title: shCaf1, biological rep1

description: Gene expression data from mouse elongating spermatids transduced with lentiviral Caf1 shRNA vector

source_name: Mouse elongating spermatids transduced with lentiviral Caf1 shRNA vector

tag: genotype


title: shCaf1, biological rep2

status: Public on Jul 11 2014

type: RNA

city: Shanghai

first: Lantao

last: Gou

address: 320 Yue Yang Road

country: China

institute: Institute of Biochemistry and Cell Biology

hyb_protocol: Array hybridization and wash was performed using GeneChip Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Testis transduction was performed in 5-week-old ICR male mice with shMiwi:GFP, shCaf1:GFP, or control pSilencer:GFP vectors.

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

treatment_protocol: GFP+ elongating spermatids were sorted from isolated total germ cells of transduced mouse testes 1 week post-transduction.

tag: tissue

value: elongating spermatids

value: wildtype

tag: age

value: adult

tag: strain

value: ICR


title: shMiwi, biological rep1

description: Gene expression data from mouse elongating spermatids transduced with lentiviral Miwi shRNA vector

source_name: Mouse elongating spermatids transduced with lentiviral Miwi shRNA vector


title: tlo1Δ/tlo2Δ + TLO2 1h 10% Serum replicate 2

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

description: Candida dubliniensis tlo1Δ/tlo2Δ versus a TLO2 complemented mutant hypha-inducing conditions (10% serum at 37˚C)

hyb_protocol: Hybridization and washing of the arrays was carried out using the Agilent Gene Expression Hybridization Kit and Gene Expression Wash Pack according the manufacturer’s instructions.

scan_protocol: Slides were scanned using the GenePix personal 4100A scanner (Axon) and data was extracted with GenePix Pro 6.1 (Axon).

data_processing: Spots were flagged absent if the signal was less than background +1 standard deviation in both fluorescent channels. Raw data was exported to GeneSpring GX12 and signals for each replicate spot were background corrected and normalized using Loess normalization. Log2 fluorescence ratios were generated for each replicate spot and averaged. Oligonucleotides were excluded from analysis if >50% of replicates in each condition were flagged absent.

organism: Candida dubliniensis

source_name: Candida dubliniensis 1h in 10% serum at 37˚C

label_protocol: Total RNA was labelled with Cy5 or Cy3 using the Agilent Quick AmpTwo-Color Labelling Kit

growth_protocol: For YEPD experiments, Candida cells were cultured in standard YEPD broth at 37˚C until they reached OD600nm 0.8. For 10% serum experiments, cultures were growth overnight in YEPD at 30˚C, washed and diluted and 2 x106 cells/ml were added to 10% serum for the indicated time.

extract_protocol: Total RNA was extracted using the Qiagen RNA minikit using a microdismembrator (Braun, Melsungen,Germany) for cell breakage.

treatment_protocol: Cells were spun down at 2,500 x g for 5 min and flash frozen in liquid Nitrogen

tag: genotype/variation

value: tlo1Δ/tlo2Δ + TLO2


title: tlo1Δ/tlo2Δ + TLO2 1h 10% Serum replicate 3


title: tlo1Δ/tlo2Δ + TLO1 1h 10% Serum replicate 3

description: Candida dubliniensis tlo1Δ/tlo2Δ versus a TLO1 complemented mutant hypha-inducing conditions (10% serum at 37˚C)

value: tlo1Δ/tlo2Δ + TLO1


title: tlo1Δ/tlo2Δ + TLO1 1h 10% Serum replicate 2


title: tlo1Δ/tlo2Δ + TLO2 1h 10% Serum replicate 1


title: tlo1Δ/tlo2Δ + TLO1 1h 10% Serum replicate 1


title: control pSilencer, biological rep1

description: Gene expression data from mouse elongating spermatids transduced with lentiviral pSilencer vector

source_name: Mouse elongating spermatids transduced with lentiviral pSilencer vector


title: Control-rep6

city: Minneapolis

first: emilyn

middle: U

last: alejandro

state: MN

department: Integrative Biology and Physiology

country: USA

institute: University of Minnesota

description: Ctrl

data_processing:
ΔCt values were calculated as the difference to the average U6 for the A and B primer pools separately. Linear models were calculated using the limma package of R/bioconductor
Fold Change worksheet reports test/control ratios (2^-(TestΔCt-controlΔCt)).

label: FAM

source_name: Islet

label_protocol: TaqMan probe label: FAM

extract_protocol: RNA was isolated by MirVana Kit (Life Technologies). See manufacturer's website.

tag: gender

value: Male

tag: diet

value: control diet


title: tlo1Δ/tlo2Δ + TLO2 YEPD replicate 3

description: Candida dubliniensis tlo1Δ/tlo2Δ versus a TLO2 complemented mutant in YEPD medium

source_name: Candida dubliniensis YEPD broth, 37˚C, OD600nm 1.0


title: tlo1Δ/tlo2Δ + TLO2 YEPD replicate 2


title: control pSilencer, biological rep2


title: cdk11 deletion mutant dye-swap rep1

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description:
biological replicate 1 of 2
cdk11-del_rep3

hyb_protocol: 750 ng of labeled cRNA was hybridized per sample, according to standard Agilent protocols.

scan_protocol: Microarrays were scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies)

data_processing: Spot quantification was carried out using Feature Extraction software v9.5 (Agilent Technologies). Following quantification, the microarray data was lowess-normalized and an expression ratio was calculated for each microarray feature by dividing the signal intensity of the channel corresponding to the deletion mutant by that of the control channel (wild-type).

organism: Schizosaccharomyces pombe

source_name: total RNA from a wild-type strain

label_protocol: For each sample, 500 µg of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye using the Low RNA Input Linear Amplification Kit (Agilent Technologies).

growth_protocol: A culture of 100ml was grown at 32°C in YES medium until mid-log phase, pelleted and snap-frozen in liquid nitrogen.

extract_protocol: RNA was prepared by acidic phenol extraction at 65°C for 1 hour with brief vortexing every 10 minutes. The water phase was re-extracted with acidic phenol-chloroform-IAA (24:24:1) and the RNA precipitated. About 250 µg of RNA were purified on Qiagen RNeasy column and eluted with 30 µl H20.

value: wild type

source_name: total RNA from a cdk11 deletion mutant

value: cdk11 deletion mutant


title: tlo1Δ/tlo2Δ 3h 10% Serum replicate 3

description: Candida dubliniensis wild type versus tlo1Δ/tlo2Δ double mutant in hypha-inducing conditions (10% serum at 37˚C)

source_name: Candida dubliniensis 3h in 10% serum at 37˚C


title: tlo1Δ/tlo2Δ + TLO2 YEPD replicate 1


title: cdk11 deletion mutant dye-swap rep2

description:
biological replicate 2 of 2
cdk11-del_rep4


title: Control-rep5

description: Ctrl


title: tlo1Δ/tlo2Δ 3h 10% Serum replicate 2


title: tlo1Δ/tlo2Δ + TLO1 1h 10% Serum replicate 4


title: Control-rep4

description: Ctrl


title: Ampelo1.0_rep2

type: genomic

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 50 °C. Hybridization was performed at 50°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST was solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: Scanning was performed on a GenePix 4400A scanner. Parameters were set in order to have 1e-6 normalized counts at the 65000 intensity level (saturation).

data_processing: Data extraction was carried out using CombiMatrix Microarray Imager software and a quantile normalization of data was performed.

molecule: genomic DNA

organism: Ampelomyces quisqualis

source_name: Ampelomyces quisqualis genomic DNA replicate2

label_protocol: Five µg of DNA were labeled using ULS labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions.

extract_protocol: Genomic DNA  were extracted from A. quisqualis conidia using  GeneElute Plant Miniprep Kit (Sigma-Aldrich).

value: CNCM-807 (commercial name AQ10)


title: tlo1Δ/tlo2Δ + TLO1 YEPD replicate 1

description: Candida dubliniensis tlo1Δ/tlo2Δ versus a TLO1 complemented mutant in YEPD medium


title: Ampelo1.0_rep1

source_name: Ampelomyces quisqualis genomic DNA replicate1


title: tlo1Δ/tlo2Δ + TLO1 YEPD replicate 2


title: tlo1Δ/tlo2Δ + TLO1 YEPD replicate 3


title: tlo1Δ/tlo2Δ 3h 10% Serum replicate 4


title: tlo1Δ/tlo2Δ 3h 10% Serum replicate 1


title: Control-rep3

description: Ctrl


title: cdk8 deletion mutant dye-swap rep1

description:
biological replicate 1 of 2
cdk8-del_rep3

source_name: total RNA from a cdk8 deletion mutant

value: cdk8 deletion mutant


title: cdk8 deletion mutant dye-swap rep2

description:
biological replicate 2 of 2
cdk8-del_rep4


title: cdk11 deletion mutant rep2

description:
biological replicate 2 of 2
cdk11-del_rep2


title: L.05-rep6

description: TEST

value: low-protein diet (LP0.5)


title: tlo1Δ/tlo2Δ 1h 10% Serum replicate 4


title: Control-rep2

description: Ctrl


title: cdk11 deletion mutant rep1

description:
biological replicate 1 of 2
cdk11-del_rep1


title: L.05-rep5

description: TEST


title: L.05-rep4

description: TEST


title: Whole Blood_Media_3h (7927538083_L)

city: London

first: Simon

last: Blankley

address: The Ridgeway

department: Division of Immunoregulation

country: United Kingdom

institute: MRC - National Insititute for Medical Research

description:
Globin RNA reduced.
7927538083_L

hyb_protocol: Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion)

scan_protocol: Illumina Iscan

data_processing: Background subtraction using Genomestudio

organism: Homo sapiens

source_name: Whole Blood

growth_protocol: 1ml Human whole blood with 100µl RPMI 1640- with GlutaMAX incubated at 37 degrees celcius and 5% C02

extract_protocol: 1ml added to 2mls Tempus solution. RNA extracted using PerfectPURE RNA Blood kit (5-PRIME), globin RNA reduced using GLOBINclear (Biosystems/Ambion)

treatment_protocol: Treated either with 1ng/ml LPS or 200ng/ml Pam3CSK4 or media alone

value: whole blood

tag: treatment

value: Media 3h

tag: volunteer id


title: L.05-rep3

description: TEST


title: tlo1Δ/tlo2Δ YEPD replicate 4

description: Candida dubliniensis wild type versus tlo1Δ/tlo2Δ double mutant in YEPD medium


title: tlo1Δ/tlo2Δ 1h 10% Serum replicate 2


title: cdk8 deletion mutant rep2

description:
biological replicate 2 of 2
cdk8-del_rep2


title: Control-rep1

description: Ctrl


title: tlo1Δ/tlo2Δ 1h 10% Serum replicate 3


title: tlo1Δ/tlo2Δ YEPD replicate 2


title: tlo1Δ/tlo2Δ 1h 10% Serum replicate 1


title: L.05-rep2

description: TEST


title: tlo1Δ/tlo2Δ YEPD replicate 1


title: L.05-rep1

description: TEST


title: SH (SOX2/HMGA2-tranduced induced neural stem cell)

city: Seoul

first: Kyung-Rok

last: Yu

address: Rm727, Bd85, Gwanak-gu

country: South Korea

institute: Seoul National University

description: miRNA expression of human SOX2/HMGA2-transduced induced neural stem cells

hyb_protocol: The labeled RNA samples were dried in a Vacuum Concentrator for one hour. Once samples are completely dried, they were prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. Arrays were hybridized in 45 µl of the mixture, and then rotated at 20 rpm for 20 h at 55°C. Agilent Gene Expression Wash Buffers 1(RT) and 2(37°C) were used after hybridization as recommended by Agilent miRNA Microarray System

