title: Liver, AIN 93W (control) diet, age 12 months, replicate 6


title: Control_070

status: Public on Aug 09 2016

type: RNA

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

country: USA

institute: The Scripps Research Institute

hyb_protocol: The Gene Titan Hybridization, Wash and Stain Kit for WT Array Plates (Affymetrix) is used to hybridize 3ug of the labeled cDNA to a multi peg Gene 1.1 ST Array Plate. The hybridization cocktail also contains Control Oligo B2 and 20X Eukaryotic Hybridization Controls as recommended by Affymetrix. Hybridization is carried out for 17 hours at 48C in the Gene Titan MC (Multichannel) Instrument ( Affymetrix). After hybridization the peg array plate is automatically washed and stained and moved to the scanner.

scan_protocol: The peg array plate is automatically moved to the Xenon laser scanner of the Titan MC instrument and scanned at default settings recommended for the peg array.

data_processing:
Probes to Import: Interrogating Probes and Control Probes, Probe filtering: skip, Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish
HuGene-1_1-st-v1.r4.pgf
HuGene-1_1-st-v1.r4.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Male Control

label_protocol: The cDNA generated from the WT Expression Kit is fragmented and biotin labeled with the Affymetrix GeneChip WT Terminal Labeling Kit ( Affymetrix). The cDNA is fragmented with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonucleaseI (APE I). The fragmented cDNA is then labeled with terminal deoxynucleotidyl transferase (TdT) and a biotin reagent.

extract_protocol: RNA Extraction from PAXgene Blood Tubes: Total RNA including small and miRNA is extracted with the PreAnalytiX  PAXgene Blood miRNA kit ( QIAGEN). A semi automated method using the QIAcube (QIAGEN) is used following manufacturer’s instructions. The quantity and quality of the RNA is assessed on a nanodrop and Agilent Bioanalyzer. miRNAeasy kit PN 217004 (Qiagen)

tag: tissue

value: Peripheral Whole Blood

tag: age


title: Control_072

source_name: Female Control


title: Control_065


title: Control_066


title: Control_064


title: Control_067


title: Control_071


title: Control_061


title: Control_060


title: Control_063


title: Control_062


title: Control_059


title: Liver, medium fat diet (25% energy), age 24 months, replicate 7

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

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

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1)

organism: Mus musculus

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

growth_protocol: Mice arrived at the age of 7 weeks and received AIN-93G for 2 weeks acclimatization period. At the age of 9 weeks, dietary intervention was started and the diets were maintained until sacrifice time points at the age of 6, 12, 24 and 28 months.

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

treatment_protocol: Prior to sacrifice each mouse was first fasted for 4 hours after which they received an intragastric gavage of 400ul of 0.5% carboxymethyl cellulose, then fasted again for another 6 hours. The animals in CR diet group were fed with half of the portion they normally received 15 min before the first fasting. During the sacrifice, after sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), liver tissue was snap-frozen and stored at -80C until further analysis.

tag: strain/background

tag: gender

value: male

value: 24 months

value: medium fat (25energy%) (MF)

tag: nafld status

value: no NAFLD


title: Control_069


title: Control_058


title: Control_053


title: Control_057


title: Liver, medium fat diet (25% energy), age 6 months, replicate 5

value: 6 months


title: Control_056


title: Control_055


title: Liver, medium fat diet (25% energy), age 24 months, replicate 4

value: NAFLD (IHTG >5%)


title: Control_052


title: Liver, medium fat diet (25% energy), age 24 months, replicate 1


title: Liver, medium fat diet (25% energy), age 24 months, replicate 3


title: Control_050


title: Control_051


title: Control_049


title: Control_054


title: Control_045


title: Control_047


title: Control_044


title: Liver, AIN 93W (control) diet, age 24 months, replicate 6

value: AIN-93W (control)


title: Liver, medium fat diet (25% energy), age 24 months, replicate 2


title: Control_046


title: Control_048


title: Liver, AIN 93W (control) diet, age 24 months, replicate 5


title: Liver, calorie restriction (30%), age 24 months, replicate 1

value: caloric restriction, 30% (CR)


title: Liver, calorie restriction (30%), age 24 months, replicate 6


title: Liver, AIN 93W (control) diet, age 24 months, replicate 4


title: Liver, calorie restriction (30%), age 24 months, replicate 5


title: Liver, calorie restriction (30%), age 24 months, replicate 3


title: Liver, AIN 93W (control) diet, age 24 months, replicate 3


title: Control_043


title: Liver, AIN 93W (control) diet, age 24 months, replicate 8


title: Liver, medium fat diet (25% energy), age 12 months, replicate 7

value: 12 months


title: Liver, medium fat diet (25% energy), age 12 months, replicate 2


title: Control_038


title: Liver, medium fat diet (25% energy), age 12 months, replicate 6


title: Control_041


title: Liver, medium fat diet (25% energy), age 12 months, replicate 1


title: Control_042


title: Liver, calorie restriction (30%), age 12 months, replicate 6


title: Liver, calorie restriction (30%), age 12 months, replicate 4


title: Control_035


title: Liver, calorie restriction (30%), age 12 months, replicate 2


title: Liver, calorie restriction (30%), age 12 months, replicate 5


title: Control_037


title: Control_036


title: Control_034


title: Control_040


title: Liver, AIN 93W (control) diet, age 12 months, replicate 7


title: Control_039


title: Liver, AIN 93W (control) diet, age 12 months, replicate 3


title: Control_031


title: Liver, AIN 93W (control) diet, age 12 months, replicate 4


title: Control_033


title: Control_029b


title: Control_030b


title: Liver, medium fat diet (25% energy), age 6 months, replicate 6


title: Liver, medium fat diet (25% energy), age 6 months, replicate 4


title: Control_028b


title: Liver, medium fat diet (25% energy), age 6 months, replicate 1


title: Liver, medium fat diet (25% energy), age 6 months, replicate 2


title: Control_026b


title: Control_027b


title: Liver, AIN 93W (control) diet, age 12 months, replicate 2


title: Liver, calorie restriction (30%), age 6 months, replicate 6


title: Control_025b


title: Liver, calorie restriction (30%), age 6 months, replicate 5


title: Control_022b


title: Liver, calorie restriction (30%), age 6 months, replicate 1


title: Control_021b


title: Control_019b


title: Liver, calorie restriction (30%), age 6 months, replicate 4


title: Liver, AIN 93W (control) diet, age 6 months, replicate 3


title: Control_024b


title: Control_023b


title: Control_016b


title: Control_013b


title: Control_017b


title: Control_018b


title: Control_012b


title: Control_014b


title: Control_011b


title: Liver, AIN 93W (control) diet, age 6 months, replicate 1


title: Liver, AIN 93W (control) diet, age 6 months, replicate 4


title: Control_008b


title: Control_010b


title: Liver, AIN 93W (control) diet, age 6 months, replicate 2


title: Control_020b


title: Control_009b


title: Control_007b


title: Control_005b


title: Control_004b


title: Control_003b


title: Control_015b


title: Control_006b


title: Control_002b


title: Fibroblasts_untreated_rep1

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

description:
FIB CTRL 1
RNA from untreated fibroblasts replicate 1

hyb_protocol: Hybridization was performed at 58 °C in GEX-HCB buffer (Illumina) at a concentration of 100 ng cRNA/μl, unsealed in a humidified chamber for 20 h.

scan_protocol: After washing and blocking, array signals were developed by a 10-min incubation in a 1 μg/ml Cy3-streptavidin and 1% blocking solution. Microarray scanning was performed in an iScan array scanner.

data_processing: The data were quantile normalized and fold-changes were calculated using R/Bioconductor scripts.

source_name: Primary dermal fibroblasts

label_protocol: Illumina Total Prep RNA Amplification Kit was used to synthesize first and second strand cDNA and for amplifying biotinylated cRNA.

growth_protocol: Fibroblasts were grown in DMEM medium, supplemented with 10% FBS, 1% penicillin-streptomycin and 1% L-glutamine. 6 hours prior to and during the treatment, treated and control fibroblasts were cultured in serum-free medium.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Mature melanosomes in PBS were added to fibroblasts for 24 hours. Control cells were not treated.

tag: cell type

value: primary dermal fibroblast

tag: cell origin

value: fibroblasts isolated from eyelid, adult donor

tag: treatment

value: control


title: Fibroblasts_treated_mature melanosomes_rep2

description:
FIB MM 2
RNA from fibroblasts treated with mature melanosomes for 24h replicate 2

value: mature melanosomes for 24h


title: Fibroblasts_treated_mature melanosomes_rep3

description:
FIB MM 3
RNA from fibroblasts treated with mature melanosomes for 24h replicate 3


title: Fibroblasts_untreated_rep2

description:
FIB CTRL 2
RNA from untreated fibroblasts replicate 2


title: Fibroblasts_treated_early melanosomes_rep1

description:
FIB EM
RNA from fibroblasts treated with early melanosomes replicate 1

value: early melanosomes


title: Sox9_XY_13.5_rep1

city: Krakow

first: Michal

last: Kolasa

address: Gronostajowa 9

country: Poland

institute: Jagiellonian University

description: Gene expression data from gonads after the sexual differentiation.

hyb_protocol: Microarrays were hybridized overnight with 5 ug biotin-labelled ss-DNA, and washed in fluidics station wash protocol: FS450_0001.

scan_protocol: GeneChip scanner 3000 7G was used.

data_processing: RMA signal intensity calculation

source_name: Supporting cells isolated from gonad of XY mouse fetus at 13.5 dpc

label_protocol: Labeling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual.

extract_protocol: Total RNA from was isolated using Trizol as described above and further purified with RNeasy Mini kit per manufacturer’s instructions (Qiagen, Valencia, CA). 200 ng total RNA was then used for GeneChip analysis. Preparation of terminal-labeled cDNA, hybridization to genome-wide murine Gene Level 1.0 ST GeneChips (Affymetrix, Santa Clara, CA, USA) and scanning of the arrays were carried out according to manufacturer’s protocols (https://www.affymetrix.com).

treatment_protocol: Female mice were time-mated and the embryos were collected. The gonads were removed and the males and females were separately pooled. The gonads were incubated in Trypsin EDTA for 10 minutes. The trypsin was replaced by PBS. The samples were stained with DAPI and FACS sorted.

