title: Lung_AF2_24hr_rep1

first: Yanli

last: Zhang

state: BEIJING

address: No.5 Dongdansantiao

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

description: Gene expression after 24hr in AF control  (for inactivated virus group) injected mouse lung

hyb_protocol: 0.875 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F-014868) 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 (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 71x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and 10% for two seperate scanning procedures).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters(protocol GE1_105_Dec08 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Lung, 24hr, AF control for inactivated H5N1 virus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit purification (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Four-week-old BALB/c mice were intra-tracheally  inoculated with 106 TCID50 of live H5N1 virus or an identical volume of inactivated H5N1 virus , 106 TCID50 of live H1N1 virus, or allantoic fluid (AF)1 control for live virus,or AF2 control for inactivated H5N1 virus with a microsyringe. After 24 h, the mice were sacrificed. The mouse lung tissue was rapidly collected and preserved in liquid nitrogen prior to RNA extraction and purification.

value: Lung

value: male

value: 4 weeks


title: Lung_live H5N1_24hr_rep1

status: Public on Jan 12 2016

type: RNA

city: Beijing

country: China

description: Gene expression after 24hr in 10^6 TCID50 live H5N1 infected mouse lung

molecule: total RNA

organism: Mus musculus

source_name: Lung, 24hr, live H5N1 virus

tag: tissue

tag: gender

tag: age


title: C41T00643E

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

hyb_protocol: 600 ng labeled product was hybridized to slides using a NimbleGen Hybridization Kit (cat. no. 05583 934 001), then hybridized for 16 h at 42 degrees.

scan_protocol: Slides were scanned using a Roche NimbleGen MS 200 scanner and data extracted with NimbleScan v.2.6.

data_processing: Arrays were normalized using the RMA implementation of the R oligo software package (Irizarry et al. 2003)

organism: Homo sapiens

source_name: Carcinoma

label_protocol: Total RNA (150 ng) was processed using a Low Input Quick Amp WT Labeling Kit (Agilent)

extract_protocol:
RNA from clinical samples was isolated as follows. Large RNAs (>200 bases) were isolated from fresh frozen tissue sample using RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer´s instructions. The small RNAs (<200 bases) were recovered from the flow-through fraction using RNeasy Micro Kit together with the RNeasy MinElute spin columns (Qiagen)(described in the Supplementary Material). Total RNA from cell lines harvested with Qiazol (Qiagen) was purified using miRNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
RNA extracted from fresh frozen tissue

value: Carcinoma


title: Jmjd4 shRNA replicate 1_gene level

city: Worcester

first: Yu-Jie

last: Hu

state: MA

address: 55 Lake Avenue North

department: Cell & Developmental Biology

country: USA

institute: UMass Medical School

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: The labled mix was hybridized to Mouse Exon 1.0 ST Arrays (Affymetrix) in the GeneChip Hybridization Oven 640 (Affymetrix) overnight at the UMass Medical School Genomic Core Facility

scan_protocol: The arrays were scanned using the GeneChip Scanner 7G (Affymetrix)

data_processing: The probe cell intesity data was processed with Affymetrix Expression Console software to generate CHP files using the Robust Multichip Analysis (RMA)-sketch algorithm workflow.

label: biotin

source_name: NIH3T3 cell line_Jmjd4 shRNA

label_protocol: Single-stranded cDNA was synthesized from 500 ng RNA using the Ambion WT kit (Life Technologies) and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: The NIH3T3 cells were maintained in DMEM high glucose medium containing 10% calf serum and 100U/ml penicillin/streptomycin in a humidfied incubactor with 5% CO2 at 37oC.

extract_protocol: The cells were directly lysed by using Trizol reagent (Invitrogen). Total RNA was isolated from TRIzol lysates using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The cells were transduced with lenviral vectors encoding shRNAs for 48 hrs and subsequently selected in media containing 2.5 μg/ml puromycin for 7 days.

tag: cell line

tag: cell type

value: fibroblast


title: 16_Sc Glucose MDM33 uptags repl2

type: genomic

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

country: Germany

institute: University of Bayreuth

description: locus: uptags

hyb_protocol: Labelled Uptag and Downtag samples were incubated with blocking oligonucleotides as described in Pan et al. (2007) dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods 41(2): 206–221. Hybridization was carried out at 50°C using Agilent's blocking agent and Hi-RPM buffer; slides were washed using Agilent's Oligo aCGH Wash Buffer 1 and 2. Cyanine dye decomposition was inhibited using Agilent's Stabilization and Drying solution.

scan_protocol: Slides were scanned on a FLA8000 microarray scanner (Fujifilm) at 5 µm resolution in confocal mode.

data_processing: Spot intensities were calculated as 'median-trimmed mean densities', background intensities were calculated from selected spot groups ('dark corners' in the Agilent array) and used to correct spot intensities; the raw data of each Cy3 and Cy5 channels were normalized to a value of 147,680,000 (total intensity normalization);

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: plate cultures

label_protocol: Uptag and Downtag sequences were amplified and labelled by asymmetric PCR as described in Pan et al. (2007) dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods 41(2): 206–221;

growth_protocol: The pooled collection of deletion strains was grown in rich media (2% glucose, 2% peptone, 1% yeast extract) to middle-log phase. The pool was transformed with either pYX223 or pYX223-MDM33 using the LiAc/PEG method and after transformation the cells were plated on solid selection media (2% agar, 2% glucose, 0.67 % yeast nitrogen base without amino acids, 30 mg / l L-leucine, 30 mg / l L-lysine, 20 mg / l uracil). After 4 days of incubation at 30°C, transformants were washed off the plates with sterile 1x PBS. The pooled transformants were then plated on selective media (2% agar, 0.67 % yeast nitrogen base without amino acids, 30 mg / l L-leucine, 30 mg / l L-lysine, 20 mg / l uracil) containing either 2% glucose or 2% galactose. After 2 (glucose) or 4 (galactose) days of incubation at 30°C cells were washed off the agar plates with sterile 1xPBS.

extract_protocol: Genomic DNA was extracted using the 'NucleoMag 96 Plant' DNA isolation kit (Machery-Nagel, Dueren, Germany)

treatment_protocol: Cells were grown either on media containing 2% glucose (control condition) or 2% galactose (induction of MDM33 overexpression).

tag: strain

tag: knockout collection

value: YSC1054 Open Biosystems

tag: plasmid

tag: carbon source

value: Glucose


title: 18_Sc Glucose MDM33 downtags repl2

description: locus: downtags


title: C24T00569E


title: Lung_AF1_24hr_rep1

description: Gene expression after 24hr in AF control (for live virus group) injected mouse lung

source_name: Lung, 24hr, AF control for live virus


title: 17_Sc Glucose MDM33 uptags repl2

description: locus: uptags


title: Lung_inactivated H5N1_24hr_rep1

description: Gene expression after 24hr in same volume of inactivated H5N1 injected mouse lung

source_name: Lung, 24hr, inactivated H5N1


title: 15_Sc Glucose MDM33 downtags repl2

description: locus: downtags


title: C39T00726E

source_name: Adenoma

value: Adenoma


title: Lung_live H1N1_24hr_rep1

description: Gene expression after 24hr in 10^6 TCID50 live H1N1 infected mouse lung

source_name: Lung, 24hr, live H1N1 virus


title: C11T00015E


title: 14_Sc Galactose empty downtags repl2

description: locus: downtags

value: Galactose


title: Jmjd6 shRNA replicate 1_gene level

source_name: NIH3T3 cell line_Jmjd6 shRNA


title: C16T00333E


title: C21T00346E


title: Control shRNA replicate 1_gene level

source_name: NIH3T3 cell line_control shRNA


title: C15T00907E


title: Jmjd6 shRNA replicate 2_gene level


title: 13_Sc Galactose empty uptags repl2

description: locus: uptags


title: Control shRNA replicate 2_gene level


title: 7_Sc Glucose empty downtags repl1

description: locus: downtags


title: C17T00959E


title: 11_Sc Galactose MDM33 downtags repl2

description: locus: downtags


title: 12_Sc Galactose MDM33 uptags repl2

description: locus: uptags


title: Human_colon_PTK7_negative_replicate_2

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: Affymetrix Human PrimeView arrays were hybridized with 8 mg of labeled dsDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual

scan_protocol: Scanning was done on an Affymetrix  GeneChip Scanner 3000

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

source_name: Normal human colonic epithelial cells, PTK7 negative surface abundance

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

growth_protocol: Cells were directly derived from human tissue samples. No tissue culture was performed prior to RNA extraction from cells

extract_protocol: RNA was extracted from FACS sorted cells using Trizol/Chloroform extraction and purification was performed using the Qiagen RNA Mini Kit (Qiagen GmbH). cDNA amplification was performed as described in Gonzalez-Roca E et al. (Plos One, 2010). CDNA library was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2)

treatment_protocol: Cells were not treated prior to RNA extraction

tag: ptk7 surface abundance

value: PTK7 negative


title: 5_Sc Glucose empty uptags repl1

description: locus: uptags


title: 8_Sc Galactose empty downtags repl1

description: locus: downtags


title: 6_Sc Galactose empty uptags repl1

description: locus: uptags


title: 3_Sc Glucose MDM33 downtags repl1

description: locus: downtags


title: 9_Sc Glucose empty uptags repl2

description: locus: uptags


title: 2_Sc Galactose MDM33 uptags repl1

description: locus: uptags


title: Human_colon_PTK7_high_replicate_2

source_name: Normal human colonic epithelial cells, PTK7 high surface abundance

value: PTK7 high


title: 10_Sc Glucose empty downtags repl2

description: locus: downtags


title: 1_Sc Glucose MDM33 uptags repl1

description: locus: uptags


title: Human_colon_PTK7_medium_replicate_2

source_name: Normal human colonic epithelial cells, PTK7 medium surface abundance

value: PTK7 medium


title: 4_Sc Galactose MDM33 downtags repl1

description: locus: downtags


title: supply_Fe_PS3

status: Public on Jan 11 2016

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: Four micrograms of labelled aRNA were hybridized to the array according to the manufacturer’s recommendations (http://www.combimatrix.com/support_docs.htm). Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C. Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS) using 4 μg of labelled aRNA. 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), 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).

