title: MIA PaCa-2 (Gem; 72 h)

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

description: Cancer - Treated 3

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

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

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: Pancreatic Cancer Cell line

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 1 µg total RNA sample and the RNA was 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: HPDE was grown keratinocyte-SFM with additional supplements while MIA PaCa-2 was grown in DMEM with 10% FBS,  2.5 % Donor Horse Serum, and 1% Penicillin-Stepromycin antibiotic. Tissue RNA were purchased from Asterand.

extract_protocol: Total RNA was extracted from cells under indicated conditions using miRVANA isolation kit from Life technologies.

treatment_protocol: Cells were treated with DZNep for 8 h (Treated 1) or 72 h (Treated 2) (1 µM) or with gemcitabine for 72 h (100 nM) (Treated 3) or with DZNep (8 h; 1 µM) followed with Gemcitabine (72 h; 100 nM) (Treated 4)

tag: cell line

value: MIA PaCa-2

tag: tissue/cell type

value: Pancreatic Cancer Cell line

tag: treated with

value: Gemcitabine for 72hrs


title: 11 vs 12 second

status: Public on Sep 03 2016

type: RNA

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

description: 11 vs 12 second

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentRNA.pdf

scan_protocol: Pixel Size : 5 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: OD : midlog

extract_protocol:
Extracted molecule : Total RNA
Extraction method : acid phenol prep http://dunham.gs.washington.edu/MDyeastRNA.pdf

tag: strain name

value: DNatA + hNatA WT

value: WT + e.v.


title: MDA Micropapillary bladder tumor MDA MP7

city: Houston

first: Li

last: Zhang

state: TX

address: 1400 Pressler, unit 1410

department: Bioinformatics

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization in the Linear Model for Microarray Data (LIMMA)

label: biotin

organism: Homo sapiens

source_name: Bladder tumor tissue embeded in parffin block

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

extract_protocol: RNA was extracted with MasterPure Complete Purification Kit from Epicentre in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: tissue

value: micropapillary bladder tumors


title: MDA Micropapillary bladder tumor MDA MP11


title: MDA Micropapillary bladder tumor MDA MP17


title: Normal Tissue

description: Normal Tissue - 1

source_name: Normal pancreatic tissue

value: Normal pancreatic tissue

tag: age

tag: tumor stage

value: IB


title: PDAC Tissue

description: Cancer Tissue - 1

source_name: Primary pancreatic cancer

value: Primary pancreatic cancer


title: MDA Micropapillary bladder tumor MDA MP6


title: Kupffer cell M0 con rep 2

city: Seoul

first: Yong-Hyun

last: Han

state: Seoul

address: Daehak-ro

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
replicate 2
SAMPLE 2

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label: Biotin

organism: Mus musculus

source_name: Primary Mouse Kupffer cell

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: Kupffer cells were isolated from 8 weeks old, male C57BL/6 mice by perfusion of liver using collagenase type IV. For isolation of Kupffer cells, non-parenchymal sufficient supernatant was centrifuged in 50%/25% percoll  The layer containing Kupffer cells was plated with RPMI 1640 with 10% FBS.

extract_protocol: Cells were harvested in RLT buffer and RNA was extracted from cultured kupffer cells using the RNeasy micro KIT (Qiagen, Valencia, CA).

treatment_protocol: KCs were treated with 10 ng/ml LPS (M1), 20 ng/ml IL-4 (M2), DMSO (Veh), 10 mM SR3335, or 5 mM SR1078 for 24 h in RPMI medium.

tag: strain

tag: gender

value: Male

value: 8 weeks

tag: cell type

value: Primary cultured Kupffer cells


title: MIA PaCa-2 (Gem:DZNep=1:10))

description: Cancer - Treated 4

value: DZNep for 8hrs followed with Gemcitabine for 72hrs


title: 6 vs 5

description: 6 vs 5

label_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentRNA.pdf

value: W303 WT

value: W303 DyNatA


title: MDA Micropapillary bladder tumor MDA MP8


title: MDA Micropapillary bladder tumor MDA MP10


title: MDA Micropapillary bladder tumor MDA MP9


title: 13 vs 12 second

description: 13 vs 12 second

value: DNatA + hNatA S37P


title: HPDE (DZNep; 72 h)

description: Normal - Treated

source_name: Human Pancreatic Ductal Epithelial Cell line

value: HPDE

value: 3-Deazaneplanocin-A (DZNep) for 72hrs


title: NIL-Bph6 leaf shealth without BPH infestation (at 0h), biological rep2

city: Wuhan

first: Jianping

last: Guo

address: Wuhan University

department: College of Life Sciences

country: China

institute: National Key Laboratory of Hybrid Rice

description: Gene expression data from 9311 leaf shealth without BPH infestation (at 0h).

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara,CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0  (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

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

growth_protocol: Plants were grown in a controlled growth chamber. The fourth leaf of 3-week-old young plants were used as the material in all experiments.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad,CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified  total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and  RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Treat plants with BPH in different time points (as indicated) then sampled in the same time points.

tag: cultivar

value: leaf shealth

tag: genotype

value: Resistant to BPH

value: four-leaf stage


title: Kupffer cell M0 con rep 1

description:
replicate 1
SAMPLE 1


title: 14 vs 12 second

description: 14 vs 12 second

value: DNatA + e.v.

value: WT + e.v.


title: 15 vs 5

description: 15 vs 5


title: MDA Micropapillary bladder tumor MDA MP5

value: micropapillary bladder tumors


title: MIA PaCa-2 (DZNep; 8 h)

description: Cancer - Treated 1

value: MIA PaCa-2

value: Pancreatic Cancer Cell line

value: 3-Deazaneplanocin-A (DZNep) for 8hrs


title: MIA PaCa-2

description: Cancer - Control

value: none (untreated control)


title: MDA Micropapillary bladder tumor MDA MP2


title: 12 vs 2 second

description: 12 vs 2 second


title: HPDE

description: Normal - Control

value: Human Pancreatic Ductal Epithelial Cell line


title: 4 vs 2 second

description: 4 vs 2 second


title: MDA Micropapillary bladder tumor MDA MP4


title: MDA Micropapillary bladder tumor MDA MP1


title: 1 vs 2 second

description: 1 vs 2 second

value: DNatA + hNatA WT


title: MDA Micropapillary bladder tumor MDA MP3


title: 3 vs 2 second

description: 3 vs 2 second


title: 2 v 12 second

description: 2 v 12 second


title: MIA PaCa-2 (DZNep; 72 h)

description: Cancer - Treated 2


title: Kupffer cell M1 LPS rep 2

description:
replicate 2
SAMPLE 4

value: Male

value: 8 weeks

value: Primary cultured Kupffer cells


title: Individual_86_1997

status: Public on Sep 02 2016

type: genomic

city: Denmark

first: Qihua

last: Tan

address: J. B. Winsløws Vej 9B

country: Denmark

institute: University of Southern Denmark

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R06C01
Sample_well: A08
Sample_plate: 8

