guide

data_processing: Illumina GenomeStudio v2011.1 Gene Expression Software Expression software

source_name: HCC95 lung cancer cells (American Type Culture Collection), transfected with LZTFL1 with bicistronic GFP

label_protocol: Illumina HumanHT-12 v4

growth_protocol: Cultured in DMEM supplemented with Glutamax, 10% fetal bovine serum and 1% pen/strep

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

value: lung cancer

tag: transfected with

tag: treated with


title: cardiac muscle P30 wt repl.1

value: cardiac muscle

tag: strain


title: H460-GFP

description:
SAMPLE 5
replicate 1

source_name: H460 lung cancer cells (American Type Culture Collection), transfected with control GFP


title: Pig 1497


title: CTY009 [V2]

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


title: Pig 1323


title: HME2-ZEB1- RAS D90


title: CTY008 [V1]


title: CTY010 [V1]


title: HME3-RAS D90

value: HMEC hTERT immortalized cell line ectopically expressing HRasG12V

value: expressed HRasG12V

value: non transformed


title: HCC95-LZTFL1-GFP+TGFβ

description:
SAMPLE 4
replicate 1

source_name: HCC95 lung cancer cells (American Type Culture Collection), transfected with LZTFL1 with bicistronic GFP and treated with TGFβ

value: TGFβ


title: Pig 1316


title: H460-LZTFL1-GFP

description:
SAMPLE 6
replicate 1

source_name: H460 lung cancer cells (American Type Culture Collection), transfected with LZTFL1 with bicistronic GFP


title: Pig 1317


title: HME2-RAS D90


title: treatment naïve OSA patient (VSO) [9249889011L]

city: Kaohsiung

first: yungche

last: chen

address: 123, Ta-Pei Rd. Niao-Sung Dist.

institute: Kaohsiung Chang Gung Memorial Hospital

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: treatment naïve OSA patient (VSO)

value: PBMC

tag: apnea hyponea index

tag: Sex

value: male

tag: hypertension

tag: eds


title: OSA patient with long-term CPAP treatment [9249889011K]

tag: age


title: HCC95GFP+TGFβ

description:
SAMPLE 2
replicate 1

source_name: HCC95 lung cancer cells (American Type Culture Collection), transfected with control GFP and treated with TGFβ


title: HME1-SNAI1-RAS D90

value: HMEC hTERT immortalized cell line ectopically expressing HRasG12V and SNAI1

value: expressed SNAI1 and HRasG12V


title: OSA patient with long-term CPAP treatment [9249889011F]


title: HME1-ZEB1-RAS D45


title: HME1-ZEB1-RAS D90


title: Pig 1315

tag: tissue

value: skeletal muscle


title: HME1-ZEB1-RAS D15

tag: cell line


title: Pig 1495

source_name: skeletal muscle (biceps brachii)_liraglutide-treated

value: liraglutide-treated pig


title: treatment naïve OSA patient (MSO) [9249889011I]

source_name: treatment naïve OSA patient (MSO)

tag: cell type


title: OSA patient with long-term CPAP treatment [9249889011E]


title: Pig 1506

value: 5 months


title: Pig 1311

value: placebo-treated pigs


title: Pig 1503


title: Pig 1492


title: HCC95-GFP

description:
SAMPLE 1
replicate 1

source_name: HCC95 lung cancer cells (American Type Culture Collection), transfected with control GFP


title: Primary snoring subject [9249889011J]

source_name: Primary snoring subject

value: female


title: OSA patient with long-term CPAP treatment [9249889011D]


title: HME1-TWIST1-RAS D90

value: HMEC hTERT immortalized cell line ectopically expressing HRasG12V and TWIST1

value: expressed TWIST1 and HRasG12V

value: transformed


title: HME1-RAS D15

value: pool normal lymphocytes


title: 101322-23

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: 50 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4 as per manufacturer's instructions.

scan_protocol: The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.

data_processing: Raw expression data were analysed using Agilent GeneSpring GX 11 (agilent Technologies, Santa Clara, CA, USA). Raw data were normalized with a quantile algorithm and the baseline was transformed to the median of all samples. Those probes with a flag value of 'Present' or 'Marginal' in >= 80% of any of the experimental categories were selected for futher analysis. The R package RankProd was used to identify differentially expressed genes. Genes were defined as differentially expressed if the percentage of false positives in 1,000 permutations of the Rank Products test was <5% and the change in expression was > 1.2x in either direction.

source_name: rectal mucosal biopsy

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate Biotin labeled (biotin-16-UTP), amplified cRNA starting from 200ng total RNA.

