title: BJHTERT-minus PDGFBB, replicate 3

city: Majadahonda

first: Cristina

last: Peña

state: Madrid

address: Joaquín Rodrigo,2

country: Spain

institute: Hospital Universitario Puerta de Hierro, Majadahonda

description: BJHTERT - PDGFBB (sample 3)

hyb_protocol: Illumina Whole-Genome Gene Expression with IntelliHyb Seal 11226030 Rev C.

scan_protocol: Standard Illumina BeadChip scanning protocol. Scan setting file: DirectHyb_HumanHT-12_V3_0.

data_processing: The data were normalised using quantile normalisation implemented in BeadStudio 3.1.3.0.

source_name: BJ-hTERT fibroblasts without stimulation

label_protocol: Illumina®TotalPrep-96 RNA Amplification kit (catalog #: 4393543).

growth_protocol: 1.2 x 10e6 BJ-hTERT fibroblasts were cultured in 10cm dish with Dulbecco's Modified Eagle Medium (DMEM; Gibco Life Technologies, Gergy-Pontoise, France) containing 1% heat-inactivated fetal calf serum (FCS), 2 mM L-glutamine, penicillin (100 units/ml) and streptomycin (100 ng/ml) at 37ºC in a 5% CO2 humidified atmosphere during 24h.

extract_protocol: TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen Inc., Hilden, Germany), followed by purification using the RNeasy Micro Kit (Qiagen Inc., Hilden, Germany).

treatment_protocol: Cultures were stimulated with or without 20ng/mL PDGF-BB (Peprotech, New Jersey, USA) for 24h prior to harvest. Unstimulated fibroblasts were used as control samples. Cultures of both unstimulated and stimulated fibroblasts were done in triplicate.

value: BJ-hTERT

tag: cell type

value: newborn foreskin fibroblasts immortalized with hTERT

tag: treatment


title: BJHTERT-plus PDGFBB, replicate 3

status: Public on Sep 10 2012

type: RNA

description: BJHTERT + PDGFBB (sample 3)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: BJ-hTERT fibroblasts stimulated with 20ng/mL PDGF-BB

tag: cell line

value: 20ng/mL PDGF-BB


title: BerryPericarp-PFS_rep3

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: berry pericarp post-fruit set, replicate 3

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Vitis vinifera cv. Corvina (clone 48) samples were collected from a 7-year-old vineyard (45° 27’ 17” N, 11° 03’ 14” E, Montorio, Verona province, Italy) during 2008/2009 growing seasons. The vineyard is at 130 m. above sea level (a.s.l.), planted on a soil with the following composition: 36% sand, 36% say and 28% silt. The replacement cane Guyot rows are north-south oriented and 41B in used as rootstock.

extract_protocol: Total RNA was extracted from ~100 mg of liquid-nitrogen-grinded tissue using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO) following the manufacturer’s protocol. For berry flesh, senescing leaf and woody stem, it was necessary to isolate RNA from ~400 mg of grinded material, while for berry pericarp and skin, seed, rachis, root, latent and winter bud, from ~200 mg.  Lithium Chloride precipitation treatment was applied to some of the total RNA samples (from winter bud, from seed and rachis at vèraison and mid-ripening, from woody stem) to remove 230wavelenght-absorbant contaminants. Briefly, LiCl solution was mixed with total RNA solution to a final concentration of 2.5 M; after over-night incubation at 4°C, a cold centrifugation and ethanol-70% washing step, total RNA was resuspended in water.

tag: cultivar

value: Corvina

tag: tissue

value: Berry Pericarp

tag: developmental stage

value: post-fruit set


title: Male 1.0 estradiol-7

city: Little Rock

first: Isabelle

last: Racine Miousse

address: 15 Children's Way

country: USA

institute: UAMS

description: mammary gene expression

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N = 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing: Cel files were generated using GCOS and utilized for analysis using GeneSpring GX 11.5.

organism: Rattus norvegicus

source_name: postnatal day 33-rat mammary gland

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Mammary gland pairs were collected and fresh frozen in liquid nitrogen. Total mammary glands RNA was isolated from the rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion.

tag: strain

value: Sprague-Dawley

tag: diet

value: 1 µg/kg/day E2

tag: gender

value: male


title: BerryPericarp-PFS_rep2

source_name: berry pericarp post-fruit set, replicate 2


title: Male 0.1 estradiol-5

description: mammary gene expression

value: 0.1 µg/kg/day E2


title: BerryPericarp-PFS_rep1

source_name: berry pericarp post-fruit set, replicate 1


title: BJHTERT-minus PDGFBB, replicate 2

description: BJHTERT - PDGFBB (sample 2)


title: BerryPericarp-FS_rep3

source_name: berry pericarp fruit set, replicate 3

value: fruit set


title: Male 0.1 estradiol-4

description: mammary gene expression


title: 3 Day Adeno-Cux2 treated 8 wk scid Male mouse liver/3 Day Adeno-CMV treated 8 wk scid Male mouse liver/Replicate#2

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: The expression profile for a pool of RNAs isolated from n=6 8 wk old male mouse livers treated with Adeno-Cux2 for 3 days vs. a pool of RNAs isolated from n=6 8 wk old male mouse livers treated with Adeno-CMV for 3 days is given as a normalized ratio.  The purpose of this comparison is to identify differences in gene expression due to overexpression of Cux2 in male mouse liver.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).

data_processing: Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1)

label: Alexa 647

organism: Mus musculus

source_name: 3 Day Adeno-CMV treated male mouse liver

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

extract_protocol: Trizol extraction of RNA

value: ICR scid

tag: Sex

value: Male

tag: age

value: 8 wk

value: Adeno-CMV (3 day)

label: Alexa 555

source_name: 3 Day Adeno-Cux2 treated male mouse liver

value: Adeno-Cux2 (3 day)


title: Male 0 estradiol-3

description: mammary gene expression

value: 0 µg/kg/day E2


title: 5 Day Adeno-Cux2 treated 8 wk scid Female mouse liver/5 Day Adeno-CMV treated 8 wk scid Female mouse liver/Replicate#1

description: The expression profile for a pool of RNAs isolated from n=4 8 wk old female mouse livers treated with Adeno-Cux2 for 5 days vs. a pool of RNAs isolated from n=4 8 wk old female mouse livers treated with Adeno-CMV for 5 days is given as a normalized ratio.  The purpose of this comparison is to identify differences in gene expression due to overexpression of Cux2 in male mouse liver.

source_name: 5 Day Adeno-CMV treated female mouse liver

value: Female

value: Adeno-CMV (5 day)

source_name: 5 Day Adeno-Cux2 treated female mouse liver

value: Adeno-Cux2 (5 day)


title: 3 Day Adeno-Cux2 treated 8 wk scid Male mouse liver/3 Day Adeno-CMV treated 8 wk scid Male mouse liver/Replicate#1

description: The expression profile for a pool of RNAs isolated from n=5 8 wk old male mouse livers treated with Adeno-Cux2 for 3 days vs. a pool of RNAs isolated from n=5 8 wk old male mouse livers treated with Adeno-CMV for 3 days is given as a normalized ratio.  The purpose of this comparison is to identify differences in gene expression due to overexpression of Cux2 in male mouse liver.


title: BerryPericarp-FS_rep2

source_name: berry pericarp fruit set, replicate 2

value: Corvina


title: Male 0 estradiol-2

description: mammary gene expression


title: BerryPericarp-FS_rep1

source_name: berry pericarp fruit set, replicate 1

value: Berry Pericarp


title: Growth plate cartilage sample 5

city: Enschede

first: Jeroen

last: Leijten

address: Drienerlolaan 5

country: Netherlands

institute: University of Twente

description: Healthy preadolescent cartilage

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 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: A customCDF Version 10 entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization. Differential gene expression was analysed based on loglinear mixed model

label: Biotin

source_name: Growth plate cartilage sample 5

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

extract_protocol: As detailed in Heinrichs C, et al. (1994) Dexamethasone increases growth hormone receptor messenger ribonucleic acid levels in liver and growth plate. Endocrinology 135: 1113-1118.

treatment_protocol: Healthy explants, all remained untreated

tag: tissue-type

value: Growth plate cartilage


title: Male 0 estradiol-1

description: mammary gene expression

value: Sprague-Dawley


title: BJHTERT-plus PDGFBB, replicate 2

description: BJHTERT + PDGFBB (sample 2)

value: BJ-hTERT

value: newborn foreskin fibroblasts immortalized with hTERT

value: 20ng/mL PDGF-BB


title: BJHTERT-plus PDGFBB, replicate 1

description: BJHTERT + PDGFBB (sample 1)


title: 5 Day Adeno-Cux2 treated 8 wk scid Male mouse liver/5 Day Adeno-CMV treated 8 wk scid Male mouse liver/Replicate#2

description: The expression profile for a pool of RNAs isolated from n=6 8 wk old male mouse livers treated with Adeno-Cux2 for 5 days vs. a pool of RNAs isolated from n=7 8 wk old male mouse livers treated with Adeno-CMV for 5 days is given as a normalized ratio.  The purpose of this comparison is to identify differences in gene expression due to overexpression of Cux2 in male mouse liver.

source_name: 5 Day Adeno-CMV treated male mouse liver

source_name: 5 Day Adeno-Cux2 treated male mouse liver


title: 5 Day Adeno-Cux2 treated 8 wk scid Female mouse liver/5 Day Adeno-CMV treated 8 wk scid Female mouse liver/Replicate#2

description: The expression profile for a pool of RNAs isolated from n=4 8 wk old female mouse livers treated with Adeno-Cux2 for 5 days vs. a pool of RNAs isolated from n=3 8 wk old female mouse livers treated with Adeno-CMV for 5 days is given as a normalized ratio.  The purpose of this comparison is to identify differences in gene expression due to overexpression of Cux2 in male mouse liver.


title: BJHTERT-minus PDGFBB, replicate 1

description: BJHTERT - PDGFBB (sample 1)


title: Stamen_rep3

source_name: pool of stamens from undisclosed flowers at 10% and 50% open flowers, replicate 3

value: Stamen


title: Stamen_rep2

source_name: pool of stamens from undisclosed flowers at 10% and 50% open flowers, replicate 2


title: Growth plate cartilage sample 4

description: Healthy preadolescent cartilage

source_name: Growth plate cartilage sample 4


title: Articular cartilage sample 8

description: Healthy preadolescent cartilage

source_name: Articular cartilage sample 8

value: Articular cartilage


title: LmSir2rp3 overexpressor vs. WT M188S2

city: Ribeirão Preto

first: Nilmar

middle: Silvio

last: Moretti

state: Sao Paulo

address: Av. Bandeirantes, 3900

department: Molecular and Cellular Biology

country: Brazil

institute: Sao Paulo University

hyb_protocol: The array was pre-hybridized  with 5X complete Denhardt, 30% deionized formamide, 6X SSPE, 0.5% SDS and 0.1 mg/ml ssDNA for 1 h at 42°C, washed several times and hybridized overnight at 42°C (2.5X modified Denhardt, 30% deionized formamide, 6X SSPE, 0.5% SDS, 0.1mg/ml ssDNA and 0.75 mg/ml yeast tRNA) as described in Rochette et al., 2008. Three biological replicates of all hybridizations were performed to account for sample heterogeneity, variation between slides and variations due to hybridization. The hybridization was performed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned in Perkin Elmer ScanArray Express scanner.

data_processing: The fluorescence signal intensities of the array and the local background were measured by the GenePix Pro 6.0 image analysis software (Axon Instruments, Union City, California). Data imported in R 2.2.1 were normalized and statistically analyzed using the LIMMA (version 2.7.3).