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 BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

tag: Sex

value: female

tag: individual id


title: Individual_86_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R06C02
Sample_well: D08
Sample_plate: 8


title: Individual_80_2007-2

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R01C02
Sample_well: G01
Sample_plate: 9

value: male


title: Individual_82_1997-2

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R04C01
Sample_well: G01
Sample_plate: 8


title: Individual_81_2007-1

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R03C02
Sample_well: G10
Sample_plate: 8


title: Individual_81_1997-2

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R04C02
Sample_well: A09
Sample_plate: 9


title: Individual_81_2007-2

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R03C02
Sample_well: G09
Sample_plate: 9


title: Individual_85_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R05C01
Sample_well: C07
Sample_plate: 8


title: Individual_84_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R06C01
Sample_well: F03
Sample_plate: 8


title: Individual_85_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R05C02
Sample_well: F07
Sample_plate: 8


title: Individual_83_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R05C01
Sample_well: H02
Sample_plate: 8


title: Individual_84_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R06C02
Sample_well: C01
Sample_plate: 9


title: Individual_83_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R05C02
Sample_well: A02
Sample_plate: 9


title: Individual_79_1997-2

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R02C01
Sample_well: G04
Sample_plate: 8


title: Individual_82_2007-2

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R03C01
Sample_well: A01
Sample_plate: 8


title: Individual_81_1997-1

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R03C01
Sample_well: H01
Sample_plate: 9


title: Individual_82_2007-1

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R04C02
Sample_well: A10
Sample_plate: 8


title: Individual_79_2007-2

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R01C01
Sample_well: A04
Sample_plate: 8


title: Individual_80_1997-2

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742087
Sentrix_position: R02C02
Sample_well: A01
Sample_plate: 9


title: Individual_82_1997-1

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R04C01
Sample_well: B01
Sample_plate: 9


title: Individual_80_1997-1

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R02C01
Sample_well: F06
Sample_plate: 8


title: Individual_80_2007-1

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R02C02
Sample_well: E04
Sample_plate: 8


title: Individual_79_1997-1

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R01C01
Sample_well: H05
Sample_plate: 8


title: Individual_77_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R05C02
Sample_well: D05
Sample_plate: 8


title: Individual_78_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R06C02
Sample_well: F04
Sample_plate: 8


title: Individual_75_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R03C02
Sample_well: E01
Sample_plate: 9


title: Individual_79_2007-1

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440140
Sentrix_position: R01C02
Sample_well: C05
Sample_plate: 8


title: Individual_76_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R04C02
Sample_well: C02
Sample_plate: 9


title: Individual_78_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R06C01
Sample_well: B03
Sample_plate: 9


title: Individual_72_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R06C02
Sample_well: H10
Sample_plate: 8


title: Individual_70_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R04C02
Sample_well: G09
Sample_plate: 8


title: Individual_73_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R01C02
Sample_well: A12
Sample_plate: 9


title: Individual_77_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R05C01
Sample_well: H03
Sample_plate: 9


title: Individual_76_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R04C01
Sample_well: C06
Sample_plate: 8


title: Individual_72_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R06C01
Sample_well: A05
Sample_plate: 9


title: Individual_73_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R01C01
Sample_well: C05
Sample_plate: 9


title: Individual_74_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R02C01
Sample_well: E04
Sample_plate: 9


title: Individual_67_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R01C01
Sample_well: H04
Sample_plate: 9


title: Individual_74_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R02C02
Sample_well: G12
Sample_plate: 9


title: Individual_69_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R03C01
Sample_well: G04
Sample_plate: 9


title: Individual_68_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R02C02
Sample_well: B02
Sample_plate: 9


title: Individual_67_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R01C02
Sample_well: D01
Sample_plate: 9


title: Individual_75_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440109
Sentrix_position: R03C01
Sample_well: E05
Sample_plate: 8


title: Individual_61_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R01C02
Sample_well: E02
Sample_plate: 8


title: Individual_62_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R02C02
Sample_well: C03
Sample_plate: 8


title: Individual_65_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R05C02
Sample_well: A02
Sample_plate: 8


title: Individual_70_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R04C01
Sample_well: A04
Sample_plate: 9


title: Individual_63_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R03C02
Sample_well: F02
Sample_plate: 8


title: Individual_71_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R05C01
Sample_well: C04
Sample_plate: 9


title: Individual_64_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R04C01
Sample_well: A03
Sample_plate: 9


title: Individual_66_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R06C02
Sample_well: C01
Sample_plate: 8


title: Individual_63_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R03C01
Sample_well: G03
Sample_plate: 9


title: Individual_66_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R06C01
Sample_well: D06
Sample_plate: 8


title: Individual_71_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R05C02
Sample_well: B10
Sample_plate: 8


title: Individual_65_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R05C01
Sample_well: F05
Sample_plate: 8


title: Individual_64_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R04C02
Sample_well: D03
Sample_plate: 8


title: Individual_68_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R02C01
Sample_well: B04
Sample_plate: 9


title: Individual_69_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806073
Sentrix_position: R03C02
Sample_well: A09
Sample_plate: 8


title: Individual_60_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R06C02
Sample_well: A06
Sample_plate: 8


title: Individual_62_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R02C01
Sample_well: B06
Sample_plate: 8


title: Individual_61_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929806074
Sentrix_position: R01C01
Sample_well: H06
Sample_plate: 8


title: Individual_57_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R03C02
Sample_well: E06
Sample_plate: 8


title: Individual_58_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R04C02
Sample_well: G05
Sample_plate: 8


title: Individual_56_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R02C02
Sample_well: E02
Sample_plate: 9


title: Individual_55_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R01C02
Sample_well: C03
Sample_plate: 9


title: Individual_60_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R06C01
Sample_well: H08
Sample_plate: 9


title: Individual_59_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R05C02
Sample_well: G06
Sample_plate: 8


title: Individual_58_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R04C01
Sample_well: G08
Sample_plate: 9


title: Individual_53_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R05C01
Sample_well: A05
Sample_plate: 8


title: Individual_59_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R05C01
Sample_well: F09
Sample_plate: 9


title: Individual_49_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R01C02
Sample_well: F12
Sample_plate: 9


title: Individual_57_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R03C01
Sample_well: E09
Sample_plate: 9


title: Individual_50_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R02C02
Sample_well: C10
Sample_plate: 9


title: Individual_52_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R04C02
Sample_well: E12
Sample_plate: 9


title: Individual_55_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R01C01
Sample_well: H10
Sample_plate: 9


title: Individual_51_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R03C02
Sample_well: A11
Sample_plate: 9


title: Individual_54_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R06C02
Sample_well: C12
Sample_plate: 9


title: Individual_49_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R01C01
Sample_well: G10
Sample_plate: 9


title: Individual_54_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R06C01
Sample_well: C04
Sample_plate: 8


title: Individual_53_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R05C02
Sample_well: B10
Sample_plate: 9


title: Individual_50_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R02C01
Sample_well: E11
Sample_plate: 9


title: Individual_56_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440139
Sentrix_position: R02C01
Sample_well: D12
Sample_plate: 9


title: Individual_48_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R06C02
Sample_well: D01
Sample_plate: 8


title: Individual_47_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R05C02
Sample_well: B02
Sample_plate: 8


title: Individual_52_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R04C01
Sample_well: A10
Sample_plate: 9


title: Individual_51_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 6929742086
Sentrix_position: R03C01
Sample_well: F11
Sample_plate: 9


title: Individual_46_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R04C02
Sample_well: D04
Sample_plate: 8


title: Individual_43_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R01C02
Sample_well: D07
Sample_plate: 9


