title: Primary patient sample_MMRC0267_1_GEP

source_name: Sample from patient MMRC0267


title: Primary patient sample_MMRC0312_1_GEP

status: Public on Jan 20 2011

type: RNA

city: Cambridge

first: Michael

middle: Anthony

last: Chapman

state: MA

address: 7 Cambridge Center

country: USA

institute: Broad Institute

description: Gene expression data from untreated cells

hyb_protocol: Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer.

data_processing: Data were extracted from CEL files by GenePattern ExpressionFileCreator version 8, using RMA with quantile normalization and background correction.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Sample from patient MMRC0312

label_protocol: 1-2 ug of Total RNA was labeled using the One-Cycle Target Labeling kit from Affymetrix as per the manufacturers suggestion.

growth_protocol: After informed consent bone marrow aspirates were collected in sodium citrate tubes at MMRC member institutions and shipped by overnight courier to the MMRC Tissue Bank (Scottsdale, Arizona).  White blood cells were collected after red cell lysis using ACK reagent.  Plasma cells were selected using CD138 and the RoboSep (StemCell Technologies) as per the manufacturers protocol.  The purified plasma cells were lysed in 1 ml of TRIzol Reagent (Life Technologies).

extract_protocol: RNA was extracted from the TRIzol suspension using the manufacturers protocol..  The RNA was subsequently cleaned-up with a Qiagen RNeasy mini or micro kit as per the manufacturers suggestion..  RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer.

treatment_protocol: No post collection treatment was performed.

tag: cell type

value: CD138-selected bone marrow cells


title: VARI126T

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression ratios were obtained from human kidney tumor cell lines.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with MBNI re-mapped CDF files, version 12.

label: biotin

source_name: Homo Sapiens

label_protocol: 10 ug of Qiagen-purified total RNA

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

tag: tissue

value: clear cell

tag: mutation

value: VHL


title: VARI144T

value: unknown


title: Primary patient sample_MMRC0298_1_GEP

source_name: Sample from patient MMRC0298


title: VARI130T


title: Primary patient sample_MMRC0282_1_GEP

source_name: Sample from patient MMRC0282


title: VARI175T


title: Normal HOSE2225

city: Boston

last: Birrer

address: 70 Blossom Street

department: Medicine

institute: MGH

description: Gene expression data from ovarian surface epithelial cells

hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).

scan_protocol: Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)

data_processing: Robust Multi-Array Analysis was performed

source_name: Ovarian surface epithelial cells

label_protocol: Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a single round of amplification

extract_protocol: Total RNA was isolated using the RNeasy Micro kit (Qiagen)

treatment_protocol: Tumor specimens were obtained from 185 previously untreated late-stage (III–IV) high-grade ovarian cancer patients. A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens were used as control

value: Normal ovarian surface epithelium


title: Primary patient sample_MMRC0272_1_GEP

source_name: Sample from patient MMRC0272


title: Primary patient sample_MMRC0264_1_GEP

source_name: Sample from patient MMRC0264


title: Normal HOSE2061


title: Primary patient sample_MMRC0259_1_GEP

source_name: Sample from patient MMRC0259


title: Primary patient sample_MMRC0283_1_GEP

source_name: Sample from patient MMRC0283


title: VARI176T


title: Normal HOSE2226


title: Primary patient sample_MMRC0268_1_GEP

source_name: Sample from patient MMRC0268


title: Primary patient sample_MMRC0281_1_GEP

source_name: Sample from patient MMRC0281


title: Primary patient sample_MMRC0258_1_GEP

source_name: Sample from patient MMRC0258


title: Primary patient sample_MMRC0277_1_GEP

source_name: Sample from patient MMRC0277


title: Primary patient sample_MMRC0280_1_GEP

source_name: Sample from patient MMRC0280


title: VARI116T


title: Primary patient sample_MMRC0250_1_GEP

source_name: Sample from patient MMRC0250


title: Primary patient sample_MMRC0256_1_GEP

source_name: Sample from patient MMRC0256


title: Normal HOSE2064


title: VARI115T


title: VARI108T


title: Primary patient sample_MMRC0252_1_GEP

source_name: Sample from patient MMRC0252


title: Primary patient sample_MMRC0260_1_GEP

source_name: Sample from patient MMRC0260


title: Primary patient sample_MMRC0249_1_GEP

source_name: Sample from patient MMRC0249


title: VARI102T

source_name: Homo Sapiens


title: Primary patient sample_MMRC0248_1_GEP

source_name: Sample from patient MMRC0248


title: Primary patient sample_MMRC0246_1_GEP

source_name: Sample from patient MMRC0246


title: Primary patient sample_MMRC0247_1_GEP

source_name: Sample from patient MMRC0247


title: VARI093T

value: ESRRG

value: PC

value: PTPRF

value: PTPRJ

value: TRAD


title: VARI094T

value: DEK

value: MAFG


title: VARI092T

value: CAD


title: VARI091T


title: Primary patient sample_MMRC0240_1_GEP

source_name: Sample from patient MMRC0240


title: Primary patient sample_MMRC0239_1_GEP

source_name: Sample from patient MMRC0239


title: Primary patient sample_MMRC0224_1_GEP

source_name: Sample from patient MMRC0224


title: VARI113T


title: Primary patient sample_MMRC0238_1_GEP

source_name: Sample from patient MMRC0238


title: Primary patient sample_MMRC0245_1_GEP

source_name: Sample from patient MMRC0245


title: Normal HOSE2237

source_name: Ovarian surface epithelial cells


title: Primary patient sample_MMRC0243_1_GEP

source_name: Sample from patient MMRC0243


title: Primary patient sample_MMRC0233_1_GEP

source_name: Sample from patient MMRC0233


title: Primary patient sample_MMRC0228_1_GEP

source_name: Sample from patient MMRC0228


title: VARI101T


title: VARI098T

value: ATRX

value: BRE

value: NIN

value: NIPBL


title: Normal HOSE2008


title: Teffs at day 10, biological rep2

city: Munich

first: Iryna

last: Prots

address: Pettenkoferstrasse 8a

department: Rheumatology

country: Germany

institute: University of Munich

description: Gene expression data from CD25+ T cells at day 10 incubated without IL4, donor 2

hyb_protocol: 15 µg of fragmented cRNA were hybridized on the GeneChip HG-U133A array (Affymetrix). Hybridization was performed in a GeneChip Hybridization Oven 640 (Affymetrix) for 16 hours at 45°C.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed in GeneSpring GX10 software (Agilent Technologies) applying a MAS5 probe summarization algorithm using default analysis settings, logarithmic transformation of the signal intensities.