label: Alexa Fluor 555

organism: Leishmania major

source_name: LmSir2rp3 overexpressor

label_protocol: cDNA was generated from 10µg of total RNAusing a random primer hexamer (GE Healthcare, Barrington) and aminoallyl-dUTPmix (Sigma-Aldrich, St. Louis) following the protocol for Superscript III (Invitrogen, Carlsbad). After 5 h of incubation at 50 C, total RNA was hydrolyzed with NaOH and EDTA for 15 min at 65 C, then pH was neutralized with HCl. cDNA was purified from unincorporated aminoallyl-dUTP using MinElute PCR purification columns (Qiagen, Hilden). Purified cDNA from either condition (Sir2rp3 and wild-type) was dried and coupled with Alexa 555 and Alexa 647 dyes (Invitrogen, Carlsbad).

growth_protocol: Promastigotes forms of Leishmania major wild-type bearing empty vector and Sir2rp3 overexpressor were cultivated in medium M199 1X (Sigma-Aldrich, St. Louis) at 26°C.

extract_protocol: Total RNA extracted using Trizol (Invitrogen, Carlsbad) following manufacturer's instructions. The quality and quantity of RNAwas assessed using RNA 6000 Nano Assay Chips (Agilent Technologies).

treatment_protocol: No treatment was performed

value: promastigote

tag: genotype

value: LmSir2rp3 overexpressor

label: Alexa Fluor 647

source_name: wild type

value: wild type


title: LmSir2rp3 overexpressor vs. WT M188S1


title: Female 10 estradiol-11

description: mammary gene expression

source_name: postnatal day 33-rat mammary gland

value: 10 µg/kg/day E2

value: female


title: LmSir2rp3 overexpressor vs. WT M188S3


title: Articular cartilage sample 7

description: Healthy preadolescent cartilage

source_name: Articular cartilage sample 7


title: Female 10 estradiol-12

description: mammary gene expression


title: Articular cartilage sample 6

description: Healthy preadolescent cartilage

source_name: Articular cartilage sample 6


title: Female 10 estradiol-10

description: mammary gene expression


title: Growth plate cartilage sample 2

description: Healthy preadolescent cartilage

source_name: Growth plate cartilage sample 2


title: Untreated 8 wk scid Male mouse liver/Untreated 8 wk scid Female mouse liver/Replicate#1

description: The expression profile for a pool of RNAs isolated from n=5 untreated 8 wk old male mouse livers vs. a pool of RNAs isolated from n=5 untreated 8 wk old female mouse livers is given as a normalized ratio.  The purpose of this comparison is to highlight sex-specific differences in untreated 8 wk old mouse liver gene expression.

source_name: Untreated 8 week scid female mouse liver

value: ICR scid

value: Female

value: 8 wk

value: untreated

source_name: Untreated 8 week scid male mouse liver

value: Male


title: Female 1.0 estradiol-9

description: mammary gene expression

value: 1 µg/kg/day E2


title: Female 1.0 estradiol-8

description: mammary gene expression

value: Sprague-Dawley


title: Growth plate cartilage sample 1

description: Healthy preadolescent cartilage

source_name: Growth plate cartilage sample 1

value: Growth plate cartilage


title: 5 Day Adeno-Cux2 treated 8 wk scid Male mouse liver/5 Day Adeno-CMV treated 8 wk scid Male mouse liver/Replicate#1

description: The expression profile for a pool of RNAs isolated from n=6 8 wk old male mouse livers treated with Adeno-Cux2 for 5 days vs. a pool of RNAs isolated from n=6 8 wk old male mouse livers treated with Adeno-CMV for 5 days is given as a normalized ratio.  The purpose of this comparison is to identify differences in gene expression due to overexpression of Cux2 in male mouse liver.

value: Adeno-CMV (5 day)

value: Adeno-Cux2 (5 day)


title: Female 0.1 estradiol-6

description: mammary gene expression

value: 0.1 µg/kg/day E2


title: Female 1.0 estradiol-7

description: mammary gene expression


title: Stamen_rep1

source_name: pool of stamens from undisclosed flowers at 10% and 50% open flowers, replicate 1

value: Corvina

value: Stamen


title: Female 0.1 estradiol-5

description: mammary gene expression


title: Untreated 8 wk scid Male mouse liver/Untreated 8 wk scid Female mouse liver/Replicate#2


title: Growth plate cartilage sample 3

description: Healthy preadolescent cartilage

source_name: Growth plate cartilage sample 3


title: Articular cartilage sample 4

description: Healthy preadolescent cartilage

source_name: Articular cartilage sample 4

value: Articular cartilage


title: Female 0.1 estradiol-4

description: mammary gene expression


title: DBA/2 mice post day 14 infection

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Gene expression data from DBA/2 mice post day 14 infection with arthroconidia of C. immitis

hyb_protocol: Purified and fragmented cRNA was hybridized to Affymetrix GeneChip MGU74Av2 microarrays (12,488 probes). GeneChips were washed and stained with streptavidin phycoerythrin according to manufacturer’s instructions.

scan_protocol: GeneChips were scanned using an Agilent Gene Array scanner.

data_processing: Once the microarray data passes quality control analysis, it was transformed to the log2 scale and normalized using the GeneChip Robust Multichip Average (GCRMA) method. The limit of detection was calculated as an expression level of 35.3, which was the 95th percentile expression level of the absent and marginal probes identified using the MAS 5 algorithm from Affymetrix.

source_name: Frozen lung tissue

label_protocol: Double-stranded cDNA was synthesized from isolated RNA. Biotinylated cRNA was in vitro transcribed from double-stranded cDNA template.

extract_protocol: RNA was extracted from frozen lung tissue and RNA quality was confirmed using agarose gels and concentration determined using a spectrophotometer.

treatment_protocol: [Infection protocol] C57BL/6 and DBA/2 mice were infected intra nasally with 50 arthroconidia of C. immitis and sacrificed at either day 10, 14, or 16 post-infection.

tag: c. immitis-infection susceptibility

value: Resistant to C. immitis infection

tag: infection with arthroconidia of c. immitis

value: yes

tag: time (post-infection)

value: post-infection day 14

value: lung


title: DBA/2 mice post day 10 infection

description: Gene expression data from DBA/2 mice post day 10 infection with arthroconidia of C. immitis

value: post-infection day 10


title: C57BL/6 mice post day 16 infection

description: Gene expression data from C57BL/6 mice post day 16 infection with arthroconidia of C. immitis

value: Sensitive to C. immitis infection

value: post-infection day 16


title: Articular cartilage sample 2

description: Healthy preadolescent cartilage

source_name: Articular cartilage sample 2


title: DBA/2 mice prior to infection

description: Gene expression data from DBA/2 mice prior to infection with arthroconidia of C. immitis

value: no

value: control


title: C57BL/6 mice prior to infection

description: Gene expression data from C57BL/6 mice prior to infection with arthroconidia of C. immitis


title: C57BL/6 mice post day 10 infection

description: Gene expression data from C57BL/6 mice post day 10 infection with arthroconidia of C. immitis


title: C57BL/6 mice post day 14 infection

description: Gene expression data from C57BL/6 mice post day 14 infection with arthroconidia of C. immitis


title: Articular cartilage sample 1

description: Healthy preadolescent cartilage

source_name: Articular cartilage sample 1


title: Female 0 estradiol-2

description: mammary gene expression

value: Sprague-Dawley

value: 0 µg/kg/day E2

value: female


title: INSGFP+ 2

status: Public on Sep 09 2012

city: Toronto

first: Michael

last: Wheeler

state: Ontario

address: 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

description:
INS:GFP+ 2
d22-differentiated hESC according to the 'Nostro Protocol', FACS sorted population

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 GeneChip. EukGE-WSv4_450 was used to stain and wash the arrays.

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

data_processing: The data were analyzed with Affymetrix Expression Console (Version 1.1) using Affymetrix default analysis settings and RMA as normalization method.

source_name: FACS sorted Insulin-positive hESC-derived cells

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: hESC differentiated according to the 'Nostro Protocol' (Development, 2011) to day 22. Human Islets obtained from the Clinical Islet Laboratory, University of Alberta and hand-picked.

extract_protocol: Qiagen RNeasy Plus Mini Kit

treatment_protocol: As described in Nostro et al., Development, 2011

tag: cell line background

tag: genotype/variation

value: expressing GFP under the insulin promoter

value: hESC-derived beta-like cells

tag: cell population

value: insulin-positive


title: Articular cartilage sample 3

description: Healthy preadolescent cartilage

source_name: Articular cartilage sample 3


title: INSGFP- 2

description:
INS:GFP- 2
d22-differentiated hESC according to the 'Nostro Protocol', FACS sorted population

source_name: FACS sorted Insulin-negative hESC-derived cells

tag: cell type

value: insulin-negative


title: Female 0 estradiol-1

description: mammary gene expression


title: R10_Brain preactive indvidual 10

status: Public on Sep 08 2012

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

description: Brain gene expression of reactive individual

hyb_protocol: Briefly, total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit. Each sample (1.65 μg of RNA) was hybridized to Zebrafish array (ID 026437, Agilent) at 65 °C for 17 hours using Agilent’s GE Hybridization Kit. Washes were conducted as recommended by the manufacturer using Agilent’s Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Microarrays slides were scanned with Agilent Technologies Scanner model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. One-channel TIFF images were imported into the Gene GeneSpring software GX 11.0.

data_processing: Percentile shift normalization was made to adjust all spot intensities in an array. This normalization takes each column in an experiment independently, and computes the median expression values for this array, across all spots. It then subtracts this value from the expression value of each entity (Bolstad et al, 2003). After Percentile normalization, all data were filtered by comparison of the standard deviation expression among groups (filter by expression). The entities that had values lesser or greater than the standard deviation value were retained. This filter procedure allowed selected genes that have outlier samples, and filter out genes that have a low variation in expression values across all samples. NULL corresponds to spot not included in the normalization.

organism: Danio rerio

source_name: Brain preactive indvidual

label_protocol: All experimental RNA samples were labeled with one dye Cy3. Each group of samples (control, proactive and reactive) was measure their individual variability in the gene expression and compared with the gene expression variability of the other samples groups labeled with the same dye (Cy3). Denatured samples of RNA were reversed transcribed and indirectly labeled with Cy3. RNA labeling, hybridizations, and scanning were performed according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from brains using 500uL of TriReagent (Molecular Research Center) following the manufacturer’s instructions. RNA concentration was quantified using Nanodrop ND-1000 and RNA integrity and quality was assessed using a Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent Technologies). The RNA integrity number (RIN) was calculated for each sample using the Agilent 2100 Expert software, only RNAs with a RIN number > 7 were processed (to reduce experimental biases). Total RNA (2μg) was used to synthesize cDNA with SuperScript III Transcriptase (Invitrogen) and oligo-dT primer (Promega).

treatment_protocol: For microarray screening of coping style in zebrafish, RNA extracted of zebrafish brains (control, n = 10), brains of zebrafish proactive trait (proactive, n = 10), brains of zebrafish reactive trait (reactive, n = 10), Individuals RNAs were hybridized and labeled (10 brain by treatment), in order to inspect the individual variability within natural population of zebrafish

value: Adults


title: R9_Brain preactive indvidual 9


title: INSGFP- 1

description:
INS:GFP- 1
d22-differentiated hESC according to the 'Nostro Protocol', FACS sorted population


title: INSGFP+ 3

description:
INS:GFP+ 3
d22-differentiated hESC according to the 'Nostro Protocol', FACS sorted population


title: INSGFP- 3

description:
INS:GFP- 3
d22-differentiated hESC according to the 'Nostro Protocol', FACS sorted population


title: INSGFP+ 1

description:
INS:GFP+ 1
d22-differentiated hESC according to the 'Nostro Protocol', FACS sorted population


title: HCLS1 shRNA

city: Hannover

first: Siarhei

last: Kandabarau

address: Carl-Neuberg-Str 1

country: Germany

institute: Hannover Medical School

description:
shRNA_HS1
Gene expression data from CD34+ cells transduced with HCLS1 shRNA.

