title: Dexa_Day5

description:
Gene expression data from adult human adipose stem cells treated ot not with a synthetic glucocorticoid
MJ_03102012_BIL_6

growth_protocol: human adipose stem cells were grwon in DMEM + FBS (10%) and antibiotics

treatment_protocol: human adipose stem cells were treated with Dexamethasone (100nM) and RNA isolated after days 0,1,2,3,4,5


title: Dexa_Day4

status: Public on Jun 12 2013

type: RNA

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description:
Gene expression data from adult human adipose stem cells treated ot not with a synthetic glucocorticoid
MJ_03102012_BIL_5

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotin

extract_protocol: Rneasy mini kit (Qiagen)

tag: cell type

value: preadipocytes

tag: tissue

value: white adipose tissue


title: Geno33_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

city: evry

first: caius

last: jose

state: essonne

address: 2 rue gaston cremieux

department: URGV

country: France

institute: transcriptomic platform

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

hyb_protocol: labelled extract quantity: 5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002). We take a subset of probes because we want the results only for Helianthus annuus specific probes.

label: Biotin

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, total RNA  .

growth_protocol: aerial - Seeds are surface-sterilized and place 2 days in soaked filter paper at 28°C. Plantlets are then transferred in 20 litre boxes (48 plantlets per box) filled with a complete hydroponic medium and grown during 15 days until treatment and harvesting. Growth chamber 14h day light at 23°C and 65% humidity, 10h night at 18°C and 65% humidity

treatment_protocol: no treatment

tag: genotype/variation

tag: agent

value: Ctl

tag: group

tag: age

tag: developmental stage (boyes et al. plant cell 2001)

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: Geno98_ABA_Grp1 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:ABA_Sunflower - compound based treatment - compound addition,aba:quantity 0.5uM time 6hour . ABA was prepared in DMS0 at a concentration of 20 mM. 500 µl were added to 20 litres of hydroponic medium (ref Massoneau 2001 Planta). 500 µl DMS0 were added to controls. Leaves of 1 plantlet per box were harvested after 6 hours and 3 plantlets (each repeat of a genotype) were pooled as one sample.

value: ABA


title: Mmu_liver_TC_CLF_VEH_0_2H_rep2

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

country: USA

institute: Michigan State University

description:
SAMPLE 19
Gene expression following 2.0 hours exposure to the vehicle control sesame oil

hyb_protocol: Hybridization was performed according the the Agilent manual G4140-90040 v. 5.7.

scan_protocol: Immediately after washing, microarrays were scannedusing a GenePix 4000B microarray scanner (Molecular Devices, Union City, CA) at 532 nm with a scan resultion of 5um.

data_processing:
Feature signal intensities and flagged features were determined using GenePix Pro 6.0 (Molecular Devices, Union City, CA).
Signal intensities normalized using a semi-parametric approach (Eckel, J. E., Gennings, C., Therneau, T. M., Burgoon, L. D., Boverhof, D. R. and Zacharewski, T. R. (2005). Bioinformatics 21(7), 1078-83.). These normalized signal intensities were then analyzed using an empirical Bayes analysis (Eckel, J. E., Gennings, C., Chinchilli, V. M., Burgoon, L. D., and Zacharewski, T. R., 2004. J Biopharm Stat 14, 647-670.) resulting in a final dataset with blank values where n ≤ 2 for a probe at each time-point.

organism: Mus musculus

source_name: Liver_sesame oil_2H

label_protocol: Cy3 Labeling was performed according to the Agilent manual G4140-90040 v. 5.7.

extract_protocol: Livers were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified spectrophotometrically (A260) and purity was assessed using the A260/A280 ratio and visual inspection on a denaturing gel.

treatment_protocol: Female ovariectomized C57BL/6 mice were gavaged daily with 300 mg/kg Clofibrate, Wy-14,643 or sesame oil vehicle control. Mice were sacrificed 2, 4, 8, 12, 18, and 24h post-dose following a single dose or 1, 4 and 14d post initial dose following daily dosing.

tag: strain

tag: gender

value: female

tag: treatment

value: sesame oil (vehicle contrrol)

value: liver

tag: time-point

value: 2 hrs post-dose following a single dose

tag: replicate


title: Bone_marrow

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

country: Japan

institute: The University of Tokyo

description: Normal bone marrow

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: Normal bone marrow

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

value: Normal bone marrow


title: Geno52_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno43_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Dexa_Day3

description:
Gene expression data from adult human adipose stem cells treated ot not with a synthetic glucocorticoid
MJ_03102012_BIL_4


title: Geno52_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Vein

description: Normal vein

source_name: Normal vein

value: Normal vein


title: Dexa_Day2

description:
Gene expression data from adult human adipose stem cells treated ot not with a synthetic glucocorticoid
MJ_03102012_BIL_3


title: Prostate

description: Normal prostate

source_name: Normal prostate

value: Normal prostate


title: Peripheral_blood_cells

description: Normal peripheral blood cells

source_name: Normal peripheral blood cells

value: Normal peripheral blood cells


title: Mmu_liver_TC_CLF_300_4D_rep1

description:
SAMPLE 15
Gene expression following 4.0 days exposure to the PPARalpha ligand Clofibrate

value: Clofibrate

value: 4 days post initial dose following daily dosing


title: Mmu_liver_TC_CLF_300_1D_rep1

description:
SAMPLE 13
Gene expression following 1.0 days exposure to the PPARalpha ligand Clofibrate

value: 1 day post initial dose


title: Mmu_liver_TC_CLF_VEH_0_1D_rep1

description:
SAMPLE 14
Gene expression following 1.0 days exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_1D


title: Dexa_Day0

description:
Gene expression data from adult human adipose stem cells treated ot not with a synthetic glucocorticoid
MJ_03102012_BIL_1

value: preadipocytes


title: Artery

description: Normal artery

source_name: Normal artery

value: Normal artery


title: Mmu_liver_TC_CLF_300_14D_rep3

description:
SAMPLE 11
Gene expression following 14.0 days exposure to the PPARalpha ligand Clofibrate

value: 14 days post initial dose following daily dosing


title: Dexa_Day1

description:
Gene expression data from adult human adipose stem cells treated ot not with a synthetic glucocorticoid
MJ_03102012_BIL_2

value: white adipose tissue


title: Geno90_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: Lymph_node

description: Normal lymph node

source_name: Normal lymph node

value: Normal lymph node


title: Mmu_liver_TC_CLF_VEH_0_14D_rep3

description:
SAMPLE 12
Gene expression following 14.0 days exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_14D

value: female

value: sesame oil (vehicle contrrol)


title: Mmu_liver_TC_CLF_300_4D_rep3

description:
SAMPLE 10
Gene expression following 4.0 days exposure to the PPARalpha ligand Clofibrate

value: liver


title: siLMO3_oligo1_0_rep2

source_name: human preadipocytes+oligo1_day0_rep2

growth_protocol: human adipose stem cells were grown in DMEM + FBS (10%) and antibiotics

treatment_protocol: human adipose stem cells were transfected with a control siRNA (siCtrl) or two different siRNA oligos targeting the gene LMO3 (siLMO3_oligo1 or siLMO3_oligo2). 40Hrs later, the transfected human adipose stem cells were induced to differentiate into mature adipocytes with a adipogenic cocktail (FullMix) and RNA isolated at day 0 or day6 after induction of differentiation.


title: Geno89_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

value: Ctl


title: Adipose

description: Normal adipose

source_name: Normal adipose

value: Normal adipose


title: Geno32_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: ABA


title: Geno104_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Lung

description: Normal lung

source_name: Normal lung

value: Normal lung


title: Mmu_liver_TC_CLF_300_1D_rep3

description:
SAMPLE 8
Gene expression following 1.0 days exposure to the PPARalpha ligand Clofibrate

value: Clofibrate


title: Trachea

description: Normal trachea

source_name: Normal trachea

value: Normal trachea


title: Mmu_liver_TC_CLF_VEH_0_4D_rep3

description:
SAMPLE 9
Gene expression following 4.0 days exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_4D

value: 4 days post initial dose following daily dosing


title: Thyroid

description: Normal thyroid

source_name: Normal thyroid

value: Normal thyroid


title: Geno89_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_VEH_0_1D_rep3

description:
SAMPLE 7
Gene expression following 1.0 days exposure to the vehicle control sesame oil

value: 1 day post initial dose


title: Geno32_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Thymus

description: Normal thymus

source_name: Normal thymus

value: Normal thymus


title: Spleen

description: Normal spleen

source_name: Normal spleen

value: Normal spleen


title: Tonsil

description: Normal tonsil

source_name: Normal tonsil

value: Normal tonsil


title: Bladder

description: Normal bladder

source_name: Normal bladder

value: Normal bladder


title: Geno119_ABA_Grp2 with array type SUNFLOWER from Affymetrix

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: Mmu_liver_TC_CLF_300_18H_rep3

description:
SAMPLE 3
Gene expression following 18.0 hours exposure to the PPARalpha ligand Clofibrate

value: female

value: 18 hrs post-dose following a single dose


title: Salivary_gland

description: Normal salivary gland

source_name: Normal salivary gland

value: Normal salivary gland


title: Geno31_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_VEH_0_18H_rep3

description:
SAMPLE 4
Gene expression following 18.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_18H

value: sesame oil (vehicle contrrol)

value: liver


title: Adrenal_gland

description: Normal adrenal gland

source_name: Normal adrenal gland

value: Normal adrenal gland


title: Mmu_liver_TC_CLF_VEH_0_24H_rep3

description:
SAMPLE 6
Gene expression following 24.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_24H

value: 24 hrs post-dose following a single dose


title: Geno78_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

value: Ctl


title: Geno31_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno72_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: ABA


title: Kidney

description: Normal kidney

source_name: Normal kidney

value: Normal kidney


title: Mmu_liver_TC_CLF_300_24H_rep3

description:
SAMPLE 5
Gene expression following 24.0 hours exposure to the PPARalpha ligand Clofibrate

value: Clofibrate


title: Gallbladder

description: Normal gallbladder

source_name: Normal gallbladder

value: Normal gallbladder


title: Geno115_ABA_Grp2 with array type SUNFLOWER from Affymetrix


title: Mmu_liver_TC_CLF_300_12H_rep3

description:
SAMPLE 2
Gene expression following 12.0 hours exposure to the PPARalpha ligand Clofibrate

value: 12 hrs post-dose following a single dose


title: Geno88_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno103_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Pancreas

description: Normal pancreas

source_name: Normal pancreas

value: Normal pancreas


title: Lu130b

description: Small lung cancer cell line

source_name: Small lung cancer cell line_Lu130

value: Small lung cancer cell

tag: cell line


title: conditional mutant strain replicate 2-2

city: Padua

first: Agnese

last: Serafini

address: Via Gabelli 63

department: Molecular Medicine

country: Italy

institute: University of Padua

description: TB79 rep 2-2

hyb_protocol: protocol described in Casonato et al., 2012 Infect. Immun. 80(9):3132.