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4900DA) using 3um resolusion

data_processing:
Raw data were extracted using the software provided by Agilent Feature Extraction Software (v11.0.1.1). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene view file, providing expression data for each gene probed on the array
Array data were filtered by gIsGeneDetected =1 in all samples ( 1 : detected ).  Selected miRNA gTotalGeneSignal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test sample and control sample was carried out using fold-change

source_name: SH

label_protocol: 100 ng total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100°C for 7min. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 2 hour.

growth_protocol: H9-NSCs, iNSCs were kept in an undifferentiated state by using 20ng/ml bFGF, EGF (Gibco), and grown on PLO/Fibronectin coated dishes.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: cell type

tag: cell line


title: SOX2 (SOX2-transduced induced neural stem cell)

description: miRNA expression of human SOX2-transduced induced neural stem cells


title: WT NSC (H9-derived neural stem cell)

description: miRNA expression of H9-derived neural stem cells

source_name: WT NSC

value: H9-derived neural stem cell


title: hDF (human dermal fibroblast)

description: miRNA expression of human dermal fibroblasts

source_name: hDF

value: adult dermal fibroblasts


title: cdk8 deletion mutant rep1

description:
biological replicate 1 of 2
cdk8-del_rep1


title: tlo1Δ/tlo2Δ YEPD replicate 3


title: Ampelo_3-6-12h_rep1

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 µg ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C. Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST was solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

source_name: 3-6-12 h (early germination), replicate 1

label_protocol: Five µg were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions.

growth_protocol:
A. quisqualis was grown on potato dextrose agar (Oxoid, UK) at 25 °C.
C. pepo seedlings were grown on filter paper for 20 days.
P. xanthii was maintained on zucchini plants grown in peat in 1-liter pots  under controlled greenhouse conditions (22 ± 3°C, 70 ± 10% relative humidity and a natural photoperiod

extract_protocol: Total RNA was extracted using the Spectrum Plant Total RNA Kit (Sigma-Aldrich, Saint Louis, MO, USA)

treatment_protocol: A dialysis set up was developed to stimulate in vitro germination of A. quisqualis conidia while avoiding any contamination with P. xanthii and C. pepo. A 12,000 Da molecular weight cut-off dialysis sack (Sigma; Milano, Italy) was filled with C. pepo leaf disks (60 discs, 5 mm diam. each) infected with P. xanthii and immersed in an aqueous suspension (500 ml) of 5 × 105 A. quisqualis conidia/ml at room temperature. The dialysis was improved by the constant stirring of the conidial suspension. Equal amounts of conidia (7.5 × 107 conidia for each collection point) were collected 3, 6, 12 h after immersion. These samples were pooled.


title: Ampelo_24-48-72h_rep1

source_name: 24-48-72 h (late germination), replicate 1

treatment_protocol: A dialysis set up was developed to stimulate in vitro germination of A. quisqualis conidia while avoiding any contamination with P. xanthii and C. pepo. A 12,000 Da molecular weight cut-off dialysis sack (Sigma; Milano, Italy) was filled with C. pepo leaf disks (60 discs, 5 mm diam. each) infected with P. xanthii and immersed in an aqueous suspension (500 ml) of 5 × 105 A. quisqualis conidia/ml at room temperature. The dialysis was improved by the constant stirring of the conidial suspension. Equal amounts of conidia (7.5 × 107 conidia for each collection point) were collected 24, 48 and 72 h after immersion. These samples were pooled.


title: Ampelo_24-48-72h_rep3

source_name: 24-48-72 h (late germination), replicate 3


title: Ampelo_24-48-72h_rep2

source_name: 24-48-72 h (late germination), replicate 2


title: Ampelo_3-6-12h_rep2

source_name: 3-6-12 h (early germination), replicate 2


title: med3Δ YEPD replicate 1

description: Candida dubliniensis wild type versus med3Δ mutant in YEPD medium


title: Ampelo_3-6-12h_rep3

source_name: 3-6-12 h (early germination), replicate 3


title: CP midgut 6 hours

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

description: Transgenic mosquito midguts were collected 6 hours after a blood meal (Cy5) and compared to wild-type mosquito midguts collected at the same time (Cy3). Raw data files are from 3 independent biological replicates and 1 pseudoreplicate (Contains an equal amount of Cy-5-labeled probe from each experimental biological replicate).

hyb_protocol: Probes prepared from the RNA of transgenic mosquitoes (labeled with Cy5-dUTP fluorescent nucleotides) were co-hybridized with probes prepared from the RNA obtained from wild-type mosquitoes (labeled with Cy3-dUTP fluorescent nucleotides).

scan_protocol: Axon GenePix 4200 AL scanner at 2 um resolution

data_processing: Background-subtracted median fluorescent values were normalized with the LOWESS normalization method, and Cy5/Cy3 ratios from replicate assays were subjected to t-tests at a significance level of p<0.05 using TIGR MIDAS and MeV software. Expression data from replicate assays were averaged with the GEPAS microarray software (http://www.gepas.org) and logarithm (base 2)-transformed.

organism: Anopheles stephensi

source_name: CP line midgut 6 hr

label_protocol: The Cy5- and Cy3-labeled probes were synthesized using the Low RNA Input Fluorescent Linear Amplification Kit from Agilent Technologies (Santa Clara, California, USA).

growth_protocol: A. stephesni Liston, VG1 and CP15 strain mosquitoes (Dong et. al 2011) were reared at 27°C in 70% humidity, and adults were maintained on a 10% sucrose solution on a 12-h light/dark cycle, according to standard rearing conditions.

extract_protocol: 5 midguts or fat bodies were collected from each treatment type.  RNA was extracted from dissected tissues using an RNeasy kit (Qiagen) according to standard methodology.

treatment_protocol: A. stephensi Liston, VG1 and CP15 mosquitoes were provided a blood meal.  6, 12 and 18 hours after feeding mosquitoes were aneshtetized on ice and midguts or carcasses were collected.

value: midgut

tag: time

value: 6 hours pbm

source_name: WT midgut

value: Wild-type


title: CP midgut 12 hours

description: Transgenic mosquito midguts were collected 12 hours after a blood meal (Cy5) and compared to wild-type mosquito midguts collected at the same time (Cy3). Raw data files are from 3 independent biological replicates and 1 pseudoreplicate (Contains an equal amount of Cy-5-labeled probe from each experimental biological replicate).

source_name: CP line midgut 12 hr

value: 12 hours pbm


title: Ampelo_0h_rep2

source_name: untreated control replicate 2

growth_protocol: A. quisqualis was grown on potato dextrose agar (Oxoid, UK) at 25 °C.

treatment_protocol: Total RNA was extracted from conidia directly collected from A. quisqualis cultures on Petri dishes (0 h). To collect A. quisqualis conidia, 21-day-old culture plates were flooded with 10 ml of sterile distilled water, and then left for 1 h while conidia oozed out of the pycnidia (Gu and Ko, 1997). Conidial suspensions were adjusted to a final concentration of 4 × 106 conidia/ml.


title: VG fat body 18 hours

description: Transgenic mosquito fat bodies were collected 18 hours after a blood meal (Cy5) and compared to wild-type mosquito fat bodies collected at the same time (Cy3). Raw data files are from 3 independent biological replicates and 1 pseudoreplicate (Contains an equal amount of Cy-5-labeled probe from each experimental biological replicate).

source_name: 18 hr

value: fat body

value: 18 hours pbm

source_name: WT fat body


title: Ampelo_0h_rep3

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

source_name: untreated control replicate 3


title: SLE85.Treg

status: Public on Jul 10 2014

city: Huntsville

first: Devin

last: Absher

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Illumina HumanMethylation450

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Illumina Genome Studio
Unmethylated (A) and methylated (B) signal intensities

source_name: CD25+CD127- Regulatory T-cells

label_protocol: Standard Illumina Protocol

extract_protocol: QIAGEN DNAeasy; Zymo EZ DNA

value: CD25+CD127- Regulatory T-cells

tag: disease state

value: Systemic Lupus Erythematosus


title: X4230.Treg

description: Illumina HumanMethylation450

value: control


title: Ampelo_0h_rep1

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 µg ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST was solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

source_name: untreated control replicate 1


title: VG fat body 12 hours

description: Transgenic mosquito fat bodies were collected 12 hours after a blood meal (Cy5) and compared to wild-type mosquito fat bodies collected at the same time (Cy3). Raw data files are from 3 independent biological replicates and 1 pseudoreplicate (Contains an equal amount of Cy-5-labeled probe from each experimental biological replicate).