title: Individual_44_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R02C02
Sample_well: B08
Sample_plate: 9


title: Individual_47_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R05C01
Sample_well: C10
Sample_plate: 8


title: Individual_39_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R03C02
Sample_well: C11
Sample_plate: 9


title: Individual_46_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R04C01
Sample_well: D04
Sample_plate: 9


title: Individual_48_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R06C01
Sample_well: A11
Sample_plate: 8


title: Individual_41_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R05C02
Sample_well: G02
Sample_plate: 8


title: Individual_40_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R04C02
Sample_well: E10
Sample_plate: 9


title: Individual_45_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R03C01
Sample_well: B05
Sample_plate: 9


title: Individual_38_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R02C02
Sample_well: C02
Sample_plate: 8


title: Individual_38_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R02C01
Sample_well: B03
Sample_plate: 8


title: Individual_42_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R06C01
Sample_well: E09
Sample_plate: 8


title: Individual_42_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R06C02
Sample_well: E03
Sample_plate: 8


title: Individual_37_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R01C02
Sample_well: E01
Sample_plate: 8


title: Individual_43_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R01C01
Sample_well: F10
Sample_plate: 9


title: Individual_33_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R03C02
Sample_well: H06
Sample_plate: 9


title: Individual_31_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R01C02
Sample_well: E05
Sample_plate: 9


title: Individual_32_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R02C02
Sample_well: C06
Sample_plate: 9


title: Individual_34_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R04C02
Sample_well: B06
Sample_plate: 9


title: Individual_39_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R03C01
Sample_well: H05
Sample_plate: 9


title: Individual_41_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R05C01
Sample_well: G08
Sample_plate: 8


title: Individual_36_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R06C02
Sample_well: A03
Sample_plate: 8


title: Individual_44_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R02C01
Sample_well: D11
Sample_plate: 9


title: Individual_36_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R06C01
Sample_well: C08
Sample_plate: 8


title: Individual_35_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R05C01
Sample_well: E07
Sample_plate: 8


title: Individual_35_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R05C02
Sample_well: G03
Sample_plate: 8


title: Northeastern Indigenous_longissimus dorsi, biological rep2

city: changchun

first: yan

last: gao

address: 5333 xian road

institute: Jilin University

description:
Gene expression data from longissimus dorsi of Northeastern Indigenous
100108-Porcine-09869A_dongbeiminzhu2.CHP
100108-Porcine-09869A_dongbeiminzhu2.CEL

hyb_protocol: The labeled cRNA was then fragmented and hybridized to the array for 16 h at 45℃ with rotation. After hybridization, the GeneChip arrays were washed, and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 and converting into TIFF images.

data_processing: Array normalization and error detection analysis were carried out using Affymetrix GeneChip Operating Software Version 1.4. Data was normalized by the algorithms supplied with the feature extraction software. After normalization, one final quality-control filter was applied, where genes showing excessive biological variability were discarded.To determine the significant differentially expressed genes, significance analysis of microarrays (SAM,version 3.02) was performed.

organism: Sus scrofa

source_name: longissimus dorsi

label_protocol: 1μg of total RNA was reverse transcribed to first- and second-strand cDNAs. After purification and testing, the double-stranded cDNA served as a template for the in vitro transcription reaction for cRNA amplification. The cRNA was labeled with biotin.

growth_protocol: Three Northeastern Indigenous and three Large White were raised in the same condition of nutrition and enviroment. They were butchered on day 150.

extract_protocol: Total RNA was isolated using the Trizol reagent (Invitrogen, Aukland, New Zealand) according to the manufacturer’s instruction for six samples.

treatment_protocol: Longissimus dorsi samples were collected from six pigs. All samples were washed briefly with PBS, and then snap frozen in liquid nitrogen for future experiments.

tag: breed

value: Northeastern Indigenous

value: boar

value: 150 days

value: muscle (longissimus dorsi)


title: Individual_45_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7310440121
Sentrix_position: R03C02
Sample_well: B05
Sample_plate: 8


title: Northeastern Indigenous_longissimus dorsi, biological rep1

description:
Gene expression data from longissimus dorsi of Northeastern Indigenous
100108-Porcine-09869A_dongbeiminzhu1.CHP
100108-Porcine-09869A_dongbeiminzhu1.CEL


title: Large White_longissimus dorsi, biological rep2

description:
Gene expression data from longissimus dorsi of Large White
100108-Porcine-09869A_dabaizhu2.CHP
100108-Porcine-09869A_dabaizhu2.CEL

value: Large White


title: Large White_longissimus dorsi, biological rep3

description:
Gene expression data from longissimus dorsi of Large White
100108-Porcine-09869A_dabaizhu3.CHP
100108-Porcine-09869A_dabaizhu3.CEL


title: Individual_33_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R03C01
Sample_well: D06
Sample_plate: 9


title: Individual_31_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R01C01
Sample_well: B09
Sample_plate: 9


title: Individual_40_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R04C01
Sample_well: F06
Sample_plate: 9


title: Large White_longissimus dorsi, biological rep1

description:
Gene expression data from longissimus dorsi of Large White
100108-Porcine-09869A_dabaizhu1.CHP
100108-Porcine-09869A_dabaizhu1.CEL


title: Individual_32_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R02C01
Sample_well: H09
Sample_plate: 9


title: Individual_30_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R06C02
Sample_well: G05
Sample_plate: 9


title: Individual_37_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398109
Sentrix_position: R01C01
Sample_well: H03
Sample_plate: 8


title: Individual_34_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398141
Sentrix_position: R04C01
Sample_well: F05
Sample_plate: 9


title: Individual_27_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R03C02
Sample_well: A06
Sample_plate: 9


title: Liver_GSGME_1143

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

hyb_protocol: After checking the quality and quantity of the labeled cRNA, cRNA was fractionated and hybridized with the Affymetrix GeneChips. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station 450. The GeneChips were then scanned with an Affymetrix GeneChip scanner 3000. All procedures were performed according to Affymetrix protocols (GeneChip expression analysis, Technical manual from Affymetrix). The quality of hybridization was assessed in all samples following the manufacturer´s recommendations.

scan_protocol: After scanning the arrays, cell intensity files containing a single intensity value for each probe cell were computed from the image data with the Affymetrix GeneChip Command Console Software.

data_processing: Probe cell intensity data were further analyzed in the Affymetrix Expression Console software using the Robust Multichip Analysis (RMA) algorithm.