scan_protocol: Microarrays were scanned using an Agilent G2565CA microarray scanner system (with Scan Control 8.1 software [Agilent Technologies]), and fluorescence intensities of the two channels at each spot were quantified using Agilent Feature Extraction 10.1 software (Agilent Technologies).

data_processing: Data were normalized with the Web-based tool DNMAD (diagnosis and normalization of spotted cDNA microarray data [http://dnmad.bioinfo.cnio.es/]) using the print-tip lowess method after background subtraction.

organism: Mycobacterium tuberculosis

source_name: H37Rv mycobacterial cells_TB79

growth_protocol: The cells were grown in 35ml of Middlebrook 7H9/ADC in presence of 100ng/ml of anhydrotetracycline in rolling cultures until OD540: 0.3-0.4

extract_protocol: Total RNA extracted using Trizol (Manganelli et al. Mol Micro, 1999) 31:715-724

treatment_protocol: anhydrotetracycline 100ng/ml for 48hrs

value: esx-3 conditional mutant

source_name: H37Rv mycobacterial cells_TB38

value: parental strain


title: Liver

description: Normal liver

source_name: Normal liver

value: Normal liver


title: Geno42_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: Geno84_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno45_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: conditional mutant strain replicate 2-1

description: TB79 rep 2-1

label_protocol: protocol described in Casonato et al., 2012 Infect. Immun. 80(9):3132.


title: Stomach

description: Normal stomach

source_name: Normal stomach

value: Normal stomach


title: conditional mutant strain replicate 1-2

description: TB79 rep 1-2


title: Colon

description: Normal colon

source_name: Normal colon

value: Normal colon


title: Small_intestine

description: Normal small intestine

source_name: Normal small intestine

value: Normal small intestine


title: Esophagus

description: Normal esophagus

source_name: Normal esophagus

value: Normal esophagus


title: conditional mutant strain replicate 1-1

description: TB79 rep 1-1


title: ES[129.3:Zscan4cEmgfp(7)] Emerald- rep1

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 4 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: Embryonic Stem Cells

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: After sorting, the samples were spun down in 15 mL Falcon tubes.  The supernatant was aspirated and 1/2 mL TRIzol reagent was added.  They were then transferred to eppendorf tubes and stored at -20C until extraction proceeded. The samples were transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample.  They were mixed by hand and allowed to stand for 2-5 min at room temperature.  The samples were then separated by centrifugation for 5 minutes at 15,300 rpm on an eppendorf centrifuge at 4C. The aqeous phase was transferred to another eppendorf, and 0.8 volumes of ice-cold isopropanol was added.  They were allowed to incubate for a minimum of 10 minutes at room temperature.  If longer, they were placed at 4C.  The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol.  The tube was spun for 5 minutes, then the ethanol was dumped out.  Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer.  ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -20C for storage.

treatment_protocol: Cells were harvested by treatment with 0.05% Trypsin (GIBCO) and mechanical dispersion to make a single cell suspension.  They were then resuspended in cell sorting medium (HyQ IMDM (Hyclone), 1% ES-qualified FBS).  Cells were sorted based upon emerald fluorescence.  Both positive and negative cells were sorted into cell sorting medium: 60% HyQ IMDM, 35% FCS, 1% Glutamax, 1% Pen/Strep, 1% Non-Essential Amino Acids, 1% Beta-mercaptoethanol, 1% Sodium Pyruvate. The cells were then spun down and immediately fixed them with TRIzol reagent (Invitrogen).  I then extracted the RNA following Invitrogen protocol.

value: ES[129.3:zscan4cEmgfp(7)] cells

value: male

tag: genetic modification

tag: individual identifier

value: Zscan4_Emarald- 1; ES[129.3:Zscan4cEmgfp(7)] Emerald- rep1; ES[129.3:zscan4cEmgfp(7)], Emerald- 01_24_07; 251411710227

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

value: Universal Mouse Reference


title: Geno45_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

value: Ctl


title: Geno4_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: ES[129.3:Zscan4cEmgfp(7)] Emerald+ rep1

value: Zscan4_Emarald+ 1; ES[129.3:Zscan4cEmgfp(7)] Emerald+ rep1; ES[129.3:zscan4cEmgfp(7)], Emerald+ 01_24_07; 251411710226


title: Tongue

description: Normal tongue

source_name: Normal tongue

value: Normal tongue


title: Geno15_ABA_Grp1 with array type SUNFLOWER from Affymetrix

value: ABA


title: Geno23_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Lu130a

description: Small lung cancer cell line

value: Small lung cancer cell


title: Geno5_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: ES[129.3:Zscan4cEmgfp(7)] Emerald- rep2

value: Zscan4_Emarald- 2; ES[129.3:Zscan4cEmgfp(7)] Emerald- rep2; ES[129.3:zscan4cEmgfp(7)], Emerald- 02_07_07; 251411710248


title: ES[129.3:Zscan4cEmgfp(7)] Emerald+ rep2

value: Zscan4_Emarald+ 2; ES[129.3:Zscan4cEmgfp(7)] Emerald+ rep2; ES[129.3:zscan4cEmgfp(7)], Emerald+ 02_07_07; 251411710247


title: Heart

description: Normal heart

source_name: Normal heart

value: Normal heart


title: Geno117_Ctl_Grp2 with array type SUNFLOWER from Affymetrix

value: vegetative

value: Leaves from the 15-day-old-plantlets


title: Skin

description: Normal skin

source_name: Normal skin

value: Normal skin


title: Geno30_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: KO skin R3

city: Heidelberg

first: Nicole

last: Amen

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: cDNA was hybridized for 16 hours onto GeneChip Mouse Gene 1.0 ST Arrays.

scan_protocol: The microarray chips were scanned with a GeneChipTM scanner 3000 due to the manufacturer´s instructions.

data_processing:
The data were analyzed using Genomatix ChipInspector (fdr=0).
ChipInspector fold changes directly generated from the CEL files.
ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.

source_name: KO skin

label_protocol: cDNA was labeled with the WT Terminal Labeling and Controls Kit (Affymetrix) due to the manufacturer´s instructions.

extract_protocol: RNA was isolated with GTC-phenol-chloroform as described earlier (Chomczynski, P. and Sacchi, N. (2006))

treatment_protocol: Full thickness skins of Ugcgf/f/K14CreERT2- and control mice (n=3, each) were excised using biopsy punches 8 mm in diameter.

value: Ugcg-depletion

value: skin (biopsy punches 8 mm in diameter)


title: KO skin R2


title: Geno44_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: KO skin R1


title: Skeletal_muscle

description: Normal skeletal muscle

source_name: Normal skeletal muscle

value: Normal skeletal muscle


title: WT skin R3

source_name: WT skin

value: control


title: Cerebellum

description: Normal cerebellum

source_name: Normal cerebellum

value: Normal cerebellum


title: Geno47_Ctl_Grp1 with array type SUNFLOWER from Affymetrix


title: Diencephalon

description: Normal diencephalon

source_name: Normal diencephalon

value: Normal diencephalon


title: WT skin R1


title: Thalamus

description: Normal thalamus

source_name: Normal thalamus

value: Normal thalamus


title: Geno2_ABA_Grp1 with array type SUNFLOWER from Affymetrix


title: Geno44_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

value: Ctl


title: Hippocampus

description: Normal hippocampus

source_name: Normal hippocampus

value: Normal hippocampus


title: Geno119_Ctl_Grp2 with array type SUNFLOWER from Affymetrix


title: Tarsal conjunctiva 273-312 card A

status: Public on Jun 11 2013

city: london

first: Tamsyn

middle: Ruth

last: Derrick

address: keppel street

country: United Kingdom

institute: london school of hygiene and tropical medicine

data_processing: QRT PCR results processed in ABI SDS 2.4 RQ manager. Plates processed individually to generate non-normalized data using the following settings: Fluorescence off scale = ON,  A well has missing data = ON, Laser power low during run = ON, Large mean squared error = >2000, Percentage of plate wells not amplified = >80, A well is empty = OFF, Bad passive reference signal > 0.6, No amplification of well = OFF, High noise spikes = >1, High relative noise = >4. Set manual threshold to 0.05 & automatic baseline --> ANALYSE ALL. Data exported and processed in R using bioconductor HTqPCR package. Samples with a global miRNA median cycle threshold of 40 and samples with poor correlation within phenotype groups were excluded. A and B card data were processed seperately due to a different number of samples in each group as a result of filtering. Data were normalised with nr.norm (rank invariant normalization) as it gave the lowest coefficient of variation for all data and the highest sample distribution homology across all of the normaliation procedures tested. Data were tested for differential expression with Limma.

label: FAM

source_name: Swab, Tarsal conjunctiva, TF

label_protocol: FAM

extract_protocol: Qiagen All-prep kits with miRNA addition

value: Tarsal conjunctiva

value: F

tag: disease status


title: WT skin R2


title: Tarsal conjunctiva G-5959 card A

value: scarred


title: Tarsal conjunctiva G-5957 card A


title: Tarsal conjunctiva 117-169 card A


title: Tarsal conjunctiva G-5958 card A


title: Tarsal conjunctiva 373-204 card A

value: M


title: Pons

description: Normal pons

source_name: Normal pons

value: Normal pons


title: Geno90_Ctl_Grp1 with array type SUNFLOWER from Affymetrix

value: vegetative


title: V6.5 clone #2 rep1

description: v6.5 Neo

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 9 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: V6.5 clone #2 rep1

extract_protocol: Total RNA was extracted using Trizol according to Invitrogen's protocol.  Cells were pelleted and 1mL Trizol reagent was added to the cell pellet.