tag: gene reported

tag: strain

value: Tg(Sox9-cre/ERT2)1Msan/J, progeny of C57BL/6

tag: Sex

tag: developmental stage


title: Sox9_XY_13.5_rep2


title: Fibroblasts_treated_mature melanosomes_rep1

description:
FIB MM 1
RNA from fibroblasts treated with mature melanosomes for 24h replicate 1


title: Control_001b


title: Sry_XX_13.5_rep3

source_name: Supporting cells isolated from gonad of XX mouse fetus at 13.5 dpc

value: Sry

value: Tg(Sry-EGFP)92Ei, progeny of CD-1

value: female


title: Sry_XX_13.5_rep2


title: Sinus Rhythm_left atrial_76

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

source_name: Human heart tissue

label_protocol: Standard Affymetrix protocol

extract_protocol: Cellular RNA Extration with TRIZOL

value: Heart

tag: condition

value: Sinus Rhythm


title: Sinus Rhythm_right atrial_42


title: Sry_XX_13.5_rep1


title: Sinus Rhythm_right atrial_92


title: Sinus Rhythm_left atrial_42


title: Sinus Rhythm_left atrial_92


title: Sinus Rhythm_right atrial_39

value: male


title: Sinus Rhythm_right atrial_76


title: Fibroblasts_untreated_rep3

description:
FIB CTRL 3
RNA from untreated fibroblasts replicate 3


title: Sinus Rhythm_left atrial_39


title: Sox9_XY_13.5_rep3


title: Mafb_XY_13.5_rep1

source_name: Interstitial cells isolated from gonad of XY mouse fetus at 13.5 dpc

value: Mafb

value: progeny of 129S6/SvEvTac on mixed background


title: Sinus Rhythm_right atrial_22


title: Mafb_XY_13.5_rep3


title: Sinus Rhythm_left atrial_22


title: Oct4_XX_13.5_rep1

source_name: Germ cells isolated from gonad of XX mouse fetus at 13.5 dpc

value: progeny of C57BL/6NJ on mixed background


title: Oct4_XY_13.5_rep2

source_name: Germ cells isolated from gonad of XY mouse fetus at 13.5 dpc


title: Mafb_XY_13.5_rep2


title: Oct4_XX_13.5_rep3


title: Oct4_XX_13.5_rep2


title: Oct4_XY_13.5_rep1


title: Sinus Rhythm_right atrial_15


title: Mafb_XX_13.5_rep2

source_name: Stromal cells isolated from gonad of XX mouse fetus at 13.5 dpc


title: Atrial Fibrillation_right atrial_34

value: Atrial Fibrillation


title: Mafb_XX_13.5_rep1


title: Sox9_XY_12.5_rep1

description: Gene expression data from gonads during the sexual differentiation.

source_name: Supporting cells isolated from gonad of XY mouse fetus at 12.5 dpc


title: Atrial Fibrillation_left atrial_34


title: Atrial Fibrillation_left atrial_33


title: Oct4_XY_12.5_rep3

source_name: Germ cells isolated from gonad of XY mouse fetus at 12.5 dpc


title: Sry_XX_12.5_rep1

source_name: Supporting cells isolated from gonad of XX mouse fetus at 12.5 dpc


title: Sox9_XY_12.5_rep2


title: Mafb_XX_13.5_rep3


title: Atrial Fibrillation_right atrial_33


title: Sox9_XY_12.5_rep3


title: Sry_XX_12.5_rep3


title: Oct4_XY_12.5_rep2


title: Sinus Rhythm_left atrial_15


title: Atrial Fibrillation_right atrial_32


title: Oct4_XY_13.5_rep3


title: Atrial Fibrillation_right atrial_29


title: Mafb_XY_12.5_rep1

source_name: Interstitial cells isolated from gonad of XY mouse fetus at 12.5 dpc


title: Mafb_XX_12.5_rep2

source_name: Stromal cells isolated from gonad of XX mouse fetus at 12.5 dpc


title: Atrial Fibrillation_left atrial_32


title: Oct4_XX_12.5_rep3

source_name: Germ cells isolated from gonad of XX mouse fetus at 12.5 dpc


title: Oct4_XX_12.5_rep2


title: Atrial Fibrillation_left atrial_20


title: Mafb_XY_12.5_rep2


title: Oct4_XY_12.5_rep1


title: Mafb_XX_12.5_rep3


title: Atrial Fibrillation_left atrial_29


title: Oct4_XX_12.5_rep1


title: Mafb_XY_12.5_rep3


title: Atrial Fibrillation_right atrial_20


title: scrambled_rep1 (miR-320c control)

hyb_protocol: GeneAtlas Hybridization, Wash and Stain kit for WT array strips (Affymetrix, cat# 901667) was used according to the manufacturer's instructions. Hybridization instrument Accublock Digital Dry Bath (LabNet, D1200) this instrument is adjust for the GeneAtlas microarray.

scan_protocol: Washing and scanning were performed in GeneAtlas instrument (Affymetrix, 00-0377 (washing fluidic station), 00-0376 (imagine station)).

data_processing: Raw data (CEL files) was processed using the Chipster software (http://chipster.csc.fi/); normalized expression values were calculated with the RMA algorithm and default parameters

source_name: primary fibroblast

label_protocol: WT terminal labeling and controls kit (Affymetrix, cat# 901524) according to the manufacturer's instructions.

growth_protocol: Primary human dermal fibroblasts were isolated from neonatal foreskins (see methods), plated onto collagen dishes and cultured in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% L-glutamine.

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

treatment_protocol: Primary fibroblast were transfected with scrambled, miR-211 or miR-320c mimic

value: primary fibroblast

value: Cells transfected with scramble miRNA as control


title: scrambled_rep2 (miR-320c control)


title: miR-320c_rep2

value: Cells transfected with miRNA-320c mimic


title: Atrial Fibrillation_right atrial_19


title: Sry_XY_11.5_rep1

description: Gene expression data from gonads before the onset of sexual differentiation.

source_name: Supporting cells isolated from gonad of XY mouse fetus at 11.5 dpc


title: Sry_XX_11.5_rep3

source_name: Supporting cells isolated from gonad of XX mouse fetus at 11.5 dpc


title: Mafb_XX_12.5_rep1


title: Atrial Fibrillation_left atrial_19


title: miR-320c_rep1


title: Sry_XX_11.5_rep2


title: Atrial Fibrillation_right atrial_14


title: scrambled_rep2 (miR-211 control)


title: scrambled_rep1 (miR-211 control)


title: miR-211_rep2

value: Cells transfected with miRNA-211 mimic


title: Sry_XY_11.5_rep2


title: HBV Infected 3

city: Miami

first: Emmanuel

last: Thomas

state: FL

address: 1550 NW 12th Ave, Papanicolaou Bldg., RM. PAP 514

department: Schiff Center for LIver Diseases

institute: University Of Miami School of Medicine

description:
eThomas6_U133Plus2_04132015.CEL
Gene expression data from primary human hepatocytes.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 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: RMA nomalization by GeneSpring GX 13.0 Software (samples 1-9 were normalized separately from samples 10-15) and basline was transformed to median of all samples

source_name: Human Primary Hepatocytes

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: Primary Human Hepatocytes Were Isolated and Plated on 12 well plates at the University of Pittsburgh in the Laboratory of Dr. David Geller and provided through the NIH funded Liver Tissue and Cell Distribution System (LTCDS)

treatment_protocol: RNA was isolated after 12, and 24 h treatment with ISD/dsDNA90 (1ug/mL) or HBV from HepG2.2.15  for 40 hours (m.o.i=50).

value: Liver

value: hepatocyte

value: HBV Infected


title: Oct4_XY_11.5_rep1

source_name: Germ cells isolated from gonad of XY mouse fetus at 11.5 dpc


title: miR-211_rep1


title: Sry_XX_11.5_rep1

value: Sry


title: Sry_XY_11.5_rep3

value: Tg(Sry-EGFP)92Ei, progeny of CD-1


title: Oct4_XX_11.5_rep2

source_name: Germ cells isolated from gonad of XX mouse fetus at 11.5 dpc

value: female


title: Cont HBV 2

description:
eThomas2_U133Plus2_04132015.CEL
Gene expression data from primary human hepatocytes.

value: Control HBV


title: HBV Infected 1

description:
eThomas4_U133Plus2_04132015.CEL
Gene expression data from primary human hepatocytes.


title: Oct4_XX_11.5_rep3


title: Oct4_XY_11.5_rep3


title: Mafb_XY_11.5_rep1

source_name: Interstitial cells isolated from gonad of XY mouse fetus at 11.5 dpc


title: Oct4_XY_11.5_rep2


title: Cont HBV 1

description:
eThomas1_U133Plus2_04132015.CEL
Gene expression data from primary human hepatocytes.


title: Oct4_XX_11.5_rep1


title: HBV Infected 2

description:
eThomas5_U133Plus2_04132015.CEL
Gene expression data from primary human hepatocytes.


title: Cont HBV 3

description:
eThomas3_U133Plus2_04132015.CEL
Gene expression data from primary human hepatocytes.


title: Mafb_XY_11.5_rep2


title: 12 hour ISD/dsDNA90 2

description:
eThomas_U133_sample5_03242014.CEL
Gene expression data from primary human hepatocytes.

value: 12 hour ISD/dsDNA90


title: 24 hour ISD/dsDNA90 2

description:
eThomas_U133_sample8_03242014.CEL
Gene expression data from primary human hepatocytes.

value: 24 hour ISD/dsDNA90


title: 12 hour ISD/dsDNA90 3

description:
eThomas_U133_sample6_03242014.CEL
Gene expression data from primary human hepatocytes.


title: 24 hour ISD/dsDNA90 1

description:
eThomas_U133_sample7_03242014.CEL
Gene expression data from primary human hepatocytes.


title: 12 hour ISD/dsDNA90 1

description:
eThomas_U133_sample4_03242014.CEL
Gene expression data from primary human hepatocytes.


title: Mafb_XX_11.5_rep3

source_name: Stromal cells isolated from gonad of XX mouse fetus at 11.5 dpc

value: Mafb


title: Cont ISD/dsDNA90 3

description:
eThomas_U133_sample3_03242014.CEL
Gene expression data from primary human hepatocytes.

value: Control ISD/dsDNA90


title: Mafb_XX_11.5_rep1

value: progeny of 129S6/SvEvTac on mixed background


title: Mafb_XY_11.5_rep3

value: male


title: Atrial Fibrillation_left atrial_14

source_name: Human heart tissue

value: Heart

value: Atrial Fibrillation


title: 24 hour ISD/dsDNA90 3

description:
eThomas_U133_sample9_03242014.CEL
Gene expression data from primary human hepatocytes.


title: Mafb_XX_11.5_rep2


title: Cont ISD/dsDNA90 2

description:
eThomas_U133_sample2_03242014.CEL
Gene expression data from primary human hepatocytes.


title: ID_13T

city: Yufu

first: Mika

last: Takahashi

address: Idaigaoka 1-1

country: Japan

institute: Oita University

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed with GeneSpring GX software(Aglrent).

source_name: tissue

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from fresh-frozen tissues, using an RNeasy mini kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions. As a normal control, the total RNAs were extracted from non-neoplastic renal cortex in tissue sections of ccRCCs.