organism: Bos taurus

source_name: Liver GSGME

label_protocol: The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

growth_protocol: For this investigation, we used liver and plasma samples collected at 1 wk postpartum of an experiment with dairy cows (Gessner et al., 2015). In that experiment, 28 primiparous and multiparous Holstein cows with an average parity number of 2.8 were used as experimental animals. The experiment was conducted at the Educational and Research Centre for Animal Husbandry Hofgut Neumuehle in Rhineland-Palatinate (Münchweiler an der Alsenz, Germany); the experimental protocol was approved by the Provincial Government of Coblenz, Germany (23 177-07/G12-20-074). The cows were assigned into 2 experimental groups, either a control group or a group supplemented with GSGME (GSGME group). Body weights (BW) of the cows did not differ before parturition (wk 8 prepartum: control group, 692 ± 21 kg; treatment group, 664 ± 21 kg; mean ± SE) or after parturition (wk 2 postpartum: control group, 657 ± 28 kg; GSGME group, 632 ± 22 kg; mean ± SE) between the 2 groups. The experimental period lasted 12 wks from wk 3 before the expected calving date of the cows to wk 9 postpartum. In the period between wk 3 prepartum and calving, a total mixed ration (TMR) was calculated to meet the demand of net energy and crude protein (CP) requirement of a dry cow with a BW of 650 kg and an assumed dry matter intake (DMI) of 12 kg/d, according to the German Society of Nutrition Physiology. After calving, all animals were offered a basal TMR calculated to meet the demand of net energy and CP requirement for producing 34 kg of milk, with an assumed daily DMI of 22 kg (Gessner et al., 2015). In the time period from 3 wk before the expected calving date until wk 9 postpartum, the basal TMR of the GSGME group were supplemented with 1% of GSGME (Antaox, Dr. Eckel, Niederzissen, Germany) based on DM content. The GSGME product used had a total flavonoid content of 52 mg gallic acid equivalents per gram. The TMR of the control group was supplemented with 1% of wheat bran for an energetic adjustment.

extract_protocol: Total RNA was isolated from liver samples using Trizol® according to the manufacturer’s protocol and stored at -80 °C. Concentration and purity of the RNA were estimated from the optical density at 260 and 280 nm, respectively, using a NanoQuant plateTM (Infinite® 200, Tecan, Mainz, Germany).

treatment_protocol: Cows were separated individually and blood samples were obtained from the vena caudalis at wk 1 (d 7 postpartum ± 2 d) using EDTA-coated collection tubes (S-Monovette, Sarstedt, Nümbrecht, Germany) and centrifuged immediately. After centrifugation the plasma was separated from the blood cells, and the plasma samples were stored at −20 °C until analysis. In addition, liver biopsies were taken after sampling of blood. Therefore, the liver biopsy site on the right side of the cow between the 11th and 12th rib on a line between the olecranon and the tuber coxae was shaved and disinfected followed by a local subcutaneous anesthesia with 5 ml of Isocaine (20.0 mg/ml procainhydrochloride + 0.025 mg/ml epinephrine, Selectavet, Weyarn-Holzolling, Germany). A small incision was made with a scalpel (carbon steel scalpel blades #11, Aesculap AG, Tuttlingen, Germany) and approximately 50 mg of liver tissue were taken with a sterile 14G biopsy needle (Dispomed Witt oHG, Gelnhausen, Germany). The liver biopsies were immediately snap-frozen in liquid nitrogen and stored at −80°C until further analysis. After the biopsy, the puncture site was treated with antiseptic spray (Oxytetracycline spray blue, Bayer Health Care AG, Leverkusen, Germany).

value: Holstein

tag: condition

value: GSGME

value: liver


title: Northeastern Indigenous_longissimus dorsi, biological rep3

description:
Gene expression data from longissimus dorsi of Northeastern Indigenous
100108-Porcine-09869A_dongbeiminzhu3.CHP
100108-Porcine-09869A_dongbeiminzhu3.CEL


title: Liver_GSGME_1124


title: Liver_GSGME_1047


title: Individual_26_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R02C02
Sample_well: A07
Sample_plate: 9


title: Individual_30_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R06C01
Sample_well: D05
Sample_plate: 9


title: Individual_29_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R05C01
Sample_well: F04
Sample_plate: 9


title: Liver_control_1150

source_name: Liver control

value: control


title: Individual_27_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R03C01
Sample_well: F01
Sample_plate: 9


title: Liver_GSGME_821


title: Individual_28_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R04C01
Sample_well: D02
Sample_plate: 9


title: Liver_control_1041


title: Liver_GSGME_741


title: Liver_control_825


title: Liver_control_1031


title: Individual_28_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R04C02
Sample_well: G06
Sample_plate: 9


title: Individual_25_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R01C02
Sample_well: G07
Sample_plate: 9


title: Liver_control_819


title: Individual_20_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R02C02
Sample_well: D11
Sample_plate: 8


title: Individual_21_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R03C02
Sample_well: B01
Sample_plate: 8


title: Liver_control_1017


title: Individual_23_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R05C02
Sample_well: G02
Sample_plate: 9


title: Individual_21_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R03C01
Sample_well: C08
Sample_plate: 9


title: Individual_19_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R01C02
Sample_well: F10
Sample_plate: 8


title: Individual_26_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R02C01
Sample_well: D08
Sample_plate: 9


title: Individual_22_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R04C02
Sample_well: H01
Sample_plate: 8


title: Individual_25_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R01C01
Sample_well: F07
Sample_plate: 9


title: Individual_24_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R06C01
Sample_well: C09
Sample_plate: 9


title: Individual_24_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R06C02
Sample_well: E03
Sample_plate: 9


title: Liver_GSGME_1001


title: Hema_replicate3

city: Florence

first: Anna

last: Laurenzana

address: Viale Morgagni 50

department: Department of Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
100 nanograms of freshly isolated total cellular RNA
cDNA samples have been generated from three independent RNA samples of A375 cellular line maintained in complete cell growth medium

hyb_protocol: NuGEN Encore Biotin Module Hybridization conditions, Affymetrix Fluidics Wasging and Staining Protocol FS450_0001

scan_protocol: Affymetrix GCS 3000 Scanner Hi Resolution 7G scanning protocol

data_processing: CHP files generated with Affymetrix Transcriptome Console v2.0

source_name: Human melanocyte cell line

label_protocol: NuGEN Ovation Pico WTA System V2; NuGEN Encore Biotin Module

growth_protocol: Primary Human Epidermal Melanocytes were grown in Medium 254CF with calcium plus Human Melanocytes Growth Supplement. The melanoma cell lines A375 and M6 were grown in Dulbecco’s modified Eagle’s medium containing 2 mM glutamine, 100 UI/ml penicillin, 100 μg/ml streptomycin and supplemented with 10 % FBS.

extract_protocol: Qiagen Mirnesay Micro Kit, Handbook 02/2012

treatment_protocol: Semi-confluent cultures of Hema, A375 snd M6 were washed twice with PBS and then processed for RNA extraction with the Qiagen Mirnesay Micro Kit

value: HeMa

value: Primary Human Epidermal Melanocytes (HeMa) were isolated from the skin of an adult donor


title: group 3, remote IPC with a late window followed by warm ischemia 24 hours later 5

first: Young Eun

last: Yoon

address: yonsei-ro 50-1

department: Urology

institute: Yonsei University

description: SAMPLE 15

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: kidney_72 hr_with late window IPC