source_name: VG line fat body 12 hr


title: SLE1078.Treg

description: Illumina HumanMethylation450


title: X11864.Treg

description: Illumina HumanMethylation450


title: X1501.Treg

description: Illumina HumanMethylation450


title: X5129.Treg

description: Illumina HumanMethylation450


title: SLE10985.Treg

description: Illumina HumanMethylation450


title: SLE11867.Treg

description: Illumina HumanMethylation450


title: X11792.Treg

description: Illumina HumanMethylation450


title: SLE11862.Treg

description: Illumina HumanMethylation450


title: X11866.Treg

description: Illumina HumanMethylation450


title: SLE5323.Treg

description: Illumina HumanMethylation450


title: X4788.Treg

description: Illumina HumanMethylation450


title: SLE1709.Treg

description: Illumina HumanMethylation450


title: SLE5428.Treg

description: Illumina HumanMethylation450


title: SLE11689.Treg

description: Illumina HumanMethylation450


title: SLE11746.Treg

description: Illumina HumanMethylation450


title: SLE10015.Treg

description: Illumina HumanMethylation450


title: X11861.Treg

description: Illumina HumanMethylation450


title: SLE11845.Treg

description: Illumina HumanMethylation450


title: X4850.Treg

description: Illumina HumanMethylation450


title: SLE4050.Treg

description: Illumina HumanMethylation450


title: X11847.Treg

description: Illumina HumanMethylation450


title: X11835.Treg

description: Illumina HumanMethylation450


title: X10576.Treg

description: Illumina HumanMethylation450


title: SLE6.Treg

description: Illumina HumanMethylation450


title: X11836.Treg

description: Illumina HumanMethylation450


title: SLE10011.Treg

description: Illumina HumanMethylation450


title: SLE1752.Treg

description: Illumina HumanMethylation450


title: SLE4555.Treg

description: Illumina HumanMethylation450


title: X4003.Treg

description: Illumina HumanMethylation450


title: SLE10786.Treg

description: Illumina HumanMethylation450


title: X4010.Treg

description: Illumina HumanMethylation450


title: X5250.Treg

description: Illumina HumanMethylation450


title: SLE4034.Treg

description: Illumina HumanMethylation450


title: SLE7.Treg

description: Illumina HumanMethylation450


title: SLE5301.Treg

description: Illumina HumanMethylation450


title: SLE1846.Treg

description: Illumina HumanMethylation450


title: X3541.Treg

description: Illumina HumanMethylation450


title: SLE1808.Treg

description: Illumina HumanMethylation450


title: SLE11862.Tnaive

description: Illumina HumanMethylation450

source_name: CD45RO-RA+ Naive T-cells

value: CD45RO-RA+ Naive T-cells


title: SLE11689.Tnaive

description: Illumina HumanMethylation450


title: SLE1169.Tnaive

description: Illumina HumanMethylation450


title: X3761.Treg

description: Illumina HumanMethylation450


title: X4788.Tnaive

description: Illumina HumanMethylation450


title: SLE4091.Tnaive

description: Illumina HumanMethylation450


title: SLE10015.Tnaive

description: Illumina HumanMethylation450


title: SLE4050.Tnaive

description: Illumina HumanMethylation450


title: SLE3686.Treg

description: Illumina HumanMethylation450


title: SLE1709.Tnaive

description: Illumina HumanMethylation450


title: X11836.Tnaive

description: Illumina HumanMethylation450


title: X4850.Tnaive

description: Illumina HumanMethylation450


title: X5129.Tnaive

description: Illumina HumanMethylation450


title: SLE11867.Tnaive

description: Illumina HumanMethylation450


title: SLE6.Tnaive

description: Illumina HumanMethylation450


title: SLE85.Tnaive

description: Illumina HumanMethylation450


title: X11792.Tnaive

description: Illumina HumanMethylation450


title: SLE11845.Tnaive

description: Illumina HumanMethylation450


title: X11835.Tnaive

description: Illumina HumanMethylation450


title: SLE10011.Tnaive

description: Illumina HumanMethylation450


title: SLE5323.Tnaive

description: Illumina HumanMethylation450


title: X11861.Tnaive

description: Illumina HumanMethylation450


title: X11847.Tnaive

description: Illumina HumanMethylation450


title: SLE10786.Tnaive

description: Illumina HumanMethylation450


title: X11864.Tnaive

description: Illumina HumanMethylation450


title: SLE11746.Tnaive

description: Illumina HumanMethylation450


title: SLE1808.Tnaive

description: Illumina HumanMethylation450


title: X3761.Tnaive

description: Illumina HumanMethylation450


title: SLE5428.Tnaive

description: Illumina HumanMethylation450


title: SLE3686.Tnaive

description: Illumina HumanMethylation450


title: SLE4034.Tnaive

description: Illumina HumanMethylation450


title: X4230.Tnaive

description: Illumina HumanMethylation450


title: X4010.Tnaive

description: Illumina HumanMethylation450


title: SLE5301.Tnaive

description: Illumina HumanMethylation450


title: X10576.Tnaive

description: Illumina HumanMethylation450


title: SLE1078.Tnaive

description: Illumina HumanMethylation450


title: SLE10985.Tnaive

description: Illumina HumanMethylation450


title: SLE7.Tnaive

description: Illumina HumanMethylation450


title: SLE4555.Tnaive

description: Illumina HumanMethylation450


title: X5250.Tnaive

description: Illumina HumanMethylation450


title: X4003.Tnaive

description: Illumina HumanMethylation450


title: SLE1846.Tnaive

description: Illumina HumanMethylation450


title: X3541.Tnaive

description: Illumina HumanMethylation450


title: X11866.Tnaive

description: Illumina HumanMethylation450


title: X4230.Tmem

description: Illumina HumanMethylation450

source_name: CD45RO+RA- Memory T-cells

value: CD45RO+RA- Memory T-cells


title: SLE1078.Tmem

description: Illumina HumanMethylation450


title: SLE10985.Tmem

description: Illumina HumanMethylation450


title: SLE4091.Tmem

description: Illumina HumanMethylation450


title: SLE5428.Tmem

description: Illumina HumanMethylation450


title: SLE4050.Tmem

description: Illumina HumanMethylation450


title: SLE1169.Tmem

description: Illumina HumanMethylation450


title: SLE11862.Tmem

description: Illumina HumanMethylation450


title: X11864.Tmem

description: Illumina HumanMethylation450


title: SLE85.Tmem

description: Illumina HumanMethylation450


title: X11861.Tmem

description: Illumina HumanMethylation450


title: SLE6.Tmem

description: Illumina HumanMethylation450


title: SLE11867.Tmem

description: Illumina HumanMethylation450


title: SLE11746.Tmem

description: Illumina HumanMethylation450


title: SLE10015.Tmem

description: Illumina HumanMethylation450


title: X11792.Tmem

description: Illumina HumanMethylation450


title: SLE5323.Tmem

description: Illumina HumanMethylation450


title: X4788.Tmem

description: Illumina HumanMethylation450


title: X11847.Tmem

description: Illumina HumanMethylation450


title: SLE1709.Tmem

description: Illumina HumanMethylation450


title: X4850.Tmem

description: Illumina HumanMethylation450


title: X11866.Tmem

description: Illumina HumanMethylation450


title: X5250.Tmem

description: Illumina HumanMethylation450


title: X10576.Tmem

description: Illumina HumanMethylation450


title: SLE11845.Tmem

description: Illumina HumanMethylation450


title: X11836.Tmem

description: Illumina HumanMethylation450


title: SLE1808.Tmem

description: Illumina HumanMethylation450


title: SLE4555.Tmem

description: Illumina HumanMethylation450


title: X11835.Tmem

description: Illumina HumanMethylation450


title: SLE4034.Tmem

description: Illumina HumanMethylation450


title: SLE11689.Tmem

description: Illumina HumanMethylation450


title: X4010.Tmem

description: Illumina HumanMethylation450


title: X3541.Tmem

description: Illumina HumanMethylation450


title: SLE10786.Tmem

description: Illumina HumanMethylation450


title: X5129.Tmem

description: Illumina HumanMethylation450


title: SLE10011.Tmem

description: Illumina HumanMethylation450


title: SLE1846.Tmem

description: Illumina HumanMethylation450


title: SLE10985.CD4

description: Illumina HumanMethylation450

source_name: CD4+ T-cells

value: CD4+ T-cells


title: X5129.CD4

description: Illumina HumanMethylation450


title: SLE5301.Tmem

description: Illumina HumanMethylation450


title: SLE11867.CD4

description: Illumina HumanMethylation450


title: SLE7.Tmem

description: Illumina HumanMethylation450


title: SLE4091.CD4

description: Illumina HumanMethylation450


title: SLE1169.CD4

description: Illumina HumanMethylation450


title: X4850.CD4

description: Illumina HumanMethylation450


title: SLE10015.CD4

description: Illumina HumanMethylation450


title: X11866.CD4

description: Illumina HumanMethylation450


title: X1501.R2.CD4

description: Illumina HumanMethylation450


title: SLE11689.CD4

description: Illumina HumanMethylation450


title: SLE5323.CD4

description: Illumina HumanMethylation450


title: SLE3686.Tmem

description: Illumina HumanMethylation450


title: X11835.CD4

description: Illumina HumanMethylation450


title: SLE1709.CD4

description: Illumina HumanMethylation450


title: SLE11845.CD4

description: Illumina HumanMethylation450


title: X3761.Tmem

description: Illumina HumanMethylation450


title: SLE10011.R2.CD4

description: Illumina HumanMethylation450


title: SLE1752.Tmem

description: Illumina HumanMethylation450


title: X4230.CD4

description: Illumina HumanMethylation450


title: X11847.CD4

description: Illumina HumanMethylation450


title: SLE11862.CD4

description: Illumina HumanMethylation450


title: SLE1078.CD4

description: Illumina HumanMethylation450


title: SLE6.CD4

description: Illumina HumanMethylation450


title: SLE85.CD4

description: Illumina HumanMethylation450


title: X4788.CD4

description: Illumina HumanMethylation450


title: SLE4050.CD4

description: Illumina HumanMethylation450


title: SLE11746.CD4

description: Illumina HumanMethylation450


title: X11864.CD4

description: Illumina HumanMethylation450


title: X11861.CD4

description: Illumina HumanMethylation450


title: X11792.CD4

description: Illumina HumanMethylation450


title: SLE10786.CD4

description: Illumina HumanMethylation450


title: X11836.CD4

description: Illumina HumanMethylation450


title: SLE4555.CD4

description: Illumina HumanMethylation450


title: SLE5428.CD4

description: Illumina HumanMethylation450


title: X5250.CD4

description: Illumina HumanMethylation450


title: X3541.CD4

description: Illumina HumanMethylation450


title: X4010.R2.CD4

description: Illumina HumanMethylation450


title: SLE1808.CD4

description: Illumina HumanMethylation450


title: X3761.CD4

description: Illumina HumanMethylation450


title: X4010.CD19

description: Illumina HumanMethylation450

source_name: CD19+ B-Cells

value: CD19+ B-Cells


title: SLE3686.R2.CD4

description: Illumina HumanMethylation450


title: X1451.CD19

description: Illumina HumanMethylation450


title: SLE11546.CD19

description: Illumina HumanMethylation450


title: X4492.CD19

description: Illumina HumanMethylation450


title: SLE4034.CD4

description: Illumina HumanMethylation450


title: SLE4440.CD19

description: Illumina HumanMethylation450


title: X10576.R2.CD4

description: Illumina HumanMethylation450


title: SLE5301.CD4

description: Illumina HumanMethylation450


title: X1690.CD19

description: Illumina HumanMethylation450


title: SLE7.CD4

description: Illumina HumanMethylation450


title: X11301.CD19

description: Illumina HumanMethylation450


title: X4003.CD4

description: Illumina HumanMethylation450


title: SLE1846.CD4

description: Illumina HumanMethylation450


title: X1433.CD19

description: Illumina HumanMethylation450


title: SLE1752.CD4

description: Illumina HumanMethylation450


title: X11471.CD19

description: Illumina HumanMethylation450