extract_protocol: RNA extraction was performed using TRIZOL (Invitrogen, Gibco (Ambion) following standard procedures. Briefly, RNA Later was drained from the biopsies on a clean wipe before submerging the biopsy in 0.5ml of TRIZOL. The biopsy was homogenised in TRIZOL, on ice, using a blender.  At this stage, an extra 0.5ml of TRIZOL was added to the homogenised biopsy, followed by 5 min incubation at room temperature. Samples were centrifuged (10 min, 12.000×g, 4°C), the supernatant fluid was extracted for 3 min with chloroform (0.2ml / ml TRIZOL ), centrifuged (15min, 12.000×g, 4°C) and the upper phase was precipated in 70% EtOH prepared in DEPC-treated milliQ water. The sample was purified on PureLink RNA cartridge (Ambion) according to manufacturer’s protocol and eluted in RNase-DNAase-free H2O.

treatment_protocol: Mucosall pinch biopsies were obtained from anatomically normal mucosa 10cm from the rectal verge and placed immediately in RNA Later (Ambion, Life Technologies, Paisley, UK) for transcriptomics, and stored at -80C

value: rectal mucosa

tag: plasma selenium concentration (µmol/l)

tag: plasma selenium status

value: Sub-optimal

value: MALE

tag: bmi


title: HME1  D90

value: HMEC hTERT immortalized cell line

value: immortalized


title: 101322-21

value: FEMALE


title: OSA patient with long-term CPAP treatment [9249889011C]

value: PBMC

value: male


title: 101322-24

value: Optimal


title: OSA patient with long-term CPAP treatment [9249889011G]


title: OSA patient with long-term CPAP treatment [9249889011H]


title: 101322-20


title: 101322-22


title: HME1-RAS D45

value: HMEC hTERT immortalized cell line ectopically expressing HRasG12V

value: expressed HRasG12V

value: non transformed


title: 101322-19


title: HME1  D45


title: Pig 1488

value: skeletal muscle

tag: treatment

value: liraglutide-treated pig

value: 5 months


title: yeast_induced_AWR5_6 h_rep2

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

hyb_protocol: Microarrays were processed as described in Hegde, P., R. Qi, et al. (2000). A concise guide to cDNA microarray analysis. Biotechniques 29(3): 548-562.

scan_protocol: Scanned in a ScanArray 4000 apparatus (Packard BioChips Technologies). The output was analyzed using GenePix Pro 6.0 software.

data_processing: Unflagged features (signal > 100, diameter >120), normalized by median of ratios.

source_name: yeast tetO:AWR5 15 µg/ml dox (repressing) 6 h

label_protocol: Total RNA (8 μg) was employed for cDNA synthesis and labelling using the indirect labelling kit (CyScribe Post-Labeling kit; GE Healthcare) with Cy3–dUTP and Cy5–dUTP fluorescent nucleotides.

extract_protocol: RNA was extracted using the yeast RiboPureTM RNA Purification Kit (Ambion) according to the manufacturer’s protocol.

tag: background strain

value: JA-awr5 (MATa ura3-5 leu2-3,112 trp1-1 his4 can-1r PPZ1 PPZ2 HAL3 tetO:AWR5::GFP::URA3)

value: dox (repressing)

tag: time

source_name: yeast tetO:AWR5 no dox (inducing)  6 h after removal dox

value: no dox (inducing)


title: yeast_induced_AWR5_6 h_rep1


title: yeast_induced_AWR5_4 h_rep2

source_name: yeast tetO:AWR5 15 µg/ml dox (repressing) 4 h

source_name: yeast tetO:AWR5 no dox (inducing) 4 h after removal dox


title: Pig 1313


title: Pig 1326


title: yeast_induced_AWR5_2 h_rep1

source_name: yeast tetO:AWR5 no dox (inducing) 2 h after removal dox

source_name: yeast tetO:AWR5 15 µg/ml dox (repressing) 2 h


title: Primary snoring subject [9249889008K]


title: 101322-18

value: rectal mucosa


title: 101322-17

value: Sub-optimal


title: OSA patient with long-term CPAP treatment [9249889008L]


title: 101322-16

value: MALE


title: treatment naïve OSA patient (VSO) [9249889011B]

value: female


title: 101322-15

value: FEMALE


title: treatment naïve OSA patient (VSO) [9249889011A]

value: PBMC


title: yeast_induced_AWR5_4 h_rep1


title: HME1-RAS D90

source_name: mammary cells

tag: retrovirus expression

tag: state

value: pool normal lymphocytes


title: Pig 1331


title: treatment naïve OSA patient (MSO) [9249882091J]