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, CA), in accordance with the manufacturer's protocol, and purified by RNeasy Mini Kit (Qiagen, Valencia, CA)

value: Yorkshire

tag: sample group

value: remote IPC with a late window followed by warm ischemia 24 hrs later

value: kidney


title: group 3, remote IPC with a late window followed by warm ischemia 24 hours later 4

description: SAMPLE 14


title: Individual_20_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R02C01
Sample_well: H12
Sample_plate: 9


title: M6_replicate2

source_name: Human melanoma cell line

tag: cell line

value: A375-M6 melanoma cells (M6) were isolated from lung metastasis of SCID bg/bg mice i.v. injected with A375 human melanoma cell line


title: Individual_22_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R04C01
Sample_well: E07
Sample_plate: 9

value: female


title: Individual_29_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398097
Sentrix_position: R05C02
Sample_well: E06
Sample_plate: 9

value: male


title: Individual_19_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R01C01
Sample_well: B12
Sample_plate: 9


title: group 3, remote IPC with a late window followed by warm ischemia 24 hours later 3

description: SAMPLE 13


title: Hema_replicate2


title: Individual_17_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R05C02
Sample_well: C07
Sample_plate: 9


title: group 3, remote IPC with a late window followed by warm ischemia 24 hours later 2

description: SAMPLE 12


title: M6_replicate3


title: M6_replicate1


title: Individual_16_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R04C02
Sample_well: D09
Sample_plate: 9


title: group 3, remote IPC with a late window followed by warm ischemia 24 hours later 1

description: SAMPLE 11


title: Individual_18_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R06C02
Sample_well: A08
Sample_plate: 9


title: Hema_replicate1


title: group 2, remote IPC with an early window followed by 90 minutes warm ischemia 4

description: SAMPLE 9

source_name: kidney_72 hr_with early window IPC

value: remote IPC with an early window followed by 90 min warm ischemia


title: A375_replicate2

value: Human melanoma cell line (A375) was derived from the skin of a 54 year-old female patient with malignant melanoma


title: group 2, remote IPC with an early window followed by 90 minutes warm ischemia 3

description: SAMPLE 8


title: group 2, remote IPC with an early window followed by 90 minutes warm ischemia 2

description: SAMPLE 7


title: A375_replicate1


title: Individual_15_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R03C02
Sample_well: F08
Sample_plate: 9


title: Individual_13_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R01C02
Sample_well: B11
Sample_plate: 8


title: Individual_14_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R02C02
Sample_well: D10
Sample_plate: 8


title: group 1, no IPC and 90 minutes warm ischemia 4

description: SAMPLE 4

source_name: kidney_72 hr_without IPC

value: no IPC and 90 min warm ischemia


title: group 1, no IPC and 90 minutes warm ischemia 3

description: SAMPLE 3


title: group 2, remote IPC with an early window followed by 90 minutes warm ischemia 1

description: SAMPLE 6


title: group 1, no IPC and 90 minutes warm ischemia 1

description: SAMPLE 1


title: group 1, no IPC and 90 minutes warm ischemia 5

description: SAMPLE 5


title: SEC-1

city: Tokyo

first: Yo

last: Mabuchi

address: 35 Shinanomachi, Shinjuku-ku

department: Physiology

country: Japan

institute: Keio University School of Medicine

description: Gene expression  in  human MSC after six weeks culture

hyb_protocol: Hybridized to an Agilent human whole-genome chip (4x44K, AMADID=14850, Agilent technologies)

scan_protocol: The genes were screened with GeneSpring GX10 (Agilent Technologies).

data_processing: We normalized the signal intensity of each chip at 75% tile according to the signals of all (=41000) spots on each chip. Then, we narrowed down the candidates in the following steps: 1) created from advanced analysis: significance; 2) entity list: significantly high in at least one sample; 3) interpretation: type; 4) experiment: GE per gene norm 5) p-value cut off: 0.05 6) post-hoc test: Tukey’s HSD; 7) selected test: one-way ANOVA; 8) p-value computation: asymptotic; 9) multiple-testing correction: Benjamini-Hochberg.

source_name: Bone Marrow, Slowly Expanding Clones 1

label_protocol: 300 ng of total RNA was labeled with Cy3.

growth_protocol: Bone marrow single LNGFR+THY-1+ cell were sorted in 96 well plate. A maximum of 5x10^6 cells were passaged at six weeks.

extract_protocol: Several human MSC clones that did not have any copy-number abnormality (two REC clones, three MEC clones, and three SEC clones) were cultured, and total RNA was extracted.We purified total RNA with an RNeasy Mini Kit (Qiagen) or RNeasy Micro Kit (Qiagen)

treatment_protocol: Standard culture medium, which consisted of DMEM supplemented with 20% FBS (Hyclone), 20 ng/ml bFGF (Peprotech) and 1% P/S, and which was changed twice weekly.

value: Bone Marrow  LNGFR+THY-1+ cell


title: SEC-4

source_name: Bone Marrow, Slowly Expanding Clones 4


title: SEC-2

source_name: Bone Marrow, Slowly Expanding Clones 2


title: Individual_16_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R04C01
Sample_well: F02
Sample_plate: 9


title: A375_replicate3


title: group 1, no IPC and 90 minutes warm ischemia 2

description: SAMPLE 2


title: Individual_18_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R06C01
Sample_well: D02
Sample_plate: 8


title: group 2, remote IPC with an early window followed by 90 minutes warm ischemia 5

description: SAMPLE 10


title: MEC-4

source_name: Bone Marrow, Moderately Expanding Clones 4


title: Individual_13_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R01C01
Sample_well: H02
Sample_plate: 9


title: Individual_23_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398100
Sentrix_position: R05C01
Sample_well: E08
Sample_plate: 9


title: Individual_17_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R05C01
Sample_well: F01
Sample_plate: 8


title: 81-176 ΔCjjptaackA-3-3

type: mixed

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

description: C. jejuni strain 81-176ΔCjjptaackA Bio Replicate 3 Tech 3

hyb_protocol: Labeled reference genomic DNA and test cDNAs were combined in 45 µl Pronto! cDNA hybridization solution (Corning, Corning, NY) and heated to 95°C for 5 min. Then, 15 µl of the hybridization mixture was put onto a microarray slide and sealed with a cover slip. The microarray slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18 h. Following hybridization, the slides were washed twice in 2× SSC, 0.1% sodium dodecyl sulfate at 42°C for 10 min, followed by twice in 1× SSC at room temperature for 10 min, and finally twice in 0.2× SSC at room temperature for 5 min. The microarray slides were dried by centrifugation at 300 × g for 10 min before scanning.

scan_protocol: Scanned on an Axon GenePix4000B scanner at 10nm resolution using GenePix software. Optimize intensities manually. Images were quantified using GenePix software (version 6.0).

data_processing: Fluorescence ratios were calculated after local background was subtracted from spot signals. To compensate for any effect of the amount of template and uneven Cy-dye incorporation, data normalization (centering) was performed by bringing the median natural logarithm of the ratios for each group of spots printed by the same pin to zero using the following equation: ln(Ti ) = ln(Ri /Gi ) - c, where T is the centered ratio, i is the gene index, R and G are the red and green intensities, respectively, and c is the 50th percentile of all red/green ratios.

organism: Campylobacter jejuni

source_name: strain WT81-176

label_protocol: 2 µg of genomic DNA were Cy5-dUTP labeled during random primed synthesis with Klenow fragment.  20 µg of total RNA were labeled during reverse transcription with random primed hexamers to cDNA with Cy3-dUTP using Stratascript (Stratagene, Palo Alto, CA) at 42°C for 16 h.

growth_protocol: Campylobacter were grown under micro-aerobic conditions (5% O2, 10% CO2, and 85% N2) at 42°C on blood agar base II medium.