hyb_protocol: After chemical fragmentation of the biotin-labeled cRNA targets, they were hybridized to Affymetrix Human Exome microarrays using the Fluidics Station 450.

scan_protocol: Microarrays were scanned using the Affymetrix Genechip Scanner 3000 with Genechip Operating Software 1.4 (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed with Affymetrix Expression Console software with RMA-sketch exon-level analysis settings.

source_name: Bone marrow CD34+ cells, HCLS1 shRNA

label_protocol: The GeneChip WT cDNA Synthesis and Amplification Kit was used to make double-stranded cDNA from total RNA, which was then labeled with biotin (GeneChip WT Terminal Labeling Kit).

growth_protocol: Cells were cultured in ex-vivo medium supplemented with 10% HSA, 20 ng/ml IL-3, 20 ng/ml IL-6, 20 ng/ml TPO, 50 ng/ml SCF and 50 ng/ml Flt-3L.

extract_protocol: Extraction of total RNA was performed using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: CD34+ hematopoietic cells were transduced with lenitvirus-based RFP-expressed shRNA constructs targeting HCLS1 mRNA (two different shRNA constructs were used simultaneously) or scrambled control shRNA. On day 4 after transduction, transduced RFP+ cells were sorted and total RNA was isolated.

tag: disease state

value: healthy

value: bone marrow

value: CD34+ cells

tag: treatment

value: HCLS1 shRNA


title: Ctrl shRNA

description:
shRNA_CTL
Gene expression data from CD34+ cells transduced with ctrl shRNA.

source_name: Bone marrow CD34+ cells, ctrl shRNA

tag: tissue

value: ctrl shRNA


title: Articular cartilage sample 5

description: Healthy preadolescent cartilage

source_name: Articular cartilage sample 5

value: Articular cartilage


title: DBA/2 mice post day 16 infection

description: Gene expression data from DBA/2 mice post day 16 infection with arthroconidia of C. immitis

tag: strain

value: Resistant to C. immitis infection

value: yes

value: post-infection day 16

value: lung


title: R7_Brain preactive indvidual 7


title: R6_Brain preactive indvidual 6


title: R5_Brain preactive indvidual 5


title: R8_Brain preactive indvidual 8


title: R4_Brain preactive indvidual 4


title: P10_Brain proactive indvidual 10

description: Brain gene expression of proactive individual

source_name: Brain proactive indvidual


title: E. coli O157:H7 at 2 h cinnamaldehyde treatment biological rep2

city: Winnipeg

first: Richard

middle: A

last: Holley

state: Manitoba

address: 250 Ellis Building

department: Department of Food Science

institute: University of Manitoba

description: Gene expression data from cinnamaldehyde treatment at 2 h

hyb_protocol: Hybridization of the cDNAs was conducted at Genome Québec Innovation Centre (McGill University, Montréal, QC, Canada) using Affymetrix Genechip® E. coli Genome 2.0 Array (Affymetrix) as described by the manufacturer.

scan_protocol: Scan procedure was carried out at McGill University & Genome Quebec Innovation Centre according to Affymetrix recommendation.

data_processing:
Raw microarray data was imported into FlexArray 1.6.1 software and statistical tests were performed (Blazejczyk M,  Miron M, Nadon R. 2007. FlexArray: A statistical data analysis software for gene expression microarrays. Genome Quebec, Montreal, Canada)
Data normalization, background correction and expression value calculation were done using the robust multi-array average algorithm (RMA). The expression fold change  (FC), treatment  minus control value ≥ 1.5 log2  with a p value ≤ 0.05 was considered as a cut-off point to determine differentially expressed genes

organism: Escherichia coli O157:H7

source_name: E. coli O157:H7 treated with 200 mg/l cinnamaldehyde, sampled at 2h of treatment

label_protocol: Labelling was performed according to the Affymetrix protocol (Affymetrix, Santa Clara, CA, US). Fragmented cDNAs were mixed with GeneChip® DNA labelling reagent at 7.5 mM (Affymetrix), reaction buffer and 60 U of terminal deoxynucleotidyl transferase (Promega, Madison, WI, US), and incubated at 37 oC for 60 min. The reaction was terminated by adding 2 µl of 0.5 M EDTA.

growth_protocol: An Overnight culture of E. coli O157:H7 was used to inoculate Brain heart infusion broth (BHIB) and incubated at 37ºC to get exponential phase cultures with absorbance at 600 nm (A600) between 0.6 to 0.7.

extract_protocol: Cultures were centrifuged and pellet was treated with TRIzol® reagent. Total RNA was extracted according to the TRIzol® manufacturer's protocol.The RNA pellet digested with DNase I and cleaned-up using RNeasy mini columns (Qiagen Sciences, Germantown, MD, US) according to the manufacturer’s protocol.

treatment_protocol: Exponential phase culture was used to incoculate duplicate flasks with or without 200 mg/l cinnamaldehyde and incubated at 37ºC for ≤ 4h. The Samples from each flask were collected at 2 and 4 h for total RNA extraction.

value: cinnamaldehyde

tag: time


title: P7_Brain proactive indvidual 7


title: E. coli O157:H7 at 4 h control biological rep2

description: Gene expression data from control at 4 h

source_name: E. coli O157:H7 control, sampled at 4h of treatment

value: control


title: P6_Brain proactive indvidual 6


title: R1_Brain preactive indvidual 1


title: R2_Brain preactive indvidual 2


title: E. coli O157:H7 at 2 h control biological rep1

description: Gene expression data from control at 2 h

source_name: E. coli O157:H7 control, sampled at 2h of treatment


title: E. coli O157:H7 at 2 h control biological rep2


title: P8_Brain proactive indvidual 8


title: E. coli O157:H7 at 4 h cinnamaldehyde treatment biological rep1

description: Gene expression data from cinnamaldehyde treatment at 4 h

source_name: E. coli O157:H7 treated with 200 mg/l cinnamaldehyde, sampled at 4h of treatment


title: E. coli O157:H7 at 4 h control biological rep1


title: P4_Brain proactive indvidual 4


title: P9_Brain proactive indvidual 9


title: P3_Brain proactive indvidual 3


title: P2_Brain proactive indvidual 2


title: P5_Brain proactive indvidual 5


title: P1_Brain proactive indvidual 1


title: Subcutaneous tumor 3

city: Melbourne

middle: Henry

last: Kershaw

state: Victoria

address: 14 St. Andrews Place

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Gene expression data from Renca cells growing subcutaneous
S.C.3

hyb_protocol: 10 ug of cRNA was hybridized overnight at 45C on Mouse Gene 1.0 chips.

scan_protocol: A Hewlett-Packard GeneArray Scanner G2500A was used to scan DNA chips.

data_processing: The data was analysed using R and Bioconductor. RMA normalisation was applied using the affy package.

source_name: Subcutaneous tumor

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

growth_protocol: Renca tumor cells were injected either subcutaneously or into the outer coretx of the kidney in BALB/c mice.

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

treatment_protocol: Tumors were taken 12 days after cell injection and snap frozen in liquid nitrogen.

tag: strain background

value: BALB/c

tag: tumor

value: Renca subcutaneous tumor


title: C9_Brain control indvidual 9

description: Brain gene expression of control individual

source_name: Brain control indvidual

tag: age


title: Retina of 5% bilberries in normal control diet (NCD+BB)

city: Kuopio

first: Otto

middle: Taavetti

last: Mykkänen

address: Yliopistonranta 1

department: Public Health and Clinical Nutrition

country: Finland

institute: University of Eastern Finland

hyb_protocol: Pooled cRNA 750 ng from 4 samples (187.5 ng) per group was hybridized at 58˚C overnight (19 h) to each array using standard Illumina protocol with 1 μg/ml streptavidin-Cy3 detection (Amersham, Piscataway, NJ, USA)

scan_protocol: The Mouse-Ref8 V2 R0 Expression BeadChips were scanned with Illumina Bead Array Reader (standard settings) and results extracted with BeadStudio v3.3.7 (Illumina Inc.San Diego, CA, USA).

data_processing:
The data was quantile normalized and resulting gene specific bead-summary data was used as the basis for the gene expression analyses in the statistical programming language R, primarily using beadarray (Dunning et al. 2007) and limma (Smyth et al.2004) packages from the Bioconductor project (Gentleman et al. 2004).
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. PubMed PMID: 15461798; PubMed Central PMCID: PMC545600.

source_name: Mouse retina

label_protocol: The Dnase treated RNA was eluted in 50 μl of water and amplified and biotinylated overnight (15 h) with Ambion's Illumina TotalPrep RNA Amplification kit

growth_protocol: Mice were housed in pairs under standard conditions for laboratory animals.

extract_protocol: Total RNA extracted using QIAzol and cleaned up with RNeasy Lipid Tissue Mini –kit (RNeasy Lipid Tissue Handbook) followed with a Dnase step (Qiagen’s Rnase-Free Dnase set). For the amount and quality  Nanodrop (ND-1000 Wilmington, DE) and BioRad’s Experion electrophoresis station were used at the DNA MicroArray Centre (Turku, Finland).

treatment_protocol: Mice were fed ad libitum with different diets and fasted 1-2 hours prior to sacrifice and collection of both retina per mice for total RNA extraction.

tag: gender

value: male

tag: mouse id

value: 18 weeks

tag: feeding time

value: 12 weeks

tag: diet id

value: D12451, Research Diets Inc.

tag: % kcal fat in diet

value: normal (10%)

tag: berrydiet

value: 5% bilberries (w/w)


title: C7_Brain control indvidual 7

value: Adults


title: Subcutaneous tumor 2

description:
Gene expression data from Renca cells growing subcutaneous
S.C.2


title: Subcutaneous tumor 1

description:
Gene expression data from Renca cells growing subcutaneous
S.C.1


title: C5_Brain control indvidual 5


title: C10_Brain control indvidual 10


title: C6_Brain control indvidual 6


title: C1_Brain control indvidual 1


title: C3_Brain control indvidual 3


title: Intrakidney tumor 2

description:
Gene expression data from Renca cells growing in kidney
lik5

source_name: Intrakidney tumor

value: Renca kidney tumor


title: C2_Brain control indvidual 2


title: Intrakidney tumor 1

description:
Gene expression data from Renca cells growing in kidney
lik4


title: Retina of high-fat diet (HFD)

value: Custom made using D12450B in Research Diets Inc.