value: male


title: 101322-12


title: 101322-14

value: Optimal


title: 101322-13


title: HME1  D15

value: HMEC hTERT immortalized cell line

value: immortalized


title: genomic DNA from PBMC osa16

city: Hsinchu

first: Tingwen

address: No. 75, Boat Street, East District

institute: National Yang Ming Chiao Tung University

description: PBMC sample from OSA patients

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: PBMC osa16

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: disease state

value: OSA


title: Primary snoring subject [9249882091H]

tag: apnea hyponea index

tag: Sex


title: treatment naïve OSA patient (MSO) [9249882091I]

tag: hypertension

tag: eds


title: genomic DNA from PBMC osa15

description: PBMC sample from OSA patients

source_name: PBMC osa15

value: Male


title: 101322-10

tag: tissue

tag: age


title: treatment naïve OSA patient (VSO) [9249882091D]

tag: cell type


title: genomic DNA from PBMC osa14

description: PBMC sample from OSA patients

source_name: PBMC osa14


title: 101322-09

tag: plasma selenium concentration (µmol/l)


title: treatment naïve OSA patient (MSO) [9249882091G]


title: treatment naïve OSA patient (MSO) [9249882091E]


title: treatment naïve OSA patient (VSO) [9249882091F]

source_name: treatment naïve OSA patient (VSO)


title: genomic DNA from PBMC osa11

description: PBMC sample from OSA patients

source_name: PBMC osa11


title: MQ6_L_1

first: Pratiti

last: Bandopadhayay

state: Massachusetts

address: 450 Brookline Ave

description: Over-express MYBQKI6 and suppress LacZ

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Gene Pattern

source_name: mNSC

label_protocol: standard Affymetrix protocol

growth_protocol: mNSC isolated from E14.5 mouse embryos

extract_protocol: Qiagen Rnase

treatment_protocol: Lentiviral over-expression

value: mouse neural stem cell

tag: genotype

value: C57BL6 wild-type E14.5 dpc mouse embryos


title: 101322-06

tag: plasma selenium status

tag: bmi


title: genomic DNA from PBMC osa13

description: PBMC sample from OSA patients

source_name: PBMC osa13


title: 101322-08


title: Primary snoring subject [9249882091C]


title: MQ6_9_3

description: Over-express MYBQKI6 and suppress Qk


title: MQ6_L_3

description: Over-express MYBQKI6 and suppress LacZ


title: genomic DNA from PBMC osa12

description: PBMC sample from OSA patients

source_name: PBMC osa12


title: 101322-04


title: 101322-05


title: OSA patient with long-term CPAP treatment [9249882091B]


title: genomic DNA from PBMC osa10

description: PBMC sample from OSA patients

source_name: PBMC osa10


title: genomic DNA from PBMC osa9

description: PBMC sample from OSA patients

source_name: PBMC osa9


title: 101322-03

source_name: rectal mucosal biopsy


title: MQ6_6_3

description: Over-express MYBQKI6 and suppress Qk


title: MQ6_5_2

description: Over-express MYBQKI6 and suppress Qk


title: MQ6_9_1

description: Over-express MYBQKI6 and suppress Qk


title: 18_QKItr_Pool_3

description: Over-express QKItr


title: MQ6_L_2

description: Over-express MYBQKI6 and suppress LacZ


title: 101322-02


title: 101322-01


title: genomic DNA from PBMC osa8

description: PBMC sample from OSA patients

source_name: PBMC osa8


title: PNF_45

scan_protocol: The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.

data_processing: Data were processed using R/Bioconductor (the lumi package), Raw data were transformed using a Variance Stabilizing Transformation, and normalized with the robust spline normalization algorithm. Probes were selected which fulfilled the criteria of Illumina probe detection p-value of <0.01.

source_name: Fibroblast case

growth_protocol: Primary nasal epithelial cells were harvested with a cytology brush and grown in Lonza BEGM epithelial growth medium supplemented with 100u/ml Penicillin and 100ug/mlStreptomycin, total RNA was isolated from all cells at P0.  Primary nasal fibroblast cells were grown from patient nasal biopsies in Sigma D571 DMEM media supplemented with 10% FCS, 100u/ml Penicillin and 100ug/mlStreptomycin, 2mM L-Glutamine and 5ml Amphotericin B, total RNA was isolated from all cells at P1.

extract_protocol: Total RNA isolated using the Machery Nagel Nucleospin kit following the manufacturer’s protocol, RNA integrity was checked using Agilent Bioanalyser.