scan_protocol: The array was scanned with an Axon GenePix® 4400A scanner and GenePix Pro 7 software (MDS Analytical Technologies). Laser was set at 33. PMT gain was set at 500.

data_processing: Raw data was extracted using GenePix  Pro 7 software (MDS Analytical Technologies). Raw data were analyzed using the open source software of the Bioconductor project (www.bioconductor.org) ) with the statistical R programming language (www.r-project.org). Background adjustment, summarization and quantile normalization were performed using limma package (DOI: 10.2202/1544-6115.1027).

organism: Solanum lycopersicum

source_name: 1-w Fe-deficiency, 1-h-supply with Fe-PS

label_protocol: Total RNA (1 µg) was amplified and labelled using the RNA ampULSe kit (Kreatech).

growth_protocol: Tomato seedling were germinated for 6 days on filter paper moistened with 1 mM CaSO4 and then grown for 14 days in a continuously aerated nutrient solution (pH adjusted at 6.0 with 1 M KOH) as reported by Tomasi at al. (2009; DOI: 10.1007/s11104-009-0069-z) being exposed to 5 μM Fe (Fe-EDTA); The nutrient solutions were renewed every three days. The controlled climatic conditions were the following: day/night photoperiod, 16/8 h; light intensity, 220 μE m-2s-1; temperature (day/night) 25/20 °C; RH 70 to 80 %.

extract_protocol: Total RNA was isolated using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich).

treatment_protocol:
21-d-old-plants were transferred for a further week to a Fe-free nutrient solution (Fe-deficient; 0 μM) and, at end of this period, for 1 h in nutrient solution with 1 μM of Fe as Fe-WEHS (supply_Fe_WEHS), Fe citrate (supply_Fe_CITRATE) and Fe-PS (supply_Fe_PS). The nutrient solutions were renewed every three days.  The controlled climatic conditions were the following: day/night photoperiod, 16/8 h; light intensity, 220 μE m-2s-1; temperature (day/night) 25/20 °C; RH 70 to 80 %.
24 hours before harvesting, all nutrient solutions were renewed and the pH was adjusted at 7.5 with 10 mM Hepes-KOH. Roots were harvested five hours after the beginning of light phase.

tag: cultivar

value: Marmande superprecoce

value: roots


title: Human_colon_PTK7_medium_replicate_1


title: Depuration Du→Op (sample 62)

city: Québec

first: Berenice

last: BOUGAS

state: QC

address: 1030 avenue de la médecine, IBIS, Pavillon Marchand

department: Biology

country: Canada

institute: Laval university

description: Perca flavescens – Yellow perch

hyb_protocol: Microarray were hybridized using Cy3/Cy5 dyes (Genisphere) as detailed in http://web.uvic.ca/grasp/microarray/protocols/Genisphere_Array_50_Protocol_Revised_v.5.pdf

scan_protocol: Microarrays were scanned using a ScanArray scanner (Packard BioScience). Spots were localized and quantified with the QuantArray 3.0 software, using the histogram quantification method and keeping the mean value of intensity for each spot.

data_processing: Data were exported in text format and were analyzed using a mixed model ANOVA and the R/MAANOVA package (Kerr and Churchill 2000)

organism: Perca flavescens

source_name: fish from depuration experiment

label_protocol: For each sample, 12 µg total RNA was reverse-transcribed and the cDNA samples labeled using the Genisphere 3DNA Array 50 Kit, Invitrogen’s Superscript II retro-transcriptase and Cyanine3 and Cyanine5 fluorescent dyes (Genisphere), following the procedures described at http://genisphere.com/products/3dna-array-detection/support (Genisphere Array 50 Protocol)

extract_protocol: Total RNA was extracted with the PureLink TM Micro-to-Midi Total RNA Purification System Kit and then treated using Amplification Grade DNase I (3 unit/μl; Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Total RNA was stored in RNAse free water at -80 °C. Quality and integrity of the total RNA were controlled using an Experion Automated Electrophoresis Station and RNA HighSens Chips (Biorad, Hercules, CA).

tag: developmental stage

value: juvenile

tag: experiment

value: depuration experiment

tag: protocol

value: Du→Op

tag: cage status

value: Caged

value: Liver


title: Depuration Du→Du (sample 64)

description: Perca flavescens – Yellow perch

value: Du→Du


title: Depuration Du→Op (sample 63)

description: Perca flavescens – Yellow perch


title: Depuration Du→Du (sample 61)

description: Perca flavescens – Yellow perch


title: supply_Fe_CITRATE3

source_name: 1-w Fe-deficiency, 1-h-supply with Fe-CITRATE


title: supply_Fe_PS1


title: Human_colon_PTK7_low_replicate_1

source_name: Normal human colonic epithelial cells, PTK7 low surface abundance

value: PTK7 low


title: supply_Fe_PS2


title: supply_Fe_CITRATE1


title: supply_Fe_WEHS3

source_name: 1-w Fe-deficiency, 1-h-supply with Fe-WEHS


title: Depuration Du→Op (sample 58)

description: Perca flavescens – Yellow perch


title: Depuration Du→Op (sample 60)

description: Perca flavescens – Yellow perch


title: Depuration Du→Du (sample 59)

description: Perca flavescens – Yellow perch


title: supply_Fe_CITRATE2


title: Human_colon_PTK7_negative_replicate_1


title: Human_colon_PTK7_high_replicate_1


title: Depuration Du→Du (sample 56)

description: Perca flavescens – Yellow perch


title: Depuration Du→Du (sample 57)

description: Perca flavescens – Yellow perch


title: supply_Fe_WEHS1


title: Depuration Du→Op (sample 53)

description: Perca flavescens – Yellow perch


title: Depuration Du→Du (sample 54)

description: Perca flavescens – Yellow perch


title: Depuration Du→Op (sample 55)

description: Perca flavescens – Yellow perch


title: supply_Fe_WEHS2


title: Depuration Du→Du (sample 49)

description: Perca flavescens – Yellow perch


title: Depuration Du→Op (sample 52)

description: Perca flavescens – Yellow perch


title: Contamination Op→Du (sample 47)

description: Perca flavescens – Yellow perch

source_name: fish from contamination experiment

value: contamination experiment

value: Op→Du


title: Contamination Op→Op (sample 48)

description: Perca flavescens – Yellow perch

value: Op→Op


title: Depuration Du→Du (sample 51)

description: Perca flavescens – Yellow perch


title: Depuration Du→Op (sample 50)

description: Perca flavescens – Yellow perch


title: Contamination Op→Op (sample 43)

description: Perca flavescens – Yellow perch


title: Contamination Op→Op (sample 45)

description: Perca flavescens – Yellow perch


title: Contamination Op→Du (sample 44)

description: Perca flavescens – Yellow perch


title: Contamination Op→Du (sample 40)

description: Perca flavescens – Yellow perch


title: Contamination Op→Du (sample 37)

description: Perca flavescens – Yellow perch


title: Cases_rep2

city: Nanchang

first: Yanmei

last: Xu

state: Jiangxi

address: No.1 Min De Road

department: Department of Clinical Laboratory

institute: the Second Affiliated Hospital of Nanchang University

description:
sample pooled from 135 females and 65 males
8104411006_R06C01
Genomic DNA extracted from ITP patients was genotyped using Illumina HumanOmniZhongHua-8 v1.0 BeadChip array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from ITP patients and healthy subjects was genotyped using Illumina HumanOmniZhongHua-8 v1.0 BeadChip array

label: C-Bio and A-DNP

source_name: ITP

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA was extracted from EDTA-anticoagulated peripheral blood using a Qiagen DNA Isolation kit (QiagenDNA GmbH, Hilden, Germany) as instruction. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer,PicoGreen and agarose gel eletrophoresis.

value: peripheral blood

tag: group

value: Case

tag: pools

value: 200 ITP patients

value: mixed

tag: race

value: Han Chinese


title: Contamination Op→Du (sample 41)

description: Perca flavescens – Yellow perch

tag: tissue


title: Contamination Op→Op (sample 42)

description: Perca flavescens – Yellow perch


title: Contamination Op→Op (sample 39)

description: Perca flavescens – Yellow perch


title: C18T00845E

source_name: Carcinoma

value: Carcinoma


title: Contamination Op→Op (sample 36)

description: Perca flavescens – Yellow perch


title: Contamination Op→Du (sample 35)

description: Perca flavescens – Yellow perch


title: Controls_rep2

description:
sample pooled from 135 females and 65 males
8104411006_R08C01
Genomic DNA extracted from healthys was genotyped using Illumina HumanOmniZhongHua-8 v1.0 BeadChip array

source_name: Healthy subjects

value: Control

value: 200 healthy subjects (age-, sex, race-matched with cases)

tag: gender


title: Dufault cage Du→Du (sample 30)

description: Perca flavescens – Yellow perch

source_name: fish from cage experiment in Lake Dufault

value: juvenile

value: cage experiment in Lake Dufault


title: Contamination Op→Du (sample 34)

description: Perca flavescens – Yellow perch

value: Caged


title: Contamination Op→Op (sample 38)

description: Perca flavescens – Yellow perch

value: Liver


title: Contamination Op→Op (sample 33)

description: Perca flavescens – Yellow perch


title: Dufault noncage Du (sample 29)

description: Perca flavescens – Yellow perch

value: Du

value: Noncaged


title: Dufault cage Du→Du (sample 31)

description: Perca flavescens – Yellow perch

value: Du→Du


title: Dufault noncage Du (sample 32)

description: Perca flavescens – Yellow perch


title: Dufault noncage Du (sample 27)

description: Perca flavescens – Yellow perch


title: Dufault cage Du→Du (sample 25)

description: Perca flavescens – Yellow perch


title: Dufault noncage Du (sample 24)