title: X11080.CD19

description: Illumina HumanMethylation450


title: SLE10643.CD19

description: Illumina HumanMethylation450


title: X11579.CD19

description: Illumina HumanMethylation450


title: X11571.CD19

description: Illumina HumanMethylation450


title: X1501.CD19

description: Illumina HumanMethylation450


title: SLE1120.CD19

description: Illumina HumanMethylation450


title: SLE5024.CD19

description: Illumina HumanMethylation450


title: X11570.CD19

description: Illumina HumanMethylation450


title: X11561.CD19

description: Illumina HumanMethylation450


title: SLE3686.CD19

description: Illumina HumanMethylation450


title: SLE11440.T2.CD19

description: Illumina HumanMethylation450


title: SLE1182.CD19

description: Illumina HumanMethylation450


title: SLE2534.CD19

description: Illumina HumanMethylation450


title: SLE11352.CD19

description: Illumina HumanMethylation450


title: X11451.CD19

description: Illumina HumanMethylation450


title: X11534.CD19

description: Illumina HumanMethylation450


title: SLE11555.CD19

description: Illumina HumanMethylation450


title: X11550.CD19

description: Illumina HumanMethylation450


title: SLE10984.CD19

description: Illumina HumanMethylation450


title: X11556.CD19

description: Illumina HumanMethylation450


title: X11463.CD19

description: Illumina HumanMethylation450


title: X11575.CD19

description: Illumina HumanMethylation450


title: X11542.CD19

description: Illumina HumanMethylation450


title: X11578.CD19

description: Illumina HumanMethylation450


title: SLE1072.CD19

description: Illumina HumanMethylation450


title: X11558.CD19

description: Illumina HumanMethylation450


title: X11568.CD19

description: Illumina HumanMethylation450


title: SLE10011.CD19

description: Illumina HumanMethylation450


title: X11560.CD19

description: Illumina HumanMethylation450


title: X11559.CD19

description: Illumina HumanMethylation450


title: SLE11586.CD19

description: Illumina HumanMethylation450


title: SLE11530.CD19

description: Illumina HumanMethylation450


title: SLE11563.CD19

description: Illumina HumanMethylation450


title: SLE3667.CD19

description: Illumina HumanMethylation450


title: X11577.CD19

description: Illumina HumanMethylation450


title: X11533.CD19

description: Illumina HumanMethylation450


title: X11573.CD19

description: Illumina HumanMethylation450


title: SLE5424.CD19

description: Illumina HumanMethylation450


title: SLE10797.CD19

description: Illumina HumanMethylation450


title: X11538.CD19

description: Illumina HumanMethylation450


title: X11432.CD19

description: Illumina HumanMethylation450


title: SLE3696.CD19

description: Illumina HumanMethylation450


title: SLE11548.CD19

description: Illumina HumanMethylation450


title: X11310.CD19

description: Illumina HumanMethylation450


title: X11436.CD19

description: Illumina HumanMethylation450


title: X11314.CD19

description: Illumina HumanMethylation450


title: SLE11585.CD19

description: Illumina HumanMethylation450


title: X4184.CD19

description: Illumina HumanMethylation450


title: SLE11453.CD19

description: Illumina HumanMethylation450


title: SLE4048.T1.CD19

description: Illumina HumanMethylation450


title: X10943.CD19

description: Illumina HumanMethylation450


title: SLE11473.CD19

description: Illumina HumanMethylation450


title: SLE10593.CD19

description: Illumina HumanMethylation450


title: X10413.CD19

description: Illumina HumanMethylation450


title: X4665.CD19

description: Illumina HumanMethylation450


title: X11246.CD19

description: Illumina HumanMethylation450


title: SLE10347.CD19

description: Illumina HumanMethylation450


title: SLE4046.CD19

description: Illumina HumanMethylation450


title: SLE1627.CD19

description: Illumina HumanMethylation450


title: X11429.CD19

description: Illumina HumanMethylation450


title: SLE1296.CD19

description: Illumina HumanMethylation450


title: X11016.CD19

description: Illumina HumanMethylation450


title: X11394.CD19

description: Illumina HumanMethylation450


title: SLE92.CD19

description: Illumina HumanMethylation450


title: X4791.CD19

description: Illumina HumanMethylation450


title: SLE4042.CD19

description: Illumina HumanMethylation450


title: X4996.CD19

description: Illumina HumanMethylation450


title: SLE10374.CD19

description: Illumina HumanMethylation450


title: SLE4090.CD19

description: Illumina HumanMethylation450


title: X11369.CD19

description: Illumina HumanMethylation450


title: SLE11440.T1.CD19

description: Illumina HumanMethylation450


title: X10576.CD19

description: Illumina HumanMethylation450


title: X10450.CD19

description: Illumina HumanMethylation450


title: SLE11439.CD19

description: Illumina HumanMethylation450


title: SLE11445.CD19

description: Illumina HumanMethylation450


title: SLE1190.T1.CD19

description: Illumina HumanMethylation450


title: X3755.CD19

description: Illumina HumanMethylation450


title: SLE1167.CD19

description: Illumina HumanMethylation450


title: X10412.CD19

description: Illumina HumanMethylation450


title: X10414.CD19

description: Illumina HumanMethylation450


title: SLE10495.CD19

description: Illumina HumanMethylation450


title: X11423.CD19

description: Illumina HumanMethylation450


title: SLE11414.CD19

description: Illumina HumanMethylation450


title: X11406.CD19

description: Illumina HumanMethylation450


title: X4136.CD19

description: Illumina HumanMethylation450


title: SLE5274.CD19

description: Illumina HumanMethylation450


title: SLE10024.CD19

description: Illumina HumanMethylation450


title: X10897.CD19

description: Illumina HumanMethylation450


title: X1501.R1.CD4

description: Illumina HumanMethylation450


title: X11301.CD4

description: Illumina HumanMethylation450


title: SLE4097.CD19

description: Illumina HumanMethylation450


title: SLE1796.CD19

description: Illumina HumanMethylation450


title: X4122.CD19

description: Illumina HumanMethylation450


title: X11560.CD4

description: Illumina HumanMethylation450


title: SLE4440.CD4

description: Illumina HumanMethylation450


title: X4492.CD4

description: Illumina HumanMethylation450


title: SLE11476.CD19

description: Illumina HumanMethylation450


title: X11080.CD4

description: Illumina HumanMethylation450


title: SLE11546.CD4

description: Illumina HumanMethylation450


title: X11406.CD4

description: Illumina HumanMethylation450


title: X4010.R1.CD4

description: Illumina HumanMethylation450


title: SLE10643.CD4

description: Illumina HumanMethylation450


title: X11579.CD4

description: Illumina HumanMethylation450


title: X11561.CD4

description: Illumina HumanMethylation450


title: X11571.CD4

description: Illumina HumanMethylation450


title: SLE11352.CD4

description: Illumina HumanMethylation450


title: SLE11440.T2.CD4

description: Illumina HumanMethylation450


title: X4136.CD4

description: Illumina HumanMethylation450


title: X11570.CD4

description: Illumina HumanMethylation450


title: X11471.CD4

description: Illumina HumanMethylation450


title: X11534.CD4

description: Illumina HumanMethylation450


title: SLE1182.CD4

description: Illumina HumanMethylation450


title: SLE1120.CD4

description: Illumina HumanMethylation450


title: SLE11555.CD4

description: Illumina HumanMethylation450


title: X11542.CD4

description: Illumina HumanMethylation450


title: SLE11530.CD4

description: Illumina HumanMethylation450


title: X11463.CD4

description: Illumina HumanMethylation450


title: SLE2534.CD4

description: Illumina HumanMethylation450


title: X11556.CD4

description: Illumina HumanMethylation450


title: SLE1072.CD4

description: Illumina HumanMethylation450


title: SLE5422.CD4

description: Illumina HumanMethylation450


title: SLE4048.T2.CD4

description: Illumina HumanMethylation450


title: SLE3686.R1.CD4

description: Illumina HumanMethylation450


title: X11558.CD4

description: Illumina HumanMethylation450


title: X11575.CD4

description: Illumina HumanMethylation450


title: SLE11563.CD4

description: Illumina HumanMethylation450


title: SLE10984.CD4

description: Illumina HumanMethylation450


title: X11559.CD4

description: Illumina HumanMethylation450


title: X11451.CD4

description: Illumina HumanMethylation450


title: SLE1121.CD4

description: Illumina HumanMethylation450


title: X11578.CD4

description: Illumina HumanMethylation450


title: X11538.CD4

description: Illumina HumanMethylation450


title: SLE3667.CD4

description: Illumina HumanMethylation450


title: SLE10494.CD19

description: Illumina HumanMethylation450


title: X10436.CD19

description: Illumina HumanMethylation450


title: SLE11586.CD4

description: Illumina HumanMethylation450


title: X11577.CD4

description: Illumina HumanMethylation450


title: X11432.CD4

description: Illumina HumanMethylation450


title: SLE1190.T2.CD4

description: Illumina HumanMethylation450


title: SLE5424.CD4

description: Illumina HumanMethylation450


title: SLE11548.CD4

description: Illumina HumanMethylation450


title: SLE10797.CD4

description: Illumina HumanMethylation450


title: X11533.CD4

description: Illumina HumanMethylation450


title: SLE11585.CD4

description: Illumina HumanMethylation450


title: X11550.CD4

description: Illumina HumanMethylation450


title: X11573.CD4

description: Illumina HumanMethylation450


title: SLE10011.R1.CD4

description: Illumina HumanMethylation450


title: X11568.CD4

description: Illumina HumanMethylation450


title: X3968.CD19

description: Illumina HumanMethylation450


title: SLE5024.CD4

description: Illumina HumanMethylation450


title: X4184.CD4

description: Illumina HumanMethylation450


title: X11314.CD4

description: Illumina HumanMethylation450


title: SLE10593.CD4

description: Illumina HumanMethylation450


title: SLE10347.CD4

description: Illumina HumanMethylation450


title: X11246.CD4

description: Illumina HumanMethylation450


title: SLE4048.T1.CD4

description: Illumina HumanMethylation450


title: wildtype_Mycelia, PDB pH5.0-pH7.0, replicate 3

city: Cordoba

first: Carmen

last: Ruiz Roldan

address: Campus de Rabanales

department: Genetics

country: Spain

institute: University of Cordoba

description:
Mycelia shifted for 3 min to PDB pH 5.0 and then transferred to PDB pH 7.0 for 30 min
wt-3

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 110 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Fusarium oxysporum custom Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

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

organism: Fusarium oxysporum

source_name: Mycelia, PDB pH5.0-pH7.0, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One-Color Microarray-Based Gene Expression Analysis v 6.5 kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Freshly obtained microconidia were germinated for 14 hours (wt) or 20 hours (Δcon7-1 mutant) in PDB pH7.0.

extract_protocol: Total RNA was extracted from F. oxysporum mycelia following previously reported protocols (Chomczynski and Sacchi, 1987).

treatment_protocol: Mycelia were harvested by filtration, washed three times in sterile ddH2O, and transferred for 30 min to fresh PDB pH5.0, and then transferred to PDB pH7.0 for 30 min.

value: wt

value: mycelia


title: sample from recurrent patient (sample #20)

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: Labeled RNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by quantile normalization.

source_name: prostate cancer

label_protocol: 100 ng of total RNA from recurrent and non-recurrent samples were labeled with Cy3 by using Agilent miRNA labeling kit following manufacturer’s protocol.