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

growth_protocol: Cell cultures were conducted in RPMI 1640 medium supplemented with penicillin G/streptomycin (50 U/ml), L-glutamine (2 mM), and 10% NHS at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated using the RNeasy Minikit (Qiagen, Hilden, Germany) with an additional DNA digestion step (RNase Free DNase Set; Qiagen) according to the manufacturer's instructions.

treatment_protocol: Purified naive CD25- CD4 T cells were incubated at a concentration of 1 x 106/ml in the presence of 1 x 106/ml irradiated  (30 Gy) autologous feeder cells in a final volume of 2 ml in 24-well cell culture plates for 3, 5, 7 and 10 days. IL-4 at a final concentration of 6.25 ng/ml was added or not to the cultures to generate Tregs or Teffs, respectively.

tag: time

value: day 10

tag: treatment

value: no IL4

tag: cell surface marker

tag: individual

value: donor 2

value: CD25+ T cell


title: Primary patient sample_MMRC0242_1_GEP

source_name: Sample from patient MMRC0242

value: CD138-selected bone marrow cells


title: Primary patient sample_MMRC0226_1_GEP

source_name: Sample from patient MMRC0226


title: VARI086T

value: clear cell

value: CTSZ

value: STCH

value: VHL


title: VARI088T

value: ADSS


title: Primary patient sample_MMRC0227_1_GEP

source_name: Sample from patient MMRC0227


title: VARI090T

value: CLSPN


title: CD25- T cells at day 10 incubated without IL4, biological rep1

description: Gene expression data from CD25- T cells at day 10 incubated without IL4, donor 1

value: donor 1

value: CD25- T cell


title: Primary patient sample_MMRC0207_1_GEP

source_name: Sample from patient MMRC0207


title: Tregs at day 10, biological rep3

description: Gene expression data from CD25+ T cells at day 10 incubated with IL4, donor 3

value: donor 3


title: CD25- T cells at day 10 incubated without IL4, biological rep2

description: Gene expression data from CD25- T cells at day 10 incubated without IL4, donor 2


title: CD25- T cells at day 10 incubated without IL4, biological rep3

description: Gene expression data from CD25- T cells at day 10 incubated without IL4, donor 3


title: Teffs at day 10, biological rep1

description: Gene expression data from CD25+ T cells at day 10 incubated without IL4, donor 1


title: Tregs at day 10, biological rep2

description: Gene expression data from CD25+ T cells at day 10 incubated with IL4, donor 2


title: Primary patient sample_MMRC0203_1_GEP

source_name: Sample from patient MMRC0203


title: Primary patient sample_MMRC0208_1_GEP

source_name: Sample from patient MMRC0208


title: Tregs at day 10, biological rep1

description: Gene expression data from CD25+ T cells at day 10 incubated with IL4, donor 1


title: Primary patient sample_MMRC0244_1_GEP

source_name: Sample from patient MMRC0244


title: Primary patient sample_MMRC0204_1_GEP

source_name: Sample from patient MMRC0204


title: CD25- T cells at day 10 incubated with IL4, biological rep1

description: Gene expression data from CD25- T cells at day 10 incubated with IL4, donor 1


title: Primary patient sample_MMRC0201_1_GEP

source_name: Sample from patient MMRC0201


title: CD25- T cells at day 10 incubated with IL4, biological rep2

description: Gene expression data from CD25- T cells at day 10 incubated with IL4, donor 2


title: CD25- T cells at day 10 incubated with IL4, biological rep3

description: Gene expression data from CD25- T cells at day 10 incubated with IL4, donor 3


title: Primary patient sample_MMRC0194_1_GEP

source_name: Sample from patient MMRC0194


title: VARI076T

source_name: Homo Sapiens

value: unknown


title: Primary patient sample_MMRC0220_1_GEP

source_name: Sample from patient MMRC0220


title: VARI085T


title: Primary patient sample_MMRC0200_1_GEP

source_name: Sample from patient MMRC0200


title: VARI074T


title: Primary patient sample_MMRC0206_1_GEP

source_name: Sample from patient MMRC0206


title: VARI084T

value: PML


title: VARI083T


title: VARI075T


title: Primary patient sample_MMRC0198_1_GEP

source_name: Sample from patient MMRC0198


title: Teffs at day 7, biological rep2

description: Gene expression data from CD25+ T cells at day 7 incubated without IL4, donor 2

value: day 7


title: Teffs at day 7, biological rep1

description: Gene expression data from CD25+ T cells at day 7 incubated without IL4, donor 1


title: Primary patient sample_MMRC0184_1_GEP

source_name: Sample from patient MMRC0184


title: Primary patient sample_MMRC0197_1_GEP

source_name: Sample from patient MMRC0197


title: Primary patient sample_MMRC0187_1_GEP

source_name: Sample from patient MMRC0187


title: VARI072T


title: CD25- T cells at day 7 incubated without IL4, biological rep3

description: Gene expression data from CD25- T cells at day 7 incubated without IL4, donor 3


title: Primary patient sample_MMRC0195_1_GEP

description: Gene expression data from untreated cells

source_name: Sample from patient MMRC0195


title: Primary patient sample_MMRC0196_1_GEP

source_name: Sample from patient MMRC0196


title: VARI068T

description: Gene expression ratios were obtained from human kidney tumor cell lines.


title: Teffs at day 7, biological rep3

description: Gene expression data from CD25+ T cells at day 7 incubated without IL4, donor 3


title: Primary patient sample_MMRC0186_1_GEP

source_name: Sample from patient MMRC0186


title: Primary patient sample_MMRC0191_1_GEP

source_name: Sample from patient MMRC0191


title: Primary patient sample_MMRC0189_1_GEP

source_name: Sample from patient MMRC0189


title: Primary patient sample_MMRC0185_1_GEP

source_name: Sample from patient MMRC0185


title: Primary patient sample_MMRC0192_1_GEP

source_name: Sample from patient MMRC0192


title: Primary patient sample_MMRC0183_1_GEP

source_name: Sample from patient MMRC0183


title: VARI070T

value: APC

value: BCOR

value: NOV

value: PDHX


title: Primary patient sample_MMRC0180_1_GEP

source_name: Sample from patient MMRC0180

value: CD138-selected bone marrow cells


title: Primary patient sample_MMRC0182_1_GEP

source_name: Sample from patient MMRC0182


title: VARI058T

source_name: Homo Sapiens

value: clear cell


title: Primary patient sample_MMRC0181_1_GEP

source_name: Sample from patient MMRC0181


title: VARI062T


title: Tregs at day 7, biological rep2

description: Gene expression data from CD25+ T cells at day 7 incubated with IL4, donor 2

value: donor 2

value: CD25+ T cell


title: Primary patient sample_MMRC0172_1_GEP

source_name: Sample from patient MMRC0172


title: Primary patient sample_MMRC0175_1_GEP

source_name: Sample from patient MMRC0175


title: VARI061T


title: Primary patient sample_MMRC0176_1_GEP

source_name: Sample from patient MMRC0176


title: Tregs at day 7, biological rep3

description: Gene expression data from CD25+ T cells at day 7 incubated with IL4, donor 3


title: Tregs at day 7, biological rep1

description: Gene expression data from CD25+ T cells at day 7 incubated with IL4, donor 1


title: Primary patient sample_MMRC0173_1_GEP

source_name: Sample from patient MMRC0173


title: CD25- T cells at day 7 incubated without IL4, biological rep2

description: Gene expression data from CD25- T cells at day 7 incubated without IL4, donor 2

value: no IL4


title: CD25- T cells at day 7 incubated without IL4, biological rep1

description: Gene expression data from CD25- T cells at day 7 incubated without IL4, donor 1


title: VARI055T

value: VHL


title: Primary patient sample_MMRC0179_1_GEP

source_name: Sample from patient MMRC0179


title: VARI051T

value: PTPLB


title: Primary patient sample_MMRC0168_1_GEP

source_name: Sample from patient MMRC0168


title: VARI056T


title: Primary patient sample_MMRC0170_1_GEP

source_name: Sample from patient MMRC0170


title: CD25- T cells at day 7 incubated with IL4, biological rep1

description: Gene expression data from CD25- T cells at day 7 incubated with IL4, donor 1