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in ES standard medium with LIF for 3 days.

tag: clone

value: ES cell line V6.5

value: hybrid from C57Bl/6 x 129

value: male

tag: transfection

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

tag: reference

value: Universal Mouse Reference (total RNA from 11 cultured cell lines) plus 129ES cell RNA (Lif+)


title: V6.5 ZERT2 clone #18 (Tmx-) rep1

description: v6.5 ERT2 ES

source_name: V6.5 ZERT2 clone #18 (Tmx-) rep1

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in ES standard medium with LIF for 2 days.

tag: tamoxifen induction

value: no


title: V6.5 ZERT2 clone #18 (Tmx+) rep3

description: v6.5 ERT2 TAM

source_name: V6.5 ZERT2 clone #18 (Tmx+) rep3

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in ES standard medium(LIF+) with Tamoxifen(200nM) for 2 days.

value: yes


title: V6.5 ZERT2 clone #18 (Tmx+) rep1

description: v6.5 ERT2 TAM

source_name: V6.5 ZERT2 clone #18 (Tmx+) rep1


title: V6.5 ZERT2 clone #18 (Tmx-) rep3

description: v6.5 ERT2 ES

source_name: V6.5 ZERT2 clone #18 (Tmx-) rep3


title: V6.5 ZERT2 clone #18 (Tmx-) rep2

description: v6.5 ERT2 ES

source_name: V6.5 ZERT2 clone #18 (Tmx-) rep2


title: Whole_Brain

description: Normal whole brain

source_name: Normal whole brain

tag: tissue

value: Normal whole brain


title: V6.5 ZERT2 clone #18 (Tmx+) rep2

description: v6.5 ERT2 TAM

source_name: V6.5 ZERT2 clone #18 (Tmx+) rep2


title: V6.5 clone #2 rep3

description: v6.5 Neo

source_name: V6.5 clone #2 rep3

value: control


title: Cerebral_cortex

description: Normal cerebral cortex

source_name: Normal cerebral cortex

value: Normal cerebral cortex


title: V6.5 clone #2 rep2

description: v6.5 Neo

source_name: V6.5 clone #2 rep2


title: Tarsal conjunctiva G-5919 card A


title: Tarsal conjunctiva G-5788 card A


title: Tarsal conjunctiva G-5960 card A


title: Tarsal conjunctiva G-5666 card A


title: Tarsal conjunctiva G-5817 card A


title: Tarsal conjunctiva G-5624 card A


title: Tarsal conjunctiva G-5637 card A


title: Tarsal conjunctiva G-5650 card A


title: Tarsal conjunctiva G-5789 card A


title: Tarsal conjunctiva G-5648 card A


title: Tarsal conjunctiva G-5602 card A


title: Tarsal conjunctiva G-5646 card A


title: Tarsal conjunctiva G-5532 card A


title: Tarsal conjunctiva G-5594 card A


title: Tarsal conjunctiva G-5524 card A


title: Tarsal conjunctiva G-5636 card A


title: Tarsal conjunctiva G-5606 card A


title: Tarsal conjunctiva G-5529 card A


title: Tarsal conjunctiva G-5521 card A


title: Tarsal conjunctiva G-5398 card A


title: Tarsal conjunctiva G-5402 card A


title: Tarsal conjunctiva G-5428 card A


title: Tarsal conjunctiva G-5388 card A


title: Tarsal conjunctiva G-5485 card A


title: Tarsal conjunctiva G-5623 card A


title: Tarsal conjunctiva G-5581 card A


title: Tarsal conjunctiva F-1617 card A


title: Tarsal conjunctiva G-5523 card A


title: Tarsal conjunctiva G-5500 card A


title: Tarsal conjunctiva F-1588 card A


title: Tarsal conjunctiva F-1217 card A


title: Tarsal conjunctiva F-1233 card A


title: Tarsal conjunctiva F-0778 card A


title: Tarsal conjunctiva G-5327 card A


title: Mmu_liver_TC_CLF_VEH_0_4H_rep1

description:
SAMPLE 1
Gene expression following 4.0 hours exposure to the vehicle control sesame oil

source_name: Liver_sesame oil_4H

value: female

value: sesame oil (vehicle contrrol)

value: liver

value: 4 hrs post-dose following a single dose


title: C57BL/6J_XY_E12.0_gonad_rep3

city: Durham

first: Anirudh

last: Natarajan

state: NC

address: 4034 GSRBII Building, Research Drive

institute: Duke University Medical Center

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BeadArray,a package in BioConductor, in R [version of R 2.12.0 and beadarray version 2.0.6].

source_name: C57BL/6J, XY, E12.0 Gonad

label_protocol: From each total RNA sample, mRNA was selectively reverse transcribed with oligo(dT) primers to T7-labelled cDNA, and then amplified by in vitro transcription (IVT) to produce biotinylated cRNA using the Illumina TotalPrep Amplification Kit (Ambion/ Life Technologies, cat no. AMIL1791) according to manufacturer’s instructions.

extract_protocol: Total RNA was first extracted from individual pairs of E11.0-E12.0 XX and XY gonads (separated from mesonephroi) with the RNeasy Micro kit with on-column DNase digestion (QIAGEN, cat no. 74004) following the manufacturer’s protocol. Total RNA was eluted in 14 ul RNase-free water (not DEPC- treated), and 2 ul were used to quantify RNA concentration on a NanoDrop ND-2000 (Thermo Scientific). Only samples with > 100 ng of total RNA and an A280:A260 ratio of >1.6 were included in the expression analyses.

tag: Sex

value: XY

tag: Stage


title: C57BL/6J_XY_E11.8_gonad_rep3

description: replicate 3

source_name: C57BL/6J, XY, E11.8 Gonad


title: C57BL/6J_XY_E12.0_gonad_rep1

description: replicate 1


title: C57BL/6J_XY_E11.2_gonad_rep2

description: replicate 2

source_name: C57BL/6J, XY, E11.2 Gonad


title: C57BL/6J_XY_E11.4_gonad_rep1

description: replicate 1

source_name: C57BL/6J, XY, E11.4 Gonad


title: F1 saline Rep2

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: For each sample, 1.65ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: F1 uterus, saline treated

label_protocol: Starting with 500ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer's protocol.

extract_protocol: Frozen uterine tissue from three animals per treatment group was pulverized, then homogenized in Trizol (Invitrogen, Carlsbad, CA), and RNA was prepared according to the manufacturer's protocol. Isolated RNA was then further purified using the QIAGEN (Valencia, CA) RNeasy mini prep kit clean-up protocol.

treatment_protocol: Animals were ovariectomized at NIEHS, rested for 1 to 2 wk, and then subjected to treatment with either E2 (40.0 μg/kg BW injected i.p.) in 0.1 ml saline containing 0.25% ethanol, or ethanol/saline vehicle. Animals were euthanized and tissue collected at 2 or 24 h after injection.

value: F1 from C57BL/6 x C3H/HeJ

value: uterus

tag: age

value: 8 weeks

value: ethanol/saline vehicle


title: C57BL/6J_XY_E12.0_gonad_rep2

description: replicate 2

tag: strain


title: C57BL/6J_XY_E11.8_gonad_rep2

description: replicate 2


title: C57BL/6J_XY_E11.4_gonad_rep2

description: replicate 2


title: F1 saline Rep1

tag: gender


title: C57BL/6J_XY_E11.6_gonad_rep3

description: replicate 3

source_name: C57BL/6J, XY, E11.6 Gonad


title: C57BL/6J_XY_E11.2_gonad_rep4

description: replicate 4


title: F1 saline Rep3

tag: treatment


title: F1 E2 2hr Rep 3

source_name: F1 uterus, E2 treated for 2hr

value: 17β-estradiol (E2)