description: Perca flavescens – Yellow perch


title: Dufault cage Du→Du (sample 28)

description: Perca flavescens – Yellow perch


title: Dufault cage Du→Du (sample 20)

description: Perca flavescens – Yellow perch


title: Dufault noncage Du (sample 26)

description: Perca flavescens – Yellow perch


title: Dufault cage Du→Du (sample 23)

description: Perca flavescens – Yellow perch


title: Human_colon_PTK7_low_replicate_2

value: PTK7 low


title: Dufault noncage Du (sample 22)

description: Perca flavescens – Yellow perch


title: Dufault noncage Du (sample 19)

description: Perca flavescens – Yellow perch


title: Controls_rep1

description:
sample pooled from 135 females and 65 males
8104411006_R07C01
Genomic DNA extracted from healthys was genotyped using Illumina HumanOmniZhongHua-8 v1.0 BeadChip array


title: Dufault noncage Du (sample 17)

description: Perca flavescens – Yellow perch


title: Opasatica noncage Op (sample 16)

description: Perca flavescens – Yellow perch

source_name: fish from cage experiment in Lake Opasatica

value: cage experiment in Lake Opasatica

value: Op


title: Opasatica cage Op→Op (sample 14)

description: Perca flavescens – Yellow perch

value: Op→Op


title: Opasatica cage Op→Op (sample 15)

description: Perca flavescens – Yellow perch


title: Dufault cage Du→Du (sample 21)

description: Perca flavescens – Yellow perch


title: Opasatica noncage Op (sample 10)

description: Perca flavescens – Yellow perch


title: Opasatica noncage Op (sample 11)

description: Perca flavescens – Yellow perch


title: Opasatica cage Op→Op (sample 8)

description: Perca flavescens – Yellow perch


title: Opasatica noncage Op (sample 7)

description: Perca flavescens – Yellow perch


title: Opasatica noncage Op (sample 6)

description: Perca flavescens – Yellow perch


title: Dufault cage Du→Du (sample 18)

description: Perca flavescens – Yellow perch


title: Opasatica cage Op→Op (sample 5)

description: Perca flavescens – Yellow perch


title: Opasatica noncage Op (sample 1)

description: Perca flavescens – Yellow perch


title: Opasatica cage Op→Op (sample 3)

description: Perca flavescens – Yellow perch


title: Opasatica cage Op→Op (sample 2)

description: Perca flavescens – Yellow perch


title: Cases_rep1

description:
sample pooled from 135 females and 65 males
8104411006_R05C01
Genomic DNA extracted from ITP patients was genotyped using Illumina HumanOmniZhongHua-8 v1.0 BeadChip array

value: peripheral blood

value: Case

value: 200 ITP patients


title: Opasatica cage Op→Op (sample 12)

description: Perca flavescens – Yellow perch


title: Opasatica noncage Op (sample 13)

description: Perca flavescens – Yellow perch


title: Opasatica cage Op→Op (sample 9)

description: Perca flavescens – Yellow perch


title: Opasatica noncage Op (sample 4)

description: Perca flavescens – Yellow perch


title: subject 19_Baseline_NL

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 8.

source_name: skin biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: Skin biopsies of 3 mm were obtained from inflammatory lesions in all 17 patients. Additionally, an extra biopsy from clinically healthy skin of the upper arm or leg was obtained from 13 patients.  Biopsies were immediately frozen in liquid nitrogen and subsequently stored at –80oC until RNA preparation.

tag: subject

tag: visit

value: Baseline

tag: skin

value: non-lesion


title: subject 16_Baseline_NL


title: subject 15_Baseline_NL


title: subject 10_Baseline_NL


title: subject 17_Baseline_NL


title: subject 4_Baseline_NL


title: subject 19_Baseline_LS

value: lesion


title: subject 7_Baseline_NL


title: subject 13_Baseline_NL


title: subject 18_Baseline_NL


title: subject 12_Baseline_NL


title: subject 8_Baseline_NL


title: subject 9_Baseline_NL


title: subject 18_Baseline_LS


title: subject 15_Baseline_LS


title: subject 13_Baseline_LS


title: subject 6_Baseline_NL


title: subject 16_Baseline_LS


title: subject 12_Baseline_LS


title: subject 17_Baseline_LS


title: LNCaP siLUC FBS Rep #3

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 22

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio

source_name: LNCaP siLUC FBS Rep #3

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS and 1% PS.

extract_protocol: Total RNA were extracted using Trizol according to manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: LNCaP cells were transfected with siRNA against luciferase and GATA2, respectively. 72 h post-transfection, cells were cultured in medium containing 10% charcoal-stripped FBS or FBS for 3 days, and then were harvested for RNA extraction.

tag: cell line

value: LNCaP


title: LNCaP siGATA2 FBS Rep #3

description: SAMPLE 24

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

source_name: LNCaP siGATA2 FBS Rep #3


title: MCF7LacZ

city: Nagakute

first: Kenji

last: Kasai

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Pathology

country: Japan

institute: Aichi Medical University School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G4851B) 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 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MCF-7 expressing LacZ.

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

extract_protocol: Not provided.

tag: cell type

tag: genotype/variation

value: expressing LacZ


title: subject 8_Baseline_LS


title: MCF7TSHZ2

source_name: MCF-7 expressing TSHZ2.

value: expressing TSHZ2


title: subject 10_Baseline_LS


title: LNCaP siGATA2 FCS Rep #3

description: SAMPLE 23

source_name: LNCaP siGATA2 FCS Rep #3

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

growth_protocol: Cells were maintained in phenol free RPMI +5%FCS+ 1% P/S.

treatment_protocol: LNCaP cells were transfected with siRNA against luciferase and GATA2, respectively. 72 h post-transfection, cells were cultured in phenol free RPMI +5%FCS+ 1% P/S, and then were harvested for RNA extraction.


title: subject 6_Baseline_LS


title: Contamination Op→Du (sample 46)

description: Perca flavescens – Yellow perch

value: juvenile

value: contamination experiment

value: Op→Du

value: Caged

value: Liver


title: LNCaP siGATA2 FBS Rep #2

description: SAMPLE 20

source_name: LNCaP siGATA2 FBS Rep #2


title: subject 4_Baseline_LS


title: LNCaP siLUC FCS Rep #3

description: SAMPLE 21

source_name: LNCaP siLUC FCS Rep #3


title: subject 1_Baseline_LS


title: LNCaP siLUC FCS Rep #2

description: SAMPLE 17

source_name: LNCaP siLUC FCS Rep #2


title: subject 9_Baseline_LS


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-pos overexpression Dnmt3b MLL-AF9-85-0-ckit-pos

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

description: Gene expression data from MLL-AF9 induced leukemia from bone marrow with Dnmt3b overexpression ckit-pos

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's specifications (Affymetrix Inc., Santa Clara, CA, USA)

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console software Build 1.3.1.187.

source_name: leukemic spleen

label_protocol: The samples were labeled according to the Affymetrix GeneChip WT Terminal Labeling protocol (Affymetrix UK Ltd., High Wycombe, UK).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAgen Hilden). RNA quality was approved using the Agilent RNA 6000 Nano Kit (Agilent Technologies).

tag: dnmt3b overexpression

tag: ckit facs

value: ckit-pos

tag: oncogene


title: LNCaP siLUC FBS Rep #2

description: SAMPLE 18

source_name: LNCaP siLUC FBS Rep #2


title: LNCaP siGATA2 FCS Rep #1

description: SAMPLE 15

source_name: LNCaP siGATA2 FCS Rep #1


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-neg overexpression Dnmt3b MLL-AF9-85-0-ckit-neg

description: Gene expression data from MLL-AF9 induced leukemia from bone marrow with Dnmt3b overexpression ckit-neg

value: ckit-neg


title: subject 5_Baseline_LS


title: LNCaP siGATA2 FBS Rep #1

description: SAMPLE 16

source_name: LNCaP siGATA2 FBS Rep #1


title: LNCap R1881 Rep #3

description: SAMPLE 12

source_name: LNCap R1881 Rep #3

growth_protocol: Cells were maintained in phenol free RPMI +5%FCS+ 1% P/S + R1881 24hr.

treatment_protocol: LNCaP cells were transfected with siRNA against luciferase and GATA2, respectively. 72 h post-transfection, cells were cultured in phenol free RPMI +5%FCS+ 1% P/S + R1881 24hr, and then were harvested for RNA extraction.


title: LNCaP siLUC FBS Rep #1

description: SAMPLE 14

source_name: LNCaP siLUC FBS Rep #1


title: subject 3_Baseline_LS


title: subject 2_Baseline_LS


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-neg overexpression Dnmt3b MLL-AF9-81-0-ckit-neg


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-pos overexpression Dnmt3b MLL-AF9-83-0-ckit-pos


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-pos overexpression Dnmt3b MLL-AF9-81-0-ckit-pos


title: LNCaP siLUC FCS Rep #1

description: SAMPLE 13

source_name: LNCaP siLUC FCS Rep #1


title: LNCaP siGATA2 FCS Rep #2

description: SAMPLE 19

source_name: LNCaP siGATA2 FCS Rep #2


title: LNCap EtOH Rep #3

description: SAMPLE 11

source_name: LNCap EtOH Rep #3

growth_protocol: Cells were maintained in phenol free RPMI +5%FCS+ 1% P/S + EtOH.

treatment_protocol: LNCaP cells were transfected with siRNA against luciferase and GATA2, respectively. 72 h post-transfection, cells were cultured in phenol free RPMI +5%FCS+ 1% P/S + EtOH, and then were harvested for RNA extraction.