value: donor 1


title: CD25- T cells at day 7 incubated with IL4, biological rep3

description: Gene expression data from CD25- T cells at day 7 incubated with IL4, donor 3

value: CD25- T cell


title: Primary patient sample_MMRC0169_1_GEP

source_name: Sample from patient MMRC0169


title: Primary patient sample_MMRC0164_1_GEP

source_name: Sample from patient MMRC0164


title: Primary patient sample_MMRC0163_1_GEP

source_name: Sample from patient MMRC0163


title: Primary patient sample_MMRC0161_1_GEP

source_name: Sample from patient MMRC0161


title: Teffs at day 5, biological rep1

description: Gene expression data from CD25+ T cells at day 5 incubated without IL4, donor 1

value: day 5


title: Primary patient sample_MMRC0174_1_GEP

source_name: Sample from patient MMRC0174


title: VARI049T


title: Primary patient sample_MMRC0160_1_GEP

source_name: Sample from patient MMRC0160


title: Teffs at day 5, biological rep3

description: Gene expression data from CD25+ T cells at day 5 incubated without IL4, donor 3

value: donor 3


title: VARI039T

value: PTEN

value: SPIB


title: Primary patient sample_MMRC0155_1_GEP

source_name: Sample from patient MMRC0155


title: VARI045T


title: CD25- T cells at day 7 incubated with IL4, biological rep2

description: Gene expression data from CD25- T cells at day 7 incubated with IL4, donor 2

value: day 7


title: Primary patient sample_MMRC0165_1_GEP

source_name: Sample from patient MMRC0165


title: Primary patient sample_MMRC0167_1_GEP

source_name: Sample from patient MMRC0167


title: CD25- T cells at day 5 incubated without IL4, biological rep3

description: Gene expression data from CD25- T cells at day 5 incubated without IL4, donor 3


title: Primary patient sample_MMRC0153_1_GEP

source_name: Sample from patient MMRC0153


title: Primary patient sample_MMRC0156_1_GEP

source_name: Sample from patient MMRC0156


title: Primary patient sample_MMRC0159_1_GEP

source_name: Sample from patient MMRC0159


title: Primary patient sample_MMRC0171_1_GEP

source_name: Sample from patient MMRC0171


title: CD25- T cells at day 5 incubated without IL4, biological rep2

description: Gene expression data from CD25- T cells at day 5 incubated without IL4, donor 2


title: VARI034T

source_name: Homo Sapiens


title: Primary patient sample_MMRC0149_1_GEP

source_name: Sample from patient MMRC0149


title: Primary patient sample_MMRC0150_1_GEP

source_name: Sample from patient MMRC0150


title: VARI047T

value: MLL


title: Primary patient sample_MMRC0158_1_GEP

source_name: Sample from patient MMRC0158


title: CD25- T cells at day 5 incubated with IL4, biological rep3

description: Gene expression data from CD25- T cells at day 5 incubated with IL4, donor 3


title: Primary patient sample_MMRC0141_1_GEP

source_name: Sample from patient MMRC0141


title: VARI033T

value: DGKQ

value: GNAZ

value: TRIO

value: UMPS


title: VARI029T

value: clear cell

value: unknown


title: VARI037T

value: OCRL


title: VARI030T

value: ARNT

value: ICK

value: VHL


title: Primary patient sample_MMRC0139_1_GEP

source_name: Sample from patient MMRC0139

value: CD138-selected bone marrow cells


title: CD25- T cells at day 5 incubated with IL4, biological rep2

description: Gene expression data from CD25- T cells at day 5 incubated with IL4, donor 2

value: day 5

value: donor 2

value: CD25- T cell


title: Primary patient sample_MMRC0145_1_GEP

description: Gene expression data from untreated cells

source_name: Sample from patient MMRC0145


title: Teffs at day 5, biological rep2

description: Gene expression data from CD25+ T cells at day 5 incubated without IL4, donor 2

value: no IL4

value: CD25+ T cell


title: Primary patient sample_MMRC0148_1_GEP

source_name: Sample from patient MMRC0148


title: VARI028T

description: Gene expression ratios were obtained from human kidney tumor cell lines.


title: Primary patient sample_MMRC0147_1_GEP

source_name: Sample from patient MMRC0147


title: Tregs at day 5, biological rep2

description: Gene expression data from CD25+ T cells at day 5 incubated with IL4, donor 2


title: Primary patient sample_MMRC0162_1_GEP

source_name: Sample from patient MMRC0162


title: Primary patient sample_MMRC0154_1_GEP

source_name: Sample from patient MMRC0154


title: VARI027T


title: Primary patient sample_MMRC0144_1_GEP

source_name: Sample from patient MMRC0144


title: Primary patient sample_MMRC0136_1_GEP

source_name: Sample from patient MMRC0136


title: Tregs at day 5, biological rep1

description: Gene expression data from CD25+ T cells at day 5 incubated with IL4, donor 1

value: donor 1


title: Primary patient sample_MMRC0140_1_GEP

source_name: Sample from patient MMRC0140


title: Primary patient sample_MMRC0137_1_GEP

source_name: Sample from patient MMRC0137


title: Teffs at day 3, biological rep1

description: Gene expression data from CD25+ T cells at day 3 incubated without IL4, donor 1

value: day 3


title: VARI025T


title: VARI026T

value: MGA


title: CD25- T cells at day 3 incubated without IL4, biological rep3

description: Gene expression data from CD25- T cells at day 3 incubated without IL4, donor 3

value: donor 3


title: Tregs at day 5, biological rep3

description: Gene expression data from CD25+ T cells at day 5 incubated with IL4, donor 3


title: VARI021T


title: Primary patient sample_MMRC0133_1_GEP

source_name: Sample from patient MMRC0133


title: Primary patient sample_MMRC0125_1_GEP

source_name: Sample from patient MMRC0125


title: Teffs at day 3, biological rep3

description: Gene expression data from CD25+ T cells at day 3 incubated without IL4, donor 3


title: CD25- T cells at day 3 incubated without IL4, biological rep2

description: Gene expression data from CD25- T cells at day 3 incubated without IL4, donor 2


title: VARI024T

source_name: Homo Sapiens


title: Primary patient sample_MMRC0123_1_GEP

source_name: Sample from patient MMRC0123


title: VARI031T


title: Primary patient sample_MMRC0131_1_GEP

source_name: Sample from patient MMRC0131


title: Primary patient sample_MMRC0111_1_GEP

source_name: Sample from patient MMRC0111


title: Tregs at day 3, biological rep1

description: Gene expression data from CD25+ T cells at day 3 incubated with IL4, donor 1


title: Primary patient sample_MMRC0107_1_GEP

source_name: Sample from patient MMRC0107


title: CD25- T cells at day 5 incubated without IL4, biological rep1

description: Gene expression data from CD25- T cells at day 5 incubated without IL4, donor 1


title: VARI008T


title: CD25- T cells at day 5 incubated with IL4, biological rep1

description: Gene expression data from CD25- T cells at day 5 incubated with IL4, donor 1


title: Primary patient sample_MMRC0124_1_GEP

source_name: Sample from patient MMRC0124


title: Primary patient sample_MMRC0108_1_GEP

source_name: Sample from patient MMRC0108


title: VARI013T


title: Tregs at day 3, biological rep2

description: Gene expression data from CD25+ T cells at day 3 incubated with IL4, donor 2