tag: treatment duration

value: 2 hr


title: F1 E2 2hr Rep 2


title: F1 E2 24hr Rep2

source_name: F1 uterus, E2 treated for 24hr

value: 24 hr


title: C57BL/6J_XY_E11.6_gonad_rep1

description: replicate 1


title: C57BL/6J_XY_E11.0_gonad_rep1

description: replicate 1

source_name: C57BL/6J, XY, E11.0 Gonad


title: C57BL/6J_XY_E11.0_gonad_rep2

description: replicate 2


title: C57BL/6J_XY_E11.2_gonad_rep3

description: replicate 3


title: C57BL/6J_XX_E12.0_gonad_rep3

description: replicate 3

source_name: C57BL/6J, XX, E12.0 Gonad

value: XX


title: C57BL/6J_XY_E11.6_gonad_rep2

description: replicate 2


title: C57BL/6J_XY_E11.0_gonad_rep3

description: replicate 3


title: F1 E2 24hr Rep 3


title: C57BL/6J_XY_E11.4_gonad_rep3

description: replicate 3


title: C57BL/6J_XY_E11.8_gonad_rep1

description: replicate 1


title: C57BL/6J_XY_E11.2_gonad_rep1

description: replicate 1


title: F1 E2 2hr Rep 1


title: C57BL/6J_XX_E12.0_gonad_rep1

description: replicate 1


title: C57BL/6J_XX_E12.0_gonad_rep2

description: replicate 2


title: F1 E2 24hr Rep 1


title: C57BL/6J_XX_E11.8_gonad_rep3

description: replicate 3

source_name: C57BL/6J, XX, E11.8 Gonad


title: C57BL/6J_XX_E11.8_gonad_rep1

description: replicate 1


title: C57BL/6J_XX_E11.8_gonad_rep2

description: replicate 2


title: C3H E2 24hr Rep3

source_name: C3H uterus, E2 treated for 24hr


title: B6 saline Rep3

source_name: B6 uterus, saline treated


title: C3H E2 2hr Rep1

source_name: C3H uterus, E2 treated for 2hr


title: C3H E2 2hr Rep2


title: C3H saline Rep1

source_name: C3H uterus, saline treated


title: C57BL/6J_XX_E11.6_gonad_rep2

description: replicate 2

source_name: C57BL/6J, XX, E11.6 Gonad


title: B6 saline Rep2


title: C3H E2 24hr Rep2


title: C3H E2 24hr Rep1


title: C3H E2 2hr Rep3


title: C57BL/6J_XX_E11.6_gonad_rep3

description: replicate 3


title: C3H saline Rep2


title: C3H saline Rep3


title: C57BL/6J_XX_E11.4_gonad_rep3

description: replicate 3

source_name: C57BL/6J, XX, E11.4 Gonad


title: B6 E2 2hr Rep2

source_name: B6 uterus, E2 treated for 2hr


title: B6 E2 24hr Rep3

source_name: B6 uterus, E2 treated for 24hr


title: B6 saline Rep1


title: B6 E2 2hr Rep3


title: C57BL/6J_XX_E11.4_gonad_rep2

description: replicate 2


title: B6 E2 24hr Rep2


title: C57BL/6J_XX_E11.4_gonad_rep1

description: replicate 1


title: B6 E2 24hr Rep1


title: C57BL/6J_XX_E11.6_gonad_rep1

description: replicate 1


title: C57BL/6J_XX_E11.2_gonad_rep3

description: replicate 3

source_name: C57BL/6J, XX, E11.2 Gonad


title: Lipofectamine only control, replicate 1

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: Lipofectamine only control, biological replicate 1 of 3

hyb_protocol: For each sample, 750 ng of biotinylated cRNA were hybridized in a BeadChip Hyb Chamber with rocking 16 h at 58ºC. The day after the bead arrays were washed with Illumina proprietary washing solutions in a Hybex waterbath: first with static incubation for 10 min at 55ºC in E1BC solution, followed by 10 rinses by dipping in the same solution and shaking 5 min at 90 rpm in an orbital shaker; the next wash was by dipping 10 times in 100% ethanol and shaking 10 min at 110 rpm in an orbital shaker; this was followed by another wash in E1BC solution with 10 dippings followed by 2 min shaking at 90 rpm. Washed bead arrays were blocked in E1 buffer 10 min in rocking incubator and 10 additional minutes with 2 ml of E1 buffer plus streptavidin-Cy3. The fluorescent reagent was washed away with E1BC solution with 10 dippings plus 5 min shaking at 140 rpm. Finally beadarrays were dried by centrifugation 4 min at 275 rcf, followed by scanning in a Illumina Beadstation.

scan_protocol: The Beadscan software was used to control de scanner, generate .tif images and extract the raw data as tabulated text files. Default settings for DirectHyb Gene Expression were used.

data_processing: The raw data was summarized per probe using GenomeStudio 1.6.0 software Gene Expression module and the summary data file was processed using the PILLA web einterface tool (Lozano et al, unpublished), an implementation of the Lumi package (Du et al, 2008) developed within the Bioconductor project in the R statistical programming environment (Gentleman et al, 2004). Data were normalized using the rsn method and vst as the variance stabilization method. The log2 intensities were median centered and log ratios were computed as differences in log2 intensities for each probe. The SAM  (significance analysis of microarrays) two class unpaired comparison test was applied with 100 permutations to detect statistically significant differences in gene expression between treated and control conditions (Tusher et al, 2001).

label: biotin / streptavidin-Cy3

label_protocol: For each sample 200 ng of total RNA were reverse transcribed, amplified by in vitro transcription and labelled with biotin-UTP using the Illumina Total Prep RNA amplification kit (IL1791, Ambion) following the manufacturer's instructions. Labelled sample quality was assessed by spectrophotometry and bioanalyzer. After preheating at 65ºC for 5 min.

growth_protocol: Neuro2a cell were maintanied in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 4.5 g/l glucose, 10% FBS, and antibiotics.

extract_protocol: Total RNA was extracted using the RNAsy Kit (Qiagen). RNA concentration was measured with a small volume spectrophotometer (Nanodrop). The quality of the RNA was analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay, with RIN ranging between 9.2 and 9.8.

treatment_protocol: Cells were plated at 0.25x106 cells/ml transfected the next day using Lipofectamine 2000 reagent in Optimem medium, following the manufacturer’s instructions (Invitrogen-Life Technologies).

tag: cell type

tag: genotype/variation

value: negative control for transfection


title: Scrambled siRNA control, replicate 3

description: Scrambled siRNA control, biological replicate 3 of 3

value: negative control for loss of function


title: Lipofectamine only control, replicate 3

description: Lipofectamine only control, biological replicate 3 of 3


title: Prnp overexpression, replicate 3

description: Prnp overexpression with lentiviral vector, biological replicate 3 of 3

value: gain of function


title: C57BL/6J_XX_E11.2_gonad_rep2

description: replicate 2


title: C57BL/6J_XX_E11.0_gonad_rep1

description: replicate 1

source_name: C57BL/6J, XX, E11.0 Gonad


title: Prnp knock down, replicate 2

description: Prnp inhibition with siRNA, biological replicate 2 of 3

value: loss of function


title: 129S1/SvImJ_XY_E12.0_gonad_rep1

description: replicate 1

source_name: 129S1/SvImJ, XY, E12.0 Gonad


title: Scrambled siRNA control, replicate 1

description: Scrambled siRNA control, biological replicate 1 of 3


title: C57BL/6J_XX_E11.0_gonad_rep3

description: replicate 3


title: C57BL/6J_XX_E11.2_gonad_rep1

description: replicate 1


title: Lipofectamine only control, replicate 2

description: Lipofectamine only control, biological replicate 2 of 3


title: Prnp overexpression, replicate 2

description: Prnp overexpression with lentiviral vector, biological replicate 2 of 3


title: B6 E2 2hr Rep1

value: female


title: Scrambled siRNA control, replicate 2

description: Scrambled siRNA control, biological replicate 2 of 3


title: Prnp knock down, replicate 3

description: Prnp inhibition with siRNA, biological replicate 3 of 3


title: 129S1/SvImJ_XY_E12.0_gonad_rep2

description: replicate 2


title: 129S1/SvImJ_XY_E11.8_gonad_rep3

description: replicate 3

source_name: 129S1/SvImJ, XY, E11.8 Gonad


title: Pusa 1342, non-aromatic parent, biological rep 4

city: new delhi

first: vinita

last: pachauri

state: delhi

address: pusa campus

department: rice genome

country: India

institute: NRCPB

description: gene expression data from non-aromatic parent (Pusa 1342)

hyb_protocol: 10 µg of fragmented cRNA was hybridized and then washed and stained with streptavidin-phycoerythrin in the Affymetrix fluidics station 450.

scan_protocol: Probe genechips were scanned in a GeneChip Scanner 3000.

data_processing: The array data was analyzed using GeneChip Operating System (GCOS 1.2) and GeneSpring software version GX 9.0.6. A default target intensity value (TGT) setting of n = 500 was used while scaling factor for the arrays ranged from 3.1–8.5. The detection calls (present, absent or marginal) for the probe sets were made by GCOS. Probe level normalization was performed using robust multichip average (RMA) algorithm of GeneSpring and only those probes with expression levels above the background levels with statistical significance (P < 0.01) were recorded as “present”. For false discovery rate (FDR), the Benjamini and Hochberg (1995) algorithm with a cutoff setting of <2% was applied. Fold changes >2 were considered as significant.

organism: Oryza sativa

source_name: non-aromatic parent (Pusa 1342)

label_protocol: cRNA was tagged with biotin using IVT labeling kit provided by Affymetrix

growth_protocol: Seeds grown in experimental field under natural conditions.

extract_protocol: Total RNA extracted fro leaves using Qiagen Rneasy kit following the manufacturers' instructions.

treatment_protocol: No treatment was given to any plants. They were grown in natural conditions.

value: fresh healthy leaves

tag: genotype

value: non-aromatic rice variety

value: leaf samples after 25 days of transplanting seedlings in experimental field


title: Prnp overexpression, replicate 1

description: Prnp overexpression with lentiviral vector, biological replicate 1 of 3


title: Prnp knock down, replicate 1

description: Prnp inhibition with siRNA, biological replicate 1 of 3


title: Pusa 1342, non-aromatic parent, biological rep 3


title: Pusa 1342, non-aromatic parent, biological rep 2


title: 129S1/SvImJ_XY_E11.8_gonad_rep1

description: replicate 1

value: XY


title: 129S1/SvImJ_XY_E11.6_gonad_rep3

description: replicate 3

source_name: 129S1/SvImJ, XY, E11.6 Gonad


title: Pusa 1121, aromatic parent, biological rep 4

description: gene expression data from aromatic parent (Pusa 1121)

source_name: aromatic parent (Pusa 1121)

value: basmati rice variety


title: Paired low-metastatic 95C and high-metastatic 95D cell cultured in RPMI 1640 replicate 1

city: Shanghai

first: Gentao

last: Liu

address: 507 Zhengmin Rd

country: China

institute: Tongji University School of Medicine

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.

source_name: 95C cell line

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA was extracted using the TRIzol® Reagent (Invitrigen Corporation, America), following the manufacturer's recommended protocol.