extract_protocol: Campylobacter genomic DNA was prepared with the Qiagen Dneasy Blood and Tissue kit. To isolate total RNA,  log phase cultures suspended in 10X stop solution (95% ethanol plus 5% phenol), incubated on ice for 20 min, pelleted by centrifugation.  Pellets were suspended in 1 mL of RiboZol (Amresco) and RNA was removed by chloroform extraction. Total RNA (60 μg) was treated with DNaseI (Invitrogen) and then purified through an RNeasy Mini Column (Qiagen) according to the manufacturer’s specifications.

tag: genotype/variation

value: wild-type

source_name: strain 81-176ΔCjjptaackA

value: mutant


title: Individual_15_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R03C01
Sample_well: D03
Sample_plate: 9


title: 81-176 ΔCjjptaackA-3-2

description: C. jejuni strain 81-176ΔCjjptaackA Bio Replicate 3 Tech 2


title: MEC-3

source_name: Bone Marrow, Moderately Expanding Clones 3


title: 81-176 ΔCjjptaackA-3-1

description: C. jejuni strain 81-176ΔCjjptaackA Bio Replicate 3 Tech 1


title: REC-3

source_name: Bone Marrow, Rapidly Expanding Clones 3


title: MEC-1

source_name: Bone Marrow, Moderately Expanding Clones 1


title: 81-176 ΔCjjptaackA-2-3

description: C. jejuni strain 81-176ΔCjjptaackA Bio Replicate 2 Tech 3


title: Individual_14_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398133
Sentrix_position: R02C01
Sample_well: F03
Sample_plate: 9

source_name: Whole blood


title: REC-1

source_name: Bone Marrow, Rapidly Expanding Clones 1


title: 81-176 ΔCjjptaackA-2-2

description: C. jejuni strain 81-176ΔCjjptaackA Bio Replicate 2 Tech 2


title: Individual_8_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R02C02
Sample_well: G07
Sample_plate: 8


title: 81-176 ΔCjjptaackA-2-1

description: C. jejuni strain 81-176ΔCjjptaackA Bio Replicate 2 Tech 1


title: brain NAc_shock sensitive_rep6

city: Baltimore

first: Jean Lud

last: Cadet

state: MD

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

description: whole transcript gene expression profiling on rats that self administer methamphetamine and use footshocks as adverse consequences

hyb_protocol: Following fragmentation, 5.5 ug of ss DNA were hybridized for 16 hr at 45C on GeneChip Rat Transcriptome 1.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Expression Console Software using Affymetrix default analysis settings.

organism: Rattus norvegicus

source_name: Nacc tissue_shock_sensitive

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Plus Reagent Kit Manual, Affymetrix).

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

treatment_protocol: Male Sprague-Dawley rats (Charles River Labs, Raleigh, NC, USA), weighing 350-400g were used in the experiments.  Animals were housed in a humidity and temperature-controlled (22.2 + 0.2ºC) room with free access to food and water.

value: brain

tag: brain region

value: Nucleus accumbens

value: Sprague Dawley

tag: weight


title: brain NAc_shock sensitive_rep4

tag: tissue


title: Individual_11_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R05C02
Sample_well: D10
Sample_plate: 9


title: brain NAc_shock sensitive_rep5


title: Individual_12_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R06C02
Sample_well: B11
Sample_plate: 9


title: 81-176 ΔCjjptaackA-1-3

description: C. jejuni strain 81-176ΔCjjptaackA Bio Replicate 1 Tech 3


title: Individual_10_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R04C02
Sample_well: H11
Sample_plate: 9


title: Individual_9_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R03C01
Sample_well: C09
Sample_plate: 8


title: Individual_9_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R03C02
Sample_well: G11
Sample_plate: 9


title: Individual_7_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R01C02
Sample_well: A07
Sample_plate: 8


title: 81-176 ΔCjjptaackA-1-2

description: C. jejuni strain 81-176ΔCjjptaackA Bio Replicate 1 Tech 2


title: 81-176 ΔCjjptaackA-1-1

description: C. jejuni strain 81-176ΔCjjptaackA Bio Replicate 1 Tech 1


title: Individual_10_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R04C01
Sample_well: E08
Sample_plate: 8


title: WT81-176-3-3

description: C. jejuni strain 81-176 wildtype Bio Replicate 3 Tech 3

growth_protocol: Precultures of Campylobacter were grown under micro-aerobic conditions (5% O2, 10% CO2, and 85% N2) at 42°C in Heart Infusion broth (HI) , diluted to an A550 of 0.02 in 5 ml of HI, and incubated on a gyratory shaker (150 rpm) under microaerobic conditions at 42°C to stationary phase (A550 of 1.0-1.4) .


title: Individual_11_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R05C01
Sample_well: B04
Sample_plate: 8


title: brain NAc_shock sensitive_rep1


title: brain NAc_shock sensitive_rep3


title: Individual_7_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R01C01
Sample_well: F09
Sample_plate: 8


title: brain NAc_shock resistant_rep6

source_name: Nacc tissue_shock_resistant


title: WT81-176-3-2

description: C. jejuni strain 81-176 wildtype Bio Replicate 3 Tech 2


title: WT81-176-3-1

description: C. jejuni strain 81-176 wildtype Bio Replicate 3 Tech 1


title: WT81-176-2-1

description: C. jejuni strain 81-176 wildtype Bio Replicate 2 Tech 1


title: WT81-176-2-3

description: C. jejuni strain 81-176 wildtype Bio Replicate 2 Tech 3


title: WT81-176-2-2

description: C. jejuni strain 81-176 wildtype Bio Replicate 2 Tech 2


title: brain NAc_shock resistant_rep5

description: whole transcript gene expression profiling on rats that self administer methamphetamine and use footshocks as adverse consequences


title: Individual_5_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R05C02
Sample_well: D09
Sample_plate: 8


title: Individual_8_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R02C01
Sample_well: H08
Sample_plate: 8


title: Individual_6_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R06C02
Sample_well: F08
Sample_plate: 8


title: Individual_12_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398091
Sentrix_position: R06C01
Sample_well: H04
Sample_plate: 8


title: WT81-176-1-3

description: C. jejuni strain 81-176 wildtype Bio Replicate 1 Tech 3


title: WT81-176-1-2

description: C. jejuni strain 81-176 wildtype Bio Replicate 1 Tech 2


title: brain NAc_shock resistant_rep2


title: brain NAc_shock resistant_rep3


title: brain NAc_shock resistant_rep1


title: brain NAc_shock resistant_rep4


title: Individual_4_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R04C02
Sample_well: C11
Sample_plate: 8


title: brain NAc_control_rep6

source_name: Nacc tissue_control


title: WT81-176-1-1

description: C. jejuni strain 81-176 wildtype Bio Replicate 1 Tech 1


title: Individual_2_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R02C02
Sample_well: B07
Sample_plate: 9


title: brain NAc_shock sensitive_rep2


title: Individual_3_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R03C02
Sample_well: E10
Sample_plate: 8


title: Individual_6_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R06C01
Sample_well: H09
Sample_plate: 8


title: WL CD11c+ ATM, rep 1

status: Public on Sep 01 2016

city: Ann Arbor

first: Carey

middle: N

last: Lumeng

state: MI

address: 109 Zina Pitcher Place

department: Pediatrics

institute: University of Michigan

description: FACS Sorted Live cells

hyb_protocol: Following Labeling procedure, 2.5 ug of Biotinylated cDNA were hybridized at 48C – WT on Mouse Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515)

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical environment v3.0.0. RMA was used to fit log2 transformed expression values.