title: VARI015T


title: Primary patient sample_MMRC0112_1_GEP

source_name: Sample from patient MMRC0112


title: CD25- T cells at day 3 incubated with IL4, biological rep3

description: Gene expression data from CD25- T cells at day 3 incubated with IL4, donor 3


title: CD25- T cells at day 3 incubated with IL4, biological rep2

description: Gene expression data from CD25- T cells at day 3 incubated with IL4, donor 2


title: Primary patient sample_MMRC0122_1_GEP

source_name: Sample from patient MMRC0122


title: Primary patient sample_MMRC0134_1_GEP

source_name: Sample from patient MMRC0134


title: Primary patient sample_MMRC0100_1_GEP

source_name: Sample from patient MMRC0100


title: VARI016T

value: MERTK


title: Primary patient sample_MMRC0138_1_GEP

source_name: Sample from patient MMRC0138


title: Primary patient sample_MMRC0128_1_GEP

source_name: Sample from patient MMRC0128


title: Primary patient sample_MMRC0135_1_GEP

source_name: Sample from patient MMRC0135


title: VARI006T

value: clear cell


title: Primary patient sample_MMRC0110_1_GEP

source_name: Sample from patient MMRC0110


title: Primary patient sample_MMRC0102_1_GEP

source_name: Sample from patient MMRC0102


title: Primary patient sample_MMRC0104_1_GEP

source_name: Sample from patient MMRC0104


title: VARI007T

source_name: Homo Sapiens

value: DGKK

value: TEK


title: Primary patient sample_MMRC0097_1_GEP

source_name: Sample from patient MMRC0097


title: Teffs at day 3, biological rep2

description: Gene expression data from CD25+ T cells at day 3 incubated without IL4, donor 2


title: Primary patient sample_MMRC0101_1_GEP

description: Gene expression data from untreated cells

source_name: Sample from patient MMRC0101


title: CD25- T cells at day 3 incubated without IL4, biological rep1

description: Gene expression data from CD25- T cells at day 3 incubated without IL4, donor 1


title: Primary patient sample_MMRC0098_1_GEP

source_name: Sample from patient MMRC0098


title: Primary patient sample_MMRC0105_1_GEP

source_name: Sample from patient MMRC0105


title: Primary patient sample_MMRC0094_1_GEP

source_name: Sample from patient MMRC0094


title: naive T cells at day 0, biological rep1

description: Gene expression data from naive T cells at day 0, donor 1

source_name: naive T cells at day 0, donor 1

value: day 0

value: naive T cell


title: Primary patient sample_MMRC0093_1_GEP

source_name: Sample from patient MMRC0093


title: Primary patient sample_MMRC0109_1_GEP

source_name: Sample from patient MMRC0109


title: Primary patient sample_MMRC0091_1_GEP

source_name: Sample from patient MMRC0091


title: Primary patient sample_MMRC0090_1_GEP

source_name: Sample from patient MMRC0090


title: Tregs at day 3, biological rep3

description: Gene expression data from CD25+ T cells at day 3 incubated with IL4, donor 3


title: Primary patient sample_MMRC0099_1_GEP

source_name: Sample from patient MMRC0099


title: Primary patient sample_MMRC0095_1_GEP

source_name: Sample from patient MMRC0095


title: naive T cells at day 0, biological rep3

description: Gene expression data from naive T cells at day 0, donor 3

source_name: naive T cells at day 0, donor 3


title: VARI005T

description: Gene expression ratios were obtained from human kidney tumor cell lines.

value: VHL


title: naive T cells at day 0, biological rep2

description: Gene expression data from naive T cells at day 0, donor 2

source_name: naive T cells at day 0, donor 2


title: VARI003T


title: Primary patient sample_MMRC0103_1_GEP

source_name: Sample from patient MMRC0103

value: CD138-selected bone marrow cells


title: VARI004T


title: Primary patient sample_MMRC0106_1_GEP

source_name: Sample from patient MMRC0106


title: Primary patient sample_MMRC0096_1_GEP

source_name: Sample from patient MMRC0096


title: Primary patient sample_MMRC0089_1_GEP

source_name: Sample from patient MMRC0089


title: Primary patient sample_MMRC0088_1_GEP

source_name: Sample from patient MMRC0088


title: CD25- T cells at day 3 incubated with IL4, biological rep1

description: Gene expression data from CD25- T cells at day 3 incubated with IL4, donor 1


title: Primary patient sample_MMRC0087_1_GEP

source_name: Sample from patient MMRC0087


title: Primary patient sample_MMRC0092_1_GEP

source_name: Sample from patient MMRC0092


title: iPSCs-HLCs_4_P1_Passage 15_replicate 2

city: Berlin

first: Justyna

last: Jozefczuk

address: Ihnestrasse 63

department: Vertebrate Genomics

institute: Max Planck Institute for Molecular Genetics

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina)

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.

tag: strain

value: iPS4-derived hepatocyte-like cells (protocol 1)

tag: developmental stage

value: Passage 15

value: iPSCs-derived hepatocyte-like cells (protocol 1)


title: SN12C_siRNA

source_name: Homo Sapiens

tag: cell line

value: PBRM siRNA


title: TK10_siRNA


title: iPSCs-HLCs_4_P1_Passage 15_replicate 1

description: replicate 1


title: SN12C_Mock

value: Mock


title: iPSCs-HLCs_2_P1_Passage 15_replicate 2

description: replicate 2

value: iPS2-derived hepatocyte-like cells (protocol 1)


title: TK10_Mock


title: iPSCs-HLCs_2_P1_Passage 15_replicate 1

description: replicate 1


title: hESCs-HLCs_P1_Passage 60_replicate 2

description: replicate 2

value: H1-derived hepatocyte-like cells (protocol 1)