tag: sample group

value: case

value: Primary Nasal Fibroblast Cells


title: 17_MYBQKI6_Pool_3

description: Over-express MYBQKI6


title: treatment naïve OSA patient (MSO) [9249882091A]

source_name: treatment naïve OSA patient (MSO)


title: genomic DNA from PBMC osa6

description: PBMC sample from OSA patients

source_name: PBMC osa6


title: treatment naïve OSA patient (VSO) [9249882080K]


title: treatment naïve OSA patient (VSO) [9249882080L]


title: 16_MYBQKI5_Pool_3

description: Over-express MYBQKI5


title: MQ6_6_1

description: Over-express MYBQKI6 and suppress Qk


title: genomic DNA from PBMC osa5

description: PBMC sample from OSA patients

source_name: PBMC osa5


title: treatment naïve OSA patient (VSO) [9249889008J]


title: 14_eGFP_Pool_3R2

description: Over-express eGFP


title: Primary snoring subject [9249882080J]

source_name: Primary snoring subject


title: 15_MYB-tr_Pool_3

description: Over-express MYBtr


title: PNF_44


title: treatment naïve OSA patient (MSO) [9249882080I]


title: genomic DNA from PBMC osa3

description: PBMC sample from OSA patients

source_name: PBMC osa3


title: genomic DNA from PBMC osa2

description: PBMC sample from OSA patients

source_name: PBMC osa2


title: OSA patient with long-term CPAP treatment [9249882080H]


title: PNF_43


title: OSA patient with long-term CPAP treatment [9249882080G]


title: 13_eGFP_Pool_3R1

description: Over-express eGFP


title: genomic DNA from PBMC osa4

description: PBMC sample from OSA patients

source_name: PBMC osa4


title: genomic DNA from PBMC osa1

description: PBMC sample from OSA patients

source_name: PBMC osa1


title: PNEC_44

source_name: Epithelial case

value: Primary Nasal Epithelial Cells


title: PNEC_43


title: treatment naïve OSA patient (VSO) [9249889008I]

source_name: treatment naïve OSA patient (VSO)


title: 12_QKItr_Pool_2

description: Over-express QKItr

source_name: mNSC


title: treatment naïve OSA patient (MSO) [9249889008H]


title: genomic DNA from PBMC C7

description: normal PBMC sample

source_name: PBMC C7

value: normal


title: PNF_42

source_name: Fibroblast control

value: control


title: PNEC_45


title: yeast_induced_AWR5_2 h_rep2

source_name: yeast tetO:AWR5 15 µg/ml dox (repressing) 2 h

tag: background strain

value: JA-awr5 (MATa ura3-5 leu2-3,112 trp1-1 his4 can-1r PPZ1 PPZ2 HAL3 tetO:AWR5::GFP::URA3)

tag: treatment

value: dox (repressing)

tag: time

source_name: yeast tetO:AWR5 no dox (inducing) 2 h after removal dox

value: no dox (inducing)


title: 11_MYBQKI6_Pool_2

description: Over-express MYBQKI6


title: 10_MYBQKI5_Pool_2

description: Over-express MYBQKI5


title: genomic DNA from PBMC C5

description: normal PBMC sample

source_name: PBMC C5

tag: gender

value: PBMC


title: 9_MYB-tr_Pool_2

description: Over-express MYBtr


title: treatment naïve OSA patient (MSO) [9249889008F]

value: male


title: PNF_41

source_name: Fibroblast case


title: OSA patient with long-term CPAP treatment [9249889008E]

value: female


title: genomic DNA from PBMC C4

description: normal PBMC sample

source_name: PBMC C4

tag: disease state


title: treatment naïve OSA patient (VSO) [9249889008G]

tag: apnea hyponea index


title: PNF_40


title: OSA patient with long-term CPAP treatment [9249889008D]

tag: Sex


title: PNEC_42

source_name: Epithelial control


title: genomic DNA from PBMC C1

description: normal PBMC sample

source_name: PBMC C1


title: PNEC_41


title: 7_eGFP_Pool_2R1

description: Over-express eGFP


title: OSA patient with long-term CPAP treatment [9249889008C]