source_name: CD11c+ ATM from Gonadal Adipose Tissue from weight loss WL mice

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 50 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 2.5 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6).

growth_protocol: Male C57Bl/6 mice were fed either normal diet (ND), high fat diet (HFD; 60% fat), or underwent a weight loss (WL) protocol by withdrawal of HFD for 8 weeks after 12 weeks of feeding.

extract_protocol: FACS sorted live cells were isolated in media prior to centrifugation and RNA purification.

treatment_protocol: Gonadal/Epididymal adipose tissue was minced and collagenase digested to obtain single cell suspensions of stromal cells prior to staining.

value: Male

value: Gonadal Adipose Tissue

tag: body weight

value: Weight Loss

value: Macrophage


title: Individual_1_2007

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R01C02
Sample_well: H07
Sample_plate: 9


title: WL CD11c- ATM, rep 2

description: FACS Sorted Live cells

source_name: CD11c- ATM from Gonadal Adipose Tissue from weight loss WL mice


title: brain NAc_control_rep1


title: HFD PA, rep 3

description: FACS Sorted Live cells

source_name: PA from Gonadal Adipose Tissue from from obese HFD fed mice

value: Obese

value: Preadiopcyte


title: brain NAc_control_rep3


title: WL CD11c+ ATM, rep 2

description: FACS Sorted Live cells


title: brain NAc_control_rep4


title: brain NAc_control_rep2


title: WL CD11c- ATM, rep 1

description: FACS Sorted Live cells


title: Finding novel targets regulated by AR in breast cancer cells_2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: WCE DNA prepared from MDA-MB-453 cells after 24 hours of DHT treatment

hyb_protocol: 4µg each of Cy3-labeled WCE was combined with Cy5-labeled IP DNA samples and Human Cot-1 DNA (1mg/ml) (Invitrogen-catalogue no. 15279-011), Agilent 10X Blocking agent (Part Number 5188-6416) and Hybridization buffer (Part Number 5188-6420) were added to it. The total hybridization volume was 260µl. The labeled samples in above hybridization mix were denatured at 95oC for 3 minutes and incubated at 37oC for 30 minutes.

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

data_processing: Data extraction done using Agilent Feature extraction software and Feature extracted raw data was analyzed using Data analysis was done using Agilent Genomic Workbench Lite Edition 6.5 (Methylation Application-Linear Normalization)

source_name: MDA-MB-453 cell line_input

label_protocol: Agilent Suretag Genomic DNA Labeling Kit (Part no : 5190-3399) was used for labeling. Protocol inclu random primers and the exo- Klenow fragment to differentially label genomic DNA samples with fluorescent- labeled nucleotides.1µg of each amplified WCE and IP DNA were mixed with 5µl of Random primers and incubated at 95oC for 3 minutes followed by  incubation  at 4oC for  5 minutes.19µl of labeling master mix containing Cy5-dUTP(For IP samples) or Cy3-dUTP(For WCE samples), dNTP, Buffer and Klenow, were added to the denatured DNA sample and incubated at 37oC for 2 hours followed by enzyme inactivation at 65oC for 10 minutes

extract_protocol: The cell nuclei  were subjected to chromatin digestion so as to give a smear of DNA prominently lying in range of 200–500bp by incubating at 37°C for 10 minutes with EZ-Zyme Enzymatic cocktail, provided with the EZ-Zyme Chromatin Prep Kit (Millipore). Androgen Receptor antibody ChIP Validated Antibody (Millipore catalog number 06-680, lot/batch number 2167784) were added separately and incubated for 2 hour at 30°C followed by incubation with fresh Protein A agarose magnetic beads. Cleaved chromatin was immunoprecipitated using the Magna ChIP A/G kit (Millipore).

tag: dna shearing

value: Unsheared DNA

tag: chip antibody

value: none (input DNA)

value: DNA sheared in the range of 250-500bp


title: HFD ATDC, rep 3

description: FACS Sorted Live cells

source_name: ATDC from Gonadal Adipose Tissue from from obese HFD fed mice

tag: gender

tag: strain

value: Dendritic Cell


title: HFD ATDC, rep 1

description: FACS Sorted Live cells

tag: cell type


title: brain NAc_control_rep5

value: male


title: HFD PA, rep 2

description: FACS Sorted Live cells


title: HFD ATDC, rep 2

description: FACS Sorted Live cells


title: HFD PA, rep 1

description: FACS Sorted Live cells


title: Finding novel targets regulated by AR in breast cancer cells_1

value: Androgen Receptor antibody ChIP Validated Antibody


title: HFD CD11c- ATM, rep 2

description: FACS Sorted Live cells

source_name: CD11c- ATM from Gonadal Adipose Tissue from obese HFD fed mice


title: HFD CD11c- ATM, rep 1

description: FACS Sorted Live cells


title: HFD CD11c- ATM, rep 3

description: FACS Sorted Live cells


title: HFD CD11c+ ATM, rep 1

description: FACS Sorted Live cells

source_name: CD11c+ ATM from Gonadal Adipose Tissue from obese HFD fed mice


title: Individual_3_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R03C01
Sample_well: D07
Sample_plate: 8

value: female


title: HFD CD11c+ ATM, rep 2

description: FACS Sorted Live cells


title: ND PA, rep 3

description: FACS Sorted Live cells

source_name: PA from Gonadal Adipose Tissue from lean ND fed mice

value: Lean


title: Individual_2_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R02C01
Sample_well: B07
Sample_plate: 8


title: HFD CD11c+ ATM, rep 3

description: FACS Sorted Live cells


title: ND PA, rep 2

description: FACS Sorted Live cells


title: ND PA, rep 1

description: FACS Sorted Live cells


title: ND ATDC, rep 2

description: FACS Sorted Live cells

source_name: ATDC from Gonadal Adipose Tissue from lean ND fed mice


title: ND CD11c- ATM, rep 2

description: FACS Sorted Live cells

source_name: CD11c- ATM from Gonadal Adipose Tissue from lean ND fed mice


title: ND CD11c- ATM, rep 1

description: FACS Sorted Live cells


title: ND ATDC, rep 1

description: FACS Sorted Live cells


title: Individual_1_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R01C01
Sample_well: H07
Sample_plate: 8


title: Individual_5_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R05C01
Sample_well: B09
Sample_plate: 8


title: Vehicle_1 [72 hr]

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: Gene expression data from F1 mice treated with Vehicle

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

source_name: F1 mice treated with Vehicle, biological replicate 1

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: 10-12 week old C57Bl/6 and B6D2F1 mice were purchased from the Jackson Laboratoires.  To initiate GVHD, splenocytes equaling 4X10^7 T cells were i.v. injected into F1 host mice.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: F1 mice (n=4-5) were treated i.p. with 15μg/kg TCDD on day 0, or vehicle or 10mg/kg Cl-BBQ on days 0, 1 and 2. Mice were sacrificed on day 3 and alloresponding CD4+ T cells (at least 2 cell divisions based on CFSE dilution) were isolated by pan-CD4 microbeads followed by FACS sorting.