value: Passage 60

value: hESCs-derived hepatocyte-like cells


title: Primary patient sample_MMRC0079_1_GEP

source_name: Sample from patient MMRC0079


title: 786-O_Mock


title: Primary patient sample_MMRC0084_1_GEP

source_name: Sample from patient MMRC0084


title: Fetal liver 2_18th week of gestation_replicate 2

description: replicate 2

source_name: single male donor

value: Stratagene, MVP total RNA

value: 18th week of gestation

value: fetal liver


title: Primary patient sample_MMRC0082_1_GEP

source_name: Sample from patient MMRC0082


title: Primary patient sample_MMRC0086_1_GEP

source_name: Sample from patient MMRC0086


title: Primary patient sample_MMRC0078_1_GEP

source_name: Sample from patient MMRC0078


title: Primary patient sample_MMRC0077_1_GEP

source_name: Sample from patient MMRC0077


title: Primary patient sample_MMRC0064_1_GEP

source_name: Sample from patient MMRC0064


title: Primary patient sample_MMRC0070_1_GEP

source_name: Sample from patient MMRC0070


title: Primary patient sample_MMRC0080_1_GEP

source_name: Sample from patient MMRC0080


title: Primary patient sample_MMRC0083_1_GEP

source_name: Sample from patient MMRC0083


title: Primary patient sample_MMRC0069_1_GEP

source_name: Sample from patient MMRC0069


title: Primary patient sample_MMRC0081_1_GEP

source_name: Sample from patient MMRC0081


title: Primary patient sample_MMRC0073_1_GEP

source_name: Sample from patient MMRC0073


title: Primary patient sample_MMRC0076_1_GEP

source_name: Sample from patient MMRC0076


title: 786-O_siRNA


title: Primary patient sample_MMRC0068_1_GEP

source_name: Sample from patient MMRC0068


title: Primary patient sample_MMRC0075_1_GEP

source_name: Sample from patient MMRC0075


title: Primary patient sample_MMRC0072_1_GEP

source_name: Sample from patient MMRC0072


title: Primary patient sample_MMRC0063_1_GEP

source_name: Sample from patient MMRC0063


title: Primary patient sample_MMRC0060_1_GEP

source_name: Sample from patient MMRC0060


title: Primary patient sample_MMRC0057_1_GEP

source_name: Sample from patient MMRC0057


title: Primary patient sample_MMRC0059_1_GEP

source_name: Sample from patient MMRC0059


title: Primary patient sample_MMRC0061_1_GEP

source_name: Sample from patient MMRC0061


title: Primary patient sample_MMRC0050_1_GEP

source_name: Sample from patient MMRC0050


title: iPSCs_2_Passage 10_replicate 1

description: replicate 1

source_name: iPS2 from HFF1

value: Passage 10

value: iPSCs


title: Fetal liver 2_18th week of gestation_replicate 1

description: replicate 1

source_name: single male donor


title: hESCs-HLCs_P1_Passage 60_replicate 1

description: replicate 1


title: iPSCs_4_Passage 10_replicate 1

description: replicate 1

source_name: iPS4 from HFF1


title: Primary patient sample_MMRC0049_1_GEP

source_name: Sample from patient MMRC0049


title: Primary patient sample_MMRC0048_1_GEP

source_name: Sample from patient MMRC0048


title: Primary patient sample_MMRC0053_1_GEP

source_name: Sample from patient MMRC0053


title: Primary patient sample_MMRC0052_1_GEP

source_name: Sample from patient MMRC0052


title: 14_U133A

first: Bin

last: Zheng

address: 65 Landsdowne Street

department: Center for Neurologic Diseases

institute: Brigham and Women's hospital

hyb_protocol: Standard Affymetrix protocols.

scan_protocol: Standard Affymetrix protocols.

data_processing: The data were processed and scaled to a target intensity of 100 for all probe sets by MAS5 in Biocondutor affy package.

source_name: SN, PD

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

growth_protocol: None.

treatment_protocol: None.

tag: age

value: substantia nigra

tag: diagnosis

value: Parkinson's disease


title: 5164_U133A


title: Primary patient sample_MMRC0045_1_GEP

source_name: Sample from patient MMRC0045

value: CD138-selected bone marrow cells


title: 4831_U133A


title: Primary patient sample_MMRC0042_1_GEP

source_name: Sample from patient MMRC0042


title: Primary patient sample_MMRC0046_1_GEP

source_name: Sample from patient MMRC0046


title: Primary patient sample_MMRC0041_1_GEP

source_name: Sample from patient MMRC0041


title: Primary patient sample_MMRC0043_1_GEP

source_name: Sample from patient MMRC0043


title: 290_U133A

source_name: SN, control

tag: sample type

value: control


title: Primary patient sample_MMRC0047_1_GEP

source_name: Sample from patient MMRC0047


title: 2729_U133A


title: Primary patient sample_MMRC0054_1_GEP

source_name: Sample from patient MMRC0054


title: Primary patient sample_MMRC0074_1_GEP

source_name: Sample from patient MMRC0074


title: 287_U133A


title: Primary patient sample_MMRC0039_1_GEP

source_name: Sample from patient MMRC0039


title: Primary patient sample_MMRC0055_1_GEP

source_name: Sample from patient MMRC0055


title: Primary patient sample_MMRC0056_1_GEP

source_name: Sample from patient MMRC0056


title: Primary patient sample_MMRC0058_1_GEP

source_name: Sample from patient MMRC0058


title: Primary patient sample_MMRC0065_1_GEP

source_name: Sample from patient MMRC0065


title: Primary patient sample_MMRC0051_1_GEP

source_name: Sample from patient MMRC0051


title: Primary patient sample_MMRC0062_1_GEP

source_name: Sample from patient MMRC0062


title: Primary patient sample_MMRC0040_1_GEP

source_name: Sample from patient MMRC0040


title: 2721_U133A

source_name: SN, PD


title: hESCs_Passage 56_replicate 1

description: replicate 1

value: Passage 56

value: hESCs


title: Primary patient sample_MMRC0085_1_GEP

source_name: Sample from patient MMRC0085


title: Primary patient sample_MMRC0071_1_GEP

source_name: Sample from patient MMRC0071


title: hESCs_Passage 56_replicate 2

description: replicate 2


title: iPSCs_2_Passage 10_replicate 2

description: replicate 2

source_name: iPS2 from HFF1


title: 3059_U133A


title: Fetal liver 1_18th week of gestation_replicate 2

description: replicate 2

source_name: single male donor


title: hESCs_Passage 55_replicate 2

description: replicate 2

value: Passage 55


title: HFF1-b_Neonatal, Passage 4_replicate 2

description: replicate 2

value: HFF1 (purchased from ATCC)

value: Neonatal, Passage 4

value: neonatal foreskin fibroblasts


title: HFF1-a_Neonatal, Passage 4_replicate 1

description: replicate 1


title: hESCs-HLCs_P2_Passage 60_replicate 2

description: replicate 2

value: H1-derived hepatocyte-like cells (protocol 2)

value: Passage 60


title: hESCs_Passage 55_replicate 1

description: replicate 1


title: iPSCs_4_Passage 10_replicate 2

description: replicate 2

source_name: iPS4 from HFF1


title: hESCs-HLCs_P2_Passage 60_replicate 1

description: replicate 1

value: hESCs-derived hepatocyte-like cells


title: 2525_U133A


title: Fetal liver 1_18th week of gestation_replicate 1

description: replicate 1

value: Stratagene, MVP total RNA

value: 18th week of gestation


title: hESCs_Passage 60_replicate 3

description: replicate 3


title: Primary patient sample_MMRC0044_1_GEP

source_name: Sample from patient MMRC0044


title: 252_U133A

source_name: SN, control


title: hESCs-HLCs_P2_Passage 60_replicate 3

description: replicate 3


title: hESCs_Passage 60_replicate 2

description: replicate 2


title: Primary patient sample_MMRC0038_1_GEP

source_name: Sample from patient MMRC0038


title: Primary patient sample_MMRC0036_1_GEP

source_name: Sample from patient MMRC0036


title: hESCs-HLCs_P1_Passage 53_replicate 2

description: replicate 2

value: H1-derived hepatocyte-like cells (protocol 1)