extract_protocol: Trizol extraction of total RNA

value: prostate cancer

tag: disease status

value: recurrent


title: SLE3696.CD4

description: Illumina HumanMethylation450


title: X11429.CD4

description: Illumina HumanMethylation450


title: X4791.CD4

description: Illumina HumanMethylation450


title: X11394.CD4

description: Illumina HumanMethylation450


title: X10943.CD4

description: Illumina HumanMethylation450


title: sample from recurrent patient (sample #16)


title: X11310.CD4

description: Illumina HumanMethylation450


title: SLE11476.CD4

description: Illumina HumanMethylation450


title: X11016.CD4

description: Illumina HumanMethylation450


title: Δcon7-1mutant_Mycelia, PDB pH5.0-pH7.0, replicate 2

description:
Mycelia shifted for 3 min to PDB pH 5.0 and then transferred to PDB pH 7.0 for 30 min
Δcon7-1-2

source_name: Mycelia, PDB pH5.0-pH7.0, replicate 2

value: Δcon7-1 mutant


title: SLE1627.CD4

description: Illumina HumanMethylation450


title: SLE11473.CD4

description: Illumina HumanMethylation450


title: X10413.CD4

description: Illumina HumanMethylation450


title: SLE11453.CD4

description: Illumina HumanMethylation450


title: SLE10374.CD4

description: Illumina HumanMethylation450


title: sample from recurrent patient (sample #12)


title: SLE10494.CD4

description: Illumina HumanMethylation450


title: sample from recurrent patient (sample #8)


title: Δcon7-1mutant_Mycelia, PDB pH5.0-pH7.0, replicate 3

description:
Mycelia shifted for 3 min to PDB pH 5.0 and then transferred to PDB pH 7.0 for 30 min
Δcon7-1-3


title: SLE4046.CD4

description: Illumina HumanMethylation450


title: sample from recurrent patient (sample #11)


title: SLE4042.CD4

description: Illumina HumanMethylation450


title: X4665.CD4

description: Illumina HumanMethylation450


title: SLE1296.CD4

description: Illumina HumanMethylation450


title: SLE92.CD4

description: Illumina HumanMethylation450


title: sample from recurrent patient (sample #7)


title: sample from recurrent patient (sample #4)


title: X4996.CD4

description: Illumina HumanMethylation450


title: sample from recurrent patient (sample #15)


title: wildtype_Mycelia, PDB pH5.0-pH7.0, replicate 2

description:
Mycelia shifted for 3 min to PDB pH 5.0 and then transferred to PDB pH 7.0 for 30 min
wt-2


title: sample from recurrent patient (sample #14)


title: X11436.CD4

description: Illumina HumanMethylation450


title: sample from recurrent patient (sample #3)


title: sample from recurrent patient (sample #19)


title: sample from recurrent patient (sample #10)


title: X10576.R1.CD4

description: Illumina HumanMethylation450


title: sample from recurrent patient (sample #18)


title: wildtype_Mycelia, PDB pH5.0-pH7.0, replicate 1

description:
Mycelia shifted for 3 min to PDB pH 5.0 and then transferred to PDB pH 7.0 for 30 min
wt-1

source_name: Mycelia, PDB pH5.0-pH7.0, replicate 1


title: sample from recurrent patient (sample #6)


title: Δcon7-1mutant_Mycelia, PDB pH5.0-pH7.0, replicate 1

description:
Mycelia shifted for 3 min to PDB pH 5.0 and then transferred to PDB pH 7.0 for 30 min
Δcon7-1-1


title: MDAMB157

city: Boston

first: Sergey

last: Lezhnin

state: MA

address: 33 AVENUE LOUIS PASTEUR

department: Molecular Profiling

institute: Merck Research Laboratories

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45oC with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Standard RMA pipleline as implemented in APT (Affymetrix Power Tools software) using default settings

label: Biotin

source_name: breast cancer cell line MDAMB157

label_protocol: Nugen amplification protocol

growth_protocol: Cell lines were grown as recommended by vendor ATCC

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

treatment_protocol: No treatment

value: Breast Cancer


title: KPL1

source_name: breast cancer cell line KPL1


title: SVCT

source_name: breast cancer cell line SVCT

value: SVCT


title: X10436.CD4

description: Illumina HumanMethylation450


title: sample from recurrent patient (sample #17)


title: sample from recurrent patient (sample #2)


title: sample from recurrent patient (sample #13)


title: ZR7530

source_name: breast cancer cell line ZR7530


title: MB157

source_name: breast cancer cell line MB157


title: sample from recurrent patient (sample #9)


title: X10450.CD4

description: Illumina HumanMethylation450


title: HMT3522S1

source_name: breast cancer cell line HMT3522S1


title: M4A4

source_name: breast cancer cell line M4A4


title: sample from recurrent patient (sample #5)


title: sample from recurrent patient (sample #1)


title: sample from non-recurrent patient (sample #16)

value: non-recurrent


title: sample from non-recurrent patient (sample #12)


title: X11369.CD4

description: Illumina HumanMethylation450


title: MDAMB453

source_name: breast cancer cell line MDAMB453


title: sample from non-recurrent patient (sample #4)


title: X10897.CD4

description: Illumina HumanMethylation450


title: sample from non-recurrent patient (sample #8)


title: sample from non-recurrent patient (sample #20)


title: sample from non-recurrent patient (sample #15)


title: sample from non-recurrent patient (sample #19)


title: sample from non-recurrent patient (sample #3)


title: sample from non-recurrent patient (sample #7)


title: sample from non-recurrent patient (sample #6)


title: sample from non-recurrent patient (sample #18)


title: SLE11445.CD4

description: Illumina HumanMethylation450


title: HS605T

source_name: breast cancer cell line HS605T


title: sample from non-recurrent patient (sample #10)


title: HS739T

source_name: breast cancer cell line HS739T


title: MDAMB436

source_name: breast cancer cell line MDAMB436


title: HS578T

source_name: breast cancer cell line HS578T


title: sample from non-recurrent patient (sample #11)


title: SLE1796.CD4

description: Illumina HumanMethylation450

source_name: CD4+ T-cells


title: UACC893

source_name: breast cancer cell line UACC893


title: BT20

source_name: breast cancer cell line BT20


title: sample from non-recurrent patient (sample #2)

source_name: prostate cancer


title: SLE4090.CD4

description: Illumina HumanMethylation450


title: sample from non-recurrent patient (sample #13)


title: SLE11440.T1.CD4

description: Illumina HumanMethylation450


title: HCC38

source_name: breast cancer cell line HCC38


title: SLE1167.CD4

description: Illumina HumanMethylation450


title: sample from non-recurrent patient (sample #17)


title: sample from non-recurrent patient (sample #5)


title: sample from non-recurrent patient (sample #9)


title: HS579MG

source_name: breast cancer cell line HS579MG


title: PBMC_rabbit5_PMA+Iono_24hours

city: JOUY EN JOSAS

first: Vincent

last: Jacquier

address: INRA CEA GABI GIS Domaine de Vilvert bat 320

department: GABI

country: France

institute: INRA

hyb_protocol: For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 6.0 pmol Cy3/µg of cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent Fragmentation Buffer and 10x Agilent Blocking Agent and following the manufacturer’s instructions. Subsequently, 25 µl of 2x Agilent Hybridization Buffer were added to the fragmentation mixture and hybridized to a Rabbit Custom Gene Expression Microarrays (Agilent Technologies, design ID : 042421) for 17 hours at 65°C in a rotating Agilent hybridization oven (Agilent Technologies). After hybridization, microarrays were washed 1 minute at room temperature with the GE Wash Buffer 1 (Agilent Technologies) and 1 minute at 37°C using the GE Wash Buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Immediately after washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies), and using a scan protocol with a resolution of 3 µm and a dynamic range of 20 bit.

data_processing:
The resulting .tiff images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) and using the GE2_107_Sep09 protocol. Features flagged as ‘Feature Non-uniform’ outliers were excluded.
Data were normalized using intra-array median substraction and log2 transformation.

organism: Oryctolagus cuniculus

source_name: PBMC rabbit5 PMA+Ionomycin 24hours

label_protocol: Cyanine-3 (Cy3) labeled cRNAs were prepared from 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's protocol, and followed by an RNeasy column purification (Qiagen, Valencia, CA).  Specific activities and cRNA yields were checked with the NanoDrop ND-1000 spectrophotometer.

extract_protocol: RNAs were prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) and following the manufacturer's recommendations. The protocol included a DNase digestion step. RNAs were quantified using a NanoDrop-1000 spectrophotometer and their integrity was checked using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 5 x 10^5 PBMCs were suspended into RPMI 1640 medium (BioWhittaker, Belgium) and containing 200 mM/L of L-glutamine (Sigma-Aldrich, St. Louis, MO, USA), 10% heat inactivated FBS, 1% penicillin and streptomycin (Invitrogen, Life Technologies, Camarillo, CA, USA). PBMCs were stimulated or not stimulated with 1 ug/mL of LPS or a mixture of PMA (Sigma, France) at 10 ng/mL and ionomycin (Sigma, France) at 1 μg/mL. After 4hours to 24hours of incubation at 37°C and 5% CO2, cells were harvested for RNA extraction.

value: blood

value: Peripheral Blood Mononuclear Cell

tag: stimulation

value: PMA + Ionomycin

tag: time of stimulation

value: 24 hours


title: sample from non-recurrent patient (sample #1)


title: PBMC_rabbit5_Control_24hours

source_name: PBMC rabbit5 Control 24hours

value: Control


title: X10414.CD4

description: Illumina HumanMethylation450

value: control


title: X4122.CD4

description: Illumina HumanMethylation450


title: SLE11439.CD4

description: Illumina HumanMethylation450

value: Systemic Lupus Erythematosus


title: sample from non-recurrent patient (sample #14)