value: high-fat diet (45%)


title: Intrakidney tumor 3

description:
Gene expression data from Renca cells growing in kidney
lik6


title: C4_Brain control indvidual 4


title: MCF7-shSTAT3-nutlin3a_4h-3

status: Public on Sep 07 2012

city: Stockholm

first: Fedor

last: Nikulenkov

address: Nobels vag 16

country: Sweden

institute: Fedor Nikulenkov

description: tumor cell line

hyb_protocol: Labeled cRNA was fragmented in fragmentation buffer (5x buffer:200 mM Tris-acetate (pH 8.1)/500nM KOAc/150 mM MgOAc) before hybridization on the array. Fragmented cRNA was hybridized to the nicroarrays in 90ul hybridization solution. GeneTitan Hybridization, Wash and Stain kit for 3`IVT arrays (Affymetrix) was used for preparing hybridization mixes and processing plate array in GeneTitan

scan_protocol: Human Genome U219 array plate was processed in GeneTitan according to manufacturer's instructions

data_processing: The data were analyzed with RMA method in R

source_name: MCF7 cell line

label_protocol: cRNA synthesis was made using 3`IVT Express kit (Affymetrix) following manufacterer's instructions and starting with 200ng of total RNA

growth_protocol: MCF7 is a human breast carcinoma line in 10% FCS DMEM media

extract_protocol: Total RNA from cell pellets was isolated with Rneasy Mini Kit (Qiagen), following the manufacterer's instructon. A fraction was quantitated by spectrophotometric measure using NanoDrop. RNA integrity was evaluated in agarose gel electrophoresis.

treatment_protocol: Cell lines were treated with 10 μM nutlin3a for 8 or 4h before analysis. Knock-down of STAT3 was performed using lentivirus system. MCF7 cells were infected with shContr or shSTAT3 and selected using puromicin selectivity marker. Obtained stably depleted clones were treated  with nutlin3a for 4h, harvested and subjected for microarrays.

tag: cell line

value: infected with shSTAT3 and then treated with 10 μM nutlin3a for 4h


title: MCF7-shSTAT3-nutlin3a_4h-2

description: tumor cell line


title: Retina of normal control diet (NCD)

value: D12450B, Research Diets Inc.


title: MCF7-shSTAT3-Contr_4h-3

description: tumor cell line

value: infected with shSTAT3


title: MCF7-shSTAT3-nutlin3a_4h-1

description: tumor cell line


title: MCF7-shSTAT3-Contr_4h-2

description: tumor cell line


title: Retina of 5% bilberries in high-fat diet (HFD+BB)

value: Custom made using D12451 in Research Diets Inc.


title: MCF7-shContr-nutlin3a_4h-2

description: tumor cell line

value: infected with shContr and then treated with 10 μM nutlin3a for 4h


title: MCF7-shSTAT3-Contr_4h-1

description: tumor cell line


title: MCF7-shContr-nutlin3a_4h-3

description: tumor cell line


title: MCF7-shContr-nutlin3a_4h-1

description: tumor cell line


title: MCF7-shContr-Contr_4h-2

description: tumor cell line

value: infected with shContr


title: R3_Brain preactive indvidual 3

description: Brain gene expression of reactive individual


title: Female 0 estradiol-3

description: mammary gene expression

source_name: postnatal day 33-rat mammary gland

value: Sprague-Dawley

tag: diet

value: 0 µg/kg/day E2

value: female


title: MCF7-shContr-Contr_4h-3

description: tumor cell line


title: MCF7-nutlin3a_8h-3

description: tumor cell line

value: 10 μM nutlin3a for 8h


title: MCF7-Contr_8h-3

description: tumor cell line


title: MCF7-nutlin3a_8h-2

description: tumor cell line


title: MCF7-nutlin3a_8h-1

description: tumor cell line


title: MCF7-Contr_8h-2

description: tumor cell line


title: L. lactis LL52 CGH M17 replicate 2

type: genomic

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

description: [L. lactis LL52 CGH on M17 replicate 2]

hyb_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

data_processing: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France, http://biopuce.insa-toulouse.fr). Data were normalized by the all spot’s mean with Bioplot software.

molecule: genomic DNA

organism: Lactococcus lactis

source_name: L. lactis LL52 CGH M17

growth_protocol: see manuscript in preparation Tan-a-ram et al. 2010. Diversity of dairy Lactococcus lactis subsp. lactis: an integrated approach combining phenotypic, genomic and transcriptomic analyses.


title: L. lactis LL52 CGH M17 replicate 1

description: [L. lactis LL52 CGH on M17 replicate 1]

scan_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

extract_protocol: see manuscript in preparation Tan-a-ram et al. 2010. Diversity of dairy Lactococcus lactis subsp. lactis: an integrated approach combining phenotypic, genomic and transcriptomic analyses.


title: L. lactis S86 CGH M17 replicate 2

description: [L. lactis S86 CGH on M17 replicate 2]

source_name: L. lactis S86 CGH M17

label_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.


title: L. lactis IL1403 CGH M17 replicate 3

description: [L. lactis IL1403 CGH on M17 replicate 3]

source_name: L. lactis IL1403 CGH M17


title: L. lactis LL08 CGH M17 replicate 3

description: [L. lactis LL08 CGH on M17 replicate 3]

source_name: L. lactis LL08 CGH M17


title: L. lactis LL08 CGH M17 replicate 2

description: [L. lactis LL08 CGH on M17 replicate 2]


title: L. lactis LL52 CGH M17 replicate 3

description: [L. lactis LL52 CGH on M17 replicate 3]


title: MCF7-shContr-Contr_4h-1

description: tumor cell line


title: L. lactis S86 CGH M17 replicate 1

description: [L. lactis S86 CGH on M17 replicate 1]


title: L. lactis IL1403 CGH M17 replicate 2

description: [L. lactis IL1403 CGH on M17 replicate 2]


title: L. lactis S86 CGH M17 replicate 3

description: [L. lactis S86 CGH on M17 replicate 3]


title: L. lactis IL1403 CGH M17 replicate 1

description: [L. lactis IL1403 CGH on M17 replicate 1]


title: L. lactis LL08 CGH M17 replicate 1

description: [L. lactis LL08 CGH on M17 replicate 1]


title: L. lactis LD61 CGH M17 replicate 2

description: [L. lactis LD61 CGH on M17 replicate 2]

source_name: L. lactis LD61 CGH M17


title: MCF7-Contr_8h-1

description: tumor cell line


title: L. lactis LD55 CGH M17 replicate 3

description: [L. lactis LD55 CGH on M17 replicate 3]

source_name: L. lactis LD55 CGH M17


title: L. lactis UCMA5713 CGH M17 replicate 3

description: [L. lactis UCMA5713 CGH on M17 replicate 3]

source_name: L. lactis UCMA5713 CGH M17


title: E. coli O157:H7 at 4 h cinnamaldehyde treatment biological rep2

value: cinnamaldehyde


title: L. lactis LD55 CGH M17 replicate 1

description: [L. lactis LD55 CGH on M17 replicate 1]


title: L. lactis LD61 CGH M17 replicate 3

description: [L. lactis LD61 CGH on M17 replicate 3]


title: L. lactis LD61 CGH M17 replicate 1

description: [L. lactis LD61 CGH on M17 replicate 1]


title: L. lactis UCMA5713 CGH M17 replicate 2

description: [L. lactis UCMA5713 CGH on M17 replicate 2]


title: L. lactis S86 Transcriptome cheese replicate 3

description: [L. lactis S86 Transcriptome on cheese replicate 3]

source_name: L. lactis S86


title: L. lactis UCMA5713 CGH M17 replicate 1

description: [L. lactis UCMA5713 CGH on M17 replicate 1]


title: L. lactis LD55 CGH M17 replicate 2

description: [L. lactis LD55 CGH on M17 replicate 2]


title: L. lactis S86 Transcriptome cheese replicate 2

description: [L. lactis S86 Transcriptome on cheese replicate 2]


title: L. lactis LD61 Transcriptome cheese replicate 2

description: [L. lactis LD61 Transcriptome on cheese replicate 2]

source_name: L. lactis LD61


title: L. lactis LL52 Transcriptome cheese replicate 3

description: [L. lactis LL52 Transcriptome on cheese replicate 3]

source_name: L. lactis LL52


title: L. lactis S86 Transcriptome cheese replicate 1

description: [L. lactis S86 Transcriptome on cheese replicate 1]


title: L. lactis LL52 Transcriptome cheese replicate 2

description: [L. lactis LL52 Transcriptome on cheese replicate 2]


title: L. lactis LD61 Transcriptome cheese replicate 1

description: [L. lactis LD61 Transcriptome on cheese replicate 1]


title: L. lactis LL52 Transcriptome cheese replicate 1

description: [L. lactis LL52 Transcriptome on cheese replicate 1]


title: E. coli O157:H7 at 2 h cinnamaldehyde treatment biological rep1

description: Gene expression data from cinnamaldehyde treatment at 2 h

source_name: E. coli O157:H7 treated with 200 mg/l cinnamaldehyde, sampled at 2h of treatment


title: L. lactis LD55 Transcriptome cheese replicate 1

description: [L. lactis LD55 Transcriptome on cheese replicate 1]

source_name: L. lactis LD55


title: L. lactis LD55 Transcriptome cheese replicate 3

description: [L. lactis LD55 Transcriptome on cheese replicate 3]


title: L. lactis LD55 Transcriptome cheese replicate 2

description: [L. lactis LD55 Transcriptome on cheese replicate 2]


title: L. lactis LL08 Transcriptome cheese replicate 3

description: [L. lactis LL08 Transcriptome on cheese replicate 3]

source_name: L. lactis LL08


title: L. lactis UCMA5713 Transcriptome cheese replicate 1

description: [L. lactis UCMA5713 Transcriptome on cheese replicate 1]

source_name: L. lactis UCMA5713


title: L. lactis LL08 Transcriptome cheese replicate 2

description: [L. lactis LL08 Transcriptome on cheese replicate 2]


title: L. lactis LL08 Transcriptome cheese replicate 1

description: [L. lactis LL08 Transcriptome on cheese replicate 1]


title: L. lactis UCMA5713 Transcriptome cheese replicate 3

description: [L. lactis UCMA5713 Transcriptome on cheese replicate 3]


title: L. lactis LD61 Transcriptome cheese replicate 3

description: [L. lactis LD61 Transcriptome on cheese replicate 3]


title: L. lactis UCMA5713 Transcriptome cheese replicate 2

description: [L. lactis UCMA5713 Transcriptome on cheese replicate 2]


title: Cell line Number 38 rs7222094 genotypeTT stim

city: Stanford

first: Simone

last: Thair

state: CA

address: P226 1201 Welch Rd

department: Emergency Medicine

institute: Stanford University

hyb_protocol: Standard Illumina Whole Genome Gene Expression Direct Hybridization Protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Normalization and fold change were calculated using FlexArray v. 1.4.1 Software package available from Genome Quebec Canada

source_name: B lymphoblastoid cell line stimulated with cytomix for 6 hours

label_protocol: Standard Illumina TotalPrep RNA amplification kit

growth_protocol: Standard tissue culture protocol according to Coriell Respository recommendations

extract_protocol: Column extraction using QIAgen RNEasy kit.

treatment_protocol: Stimulation with Cytomix for 6 hours, 3 biological replicates.