title: LNCap R1881 Rep #2

description: SAMPLE 10

source_name: LNCap R1881 Rep #2


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-neg overexpression Dnmt3b MLL-AF9-83-0-ckit-neg


title: subject 7_Baseline_LS

source_name: skin biopsy


title: LNCap EtOH Rep #2

description: SAMPLE 9

source_name: LNCap EtOH Rep #2


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-pos MLL-AF9-79-0-ckit-pos

description: Gene expression data from MLL-AF9 induced leukemia from bone marrow ckit-pos

value: WT


title: LNCap R1881 Rep #1

description: SAMPLE 8

source_name: LNCap R1881 Rep #1


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-neg MLL-AF9-75-0-ckit-neg

description: Gene expression data from MLL-AF9 induced leukemia from bone marrow ckit-neg


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-neg MLL-AF9-79-0-ckit-neg


title: LNCaP shFOXA1 FBS Rep #2

description: SAMPLE 4

source_name: LNCaP shFOXA1 FBS Rep #2


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-neg MLL-AF9-73-0-ckit-neg


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-pos MLL-AF9-75-0-ckit-pos


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta flx/flx cells, biological rep 3

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta flx/flx cells, biological rep 3

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm with Partek Genomic Suite 6.6 software.

source_name: Purified cells from engrafted bone marrow GSK3 alpha -/- beta flx/flx cells

growth_protocol: congenic grafted primary mouse tissue

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: 5 week post-transplanted recipient mice (CD45.1) with either Lin- bone marrow GSK3 alpha +/+ beta +/flx, alpha+/+ beta flx/flx, alpha -/- beta +/+ or  alpha-/- beta  fx/flx Rosa26-CreERTM cells (CD45.2) were induced 3 times with intraperitoneal injections of Tamoxifen (75mg/kg) at intervals of two to three days. Mice were sacrificed and analyzed 4 weeks after injection.

value: bone marrow

value: sorted fraction:Lin-/Sca1+/c-kit+

tag: background strain

tag: genotype

value: GSK3 alpha -/- beta flx/flx Rosa26-CreERTM

value: male


title: LNCaP GIPZ FCS

description: SAMPLE 5

source_name: LNCaP GIPZ FCS


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta +/+ cells, biological rep 2

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta +/+ cells, biological rep 2

source_name: Purified cells from engrafted bone marrow GSK3 alpha -/- beta +/+ cells

label_protocol: In accordance with manufacturer's protocols

value: GSK3 alpha -/- beta +/+ Rosa26-CreERTM


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta +/+ cells, biological rep 3

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta +/+ cells, biological rep 3


title: LNCaP shFOXA1 FCS

description: SAMPLE 6

source_name: LNCaP shFOXA1 FCS


title: Gene expression MLL-AF9 induced leukemic bone marrow ckit-pos MLL-AF9-73-0-ckit-pos

source_name: leukemic spleen


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta flx/flx cells, biological rep 2

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta flx/flx cells, biological rep 2


title: PGCLCs Day4 Nanog rep 2

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description:
replicate 2
SAMPLE6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data values were initially transformed by Variance Stabilization Transformation (VST) using the Bioconductor lummi package, and the data matrix was quantile-normalized. Differential expression was evaluated by the Bioconductor R limma package. For any comparison, only probes which are detected in all samples (p-value > 0.0)  are considered. P values were corrected for multiple testing using FDR.

source_name: D4 Nanog-PGCLCs

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

growth_protocol: ESCs were maintained in N2B27 2i LIF medium on a fibronectin-coated dish. EpiLC differentiation was performed as reported previously (Hayashi et al., Cell, 2011).

extract_protocol: total RNA was extracted using Qiagen Rneasy mini kit according to manufacturer's instruction

treatment_protocol: EpiLCs were transferred to a low-cell binding U bottom 96 well plate (Nunc) in GK15 medium with 0.7 µg/ml Doxycycline to induce Nanog PGCLC.

value: PGCLCs

value: Male

tag: strain

tag: transgene

value: Nanog


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta flx/flx cells, biological rep 1

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta flx/flx cells, biological rep 1


title: LNCaP GIPZ FBS Rep #2

description: SAMPLE 3

source_name: LNCaP GIPZ FBS Rep #2

value: LNCaP


title: LNCaP shFOXA1 FBS Rep #1

description: SAMPLE 2

source_name: LNCaP shFOXA1 FBS Rep #1


title: mESCs 2i LIF rep 2

description:
replicate 2
SAMPLE2

source_name: 2i LIF mESCs

value: mESCs


title: LNCaP GIPZ  FBS Rep #1

description: SAMPLE 1

source_name: LNCaP GIPZ  FBS Rep #1


title: mESCs 2i LIF rep 1

description:
replicate 1
SAMPLE1


title: PGCLCs Day4 Cytokines rep 1

description:
replicate 1
SAMPLE3

source_name: D4 Ck-PGCLCs


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha+/+ beta +/flx cells, biological rep 2

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha+/+ beta +/flx cells, biological rep 2

source_name: Purified cells from engrafted bone marrow GSK3 alpha+/+ beta +/flx cells

value: GSK3 alpha+/+ beta +/flx Rosa26-CreERTM


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha+/+ beta +/flx cells, biological rep 1

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha+/+ beta +/flx cells, biological rep 1


title: PGCLCs Day4 Nanog rep 1

description:
replicate 1
SAMPLE5


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha+/+ beta flx/flx cells, biological rep 2

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha+/+ beta flx/flx cells, biological rep 2

source_name: Purified cells from engrafted bone marrow GSK3 alpha+/+ beta flx/flx cells

value: GSK3 alpha+/+ beta flx/flx Rosa26-CreERTM


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha+/+ beta flx/flx cells, biological rep 1

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha+/+ beta flx/flx cells, biological rep 1


title: PGCLCs Day4 Cytokines rep 2

description:
replicate 2
SAMPLE4


title: Lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta +/+ cells, biological rep 1

description: Gene expression data from lineage negative, Sca1+, cKit+ cells from engrafted Lin- bone marrow GSK3 alpha -/- beta +/+ cells, biological rep 1


title: LNCap EtOH Rep #1

description: SAMPLE 7

source_name: LNCap EtOH Rep #1


title: Epithelial ovarian cancer 1-1203

status: Public on Jan 10 2016

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Fragmented and biotin labeled cDNA was hybridized to Affymetrix Human Gene 1.0 ST arrays for 18 hours at 45C with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0007 fluidics protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalization using R package Affy 1.42.3
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Frozen archival epithelial ovarian cancer tumors samples

label_protocol: Samples were enzymatically fragmented and biotinylated using the NuGEN Applause WT-Amp ST System and Encore Biotin Module.

extract_protocol: Total RNA was extracted by Qiagen miRNEasy Mini kit according to the manufacturer's instructions.