value: Low-metastatic large cell lung carcinoma cell line 95C

source_name: 95D cell line (high-metastatic )

value: High-metastatic large cell lung carcinoma cell line 95D


title: 129S1/SvImJ_XY_E11.4_gonad_rep3

description: replicate 3

source_name: 129S1/SvImJ, XY, E11.4 Gonad


title: Pusa 1342, non-aromatic parent, biological rep 1


title: 129S1/SvImJ_XY_E11.6_gonad_rep2

description: replicate 2


title: Tarsal conjunctiva G-5957 card B

description: F

source_name: Swab, Tarsal conjunctiva, TF

value: Tarsal conjunctiva

value: F

value: scarred


title: Pusa 1121, aromatic parent, biological rep 2


title: C57BL/6J_XX_E11.0_gonad_rep2

description: replicate 2


title: Tarsal conjunctiva G-5959 card B

description: F


title: Pusa 1121, aromatic parent, biological rep 3


title: Bulk of non-aromatic RILs, biological rep 3

description: gene expression data from bulk of non-aromatic RILs

source_name: bulk of six non-aromatic RILs

value: recombinant inbred line


title: Tarsal conjunctiva G-5919 card B

description: F


title: 129S1/SvImJ_XY_E11.8_gonad_rep2

description: replicate 2


title: Bulk of non-aromatic RILs, biological rep 1


title: 129S1/SvImJ_XY_E11.4_gonad_rep2

description: replicate 2


title: Tarsal conjunctiva G-5960 card B

description: F

value: control


title: Bulk of non-aromatic RILs, biological rep 4


title: 129S1/SvImJ_XY_E11.4_gonad_rep1

description: replicate 1


title: 129S1/SvImJ_XY_E11.2_gonad_rep1

description: replicate 1

source_name: 129S1/SvImJ, XY, E11.2 Gonad


title: 129S1/SvImJ_XY_E11.2_gonad_rep2

description: replicate 2


title: 129S1/SvImJ_XY_E11.2_gonad_rep3

description: replicate 3


title: Tarsal conjunctiva G-5666 card B

description: F


title: 129S1/SvImJ_XY_E11.6_gonad_rep1

description: replicate 1


title: Tarsal conjunctiva G-5650 card B

description: F


title: Tarsal conjunctiva G-5648 card B

description: F


title: Bulk of non-aromatic RILs, biological rep 2


title: Bulk of highly aromatic RILs, biological rep 3

description: gene expression data from bulk of highly aromatic RILs

source_name: bulk of six highly aromatic RILs


title: Pusa 1121, aromatic parent, biological rep 1


title: Tarsal conjunctiva G-5646 card B

description: F


title: Bulk of highly aromatic RILs, biological rep 4


title: Bulk of highly aromatic RILs, biological rep 1


title: Tarsal conjunctiva G-5637 card B

description: F


title: Bulk of highly aromatic RILs, biological rep 2


title: 6h EGF replicate 2

description:
Sample name: 6h-EGF-2
6h time point, biological replicate 2 of 3. HeLa cells treated with EGF.

hyb_protocol: Samples were hybridized in a volume of 45 ul to the Human miRNA V1 Oligo Microarray (Agilent) for 20 hours at 55°C and with 20 rpm rotation. Post-hybridization washes were in GE Wash Buffer 1 (Agilent) at RT to remove the coverslip, followed by one wash with GE Wash Buffer 1 (Agilent) at RT for 5 min and one wash with GE Wash Buffer 2 (Agilent) at 37ºC for 5 min.

scan_protocol: Arrays were scanned on an Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for miRNA microarrays at 100% PMT setting and 5 um resolution. Image derived raw intensity data was extracted using Agilent Feature Extraction Software (Agilent).

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The different arrays were scaled by quantile method without background correction. Differentially expressed genes between the treated and control condition were chosen using as cut off criteria a SAM FDR of 5% and an average absolute fold change (|FC|) above 1.2 .

source_name: Cervical cancer cell line (HeLa)

label_protocol: Total RNA (0.5 ug) was dephosphorylated with CIP at 37ºC for 30 min, samples were denaturated and then ligation was  carried out for 2 hours at 16ºC, where a molecule of Cyanine 3-pCp is incorporated to the 3’ end of RNA molecules. Labelled RNA was dried, resuspended with Hybridisation Buffer and Blocking Agent, incubated 10 min at 100ºC and transferred to an ice water bath for 5 min prior to hybridization.

growth_protocol: HeLa cells were cultured at 37ºC in a 95/5 Air/CO2 water saturated  atmosphere in Dulbecco’s  modified  Eagle’s medium (DMEM) containing 10% heat inactivated foetal bovine serum (FBS), 2 mM  L-glutamine and 100U/ml Penicilin/streptomycine (complete growth medium).

extract_protocol: Total RNA from HeLa cells was extracted using the miRvana RNA Isolation kit (Ambion) following manufacturer's instructions. RNA quantification was performed with a Nanodrop spectrophotometer, and the RNA integrity was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE). All RNAs used had RIN (RNA integrity number) ranging between 9.3 and 10, and 28S/18S ratios between 1.67 and 2.07.

treatment_protocol: For treatments, the cells were transferred  to 60 mm dishes and cultured for 48h in complete growth medium, after which they were starved for 24h in DMEM containing 2% FBS. After serum deprivation, cells were cultured without EGF addition into the medium or were stimulated with EGF (150 ng/ml) for 6 hours.

tag: cell line

value: HeLa

tag: agent

value: EGF


title: Tarsal conjunctiva G-5636 card B

description: F

tag: disease status


title: 6h EGF replicate 1a

description:
Sample name: 6h-EGF-1a
6h time point, biological replicate 1 of 3, technical replicate 1 of 2. HeLa cells treated with EGF.


title: 6h Control replicate 3

description:
Sample name: 6h-Ctrl-3
6h time point, biological replicate 3 of 3. HeLa cells untreated controls.


title: Tarsal conjunctiva G-5624 card B

description: F


title: 129S1/SvImJ_XY_E11.0_gonad_rep3

description: replicate 3

source_name: 129S1/SvImJ, XY, E11.0 Gonad


title: 6h Control replicate 2

description:
Sample name: 6h-Ctrl-2
6h time point, biological replicate 2 of 3. HeLa cells untreated controls.


title: Tarsal conjunctiva G-5788 card B

description: F


title: 6h EGF replicate 3

description:
Sample name: 6h-EGF-3
6h time point, biological replicate 3 of 3. HeLa cells treated with EGF.


title: Tarsal conjunctiva G-5623 card B

description: F


title: 129S1/SvImJ_XY_E11.0_gonad_rep2

description: replicate 2


title: Tarsal conjunctiva G-5606 card B

description: F


title: 6h Control replicate 1a

description:
Sample name: 6h-Ctrl-1a
6h time point, biological replicate 1 of 3, technical replicate 1 of 2. HeLa cells untreated controls.


title: Tarsal conjunctiva G-5594 card B

description: M

value: M


title: 129S1/SvImJ_XX_E12.0_gonad_rep3

description: replicate 3

source_name: 129S1/SvImJ, XX, E12.0 Gonad

value: XX


title: 129S1/SvImJ_XY_E11.0_gonad_rep1

description: replicate 1


title: Tarsal conjunctiva G-5581 card B

description: F


title: 6h EGF replicate 1b

description:
Sample name: 6h-EGF-1b
6h time point, biological replicate 1 of 3, technical replicate 2 of 2. HeLa cells treated with EGF.


title: Tarsal conjunctiva G-5529 card B

description: F


title: 129S1/SvImJ_XY_E11.0_gonad_rep4

description: replicate 4


title: Tarsal conjunctiva G-5524 card B

description: M


title: 129S1/SvImJ_XX_E12.0_gonad_rep2

description: replicate 2


title: 129S1/SvImJ_XX_E12.0_gonad_rep1

description: replicate 1


title: MP-GUS_line4_rep1

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

address: Yayoi 1-1-1

department: Biotechnology Research Center

description: Gene expression in a control line (MP-GUS line #4)

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Rice Gene Expression 4x44k Microarrays (G1529F015241) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (eXtended Dynamic range scan, Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 021169_D_F_20080807) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Arabidopsis thaliana

source_name: MP-GUS line 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1000 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked using a Spectrophotometer.

growth_protocol: Seeds from hemizygous MP:Dof5.8 lines and homozygous MP:GUS lines were sown on agar plates containing 10 ug/ml glufosinate ammonium. After stratification for 4 days, the plates were transferred to a growth chamber set to a continuous light condition at 23°C. Shoots were collected from 4-day-old glufosinate ammonium-resistant seedlings.

extract_protocol: Total RNA was isolated using TRIzol reagent and then treated with DNase I. RNA was purified using the RNeasy mini kit (QIAGEN). The quality of RNA was checked by measuring absorbance at 230, 260 and 280 nm using a spectrophotometer.

tag: organ

value: shoot

tag: line


title: Tarsal conjunctiva G-5523 card B

description: M


title: Tarsal conjunctiva G-5532 card B

description: F


title: 129S1/SvImJ_XX_E11.8_gonad_rep3

description: replicate 3

source_name: 129S1/SvImJ, XX, E11.8 Gonad


title: MP-Dof5.8_line4_rep1

description: Gene expression in a Dof5.8-overexpressing Arabidopsis (MP-Dof5.8 line #4)

source_name: MP-Dof5.8 line 4


title: 129S1/SvImJ_XY_E11.0_gonad_rep5

description: replicate 5


title: 6h Control replicate 1b

description:
Sample name: 6h-Ctrl-1b
6h time point, biological replicate 1 of 3, technical replicate 2 of 2. HeLa cells untreated controls.


title: MP-Dof5.8_line3_rep3

description: Gene expression in a Dof5.8-overexpressing Arabidopsis (MP-Dof5.8 line #3)

source_name: MP-Dof5.8 line 3


title: 129S1/SvImJ_XX_E11.6_gonad_rep2

description: replicate 2

source_name: 129S1/SvImJ, XX, E11.6 Gonad


title: 129S1/SvImJ_XX_E11.6_gonad_rep1

description: replicate 1


title: MP-GUS_line1_rep2

description: Gene expression in a control line (MP-GUS line #1)

source_name: MP-GUS line 1


title: 129S1/SvImJ_XX_E11.4_gonad_rep2

description: replicate 2

source_name: 129S1/SvImJ, XX, E11.4 Gonad


title: 129S1/SvImJ_XX_E11.8_gonad_rep2

description: replicate 2


title: 129S1/SvImJ_XX_E11.6_gonad_rep3

description: replicate 3


title: Tarsal conjunctiva G-5500 card B

description: F


title: MP-GUS_line1_rep3


title: MP-GUS_line1_rep1


title: flow sorted cells form MUT E12.5 1

city: Corvallis

first: Adam

middle: Lee

last: Campbell

state: OR

address: 301 Pharmacy Building

department: College of Pharmacy

institute: Oregon State University

description: Pitx2 Mutant 1

hyb_protocol: 10 µg biotin labeled cRNA along with Affymetrix eukaryotic hybridization controls were hybridized for 16 hours in an Affymetrix GeneChip Hybridization Oven 640 at 45C.  Washing, staining with phycoerithryn-streptavidin follow the GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731) protocols using AGCC software (possibly GCOS for older than fall 2009) with a Affymetrix GeneChip® Fluidics Station and a GeneChip® Scanner 3000 with autoloader.