value: kidney

tag: tumor state

value: tumor(high)


title: Sry_XX_12.5_rep2


title: ID_22T

value: tumor(low)


title: ID_18T


title: CBS138 wild type pH7.4 rep.2

city: Nagasaki

first: Hiroshi

last: Nishikawa

address: 1-7-1 Sakamoto

institute: Nagasaki University Graduate School of Biomedical Sciences

description: This sample is of Candida glabrata CBS138 wild type in SC broth (pH7.4). It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Nakaseomyces glabratus CBS 138

source_name: Candida glabrata CBS138 wild type

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

growth_protocol: Candida glabrata CBS138 was grown to log phase at 30°C in SC broth (pH5.0 and 7.4).

extract_protocol: Total RNA were extracted using RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of RNA was checked with a RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer.

treatment_protocol: Candida glabrata CBS138 delta-vph2 was grown to log phase at 30°C in SC broth (pH5.0 and 7.4).

tag: genotype/variation

value: wild type

tag: phenotype

value: normal

tag: growth protocol


title: ID_21T

tag: tissue


title: ID_14T


title: ID_19T


title: ID_11T


title: ID_20T


title: ID_15T


title: ID_23T


title: CBS138 delta-vph2 pH5.0 rep.2

description: This sample is of Candida glabrata CBS138 delta-vph2 in SC broth (pH5.0). It is the second of two delta-vph2 mutant biological replicates used in this experiment, each from separate cultures.

source_name: Candida glabrata CBS138 delta-vph2

value: loss of V-ATPase activity


title: ID_17T


title: CBS138 delta-vph2 pH7.4 rep.1

description: This sample is of Candida glabrata CBS138 delta-vph2 in SC broth (pH7.4). It is the first of two delta-vph2 mutant biological replicates used in this experiment, each from separate cultures.


title: Cont ISD/dsDNA90 1

description:
eThomas_U133_sample1_03242014.CEL
Gene expression data from primary human hepatocytes.

value: Liver

value: hepatocyte


title: ID_9T


title: CBS138 wild type pH5.0 rep.2

description: This sample is of Candida glabrata CBS138 wild type in SC broth (pH5.0). It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.


title: ID_10T


title: ID_12T


title: CBS138 delta-vph2 pH7.4 rep.2

description: This sample is of Candida glabrata CBS138 delta-vph2 in SC broth (pH7.4). It is the second of two delta-vph2 mutant biological replicates used in this experiment, each from separate cultures.


title: CBS138 wild type pH7.4 rep.1


title: ID_8T


title: ID_7T


title: ID_6T


title: CBS138 wild type pH5.0 rep.1

description: This sample is of Candida glabrata CBS138 wild type in SC broth (pH5.0). It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: CBS138 delta-vph2 pH5.0 rep.1

description: This sample is of Candida glabrata CBS138 delta-vph2 in SC broth (pH5.0). It is the first of two delta-vph2 mutant biological replicates used in this experiment, each from separate cultures.


title: TO-/- 1g treated rep.2

city: Montréal

first: Anne

last: Camirand

state: QC

address: 1001 Décarie Blvd mail drop EM 1.3229

country: Canada

institute: McGill University

description:
replicate 2
SAMPLE 16

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data were normalized with the Lumi package of FlexArray v1.5 software and analyzed with EB Wright and Simon statistical analysis.

source_name: Trabecular osteoblasts from embryo tibia

label_protocol: Biotinylated cDNA was synthesised with Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, purified and treated with DNAse1 (Qiagen Rneasy kit) according to protocol.  Quality was checked with Agilent Bioanalyser.

tag: protocol

value: Daily 2h treatment with 10-8 PTHrP1-36 peptide

tag: age

value: embryo (1 day pre-birth)

value: Pthrp-/- ablated

value: osteoblasts from femur


title: Nestin negative cells-5

city: Philadelphia

first: Zeng-jie

last: Yang

state: Pennsylvania

address: 333  Cottman Avenue

department: Cancer Biology Program

institute: Fox Chase Cancer Center

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

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

source_name: medulloblastoma cells

growth_protocol: Cells were directly isolated from mouse cerebella without additional culture.

extract_protocol: 1X10E6 cells were used to exact total RNA with Trizol kit  according to the manufacturer's instructions.. The quality of extracted RNA was examined by Nanodrop. RNAs with OD260/280>1.8, <2.0 were used for labelling and hybridization.

treatment_protocol: No treatment prior to RNA extraction.

tag: tissue type

value: medulloblastoma

value: GNPs (granule neuron precursors)

tag: genotype

value: postnatal day 7

value: Nestin-


title: Nestin negative cells-1

tag: cell type


title: TO-/- 0g treated rep.2

description:
replicate 2
SAMPLE 14


title: ID_5T


title: Nestin negative cells-4


title: ID_3T


title: Nestin positive cells-3

value: Nestin+


title: ID_2T

value: kidney


title: Nestin positive cells-5


title: ID_18N


title: TO-/- 1g no treatment rep.2

description:
replicate 2
SAMPLE 15

value: no treatment


title: ID_4T

value: tumor(low)


title: Nestin positive cells-4


title: DCL_Treatment_liver_day14_5

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

country: Germany

institute: Hannover Medical School

hyb_protocol: Hybridization, staining, and washing were performed according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA).

scan_protocol: The Affymetrix GeneChip Mouse 430 2.0 was used for microarray analysis and was scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: The microarray intensity files (.cel file) were analysed by using the GenPlex gene expression analysis software (http://genplex.co.kr) and GeneXpalin 3.0 software (http://genexplain-platform.com). Data normalization was performed using MAS 5.0 and Global Median normalization. Differentially expressed genes were determined based on the filtering criteria >1.5 and <-1.5 fold change and P < 0.05.

label: Biotin

source_name: Liver

label_protocol: Microarray studies were performed with an initial amount of 250 ng total RNA. All steps of cDNA synthesis and biotin labeling were performed according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA).

extract_protocol: The liver was explanted and snap-frozen in liquid nitrogen. Liver samples were subsequently stored in a deep freezer until RNA extraction. Frozen liver samples were immediately added to the RLT buffer containing β‑mercaptoethanol and homogenized using a TissueLyser (Qiagen, Hilden, Germany). Total RNA from each tissue was isolated and purified using the RNase mini kit (Qiagen) according to the manufacturer’s recommendation. The concentration of total RNA was assessed using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE), and RNA integrity was determined with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57BL6- mice (males, 8 weeks old) (n=5 for each group) were purchased and maintained under laboratory conditions. The diclofenac sodium was administered daily by intraperitoneal injection of 30 mg/kg (low dose) for up to 14 days. Control mice (n=5) were administered corresponding quantities of saline. The mice were sacrificed at 24h (day 1), 72h (day 3) or 14 days after vehicle or diclofenac administration.

value: diclofenac sodium


title: ID_1T


title: TO-/- 1g treated rep.1

description:
replicate 1
SAMPLE 12


title: DCL_Treatment_liver_day14_4


title: Nestin positive cells-1


title: TO-/- 0g no treatment rep.2

description:
replicate 2
SAMPLE 13


title: ID_13N

value: normal


title: ID_16N


title: TO-/- 0g treated rep.1

description:
replicate 1
SAMPLE 10


title: TO-/- 1g no treatment rep.1

description:
replicate 1
SAMPLE 11


title: Sox7_High_r1

city: Manchester

first: Valerie

last: Kouskoff

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: RNA expression value

hyb_protocol: Labeled RNA was hybridised to GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix), following the manufacturer’s instructions

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Background adjustment, quantile normalization and summarization of probe-level intensity were performed with the Robust Multi-array Average (RMA) algorithm.

source_name: Sox7 inducible transgenic mice

label_protocol: 1µg or RNA was used to produce biotinylated sense-strand DNA with the Whole Transcript Sense Target Labelling Assay (Affymetrix)

growth_protocol: Single cell suspensions obtained from bone marrow (from Sox7 inducible transgenic mice) were  serially passaged on irradiated OP9 (30cGy) stroma layer in RPMI supplemented with 20% foetal calf serum, 2 mM L-Glutamine, 5 μg/ml Kit ligand, 2 μg/ml Interleukin-7 and 5 μg/ml FLT3. When indicated, 1 μg/ml of doxycycline (Dox) was added to the medium. After 10-12 passages, the two subpopulations expressing low and high level of SOX7::GFP where isolated by sorting based on SOX7::GFP and cKIT expression level.

extract_protocol: RNA was isolated from the cells using an RNeasy kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Bone marrow cells were serially passaged on irradiated OP9 stroma layer in the presence or in the absence of doxycycline to induce SOX7 expression

value: bone marrow cells

tag: sox7 level

value: high

tag: cell line

tag: derivative


title: Sox7_Low_r2

description: RNA expression value

value: low


title: ID_11N


title: TO+/+ 1g treated rep.2

description:
replicate 2
SAMPLE 8

value: Daily 2h treatment with 10-8 PTHrP1-36 peptide

value: Pthrp+/+ wild-type

tag: strain


title: TO-/- 0g no treatment rep.1

description:
replicate 1
SAMPLE 9

value: embryo (1 day pre-birth)

value: Pthrp-/- ablated


title: Control_liver_day14_3

tag: treatment

value: saline


title: Sox7_Low_r1

description: RNA expression value


title: TO+/+ 0g no treatment rep.2

description:
replicate 2
SAMPLE 5

value: osteoblasts from femur


title: TO+/+ 0g treated rep.2

description:
replicate 2
SAMPLE 6


title: Whole cells WM3314_rep1

description:
Cellular RNA of WM3314 melanoma cells
WC 3314

hyb_protocol: Hybridization was performed in a SureHyb chamber at 55°C for 20h.

scan_protocol: Microarray scanning was performed using the Agilent Scanner G2505C.

source_name: WM3314 melanoma cells

label_protocol: Samples were labeled according to the Agilent miRNA Complete Labeling and Hyb kit protocol.

growth_protocol: MNT-1, WM3682 and WM3314 cells were cultured in DMEM medium supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% L-glutamine.

extract_protocol: RNA of WM3682 and WM3314 cells and melanosomes was extracted with Trizol reagent. RNA from MNT-1 exosomes and secreted melanosomes was isolated using the miRNeasy Mini Kit from Qiagen. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Melanosomes of WM3682 and WM3314 cells were treated with RNase for 10 min at 37 °C, followed by the addition of RNase inhibitor.