tag: time point

value: 72 hr

tag: host strain

value: Spleen and lymph node

tag: treatment

value: Vehicle treated


title: TCDD_1 [72 hr]

description: Gene expression data from F1 mice treated with TCDD

source_name: F1 mice treated with TCDD, biological replicate 1

value: TCDD treated


title: TCDD_2 [72 hr]

source_name: F1 mice treated with TCDD, biological replicate 2


title: Vehicle_3 [72 hr]

source_name: F1 mice treated with Vehicle, biological replicate 3


title: Vehicle_2 [72 hr]

source_name: F1 mice treated with Vehicle, biological replicate 2


title: BBQ_5 [72 hr]

description: Gene expression data from F1 mice treated with Cl-BBQ

source_name: F1 mice treated with Cl-BBQ, biological replicate 5

value: BBQ treated


title: BBQ_4 [72 hr]

source_name: F1 mice treated with Cl-BBQ, biological replicate 4


title: Vehicle_4 [72 hr]

source_name: F1 mice treated with Vehicle, biological replicate 4


title: TCDD_4 [72 hr]

source_name: F1 mice treated with TCDD, biological replicate 4


title: TCDD_3 [72 hr]

source_name: F1 mice treated with TCDD, biological replicate 3


title: Plasma_HACI_rep6

city: shanghai

first: tian

last: chunou

address: 168 changhai road

department: Neurosurgery Department

institute: Changhai Hospital, Second Military Medical University, China

description: microRNA expression in human plasma of patients with hyperacute cerebral infarction with stroke onset in 6 hours

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing:
Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6 (Agilent technologies, Santa Clara, CA, US).
When the difference of one microRNA in certain sample between the signal detected by probe and background signal was not significant, it would be marked with “absent” and given a identical value, such as “-3.1303349”.

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVanaTM PARISTM(Cat # AM1556, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Total RNA was quantified using a NanoDrop-2000 spectrophotometer.

treatment_protocol: Blood samples from the HACI group and the HVT group were obtained and immediately centrifuged. The supernatants were transferred to RNase-free tubes and stored at -80°C.

tag: disease state

value: HACI

value: Plasma

tag: age

tag: clinical outcome (mrs on discharge)

tag: stroke subtype (toast)

value: cardioembolic infarct

tag: stroke subtype (ocsp)

value: total anterior circulation infarction


title: Plasma_HVT_rep1

description: microRNA expression in human plasma of healthy controls

value: control


title: Plasma_HACI_rep5

value: undetermined etiology


title: Plasma_HVT_rep3


title: Plasma_HVT_rep4


title: Plasma_HVT_rep2


title: Individual_4_1997

description:
#Individual ID: unique ID for each participant
Sentrix_id: 7497398092
Sentrix_position: R04C01
Sample_well: B08
Sample_plate: 8

source_name: Whole blood

tag: Sex

tag: individual id


title: Plasma_HACI_rep2

tag: tissue

value: partial anterior circulation infarction


title: BBQ_3 [72 hr]

source_name: F1 mice treated with Cl-BBQ, biological replicate 3


title: Plasma_HACI_rep7


title: Plasma_HACI_rep1

value: posterior circulation infarct


title: Plasma_HACI_rep4

value: male

value: large artery atherosclerosis


title: Plasma_HACI_rep3

value: female


title: BBQ_1 [72 hr]

source_name: F1 mice treated with Cl-BBQ, biological replicate 1


title: BBQ_2 [72 hr]

source_name: F1 mice treated with Cl-BBQ, biological replicate 2


title: 254706910050_b2 - BIG1.NOCO.TR2 vs WT.NOCO.TR2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: What are the gene networks associated with BIGUN function during Hyaloperonospora arabidopsidis infection?

hyb_protocol: WT.NOCO.TR2 Cy5 / BIG1.NOCO.TR2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Media: soil Hygrometry: 60% Temperature: 21°C Light: 25 klux

extract_protocol: WT.NOCO.TR2:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Hyaloperonospora arabidopsidis - environmental treatment - pathogen infection,hyaloperonospora arabidopsidis:quantity 5000 time 7day . Rosettes of 5 weeks old plants were sprayed with a total amount of 1mL of 5000 spores /mL from freshly cultured Hyaloperonospora arabidopsidis.

tag: cultivar

value: columbia

value: leaf

tag: genotype

value: wildtype

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

value: boyes 3.90

value: bigun 1 mutant


title: 254706910050_b1 - WT.NOCO.TR2 vs BIG1.NOCO.TR2

hyb_protocol: BIG1.NOCO.TR2 Cy5 / WT.NOCO.TR2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910049_b4 - BIG2.NOCO.TR1 vs WT.NOCO.TR1

hyb_protocol: WT.NOCO.TR1 Cy5 / BIG2.NOCO.TR1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: WT.NOCO.TR1:100mg. (Qiagen_RNeasy.pdf)

value: bigun 2 mutant


title: 254706910050_b3 - WT.NOCO.TR2 vs BIG2.NOCO.TR2

hyb_protocol: BIG2.NOCO.TR2 Cy5 / WT.NOCO.TR2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910050_b4 - BIG2.NOCO.TR2 vs WT.NOCO.TR2

hyb_protocol: WT.NOCO.TR2 Cy5 / BIG2.NOCO.TR2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910049_b3 - WT.NOCO.TR1 vs BIG2.NOCO.TR1

hyb_protocol: BIG2.NOCO.TR1 Cy5 / WT.NOCO.TR1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910037_b2 - BIG1.NOCO.TR3 vs WT.NOCO.TR3

hyb_protocol: WT.NOCO.TR3 Cy5 / BIG1.NOCO.TR3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: WT.NOCO.TR3:100mg. (Qiagen_RNeasy.pdf)


title: 254706910037_b4 - BIG2.NOCO.TR3 vs WT.NOCO.TR3

hyb_protocol: WT.NOCO.TR3 Cy5 / BIG2.NOCO.TR3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910049_b1 - WT.NOCO.TR1 vs BIG1.NOCO.TR1

hyb_protocol: BIG1.NOCO.TR1 Cy5 / WT.NOCO.TR1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Patient 1_Tumoral

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

source_name: Red fluorescence glioma

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by submitter

value: Red fluorescence glioma


title: 254706910037_b3 - WT.NOCO.TR3 vs BIG2.NOCO.TR3

hyb_protocol: BIG2.NOCO.TR3 Cy5 / WT.NOCO.TR3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910049_b2 - BIG1.NOCO.TR1 vs WT.NOCO.TR1

hyb_protocol: WT.NOCO.TR1 Cy5 / BIG1.NOCO.TR1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: WL CD11c+ ATM, rep 3

description: FACS Sorted Live cells

source_name: CD11c+ ATM from Gonadal Adipose Tissue from weight loss WL mice

tag: gender

value: Male

value: Gonadal Adipose Tissue

tag: body weight

value: Weight Loss

value: Macrophage


title: 254706910037_b1 - WT.NOCO.TR3 vs BIG1.NOCO.TR3

hyb_protocol: BIG1.NOCO.TR3 Cy5 / WT.NOCO.TR3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Patient 7_Tumoral


title: Patient 7_Normal

source_name: Non-fluorescence brain

value: Non-fluorescence brain


title: 254706910035_b3 - WT.NT.TR2 vs BIG2.NT.TR2

hyb_protocol: BIG2.NT.TR2 Cy5 / WT.NT.TR2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: BIG2.NT.TR2:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

extract_protocol: WT.NT.TR2:100mg. (Qiagen_RNeasy.pdf)