tag: cell line number

tag: snp

tag: genotype

value: TT

value: stimulated with cytomix for 6 hours

tag: cell type

value: B lymphoblastoid


title: Cell line Number 22 rs7222094 genotypeCT stim

value: CT

tag: treatment


title: Cell line Number 16 rs7222094 genotypeCT stim


title: Cell line Number 36 rs7222094 genotypeCT stim


title: Cell line Number 37 rs7222094 genotypeCT cont

source_name: B lymphoblastoid cell line control


title: Cell line Number 38 rs7222094 genotypeTT cont


title: Cell line Number 36 rs7222094 genotypeCT cont


title: Cell line Number 54 rs7222094 genotypeCC cont

value: CC


title: Cell line Number 16 rs7222094 genotypeCT cont


title: Cell line Number 37 rs7222094 genotypeCT stim


title: Cell line Number 32 rs7222094 genotypeTT cont


title: C8_Brain control indvidual 8

description: Brain gene expression of control individual

source_name: Brain control indvidual

value: Adults


title: Cell line Number 31 rs7222094 genotypeCT stim


title: Cell line Number 39 rs7222094 genotypeTT stim


title: Cell line Number 51 rs7222094 genotypeCT stim


title: Cell line Number 51 rs7222094 genotypeCT cont


title: Cell line Number 21 rs7222094 genotypeCT cont


title: Cell line Number 31 rs7222094 genotypeCT cont


title: Cell line Number 15 rs7222094 genotypeCT stim


title: Cell line Number 21 rs7222094 genotypeCT stim


title: Cell line Number 35 rs7222094 genotypeTT cont


title: Cell line Number 22 rs7222094 genotypeCT cont


title: Cell line Number 32 rs7222094 genotypeTT stim


title: Cell line Number 39 rs7222094 genotypeTT cont


title: Cell line Number 10 rs7222094 genotypeTT stim


title: Cell line Number 10 rs7222094 genotypeTT cont


title: Cell line Number 15 rs7222094 genotypeCT cont


title: Cell line Number 30 rs7222094 genotypeCT cont


title: Cell line Number 54 rs7222094 genotypeCC stim


title: Cell line Number 35 rs7222094 genotypeTT stim


title: Cell line Number 30 rs7222094 genotypeCT stim


title: Cell line Number 20 rs7222094 genotypeTT cont


title: Cell line Number 14 rs7222094 genotypeTT cont


title: cHF+F+ROSI, replicate 7, part 2

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

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

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

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

data_processing:
Images were quantified using Agilent Feature Extraction Software (v 10.5.5.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.
series suplementary file contains normalized log2 value of sample over reference pool (minus bad spots)

source_name: Gastrocnemius muscle, high fat diet +LC n-3 PUFA + rosiglitazone (10mg/kg diet), sacrificed after 'diet-switch protocol'

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010). The group cHF+ROSI was also included in study GSE36716; therefore, all animals of cHF+ROSI were individually used in duplicate for labelling and hybridisation.

extract_protocol: Total RNA was isolated from gastrocnemius muscle stored in RNAlater Solution (Ambion) using TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instruction. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with Experion automated electrophoresis system (BioRad).

treatment_protocol: Animals were fed a purified high-fat diet (cHF) supplemented with rosiglitazone (10mg/kg diet; cHF+ROSI), with or without supplementation of long chain n-3 PUFA (+F). All  groups received the diet ad-libitum during the 8 weeks intervention. Animals were fasted during 10hr in the light phase, and re-fed Chow diet during the subsequent night. The next morning, animals were anaestetized and sacrificed.

value: cHF diet supplemented with n-3 LC PUFA and rosiglitazone

tag: tissue

value: gastrocnemius muscle

tag: strain

value: male

value: adult

value: control reference pool (all diets including cHF+ROSI at a higher dose)


title: Cell line Number 13 rs7222094 genotypeCC cont


title: cHF+F+ROSI, replicate 3, part 2

source_name: reference pool (all diets including cHF+ROSI at a higher dose)


title: Cell line Number 34 rs7222094 genotypeCT stim


title: cHF+F+ROSI, replicate 1, part 2


title: cHF+F+ROSI, replicate 8, part 2


title: cHF+ROSI, replicate 4, part 2

source_name: Gastrocnemius muscle, high fat diet + rosiglitazone (10mg/kg diet), sacrificed after 'diet-switch protocol'

value: cHF diet supplemented with rosiglitazone


title: Cell line Number 28 rs7222094 genotypeCC cont


title: Cell line Number 34 rs7222094 genotypeCT cont


title: cHF+F+ROSI, replicate 6, part 2


title: cHF+ROSI, replicate 5, part 2


title: Cell line Number 20 rs7222094 genotypeTT stim


title: cHF+F+ROSI, replicate 2, part 2


title: Cell line Number 14 rs7222094 genotypeTT stim


title: cHF+F+ROSI, replicate 5, part 2


title: Cell line Number 50 rs7222094 genotypeTT stim


title: cHF+F+ROSI, replicate 4, part 2


title: Cell line Number 9 rs7222094 genotypeTT cont


title: Cell line Number 13 rs7222094 genotypeCC stim


title: cHF+ROSI, replicate 8, part 2


title: cHF+ROSI, replicate 3, part 2


title: cHF+ROSI, replicate 2, part 2


title: Cell line Number 9 rs7222094 genotypeTT stim


title: cHF+ROSI, replicate 6, part 2


title: Cell line Number 50 rs7222094 genotypeTT cont


title: cHF+ROSI, replicate 7, part 2


title: Cell line Number 19 rs7222094 genotypeTT cont


title: cHF+ROSI, replicate 8, part 1

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations using a Cy5-dyesaver as published (Anal Biochem 2007_363_315).

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010). Here, the additional group receiving cHF+ROSI at 100 mg/kg diet was not included in normalization and data analysis, so these arrays are therefore lacking in the list. Samples were nevertheless included for the Cy3 labelling and therefore included in the (Cy3) reference pool.

treatment_protocol: Animals were fed a purified high-fat diet as a control (cHF), or either supplemented with long chain n-3 PUFA (cHF+F), or rosiglitazone (10 mg/kg diet; cHF+ROSI). An additional group received cHF+ROSI with a higher dose of rosiglitazone 100 mg/kg diet). All  groups received the diet ad-libitum during the 8 weeks intervention. Animals were fasted during 10hr in the light phase, and re-fed Chow diet during the subsequent night. The next morning, animals were anaestetized and sacrificed. The combination treatment group receiving both LC n-3 PUFA and low dose rosiglitazone (cHF+F+ROSI) is presented in another GEO study, GSE36717.

source_name: reference pool (all 2 diets)

value: reference pool (all 2 diets)


title: Cell line Number 8 rs7222094 genotypeTT stim


title: Cell line Number 19 rs7222094 genotypeTT stim


title: cHF+ROSI, replicate 7, part 1


title: Cell line Number 7 rs7222094 genotypeCT cont


title: Cell line Number 53 rs7222094 genotypeCT cont


title: Cell line Number 53 rs7222094 genotypeCT stim


title: cHF+ROSI, replicate 3, part 1


title: cHF+ROSI, replicate 1, part 2


title: cHF+F, replicate 7, part 1

source_name: Gastrocnemius muscle, high fat diet +LC n-3 PUFA, sacrificed after 'diet-switch protocol'

value: cHF diet supplemented with n-3 LC-PUFA concentrate


title: Cell line Number 7 rs7222094 genotypeCT stim


title: Cell line Number 8 rs7222094 genotypeTT cont


title: Cell line Number 49 rs7222094 genotypeCC cont


title: cHF+F, replicate 6, part 1


title: cHF+ROSI, replicate 5, part 1


title: Cell line Number 49 rs7222094 genotypeCC stim


title: cHF+ROSI, replicate 6, part 1


title: cHF+F, replicate 4, part 1


title: Cell line Number 45 rs7222094 genotypeTT stim


title: cHF+F, replicate 5, part 1


title: cHF+ROSI, replicate 2, part 1


title: cHF+ROSI, replicate 1, part 1


title: cHF+ROSI, replicate 4, part 1


title: cHF+F, replicate 8, part 1


title: Cell line Number 4 rs7222094 genotypeCC stim


title: Cell line Number 45 rs7222094 genotypeTT cont


title: cHF+F, replicate 2, part 1


title: Cell line Number 68 rs7222094 genotypeCC cont


title: Cell line Number 68 rs7222094 genotypeCC stim


title: Cell line Number 27 rs7222094 genotypeTT stim


title: control high fat cHF, replicate 7, part 1

source_name: Gastrocnemius muscle, control high fat diet, sacrificed after 'diet-switch protocol'

value: high fat cHF diet


title: control high fat cHF, replicate 8, part 1


title: Cell line Number 27 rs7222094 genotypeTT cont


title: Cell line Number 29 rs7222094 genotypeTT stim


title: control high fat cHF, replicate 6, part 1


title: cHF+F, replicate 1, part 1


title: Cell line Number 67 rs7222094 genotypeCT stim


title: Cell line Number 67 rs7222094 genotypeCT cont


title: Cell line Number 80 rs7222094 genotypeCT cont


title: control high fat cHF, replicate 4, part 1


title: cHF+F, replicate 3, part 1


title: Cell line Number 3 rs7222094 genotypeCT cont


title: Cell line Number 80 rs7222094 genotypeCT stim


title: Cell line Number 62 rs7222094 genotypeTT stim


title: control high fat cHF, replicate 5, part 1


title: control high fat cHF, replicate 2, part 1


title: pbMEC_S. aureus_6h_rep3

city: Dummerstorf

first: Juliane

last: Guenther

address: Wilhelm-Stahl-Allee 2

institute: Leibniz-Institute for Farm Animal Biology (FBN)

description: Gene expression data from primary bovine mammary epithelial cells challenged with heat-inactivated particles of S. aureus strain 1027 for 6h

hyb_protocol: 10 µg of biotin labelled, purified and fragmented cRNA was then hybridized onto GeneChip® Bovine Genome Arrays (Affymetrix) during a 16-hour incubation at 45°C. Posthybridization staining and washing was performed using an automated protocol on the Fluidics Station 450 (Affymetrix)

scan_protocol: Arrays were scanned with a GeneChip® scanner 3000 7G

data_processing: Background correction, normalization and summation was performed using GCRMA. Only such genes were further processed exhibiting at least three present-calls. The gene expression values for the various points in time were estimated with a linear model. In order to account for multiple testing, the false discovery rate approach was used and we selected only the genes with a q-value ≤ 0.05. In a further filtering step, only genes with a fold-change ≥ 2 in the time profile were kept.

organism: Bos taurus

source_name: pbMEC callenged with S. aureus for 6h

label_protocol: cDNA was linearly amplified with T7-RNA polymerase in an in vitro transcription (IVT) reaction, and labeled with biotinylated ribonucleotides (GeneChip® IVT Labeling Kit, Affymetrix)

value: primary bovine mammary epithelial cells

value: heat inactivated S. aureus

tag: time

value: 6 h


title: control high fat cHF, replicate 3, part 1

tag: age


title: Cell line Number 29 rs7222094 genotypeTT cont

value: TT


title: control high fat cHF, replicate 1, part 1

tag: gender


title: Cell line Number 62 rs7222094 genotypeTT cont

value: B lymphoblastoid


title: Cell line Number 3 rs7222094 genotypeCT stim

value: CT

value: stimulated with cytomix for 6 hours


title: pbMEC_S. aureus_24h_rep3

description: Gene expression data from primary bovine mammary epithelial cells challenged with heat-inactivated particles of S. aureus strain 1027 for 24h

source_name: pbMEC callenged with S. aureus for 24h


title: pbMEC_S. aureus_1h_rep3

description: Gene expression data from primary bovine mammary epithelial cells challenged with heat-inactivated particles of S. aureus strain 1027 for 1h

source_name: pbMEC callenged with S. aureus for 1h

value: 1 h


title: pbMEC_S. aureus_3h_rep3

description: Gene expression data from primary bovine mammary epithelial cells challenged with heat-inactivated particles of S. aureus strain 1027 for 3h

source_name: pbMEC callenged with S. aureus for 3h

value: 3 h


title: Cell line Number 44 rs7222094 genotypeCT cont


title: pbMEC_S. aureus_0h_rep3

description: Gene expression data from unchallenged primary bovine mammary epithelial cells