tag: cell component

value: whole cells


title: ID_1N


title: Control_liver_day14_2


title: DCL_Treatment_liver_day14_2


title: Melanosomes WM3314_rep1

description:
RNA from melanosomes of WM3314 cells
MEL 3314

source_name: WM3314 melanosomes

value: melanosomes


title: ID_29N


title: Control_liver_day14_4


title: Control_liver_day14_5


title: DCL_Treatment_liver_day14_3


title: DCL_Treatment_liver_day14_1


title: ID_33N


title: ID_33T

value: tumor(high)


title: ID_29T

value: kidney


title: Sox7_High_r2

description: RNA expression value


title: Whole cells WM3682_rep1

description:
Cellular RNA of WM3682 melanoma cells
WC 3682

source_name: WM3682 melanoma cells


title: Melanosomes WM3682_rep1

description:
RNA from melanosomes of WM3682 cells
MEL 3682

source_name: WM3682 melanosomes


title: Control_liver_day14_1


title: Secreted melanosomes MNT-1_rep2

description:
RNA from secreted melanosomes of MNT-1 cells replicate 2
SMEL 2

source_name: MNT-1 secreted melanosomes

value: secreted melanosomes


title: TO+/+ 1g no treatment rep.1

description:
replicate 1
SAMPLE 3

value: no treatment


title: TO+/+ 1g treated rep.1

description:
replicate 1
SAMPLE 4


title: TO+/+ 0g treated rep.1

description:
replicate 1
SAMPLE 2


title: DCL_Treatment_liver_day3_3

value: diclofenac sodium


title: ID_31N

value: normal


title: ID_30T

value: tumor(low)


title: ID_31T


title: TO+/+ 1g no treatment rep.2

description:
replicate 2
SAMPLE 7


title: TO+/+ 0g no treatment rep.1

description:
replicate 1
SAMPLE 1


title: Secreted melanosomes MNT-1_rep1

description:
RNA from secreted melanosomes of MNT-1 cells replicate 1
SMEL 1


title: DCL_Treatment_liver_day3_2


title: DCL_Treatment_liver_day3_1


title: ID_27N


title: Control_liver_day3_2


title: Control_liver_day3_3


title: Exosomen_MNT-1_rep2

description:
RNA from MNT-1 exosomes replicate 2
EXO 2

source_name: MNT-1 exosomes

value: exosomes


title: Exosomes MNT-1_rep1

description:
RNA from MNT-1 exosomes replicate 1
EXO 1


title: ID_8N


title: ID_30N


title: ID_25N


title: DCL_Treatment_liver_day1_3


title: Control_liver_day3_1


title: ID_27T


title: ID_32T


title: DCL_Treatment_liver_day1_1


title: ID_28N


title: DCL_Treatment_liver_day1_2


title: ID_28T


title: ID_32N


title: Control_liver_day1_1


title: Control_liver_day1_2


title: ID_26N


title: ID_25T


title: Control_liver_day1_3


title: ID_26T


title: HS_CYJ8_asc

type: genomic

city: Seoul

first: Je-Keun

last: Rhee

address: 222 Banpo-daero, Seocho-Gu

country: South Korea

institute: Catholic Univ. of Korea

description:
Ascites
CYJ8_asc

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: BeadStudio software v3.2. BMIQ (Beta MIxture Quantile dilation) normalization strategy.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted by the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendation.

tag: gender

value: female

tag: disease state

value: ovarian serous adenocarcinoma

tag: Stage

value: IVB

tag: individual id

value: ascites


title: ID_24N

tag: tumor state


title: ox40l-/- mice treated with bleomycin, rep4

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
YA19
Gene expression data from lesional skin of ox40l-/- male mice injected for 3 weeks with bleomycin.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 2.0 ST Array. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were RMA normalized with Bioconductor.

source_name: lesional skin of mouse injected with bleomycin for 3 weeks, ox40l-/-

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the GeneChip Whole Transcript (WT) Sense Target labelling assay kit Affymetrix).

extract_protocol: Total RNA were extracted from lesional skin sample with RNeasy Mini kit with DNase I digestion according to the manufacturer's instructions.

treatment_protocol: Mice were injected with bleomycin for 3 weeks.

tag: strain/background

tag: genotype/variation

value: male

value: 9 weeks

tag: tissue

value: skin

value: bleomycin


title: HS_CYJ8_RTOV2

description:
IntraOvary
CYJ8_RTOV2

tag: age

value: Right ovary


title: ID_24T


title: 3 dpf miR-132 MO injected zebrafish

city: Shanghai

first: Jiu-lin

last: Du

address: 320 Yueyang Road

country: China

institute: Institute of Neuroscience

description:
Gene expression in miR-132 knockdown zebrafish
miR-132 MO

hyb_protocol: 1.65 ug Cy3-labeled cRNA were hybridized using Gene Expression Hybridization Kit (Agilent technologies, CA) in Hybridization Oven (Aglilent technoligies, CA), according to the manufacturer's instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, MA) with Gene Expression Wash Buffer Kit (Agilent technologies, CA), followed the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA, Agilent technologies, CA). Dye channel is set to green, PMT is 100%, Scan resolution is 5 um.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, CA)

organism: Danio rerio

source_name: 3 dpf miR-132 MO injected zebrafish

label_protocol: Total RNA was amplified and  labeled by Low Input Quick Amp Labeling Kit, One-Color, followed the manufacture's instructions. Labeled cRNA were purified by Rneasy mini kit (QIAGEN, Germany)

growth_protocol: Adult zebrafish were maintained with automatic fish housing system at 28 ºC under 14h-10h light dark cycle.

extract_protocol: RNA was prepared using Trizol (Invitrogen) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-3000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Zebrafish embryos were injected with 8 ng control, miR-132 MO. At 24 hpf, the chorion was removed by pronase. The embryos were maintained in 10% Hanks' solution.

value: miR-132 knockdown

value: embryos

value: 3 dpf


title: Rad21 shRNA2 rep1

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

hyb_protocol: Per affymetrix manual

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner LR15

data_processing: .gct files were created by RMA normalization using GenePattern (https://www.broad.harvard.edu/cancer/software/genepattern/). These files (specifically the .gct) was used for downstream analysis

source_name: post-primary plating

label_protocol: The cDNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual

growth_protocol: Bone marrow was harvested from 6-8 week old C57/BL6 animals and lineage depleted.  Cells were then infected for 24hours in liquid culture with lentiviruses in the presence of polybrene by spinoculation on retronectin coated plates.  Infected cells were selected with puromycin (1 mcg/mL) overnight and live cells isolated by flow cytometry and plated in methocult media (10,000 cells/mL) in the presence of cytokines

extract_protocol: At the end of primary plating (7 days), cells were collected and RNA collected with Trizol.  Total RNA was cleaned up using a qiagen kit.

treatment_protocol: Cells were infected with lentiviruses epressing shRNAs to Rad21.

value: Bone Marrow

tag: lentivirus

value: Rad21 shRNA #2

tag: developmental stage

value: 6-8 week old


title: ox40l+/+ mice treated with bleomycin, rep2

description:
YA17h
Gene expression data from lesional skin of ox40l+/+ male mice injected for 3 weeks with bleomycin.

source_name: lesional skin of mouse injected with bleomycin for 3 week, ox40l+/+


title: ox40l-/- mice treated with bleomycin, rep3

description:
YA18h
Gene expression data from lesional skin of ox40l-/- male mice injected for 3 weeks with bleomycin.


title: Rad21 shRNA1 rep2

value: Rad21 shRNA #1


title: ox40l+/+ mice treated with bleomycin, rep3

description:
YA18
Gene expression data from lesional skin of ox40l+/+ male mice injected for 3 weeks with bleomycin.


title: Rad21 shRNA2 rep2


title: ox40l+/+ mice treated with bleomycin, rep1

description:
YA17
Gene expression data from lesional skin of ox40l+/+ male mice injected for 3 weeks with bleomycin.


title: SNU-475

city: Daejeon

first: Yang

last: Suk-Jin

address: 125 Gwahak-ro, Yuseong-gu

institute: KRIBB (Korea Research Institute of Bioscience and Biotechnology)

description: Gene expression analysis of SNU-475 cell line under normal cell culture condition.

hyb_protocol: Labeled cRNA (750ng) was hybridized to HumanHT-12 v3 or v4 chips at 58℃ for 16 hours.

scan_protocol: After hybridizing procedures, chips were scanned using a BeadArray Reader and BeadScan software (Illumina).

data_processing: Data extraction and normalization were elevated by BeadStudio software (Illumina).

source_name: SNU-475 cells

label_protocol: Illumina TotalPrep RNA Amplification kit (Applied Biosystem/Ambion, Austin, TX, USA) was used to generate biotin-UTP labeled cRNA according to manufacturer’s instructions

growth_protocol: ATCC (ATCC, Manassas, VA) and SNU (KCLB, Seoul, Korea) were maintained in Dulbecco’s modified Eagle medium (DMEM; Gibco BRL, Grand Island, NY) or Roswell Park Memorial Institute 1640 medium (RPMI1640; GIBCO BRL). JHH cell lines obtained from JCRB were maintained in William’s E medium (GIBCO BRL). All media was supplemented with heat-inactivated 10% fetal bovine serum (GIBCO BRL) and 1× Antibiotic-Antimycotic (GIBCO BRL). Cells were cultured at 37℃ in a humidified incubator under 5% CO2.

extract_protocol: Total RNA extraction was perforemd using QIAGEN RNeasy mini kit according to manufacturer's instruction. Total RNA integrity was determined with ExperionTM RNA StdSens (BIO-RAD).

treatment_protocol: None.

tag: cell type

value: Human HCC cells


title: HS_CYJ8_OM2

description:
ExtraOvary
CYJ8_OM1

value: female

value: Omentum


title: ox40l-/- mice treated with bleomycin, rep2

description:
YA16H
Gene expression data from lesional skin of ox40l-/- male mice injected for 3 weeks with bleomycin.


title: 3 dpf control MO injected zebrafish

description:
Gene expression in control zebrafish
Ctrl MO

source_name: 3 dpf control MO injected zebrafish

value: control


title: Rad21 shRNA1 rep1


title: Empty Vector rep2

value: Empty Vector


title: HS_CYJ8_N

description:
Normal
CYJ8_N

value: ovarian serous adenocarcinoma

value: IVB

value: blood normal


title: Non-treatment

status: Public on Aug 08 2016

first: Weiguo

last: Fan

department: Institut Pasteur of Shanghai

institute: Chinese Academy of Sciences

description: NC

hyb_protocol: The pre-hybridization of HOA v6.1 arrays were rehydrated by 100% ethanol followed by deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridized on HOA v6.1 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluorescence intensity.

data_processing:
The data was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passing filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pair-wised comparisons were performed by Rosetta Resolver® System error-weighted modeling to find significant differential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: Huh7 cells, untreated

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amersham) to uridine (dUTP).

growth_protocol: Huh7 cells were purchased from ATCC and cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum (Gibco) at 37°C in a CO2 incubator.