value: Passage 53


title: Primary patient sample_MMRC0035_1_GEP

source_name: Sample from patient MMRC0035


title: 223_U133A

value: substantia nigra


title: Primary patient sample_MMRC0034_1_GEP

source_name: Sample from patient MMRC0034


title: Primary patient sample_MMRC0033_1_GEP

source_name: Sample from patient MMRC0033


title: Primary patient sample_MMRC0037_1_GEP

source_name: Sample from patient MMRC0037


title: Primary patient sample_MMRC0032_1_GEP

source_name: Sample from patient MMRC0032


title: hESCs_Passage 60_replicate 1

description: replicate 1


title: Primary patient sample_MMRC0027_1_GEP

source_name: Sample from patient MMRC0027


title: Primary patient sample_MMRC0031_1_GEP

source_name: Sample from patient MMRC0031


title: 238_U133A


title: Primary patient sample_MMRC0028_1_GEP

source_name: Sample from patient MMRC0028


title: 2515_U133A

source_name: SN, PD

value: Parkinson's disease


title: Primary patient sample_MMRC0024_1_GEP

source_name: Sample from patient MMRC0024

value: CD138-selected bone marrow cells


title: Primary patient sample_MMRC0022_1_GEP

source_name: Sample from patient MMRC0022


title: hESCs-HLCs_P1_Passage 53_replicate 1

description: replicate 1


title: 222_U133A

value: control


title: Primary patient sample_MMRC0025_1_GEP

source_name: Sample from patient MMRC0025


title: 204_U133A


title: Primary patient sample_MMRC0030_1_GEP

source_name: Sample from patient MMRC0030


title: Primary patient sample_MMRC0021_1_GEP

source_name: Sample from patient MMRC0021


title: Primary patient sample_MMRC0029_1_GEP

source_name: Sample from patient MMRC0029


title: Primary patient sample_MMRC0009_1_GEP

source_name: Sample from patient MMRC0009


title: Primary patient sample_MMRC0026_1_GEP

source_name: Sample from patient MMRC0026


title: Primary patient sample_MMRC0020_1_GEP

source_name: Sample from patient MMRC0020


title: Primary patient sample_MMRC0018_1_GEP

source_name: Sample from patient MMRC0018


title: Primary patient sample_MMRC0013_1_GEP

source_name: Sample from patient MMRC0013


title: Primary patient sample_MMRC0012_1_GEP

source_name: Sample from patient MMRC0012


title: Primary patient sample_MMRC0015_1_GEP

source_name: Sample from patient MMRC0015


title: S.LEW(10)x12x2x3x5 _2

city: Toledo

first: Bina

last: Joe

state: OH

address: 3000 Arlington avenue

department: Physiology and Pharmacology

institute: University of toledo

description: S.LEW(10)x12x2x3x5 _2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: We have used R statistical program with the affylmGUI (Affymetrix .CEL files) to do the evaluation of  data set. The data was normalized using Robust Multiarray Averaging (RMA). After normalization, Linear Model Fit was completed. Contrast parameters - Experiment versus control were used to create the 'Table of Genes Ranked in order of Differential Expression'. The p values were adjusted using the Benjamini-Hochberg method (BH).

organism: Rattus norvegicus

source_name: S.LEW(10)x12x2x3x5 Congenic Rat  fed with Low-salt (0.3%) diet

growth_protocol: All rats born on the same day were selected and weaned at 30 days of age.

treatment_protocol: After weaning all rats were fed with Low-salt (0.3%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley).

value: S.LEW(10)x12x2x3x5 Congenic Rat Heart

tag: genotype

value: Congenic rat with Dahl S background

value: 53 days old S.LEW(10)x12x2x3x5 Congenic Rat


title: Primary patient sample_MMRC0008_1_GEP

source_name: Sample from patient MMRC0008


title: Primary patient sample_MMRC0019_1_GEP

source_name: Sample from patient MMRC0019


title: hESCs-HLCs_P1_Passage 53_replicate 3

description: replicate 3


title: hESCs_Passage 53_replicate 3

description: replicate 3

value: hESCs


title: S.LEW(10)x12x2x3x5 _3

description: S.LEW(10)x12x2x3x5 _3


title: 515L

description: C

hyb_protocol: standard Affy protocols

scan_protocol: standard Affy protocols

source_name: Human dopamine

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

extract_protocol: RNA from 500 DA neurons from the SNc of each specimen were extracted using the  Picopure™ RNA isolation kit

tag: age (y)

tag: disease state


title: 114_U133A

source_name: SN, control


title: hESCs_Passage 53_replicate 2

description: replicate 2


title: 515I

description: C


title: hESCs_Passage 53_replicate 1

description: replicate 1


title: 515K

description: C


title: 178_U133A


title: 515H

description: C


title: 515G

description: PD

value: Parkinson’s disease


title: 515F

description: PD


title: S.LEW(10)x12x2x3x5 _1

description: S.LEW(10)x12x2x3x5 _1


title: 515J

description: PD


title: Primary patient sample_MMRC0014_1_GEP

source_name: Sample from patient MMRC0014


title: Dahl S Rat_3

description: Dahl S Rat_3

source_name: Dahl S Rat fed with Low-salt (0.3%) diet

value: Dahl S Rat Heart

value: Dahl salt sensitive rat

value: 53 days old Dahl S Rat


title: Primary patient sample_MMRC0016_1_GEP

source_name: Sample from patient MMRC0016


title: Primary patient sample_MMRC0010_1_GEP

source_name: Sample from patient MMRC0010


title: Primary patient sample_MMRC0002_1_GEP

source_name: Sample from patient MMRC0002


title: Primary patient sample_MMRC0017_1_GEP

source_name: Sample from patient MMRC0017


title: Primary patient sample_MMRC0005_1_GEP

source_name: Sample from patient MMRC0005


title: Dahl S Rat_2

description: Dahl S Rat_2


title: 515E

description: PD


title: Primary patient sample_MMRC0006_1_GEP

source_name: Sample from patient MMRC0006


title: granulosa cell.6h Ad-GFP +FSK/PMA

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Standard Affymetrix

source_name: ovarian granulosa cells collected from ovaries 48 h after stimulation with pregnant mare's serum gonadotropin

label_protocol: Standard Affymetrix

growth_protocol: To isolate granulosa cells, ovaries were collected from rats 48 h after PMSG administration and processed as described previously.  Briefly, granulosa cells were isolated by follicular puncture, pooled, filtered, pelleted by centrifugation at 200 x g for 5 min, and resuspended in Opti-MEM medium supplemented with 0.05 mg/ml of gentamycin and 1x ITS (insulin, transferin, and selenium). The cells were cultured in the absence or presence of various reagents discussed in detail below for different time points at 37oC in a humidified atmosphere of 5% CO2.  Forskolin (FSK) and phorbol 12-myristate 13-acetate (PMA) were added to mimic hCG action.

extract_protocol: Standard Affymetrix

treatment_protocol: The granulosa cells were exposed to Ad- NFIL3 or Ad-GFP at a multiplicity of infection (MOI) of 50 pfu/cell.  Two hours later, Medium was replaced with fresh Opti-MEM medium. At 24 h after adenovirus exposure, granulosa cells were treated with FSK (10uM) + PMA (20 nM) for 6 h before collection for RNA isolation using a RNeasy kit according to the manufacturer’s instructions (Qiagen Inc., Valencia, CA).

value: Sprague-Dawley

tag: gender

value: Female

value: Immature 24-25 days old


title: Dahl S Rat_1

description: Dahl S Rat_1


title: granulosa cell.6h Ad-GFP


title: Primary patient sample_MMRC0007_1_GEP

source_name: Sample from patient MMRC0007

tag: cell type


title: Biomaterial_BL_012_SI

city: Bologna

first: pier paolo

last: piccaluga

address: via massraenti 9

department: Hematology and Oncological Sciences "L. and A. Seràgnoli"

country: Italy

institute: University of Bologna

description: Gene expression data from patient's sample

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000.