tag: patient id

value: epithelial ovarian cancer


title: Epithelial ovarian cancer 1-1175


title: Epithelial ovarian cancer 1-1140


title: Epithelial ovarian cancer 1-1190


title: Epithelial ovarian cancer 1-1202


title: Epithelial ovarian cancer 1-1143


title: Epithelial ovarian cancer 1-1137


title: Epithelial ovarian cancer 1-1196


title: Epithelial ovarian cancer 1-1144


title: Epithelial ovarian cancer 1-1122


title: Epithelial ovarian cancer 1-1121


title: Epithelial ovarian cancer 1-1183R


title: Epithelial ovarian cancer 1-1092


title: Epithelial ovarian cancer 1-1106


title: Epithelial ovarian cancer 1-1113


title: Epithelial ovarian cancer 1-1128


title: Epithelial ovarian cancer 1-1084


title: Epithelial ovarian cancer 1-1049


title: Epithelial ovarian cancer 1-1057


title: Epithelial ovarian cancer 1-1053


title: Epithelial ovarian cancer 1-1026


title: Epithelial ovarian cancer 1-1041


title: Epithelial ovarian cancer 1-1021


title: Epithelial ovarian cancer 1-1043


title: Epithelial ovarian cancer 1-1039


title: Epithelial ovarian cancer 1-1033


title: Epithelial ovarian cancer 1-1146


title: Epithelial ovarian cancer 1-0996


title: Epithelial ovarian cancer 1-0892


title: Epithelial ovarian cancer 1-0974


title: Epithelial ovarian cancer 1-0900


title: Epithelial ovarian cancer 1-0912


title: Epithelial ovarian cancer 1-0817


title: Epithelial ovarian cancer 1-0842


title: Epithelial ovarian cancer 1-0862


title: Epithelial ovarian cancer 1-0801


title: Epithelial ovarian cancer 1-0732


title: Epithelial ovarian cancer 1-0744


title: Epithelial ovarian cancer 1-0679


title: Epithelial ovarian cancer 1-0683


title: Epithelial ovarian cancer 1-0715


title: Epithelial ovarian cancer 1-1040


title: Epithelial ovarian cancer 1-0648


title: Epithelial ovarian cancer 1-0668


title: Epithelial ovarian cancer 1-0626


title: Epithelial ovarian cancer 1-0680


title: Epithelial ovarian cancer 1-1247R


title: Epithelial ovarian cancer 1-1242


title: Epithelial ovarian cancer 1-1281


title: Epithelial ovarian cancer 1-1248


title: Epithelial ovarian cancer 1-1309


title: Epithelial ovarian cancer 1-0682


title: Epithelial ovarian cancer 1-1294


title: Epithelial ovarian cancer 1-1291


title: Epithelial ovarian cancer 1-1287


title: Epithelial ovarian cancer 1-1261


title: Epithelial ovarian cancer 1-1150


title: Epithelial ovarian cancer 1-0464


title: Epithelial ovarian cancer 1-1213


title: Epithelial ovarian cancer 1-0644


title: Epithelial ovarian cancer 1-0674


title: Epithelial ovarian cancer 1-0413


title: Epithelial ovarian cancer 1-0477


title: Epithelial ovarian cancer 1-1234


title: Epithelial ovarian cancer 1-0424


title: Epithelial ovarian cancer 1-0460


title: Epithelial ovarian cancer 1-1229


title: Epithelial ovarian cancer 1-1221


title: Epithelial ovarian cancer 1-0440


title: Epithelial ovarian cancer 1-1250


title: Epithelial ovarian cancer 1-1249


title: Epithelial ovarian cancer 1-0458


title: Epithelial ovarian cancer 1-0372


title: Epithelial ovarian cancer 1-1096


title: Epithelial ovarian cancer 1-0474R


title: Epithelial ovarian cancer 1-0378


title: Epithelial ovarian cancer 1-1184


title: Epithelial ovarian cancer 1-0461


title: Epithelial ovarian cancer 1-0453


title: Epithelial ovarian cancer 1-0444


title: Epithelial ovarian cancer 1-0455


title: Epithelial ovarian cancer 1-0586


title: Epithelial ovarian cancer 1-1243


title: Epithelial ovarian cancer 1-0380


title: Epithelial ovarian cancer 1-0585


title: Epithelial ovarian cancer 1-1206


title: Epithelial ovarian cancer 1-0493


title: D8.DI.ST2WT#4

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: Muscle

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age

value: 10 Weeks Old

tag: genetic/variation

value: ST2 WT/Foxp3-Cre

tag: separation method

value: Dissection / Trimming

tag: Sex

tag: amplification technique

value: Ambion WT Expression Kit


title: Epithelial ovarian cancer 1-0510

tag: tissue


title: Epithelial ovarian cancer 1-0203


title: Epithelial ovarian cancer 1-0355


title: Epithelial ovarian cancer 1-0422


title: Epithelial ovarian cancer 1-0237


title: D8.DI.ST2WT#2


title: D8.DI.ST2WT#3


title: Epithelial ovarian cancer 1-0590


title: Epithelial ovarian cancer 1-0352


title: Epithelial ovarian cancer 1-0156


title: Epithelial ovarian cancer 1-0286


title: Epithelial ovarian cancer 1-0116L


title: Epithelial ovarian cancer 1-0089


title: Epithelial ovarian cancer 1-0101


title: D8.DI.IL33#1

value: 99 Weeks Old

tag: genetic background

tag: treatment

value: 2 ug of rIL-33


title: D8.DI.PBS#3

value: WT

value: PBS


title: Donor 5 IRF7-siRNA medium

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

hyb_protocol: The samples were hybridized to primeview microarrays according to standard Affymetrix protocols. This was performed by Expression Analysis (Durham, NC).

scan_protocol: The samples were scanned on an Affymetrix scanner according to standard Affymetrix protocols. This was performed by Expression Analysis (Durham, NC).

data_processing: The microarray data was preprocessed in R employing the RMA algorithm. A custom chip description file (CDF) file was used (primeviewhsentrezg, version 19).

label_protocol: The Enzo Biochem IVT labeling kit was used. This was performed by Expression Analysis (Durham, NC).

growth_protocol: Primary human bronchial epithelial cells were cultured in BEGM medium. Hydrocortisone was removed from the medium 24 h prior to rhinovirus infection.

extract_protocol: Total RNA was extracted employing TRIzol.

treatment_protocol:
Subconfluent HBE cells were transfected with either 10 nM of IRF7-siRNA or a nontargeting siRNA (all-star control) for 24 hrs at 37°C using Lipofectamine RNAiMAX.
After transfection, cells were allowed to recover for 24 h, and then cultured in the presence or absence of (sucrose gradient purified) rhinovirus-16.

tag: phenotype

value: Cells were transfected with IRF7-siRNA and cultured in medium.

tag: cell type


title: D8.DI.ST2WT#1


title: Donor 5 all-star control medium

source_name: Primary human bronchial epithelial cells

value: Cells were transfected with all-star control siRNA and cultured in medium.


title: D8.DI.ST2FL#1

value: ST2 FL/Foxp3-Cre

value: Male


title: D8.DI.PBS#4


title: Epithelial ovarian cancer 1-0495


title: 10 day-old to adult comparison, rep2

city: Rouen

first: Philippe

last: Leroux

address: Boulevard Gambetta, 22

country: France

institute: INSERM-Rouen University

description: diameter < 70µm

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit on mouse full genome arrays (grid 026655_D_F_20121126). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitrile.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (v 12.6)

data_processing: Agilent Feature Extraction Software (v 12.6) was used for LOWESS normalization.

source_name: forebrain enriched microvessels

label_protocol: Agilent QuickAmp Labeling kit was used according to the manufacturer instructions (catalog number 5190-0443) with 100ng of total RNA.

extract_protocol: Total RNA were extracted using RNeasy Micro kit (Qiagen)

treatment_protocol: Microvessel were isolated from total forebrain by Dounce homogenization, density sedimentation and filtration allowing < 70µm particles recovery

value: forebrain enriched microvessels

value: 10 day old

source_name: total RNA

value: Adult


title: D8.DI.ST2FL#4


title: D8.DI.ST2FL#2


title: D8.DI.ST2FL#3


title: Donor 4 IRF7-siRNA medium

value: Primary human bronchial epithelial cells


title: Donor 4 all-star control medium


title: Donor 4 all-star control rhinovirus

value: Cells were transfected with all-star control siRNA and cultured with rhinovirus.


title: D8.DI.IL33#2


title: D8.DI.PBS#2


title: Donor 3 all-star control rhinovirus


title: D8.DI.IL33#4


title: 5 day-old to 10 day-old comparison, rep2

description: diameter < 70µm

value: 5 day old


title: Donor 5 all-star control rhinovirus


title: D8.DI.PBS#1


title: D8.DI.IL33#3


title: 5 day-old to adult comparison, rep2

description: diameter < 70µm

value: 5 day-old


title: Donor 4 IRF7-siRNA rhinovirus

value: Cells were transfected with IRF7-siRNA and cultured with rhinovirus.


title: Donor 3 IRF7-siRNA rhinovirus


title: 5 day-old to 10 day-old comparison, rep1

description: diameter < 70µm


title: Donor 5 IRF7-siRNA rhinovirus


title: Donor 2 all-star control rhinovirus


title: Donor 1 IRF7-siRNA rhinovirus


title: 10 day-old to adult comparison, dye swwap, rep2

description: diameter < 70µm


title: Donor 1 all-star control rhinovirus


title: Donor 2 IRF7-siRNA rhinovirus


title: Micu1 knockdown mouse 4

city: Philadelphia

first: Egle

last: Juskeviciute

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

hyb_protocol: Mouse Gene 2.0 ST Array were hybridized with 5 μg of fragmented and biotin-labeled cDNA in 220 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h. Arrays were then washed and stained using Gene chip Fluidic Station 450, using Affymetrix GeneChip hybridization wash & stain kit.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Raw gene expression data was normalized using RMA in Affymetrix Expression Console.

source_name: Micu1 knockdown mouse liver sample

label_protocol: 50 ng of total RNA was reverse transcribed using a chimeric cDNA/mRNA primer, and a second complementary cDNA strand was synthesized. Purified cDNA was then amplified with ribo-SPIA enzyme and SPIA DNA/RNA primers (NuGEN Technologies, San Carlos, CA). Amplified cDNA was purified with Qiagen MinElute reaction cleanup kit. 5 μg of cDNAs were fragmented and chemically labeled with biotin to generate biotinylated cDNA using FL-Ovation cDNA biotin module (NuGen Technologies).

extract_protocol: Total RNA was isolated using  Animal Tissue RNA Purification Kit (Norgen Biotek, ) and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100.

treatment_protocol: 10-12 weeks old MICU1loxp/loxp male mice were injected via the tail vein with AAV8-TBG-Cre or AAV8-TBG-Null (1.3x1011 pfu/mouse) (Penn Vector Core). Liver samples were collected 3-5 weeks after injection at which time MICU1 knockdown was confirmed at the mRNA and protein level. Liver tissue was freeze-clamped in liquid nitrogen and stored at -80 degrees C.

tag: background


title: Donor 3 IRF7-siRNA medium


title: Micu1 knockdown mouse 3


title: Donor 3 all-star control medium


title: 10 day-old to adult comparison, dye swwap , rep1

description: diameter < 70µm


title: Donor 2 IRF7-siRNA medium


title: 5 day-old to adult comparison, rep1

description: diameter < 70µm


title: 10 day-old to adult comparison, rep1

description: diameter < 70µm


title: Control mouse 2

source_name: Control mouse liver sample


title: Donor 1 IRF7-siRNA medium


title: Control mouse 1


title: pre-vaccination blood sample from donor 2093

status: Public on Jan 09 2016

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

description: pre-vaccination blood transcriptional profilling

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: The data were analyzed with preprocessed in R using the RMA normalization method.

source_name: Blood sample from donor 2093

label_protocol: Nugen amplification protocol

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.

value: Blood

tag: donor

tag: donor set

tag: vaccination time

value: pre-vaccination

tag: visit number

tag: hepatitis b average concentration (unit)

value: mIU/mL

tag: hepatitis b average concentration (pre-vax)

tag: hepatitis b average concentration (post-vax)