tag: hypertension


title: genomic DNA from PBMC C2

description: normal PBMC sample

source_name: PBMC C2


title: 6_QKItr_Pool_1

description: Over-express QKItr


title: PNEC_40


title: 5_MYBQKI6_Pool_1

description: Over-express MYBQKI6


title: MCL 958

city: Barcelona

first: Pedro

last: Jares

address: c/ Villarroel 170

department: Genomics Unit

institute: IDIBAPS

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

source_name: MCL 958

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: disease

value: primary MCL


title: 3_MYB-tr_Pool_1

description: Over-express MYBtr


title: 4_MYBQKI5_Pool_1

description: Over-express MYBQKI5


title: treatment naïve OSA patient (MSO) [9249889008B]

source_name: treatment naïve OSA patient (MSO)

tag: eds


title: MCL 987

source_name: MCL 987


title: PNEC_39


title: MCL207P


title: treatment naïve OSA patient (MSO) [9249889008A]

tag: age


title: treatment naïve OSA patient (VSO) [9249882091L]

tag: cell type


title: MCL101P


title: treatment naïve OSA patient (MSO) [9249882091K]


title: MCL153P


title: PNEC_38


title: 2_eGFP_Pool_1R2

description: Over-express eGFP


title: PNEC_37


title: PNF_38


title: 8_eGFP_Pool_2R2

description: Over-express eGFP


title: Primary snoring subject [9249882080F]

source_name: Primary snoring subject


title: MCL127P


title: MLN152


title: genomic DNA from PBMC osa7

last: Chen

description: PBMC sample from OSA patients

source_name: PBMC osa7


title: PNF_37


title: PNF_30


title: treatment naïve OSA patient (MSO) [9249882080D]


title: treatment naïve OSA patient (VSO) [9249882080C]

source_name: treatment naïve OSA patient (VSO)


title: GRANTA

source_name: GRANTA

tag: cell line

value: GRANTA


title: treatment naïve OSA patient (MSO) [9249882080B]


title: 1_eGFP_Pool_1R1

description: Over-express eGFP

source_name: mNSC

tag: genotype


title: JVM2


title: MINO

source_name: MINO

value: MINO


title: PNEC_30


title: PNEC_29


title: UPN1


title: PNF_29

source_name: Fibroblast control


title: PNEC_16


title: treatment naïve OSA patient (MSO) [9249882080E]


title: treatment naïve OSA patient (MSO) [9249882080A]


title: PNF_16


title: PNF_15


title: JEKO

source_name: JEKO

value: JEKO


title: HBL2


title: PNEC_15

source_name: Epithelial case


title: RNA from HCT116 cells treated with TNF-α/IFN-ɣ and silibinin rep2

city: Singapore

first: Lee

middle: Guat Lay

last: Caroline

address: 11 Hospital Drive

department: Department of Biochemistry, National University of Singapore

country: Singapore

institute: National Cancer Centre Singapore

description: replicate 2

data_processing: The data were normalised using quantile normalisation with Partek Genomic Suite version 6.6

source_name: Silibinin & TNF-α/IFN-ɣ treatment

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.

tag: sample type

value: colorectal cancer

value: treated with TNF-α/IFN-ɣ and silibinin


title: PB naive4

source_name: PB naive4

value: PB naive B-cell


title: PNF_14

source_name: Fibroblast case

value: case

value: Primary Nasal Fibroblast Cells


title: RNA from HCT116 cells treated with TNF-α/IFN-ɣ rep2

description: replicate 2

source_name: TNF-α/IFN-ɣ treatment

value: treated with TNF-α/IFN-ɣ


title: Spleen8

value: Spleen


title: PNEC_14

value: Primary Nasal Epithelial Cells


title: PB naive3

source_name: PB naive3


title: RNA from HCT116 cells treated with TNF-α/IFN-ɣ rep1

description: replicate 1


title: PNF_13

value: control


title: Spleen7


title: PNEC_13

source_name: Epithelial control


title: PNF_12


title: LN10

value: Lymph Node


title: RNA from HCT116 cells rep2

description: replicate 2

source_name: no treatment


title: LN9


title: Spleen6


title: RNA from HCT116 cells treated with TNF-α/IFN-ɣ and silibinin rep1

description: replicate 1


title: Primary prostate p53-/- Rb∆f/∆f Pten∆f/∆f 4

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description:
Gene expression of p53-/- prostate cells in the depletion of  Rb and Pten
Cre 4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Whole Genome Microarray 8x60K (G4852A) 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 by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Entities having Detected flag across all samples were extracted.

source_name: Prostate, Cre

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions with some changes. 3rd Spike mix was made by diluted 2nd Spike-Mix 10 times, and 1.8 ul of 3rd Spike-Mix was added to samples. Cy3 labeled cRNA was synthesized at 40°C for 20 hours and purified by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Prostate cells were cultured in FBS lack Prostacult media supplemented with bFGF and bEGF