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Huh7 cells were seeded into 6-well plates at a density of 6x10^5 cells/well and cultured overnight before treatment with either 10 U/ml of IFN-α or 20 ng/ml of IFN-λ1 (IL29) or IFN-λ4 for 6h or 16h.

tag: cell line

tag: time point


title: ox40l-/- mice treated with bleomycin, rep1

description:
YA16
Gene expression data from lesional skin of ox40l-/- male mice injected for 3 weeks with bleomycin.

value: male

value: 9 weeks

value: skin

value: bleomycin


title: HS_CYJ6_OM

description:
ExtraOvary
CYJ6_OM

value: IIIC


title: Empty Vector rep1

value: Bone Marrow

tag: strain


title: HS_CYJ6_asc

description:
Ascites
CYJ6_asc

value: ascites


title: IFN-λ1-6h

source_name: Huh7 cells, IFN-lambda-1, 6h

tag: treatment


title: HS_CYJ4_asc

description:
Ascites
CYJ4_asc


title: HS_CYJ6_RTOV3

description:
IntraOvary
CYJ6_RTOV3

value: Right ovary


title: IFN-α-6h

source_name: Huh7 cells, IFN-alpha, 6h

value: IFN-alpha


title: HS_CYJ4_LTOV1

description:
IntraOvary
CYJ4_LTOV1

value: Left ovary


title: IFN-λ1-16h

source_name: Huh7 cells, IFN-lambda-1, 16h


title: HS_CYJ6_N

description:
Normal
CYJ6_N

value: female


title: IFN-α-16h

source_name: Huh7 cells, IFN-alpha, 16h


title: Cypermethrin_copepodid_rep4

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

hyb_protocol: Samples were hybridized to oligonucleotide microarrays as per manufacturers' instructions for Low-Input Quick Amp kits (Agilent; v6.5). Arrays were designed using previously annotated ESTs from both Pacific and Atlantic L. salmonis (Yasuike et al. 2012; eArray design ID 024389; Agilent).

scan_protocol: Scanned at 5 micrometer resolution on a ScanArray Express (Perkin Elmer) and quantified on Imagene (v8.1; BioDiscovery).

data_processing: For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed in GeneSpring GX11 (Agilent). Each array was normalized using an intensity-dependent Lowess normalization. All entities on the array are presented in the attached matrix file here, however, for the analysis, quality control filters for each of the three experiments retained probes that pass the following criteria in at least 65% of the samples in any one condition: raw signal ≥ 500 in both channels and no poor quality flags.

organism: Lepeophtheirus salmonis

source_name: Copepodid lice (Atlantic Canada)

label_protocol: Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created for each of the above experiments, ensuring each experimental condition was included in the pool.

growth_protocol: Sea lice (L. salmonis) were collected from BMA2a in the Bay of Fundy, New Brunswick (NB) Canada in July 2014. Gravid females were returned to the Huntsman Marine Science Center, NB in chilled coolers for egg string removal and culture. Egg strings were placed in a flow-through hatch system and allowed to develop to the infective copepodid stage. At this time, lice were transported to the Atlantic Veterinary College, UPEI for in vitro bioassay procedures.

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol reagent® (Life Technologies), on-column DNase digestion (QIAGEN) followed by RNEasy column purification as per manufacturers’ instructions (QIAGEN). Purified total RNA was tested by agarose gel and automated electrophoresis (Experion; Bio-Rad) and spec.

treatment_protocol: Stock cyeprmethrin was prepared to 1 mg/L using fresh sea water. Stock solution was further diluted to 10 ug/L for a working solution. A 10-fold dilution of cypermethrin working solution was then used for all exposures. Final cypermethrin concentration was 1.0 ppb (ug/L) with n = 6 pools of 500 copepodids. Exposure time was 24 hours before collection using 80um mesh filters and scraping copepodids into a  tube (~500 copepodids/tube) and kept at -80 degrees Celcius until RNA extraction (12 individual extractions).

tag: cypermethrin concentaion (ppb)

source_name: all condition reference pool

tag: sample type

value: reference pool


title: IFN-λ4-16h

source_name: Huh7 cells, IFN-lambda-4, 16h


title: Cypermethrin_copepodid_rep6


title: Cypermethrin_copepodid_rep3


title: HS_CYJ1_N

description:
Normal
CYJ1_N

tag: gender

tag: disease state


title: HS_CYJ1_RTOV

description:
IntraOvary
CYJ1_RTOV

tag: Stage

tag: individual id


title: HS_CYJ4_OM3

description:
ExtraOvary
CYJ4_OM3

value: Omentum


title: Cypermethrin_copepodid_rep5


title: HS_CYJ4_N

description:
Normal
CYJ4_N


title: Cypermethrin_copepodid_rep2


title: Control_copepodid_rep6


title: Cypermethrin_copepodid_rep1


title: Control_copepodid_rep5


title: IFN-λ4-6h

source_name: Huh7 cells, IFN-lambda-4, 6h


title: Control_copepodid_rep4


title: D09

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Non-smoker control

hyb_protocol: The hybridization and subsequent washing and staining were performed on the Affymetrix GeneTitan platform.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing:
The data was normalised using Robust Multichip Average (RMA) method that include background adjustment, quantile normalization and final summarization of 11 oligonucleotides per transcript using the median polish algorithm
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.29167

source_name: non-smoker_placental tissue

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

extract_protocol: Total RNA was isolated from frozen placental specimens by homogenizaion in Trizol.

treatment_protocol: placental biopsy specimens were stored in RNALater at -80C until time until  total RNA extraction

tag: subject status

value: pregnant non-smokers

tag: tissue type

value: frozen placental biopsy


title: Control_copepodid_rep3


title: Control_copepodid_rep1


title: G09

description: Non-smoker control


title: F09

description: Smoker - Case

source_name: smoker_placental tissue

value: pregnant smoker


title: HS_CYJ1_asc

description:
Ascites
CYJ1_asc

value: ovarian serous adenocarcinoma

tag: tissue


title: HS_CYJ1_OM2

description:
ExtraOvary
CYJ1_OM2

tag: age


title: Liver_19W_rep1

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: wild type (19 months)

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

data_processing: Gene expression data generated by the Affymetrix MOE430 chip (two duplicates per condition) was imported to GeneSpring for analysis. Absence and presence call for each prob was made by MAS5. To call differentiated expressed (DE) genes between any two interested conditions (FC > 1.5 and p-value < 0.05; t-test), probes labeled by absence on both duplicates in either condition were discarded.

source_name: wild type (19 months)

growth_protocol: Mice are maintained at a 12-h light environment. At the experiments time, mice were sacrificedbetween 9AM to 11AM by Avertin injection, blood were drained.

extract_protocol: Samples were extracted with STAT-60TM (Tel-Test, Inc.) to retrieve total RNA. The RNA was purified one more step further with RNeasyR Mini Kit (Qiagen). RNA Analyzer (Aglient) was used to check RNA quality.

treatment_protocol: Fresh liver samples were immersed in RNALater (Ambion) for overnight.

tag: genotype/variation

value: wild type

value: 19 months

value: mix genetic background of 129/FVB/Black Swiss

value: Liver


title: Liver_12W_rep2

description: wild type (12 months)

source_name: wild type (12 months)

value: 12 months


title: Liver_3W_rep1

description: wild type (3 months)

source_name: wild type (3 months)

value: 3 months


title: Liver_3M_rep1

description: sirt1 KO (3 months)

source_name: sirt1 KO (3 months)

value: sirt1 KO


title: Liver_3M_rep2

description: sirt1 KO (3 months)


title: Liver_3W_rep2

description: wild type (3 months)


title: Liver_12W_rep1

description: wild type (12 months)


title: Liver_19W_rep2

description: wild type (19 months)


title: DMSO-Oleate,  biological rep2

city: Orlando

first: Rick

last: Vega

address: 303 E. Princeton

institute: AdventHealth

description: Gene expression data

hyb_protocol: Following fragmentation, sscDNA were hybridized for 16 hours at 45°C on Affymetrix Human Gene 1.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner.

data_processing: The data were normalized using RMA normalization approach with Affymetrix Expression Console.

source_name: Primary skeletal myotube

label_protocol: Biotinylated sscDNA were prepared according to the standard Affymetrix protocol from 400ng total RNA.

growth_protocol: Primary human skeletal myoblasts are cultured in low glucose DMEM supplemented with 10% fetal bovine serum. When the cells reach 80-90% confluency, the cells are switched to differentiation media composed of alpha-MEM with 2% fetal bovine serum. This media is replaced every other day. Oleate and compound treatment was started on day 7 following differentiaiton.

extract_protocol: Total RNA was extracted using RNA-bee (Amsbio, Lake Forest, CA) and cleaned up using Rneasy columns (Qiagen, Valencia CA) following the manufacturers' protocols.

treatment_protocol: Following differentiation, human skeletal myotubes were treated with BSA + DMSO vehicle control, 100micromolar oleic acid complexed to BSA + DMSO vehicle control, 100micromolar oleate + 10micromolar SBI-477, or 100micromolar oleate + 1micromolar A922500 for 24 hours.

tag: cells

value: Normal adult male


title: SBI-477-Oleate,  biological rep1

description: Gene expression data

value: 100micromolar oleate + 10micromolar SBI-477


title: DGATi-Oleate,  biological rep2

description: Gene expression data

value: 100micromolar oleate + 1micromolar A922500


title: breast-tum-nit-83-EB

city: Edinburgh

first: Dominic

middle: Andrew

last: Pearce

address: University of Edinburgh Cancer Research UK Centre (ECRC)

department: Institute of Genetics and Molecular Medicine

institute: The University of Edinburgh

hyb_protocol: Labelled cDNA was hybridized to Illumina Human HT-12 version 3 and version 4 whole-genome expression bead arrays according to the standard protocol for NuGEN labelled samples

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using lumi R package

source_name: Primary breast tumour, no-intervening treatment, excision biopsy

label_protocol: Biotinylated using the IL Encore Biotin Module (NuGEN)

extract_protocol: RNA extraction using the RNeasy Mini Kit with RNAse Free DNAse treatment (Qiagen).

value: Female

tag: inter-biopsy-interval-(days)

tag: grade

tag: biopsy-type

value: EB

tag: ihc-substype

value: er

tag: er-allred

tag: pr-allred

tag: size-mm


title: breast-tum-nit-79-CB

source_name: Primary breast tumour, no-intervening treatment, core biopsy

tag: gender

value: CB


title: DGATi-Oleate,  biological rep1

description: Gene expression data

tag: treatment


title: breast-tum-nit-83-CB


title: SBI-477-Oleate,  biological rep2

description: Gene expression data


title: breast-tum-nit-78-EB


title: breast-tum-nit-78-CB


title: breast-tum-nit-82-CB


title: breast-tum-nit-77-EB

value: tripleneg


title: FF_RI25

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description: FF Samples are also available in Array Express as E-MEXP-3252

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.  Since CORE Affymetrix annotations were used for these Exon Array, 22,011 lines (i.e., transcript cluster IDs) were expected.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: breast