title: Control mouse 3

tag: genotype


title: pre-vaccination blood sample from donor 2106

source_name: Blood sample from donor 2106

tag: age


title: Donor 1 all-star control medium


title: Micu1 knockdown mouse 1


title: Donor 2 all-star control medium


title: Micu1 knockdown mouse 2


title: Control mouse 4


title: pre-vaccination blood sample from donor 2100

source_name: Blood sample from donor 2100


title: pre-vaccination blood sample from donor 2107

source_name: Blood sample from donor 2107


title: pre-vaccination blood sample from donor 2082

source_name: Blood sample from donor 2082


title: pre-vaccination blood sample from donor 2071

source_name: Blood sample from donor 2071


title: pre-vaccination blood sample from donor 2088

source_name: Blood sample from donor 2088


title: pre-vaccination blood sample from donor 2074

source_name: Blood sample from donor 2074


title: pre-vaccination blood sample from donor 2099

source_name: Blood sample from donor 2099


title: pre-vaccination blood sample from donor 2086

source_name: Blood sample from donor 2086


title: pre-vaccination blood sample from donor 2073

source_name: Blood sample from donor 2073


title: pre-vaccination blood sample from donor 2103

source_name: Blood sample from donor 2103


title: pre-vaccination blood sample from donor 2066

source_name: Blood sample from donor 2066


title: pre-vaccination blood sample from donor 2101

source_name: Blood sample from donor 2101


title: pre-vaccination blood sample from donor 2098

source_name: Blood sample from donor 2098


title: pre-vaccination blood sample from donor 2067

source_name: Blood sample from donor 2067


title: pre-vaccination blood sample from donor 2070

source_name: Blood sample from donor 2070


title: pre-vaccination blood sample from donor 2095

source_name: Blood sample from donor 2095


title: pre-vaccination blood sample from donor 2109

source_name: Blood sample from donor 2109


title: pre-vaccination blood sample from donor 2061

source_name: Blood sample from donor 2061


title: pre-vaccination blood sample from donor 2072

source_name: Blood sample from donor 2072


title: pre-vaccination blood sample from donor 2094

source_name: Blood sample from donor 2094


title: pre-vaccination blood sample from donor 2089

source_name: Blood sample from donor 2089


title: pre-vaccination blood sample from donor 2058

source_name: Blood sample from donor 2058


title: pre-vaccination blood sample from donor 2087

source_name: Blood sample from donor 2087


title: pre-vaccination blood sample from donor 2090

source_name: Blood sample from donor 2090


title: pre-vaccination blood sample from donor 2060

source_name: Blood sample from donor 2060


title: pre-vaccination blood sample from donor 2091

source_name: Blood sample from donor 2091


title: pre-vaccination blood sample from donor 2059

source_name: Blood sample from donor 2059


title: pre-vaccination blood sample from donor 2078

source_name: Blood sample from donor 2078


title: pre-vaccination blood sample from donor 2065

source_name: Blood sample from donor 2065


title: pre-vaccination blood sample from donor 2062

source_name: Blood sample from donor 2062


title: pre-vaccination blood sample from donor 2063

source_name: Blood sample from donor 2063


title: pre-vaccination blood sample from donor 2084

source_name: Blood sample from donor 2084


title: pre-vaccination blood sample from donor 2057

source_name: Blood sample from donor 2057


title: pre-vaccination blood sample from donor 2077

source_name: Blood sample from donor 2077


title: pre-vaccination blood sample from donor 2104

source_name: Blood sample from donor 2104


title: pre-vaccination blood sample from donor 2079

source_name: Blood sample from donor 2079


title: pre-vaccination blood sample from donor 2092

source_name: Blood sample from donor 2092


title: pre-vaccination blood sample from donor 2105

source_name: Blood sample from donor 2105


title: pre-vaccination blood sample from donor 2085

source_name: Blood sample from donor 2085


title: pre-vaccination blood sample from donor 2076

source_name: Blood sample from donor 2076


title: pre-vaccination blood sample from donor 2075

source_name: Blood sample from donor 2075


title: pre-vaccination blood sample from donor 1035

source_name: Blood sample from donor 1035


title: pre-vaccination blood sample from donor 2014

source_name: Blood sample from donor 2014


title: pre-vaccination blood sample from donor 1072

source_name: Blood sample from donor 1072


title: pre-vaccination blood sample from donor 1018

source_name: Blood sample from donor 1018


title: pre-vaccination blood sample from donor 2040

source_name: Blood sample from donor 2040


title: pre-vaccination blood sample from donor 2047

source_name: Blood sample from donor 2047


title: pre-vaccination blood sample from donor 2083

source_name: Blood sample from donor 2083


title: pre-vaccination blood sample from donor 2041

source_name: Blood sample from donor 2041


title: pre-vaccination blood sample from donor 1001

source_name: Blood sample from donor 1001


title: pre-vaccination blood sample from donor 1064

source_name: Blood sample from donor 1064


title: pre-vaccination blood sample from donor 2024

source_name: Blood sample from donor 2024


title: pre-vaccination blood sample from donor 1041

source_name: Blood sample from donor 1041


title: pre-vaccination blood sample from donor 1029

source_name: Blood sample from donor 1029


title: pre-vaccination blood sample from donor 1019

source_name: Blood sample from donor 1019


title: pre-vaccination blood sample from donor 2046

source_name: Blood sample from donor 2046


title: pre-vaccination blood sample from donor 2050

source_name: Blood sample from donor 2050


title: pre-vaccination blood sample from donor 2051

source_name: Blood sample from donor 2051


title: pre-vaccination blood sample from donor 2035

source_name: Blood sample from donor 2035


title: pre-vaccination blood sample from donor 2081

source_name: Blood sample from donor 2081


title: pre-vaccination blood sample from donor 2022

source_name: Blood sample from donor 2022


title: pre-vaccination blood sample from donor 2056

source_name: Blood sample from donor 2056


title: pre-vaccination blood sample from donor 2053

source_name: Blood sample from donor 2053


title: pre-vaccination blood sample from donor 2037

source_name: Blood sample from donor 2037


title: pre-vaccination blood sample from donor 2044

source_name: Blood sample from donor 2044


title: pre-vaccination blood sample from donor 1045

source_name: Blood sample from donor 1045


title: pre-vaccination blood sample from donor 2039, technical replicate

source_name: Blood sample from donor 2039


title: pre-vaccination blood sample from donor 2021

source_name: Blood sample from donor 2021


title: pre-vaccination blood sample from donor 1063

source_name: Blood sample from donor 1063


title: pre-vaccination blood sample from donor 1040

source_name: Blood sample from donor 1040


title: pre-vaccination blood sample from donor 1046

source_name: Blood sample from donor 1046


title: pre-vaccination blood sample from donor 1065

source_name: Blood sample from donor 1065


title: pre-vaccination blood sample from donor 1048

source_name: Blood sample from donor 1048


title: pre-vaccination blood sample from donor 1021

source_name: Blood sample from donor 1021


title: pre-vaccination blood sample from donor 1025

source_name: Blood sample from donor 1025


title: pre-vaccination blood sample from donor 1016

source_name: Blood sample from donor 1016


title: pre-vaccination blood sample from donor 1071

source_name: Blood sample from donor 1071


title: pre-vaccination blood sample from donor 1042, technical replicate

source_name: Blood sample from donor 1042


title: pre-vaccination blood sample from donor 1037, technical replicate

source_name: Blood sample from donor 1037


title: pre-vaccination blood sample from donor 2032

source_name: Blood sample from donor 2032


title: pre-vaccination blood sample from donor 2019

source_name: Blood sample from donor 2019


title: pre-vaccination blood sample from donor 1050

source_name: Blood sample from donor 1050


title: pre-vaccination blood sample from donor 1057

source_name: Blood sample from donor 1057


title: pre-vaccination blood sample from donor 1067

source_name: Blood sample from donor 1067


title: pre-vaccination blood sample from donor 2036

source_name: Blood sample from donor 2036


title: pre-vaccination blood sample from donor 1020

source_name: Blood sample from donor 1020


title: pre-vaccination blood sample from donor 2017

source_name: Blood sample from donor 2017


title: pre-vaccination blood sample from donor 1060

source_name: Blood sample from donor 1060


title: pre-vaccination blood sample from donor 2042

source_name: Blood sample from donor 2042


title: pre-vaccination blood sample from donor 1058

source_name: Blood sample from donor 1058


title: pre-vaccination blood sample from donor 2027

source_name: Blood sample from donor 2027


title: pre-vaccination blood sample from donor 1036

source_name: Blood sample from donor 1036


title: pre-vaccination blood sample from donor 1017

source_name: Blood sample from donor 1017


title: pre-vaccination blood sample from donor 2049

source_name: Blood sample from donor 2049


title: pre-vaccination blood sample from donor 1069

source_name: Blood sample from donor 1069


title: pre-vaccination blood sample from donor 1026

source_name: Blood sample from donor 1026


title: pre-vaccination blood sample from donor 1070

source_name: Blood sample from donor 1070


title: pre-vaccination blood sample from donor 2003

source_name: Blood sample from donor 2003


title: pre-vaccination blood sample from donor 2055

source_name: Blood sample from donor 2055


title: pre-vaccination blood sample from donor 1030

source_name: Blood sample from donor 1030


title: pre-vaccination blood sample from donor 1066

source_name: Blood sample from donor 1066


title: pre-vaccination blood sample from donor 2012

source_name: Blood sample from donor 2012


title: pre-vaccination blood sample from donor 2052

source_name: Blood sample from donor 2052


title: pre-vaccination blood sample from donor 1061

source_name: Blood sample from donor 1061


title: pre-vaccination blood sample from donor 1043

source_name: Blood sample from donor 1043


title: pre-vaccination blood sample from donor 1054

source_name: Blood sample from donor 1054


title: pre-vaccination blood sample from donor 2004

source_name: Blood sample from donor 2004


title: pre-vaccination blood sample from donor 1055

source_name: Blood sample from donor 1055


title: pre-vaccination blood sample from donor 2001

source_name: Blood sample from donor 2001


title: pre-vaccination blood sample from donor 2018

source_name: Blood sample from donor 2018


title: pre-vaccination blood sample from donor 1042

source_name: Blood sample from donor 1042


title: pre-vaccination blood sample from donor 1005

source_name: Blood sample from donor 1005


title: pre-vaccination blood sample from donor 2039

source_name: Blood sample from donor 2039


title: pre-vaccination blood sample from donor 1004

source_name: Blood sample from donor 1004