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (#74106, Qiagen) according to the manufacturer’s instruction. RNA was quantified, and quality was monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Prostate cells were infected with adeno virus (lacZ) as a control or adeno virus (Cre) for deleting Rb and/or Pten overnight followed by changing of media. RNA was extracted after infection by 48 hours.

tag: tissue

value: prostate

value: Primary prostate p53-/- Rb deltaf/deltaf Pten deltaf/deltaf 4

tag: rb status

value: Deleted

tag: pten status


title: PNF_11

tag: sample group


title: Primary prostate p53-/- Rb∆f/∆f Pten∆f/∆f 3

description:
Gene expression of p53-/- prostate cells in the depletion of  Rb and Pten
Cre 3

value: Primary prostate p53-/- Rb deltaf/deltaf Pten deltaf/deltaf 3


title: PB naïve 2

source_name: PB naïve 2


title: PNEC_12


title: Primary prostate p53-/- Rb∆f/∆f Pten∆f/∆f 1

description:
Gene expression of p53-/- prostate cells in the depletion of  Rb and Pten
Cre 1

value: Primary prostate p53-/- Rb deltaf/deltaf Pten deltaf/deltaf 1


title: PNEC_11


title: CD19+ 6


title: Primary prostate p53-/- Rb∆f/∆f Pten∆f/∆f 2

description:
Gene expression of p53-/- prostate cells in the depletion of  Rb and Pten
Cre 2

value: Primary prostate p53-/- Rb deltaf/deltaf Pten deltaf/deltaf 2


title: PNF_9


title: RNA from HCT116 cells rep1

description: replicate 1

tag: treatment


title: PNEC_9


title: Primary prostate p53-/- Rbf/f Ptenf/f 2

description:
Gene expression of control p53-/- prostate cells in the presence of  Rb and Pten
lacZ 2

source_name: Prostate, lacZ

value: Primary prostate p53-/- Rbf/f Ptenf/f 2

value: Intact


title: Spleen5


title: LN8


title: PB naïve 1

source_name: PB naïve 1


title: Primary prostate p53-/- Rbf/f Ptenf/f 4

description:
Gene expression of control p53-/- prostate cells in the presence of  Rb and Pten
lacZ 4

value: Primary prostate p53-/- Rbf/f Ptenf/f 4


title: LN7


title: Primary prostate p53-/- Rbf/f Ptenf/f 1

description:
Gene expression of control p53-/- prostate cells in the presence of  Rb and Pten
lacZ 1

value: Primary prostate p53-/- Rbf/f Ptenf/f 1


title: LN6


title: miR-125a (+/-) MPD-1

city: Suita

first: Naoya

last: Tatsumi

state: Osaka

address: 1-7 Yamada-Oka

department: Functional Diagnostic Science

institute: Osaka University Graduate School of Medicine

hyb_protocol: The biotin-labeled aRNA was fragmented to uniform size and added to bioarrays.

scan_protocol: The bioarrays were washed, exposed to Cy5-streptavidin and scanned using GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA).

data_processing: The scanned image information was converted into spot intensity values using CodeLink™ Expression Analysis software v5.0 (Applied Microarrays, Tempe, AZ) and normalized by quantile method.

label: Biotin

label_protocol: Biotinylated aRNA was synthesized with two round amplification steps via TargetAmpTM2-round Aminoallyl-aRNA Amplification Kit (Illumina, Inc.) and Biotin-X-X-NHS kit (Illumina, Inc).

extract_protocol: Total RNA was extracted from the FACS-sorted Lin-Sca1+cKit+Flt3- hematopoietic stem cells from BM of miR-125a (+/+), miR-125a (+/-) MPD and miR-125a (-/-) MPD mice with TRIZOL (Invitrogen).

tag: strain/background

tag: genotype/variation

tag: disease status

value: myeloproliferative disorder (MPD)

value: hematopoietic stem cells (HSCs)


title: LN5


title: PNF_7

value: case

value: Primary Nasal Fibroblast Cells


title: PNEC_7

value: Primary Nasal Epithelial Cells


title: PNF_8

value: control


title: medulloblastoma_MB_31

city: Seoul

first: Seung-Ki

last: Kim

address: Jonrro-gu

country: South Korea

institute: Seoul National University

hyb_protocol: Agilent Human miRNA Microarray Kit (V2) was used as a miRNA microarray chip for hybridization. The RNA labeling and hybridization were performed according to the manufacturer's instructions.