source_name: unstimulated pbMEC, control

value: control


title: Cell line Number 44 rs7222094 genotypeCT stim


title: Cell line Number 66 rs7222094 genotypeTT stim


title: Cell line Number 43 rs7222094 genotypeTT cont


title: Cell line Number 52 rs7222094 genotypeCT stim


title: pbMEC_S. aureus_3h_rep2


title: Cell line Number 66 rs7222094 genotypeTT cont


title: pbMEC_S. aureus_6h_rep2


title: Cell line Number 43 rs7222094 genotypeTT stim


title: Cell line Number 65 rs7222094 genotypeCT cont


title: Cell line Number 33 rs7222094 genotypeTT cont


title: Cell line Number 6 rs7222094 genotypeTT cont


title: Cell line Number 2 rs7222094 genotypeTT stim


title: Cell line Number 65 rs7222094 genotypeCT stim


title: Cell line Number 33 rs7222094 genotypeTT stim


title: Cell line Number 79 rs7222094 genotypeTT cont


title: Cell line Number 2 rs7222094 genotypeTT cont


title: pbMEC_S. aureus_1h_rep2


title: pbMEC_S. aureus_24h_rep2


title: pbMEC_S. aureus_6h_rep1


title: Cell line Number 79 rs7222094 genotypeTT stim


title: Cell line Number 52 rs7222094 genotypeCT cont


title: Cell line Number 61 rs7222094 genotypeCT stim


title: Cell line Number 28 rs7222094 genotypeCC stim

value: CC


title: Cell line Number 6 rs7222094 genotypeTT stim


title: Cell line Number 61 rs7222094 genotypeCT cont


title: pbMEC_S. aureus_3h_rep1


title: pbMEC_S. aureus_1h_rep1


title: pbMEC_S. aureus_0h_rep2


title: pbMEC_S. aureus_24h_rep1


title: pbMEC_S. aureus_0h_rep1


title: Cell line Number 60 rs7222094 genotypeCT cont


title: Cell line Number 60 rs7222094 genotypeCT stim


title: Cell line Number 78 rs7222094 genotypeCT stim


title: Cell line Number 4 rs7222094 genotypeCC cont


title: pbMEC_E. coli_1h_rep3

description: Gene expression data from primary bovine mammary epithelial cells challenged with heat-inactivated particles of E. coli strain 1303 for 1h

source_name: pbMEC callenged with E. coli for 1h

value: heat inactivated E. coli


title: pbMEC_E. coli_0h_rep3


title: pbMEC_E. coli_3h_rep3

description: Gene expression data from primary bovine mammary epithelial cells challenged with heat-inactivated particles of E. coli strain 1303 for 3h

source_name: pbMEC callenged with E. coli for 3h


title: pbMEC_E. coli_24h_rep3

description: Gene expression data from primary bovine mammary epithelial cells challenged with heat-inactivated particles of E. coli strain 1303 for 24h

source_name: pbMEC callenged with E. coli for 24h


title: pbMEC_E. coli_6h_rep3

description: Gene expression data from primary bovine mammary epithelial cells challenged with heat-inactivated particles of E. coli strain 1303 for 6h

source_name: pbMEC callenged with E. coli for 6h


title: pbMEC_E. coli_6h_rep2


title: Cell line Number 77 rs7222094 genotypeCT stim

source_name: B lymphoblastoid cell line stimulated with cytomix for 6 hours


title: Cell line Number 76 rs7222094 genotypeTT stim


title: Cell line Number 58 rs7222094 genotypeCT cont

source_name: B lymphoblastoid cell line control


title: Cell line Number 73 rs7222094 genotypeTT cont


title: Cell line Number 74 rs7222094 genotypeTT cont


title: Cell line Number 1 rs7222094 genotypeCC cont


title: Cell line Number 59 rs7222094 genotypeCT cont


title: Cell line Number 78 rs7222094 genotypeCT cont


title: Cell line Number 76 rs7222094 genotypeTT cont


title: Cell line Number 59 rs7222094 genotypeCT stim


title: Cell line Number 73 rs7222094 genotypeTT stim


title: pbMEC_E. coli_24h_rep2


title: Cell line Number 74 rs7222094 genotypeTT stim


title: Cell line Number 81 rs7222094 genotypeTT cont


title: Cell line Number 58 rs7222094 genotypeCT stim


title: Cell line Number 1 rs7222094 genotypeCC stim


title: pbMEC_E. coli_1h_rep2


title: Cell line Number 81 rs7222094 genotypeTT stim


title: Cell line Number 48 rs7222094 genotypeTT stim


title: Cell line Number 77 rs7222094 genotypeCT cont


title: pbMEC_E. coli_3h_rep2


title: Cell line Number 82 rs7222094 genotypeCT cont


title: Cell line Number 48 rs7222094 genotypeTT cont


title: pbMEC_E. coli_0h_rep2


title: Cell line Number 47 rs7222094 genotypeCC stim


title: pbMEC_E. coli_3h_rep1


title: pbMEC_E. coli_6h_rep1


title: Cell line Number 47 rs7222094 genotypeCC cont


title: Cell line Number 55 rs7222094 genotypeTT cont


title: Cell line Number 83 rs7222094 genotypeTT cont


title: STAT4 KO at D0, IFNa treated, biological rep2

city: Providence

first: M. Pilar

last: Gil

state: Rhode Island

address: 75 Waterman St

institute: Brown University

description: Gene expression data from STAT4 KO CD8 T cells treated with IFNalpha for 90 minutes

hyb_protocol: Preparation of cRNA and hybridization to the Mouse 430A array were performed as described by the manufacturer (Affymetrix).

scan_protocol: Stained chips were read and analyzed using an Affymetrix 6 GeneChip scanner. Data acquisition was carried out at Brown and Yale Universities.

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.

source_name: CD8 T cells from STAT4-deficient mice treated with IFNalpha for 90 minutes

extract_protocol: CD8 T cells were isolated by negative selection using MACS enrichment kits and the program DepleteS on the AutoMACS instrument (Milteny Biotec). Purity was >85%.RNA was then extracted with the RNAeasy kit from Qiagen using on column digestion with DNAse I (Qiagen).

value: CD8 T cells

value: STAT4 KO

value: 8 to 12 wks of age

value: IFNalpha for 90 minutes


title: Cell line Number 56 rs7222094 genotypeTT stim


title: Cell line Number 82 rs7222094 genotypeCT stim


title: pbMEC_E. coli_0h_rep1


title: Cell line Number 18 rs7222094 genotypeTT cont


title: pbMEC_E. coli_24h_rep1


title: Cell line Number 83 rs7222094 genotypeTT stim


title: Cell line Number 46 rs7222094 genotypeTT stim


title: Cell line Number 56 rs7222094 genotypeTT cont


title: Cell line Number 26 rs7222094 genotypeCC cont


title: Cell line Number 26 rs7222094 genotypeCC stim


title: Cell line Number 55 rs7222094 genotypeTT stim


title: Cell line Number 18 rs7222094 genotypeTT stim


title: STAT4 KO at D0, IFNa treated, biological rep3

label_protocol: Preparation of cRNA and hybridization to the Mouse 430A array were performed as described by the manufacturer (Affymetrix).


title: STAT4 KO at D0, untreated, biological rep3

description: Gene expression data from STAT4 KO CD8 T cells

source_name: CD8 T cells from STAT4-deficient mice


title: pbMEC_E. coli_1h_rep1


title: Cell line Number 25 rs7222094 genotypeTT cont


title: STAT4 KO at D0, IFNa treated, biological rep1


title: Cell line Number 25 rs7222094 genotypeTT stim


title: Cell line Number 24 rs7222094 genotypeCT cont


title: Cell line Number 23 rs7222094 genotypeCT cont


title: Cell line Number 24 rs7222094 genotypeCT stim


title: STAT4 KO at D0, untreated, biological rep2


title: Cell line Number 46 rs7222094 genotypeTT cont


title: Cell line Number 42 rs7222094 genotypeCT cont


title: STAT1 KO at D0, untreated, biological rep3

description: Gene expression data from STAT1 KO CD8 T cells

source_name: CD8 T cells from STAT1-deficient mice

value: STAT1 KO


title: STAT4 KO at D0, untreated, biological rep1


title: Cell line Number 42 rs7222094 genotypeCT stim


title: STAT1 KO at D0, IFNa treated, biological rep1

description: Gene expression data from STAT1 KO CD8 T cells treated with IFNalpha for 90 minutes

source_name: CD8 T cells from STAT1-deficient mice treated with IFNalpha for 90 minutes


title: Cell line Number 57 rs7222094 genotypeCT stim


title: Cell line Number 85 rs7222094 genotypeCC cont


title: WT at D8, IFNa treated, biological rep3

description: Gene expression data from WT CD8 T cells after 8 days of LCMV infection treated with IFNalpha for 90 minutes

source_name: CD8 T cells from WT mice after 8 days of LCMV infection treated with IFNalpha for 92

value: WT

value: after 8 days of LCMV infection and treated with IFNalpha for 90 minutes


title: STAT1 KO at D0, untreated, biological rep2


title: STAT1 KO at D0, untreated, biological rep1


title: STAT1 KO at D0, IFNa treated, biological rep2


title: Cell line Number 41 rs7222094 genotypeCC cont


title: Cell line Number 23 rs7222094 genotypeCT stim


title: Cell line Number 57 rs7222094 genotypeCT cont


title: Cell line Number 85 rs7222094 genotypeCC stim


title: WT at D8, untreated, biological rep3

description: Gene expression data from WT CD8 T cells after 8 days of LCMV infection

source_name: CD8 T cells from WT mice after 8 days of LCMV infection

value: after 8 days of LCMV infection


title: Cell line Number 41 rs7222094 genotypeCC stim


title: WT at D8, IFNa treated, biological rep2

source_name: CD8 T cells from WT mice after 8 days of LCMV infection treated with IFNalpha for 91


title: Cell line Number 5 rs7222094 genotypeCC cont


title: WT at D8, IFNa treated, biological rep1

source_name: CD8 T cells from WT mice after 8 days of LCMV infection treated with IFNalpha for 90


title: Ero1-C104A/C131A non-induced biological repA

city: Copenhagen N

first: Henning Gram

last: Hansen

address: Ole Maaløesvej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

hyb_protocol: The labeled samples were hybridized to the Human Gene 1.0 ST GeneChip array (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450.

scan_protocol: The arrays were scanned in the Affymetrix GeneArray® 3000 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol.

data_processing: Cell intensity files (CEL files) were generated in the GeneChip® CommandConsole® Software (AGCC) (Affymetrix, Santa Clara, CA, USA). The raw data was RMA-normalized using the R Bioconductor package 'affy' and used for a 2-way ANOVA with the cell line and induction status used as factors.

source_name: Inducible stable HEK 293 Flp-In T-REx Ero1alpha-C104A/C131A cells, expression not induced

label_protocol: Biotinylated cDNA were prepared by amplifying and labeling 250 ng RNA using the Ambion WT Expression Kit (Applied Biosystems) according to manufacturer’s guidelines.

growth_protocol: Doxycline-inducible Flp-In T-REx HEK-293 cell lines were grown in a-minimal essential medium (Invitrogen), supplemented with 10% FCS, 100 mg/mL hygromycin B (Invitrogen) and 15 mg/mL blasticidin (Invivogen) at 37°C, 5% CO2.

extract_protocol: RNA was extracted using TRI Reagent (Sigma) according to the manufacturer’s instructions.

treatment_protocol: Ero1α expression was either not induced or induced for 24 h using 1 mg/mL doxycline (Sigma).