title: HCC1395

source_name: breast cancer cell line HCC1395


title: X10412.CD4

description: Illumina HumanMethylation450

value: CD4+ T-cells


title: PBMC_rabbit5_PMA+Iono_4hours

source_name: PBMC rabbit5 PMA+Ionomycin 4hours

value: 4 hours


title: VP229

source_name: breast cancer cell line VP229


title: CAL148

source_name: breast cancer cell line CAL148


title: X3968.CD4

description: Illumina HumanMethylation450


title: PBMC_rabbit5_LPS_24hours

source_name: PBMC rabbit5 LPS 24hours

value: LPS


title: PBMC_rabbit5_LPS_4hours

source_name: PBMC rabbit5 LPS 4hours


title: X11423.CD4

description: Illumina HumanMethylation450


title: ZR751

source_name: breast cancer cell line ZR751


title: PBMC_rabbit5_Control_4hours

source_name: PBMC rabbit5 Control 4hours


title: HCC1569

source_name: breast cancer cell line HCC1569


title: MDAMB468

source_name: breast cancer cell line MDAMB468


title: PBMC_rabbit4_PMA+Iono_24hours

source_name: PBMC rabbit4 PMA+Ionomycin 24hours


title: PBMC_rabbit4_Control_4hours

source_name: PBMC rabbit4 Control 4hours


title: PBMC_rabbit4_Control_24hours

source_name: PBMC rabbit4 Control 24hours


title: PBMC_rabbit4_LPS_24hours

source_name: PBMC rabbit4 LPS 24hours


title: PBMC_rabbit4_LPS_4hours

source_name: PBMC rabbit4 LPS 4hours


title: PBMC_rabbit4_PMA+Iono_4hours

source_name: PBMC rabbit4 PMA+Ionomycin 4hours


title: HCC1187

source_name: breast cancer cell line HCC1187


title: PBMC_rabbit2_Control_24hours

source_name: PBMC rabbit2 Control 24hours


title: SUM149PT

source_name: breast cancer cell line SUM149PT


title: HS362T

source_name: breast cancer cell line HS362T


title: PBMC_rabbit2_PMA+Iono_24hours

source_name: PBMC rabbit2 PMA+Ionomycin 24hours


title: FR2

source_name: breast cancer cell line FR2


title: EVSAT

source_name: breast cancer cell line EVSAT

value: EVSAT


title: HCC1143

source_name: breast cancer cell line HCC1143


title: SLE10024.CD4

description: Illumina HumanMethylation450

source_name: CD4+ T-cells


title: MDAMB175VII

source_name: breast cancer cell line MDAMB175VII


title: SLE4097.CD4

description: Illumina HumanMethylation450


title: EFM192B

source_name: breast cancer cell line EFM192B


title: PBMC_rabbit2_LPS_24hours

source_name: PBMC rabbit2 LPS 24hours


title: PBMC_rabbit2_Control_4hours

source_name: PBMC rabbit2 Control 4hours


title: SLE10495.CD4

description: Illumina HumanMethylation450


title: SLE1190.T1.CD4

description: Illumina HumanMethylation450


title: SLE11414.CD4

description: Illumina HumanMethylation450


title: MDAMB435S

source_name: breast cancer cell line MDAMB435S


title: SLE5274.CD4

description: Illumina HumanMethylation450


title: PBMC_rabbit2_PMA+Iono_4hours

source_name: PBMC rabbit2 PMA+Ionomycin 4hours


title: PBMC_rabbit1_Control_24hours

source_name: PBMC rabbit1 Control 24hours


title: PBMC_rabbit2_LPS_4hours

source_name: PBMC rabbit2 LPS 4hours


title: X4492.CD14

description: Illumina HumanMethylation450

source_name: CD14+ Monocytes

value: CD14+ Monocytes


title: EFM192C

source_name: breast cancer cell line EFM192C


title: X1501.CD14

description: Illumina HumanMethylation450


title: X3755.CD4

description: Illumina HumanMethylation450


title: MDAMB361

source_name: breast cancer cell line MDAMB361


title: PBMC_rabbit1_PMA+Iono_24hours

source_name: PBMC rabbit1 PMA+Ionomycin 24hours


title: HCC70

source_name: breast cancer cell line HCC70


title: MDAMB231

source_name: breast cancer cell line MDAMB231


title: CAL51

source_name: breast cancer cell line CAL51


title: X4136.CD14

description: Illumina HumanMethylation450


title: PBMC_rabbit1_Control_4hours

source_name: PBMC rabbit1 Control 4hours


title: X1433.CD14

description: Illumina HumanMethylation450


title: X1690.CD14

description: Illumina HumanMethylation450


title: XTW.CD14

description: Illumina HumanMethylation450


title: X11573.R2.CD14

description: Illumina HumanMethylation450


title: X11579.CD14

description: Illumina HumanMethylation450


title: SLE4440.CD14

description: Illumina HumanMethylation450


title: HMT3522T42

source_name: breast cancer cell line HMT3522T42


title: PBMC_rabbit1_PMA+Iono_4hours

source_name: PBMC rabbit1 PMA+Ionomycin 4hours


title: X1451.CD14

description: Illumina HumanMethylation450


title: VP267

source_name: breast cancer cell line VP267


title: PBMC_rabbit1_LPS_4hours

source_name: PBMC rabbit1 LPS 4hours


title: X11561.CD14

description: Illumina HumanMethylation450


title: AU565

source_name: breast cancer cell line AU565


title: SLE5024.CD14

description: Illumina HumanMethylation450


title: X11570.CD14

description: Illumina HumanMethylation450


title: SLE11440.T2.CD14

description: Illumina HumanMethylation450


title: NM2C5

source_name: breast cancer cell line NM2C5


title: COLO824

source_name: breast cancer cell line COLO824


title: OCUBM

source_name: breast cancer cell line OCUBM

value: OCUBM


title: CAL120

source_name: breast cancer cell line CAL120


title: MCF102A

source_name: breast cancer cell line MCF102A


title: DU4475

source_name: breast cancer cell line DU4475


title: SLE11555.CD14

description: Illumina HumanMethylation450

source_name: CD14+ Monocytes


title: BT549

source_name: breast cancer cell line BT549


title: EFM192A

source_name: breast cancer cell line EFM192A


title: MT3

source_name: breast cancer cell line MT3


title: HCC1937

source_name: breast cancer cell line HCC1937


title: CAMA1

source_name: breast cancer cell line CAMA1


title: SLE11352.CD14

description: Illumina HumanMethylation450


title: PBMC_rabbit1_LPS_24hours

source_name: PBMC rabbit1 LPS 24hours


title: MCF12A

source_name: breast cancer cell line MCF12A


title: SLE1182.CD14

description: Illumina HumanMethylation450


title: X11463.CD14

description: Illumina HumanMethylation450


title: OCUBF

source_name: breast cancer cell line OCUBF

value: OCUBF


title: SKBR3

source_name: breast cancer cell line SKBR3

value: Breast Cancer


title: SW527

source_name: breast cancer cell line SW527


title: HCC1954

source_name: breast cancer cell line HCC1954


title: SLE3686.CD14

description: Illumina HumanMethylation450


title: X11534.CD14

description: Illumina HumanMethylation450


title: X11542.CD14

description: Illumina HumanMethylation450


title: X11550.CD14

description: Illumina HumanMethylation450


title: SLE11563.CD14

description: Illumina HumanMethylation450


title: MFM223

source_name: breast cancer cell line MFM223


title: SLE4048.T2.CD14

description: Illumina HumanMethylation450


title: HCC1806

source_name: breast cancer cell line HCC1806


title: T47D

source_name: breast cancer cell line T47D


title: X11571.CD14

description: Illumina HumanMethylation450


title: SLE5422.CD14

description: Illumina HumanMethylation450


title: SLE2534.CD14

description: Illumina HumanMethylation450


title: X11556.CD14

description: Illumina HumanMethylation450


title: SLE10984.CD14

description: Illumina HumanMethylation450


title: X11575.CD14

description: Illumina HumanMethylation450


title: SLE11530.CD14

description: Illumina HumanMethylation450


title: X11558.CD14

description: Illumina HumanMethylation450


title: Mouse_macrophage_cell_line_J774_stimulated_with_C1q_whole_molecule_rep2

city: Notre Dame

first: Erliang

last: Zeng

state: IN

address: 384 Fitzpatrick Hall

institute: University of Notre Dame

hyb_protocol: Labeled product was resuspended in hybridization buffer containing alignment ologos and unique sample tracking controls, loaded onto a murine gene expression microarray designed by NimbleGen, and hybridized overnight.

scan_protocol: After extensive washing, the array microchips were dried and then scanned using a NimbleGen MS 200 Microarray Scanner.

data_processing: Array data was extracted and analyzed using NimbleSan software v2.5 (Roche NimbleGen, Inc.). The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5.

source_name: Mouse macrophage cell line (J774) stimulated with C1q (whole molecule)

label_protocol: Randomly selected RNA samples were analyzed with an Agilent 2100 Bioanalyser to verify sample integrity prior to labeling. cDNA was labeled with Cy3 using NimbleGen One-color DNA labeling kits according to manufacturer's instructions (Roche NimbleGen, Inc., Madison, WI), lyophilized, and stored at -20°C  overnight.

extract_protocol: The total RNA was isolated from mouse macrophages with Trizol (Sigma, St. Louis, MO) and was precipitated with sodium acetate and washed with ethanol to remove contaminants. Randomly selected RNA samples were analyzed with an Agilent 2100 Bioanalyser to verify sample integrity prior to cDNA synthesis. Double stranded cDNA was generated using the TransPlex Complete Whole Transcriptome Amplification Kit (Sigma, St. Louis, MO) according to the manufacturer's instructions and resulting product was precipitated with sodium acetate, washed with ethanol to remove residual primers and nucleotides, and stored at -20°C until labeled.

value: Mouse macrophage cell line (J774)


title: SLE3667.CD14

description: Illumina HumanMethylation450


title: SLE10643.CD14

description: Illumina HumanMethylation450


title: Mouse_macrophage_stimulated_with_C1q_whole_molecule_rep2

source_name: Mouse macrophage stimulated with C1q (whole molecule)

value: Mouse bone marrow macrophage


title: SLE11586.CD14

description: Illumina HumanMethylation450

source_name: CD14+ Monocytes


title: Mouse_macrophage_stimulated_with_C1q_whole_molecule_rep1


title: SLE1190.T2.CD14

description: Illumina HumanMethylation450


title: X11559.CD14

description: Illumina HumanMethylation450


title: X11568.CD14

description: Illumina HumanMethylation450


title: X11578.CD14

description: Illumina HumanMethylation450


title: SLE1121.CD14

description: Illumina HumanMethylation450


title: SLE10593.CD14

description: Illumina HumanMethylation450


title: X11573.R1.CD14

description: Illumina HumanMethylation450


title: Mouse_macrophage_stimulated_with_C1q_whole_molecule_rep3


title: X11538.CD14

description: Illumina HumanMethylation450


title: SLE11548.CD14

description: Illumina HumanMethylation450


title: X11533.CD14

description: Illumina HumanMethylation450


title: SLE10011.CD14

description: Illumina HumanMethylation450


title: SLE1072.CD14

description: Illumina HumanMethylation450


title: SLE5424.CD14

description: Illumina HumanMethylation450


title: SLE10797.CD14

description: Illumina HumanMethylation450


title: Mouse_macrophage_stimulated_with_C1qtail_tail_portion_of_C1q_protein_rep1

source_name: Mouse macrophage stimulated with C1qtail (tail portion of C1q protein)


title: X11432.CD14

description: Illumina HumanMethylation450


title: X11577.CD14

description: Illumina HumanMethylation450


title: SLE3696.CD14

description: Illumina HumanMethylation450


title: Mouse_macrophage_stimulated_with_heat_inactivated_C1q_control_rep1

source_name: Mouse macrophage stimulated with heat inactivated C1q (control)


title: X11560.CD14

description: Illumina HumanMethylation450


title: Mouse_macrophage_cell_line_J774_stimulated_with_C1q_whole_molecule_rep3


title: Mouse_macrophage_stimulated_with_C1qtail_tail_portion_of_C1q_protein_rep2


title: Mouse_macrophage_cell_line_J774_stimulated_with_C1q_whole_molecule_rep1


title: Mouse_macrophage_stimulated_with_C1qtail_tail_portion_of_C1q_protein_rep3


title: Mouse_macrophage_stimulated_with_heat_inactivated_C1q_control_rep2


title: OKF4 Primary

city: Vancouver

first: Christopher

middle: Trevor Daniel

last: Dickman

state: BC

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Center

description: Normal

hyb_protocol: Performed as per Agilent protocol

scan_protocol: Scanned using Axon GenePix 4000B scanners at 5um resolution.

data_processing: Array images normalized using GenePix Pro 6.1 software and each array was median normalized.