title: pre-vaccination blood sample from donor 1010

source_name: Blood sample from donor 1010


title: pre-vaccination blood sample from donor 2009

source_name: Blood sample from donor 2009


title: pre-vaccination blood sample from donor 2011

source_name: Blood sample from donor 2011


title: pre-vaccination blood sample from donor 2033

source_name: Blood sample from donor 2033


title: pre-vaccination blood sample from donor 2010

source_name: Blood sample from donor 2010


title: pre-vaccination blood sample from donor 2016

source_name: Blood sample from donor 2016


title: pre-vaccination blood sample from donor 1049

source_name: Blood sample from donor 1049


title: pre-vaccination blood sample from donor 2025

source_name: Blood sample from donor 2025


title: pre-vaccination blood sample from donor 1031

source_name: Blood sample from donor 1031


title: pre-vaccination blood sample from donor 2023

source_name: Blood sample from donor 2023


title: pre-vaccination blood sample from donor 1059

source_name: Blood sample from donor 1059


title: pre-vaccination blood sample from donor 2029, technical replicate

source_name: Blood sample from donor 2029


title: pre-vaccination blood sample from donor 2026

source_name: Blood sample from donor 2026


title: pre-vaccination blood sample from donor 2006

source_name: Blood sample from donor 2006


title: pre-vaccination blood sample from donor 1024

source_name: Blood sample from donor 1024


title: pre-vaccination blood sample from donor 1014

source_name: Blood sample from donor 1014


title: pre-vaccination blood sample from donor 2020

source_name: Blood sample from donor 2020


title: pre-vaccination blood sample from donor 1015

source_name: Blood sample from donor 1015


title: pre-vaccination blood sample from donor 1051

source_name: Blood sample from donor 1051


title: pre-vaccination blood sample from donor 1053

source_name: Blood sample from donor 1053


title: pre-vaccination blood sample from donor 1022

source_name: Blood sample from donor 1022


title: pre-vaccination blood sample from donor 1007

source_name: Blood sample from donor 1007


title: pre-vaccination blood sample from donor 2015

source_name: Blood sample from donor 2015


title: pre-vaccination blood sample from donor 1027

source_name: Blood sample from donor 1027


title: pre-vaccination blood sample from donor 1032, technical replicate

source_name: Blood sample from donor 1032


title: pre-vaccination blood sample from donor 2031

source_name: Blood sample from donor 2031


title: pre-vaccination blood sample from donor 2048

source_name: Blood sample from donor 2048


title: pre-vaccination blood sample from donor 1039

source_name: Blood sample from donor 1039


title: pre-vaccination blood sample from donor 1011

source_name: Blood sample from donor 1011


title: pre-vaccination blood sample from donor 1038

source_name: Blood sample from donor 1038


title: pre-vaccination blood sample from donor 1056

source_name: Blood sample from donor 1056


title: pre-vaccination blood sample from donor 1047

source_name: Blood sample from donor 1047


title: pre-vaccination blood sample from donor 1028

source_name: Blood sample from donor 1028


title: pre-vaccination blood sample from donor 1044

source_name: Blood sample from donor 1044


title: pre-vaccination blood sample from donor 1023

source_name: Blood sample from donor 1023


title: pre-vaccination blood sample from donor 1068

source_name: Blood sample from donor 1068


title: pre-vaccination blood sample from donor 1062

source_name: Blood sample from donor 1062


title: pre-vaccination blood sample from donor 2013

source_name: Blood sample from donor 2013


title: pre-vaccination blood sample from donor 2054

source_name: Blood sample from donor 2054


title: pre-vaccination blood sample from donor 2034

source_name: Blood sample from donor 2034


title: pre-vaccination blood sample from donor 1032


title: pre-vaccination blood sample from donor 1037

source_name: Blood sample from donor 1037


title: pre-vaccination blood sample from donor 1008

source_name: Blood sample from donor 1008


title: pre-vaccination blood sample from donor 2005

source_name: Blood sample from donor 2005


title: pre-vaccination blood sample from donor 1009

source_name: Blood sample from donor 1009


title: pre-vaccination blood sample from donor 2029

source_name: Blood sample from donor 2029


title: pre-vaccination blood sample from donor 2043

source_name: Blood sample from donor 2043


title: pre-vaccination blood sample from donor 1052

source_name: Blood sample from donor 1052


title: pre-vaccination blood sample from donor 2007

source_name: Blood sample from donor 2007


title: FBK1

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in prefrontal cortex of prenatally betamethasone postnatally ketamine treated P15 female rat

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two rats were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Sample tables contain normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control featrure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal.

organism: Rattus norvegicus

source_name: Treated (prenatally (G15) exposed to betamethasone_postnatally (P14) treated with ketamine) P15 female rat prefrontal cortex_Replicate 1

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Time-pregnant Sprague-Dawley rats were purchased from approved source (Taconic Farms, Germantown, NY). The rats were housed individually during the remainder of their pregnancy in the animal facility with free access to standard rat chow and water on the regular 12 hour light-dark cycle with the lights on at 07:00 am.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE).

treatment_protocol: On G15, some pregnant rats received 2 injections of betamethasone (Sigma-Aldrich, St. Louis, MO) at 0.4 mg/kg each at 08:30 and 18:30; controls received vehicle (normal saline) instead. Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four females. On P14 rats exhibiting infantile spasms received 35mg/kg ketamine or saline.

tag: Sex

value: female

tag: strain

value: Sprague-Dawley

value: prefrontal cortex

tag: developmental stage


title: FBK2

source_name: Treated (prenatally (G15) exposed to betamethasone_postnatally (P14) treated with ketamine) P15 female rat prefrontal cortex_Replicate 2

tag: tissue


title: FBK4

source_name: Treated (prenatally (G15) exposed to betamethasone_postnatally (P14) treated with ketamine) P15 female rat prefrontal cortex_Replicate 4


title: FBS1

description: Gene expression in prefrontal cortex of prenatally betamethasone postnatally saline treated P15 female rat

source_name: Primed (prenatally (G15) exposed to betamethasone_postnatally (P14) exposed to saline) P15 female rat prefrontal cortex_Replicate 1


title: FBS2

source_name: Primed (prenatally (G15) exposed to betamethasone_postnatally (P14) exposed to saline) P15 female rat prefrontal cortex_Replicate 2


title: FBK3

source_name: Treated (prenatally (G15) exposed to betamethasone_postnatally (P14) treated with ketamine) P15 female rat prefrontal cortex_Replicate 3


title: pre-vaccination blood sample from donor 2045

source_name: Blood sample from donor 2045


title: pre-vaccination blood sample from donor 1033

source_name: Blood sample from donor 1033


title: FBS4

source_name: Primed (prenatally (G15) exposed to betamethasone_postnatally (P14) exposed to saline) P15 female rat prefrontal cortex_Replicate 4


title: FSS2

description: Gene expression in prefrontal cortex of prenatally saline postnatally saline treated P15 female rat

source_name: Control (prenatally (G15) exposed to saline_postnatally (P14) exposed to saline) P15 female rat prefrontal cortex_Replicate 2


title: duodenal enteroendocrine cells 2

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

hyb_protocol: standard illumina protocol

scan_protocol: standard illumina protocol

data_processing: We used GenomeStudio to extract raw gene expression data from the BeadChip arrays.  We then used the lumi R package to transform the data using the variance-stabilizing transformation (VST) algorithm and to perform quantile-normalization. We performed pairwise comparisons between genes in each tissue pair using the limma R package, using empirical Bayes smoothing of standard errors.

source_name: duodenal EE cells

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

growth_protocol: FACS purified primary mouse cells. R26-floxed-rtTA, R26-floxed-GFP, R26-rtTA, CAG-rtTA, Ngn3-Cre, and NSG mouse strains were obtained from the Jackson laboratories. Ngn3-GFP and Cdx2(fl/fl)  mice have been described previously (Lee, et al. Genes Dev 2002, Verzi, et al. Mol Cel Biol 2013). The TetO-NPMcherry mouse lines were made by standard pronuclear injection at the Harvard Genomic Modification Facility (Cambridge, MA) using a polycistronic construct that co-expresses Ngn3, Pdx1, Mafa, and the Cherry fluorescent protein.  We validated the transgenic lines by crossing the founders with R26-rtTA, applying Doxycycline (2mg/ml in drinking water) for 10 days, and analyzing tissues for Cherry fluorescence.  Two independent transgenic lines with robust global Cherry induction were identified and used in our experiments, which yielded similar results.

extract_protocol: RNA was extracted with TriZol reagent (Invitrogent).

treatment_protocol: To dissociate tissues into single cells for FACS purification, we modified published protocols (Talchai, et al. Diabetes 2015, Reimann, et al. Cell Metab 2008).  Briefly, duodenum and colon tissues were cut into small pieces, incubated with 10 mM EDTA for 30 min, and mechanically dissociated by pipetting.  The released epithelial clusters were digested with dispase for 15 minutes into single cells.  For antral stomach, the minced tissues were incubated in 10mM EDTA for 2 hours, followed by pipetting to release the glands.  The glands were further incubated with Accutase® for 30 minutes into single cells.  GFP+ cells were isolated by fluorescent activated cell sorting (FACS) with FACSaria (BD Bioscience).

value: FACS purified GFP+ cells

value: duodenum

tag: genotype/variation

value: adult


title: FBS3

source_name: Primed (prenatally (G15) exposed to betamethasone_postnatally (P14) exposed to saline) P15 female rat prefrontal cortex_Replicate 3


title: colon enteroendocrine cells 1

source_name: colonic EE cells

value: colon


title: colon enteroendocrine cells 2


title: duodenal enteroendocrine cells 1


title: gastric enteroendocrine cells 3

source_name: gastric EE cells

value: pylorus stomach


title: FSS4

source_name: Control (prenatally (G15) exposed to saline_postnatally (P14) exposed to saline) P15 female rat prefrontal cortex_Replicate 4


title: duodenal enteroendocrine cells 3


title: Dll1-/- CD4

city: Tokushima

first: Takahiro

last: Furukawa

address: Kuramoto-Cho 2-50-1

institute: Tokushima University

description: Gene expresson after 2days in stimulated CD4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >11.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Oligo Microarrays (G4858A#28005) 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: lymphocyte, stimulation, 2days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20 n`g RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (G2938C, Agilent Technologies, Santa Clara, CA).