scan_protocol: scanned with the Agilent microarray scanner

data_processing:
Agilent Feature Extraction Software-generated raw data files are not available.   Instead, the intermediate data extracted from GeneView program are linked below.
A small constant, 16, was added to the scanned raw expression values, ensuring that all the expression values were greater than zero before log2 transformation. The log2-transformed data were normalized by quantile normalization method using R/Bioconductor

source_name: primary tumor tissue

extract_protocol: The total gene signals were extracted using Agilent Feature Extraction software

tag: disease state

value: medulloblastoma

tag: gender

value: female

tag: age (years)


title: PNF_6


title: Primary prostate p53-/- Rbf/f Ptenf/f 3

description:
Gene expression of control p53-/- prostate cells in the presence of  Rb and Pten
lacZ 3

value: prostate

value: Primary prostate p53-/- Rbf/f Ptenf/f 3


title: miR-125a (+/+) control-1

source_name: HSC, wild-type


title: LN4

value: Lymph Node


title: PNF_5


title: medulloblastoma_MB_30

label_protocol: Agilent Human miRNA Microarray Kit (V2) was used as a miRNA microarray chip for hybridization. The RNA labeling and hybridization were performed according to the manufacturer's instructions.


title: medulloblastoma_MB_29

value: male


title: medulloblastoma_MB_28


title: miR-125a (-/-) MPD-1


title: medulloblastoma_MB_27


title: CD19+ 5


title: medulloblastoma_MB_26


title: Spleen4

value: Spleen


title: medulloblastoma_MB_25


title: medulloblastoma_MB_24


title: PNEC_5


title: PNF_4


title: PNEC_4


title: medulloblastoma_MB_22


title: medulloblastoma_MB_23


title: PNEC_3


title: PNF_3


title: medulloblastoma_MB_21


title: Spleen3


title: LN3


title: PNEC_2


title: medulloblastoma_MB_20


title: medulloblastoma_MB_19


title: CD19+ 3


title: medulloblastoma_MB_18


title: CD19+ 2


title: Activated B cells from subject 155

city: Atlanta

first: Ali

middle: Hassan

last: Ellebedy

state: GA

address: 1462 Clifton Rd NE

institute: Emory University

source_name: PBMCs - Day 7

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

value: Activated B cells


title: PNEC_1


title: PNF_2


title: Tonsil3

value: Tonsil


title: Tonsil1


title: Antibody secreting cells from subject 155

value: Antibody secreting cells


title: Tonsil2


title: LN2


title: Naïve B cells from subject 155

value: Naïve B cells


title: Spleen2


title: medulloblastoma_MB_17


title: Spleen1


title: MCL214

tag: disease

value: primary MCL


title: CD19+ 1


title: medulloblastoma_MB_16


title: Resting memory B cells from subject 155

value: Resting memory B cells


title: Antibody secreting cells from subject 157


title: Resting memory B cells from subject 157


title: MCL213


title: Antibody secreting cells from subject 162


title: medulloblastoma_MB_11


title: medulloblastoma_MB_12


title: medulloblastoma_MB_13


title: Activated B cells from subject 157


title: medulloblastoma_MB_10


title: medulloblastoma_MB_15


title: medulloblastoma_MB_09


title: Naïve B cells from subject 157


title: CD19+ 4


title: Activated B cells from subject 162


title: medulloblastoma_MB_08


title: Naïve B cells from subject 162


title: Resting memory B cells from subject 162


title: medulloblastoma_MB_07


title: MCL 1180


title: MCL 1194


title: medulloblastoma_MB_06


title: Antibody secreting cells from subject 163


title: MCL 1178


title: medulloblastoma_MB_05


title: MCL 1172


title: MCL 1179


title: Human adult Monocyte_transwell cocultured with NRBCs_LPS 100ng/ml_36h_rep1

city: Fukuoka

first: Cui

middle: Li

last: Li

department: Pediatrics

institute: Kyushu university

description: Gene expression of monocytes by LPS stimulation for 36h in the presence of NRBCs

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: Human adult monocytes, cord blood NRBCs

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: Fresh human monocytes were stimulated with LPS (100ng/ml) alone or transwell cocultured with NRBCs, which derived from cord blood  for 36h.  Monocytes were  collected after culture.