tag: parental cell line

value: HEK 293 Flp-In T-REx

tag: construct stably transfected into cell line

tag: overexpression induced with doxycline

value: No


title: Ero1-WT induced biological repC

source_name: Inducible stable HEK 293 Flp-In T-REx Ero1alpha-WT cells, expression induced with doxycycline for 24 h

value: Yes


title: Cell line Number 5 rs7222094 genotypeCC stim

value: stimulated with cytomix for 6 hours

value: B lymphoblastoid


title: Ero1-C104A/C131A induced biological repA

source_name: Inducible stable HEK 293 Flp-In T-REx Ero1alpha-C104A/C131A cells, expression induced with doxycycline for 24 h


title: Ero1-C104A/C131A induced biological repC


title: Ero1-C104A/C131A non-induced biological repB


title: Ero1-C104A/C131A induced biological repB


title: Ero1-C104A/C131A non-induced biological repC


title: WT at D8, untreated, biological rep2


title: WT at D8, untreated, biological rep1


title: Cell line Number 72 rs7222094 genotypeTT cont

value: TT


title: WT at D0, IFNa treated, biological rep3

description: Gene expression data from WT CD8 T cells treated with IFNalpha for 90 minutes

source_name: CD8 T cells from WT mice treated with IFNalpha for 90 minutes


title: Cell line Number 12 rs7222094 genotypeCT cont

value: CT


title: Ero1-WT induced biological repB


title: Ero1-WT induced biological repA


title: Ero1-WT non-induced biological repC

source_name: Inducible stable HEK 293 Flp-In T-REx Ero1alpha-WT cells, expression not induced


title: Cell line Number 12 rs7222094 genotypeCT stim


title: Cell line Number 84 rs7222094 genotypeCT stim


title: WT at D0, IFNa treated, biological rep4


title: Cell line Number 72 rs7222094 genotypeTT stim


title: WT at D0, IFNa treated, biological rep1


title: Cell line Number 84 rs7222094 genotypeCT cont


title: Ero1-WT non-induced biological repA


title: WT at D0, untreated, biological rep3

description: Gene expression data from WT CD8 T cells

source_name: CD8 T cells from WT mice


title: WT at D0, untreated, biological rep2


title: WT at D0, IFNa treated, biological rep2


title: Cell line Number 71 rs7222094 genotypeCT stim


title: Cell line Number 64 rs7222094 genotypeCT stim


title: WT at D0, untreated, biological rep1


title: Cell line Number 71 rs7222094 genotypeCT cont


title: Cell line Number 64 rs7222094 genotypeCT cont


title: iTreg_IFNg_48hr_rep2

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

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

source_name: in vitro generated Treg, 48hr, IFNg conditions

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: CD4+ CD25+ T cells were purified from a combined preparation of spleen and lymph node using T cell columns (R & D) followed by negative selection on CD4 column (Miltenyi Biotech) and negative selection on CD25 columns (Miltenyi Biotech).

extract_protocol: Total RNA was isolated using the Qiagen Rneasy Plus Kit

treatment_protocol: Negatively selected CD4+ CD25+ Tcells were rested for 30 min in complete RPMI (cRPMI) (1% penicillin/streptomycin, 2mM L-glutamine, 10% fetal bovine serum, 0.1% beta-mercaptoethanol, 1% non-essential amino acids, 1mM sodium pyruvate and 20mM HEPES). Cells were cultured at 1x10^6/mL in αCD3-coated (1μg/mL; clone 145-2C11; eBioscience) 96-well U-bottom plates (Costar) in cRPMI containing αCD28 (1μg/mL; clone 37.51; eBioscience), recombinant human (rHu)TGF-β2 (5ng/mL, eBioscience), with or without (rHu IL-2; 100U/mL; Proleukin), anti-IFNγ (10μg/mL; clone XMG1.2) and anti-IL-4 (10 μg/mL; clone 11B11) blocking antibodies, recombinant mouse (rM)IL-27 (50ng/mL; Amgen), and with or without rM-IFN-γ (50ng/mL; R&D). Media was added every 2 days with initial cytokines and neutralizing antibodies.

value: Female

value: CD4+CD25+ T cells purified from spleen and lymph node by magnetic bead selection

value: IFNg conditions

tag: collection timepoint


title: iTreg_IL27_48hr_rep3

description: replicate 3

source_name: in vitro generated Treg, 48hr, IL27 conditions

value: IL27 conditions


title: iTreg_IFNg_48hr_rep1

description: replicate 1


title: iTreg_IFNg_48hr_rep3

description: replicate 3


title: ES_KSP-negative_2

city: Tokyo

first: Ryuji

last: Morizane

address: 35 shinanomachi, shinjukuku

department: Internal Medicine

country: Japan

institute: Keio University School of Medicine

description: Gene expression data from differentiated ES cells

hyb_protocol: Hybridization was carried out by use of GeneChip Hybridization and wash and Stain Kit (Affymetrix) according to the manufacture's protocol.

scan_protocol: Mouse Genome 430 2.0 Array (Affymetrix) was used for scan.

data_processing: MAS5.0-generated CHP files. Data was analyzed by Gene Spring (Agilent).

source_name: ES cells negative for KSP

label_protocol: Labeling was carried out by use of two-cycle cDNA Synthesis Kit (Affymetrix), MEGAscript T7 Kit (Ambion), IVT cRNA Cleanup Kit (Affymetrix), GeneChip IVT Labeling Kit (Affymetrix) according to the manufacture's protocol.

extract_protocol: Total RNA was isolated by use of Rneasy Mini Kit (QIAGEN) according to the manufacture's protocol.

value: ES cell line EB3

value: Differentiated ES cells

tag: ksp status

value: KSP-negative


title: Cell line Number 40 rs7222094 genotypeTT cont

source_name: B lymphoblastoid cell line control


title: ES_KSP-negative_1

tag: cell line


title: Cell line Number 70 rs7222094 genotypeTT cont


title: ES_KSP-positive_2

source_name: ES cells positive for KSP

value: KSP-positive


title: Cell line Number 40 rs7222094 genotypeTT stim

source_name: B lymphoblastoid cell line stimulated with cytomix for 6 hours


title: iTreg_IL27_48hr_rep1

description: replicate 1


title: iTreg_IL27_48hr_rep2

description: replicate 2


title: iTreg_neutral_48hr_rep2

description: replicate 2

source_name: in vitro generated Treg, 48hr, neutral conditions

value: neutral conditions


title: Cell line Number 75 rs7222094 genotypeCT cont


title: Cell line Number 75 rs7222094 genotypeCT stim


title: iTreg_neutral_48hr_rep3

description: replicate 3


title: Cell line Number 70 rs7222094 genotypeTT stim


title: nTreg Foxo1 WT, rep1

city: New York

first: Willey

last: Liao

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

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

scan_protocol: Arrays were scanned using GeneChip Affymetrix scanner 3000 7G

data_processing: The data was analyzed using the RMA and limma methods to assess differential expression [R version 2.15; packages: affy 1.34.0, affyPLM 1.32.0, limma 3.12.1, mouse_4302.db 2.7.1, biomaRt 2.12.0]

source_name: nTreg cells WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

extract_protocol: total RNA was extracted from cells using miRNeasy kit from Qiagen for RNA extraction

tag: genotype/variation

value: Wild type

value: Regulatory T cells


title: Cell line Number 17 rs7222094 genotypeCT stim

tag: cell line number


title: ES_KSP-positive_1


title: iTreg_IFNg_10hr_rep2

description: replicate 2

source_name: in vitro generated Treg, 10hr, IFNg treatment


title: Cell line Number 17 rs7222094 genotypeCT cont

tag: snp


title: iTreg_IFNg_10hr_rep3

description: replicate 3


title: iTreg_neutral_48hr_rep1

description: replicate 1


title: nTreg, Constitutively Active Foxo1

source_name: nTreg cells, Foxo1AAA mice

value: Foxo1AAA mice


title: nTreg Foxo1 KO, rep1

source_name: nTreg cells Foxo1KO


title: iTreg_IL27_10hr_rep3

description: replicate 3

source_name: in vitro generated Treg, 10hr, IL27 treatment


title: telavancin resistant strain vs. parent strain-rep3

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

state: IL

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

description: Analysis used MED1951 RNA as control samples for comparison to MED1952 S. aureus RNA samples.

hyb_protocol: Arrays were blocked in 1% SDS, 5 X SSC and 1 mg/ml BSA at 42C for 1 h.  Arrays were then washed 2X for 5 min in 0.1X SSC and 2X for 30 sec in sterile double-distilled water.  Arrays were hybirdized to Cy-labeled cDNAs denatured at 05C in 10 mM EDTA for 5 min and mixed with 40 ul hybridization buffer (Ambion) before loading under a caverslip on the array and sealing in hybridization cassettes.  Hybridization was carried out at 47C for 18 h.  Afterwards, array slides were washed in 2X SSC, 0.5% SDS at 37C for 5 min, followed by stringency washes 2X in 0.1X SSC at 37C for 2.5 min each, and 2X in 0.1X SSC at room temperature for 2.5 min each.

scan_protocol: Arrays were scanned using an Axon 4000b, and images analyzed using GenePix 6.0.

data_processing: Intensity of spots are quantified by using Spotfinder. Low intensity filter in MIDAS is used to filter out points with intensity less than 1000. Array intensity data was log2-transformed, and normalized using the Lowess algorithm.  Statistical analysis was performed using a significance analysis of microarrays (SAM, MultiExperiment Viewer, ver. 4.0) unpaired contrast.  A d-statistic was calculated for each gene based on repeated permutations, and a false discovery rate FDR of 0.01 was used to assign a critical cutoff for significance. Those control genes At1g01880 and Obsolete genes are removed before SAM analysis.

organism: Staphylococcus aureus

source_name: sample collected at OD600 at 0.4

label_protocol: Amino-allyl labeled cDNA was dried and then suspended in 0.1 M sodium carbonate (pH 9.3) and coupled with either Cy3 or Cy5 (swapped between balanced samples, N=4).  Uncoupled dye was removed by column purification (Qiagen).

growth_protocol: Cultures were initiated from overnight cultures in MHB into fresh MHB at 1:100 and grown to OD600=0.4.

extract_protocol: Samples were added to RNA Protect (Qiagen, Valencia, CA) and processed according to the manufacturer's instructions.  Cells were harvested by centrifugation (8,000 X g, 20 min, 4C) and then resuspended in 1 ml Trizol (Invitrogen, Carlsbad, CA) and processed in an FP120 FastPrep cell disruptor (MP Biomedicals, Irvine, CA).  Chloroform was subsequently added to the lysates, followed by centrifugation (16,000 X g, 15 min, 4C) and RNA was precipitated 1:1 (vol/vol) in 100% ethyl alcohol.  The RNA was then purified using the RNeasy™ kit (Qiagen) according to the manufacturer's instructions. Contaminating DNA was removed from purified RNA using DNAfree (Ambion, Austin, TX).  cDNA was produced using SuperScript II Reverse Transcriptase (Invitrogen) from 2 µg of total RNA combined with random hexamers, 0.25 mM deoxynucleoside triphosphate, and 0.25 mM aminoallyl-dUTP.