source_name: OKF4 Primary

label_protocol: Agilent Low Input Labeling Kit

extract_protocol: Total RNA was extracted using TRIZol protocol, followed by Dnase I treatment

tag: tissue of origin

value: Floor of Mouth

tag: source

value: Cell Line

value: Normal


title: Mouse_macrophage_stimulated_with_heat_inactivated_C1q_control_rep3


title: OKP7 Primary

description: Normal

source_name: OKP7 Primary

value: Soft Palate


title: OKF4 TERT

description: Immortalized Normal

source_name: OKF4 TERT


title: DOK

description: Dysplasia

source_name: DOK

value: Tongue

value: Dysplasia


title: OKF4 E6E7

description: Immortalized Normal

source_name: OKF4 E6E7


title: Scap_PN1_KO16

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Scap1/2 deletion from mouse whole lung at PN1

hyb_protocol: Based on Affymetrix protocols

scan_protocol: Based on Affymetrix protocols

data_processing:
Quantile normalized gene level expression values from Gene Spring
MoGene-1_0-st-v1.r4.pgf

source_name: Mouse lung KO

label_protocol: Based on Affymetrix protocols

growth_protocol: Mouse whole lung isolated from day 17.5, 18.5 and PN1 mouse embryos

extract_protocol: E17.5 and E18.5 mice were delivered by Cesarean section with anesthesia followed by exsanguination.  PN1 mice were taken on the day of birth and euthanized with pentobarbital followed by exsanguination.   .Phenotypes were manually identified as knock out or mutants.

treatment_protocol: Insig-/-, Scap-/-, control littermates

tag: tissue

value: Whole Lung

tag: genotype

value: Scap-/-


title: Scap_PN1_C15

description: Control from mouse whole lung at PN1

source_name: Mouse lung control

tag: age

value: Control


title: OKF6 E6E7

description: Immortalized Normal

source_name: OKF6 E6E7


title: Scap_PN1_KO18


title: OKF6 Tert 2

description: Immortalized Normal

source_name: OKF6 Tert 2


title: OKF6 Tert 1

description: Immortalized Normal

source_name: OKF6 Tert 1


title: Scap_PN1_KO17


title: Scap_PN1_C14

description: Control from mouse whole lung at PN1


title: Scap_PN1_C13

description: Control from mouse whole lung at PN1


title: OKP7 bmi Tert

description: Immortalized Normal

source_name: OKP7 bmi Tert


title: POE9n Tert

description: Immortalized Dysplasia

source_name: POE9n Tert


title: Scap_E18.5_KO12

description: Scap1/2 deletion from mouse whole lung at E18.5


title: WT-60_CuR1-60

city: Raleigh

first: Garrett

last: Wheaton

address: 840 Main Campus Dr. Rm 3304

department: Chemical Engineering

institute: North Carolina State University

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42°C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95°C in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42°C to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42°C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42°C for 4 min with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT for 4 min with 0.5X SSC w/ 0.2% SDS. 2 wash cycles at RT for 2 min each with 0.5X SSC. 1 wash cycle at RT for 1 min with 0.05X SSC.

scan_protocol: Images were aquired with a GenePix 4000B scanner (Molecular Devices) using 532 nm and 635 nm lasers simultaneously. An automatic photomultiplier (PMT) gain adjustment was used to balance the 532 nm and 635 nm channels prior to scanning the whole slide. A pixel size of 10 microns was selected for the image resolution. Separate images were saved for the 532 and 635 nm scans, and analyzed together using GenePix Pro (v6.0) software.

data_processing: Signals for each channel were obtained using GenePix Pro (v6.0) using circular features and were background subtracted using the median local intensity around the spot. Once all the slides were quantitated, data from the loop was analyzed with JMP Genomics 5.0 (SAS, NC), normalized using ANOVA to estimate the global fixed effects of dye & treatment and the random effects array and block followed by using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

label: Cy™3 dye (GE Healthcare)

organism: Metallosphaera sedula DSM 5348

source_name: Cell Pellet

label_protocol: Producing cDNA: In a sterile PCR tube add 20 ug RNA with 6 ug random primers. Then add nuclease free water so the volume is 10 uL. Incubate at 70°C for 10 min. Place tube on ice for 1 min. Add 8 uL of RT Master Mix (recipe below) to each tube and swirl to mix. Quick spin before incubation. RT Master Mix: 4uL 5X strand buffer, 1uL 0.1M DTT, 1uL dNTP mix (see below), 2uL superscript III Invitrogen. dNTP mix: 3uL dATP (100mM), 3uL dGTP (100mM), 3uL dCTP(100mM), 1.8uL dTTP (100mM), 2.4uL aa-dUTP(50mM) Ambion, 6.8uL nuclease free water. Incubate at 46°C for at least 3 hours. Hydrolyze RNA by adding 10uL 1N NaOH to each tube. To stop reaction add 10 uL 0.5M EDTA to each tube. Mix and incubate at 65°C for 15 min. Add 10uL 1N HCl to each tube neutralize reaction mix. Transfer samples into labeled tubes of appropriate sizes. Add five volumes PB Buffer (Qiagen) to each tube and mix well. Add 300 ul of RT product to a labeled Qiagen PCR cleanup column. Spin at 1,000 rpm for 15 sec., empty collection tube, and repeat until all of the solution has passed through the column. Complete wash One, add 750 ul of phosphate wash buffer (recipe below) to column and spin at 13,000 rpm for 1 min., empty tube. Complete wash Two, add 750 ul of phosphate wash buffer to column and spin at 13,000 rpm for 1 min., empty tube. Phosphate wash buffer: 0.1mL 1M KPO4( pH 8.5), 3.05mL autoclaved dH2O and 16.85mL 95% EtOH. Spin an additional 1 min. with the same collection tube and discard the flow through. Transfer to new 1.5 mL tube, add 60uL phosphate elution buffer to the membrane and incubate @ R. T. for 1 min. Spin at 13,000 rpm. Phosphate elution buffer: 4mM KPO4. Repeat phosphate elution into same tube using 60uL. Fluorescent Labeling: Dry all RT samples completely in speed vac. Resuspend each dried sample cDNA in 4.5 uL of 0.1M sodium carbonate buffer, pH 9.0. Mix up and down with pipette for good mixing. Dissolve and mix thoroughlythe Cy™ dye to be used with 20uL of DMSO. Tpically Cye dyes contain four applications in each vial. Mix 4.5 uL of dye with prepared cDNA sample. Incubate in the dark for 2 hour @ R.T. Mix RT-PCR products with 35uL 100mM NaOAc PH 5.2 and mix by vortexing. Mix with 250uL Qiagen Buffer PB and filter through spin columns (13,000 rpm). Wash spin column with 750 uL of Buffer PE (Qiagen). Spin an additional 1 min. with the same collection tube and discard the flow through. Elute labeled cDNA 2 times with 30 uL of EB Buffer (Qiagen). Combine different labeled probes Speed vacuum sample until dry (not too dry, i.e. don’t leave in speed vacuum for over 1 hour). Combine different labeled probes and speed vacuum sample until dry. Resuspend samples in 29uL sterilized dH2O.

growth_protocol: Metallosphaera cells inoculated at a density of 2.0x107 cells/mL and cultured aerobically in DSM88 medium adjusted to a pH of 2.0 using sulfuric acid, supplemented 0.05% (w/v) tryptone and 25 mg/L uracil, and incubated at 70°C in oil bath with a shaking rate of 100 rpm. Metallosphaera cells were challenged with 2 mM copper sulfate in mid log phase at a cell density of 1.0x108 cells/mL.

extract_protocol: Cells were cooled to T < 10°C using dry ice and ethanol mix and harvested by centrifugation (6080xg, 10 min at 4°C), washed with TE buffer, and pellets were stored at -80°C. Total RNA was isolated using a modified Trizol (Invitrogen) protocol in combination with an RNAeasy kit (Qiagen). RNA quality was determined by running it on 1% Agarose gel. The biological replicates were pooled prior to cDNA construction.

treatment_protocol: Harvest of copper challenged cells occurred after 60 minutes of shock at a density of 1.0x108 cells/mL.

tag: genotype/variation

value: wild type

tag: growth conditions

value: Heterotrophic growth with 0.2 wt% Yeast extract

value: 60 minutes post 2.0 mM copper challenge

label: Cy™5 dye (GE Healthcare)

organism: Metallosphaera sedula


title: WT-15_WT-60

treatment_protocol: Harvest of copper challenged cells occurred after 15  and 60 minutes of shock at a density of 1.0x108 cells/mL.

value: 15 minutes post 2.0 mM copper challenge


title: WT-15_CuR1-15

treatment_protocol: Harvest of copper challenged cells occurred after 15 minutes of shock at a density of 1.0x108 cells/mL.


title: WT_CuR1

label: Cy™3, Cy™5 dye (GE Healthcare)

growth_protocol: Metallosphaera cells inoculated at a density of 2.0x107 cells/mL and cultured aerobically in DSM88 medium adjusted to a pH of 2.0 using sulfuric acid, supplemented 0.05% (w/v) tryptone and 25 mg/L uracil, and incubated at 70°C in oil bath with a shaking rate of 100 rpm.

treatment_protocol: Harvest of cells occurred at a cell density of 1.0x108 cells/mL.

value: normal conditions


title: Scap_E18.5_KO11


title: CuR1-15_CuR1-60


title: Scap_E18.5_C9

description: Control from mouse whole lung at E18.5

source_name: Mouse lung Control


title: Scap_E17.5_KO4

description: Scap1/2 deletion from mouse whole lung at E17.5


title: Scap_E18.5_KO10


title: Scap_E18.5_C8

description: Control from mouse whole lung at E18.5


title: Scap_E17.5_KO6


title: SLE10347.CD14

description: Illumina HumanMethylation450

source_name: CD14+ Monocytes

value: CD14+ Monocytes

value: Systemic Lupus Erythematosus


title: Scap_E18.5_C7

description: Control from mouse whole lung at E18.5


title: Scap_E17.5_KO5


title: SLE11585.CD14

description: Illumina HumanMethylation450


title: Scap_E17.5_C3

description: Control from mouse whole lung at E17.5


title: Mesp1_H2BGFP+ cells at E6.5, Biological rep2

city: Bruxelles

first: Samira

last: Chabab

address: 808, Route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

description: Gene expression data from embryos at E6.5

hyb_protocol: Affymetrix MG-430 PM array strips were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual

scan_protocol: Arrays were scanned with GeneAtlasImaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)

source_name: Mouse Embryos

label_protocol: cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines.

extract_protocol: RNA isolation and cDNA amplification was performed as described by Gonzalez-Roca et al. (2010). In brief, 50 cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt).RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich). For monitoring amplification, SYBR Green was added to the reaction; it was stopped after 25 cycles when SYBR Green signal reached a plateau. cDNA was purified using Genelute PCR Clean-Up kit (Sigma Aldrich).