data_processing: The data were analyzed with Affymetrix GCOS. Normalization: RMA.  Baseline Transformation: Median of all samples.

source_name: Endemic Burkitt lymphoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Samples were taken at diagnosis from untreated patients

tag: tissue

value: Lymph-node biopsy

value: African patient

value: Children


title: Primary patient sample_MMRC0001_1_GEP

source_name: Sample from patient MMRC0001


title: Biomaterial_BL_001_BO

source_name: Sporadic Burkitt lymphoma

value: European patient

value: Adult


title: granulosa cell.6h Ad-NFIL3 +FSK/PMA


title: Biomaterial_BL_010_SI


title: Primary patient sample_MMRC0011_1_GEP

source_name: Sample from patient MMRC0011

value: CD138-selected bone marrow cells


title: Biomaterial_BL_011_SI


title: WT_4

city: Frederick

first: Stephanie

middle: Kaye

last: Watkins

state: MD

address: 1050 Boyles St.

department: CIP/LMI

institute: NCI-Frederick

description: Dendritic cells Wildtype Mouse 4

hyb_protocol: replicates of each group were hybridized to Affymetrix mouse Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs

scan_protocol: Wash and stain were performed on Affymetrix Fluidics Station 450 and scanned on Affymetrix GeneChip scanner 3000

data_processing: Data were collected using Affymetrix AGCC software. Statistical and clustering analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.

organism: Mus musculus

source_name: Wild Type Mouse 4

label_protocol: 200 ng of RNA was reverse transcribed with random hexamer primer, amplified and terminal labeled with biotin using Affymetrix Whole Transcript Sense Target Labeling kit according to manufacturer’s protocol

extract_protocol:
RNA was isolated using the qiagen RNAeasy mini spin colomn according to manufacturer's instuctions.
RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: Cells were purified from digested prostates by magnetic beads >90% purity was confirmed

value: male

value: dendritic cells

tag: genotype/variation

value: Wildtype


title: Biomaterial_HIV-BL_002_BO

source_name: Immunodeficiency associated Burkitt lymphoma


title: Biomaterial_HIV-BL_001_BO


title: Biomaterial_BL_013_SI


title: 515C

description: C

source_name: Human dopamine

value: control


title: Biomaterial_BL_009_SI


title: Primary patient sample_MMRC0004_1_GEP

source_name: Sample from patient MMRC0004


title: 515D

description: PD

value: Parkinson’s disease


title: WT_3

description: Dendritic cells Wildtype Mouse 3

source_name: Wild Type Mouse 3


title: Biomaterial_BL_007_SI


title: 515B

description: PD


title: Biomaterial_BL_008_SI


title: Biomaterial_BL_004_SI


title: 459F

description: PD


title: Biomaterial_BL_006_SI


title: Primary patient sample_MMRC0003_1_GEP

source_name: Sample from patient MMRC0003


title: WT_1

description: Dendritic cells Wildtype Mouse 1

source_name: Wild Type Mouse 1


title: Biomaterial_BL_005_SI


title: NT_6

description: Dendritic cells Tumor Bearing TRAMP mouse 6

source_name: TRAMP Mouse 6

value: TRAMP Transgenic


title: 459E

description: PD


title: WT_2

description: Dendritic cells Wildtype Mouse 2

source_name: Wild Type Mouse 2


title: Ko_1210

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: according to manufacturer

scan_protocol: according to manufacturer

data_processing: MAS5 algorithm, overall intensity targeted to 500

source_name: purification of basal epidermal cells from E16.5 embryos

label_protocol: 3 prime IVT express

extract_protocol: trizol

treatment_protocol: FACS purification of basal epidermal cells from E16.5 SRF fl/fl ROSA26 YFP fl/fl  K14-Cre (cKO) or SRF fl/+ ROSA26 YFP fl/fl  K14-Cre (WT) was performed on a FACS Vantage SE system equipped with FACS DiVa software (BD Biosciences). Cells were gated for single events and viability and then sorted according to α6 integrin-PE expression and YFP.

value: SRF fl/fl ROSA26 YFP fl/fl  K14-Cre


title: Biomaterial_BL_003_SI


title: 459C

description: C


title: NT_5

description: Dendritic cells Tumor Bearing TRAMP mouse 5

source_name: TRAMP Mouse 5


title: 459B

description: C


title: NT_4

description: Dendritic cells Tumor Bearing TRAMP mouse 4

source_name: TRAMP Mouse 4


title: NT_3

description: Dendritic cells Tumor Bearing TRAMP mouse 3

source_name: TRAMP Mouse 3


title: alpha-IFN Treated - repeat 2 - mAdbID:91929

status: Public on Jan 19 2011

city: Bethesda

first: Angel

middle: N

last: Morrow

address: 9000 Rockville Pike

institute: NIH/NIAID

description: mAdb experiment ID: 91929

hyb_protocol: Sample Hybridization Protocol Other: Hybridization of sample onto arrays was carried out using a MAUI Hybridization System (BioMicro Systems, Salt Lake City, Utah).

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 15 LaserPower: 3.17871;; 2.78137 Temperature: 23.0625 Scanning Protocol Other: Arrays were washed, dried and then scanned using an Axon GenePix 4200A microarray scanner along with GenePix Pro image analysis software (Molecular Devices, Sunnyvale, CA).

data_processing:
mAdb Dataset Extraction
Calculation Method: Default Ratio: ChanB/ChanA (Cy5/Cy3). Signal calculation: Mean Intensity minus Median Background. Any features designated Control were excluded. Normalization method: Precalculated 50th Percentile (Median). Spot Filter Options: Include Spots not flagged BAD or Not Found. Data was extracted and aligned by the Inventory Well ID. Within array multiple occurrences of Well ID were reduced to a single instance by selecting the one with the strongest signal (Chan A + Chan B). Note: For all GenePix results from Axon scanned arrays Chan A is CY3 and Chan B is CY5. Ratios were further log2 transformed.

source_name: Control

label_protocol:
Cy3 Labeling Protocol
Other: Total RNA (5µg) was reverse transcribed using 5'-amino-modified oligo (dT) primer along with reagents from FairPlay III Microarray Indirect Labeling kit (Stratagene, La Jolla, CA). Dye coupling was performed using Cy3 obtained from Amersham Biosciences (Piscataway, NJ).

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was purified using RNeasy Mini kits (Qiagen, Valencia, CA).

value: lung

value: lung epithelial cells

source_name: alpha-IFN treated

label_protocol:
Cy5 Labeling Protocol
Other: Total RNA (5µg) was reverse transcribed using 5'-amino-modified oligo (dT) primer along with reagents from FairPlay III Microarray Indirect Labeling kit (Stratagene, La Jolla, CA). Dye coupling was performed using Cy5 obtained from Amersham Biosciences (Piscataway, NJ).

treatment_protocol:
Treatment type: compound
Agent: alpha-IFN (alpha-Interferon)
Treatment dose: 10 IU/ml
Treatment time: 24 hours
Treatment temperature: 37C
In-vitro treatment: Three million A549 cells were seeded overnight in 10mL complete RPMI and treated with alpha-IFN as indicated for 24h.


title: KO_1261


title: GBM51

type: genomic

city: Rennes

first: Amandine

last: Etcheverry

address: 2 rue Henri Le Guilloux

country: France

institute: CNRS UMR 6290 - IGDR

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

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio software 2008.1. The beta values were calculated as follows: "For each interrogated CpG site, methylation status is calculated by dividing the signal from the methylated probe (M) by the sum of signals for both methylated and unmethylated (U) probes (GenomeStudio 2008.1, Illumina Inc.): b = Max(M,0) / [Max(M,0) +  Max(U,0) + 100]. This b-value provides a continuous and quantitative measurement of DNA methylation, ranging from 0 (completely unmethylated) to 1 (completely methylated)."