tag: gender

value: 8 weeks


title: WT CD4

value: wild type


title: gastric enteroendocrine cells 2

tag: cell type


title: FSS3

source_name: Control (prenatally (G15) exposed to saline_postnatally (P14) exposed to saline) P15 female rat prefrontal cortex_Replicate 3


title: FSS1

source_name: Control (prenatally (G15) exposed to saline_postnatally (P14) exposed to saline) P15 female rat prefrontal cortex_Replicate 1


title: Chamelea gallina collected in T7 in September T7SE2

status: Public on Jan 08 2016

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

institute: University of Padova

description: Chamelea gallina

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.6.1 statistical software

organism: Chamelea gallina

source_name: digestive gland of C. gallina collected in T7 in September

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples (pools of 5 digestive gland)

tag: condition

value: C. gallina collected in T7 in September

value: digestive gland


title: Chamelea gallina collected in T7 in August T7AU2

description: Chamelea gallina

source_name: digestive gland of C. gallina collected in T7 in August

value: C. gallina collected in T7 in August


title: Chamelea gallina collected in T7 in September T7SE1

description: Chamelea gallina


title: Rbpj-/- CD4

value: Rbpj-/-


title: adipocyte dmso1 6h (control for resveratrol treatment)

city: Suwon

first: Seo-Hyuk

last: Chang

address: 2066, Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

description:
dmso1
Gene expression data from DMSO1 (control to resveratrol treated sample) treated fully differentiated C3H10T1/2 cell

hyb_protocol: Following fragmentation, 15ug of aRNA were hybridized for 16h at 45c on gene chip mouse genome array.

scan_protocol: Genechips were scanned using the Affymetrix Genechip scanner 300 7G.

data_processing:
Data were analyzed with RMA (Robust multi-array analysis) using Affymetrix default analysis settings and global scaling as normalization method
The normalized, and log transformed intensity values were then analyzed using genespring GX 13.o.

source_name: C3H10T1/2 cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA.

growth_protocol: C3H10T1/2 cells were differentiated with standard protocol. Fully differentiated C3H10T1/2 cells were treated with small molecules.

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

treatment_protocol: Fully differentiated C3H10T1/2 cells were refreshed with fresh media day before treatment. Indicated small molecules were treated for 6h.

tag: cell line

value: fully differentiated C3H10T1/2 adipocytes

tag: treated with

value: DMSO for 6hrs


title: gastric enteroendocrine cells 1

value: FACS purified GFP+ cells from the pylorus stomach of Ngn3-GFP adult mice


title: Chamelea gallina collected in T7 in September T7SE3

description: Chamelea gallina


title: Chamelea gallina collected in T7 in August T7AU5

description: Chamelea gallina


title: Chamelea gallina collected in T7 in August T7AU3

description: Chamelea gallina


title: adipocyte resveratrol 6h

description:
resveratrol
Gene expression data from resveratrol treated fully differentiated C3H10T1/2 cell

value: resveratrol for 6hrs


title: adipocyte dmso 6h

description:
dmso
Gene expression data from DMSO treated fully differentiated C3H10T1/2 cell


title: Chamelea gallina collected in T7 in September T7SE4

description: Chamelea gallina


title: Chamelea gallina collected in T7 in August T7AU1

description: Chamelea gallina


title: adipocyte butein 6h

description:
butein
Gene expression data from butein treated fully differentiated C3H10T1/2 cell

value: butein for 6hrs


title: Chamelea gallina collected in T7 in July T7JU3

description: Chamelea gallina

source_name: digestive gland of C. gallina collected in T7 in July

value: C. gallina collected in T7 in July


title: adipocyte sulfuretin 6h

description:
sulfuretin
Gene expression data from sulfuretin treated fully differentiated C3H10T1/2 cell

value: sulfuretin for 6hrs


title: 3h_control_vs_AA_1

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: Potato cultivar Russet Norkotah was grown in a growth chamber at 16 hour light/8 hour dark at 22°C fertilized with Osmocote.  Plants were from tissue culture, transplanted to soil and used approximately 4 weeks after transplanting.  RNA was extracted from leaves using Trizol.  Plants were sprayed with one of four treatments, either 1mM salicylic acid, 100 µM methyl jasmonate, 1 mg/ml arachidonic acid or 100 µM methyl jasmonate plus 1 mM salicylic acid together.   Samples were harvested at 3, 24 and 72 hours after spraying.  Each salicylic acid or arachidonic acid treatment has 3 biological replicates done in parallel, using leaves pooled from 2 plants.  The control for SA or AA treated plants were water sprayed plants, from which leaves of 3 different plants were pooled at each timepoint, done side-by-side with the treated samples. Methyl jasmonate or MJ+SA treatments had 2 biological replicates each, using leaves pooled from 2 plants. A separate set of water sprayed plants (from the SA and AA control treatments) were used as controls, and pooled leaves from 3 plants were used at each time-point, and done in parallel with the treated samples.

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Solanum tuberosum

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: Growth chamber, 16h light/8h dark at 22C, fertilized with osmocoat

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: 3h, 1mg/ml arachidonic acid

tag: Solanum tuberosum, Leaves, petioles, Biotic stress

treatment_protocol: 3h, water sprayed control


title: Chamelea gallina collected in T7 in July T7JU5

description: Chamelea gallina


title: Chamelea gallina collected in T7 in September T7SE5

description: Chamelea gallina


title: Chamelea gallina collected in T7 in July T7JU2

description: Chamelea gallina


title: Chamelea gallina collected in T4 in September T4SE5

description: Chamelea gallina

source_name: digestive gland of C. gallina collected in T4 in September

value: C. gallina collected in T4 in September


title: Chamelea gallina collected in T7 in August T7AU4

description: Chamelea gallina


title: Breast 763

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2. The 'complete.betas.nocurelung.txt' contains unmethylated and methylated signal intensities along with average Beta and P-val

label: Cy3, Cy5

source_name: Breast

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

tag: disease state

value: normal


title: Breast 761


title: Chamelea gallina collected in T4 in September T4SE3

description: Chamelea gallina


title: Chamelea gallina collected in T4 in September T4SE2

description: Chamelea gallina


title: Chamelea gallina collected in T7 in July T7JU1

description: Chamelea gallina


title: Chamelea gallina collected in T4 in September T4SE4

description: Chamelea gallina


title: Chamelea gallina collected in T4 in July T4JU5

description: Chamelea gallina

source_name: digestive gland of C. gallina collected in T4 in July

value: C. gallina collected in T4 in July


title: Chamelea gallina collected in T4 in August T4AU5

description: Chamelea gallina

source_name: digestive gland of C. gallina collected in T4 in August

value: C. gallina collected in T4 in August


title: Breast 760


title: Breast 762


title: Chamelea gallina collected in T7 in July T7JU4

description: Chamelea gallina


title: Chamelea gallina collected in T4 in September T4SE1

description: Chamelea gallina


title: Chamelea gallina collected in T4 in August T4AU1

description: Chamelea gallina


title: Chamelea gallina collected in T4 in August T4AU2

description: Chamelea gallina


title: Chamelea gallina collected in T4 in July T4JU2

description: Chamelea gallina


title: Chamelea gallina collected in T4 in July T4JU1

description: Chamelea gallina


title: Chamelea gallina collected in T4 in August T4AU4

description: Chamelea gallina


title: Breast 758


title: Chamelea gallina collected in T4 in July T4JU3

description: Chamelea gallina


title: Chamelea gallina collected in T4 in August T4AU3

description: Chamelea gallina


title: Chamelea gallina collected in T4 in July T4JU4

description: Chamelea gallina


title: pre-vaccination blood sample from donor 2030

source_name: Blood sample from donor 2030

value: Blood

tag: donor

tag: donor set

tag: vaccination time

value: pre-vaccination

tag: visit number

tag: hepatitis b average concentration (unit)

value: mIU/mL


title: Breast 759


title: Breast 756


title: Breast 757


title: Breast 752


title: Breast 754


title: pre-vaccination blood sample from donor 1013

source_name: Blood sample from donor 1013

tag: hepatitis b average concentration (pre-vax)

tag: hepatitis b average concentration (post-vax)

tag: age


title: Breast 748


title: Breast 749


title: leaves_vs_roots_rep_3_vs_4

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

hyb_protocol: All of the hybridization, washing and drying steps were performed in 2x105K Chambers in an HS 4800 Pro (Tecan) automatic hybridization station according to the manufacturer’s guidelines regarding Agilent microarrays treatment. A Gene Expression Hybridization Kit (Agilent) and Gene Expression Wash Buffer Kit solutions (Agilent) were used for the hybridization and washing steps, respectively.

scan_protocol: The intensity data were collected with 4200AL GenePix scanner and GenePix Pro 6.1 software at 5 µm resolution, at green and red channel.

data_processing: The scans were processed with GenePix Pro 6.1 software using morphological opening background method. Intensity data were analyzed with R/Bioconductor limma package. Background was subtracted (offset 10). Loess within-array normalization and Aquantile between-array normalization was applied.

organism: Nicotiana benthamiana

label_protocol: Labeled cRNA samples were prepared from 200 ng RNA each, using Quick Amp Labeling Kit (Agilent). The labeling efficiency was monitored with Nanodrop 2000 spectrophotometer.

growth_protocol: N. benthamiana plants were grown in growth chambers at 22°C/20°C (day/night).

extract_protocol: Samples from 4 biological replicates (individual plants) were obtained. Total RNA was extracted from frozen Nicotiana benthamiana leaves and roots using spin-columns (RNeasy Plant Mini Kit, QIAGEN) and DNase-digested with TURBO DNA-free kit (Ambion) according to the manufacturers’ standard protocols. RNA quality was determined using Nanodrop 2000 and 2100 Bioanalyzer (Agilent). All of the samples used for the study were pure (A260/A280 ≥ 1.9; A260/A230 ≥ 2) and showed no visible signs of degradation.

treatment_protocol: Roots and leaves were collected from 6-weeks-old plants.

tag: tissue

value: roots

value: leaves


title: leaves_vs_roots_rep_4_vs_1


title: leaves_vs_roots_rep_1_vs_2


title: Breast 755


title: leaves_vs_roots_rep_2_vs_3


title: White matter 744

source_name: Central Nervous System


title: BC 657

value: cancer