value: PBMNC and CBMNC

tag: cell

value: Monocyte


title: Human adult Monocyte_LPS 100ng/ml_36h_rep1

description: Gene expression of monocytes by LPS stimulation for 36h

source_name: Human adult monocytes

value: PBMNC

value: LPS stimulation for 36h


title: Resting memory B cells from subject 163

tag: cell type


title: medulloblastoma_MB_03

value: medulloblastoma


title: MCL 1176


title: Caco-2_4h_50µg/mL_of_polymeric nanoparticles (Eudragit® RLPO)_rep4

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

institute: Université de lorraine

description:
Gene expression in Caco-2 cells after 4 h in presence of polymeric nanoparticles exposure (Eudragit® RL PO, 50µg/mL)
S35_1_1

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA (specific activity > 10 pmol Cy3 / µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2 x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Human GE v2 8x60K (Agilent Technologies, Santa Clara, CA, USA) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent Technologies, Santa Clara, CA, USA), and immediately dried by brief immersion in acetonitrile.

scan_protocol: Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing:
The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent Technologies, Santa Clara, CA, USA) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20140326) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.
Normalized signal intensity by Genespring (version 13.0, Agilent Technologies, Santa Clara, CA, USA)

source_name: Caco-2, 4 h, 50µg/mL of polymeric nanoparticles (Eudragit® RLPO), replicate 4

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (version 6.6, Agilent Technologies, Santa Clara, CA, USA) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN, Venlo, NL). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyzer).

growth_protocol: Caco-2 human colon epithelial-like cell line is derived from a sample of a 72 years old man suffering from colorectal adenocarcinoma and was obtained from American Type Culture Collection (ATCC, HTB-37™, Manassas, VA, USA). Cells were grown in EMEM culture medium (Sigma Aldrich, Saint Quentin Fallavier, France) supplemented with 20% of heat-inactivated fetal bovine serum (Eurobio, Les Ullis, France) and 1% non-essential amino acids, as well as penicillin (100U/mL) and 1mM sodium pyruvate (all from Sigma Aldrich, Saint Quentin Fallavier, France). Cells were incubated at 37°C under a 5 % CO2 atmosphere, and diluted by half once a week and medium was change every 3 days. Passage 39 was used.

extract_protocol: The quality of RNA extracted by RNeasy® Mini Kit (Qiagen, Venlo, NL) was determined by spectrophotometry (A260nm/A280nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 8, Agilent 2100 Bioanalyzer, Santa Clara, CA, USA).

treatment_protocol: Caco-2 cells at a density of 3x105 cells/mL were incubated without (control) or with S-nitrosoglutathione (GSNO, 1.4 µM), or with Eudragit RL PO polymeric nanoparticles (NP-ERL, 50 μg/mL), or with GSNO loaded Eudragit RL PO polymeric nanoparticles (NP-GSNO, 50 μg/mL, corresponding 1.4 µM GSNO) for 4h. GSNO and nanoparticles was prepared by W. Wu and Professor R. Schneider in LRGP UPR-CNRS 3349 and EA 3452 CITHEFOR laboratories (Lorraine University, France).

value: Colon

value: Male

tag: age

value: 72 years

tag: cell line

value: Caco-2 colon epithelial-like cell line

tag: agent

value: nanoparticles


title: Activated B cells from subject 163


title: MCL 1171


title: Naïve B cells from subject 163


title: LN1

value: Lymph Node


title: MCL 1169


title: medulloblastoma_MB_02

value: female


title: Caco-2_4h_50µg/mL_of_polymeric nanoparticles (Eudragit® RLPO)_rep2

description:
Gene expression in Caco-2 cells after 4 h in presence of polymeric nanoparticles exposure (Eudragit® RL PO, 50µg/mL)
S46_1_1

source_name: Caco-2, 4 h, 50µg/mL of polymeric nanoparticles (Eudragit® RLPO), replicate 2

tag: tissue


title: Caco-2_4h_50µg/mL_of_polymeric nanoparticles (Eudragit® RLPO)_rep3

description:
Gene expression in Caco-2 cells after 4 h in presence of polymeric nanoparticles exposure (Eudragit® RL PO, 50µg/mL)
S35_1_2

source_name: Caco-2, 4 h, 50µg/mL of polymeric nanoparticles (Eudragit® RLPO), replicate 3


title: MCL 1166


title: blood-mid-74

scan_protocol: The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol  The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.  The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.

source_name: whole blood, fatigue level: Mid

extract_protocol: Total RNA isolated from peripheral whole blood using PAXgene Blood miRNA kit [PreAnalytix GmbH, Switzerland] following manufacturer’s protocol, RNA integrity checked using Agilent Bioanalyser.

value: whole blood

tag: fatigue status

value: Mid

tag: patient group

value: Patient

value: Female


title: medulloblastoma_MB_01


title: blood-low-21

source_name: whole blood, fatigue level: Low

value: Low