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Human FF tumor

extract_protocol: Total RNA was extracted using Rneasy mini kit (Qiagen)

value: FF breast angiosarcomas

tag: etiology

value: radiation induced


title: FF_RI27


title: BSA-Control,  biological rep2

description: Gene expression data

value: BSA + DMSO vehicle control


title: breast-tum-nit-79-EB


title: Control_copepodid_rep2

tag: cypermethrin concentaion (ppb)

tag: sample type

value: reference pool


title: breast-tum-nit-82-EB


title: FF_RI26


title: DMSO-Oleate,  biological rep1

description: Gene expression data

value: 100micromolar oleic acid complexed to BSA + DMSO vehicle control


title: FF_RI18


title: FF_RI16


title: breast-tum-nit-77-CB


title: breast-tum-nit-72-EB


title: breast-tum-nit-74-CB


title: breast-tum-nit-72-CB


title: breast-tum-nit-73-CB


title: FF_RI20


title: BSA-Control,  biological rep1

description: Gene expression data


title: breast-tum-nit-74-EB


title: breast-tum-nit-73-EB


title: breast-tum-nit-71-CB


title: breast-tum-nit-71-EB


title: breast-tum-nit-70-CB


title: breast-tum-nit-70-EB


title: breast-tum-nit-67-EB


title: FF_RI13


title: breast-tum-nit-67-CB


title: FF_RI12


title: breast-tum-nit-65-CB


title: FF_RI09


title: FF_RI08


title: breast-tum-nit-59-CB


title: breast-tum-nit-58-EB


title: FF_RI14


title: breast-tum-nit-59-EB


title: FF_RI07


title: breast-tum-nit-64-EB


title: breast-tum-nit-54-EB


title: FF_RI04


title: breast-tum-nit-41-EB


title: breast-tum-nit-53-EB


title: breast-tum-nit-42-EB


title: FF_RI15


title: FF_RI06


title: FF_RI01


title: breast-tum-nit-53-CB


title: FF_RI05


title: breast-tum-nit-39-EB


title: breast-tum-nit-65-EB


title: breast-tum-nit-54-CB


title: breast-tum-nit-41-CB


title: breast-tum-nit-39-CB


title: E09

description: Smoker - Case

tag: subject status

value: pregnant smoker

tag: tissue type

value: frozen placental biopsy


title: breast-tum-nit-58-CB

tag: age


title: FF_RI02

tag: tissue


title: breast-tum-nit-42-CB


title: breast-tum-nit-35-EB


title: breast-tum-nit-35-CB


title: FF_PR08

value: primary


title: FF_PR05


title: FF_PR06


title: breast-tum-nit-25-CB


title: breast-tum-nit-34-CB


title: breast-tum-nit-34-EB


title: breast-tum-nit-24-EB


title: breast-tum-nit-25-EB


title: breast-tum-nit-24-CB


title: FF_PR07


title: FF_PR03


title: breast-tum-nit-64-CB


title: breast-tum-nit-23-EB


title: breast-tum-nit-23-CB


title: RI31

label_protocol: Samples were enzymatically fragmented and biotinylated using the Ovation WTA FFPE method

growth_protocol: Human FFPE tumor

extract_protocol: operation or biopsy. Rneasy FFPE kit (Qiagen).

value: FFPE breast angiosarcomas


title: FF_PR02


title: Mus_musculus_skeletal_muscle_Old_KO_replicate_4

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

source_name: Mus musculus skeletal muscle, Old individual, KO genotype

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Mice were kept under under a 12-h dark/light cycle and were provided a standard chow diet and water ad libitum

extract_protocol: RNA was extracted by using a protocol combining Trizol reagent (Invitrogen) with RNeasy  Mini Kit columns (Qiagen)

treatment_protocol: Quadriceps muscle was excissed and snap frozen in liquid nitrogen. Samples were stored at -80 degrees

value: Old

tag: genotype

value: Mfn2 KO

tag: family

value: Other

value: skeletal muscle


title: breast-tum-nit-19-CB

value: Female

tag: inter-biopsy-interval-(days)

tag: grade


title: Mus_musculus_skeletal_muscle_Old_KO_replicate_2

value: A


title: RI29


title: breast-tum-nit-18-CB

tag: biopsy-type

value: CB

tag: ihc-substype

value: er


title: RI27


title: breast-tum-nit-19-EB

value: EB

tag: er-allred

tag: pr-allred


title: breast-tum-nit-18-EB

tag: gender

tag: size-mm


title: Mus_musculus_skeletal_muscle_Old_KO_replicate_3


title: Mus_musculus_skeletal_muscle_Old_KO_replicate_1


title: RI30

tag: etiology

value: radiation induced


title: Mus_musculus_skeletal_muscle_Old_Control_replicate_4

source_name: Mus musculus skeletal muscle, Old individual, Control genotype

value: Control


title: Mus_musculus_skeletal_muscle_Old_Control_replicate_3

value: B


title: Mus_musculus_skeletal_muscle_Old_Control_replicate_2


title: RI26


title: Mus_musculus_skeletal_muscle_Old_Control_replicate_1


title: breast-tum-nit-17-EB


title: RI25


title: breast-tum-nit-17-CB


title: RI20


title: RI18


title: RI17


title: Mus_musculus_skeletal_muscle_Young_KO_replicate_4

source_name: Mus musculus skeletal muscle, Young individual, KO genotype

value: Young


title: Mus_musculus_skeletal_muscle_Young_KO_replicate_2

value: D


title: RI16


title: RI13


title: Mus_musculus_skeletal_muscle_Young_Control_replicate_3

source_name: Mus musculus skeletal muscle, Young individual, Control genotype


title: breast-tum-nit-14-EB


title: Mus_musculus_skeletal_muscle_Young_Control_replicate_4


title: RI14


title: breast-tum-nit-14-CB


title: RI12


title: RI15


title: Mus_musculus_skeletal_muscle_Young_KO_replicate_1

value: C


title: breast-tum-nit-16-EB

value: tripleneg


title: Mus_musculus_skeletal_muscle_Young_Control_replicate_1


title: Mus_musculus_skeletal_muscle_Young_Control_replicate_2


title: breast-tum-nit-10-EB


title: Mus_musculus_skeletal_muscle_Young_KO_replicate_3


title: breast-tum-nit-5-CB


title: breast-tum-nit-1-EB


title: breast-tum-nit-10-CB


title: breast-tum-nit-1-CB


title: breast-tum-nit-16-CB


title: breast-tum-nit-5-EB


title: RI09

value: FFPE breast angiosarcomas


title: RI11


title: 1291_4082_21504_4421LM1

city: East Lansing

first: Eran

middle: Robert

last: Andrechek

state: MI

address: 567 Wilson Rd. Room 2120

department: Physiology

institute: Michigan State University

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Normalization was with Affymetrix Expression Console using build 1.2.1.20.

source_name: Lung metastasis

label_protocol: standard affymetrix protocol

growth_protocol: MMTV-Myc tumors were induced in the indicated E2F wildtype or knockout background.

extract_protocol: Rneasy was used to extract RNA following manufacturer guidelines.

treatment_protocol: Lung metastases were extracted at endpoint and were flash frozen.

value: Lung metastasis

tag: strain

value: FVB

value: Myc E2F3 Het


title: 1291_4082_21697_4421-LM3


title: RI08


title: 1291_4082_21494_4010LM

value: Myc E2F2 KO


title: RI10


title: breast-tum-nit-28-EB

data_processing: The data were log2 transformed and normalised via quantile normalisation using lumi R package

value: Female


title: RI02


title: 1291_4082_21484_4128LM


title: RI01


title: 1291_4082_21489_4332LM


title: 1291_4082_21499_4421LM2


title: RI05


title: breast-tum-nit-28-CB


title: RI06


title: PR09

value: primary


title: RI04


title: breast-tum-nit-15-CB

value: CB


title: RI03


title: RI07


title: PR07


title: PR08


title: PR06


title: PR11


title: breast-tum-nit-15-EB

value: er


title: breast-tum-nit-9-EB

value: EB


title: breast-tum-nit-32-EB


title: PR05


title: Primed with MDA-MB-231

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

description:
Test
exosomal RNA

data_processing:
The normalization and all the data analysis were performed according to the manufacturer's instructions using their web-based software package.
For the normalization it uses the average of six housekeeping genes: SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A, RNU6-6P.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: MSCs, primed with MDA-MB-231

label_protocol: The Human miFinder miRNA PCR Array (Qiagen, Valencia, CA) was run according to manufactures instructions with RNA isolated using the miRNeasy Mini Kit. RNA (250 ng) was converted to cDNA with the miScript II reverse transcription reaction using HiSpec Buffer. The cDNA was used as templates in real-time PCR using the Human miRNome miScript miRNA PCR Array (miScript). The PCR array used the miScript SYBR Green PCR Kit.

extract_protocol: RNA was isolated using the miRNeasy Mini Kit.

tag: cell type

value: MSCs primed with MDA-MB-231

tag: time


title: Naïve MSCs

description:
Control
exosomal RNA

source_name: MSCs, bone marrow-derived

value: Naïve MSCs


title: PR01


title: PR10


title: breast-tum-nit-9-CB


title: PR03


title: Primed with T47D

description:
Test
exosomal RNA

source_name: MSCs, primed with T47D

value: MSCs primed with T47D


title: UM_26

status: Public on Aug 07 2016

city: Leiden

first: Theodorus

middle: Huibertus

last: van Essen

address: Albinusdreef 2

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Background correction, normalization and transformation was performed with the 'rsn' function of the lumi package v2.12.0

source_name: tissue sample of uveal melanoma of enucleated eye

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amp kit for Illumina arrays

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

tag: age at enucleation (years)

tag: death due to metastasis

value: death due to other cause

tag: chromosome 3 status

value: Disomy 3

tag: follow-up (months)

tag: hc10 (hla-b/c)-positive (percentage)

tag: hca2 (hla-a)-positive (percentage)

tag: tal.1b5 (hla-dr)-positive (percentage)


title: UM_22

value: death due to metas

value: Monosomy 3


title: UM_23

value: alive


title: UM_28


title: UM_19


title: UM_25


title: UM_24


title: UM_18


title: UM_16


title: PR02

tag: tissue

value: FFPE breast angiosarcomas


title: UM_17


title: UM_13


title: UM_20


title: UM_14


title: UM_15


title: UM_12


title: UM_08


title: UM_27


title: UM_09


title: UM_11


title: UM_07


title: UM_05


title: UM_06


title: UM_02


title: UM_10


title: UM_21


title: UM_03


title: UM_01


title: ΔphoU;Pvan-phoU -vanillate/+vanillate 16 hours depletion rep 1

status: Public on Aug 06 2016

city: Cambridge

first: Michael

last: Laub

address: 31 Ames St

institute: MIT

description: Cells grown in PYE + vanillate to mid-log phase, washed, and released into PYE + or - vanillate and grown in mid-log phase for the specified number of hours

hyb_protocol: Agilent protocol

scan_protocol: Arrays were scanned using Agilent Technologies Scanner G2505C Arrays were scanned using Agilent Technologies Scanner G2505C

data_processing: Data were retrieved using Agilent Feature Extractor 10.6

organism: Caulobacter vibrioides NA1000

source_name: mixed population in PYE + vanillate

label_protocol: RNA was reverse transcribed into cDNA as described previously (Laub et al. 2000)

growth_protocol: Cells were grown to mid-log phase in rich medium (PYE) supplemented with 50 mM vanillate, washed, and released into PYE with or without vanillate. Cells were grown in mid-log phase for the specified number of hours before sampling.