scan_protocol: scanning followed the Affymetrix GeneChip® Expression Analysis Technical Manual (701021 Rev. 5) with a Affymetrix GeneChip® Fluidics Station and a GeneChip® Scanner 3000 with autoloader.

data_processing: Data was analysed using Filemaker Pro software and RMA normalization. See Kioussi and Gross PLoS One 2008 [PMID: 18769640] and  Kioussi et al., PNAS 2006 [PMID: 17132738] for further details

source_name: flow sorted cells form MUT E12.5 1

label_protocol: 200 ng total RNA was labeled with Biotin using Ambion MessaAMP premier kit, using manufacturers instructions

growth_protocol: Forelimb tissue were dissected from genotyped E12.5 embryos

extract_protocol: Total RNA was isolated using protocol from Qiagen Rneasy Mini Kit Handbook supplied by Manufacturer

treatment_protocol: Tissue was dissociated into single cells by enzymatic digestion with collagenase type 1, passed through 30 um filter and flow sorted on basis of GFP+

value: Flow sorted forelimb tissue


title: flow sorted cells from HET E12.5 3

description: Pitx2 Heterozygote 3

source_name: flow sorted cells from HET E12.5 3


title: flow sorted cells form MUT E12.5 2

description: Pitx2 Mutant 2

source_name: flow sorted cells form MUT E12.5 2


title: flow sorted cells form MUT E12.5 3

description: Pitx2 Mutant 3

source_name: flow sorted cells form MUT E12.5 3


title: 129S1/SvImJ_XX_E11.8_gonad_rep1

description: replicate 1


title: MP-Dof5.8_line3_rep2


title: 129S1/SvImJ_XX_E11.4_gonad_rep3

description: replicate 3


title: MP-Dof5.8_line3_rep1


title: flow sorted cells from HET E12.5 2

description: Pitx2 Heterozygote 2

source_name: flow sorted cells from HET E12.5 2


title: flow sorted cells from HET E12.5 1

description: Pitx2 Heterozygote 1

source_name: flow sorted cells from HET E12.5 1


title: 129S1/SvImJ_XX_E11.2_gonad_rep3

description: replicate 3

source_name: 129S1/SvImJ, XX, E11.2 Gonad


title: Tarsal conjunctiva G-5402 card B

description: M

source_name: Swab, Tarsal conjunctiva, TF


title: 129S1/SvImJ_XX_E11.2_gonad_rep2

description: replicate 2


title: Tarsal conjunctiva G-5398 card B

description: M


title: Tarsal conjunctiva G-5485 card B

description: F


title: Tarsal conjunctiva G-5428 card B

description: F


title: 6h EGF replicate 3 versus pool of controls

description:
Sample name: 6h-EGF-3
6h time point, biological replicate 3 of 3. HeLa cells treated with EGF versus pool of controls.

hyb_protocol: Labelled RNAs (20 µL) were combined with Hybridisation Buffer and incubated 5 min at 95ºC. Samples were hybridized in a volume of 440 ul to the miRCURY LNA microRNA Array V9.2 (Exiqon) for 16–20 hours at 65°C and 15 rpm. Post-hybridization washes were in 4x SSC at 60°C to remove the coverslip, followed by three times in 2x SSC, 0.025% SDS for 5 min each, three times in 0.8x SSC for 2 min each, and two times in 0.4x SSC for 3 min each.

scan_protocol: Microarrays were scanned on a Imagene v7.0 software

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The intensities were imported without background corection and the Hy3/Hy5 log2ratios  were normalized using lowess and scaled between arrays by quantile method. Differentially expressed genes between the treated and control condition were chosen using as cut off criteria a SAM FDR of 5% and an average absolute fold change (|FC|) above 1.2 .

source_name: Cervical cancer cell line (HeLa)

label_protocol: Total RNA (0.5 µg) was 3'-end-labeled using T4 RNA ligase and a Cy3/Cy5-labeled RNA linker for 1 hour at 30°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: HeLa cells were cultured at 37ºC in a 95/5 Air/CO2 water saturated  atmosphere in Dulbecco’s  modified  Eagle’s medium (DMEM) containing 10% heat inactivated fetal bovine serum (FBS), 2 mM  L-glutamine and 100U/ml Penicilin/streptomycine (complete growth medium).

source_name: Cervical cancer cell line (HeLa)_pool of 3 control samples

tag: common reference composition

value: pool of three replicates


title: Tarsal conjunctiva G-5327 card B

description: M

tag: tissue


title: Tarsal conjunctiva F-1617 card B

description: F


title: flow sorted cells from WT E12.5 2

description: Pitx2 Wild Type 2

source_name: flow sorted cells from WT E12.5 2


title: 129S1/SvImJ_XX_E11.2_gonad_rep1

description: replicate 1

tag: Sex


title: flow sorted cells from WT E12.5 3

description: Pitx2 Wild Type 3

source_name: flow sorted cells from WT E12.5 3


title: 129S1/SvImJ_XX_E11.0_gonad_rep3

description: replicate 3

source_name: 129S1/SvImJ, XX, E11.0 Gonad

tag: Stage


title: Tumor infiltrating CD16/32LO cells_IL-15-/- tumor_rep1

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

description: Gene expression data from tumor infiltrating cells in IL-15-/- genetic background

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using high resolution, four color GeneChip Scanner 3000 7G 4C

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: Tumor Infiltrating cells, IL-15-/-

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

growth_protocol: Tail tumors in IL-15+/+ TAX-LUC and IL-15-/- TAX-LUC mice were allowed to spontaneously emerge over the course of a year

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

treatment_protocol: Tumors were excised and homogenized. CD16/32HI and CD16/32LO tumor cells were sorted.

value: Tumor Infiltrating Immune Cells in Solid Tumor

value: IL-15-/- TAX+ LUC+

tag: age

value: 14 months


title: Tumor infiltrating CD16/32LO cells_IL-15-/- tumor_rep2

value: 12 months


title: Malignant CD16/32HI cells_IL-15-/- tumor_rep1

description: Gene expression data from malignant lymphocytes in IL-15-/- genetic background

source_name: Malignant tumor cells, IL-15-/-

value: Malignant Large Granular Lymphocytes in Solid Tumor


title: Tarsal conjunctiva G-5388 card B

description: M

value: Tarsal conjunctiva


title: 129S1/SvImJ_XX_E11.0_gonad_rep2

description: replicate 2

tag: strain


title: Tarsal conjunctiva F-1588 card B

description: M

tag: gender


title: 129S1/SvImJ_XX_E11.0_gonad_rep1

description: replicate 1


title: Malignant CD16/32HI cells_ IL-15+/+ tumor_rep2

description: Gene expression data from malignant lymphocytes in IL-15+/+ genetic background

source_name: Malignant tumor cells, IL-15+/+

value: IL-15+/+ TAX+ LUC+


title: 6h EGF replicate 2 versus pool of controls

description:
Sample name: 6h-EGF-2
6h time point, biological replicate 2 of 3. HeLa cells treated with EGF versus pool of controls.


title: 6h EGF replicate 1 versus pool of controls

description:
Sample name: 6h-EGF-1
6h time point, biological replicate 1 of 3. HeLa cells treated with EGF versus pool of controls.


title: Malignant CD16/32HI cells_IL-15-/- tumor_rep2


title: Tumor infiltrating CD16/32LO cells_IL-15+/+ tumor_rep1

description: Gene expression data from tumor infiltrating cells in IL-15+/+ genetic background

source_name: Tumor Infiltrating cells, IL-15+/+


title: flow sorted cells from WT E12.5 1

description: Pitx2 Wild Type 1

source_name: flow sorted cells from WT E12.5 1


title: 6h Control replicate 3 versus pool of controls

description:
Sample name: 6h-Ctrl-3
6h time point, biological replicate 3 of 3. HeLa cells untreated controls versus pool of controls.


title: 6h Control replicate 2 versus pool of controls

description:
Sample name: 6h-Ctrl-2
6h time point, biological replicate 2 of 3. HeLa cells untreated controls versus pool of controls.


title: 6h Control replicate 1 versus pool of controls

description:
Sample name: 6h-Ctrl-1
6h time point, biological replicate 1 of 3. HeLa cells untreated controls versus pool of controls.


title: Malignant CD16/32HI cells_IL-15+/+ tumor_rep1


title: ADSC1vs.WT

city: Xi'an

first: Min

last: Sun

address: No.1, Xinsi Road

institute: Tangdu Hospital

description: compare gene expression profiles

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: ovary

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: ADSCs were cultured in α-MEM supplemented with 10% fetal bovine serum  at 37°C with 5% CO2.

extract_protocol: Ovaries of four gruops were collected, and total RNA was extracted with Trizol Reagent (Invitrogen) and ethanol precipitation.

treatment_protocol: After establishing the POF model, the mice were randomly divided into 4 equal groups. The WT group consisted of normal control mice that received no treatment. In POF group, the mice were administered with Cyclophosphamide. In the ADSC1 group, POF mice were injected intravenously with ADSCs. In the ADSC2 group, ADSCs were injected directly into the bilateral ovaries of POF mice.The ovaries were collected one week  after treatment.