treatment_protocol: Mesp1-rtTA/Teto-H2B-GFP embryos were dissected in a dissection medium (DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS)). Cells were dissociated 3min at 37°C in Trypsin/EDTA (Tryspin 0.1%, EDTA 1mM) and resuspended into PBS supplemented with 10% FBS and 1/1000 of propidium iodide.  Living cells were selected by propidium iodide dye exclusion. Mesp1 expressing cells were sorted based on the expression of the GFP. Sorted cells were  collected into lysis buffer for RNA extraction.

tag: Stage

value: Gastrulating mouse embryos


title: Mesp1_H2BGFP- cells at E6.5, Biological rep2


title: Mesp1_H2BGFP- cells at E7.5, Biological rep2

description: Gene expression data from embryos at E7.5


title: Mesp1_H2BGFP- cells at E6.5, Biological rep1


title: Scap_E17.5_C1

description: Control from mouse whole lung at E17.5


title: Insig_E17.5_KO22

description: Insig1/2 deletion from mouse whole lung at E17.5

value: Insig-/-


title: Insig_E17.5_KO24


title: Mesp1_H2BGFP+ cells at E7.5, Biological rep2


title: Mesp1_H2BGFP+ cells at E7.5, Biological rep1


title: Mesp1_H2BGFP- cells at E7.5, Biological rep1


title: Mesp1_H2BGFP+ cells at E6.5, Biological rep1


title: Insig_E17.5_C19

description: Control from mouse whole lung at E17.5


title: Insig_E17.5_KO23


title: genomic DNA from peripheral whole blood Lean Sample 39

status: Public on Jul 09 2014

city: Uppsala

first: Markus

last: Sällman Almén

address: Box 593

department: Dept. of Neuroscience

country: Sweden

institute: Uppsala Universitet

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

scan_protocol: Arrays were imaged using Illumina's iScan reader using standard recommended Illumina scanner settings

data_processing: Genomestudio2009.2 toghether with the methylumi and limma packages from Bioconductor

label: Cy5 and Cy3

source_name: Lean individual of age 66 years

extract_protocol: genomic DNA was extracted from peripheral whole blood using phenol chloroform

tag: fto

value: AA

tag: bmi

tag: weight category

value: Lean


title: genomic DNA from peripheral whole blood Lean Sample 45

source_name: Lean individual of age 68 years


title: genomic DNA from peripheral whole blood Lean Sample 41

source_name: Lean individual of age 45 years


title: Scap_E17.5_C2

description: Control from mouse whole lung at E17.5


title: genomic DNA from peripheral whole blood Obese Sample 42

source_name: Obese individual of age 53 years

value: TT

value: Obese


title: Insig_E17.5_C21

description: Control from mouse whole lung at E17.5


title: Insig_E17.5_C20

description: Control from mouse whole lung at E17.5


title: genomic DNA from peripheral whole blood Obese Sample 38

source_name: Obese individual of age 70 years


title: genomic DNA from peripheral whole blood Lean Sample 46

source_name: Lean individual of age 53 years


title: ΔdosR/WT_Replicate2

city: Bronx

first: Michael

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

description: Biological Replicate 2

hyb_protocol: Hybrization was performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

scan_protocol: Slides were scanned using an Axon GenePix4000B microarray scanner

data_processing: Tiff images were quantified with Spotfinder software (TIGR), data normalization using total array intensity and LOWESS algorithm with  MIDAS software (TIGR)

organism: Mycolicibacterium smegmatis

source_name: in vitro batch culture

label_protocol: 10 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

growth_protocol: M. smegmatis was grown in Hartmans de Bont (HdB) minimal medium supplemented with  27 mM glycero in 120 ml sealed serum vials at 37°C with agitation (200 rpm).

extract_protocol: Samples were harvested using ice-cold glycerol-saline, cells were disrupted by bead-beating and total RNAwas extracted with TRIzol following manufacturer's instructions

treatment_protocol: M. smegmatis was grown in sealed serum vials and samples were withdrawn 10h after methylene blue decolorized.

value: ΔdosR

tag: stress

value: hypoxic atmosphere

tag: strain


title: ΔdosR/WT_Replicate3

description: Biological Replicate 3


title: ΔdosR/WT_Replicate1

description: Biological Replicate 1


title: ΔdosR/WT_Replicate4

description: Biological Replicate 4


title: genomic DNA from peripheral whole blood Lean Sample 43


title: genomic DNA from peripheral whole blood Lean Sample 40

source_name: Lean individual of age 62 years


title: genomic DNA from peripheral whole blood Obese Sample 44

source_name: Obese individual of age 48 years


title: genomic DNA from peripheral whole blood Obese Sample 35

source_name: Obese individual of age 57 years


title: genomic DNA from peripheral whole blood Lean Sample 34

source_name: Lean individual of age 67 years


title: genomic DNA from peripheral whole blood Obese Sample 31

source_name: Obese individual of age 45 years


title: genomic DNA from peripheral whole blood Lean Sample 32

source_name: Lean individual of age 47 years


title: genomic DNA from peripheral whole blood Obese Sample 36


title: genomic DNA from peripheral whole blood Obese Sample 37


title: genomic DNA from peripheral whole blood Lean Sample 33


title: genomic DNA from peripheral whole blood Lean Sample 30

source_name: Lean individual of age 69 years


title: genomic DNA from peripheral whole blood Obese Sample 29

source_name: Obese individual of age 52 years


title: genomic DNA from peripheral whole blood Obese Sample 27

source_name: Obese individual of age 64 years


title: genomic DNA from peripheral whole blood Lean Sample 28

source_name: Lean individual of age 61 years


title: genomic DNA from peripheral whole blood Lean Sample 26

source_name: Lean individual of age 59 years


title: genomic DNA from peripheral whole blood Lean Sample 22

source_name: Lean individual of age 41 years


title: genomic DNA from peripheral whole blood Obese Sample 15

source_name: Obese individual of age 43 years


title: genomic DNA from peripheral whole blood Obese Sample 20

source_name: Obese individual of age 51 years


title: genomic DNA from peripheral whole blood Lean Sample 25

source_name: Lean individual of age 51 years


title: genomic DNA from peripheral whole blood Lean Sample 10

source_name: Lean individual of age 55 years


title: genomic DNA from peripheral whole blood Obese Sample 14

source_name: Obese individual of age 62 years


title: genomic DNA from peripheral whole blood Obese Sample 17

source_name: Obese individual of age 58 years


title: genomic DNA from peripheral whole blood Obese Sample 11

source_name: Obese individual of age 69 years


title: genomic DNA from peripheral whole blood Obese Sample 12


title: genomic DNA from peripheral whole blood Obese Sample 8


title: genomic DNA from peripheral whole blood Lean Sample 19


title: genomic DNA from peripheral whole blood Lean Sample 24

source_name: Lean individual of age 43 years


title: genomic DNA from peripheral whole blood Obese Sample 23

source_name: Obese individual of age 42 years


title: genomic DNA from peripheral whole blood Obese Sample 21


title: genomic DNA from peripheral whole blood Obese Sample 18

source_name: Obese individual of age 54 years


title: genomic DNA from peripheral whole blood Obese Sample 7

source_name: Obese individual of age 56 years


title: genomic DNA from peripheral whole blood Obese Sample 13


title: genomic DNA from peripheral whole blood Obese Sample 5


title: genomic DNA from peripheral whole blood Lean Sample 1


title: genomic DNA from peripheral whole blood Lean Sample 9

source_name: Lean individual of age 46 years


title: genomic DNA from peripheral whole blood Lean Sample 6


title: genomic DNA from peripheral whole blood Obese Sample 2

source_name: Obese individual of age 50 years


title: genomic DNA from peripheral whole blood Obese Sample 4

source_name: Obese individual of age 53 years


title: HT115_WT_1

city: Manchester

first: Anna

last: Marusiak

address: Wilmslow Road

institute: CRUK Manchester Institute

description:
gene expression data after MLK4-WT induction in colon cancer cell lines harboring loss-of-function mutations in MLK4
repeat 1

hyb_protocol: Triplicate samples were hybridized in the oven at 45°C for 16 hrs with rotation at 60rpm on Affymetrix Human U133 Plus 2.0 array in Affymetrix GeneChip Hybridisation Oven 640. Washing and staining is carried out in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 with Autoloader Software used: Affymetrix GeneChip Command Console (version 4.0.0)

data_processing: The data was analysed using the method RMA implemented in the Affymetrix's tool 'apt-probeset-summarize'

source_name: cell line HT115

label_protocol: Amplified cDNA is produced from the total RNA samples using the Ovation Pico WTA System V2 (NuGEN Technologies, item 3302-60). The amplified cDNA is fragmented and labelled using the Encore Biotin Module (NuGEN Technologies, item 4200-60). A 5µg input is used.

growth_protocol: HCT15 and HT115 cells were cultured in RPMI supplemented with 10% FCS, 1% penicillin/streptomycin and 2 mM L-glutamine. Cell lines were obtained from ATCC.

extract_protocol: Cells were lysed using RLT buffer (Qiagen) and mRNA was isolated using Qiagen RNeasy Plus Mini Kit according to the manufacturer's instructions.

treatment_protocol: HCT15 and HT115 were split into 6-well plates and the next day cell lines were treated with tetracycline for 24 hours in order to induce MLK4 expression.

tag: cell line

tag: cell type

value: colorectal cancer


title: genomic DNA from peripheral whole blood Lean Sample 3

source_name: Lean individual of age 47 years


title: HT115_WT_2_Tet

description:
gene expression data after MLK4-WT induction in colon cancer cell lines harboring loss-of-function mutations in MLK4
repeat 2


title: HT115_WT_3

description:
gene expression data after MLK4-WT induction in colon cancer cell lines harboring loss-of-function mutations in MLK4
repeat 3


title: HT115_WT_1_Tet


title: genomic DNA from peripheral whole blood Lean Sample 16

source_name: Lean individual of age 58 years


title: cardiac left superior fat pads-infection with miR-206 overexpressed lentiviruses-2 weeks-rep1

city: Jinan

first: Yujiao

last: Zhang

state: Shandong province

address: Jingshi Road

department: Department of cardiology

institute: Qianfoshan Hospital affiliated to Shandong University

description: Equal quantities of RNAs from 3 dogs were mixed to generate one sample for each group to construct a small RNA library.

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

scan_protocol: GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method

organism: Canis lupus familiaris

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

growth_protocol: Animals were grown according to standard conditions.

extract_protocol: The total RNAs of each dog were extracted from the left superior fat pads area using TRIzol reagent (Invitrogen, CA, USA).Microarray-based mRNA expression profiling was performed using the Affymetrix Array (CA, USA).

value: left superior fat pads

tag: infection

value: miR-206 overexpressed lentiviruses


title: HT115_WT_2


title: HT115_314-3_Tet

description:
gene expression data after MLK4-E314K induction in colon cancer cell lines harboring loss-of-function mutations in MLK4 (control experiment)
repeat 3


title: HT115_WT_3_Tet


title: HT115_314-3


title: HT115_314-2

description:
gene expression data after MLK4-E314K induction in colon cancer cell lines harboring loss-of-function mutations in MLK4 (control experiment)
repeat 2


title: cardiac left superior fat pads-infection with control lentiviruses-rep1

source_name: cardiac left superior fat pads control

value: control lentivirus