extract_protocol: Total RNA was extracted using the RNAeasy kit (Qiagen) according to manufacturer's protoco

tag: genotype

value: ΔphoU;Pvan-phoU

tag: treatment

value: 50 mM vanillate

source_name: mixed population in PYE - vanillate

value: without vanillate


title: pstS::Tn5;ΔphoU;Pvan-phoU -vanillate/+vanillate 2 hours depletion rep 1


title: UM_04


title: pstS::Tn5;ΔphoU;Pvan-phoU -vanillate/+vanillate 16 hours depletion rep 1


title: mock_rep3

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

description: Splenic Follicular B cells from yy1 f/f mouse, no TATCRE

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the EpiCentre Nano Total-Amp kit

extract_protocol: Follicular B cells were purified from spleen by positive selection using anti-CD23 antibody and Streptavidin coated microbeads (Milteny Biotech) according to the manufacturer’s instructions.

treatment_protocol: cells from each mouse were treated with TAT-CRE in OptiMEM to delete the yy1 gene and then grown in RPMI medium along with LPS, IL4, OPI and 20% FBS for 72 hours

tag: mouse strain

value: C57BL/6 yy1 f/f

tag: transgene

value: Mock


title: Capan2 F99 cocultured gels 1

city: Lund

first: P. Olof

last: Olsson

state: Skåne

address: Medicion Village, hus 406, vånging 3

department: Labratory Medicin

country: Sweden

institute: Lund University

description:
Human Pancreatic ductal carcinoma derived cell line Capan-2 and Human skin fibroblast (F99)
Replicate 1

scan_protocol: Standard Illumina iScan N240 scanning protocol setting file: Direct Hyb

data_processing: The data were normalised using quantile normalisation with BASE

source_name: 3D collagen gel

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

growth_protocol: Cells were grown for 48 hours in DMEM with 10% hi.FBS and 0.1%PEST prior to seeding in 3-dimensional collagen gels, floated after 2 hours and maintained for 48 hrs at 37C with 5% CO2 until harvested

extract_protocol: Gels were digested in Trizol and Extracted with total RNA kit (Qiagen)

treatment_protocol: Gels were taken with forceps at 48 hrs.  Gel composition at start (0.5x 2XDMEM(SVA), 0.4x(3.1mg/ml Collagen(Purecol, BioMatrix), 0.1x 200mM HEPES ph 8.0 mixed 1:9 with 1x10^6 cells in DMEM)

tag: cell line

value: Capan-2 and human skin fibroblast (F99)


title: ΔphoU;Pvan-phoU -vanillate/+vanillate 7 hours depletion rep 1


title: ΔphoU;Pvan-phoU -vanillate/+vanillate 7 hours depletion rep 2


title: ΔphoU;Pvan-phoU -vanillate/+vanillate 5 hours depletion rep 2


title: Capan2 F99 cocultured gels 3

description:
Human Pancreatic ductal carcinoma derived cell line Capan-2 and Human skin fibroblast (F99)
Replicate 3


title: tatCre_rep2

description: Splenic Follicular B cells from yy1 f/f mouse, TATCRE treated

growth_protocol: grown in RPMI medium along with LPS, IL4, OPI and 20% FBS for 72 hours

value: TATCRE


title: tatCre_rep3


title: Capan2 gels 2

description:
Human Pancreatic ductal carcinoma derived cell line Capan-2
Replicate 2


title: mock_rep1


title: ΔphoU;Pvan-phoU -vanillate/+vanillate 2 hours depletion rep 2


title: Capan2 gels 1

description:
Human Pancreatic ductal carcinoma derived cell line Capan-2
Replicate 1


title: ΔphoU;Pvan-phoU -vanillate/+vanillate 2 hours depletion rep 1


title: ΔphoU;Pvan-phoU -vanillate/+vanillate 5 hours depletion rep 1


title: mock_rep2


title: Kat4 gels 1

description:
Human Adenocarcinoma cell line (KAT-4 aka HT-29)
Replicate 1

value: KAT-4 aka HT-29


title: Kat4 F99 cocultured gels 3

description:
Human Adenocarcinoma cell line (KAT-4 aka HT-29), human skin fibroblast (F99)
Replicate 3

value: KAT-4 aka HT-29 and human skin fibroblast (F99)


title: Kat4 F99 cocultured gels 1

description:
Human Adenocarcinoma cell line (KAT-4 aka HT-29), human skin fibroblast (F99)
Replicate 1


title: pstS::Tn5;ΔphoU;Pvan-phoU -vanillate/+vanillate 7 hours depletion rep 1


title: Kat4 gels 3

description:
Human Adenocarcinoma cell line (KAT-4 aka HT-29)
Replicate 3


title: Kat4 F99 cocultured gels 2

description:
Human Adenocarcinoma cell line (KAT-4 aka HT-29), human skin fibroblast (F99)
Replicate 2


title: tatCre_rep1


title: Capan2 gels 3

description:
Human Pancreatic ductal carcinoma derived cell line Capan-2
Replicate 3


title: breast-tum-nit-32-CB

tag: gender

value: Female

tag: age

tag: inter-biopsy-interval-(days)

tag: grade

tag: biopsy-type

value: CB

tag: ihc-substype

value: er

tag: er-allred

tag: pr-allred

tag: size-mm


title: Capan2 F99 cocultured gels 2

description:
Human Pancreatic ductal carcinoma derived cell line Capan-2 and Human skin fibroblast (F99)
Replicate 2


title: M(IL-10) macrophages from human, healthy volunteer donor#3

city: Penzberg

first: Leon

last: Pradel

address: Nonnenwald 2

institute: Roche Innovation Center Munich

hyb_protocol: Hybridization was carried out o/n @45°C for 16h

scan_protocol: GeneChip® Scanner 3000 was used in combination with the respective Genechip® Operating software v1.4

data_processing: Software utilized for primary analysis and subsequent processing of the data comprised GCOS and MAS 5.0

source_name: Local ambulance during regular blood draw

label_protocol: cRNA was labeled in accordance to the manufacturer's protocol (Affymetrix)

growth_protocol: Cells were seeded and cultured for six days in serum-free XVivo10 medium at different cell densities as described earlier and differentiated by means of the cytokines IL-4, -10, -13 or by combinations of these

extract_protocol: According to Qiagen's RNeasy Mini Kit

treatment_protocol: No treatment was applied to the sample set

tag: cell type

value: Peripheral monocytes differentiated into macrophages


title: M(IL-10) macrophages from human, healthy volunteer donor#2


title: M(IL-13,-10) macrophages from human, healthy volunteer donor#3


title: M(IL-13,-10) macrophages from human, healthy volunteer donor#1


title: M(IL-13,-10) macrophages from human, healthy volunteer donor#2


title: M(IL-10) macrophages from human, healthy volunteer donor#1


title: M(IL-4,-10) macrophages from human, healthy volunteer donor#2


title: M(IL-13) macrophages from human, healthy volunteer donor#1


title: M(IL-4,-10) macrophages from human, healthy volunteer donor#3


title: M(IL-4,-10) macrophages from human, healthy volunteer donor#1


title: M(IL-13) macrophages from human, healthy volunteer donor#3


title: M(IL-13) macrophages from human, healthy volunteer donor#2


title: Kat4 gels 2

description:
Human Adenocarcinoma cell line (KAT-4 aka HT-29)
Replicate 2


title: M(IL-4) macrophages from human, healthy volunteer donor#3


title: M(IL-4) macrophages from human, healthy volunteer donor#2


title: M(IL-4) macrophages from human, healthy volunteer donor#1


title: MCF10A si KRT81

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

description: Gene expression treatment with cassis extract

hyb_protocol: 0.6 ug of Cy3-labelled 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 Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MCF10A si KRT81

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).

treatment_protocol: MCF10A cells were purchased from American Type Culture Collection. The MCF10A were routinely cultured in mammary epithelial cell growth medium kit at 37ºC in 5% CO2.

value: Human mammary epithelial cell (MCF10A)

value: KRT81 siRNA


title: MCF10A blackcurrant

source_name: MCF10A blackcurrant

tag: agent

value: black currant extract


title: individual 46

status: Public on Aug 05 2016

city: Chicago

first: Carole

last: Ober

state: Illinois

address: 920 E 58th St

department: Human Genetics

institute: University of Chicago

description:
individual 46
04a7_4ddf

data_processing: Probe intensity was log2-transformed and quantile normalized using the lumi package in R. Probes that overlapped >1 HapMap SNPs and probes that did not have a detection P value <0.05 in at least 20% (n=12) of samples were removed. In genes with multiple probes, we used the most 3’ probe to estimate gene expression.  Of the 60 samples submitted 3 samples failed to hybridize, and one sample was removed due to sample swap

source_name: Whole blood

label_protocol: not provided.

extract_protocol: RNA was extracted from each sample using Qiagen AllPrep DNA/RNA Mini Kits