treatment_protocol: Cultures in MHB grown to OD600=0.4

value: MED1952 [laboratory-derived mutant]


title: Cell line Number 11 rs7222094 genotypeCC stim

tag: genotype

value: CC

value: stimulated with cytomix for 6 hours


title: nTreg Foxo1 KO, Constitutively Active Foxo1

source_name: nTreg cells, Foxo1KO, Foxo1AAA mice

value: Foxo1KO, Foxo1AAA mice

tag: cell type


title: Cell line Number 63 rs7222094 genotypeCT stim

value: CT

tag: treatment

value: B lymphoblastoid


title: iTreg_IFNg_10hr_rep1

description: replicate 1

value: Female

tag: tissue

value: CD4+CD25+ T cells purified from spleen and lymph node by magnetic bead selection


title: Cell line Number 63 rs7222094 genotypeCT cont


title: nTreg Foxo1 KO, rep2

tag: strain


title: telavancin resistant strain vs. parent strain-rep2


title: STAT1 KO at D0, IFNa treated, biological rep3

source_name: CD8 T cells from STAT1-deficient mice treated with IFNalpha for 90 minutes

value: CD8 T cells

value: STAT1 KO

value: 8 to 12 wks of age

value: IFNalpha for 90 minutes


title: Cell line Number 11 rs7222094 genotypeCC cont


title: iTreg_IL27_10hr_rep1

description: replicate 1

value: IL27 conditions


title: telavancin resistant strain vs. parent strain-rep1


title: InvCREER/RosaYFP 3.5days 2

city: Bruxelles

first: Cédric

last: Blanpain

address: route de Lennik 808

country: Belgium

institute: IRIBHM

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix MOE 430 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® Scanner 3000 7G (Affymetrix, software AGCC v3.1.1.1229).

data_processing: Affymetrix Expression Console software v1.1.  For normalization: RMA values in log2.

source_name: InvCREER/RosaYFP+

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).

extract_protocol: RNeasy microkit (QIAGEN).

treatment_protocol: K14-CREER/rosa-YFP and Involucrin-CREER/Rosa-YFP mice were induced with 1ug and 10ug of tamoxifen, respectively, by IP injection and sacrificed 4 days later.

tag: background/strain

value: InvCREER/RosaYFP

value: interfollicular epidermis (IFE)

value: alpha6 integrin-high/CD34-neg basal cells


title: iTreg_neutral_10hr_rep3

description: replicate 3

source_name: in vitro generated Treg, 10hr, neutral conditions

value: neutral conditions


title: nTreg Foxo1 WT, rep2

value: Wild type

value: Regulatory T cells


title: iTreg_IL27_10hr_rep2

description: replicate 2


title: Cell line Number 69 rs7222094 genotypeCT cont


title: iTreg_neutral_10hr_rep2

description: replicate 2


title: InvCREER/RosaYFP 3.5days 1


title: iTreg_neutral_10hr_rep1

description: replicate 1


title: K14CREER/RosaYFP 3.5days 1


title: Cell line Number 69 rs7222094 genotypeCT stim

value: stimulated with cytomix for 6 hours


title: K14CREER/RosaYFP 3.5days 2


title: MCF10-480min-Serum

status: Public on Sep 06 2012

city: reovot

first: roi

last: avraham

address: hertzel

country: Israel

institute: weizmann

description: microRNA expression after SERUM stimulation

hyb_protocol: Agilent protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting.

data_processing: Samples are in feature extraction format.  The expression value for each miRNA was calculated using Feature Extraction software 9.5.1. miRNAs that were not detected in more than three time points according to GeneView flags were removed. All values lower than 5 were leveled to 5. For each miRNA the intensity values were normalized across the sample set, log transformed, and calculated as fold change from time 0, and are included in the corresponding norm files. MCF10-40 EGF was removed from further analysis due to technical noise.

label_protocol: Agilent microRNA labelling kit

extract_protocol: microRNAs were prepared using the Qiagen miRneasy kit according to the manufacturer instructions


title: MCF10-120min-Serum


title: MCF10-40min-Serum


title: MCF10-0min-Serum


title: Placenta_4

description: microRNA expression in placenta- positive control

source_name: Placenta


title: ScottA vs F2365 rep4

city: Columbus

first: Hua

last: Wang

state: OH

address: 2015 Fyffe CT

department: Food Science and Technology

institute: The Ohio State University

description: Sample 4

hyb_protocol: The Standard Operating Procedures for Hybridization of Labeled cDNA probes (ftp://ftp.jcvi.org/pub/data/PFGRC/MAIN/pdf_files/protocols/M008.pdf) by the J. Craig Venter Institute was followed.

scan_protocol: Microarray slides were scanned on a GenePix 4000B microarray scanner from Molecular Devices. Gain value was acquired in automatic reading mode (3 reads).

data_processing: Scanned data from dried slides were normalized and statistical analysis was conducted using the TM4 microarray software suite from J. Craig Venter Institute.  Briefly, Midas was used to normalize the microarray using LOWESS normalization. The data were then entered into Multi Experiment Viewer (MEV) where T-Tests were performed using a p-value of p = 0.05. The UID column in MEV file corresponds to to ID column in the gpr file and IA represents Cy3 and IB represents Cy5. Please note that the array which was designed for multiple strains (including Listeria moncytogenes 4b F2365, EGD-e, 1/2a F6854, 4bH7858 and HCC23) was used for this study with the ScottA strain, which resulted in no signal/values for a large percentage of the probes on the array.

organism: Listeria monocytogenes

source_name: strong biofilm former

label_protocol: The Standard Operating Procedures for Aminoallyl Labeling of RNA (ftp://ftp.jcvi.org/pub/data/PFGRC/MAIN/pdf_files/protocols/M007.pdf) from J. Craig Venter Institute was adopted.

growth_protocol: Frozen L. monocytogenes cultures were activated  by incubating in  trypticase soy broth supplemented with 0.5% yeast extract (TSBYE) at 37°C for 18 h, and transferred at least once prior to assessments.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following manufacturer’s procedure with slight modification. Briefly, 23.75 ml of fresh TSBYE was inoculated with overnight cultures at 2.5% and grown at 37°C for 6 h until reached at OD600 of 0.6 – 0.7. One mL of aliquots were removed and placed in 4°C refrigerator for 15 min, and the cells were collected by centrifugation at 8000xg for 5 min. The cells were resuspended in 100μL of TE buffer and 6μL of lysozyme (50μg/mL) followed by incubation at 30°C for 30 min. The rest of the procedures followed manufacturer’s instruction .The extracted RNA was used within 30 min of extraction or stored at -80°C until use

treatment_protocol: No treatment was applied before extract preparation.

tag: strain background

value: ScottA

source_name: weak biofilm former


title: ScottA vs F2365 rep3

description: Sample 3


title: MCF10-60min-Serum


title: ScottA vs F2365 rep2

description: Sample 2


title: ScottA vs F2365 rep1

description: Sample 1


title: MCF10-20min-Serum


title: LbrAdeletionMutant vs ScottA rep1

description: Sample 5

source_name: LbrAdeletion mutant

value: LbrA deletion


title: MCF10-240min-EGF

description: microRNA expression after EGF stimulation


title: MCF10-40min-EGF


title: MDA-MB-231

description: microRNA expression (no EGF)

source_name: MDA-MB-231 (no EGF)


title: MCF10-240min-Serum


title: MCF10-60min-EGF


title: MCF10-0min-EGF


title: Placenta_2

value: Placenta


title: MCF10-20min-EGF


title: MCF10-120min-EGF


title: HeLa-480min-EGF

value: HeLa


title: HeLa-120min-EGF


title: HeLa-20min-EGF


title: Ero1-WT non-induced biological repB

source_name: Inducible stable HEK 293 Flp-In T-REx Ero1alpha-WT cells, expression not induced

value: HEK 293 Flp-In T-REx

value: No


title: Placenta_3


title: Placenta_1


title: HeLa-60min-EGF


title: HeLa-0min-EGF


title: Bulge SC no TAM

city: Brussels

first: KHALIL

last: KASS YOUSSEF

address: 808, Route de Lennick

institute: ULB-IRIBHM

description: WT CD34 exp1

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix MOE 430 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: The data were analyzed with R (version 2.14.0) Bioconductor fRMA (version 1.6) package with default analysis settings.

source_name: FACS sorted SmoM2+ Bulge stem cells from untreated K19ER SmoM2 mice

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

extract_protocol: Microprep kit, RNAeasy, Stratagen

treatment_protocol: K14CREER/Rosa-SmoM2-YFP and K14CREER/Rosa-SmoM2-YFP/b-catenin cKO mice were treated with tamoxifen to activate Cre-mediated recombination.

value: mixed

value: Tail epidermis

value: Bulge and outer-root sheath (ORS) cells


title: IFE no TAM, rep3

description: WT IFE exp3

source_name: FACS sorted IFE cells from untreated K14CREER/Rosa-SmoM2-YFP mice

value: basal interfollicular epidermis (IFE) cells


title: Bulge SmoM2 cells 4 weeks after TAM administration

description: 4W K19ER SmoM2 exp1

source_name: FACS sorted SmoM2+ Bulge stem cells 4wks after after tamoxifen administration to K19ER SmoM2 mice


title: SmoM2 cells IFE 4 weeks after TAM administration, rep2

description: 4W K14ER SmoM2 IFE exp2

source_name: FACS sorted SmoM2+ IFE cells 4wks after tamoxifen administration to K14CREER/Rosa-SmoM2-YFP mice


title: murine pancreatic cancer cell line B-53631

city: München

first: Günter

last: Schneider

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Technische Universität München

description: Gene expression data from murine pancreatic cancer cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the 3 GeneChip Fluidics Station F450.

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

data_processing: Raw data analysis was performed with R and Bioconductor (Gentleman et al. 2004; R Development Core Team 2007). Arrays were assessed for quality and RMA-normalized.

label_protocol: Biotinylated aRNA was prepared according to the standard GeneChip 3' IVT Express Kit (Affymetrix) protocol from 250 ng total RNA.

growth_protocol: Low passage murine pancreatic cancer cells were cultured at 37°C with 5% CO2 in DMEM medium supplemented with 10% fetal calf serum and 1% [vol/vol] P/S/A.

extract_protocol: Extraction of total RNA was performed using QIAGEN QIAshredder (#79656) and the RNeasy Mini kit (#74106) according to the manufacturer's instructions.

treatment_protocol: No special treatment was applied.

value: pancreatic cancer


title: murine pancreatic cancer cell line HEP1-53631


title: SmoM2 cells IFE 1 week after TAM administration, rep2

description: 1W K14ER SmoM2 IFE exp2

source_name: FACS sorted SmoM2+ IFE cells 1wk after tamoxifen administration to K14CREER/Rosa-SmoM2-YFP mice


title: murine pancreatic cancer cell line HEP2-53631


title: murine pancreatic cancer cell line PUL2-53631


title: SmoM2 cells IFE 4 weeks after TAM administration, rep3

description: 4W K14ER SmoM2 IFE exp3


title: SmoM2 cells IFE 3days after TAM administration, rep1

description: 3d K14ER SmoM2 IFE

source_name: FACS sorted SmoM2+ IFE cells 3 days after tamoxifen administration to K14CREER/Rosa-SmoM2-YFP mice


title: murine pancreatic cancer cell line PUL3-53631


title: SmoM2 cells IFE 10 weeks after TAM administration, rep1

description: 10W K14ER SmoM2 exp2

source_name: FACS sorted SmoM2+ IFE cells 10wks after tamoxifen administration to K14CREER/Rosa-SmoM2-YFP mice


title: SmoM2 cells IFE 1 week after TAM administration, rep3

description: 1W K14ER SmoM2 IFE exp3


title: SmoM2 bcatcLOF cells IFE 4 weeks after TAM administration, rep2

description: 4W K14ER SmoM2 bcatcLOF IFE exp2

source_name: FACS sorted SmoM2+ IFE cells 4wks after tamoxifen administration to K14ER SmoM2 bcatcLOF mice

value: K14CREER/Rosa-SmoM2-YFP/b-cat flox/flox