value: normal


title: Tumor infiltrating CD16/32LO cells_IL-15+/+ tumor_rep2


title: Somatotroph adenoma 331

status: Public on Jun 10 2013

city: Oslo

first: Tove

last: Lekva

address: Sognsvannsveien 20

department: Section of Specialized Endocrinology and Institute for Internal Medicine

country: Norway

institute: OUS-HF, Rikshospitalet

hyb_protocol: The cRNA was hybridized to HG U133 plus 2.0 Arrays (Affymetrix) followed by washing and staining on the GeneChips Fluidics Station 450 (Affymetrix)

scan_protocol: Signal intensities were detected by  Affymetrix GeneChip Scanner 3000

data_processing: The scanned images were processed using GCOS 1.4 (Affymetrix) according to the manufacturer. The resulting data sets (CEL files) were imported into ArrayAssist Expression Software (v5.2.0;Iobion Informatics LLC) and normalized using the PLIER algorithm in Array Assist to calculate relative signal values for each probe set.

source_name: Adenoma_tertile 3_SA treatment

label_protocol: Double-stranded cDNA and biotin-labeled cRNA probes were made from 5 μg of total RNA by use of GeneChip® Expression 3' Amplification One-Cycle Target Labeling kit (Affymetrix).

extract_protocol: Trizol extraction followed by Rneasy clean up kit (qiagen) was performed according to the manufacturer´s instruction

value: Male

tag: adenoma

value: pituitary

tag: e-cadherin expression

value: high

tag: treatment

value: SA


title: Somatotroph adenoma 323


title: Somatotroph adenoma 321


title: Somatotroph adenoma 330

source_name: Adenoma_tertile 3_no treatment


title: Somatotroph adenoma 320

source_name: Adenoma_tertile 1_SA treatment

value: low


title: Somatotroph adenoma 291

value: Female


title: Somatotroph adenoma 343


title: Somatotroph adenoma 253


title: Somatotroph adenoma 276

source_name: Adenoma_tertile 1_no treatment


title: Somatotroph adenoma 328


title: Somatotroph adenoma 329


title: Somatotroph adenoma 273


title: POFvs.WT

description: compare gene expression profiles

value: premature ovary failure(POF)


title: ADSC2vs.WT

description: compare gene expression profiles

value: POF mice with ADSC injected directly into the bilateral ovaries


title: Somatotroph adenoma 280


title: Somatotroph adenoma 153


title: Somatotroph adenoma 185


title: Col 0 con c

city: Erlangen

first: Christian

last: Prasch

address: Staudtstrasse 5

department: Biochemistry division

institute: FAU Universität Erlangen-Nürnberg

description: Arabidopsis, leave, control, replicate 3

hyb_protocol: After fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent Arabidopsis_v4 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2565B Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.7.1 (Agilent Technologies Germany). Data extraction using protocol GE1_v5_95_Feb07

data_processing: After importing text files via feature extraction software (Version 11.7.1; Agilent Technologies) into GeneSpring GX 11.0 (Silicon Genetics) microarray data were log2-transformed followed by normalization to the 75th percentile and corrected to the median of all samples.

source_name: 34 days post germination under control conditions

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 80mg  total RNA after the method published by Logemann et al. (1987) (One-Color Microarray-based gene expression analysis v.5.5)

growth_protocol: Three days after vernalisation in darkness at 4°C, Arabidopsis thaliana plants (ecotype Columbia) were grown on soil under short-day conditions (8 h light, 16 h dark), 60% humidity and 22°C (day) or 18/19°C (night). 12 days after germination young seedlings were transferred to single plant pots containing 160g soil. Plants were watered with defined volumes of water (see treatment protocol). Further plant cultivation was implemented in a plant climate chamber (Plant-Master PGR 3045, CLF Plant Climatics GmbH, Germany) that guarantees a diurnal rhythm of 12h of light at approximately 80 µmol m-2 s-2 and exactly 60% humidity at day and night. The temperature regime followed the light/ dark cycle with 22°C and 18°C.

extract_protocol: 34 days after germination the fresh weight of whole rosettes of differentially treated plants have been determined and individual Arabidopsis leaves were harvested and immediately frozen in liquid nitrogen. Leaves from 5-8 plants were grouped for one biological replicate. For each treatment four biological replicates have been sampled. After sampling, material was stored at -80°C.

treatment_protocol: Three weeks after germination plants were treated with the virus TuMV (see below). Control plants were treated with water to equalize damaging effects on locally infected leaves. Eight days later approximately 85% of the young Arabidopsis leaves, which had been infected systemically, showed typically virus symptoms. The obviously infected plants were exposed to drought stress by reducing water amounts (see below). After two days of mild drought influence, heat stress was applied by increasing temperature for three days (see below). Plants exposed to the different stress treatments were randomly mixed and distributed throughout the growth chamber. Harvest of plant material started four hours before the end of the light period and was completed before the start of the dark period. To avoid systematic errors, plants of different stress treatments have been sampled in a randomized fashion. Mild drought stress was controlled by using soil moisture content measurements. To determine the volumetric water content the Decagon Devices sensor was used measuring the dielectric constant of water. This constant is very different from the surrounding soil components, which allows a direct correlation between dielectric constant and water content and was subsequently used for field capacity measurements. The correlation between certain amounts of soil and the corresponding field capacity values resulted in a calibration curve. To define an upper limit, field capacity of soil moisture content was set to 100% field capacity. Therefore, plant pots were watered till saturation and measured. By contrast, the lowest field capacity was given by trying 160g soil overnight, reweighing and measuring field capacity values. Field capacity values in between were determined starting from 160g soil and watering of 10 ml water each. According to the calibration curve well-watered plants were watered according to 55% of field capacity with a deviation of 10%, whereas mild drought stress is given by 30% of field capacity with a deviation of 10%. Progressive drought-stress procedure was initiated by withholding water. Water loss was monitored by weighing each pot every day and watering after the lower limit of mild drought stress is achieved. Control plants were watered daily to maintain the soil humidity at the field capacity. Mild heat stress was applied by increasing air temperature to 32°C during the day and 28°C during the night for 3 days. Humidity of 60% was not changed and water was not restricted for plants without drought stress. Turnip mosaic virus (TuMV) infection was performed by inoculating the two largest leaves with TuMV-infected plant material ground in 5 mM sodium phosphate buffer (pH 7.2). In addition Silicon carbide powder was used to damage the leaf surface ensuring a successful virus penetration. After a few minutes the leaves were washed with water.

tag: ecotype

value: Columbia

tag: t-dna insertion line

value: no insertion (wild-type)

value: systemically infected leaves

value: 34 post germination


title: Somatotroph adenoma 192


title: N672283 treat a

description: Arabidopsis, T-DNA Insertionline, leave, virus&drought&heat, replicate 1

source_name: plants treated with virus for 13 days and exposed to five days of drought stress and parallel to heat stress for three days


title: N672283 con d

description: Arabidopsis, T-DNA insertion line, leave, control, replicate 4


title: Col 0 treat c

description: Arabidopsis, leave, virus&drought&heat, replicate 3


title: N672283 treat d

description: Arabidopsis, T-DNA Insertionline, leave, virus&drought&heat, replicate 4


title: N672283 con a

description: Arabidopsis, T-DNA insertion line, leave, control, replicate 1


title: Col 0 con b

description: Arabidopsis, leave, control, replicate 2


title: Col 0 treat a

description: Arabidopsis, leave, virus&drought&heat, replicate 1


title: N672283 treat c

description: Arabidopsis, T-DNA Insertionline, leave, virus&drought&heat, replicate 3


title: N672283 con c

description: Arabidopsis, T-DNA insertion line, leave, control, replicate 3


title: Col 0 treat b

description: Arabidopsis, leave, virus&drought&heat, replicate 2


title: control 1d (to heat)

description: Arabidopsis, leave, control, replicate 4

source_name: 37 days post germination under control conditions

extract_protocol: 34 days and 37 days after germination the fresh weight of whole rosettes of differentially treated plants have been determined and individual systemically infected Arabidopsis leaves were harvested and immediately frozen in liquid nitrogen. Leaves from 5-8 plants were grouped for one biological replicate. For each treatment four biological replicates have been sampled. After sampling, material was stored at -80°C.

treatment_protocol: Three weeks after germination plants were treated with the virus TuMV (see below). Control plants were treated with water to equalize damaging effects on locally infected leaves. Eight days later approximately 85% of the young Arabidopsis leaves, which had been infected systemically, showed typically virus symptoms. The obviously infected plants were exposed to drought stress by reducing water amounts (see below). After two days of mild drought influence, heat stress was applied by increasing temperature for three days (see below). Plants exposed to the different stress treatments were randomly mixed and distributed throughout the growth chamber. Harvest of plant material started four hours before the end of the light period and was completed before the start of the dark period. To avoid systematic errors, plants of different stress treatments have been sampled in a randomized fashion. Mild drought stress was controlled by using soil moisture content measurements. To determine the volumetric water content the Decagon Devices sensor was used measuring the dielectric constant of water. This constant is very different from the surrounding soil components, which allows a direct correlation between dielectric constant and water content and was subsequently used for field capacity measurements. The correlation between certain amounts of soil and the corresponding field capacity values resulted in a calibration curve. To define an upper limit, field capacity of soil moisture content was set to 100% field capacity. Therefore, plant pots were watered till saturation and measured. By contrast, the lowest field capacity was given by trying 160g soil overnight, reweighing and measuring field capacity values. Field capacity values in between were determined starting from 160g soil and watering of 10 ml water each. According to the calibration curve well-watered plants were watered according to 55% of field capacity with a deviation of 10%, whereas mild drought stress is given by 30% of field capacity with a deviation of 10%. Progressive drought-stress procedure was initiated by withholding water. Water loss was monitored by weighing each pot every day and watering after the lower limit of mild drought stress is achieved. Control plants were watered daily to maintain the soil humidity at the field capacity. Mild heat stress was applied by increasing air temperature to 32°C during the day and 28°C during the night for 3 days. Increased air temperature of 37°C during the day and 33°C during the night for 3 days guaranteed severe heat stress. Humidity of 60% was not changed and water was not restricted for plants without drought stress. Turnip mosaic virus (TuMV) infection was performed by inoculating the two largest leaves with TuMV-infected plant material ground in 5 mM sodium phosphate buffer (pH 7.2). In addition Silicon carbide powder was used to damage the leaf surface ensuring a successful virus penetration. After a few minutes the leaves were washed with water.

value: leaves


title: TuMV 5c

description:
Arabidopsis, leave, TuMV, replicate 3

[***Sample did not pass the quality control parameter and was excluded from further analysis***]

hyb_protocol: following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent Arabidopsis_v4 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

data_processing:
After importing text files via feature extraction software (Version 11.7.1; Agilent Technologies) into GeneSpring GX 11.0 (Silicon Genetics) microarray data were log2-transformed followed by normalization to the 75th percentile and corrected to the median of all samples.  A one-way Anova (p ≤0.05, variance assumed as equal) enabled us to select genes which show differential behavior and also pronounced similarities within the groups.