tag: tissue

value: blood

tag: population

value: Hutterite

tag: eosinophil proportion

tag: neutrophil proportion

tag: monocyte proportion


title: individual 45

description:
individual 45
3919_4664

value: Amish


title: individual 48

description:
individual 48
e9d7_4846


title: individual 49

description:
individual 49
0e8f_49de


title: MCF10A si control

description: Gene expression control

source_name: MCF10A si control

tag: cell line

tag: treatment

value: control


title: individual 51

description:
individual 51
143a_4fa2


title: individual 54

description:
individual 54
f116_4d0c


title: individual 53

description:
individual 53
05fa_4dda


title: individual 44

description:
individual 44
7f6b_4501


title: individual 52

description:
individual 52
eed2_4303


title: MCF10A control

description: Gene expression control

source_name: MCF10A control


title: individual 41

description:
individual 41
d9ef_4854


title: individual 55

description:
individual 55
7939_4d90


title: individual 37

description:
individual 37
de37_4eea


title: individual 43

description:
individual 43
1b27_4c04


title: individual 56

description:
individual 56
c04d_452f


title: individual 36

description:
individual 36
0544_42f0


title: individual 39

description:
individual 39
007e_4c68


title: individual 42

description:
individual 42
02f7_4f2f


title: individual 50

description:
individual 50
09a6_4b8f


title: individual 47

description:
individual 47
350b_45cf


title: individual 35

description:
individual 35
7c29_4e48


title: individual 34

description:
individual 34
7a2a_4e20


title: individual 40

description:
individual 40
bc74_4ae1


title: individual 33

description:
individual 33
aba4_4767


title: individual 32

description:
individual 32
fe44_496e


title: individual 38

description:
individual 38
57e6_4eff


title: individual 30

description:
individual 30
a057_412a


title: individual 28

description:
individual 28
cc2e_4fd1


title: individual 25

description:
individual 25
27e8_409e


title: individual 27

description:
individual 27
3cc1_4987


title: individual 26

description:
individual 26
13d3_4db7


title: individual 29

description:
individual 29
9a4b_4a8b


title: individual 24

description:
individual 24
72f8_47bc


title: individual 19

description:
individual 19
c6bb_4ea5


title: individual 22

description:
individual 22
b2bf_4ec9


title: individual 12

description:
individual 12
0cc1_4f17


title: individual 13

description:
individual 13
334e_404b


title: individual 8

description:
individual 8
b0f4_4029


title: individual 16

description:
individual 16
4949_4911


title: individual 20

description:
individual 20
9711_48a9


title: individual 15

description:
individual 15
8246_41d7


title: individual 23

description:
individual 23
c164_43a5


title: individual 14

description:
individual 14
baac_40c8


title: individual 18

description:
individual 18
b8ea_4d8f


title: individual 17

description:
individual 17
54f4_4a7c


title: individual 5

description:
individual 5
29f4_4128


title: individual 7

description:
individual 7
0c77_42a8


title: individual 9

description:
individual 9
8893_40a7


title: individual 6

description:
individual 6
63c8_47f4


title: individual 11

description:
individual 11
3833_4520


title: individual 21

description:
individual 21
05cf_474a


title: individual 4

description:
individual 4
3dec_4ff1


title: individual 3

description:
individual 3
1dc0_464c


title: individual 10

description:
individual 10
adca_494a


title: individual 2

description:
individual 2
df23_4648


title: individual 1

description:
individual 1
98b7_4ac7


title: 16472 wild type F

city: Ann Arbor

first: Sally

middle: Ann

last: Camper

address: 1241 Catherine St

institute: University of Michigan

hyb_protocol: 1500 ng cRNA was direct hybridized for 18 hours at 58 C by standard Illumina protocol.

scan_protocol: Signal intensity recorded with an Illumina iScan by standard protocol.

data_processing: Image data was analyzed and quantile normalized with Illumina Genome Studio (v2011.1, Data Analysis Software package with Gene Expression Module v1.9.0)

source_name: Mouse pituitary gland

label_protocol: Biotin-labelled cRNA was generated using 500 ng RNA with the Illumina TotalPrep RNA Amplification kit.

extract_protocol: RNA was extracted from homogenized tissue using the RNAqueous 4PCR kit and treated with DNAse I. RNA was quantified with Nanodrop and quality was assessed with 2100 BioAnalyzer. RNA Integrity Number was 9.50 ± 0.13 (SD), 28S/18S was 1.60 ± 0.12 (SD).

tag: strain

value: Mixed C57Bl6j 129S2SvPas

tag: age

value: 8 week

value: pituitary

tag: gender

value: female

tag: genotype

value: wild


title: bes1-D_5 days DARK_rep1

city: Madrid

first: Ana

last: Espinosa-Ruiz

state: Madrid

department: Centro Nacional de Biotecnología

institute: CSIC

description: Gene expression of bes1-D 5-days old seedlings grown in continuous dark.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: bes1-D, rep 1

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

growth_protocol: Seeds were sown in MS agar plates supplemented with 1% sucrose and vernalized for 48h in the dark at 4ºC.

extract_protocol: Samples were collected in the dark and immediately frozen in liquid nitrogen. Total RNA was extracted with Trizol reagent followed by purification with High Pure RNA purification kit (Roche) according to the manufacturer's instructions.

treatment_protocol: After vernalization, plates were tranferred to a growth chamber (22ºC, constant). After 3 hours of white light exposure, plates were wrapped in aluminium foil and seeds were grown for 5 days in the dark.

value: whole seedlings

value: 5 days


title: 16477 mutant type F

value: mutant


title: 16478 wild type M

value: male


title: bes1-D;pif4pif5_5 days DARK_rep1

description: Gene expression of bes1-D;pif4pif5 5-days old seedlings grown in continuous dark.

source_name: bes1-D;pif4pif5, rep 1


title: bes1-D;pif4pif5_5 days DARK_rep2

source_name: bes1-D;pif4pif5, rep 2


title: 16475 mutant type M


title: pif4pif5_5 days DARK_rep1

description: Gene expression of pif4pif5 5-days old seedlings grown in continuous dark.

source_name: pif4pif5, rep1


title: bes1-D;pif4pif5_5 days DARK_rep3

source_name: bes1-D;pif4pif5, rep 3


title: pif4pif5_5 days DARK_rep2

source_name: pif4pif5, rep2


title: Col-0_5 days DARK_rep3

description: Gene expression of Col-0 5-days old seedlings grown in continuous dark.

source_name: Col-0, rep 3


title: 16476 wild type F


title: 16480 wild type F


title: 16470 wild type M


title: bes1-D_5 days DARK_rep3

source_name: bes1-D, rep 3


title: 16479 mutant type M


title: Drosophila_25C_Fluctuating_35C_3

city: Aarhus

first: Jesper

middle: Givskov

last: Soerensen

address: Ny Munkegade 114

department: Bioscience

country: Denmark

institute: Aarhus University

description: Gene expression data from Drosophila developed at 25C Fluctuating and assayed at 35C

hyb_protocol: Fifteen micrograms of cDNA were fragmented and loaded onto the Affymetrix probe array cartridge. Incubation, washing and staining procedures were performed in the Affymetrix Fluidics Station 450.

scan_protocol: The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (Affymetrix Scanner 3000 7G)

data_processing: The raw data was GC-RMA normalized and further analyzed using several different approaches in R

organism: Drosophila melanogaster

label_protocol: The step was performed as described in Dyrskjot et al (2003) doi:10.1038/ng1061

growth_protocol: Flies developed on standard fly food at 15 or 25C, and at either constant or fluctuating temperatures (4 treatments)

treatment_protocol: The 4 experimental groups were either frozen directly from 20C or after being heated up to 35 C at a rate of 0.1C/min

value: Field collected lab stock

tag: developed at

value: 25C Fluctuating

tag: assayed at


title: 16474 wild type M


title: Col-0_5 days DARK_rep1

source_name: Col-0, rep 1


title: Col-0_5 days DARK_rep2

source_name: Col-0, rep 2


title: 16481 mutant type F


title: pif4oif5_5 days DARK_rep3

source_name: pif4pif5, rep3


title: 16473 mutant type F


title: 16471 mutant type M


title: 16469 mutant type F


title: bes1-D_5 days DARK_rep2

source_name: bes1-D, rep 2


title: individual 31

description:
individual 31
6372_4ec1


title: Drosophila_25C_Fluctuating_35C_1

extract_protocol: The step was performed as described in Dyrskjot et al (2003) doi:10.1038/ng1061


title: Drosophila_25C_Fluctuating_20C_3

description: Gene expression data from Drosophila developed at 25C Fluctuating and assayed at 20C


title: Drosophila_25C_Fluctuating_35C_2


title: Drosophila_25C_Constant_35C_2

description: Gene expression data from Drosophila developed at 25C constant and assayed at 35C

value: 25C constant


title: Drosophila_25C_Fluctuating_20C_1


title: Drosophila_25C_Fluctuating_20C_2


title: Drosophila_25C_Constant_20C_2

description: Gene expression data from Drosophila developed at 25C constant and assayed at 20C


title: Drosophila_15C_Fluctuating_20C_1

description: Gene expression data from Drosophila developed at 15C Fluctuating and assayed at 20C

value: 15C Fluctuating


title: Drosophila_25C_Constant_20C_1


title: Drosophila_15C_Fluctuating_35C_1

description: Gene expression data from Drosophila developed at 15C Fluctuating and assayed at 35C


title: Drosophila_25C_Constant_35C_3


title: 16468 wild type F


title: 16466 wild type M


title: 16464 wild type F


title: Drosophila_25C_Constant_35C_1


title: Drosophila_15C_Fluctuating_20C_2


title: Drosophila_15C_Fluctuating_20C_3


title: 16465 mutant type F


title: 16463 mutant type M


title: Drosophila_15C_Constant_35C_3

description: Gene expression data from Drosophila developed at 15C constant and assayed at 35C

value: 15C constant


title: 16461 mutant type F


title: 16460 wild type F


title: 16458 wild type M


title: Drosophila_15C_Fluctuating_35C_3


title: Drosophila_25C_Constant_20C_3


title: Drosophila_15C_Constant_35C_2


title: Drosophila_15C_Fluctuating_35C_2


title: 16459 mutant type M


title: Drosophila_15C_Constant_35C_1


title: Drosophila_15C_Constant_20C_1

description: Gene expression data from Drosophila developed at 15C constant and assayed at 20C


title: Drosophila_15C_Constant_20C_3


title: Drosophila_15C_Constant_20C_2


title: Donor 25 Stimulation HKLR

status: Public on Aug 04 2016

first: Vincent

last: Rouilly

state: Paris

address: 25 rue Dr Roux

institute: Institut Pasteur

hyb_protocol: NanoString nCounter, a hybridization-based multiplex assay.

scan_protocol: Data were collected and analyzed using the nCounter Digital Analyze according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA).

data_processing: To normalize we used the same method as in the positive control normalization, except that geometric means were calculated over four housekeeping genes (RPL19, TBP, POLR2A, HPRT1). These genes were selected using geNorm method.

source_name: Whole Blood

label_protocol: Biotin & color-coded tag, 100ng (5μl) of total RNA from each sample was analyzed using the Human Immunology kit v2 according to the manufacturers instructions.

growth_protocol: Incubation inside a Truculture stimulation tube (from Myriad RBM), 37C, 22h.

extract_protocol: A specific chloroform-free one step protocol was adapted for automation to guarantee a reproducible and high-throughput RNA extraction protocol.

treatment_protocol: At the end of the incubation period, upon removal of the liquid supernatant cell pellets were resuspended in 2ml Trizol LS (Sigma) and vortexed for 2min, rested for 10 min at RT before storage at -80°C.

tag: individual

value: Donor 25

tag: donor id

tag: stimulus id

value: HKLR

value: M

value: whole blood


title: 16467 mutant type M

value: Mixed C57Bl6j 129S2SvPas

value: 8 week


title: Donor 25 Stimulation HKSA

value: HKSA


title: Donor 25 Stimulation ODN

value: ODN


title: Donor 25 Stimulation GARD

value: GARD


title: Donor 25 Stimulation HKHP

value: HKHP


title: Donor 25 Stimulation r848


title: Donor 25 Stimulation BCG

value: BCG


title: Donor 25 Stimulation TNFa

value: TNFa


title: Donor 25 Stimulation LPS

value: LPS