[***Sample did not pass the quality control parameter and was excluded from further analysis***]

source_name: plants treated with virus for 13 days

extract_protocol: 34 days after germination the fresh weight of whole rosettes of differentially treated plants have been determined and individual systemically infected Arabidopsis leaves were harvested and immediately frozen in liquid nitrogen. Leaves from 5-8 plants were grouped for one biological replicate. For each treatment four biological replicates have been sampled. After sampling, material was stored at -80°C.


title: N672283 treat b

description: Arabidopsis, T-DNA Insertionline, leave, virus&drought&heat, replicate 2


title: triple 1d

description: Arabidopsis, leave, triple, replicate 4

source_name: plants treated with virus for 13 days and in parallel exposed to five days of drought stress

value: 37 post germination


title: control 1a  (to triple)

description: Arabidopsis, leave, control, replicate 1


title: control 1c (to heat)


title: heat 1d

description: Arabidopsis, leave, heat, replicate 4

source_name: plants exposed to three days of heat stress


title: control 1a (to heat)


title: heat 1b

description: Arabidopsis, leave, heat, replicate 2


title: control 1b  (to triple)


title: 129S1/SvImJ_XX_E11.4_gonad_rep1

description: replicate 1

source_name: 129S1/SvImJ, XX, E11.4 Gonad

value: XX


title: TuMV&heat 7c

description: Arabidopsis, leave, TuMV&heat, replicate 3

data_processing: After importing text files via feature extraction software (Version 11.7.1; Agilent Technologies) into GeneSpring GX 11.0 (Silicon Genetics) microarray data were log2-transformed followed by normalization to the 75th percentile and corrected to the median of all samples.  A one-way Anova (p ≤0.05, variance assumed as equal) enabled us to select genes which show differential behavior and also pronounced similarities within the groups.

source_name: plants treated with virus for 13 days and in parallel exposed to three days of heat stress


title: control 1b (to heat)


title: heat 1a

description: Arabidopsis, leave, heat, replicate 1


title: Col 0 con a


title: TuMV&drought 6c

description: Arabidopsis, leave, TuMV&drought, replicate 3


title: triple 1a

description: Arabidopsis, leave, triple, replicate 1


title: heat 1c

description: Arabidopsis, leave, heat, replicate 3


title: triple 1c

description: Arabidopsis, leave, triple, replicate 3


title: TuMV&drought&heat 8d

description: Arabidopsis, leave, TuMV&drought&heat, replicate 4

source_name: plants treated with virus for 13 days and in parallel exposed to five days of drought stress and three days of heat stress


title: control 1c  (to triple)

description: Arabidopsis, leave, control, replicate 3


title: TuMV&heat 7d

description: Arabidopsis, leave, TuMV&heat, replicate 4


title: TuMV&drought&heat 8c

description: Arabidopsis, leave, TuMV&drought&heat, replicate 3


title: TuMV&drought 6d

description: Arabidopsis, leave, TuMV&drought, replicate 4


title: TuMV 5d

description: Arabidopsis, leave, TuMV, replicate 4


title: drought&heat 4c

description: Arabidopsis, leave, drought&heat, replicate 3

source_name: plants exposed to five days of drought stress and parallel to heat stress for three days


title: triple 1b

description: Arabidopsis, leave, triple, replicate 2


title: drought&heat 4d

description: Arabidopsis, leave, drought&heat, replicate 4


title: control 1d  (to triple)


title: heat 2d

description: Arabidopsis, leave, heat, replicate 4

source_name: plants exposed to three days of heat treatment


title: drought 3c

description: Arabidopsis, leave, drought, replicate 3

source_name: plants exposed to five days of drought stress


title: TuMV&heat 7b

description: Arabidopsis, leave, TuMV&heat, replicate 2


title: control 1c


title: control 1d


title: TuMV&drought&heat 8a

description: Arabidopsis, leave, TuMV&drought&heat, replicate 1


title: TuMV&heat 7a

description: Arabidopsis, leave, TuMV&heat, replicate 1


title: TuMV 5a

description: Arabidopsis, leave, TuMV, replicate 1


title: TuMV&drought&heat 8b

description: Arabidopsis, leave, TuMV&drought&heat, replicate 2


title: TuMV 5b

description: Arabidopsis, leave, TuMV, replicate 2


title: TuMV&drought 6a

description: Arabidopsis, leave, TuMV&drought, replicate 1


title: TuMV&drought 6b

description: Arabidopsis, leave, TuMV&drought, replicate 2


title: heat 2b

description: Arabidopsis, leave, heat, replicate 2


title: heat 2c

description: Arabidopsis, leave, heat, replicate 3


title: testis BeadChip rep1

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

description: replicate 1

scan_protocol: Standard Illumina scanning protocol (iScan)

data_processing: The data were analyzed with Illumina GenomeStudio. The data with background subtraction but without further normalization.

source_name: Human Testis

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

extract_protocol: RNA was isolated from samples using Trizol, followed by clean-up and DNase I treatment. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Semen was collected then treated with PureSperm gradient centrifugation through a 50% PureSperm cushion, or Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100).

value: Human Testis

tag: sample source

value: From commercial libraries


title: drought&heat 4b

description: Arabidopsis, leave, drought&heat, replicate 2


title: heat 2a

description: Arabidopsis, leave, heat, replicate 1


title: control 1a

description: Arabidopsis, leave, control, replicate 1


title: drought 3d

description: Arabidopsis, leave, drought, replicate 4


title: control 1b

description: Arabidopsis, leave, control, replicate 2


title: drought&heat 4a

description: Arabidopsis, leave, drought&heat, replicate 1


title: sperm SCLB BeadChip rep1

description: replicate 1

source_name: Fertile Human Spermatozoa

tag: cell type

value: Fertile Human Spermatozoa

value: Semen from a normal fertile donor


title: drought 3a

description: Arabidopsis, leave, drought, replicate 1


title: sperm PS BeadChip rep1

description: replicate 1


title: sperm SCLB BeadChip rep2

description: replicate 2


title: testis BeadChip rep2

description: replicate 2


title: sperm PS BeadChip rep2

description: replicate 2


title: drought 3b

description: Arabidopsis, leave, drought, replicate 2


title: 50T, rep2

status: Public on Jun 09 2013

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: 50T replicate 2

hyb_protocol: A total hybridisation volume of 15ul is prepared for each sample and 15ul loaded into a single array on the Sentrix Human-HT12v4 BeadChip. The chip is hybridised at 58C for 16 hours in an oven with a rocking platform. After hybridisation, the chip is washed using the appropriate protocols as outlined in the Illumina manual. Upon completion of the washing, the chips are then coupled with Cy3 and scanned in the illumina BeadArray Reader.

scan_protocol: Arrays were scanned in the Illumina BeadArray Reader.

data_processing: The GenomeStudio software (version 1.9.0) was used to convert the signal on the array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was carried out in R (version 2.15.2) using the limma package (version 4.15.9).

source_name: xenograft tumor

label_protocol: Human total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 500ng was labelled using the Ambion Total Prep RNA amplification kit (Cat. No. IL1791). The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 750ng of labelled cRNA was then prepared for hybridisation to the Sentrix Human- HT12v4 BeadChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the BeadChip).

extract_protocol: RNA was extracted using Invitrogen Trizol Reagent in accordance with the prescribed protocol provided with the kit. DNase treatment was performed using the QIAGEN RNase-free DNase Set prior to RNA purification using the QIAGEN RNAeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: breast tumor xenograft

tag: tumor id


title: 23T, rep1

description: 23T replicate 1


title: 23T, rep2

description: 23T replicate 2


title: NSC_5

city: London

first: Matt

last: Burney

address: 125 Coldharbour Lane

institute: King's College London

hyb_protocol: Standard Illumina hybridization protocol to Illumina Mouse Ref-8 v2 BeadArrays.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization using the Bioconductor BeadArray library in R. Differential expression was calculated using the limma library.

source_name: mESC derived NSC

label_protocol: RNA was labelled using a TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: NSCs were derived according to monolayer protocols (Ying et al 2003) and maintained in Euromed-N medium supplemented with N2 and FGF2/EGF.

extract_protocol: Total RNA was extracted using the Qiagen RNA easy columns according to manufacturers protocols

treatment_protocol: Differentiation to neurons was performed in N2B27 for four days, followed by a replating step in Neurobasal medium supplemented with B27. Neurons were then FACS purified based on RedStar expression driven by the neuronal specific Tau promoter

value: neural stem cellsderived from mouse embryonic stem cells

tag: tau-redstar expression

value: No


title: Neuron_2

source_name: NSC derived Neuron

value: differentiated neuronal progeny

value: Yes


title: 315T, rep4

description: 315T replicate 4


title: Neuron_3


title: 50T, rep1

description: 50T replicate 1


title: NSC_2


title: NSC_1


title: 315T, rep2

description: 315T replicate 2


title: 315T, rep1

description: 315T replicate 1


title: 315T, rep3

description: 315T replicate 3


title: 838T, rep2

description: 838T replicate 2


title: NSC_3


title: NSC_4


title: 838T, rep3

description: 838T replicate 3


title: Neuron_1