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: brain

label_protocol: Standard Illumina Protocol

growth_protocol: Snap frozen tumor blocks were cryodissected in 10 um sections. To allow a paired and accurate comparison between closely related biological materials, the adjacent sections were alternatively pooled in different tubes for DNA and RNA extraction.

extract_protocol: DNA was extracted according to manufacturer's instructions (NucleoSpin Tissue Kit, Macherey Nagel).

value: brain

value: Stupp


title: GBM52


title: alpha-IFN Treated - repeat 1 - mAdbID:91427

description: mAdb experiment ID: 91427

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.39;; 2.73 Temperature: 22.25 Scanning Protocol Other: Arrays were washed, dried and then scanned using an Axon GenePix 4200A microarray scanner along with GenePix Pro image analysis software (Molecular Devices, Sunnyvale, CA).


title: BC-3 cells treated with si463

city: Erlangen

first: Frank

last: Neipel

address: Schlossgarten 4

department: Virologisches Institut

institute: Universitaetsklinikum Erlangen

description: Gene expression data from BC-3 cells with vIRF-3 knockdown

hyb_protocol: After fragmentation, cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Expression signals for each of the 54,675 probe sets and comparisons between different samples were calculated with the Affymetrix GeneChip® Operating Software (GCOS) using the MAS5 algorithm.

source_name: BC-3 cells treated with si463

label_protocol: Double-stranded cDNA was synthesized from total RNA followed by an in vitro transcription (IVT) reaction to produce biotin-labeled cRNA.

growth_protocol: KSHV positive BC-3 PEL cell lines were obtained from ATCC and cultured in RPMI 1640 supplemented with 100 U/mL Penicilin/Streptomycin, 350 mg/mL L-glutamine, 1 mM sodium pyruvate (Sigma Chemical, St Louis, MO), 0.05 mM beta-mercaptoethanol (cell culture grade; Gibco BRL, Carlsbad, CA) 20% heat-inactivated fetal calf serum (FCS; PAA Laboratories, Pasching, Austria) at 37°C and 7.5% CO2.

extract_protocol: Total cellular RNA was purified with RNeasyTM Mini columns (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: PEL cells were maintained at a density of 350,000 cells/mL for 3 days. A total of 10^6 PEL cells was then transfected with 2.6 µg siRNA using the HiPerFect (Qiagen) transfection reagent according to the manufacturer’s instructions. siRNAs siNs and si716s were chemically modified so-called stealth-siRNAs (Invitrogen). siN and si463 were standard siRNA molecules.

value: BC-3 PEL

value: B cell lymphoma

tag: sirna name

tag: sirna target sequence

value: AAGGCCAUUUGUGGGUGAAAA


title: gamma-IFN Treated - repeat 2 - mAdbID:91930

description: mAdb experiment ID: 91930

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 30;; 20 LaserPower: 3.21716;; 2.78137 Temperature: 23.1875 Scanning Protocol Other: Arrays were washed, dried and then scanned using an Axon GenePix 4200A microarray scanner along with GenePix Pro image analysis software (Molecular Devices, Sunnyvale, CA).

source_name: gamma-IFN treated

treatment_protocol:
Treatment type: compound
Agent: gamma-IFN (gamma-Interferon)
Treatment dose: 10 IU/ml
Treatment time: 24 hours
Treatment temperature: 37C
In-vitro treatment: Three million A549 cells were seeded overnight in 10mL complete RPMI and treated with gamma-IFN as indicated for 24h.


title: GBM47

tag: treatment


title: GBM53


title: GBM48


title: GBM46


title: het_1210

source_name: basal epidermal cells from E16.5 embryos


title: alpha-IFN Treated - repeat 3 - mAdbID:91932

description: mAdb experiment ID: 91932

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 15 LaserPower: 3.25989;; 2.80273 Temperature: 23.4375 Scanning Protocol Other: Arrays were washed, dried and then scanned using an Axon GenePix 4200A microarray scanner along with GenePix Pro image analysis software (Molecular Devices, Sunnyvale, CA).


title: GBM50


title: gamma-IFN Treated - repeat 3 - mAdbID:91931

description: mAdb experiment ID: 91931

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 25 LaserPower: 3.26843;; 2.81555 Temperature: 23.75 Scanning Protocol Other: Arrays were washed, dried and then scanned using an Axon GenePix 4200A microarray scanner along with GenePix Pro image analysis software (Molecular Devices, Sunnyvale, CA).


title: gamma-IFN Treated - repeat 1 - mAdbID:91428

description: mAdb experiment ID: 91428

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 30;; 20 LaserPower: 3.42224;; 2.78137 Temperature: 22.25 Scanning Protocol Other: Arrays were washed, dried and then scanned using an Axon GenePix 4200A microarray scanner along with GenePix Pro image analysis software (Molecular Devices, Sunnyvale, CA).


title: BC-3 cells treated with siNs

description: Gene expression data from BC-3 cells without vIRF-3 knockdown (control siRNA)

source_name: BC-3 cells treated with siNs

value: siNs

value: AAGACUACCGUUGUAUAGUAG


title: het_1261


title: Biomaterial_BL_001_SI

source_name: Endemic Burkitt lymphoma

value: Lymph-node biopsy

value: African patient

value: Children


title: BC-3 cells treated with si716s

source_name: BC-3 cells treated with si716s

value: AAGAUGACCUCACACUGCUUGAUAA


title: NT_2

description: Dendritic cells Tumor Bearing TRAMP mouse 2

source_name: TRAMP Mouse 2

value: male

value: dendritic cells


title: GBM55


title: GBM39

tag: integrative analysis

value: gene expression data available


title: GBM38


title: GBM54


title: GBM49


title: BC-3 cells treated with siN

source_name: BC-3 cells treated with siN

value: siN


title: GBM43


title: Biomaterial_BL_002_SI


title: GBM45


title: GBM35


title: GBM44


title: GBM40


title: GBM33


title: NT_1

description: Dendritic cells Tumor Bearing TRAMP mouse 1

source_name: TRAMP Mouse 1

value: TRAMP Transgenic


title: GBM42


title: GBM41


title: GBM37


title: GBM32


title: GBM27


title: GBM36


title: GBM31


title: GBM26


title: GBM28


title: 459D

description: C

source_name: Human dopamine

value: control


title: 459A

description: C


title: GBM25

value: brain


title: GBM30

value: Stupp


title: GBM18


title: GBM22


title: GBM9


title: GBM23


title: GBM8_2

description: Technical replicate


title: GBM6


title: GBM4


title: GBM7


title: GBM13


title: GBM21


title: GBM2


title: GBM5


title: Oregon-R_wt_1_a (1631824019-A1)

city: East Lansing

first: Ian

last: Dworkin

address: 203 Natural Science Bldg. Michigan State University

department: Zoology

institute: Michigan State University

scan_protocol: Standard Illumina scanning protocol using BeadStudio version 3.0.14 ( llumina Inc)

data_processing: The data were median normalised using custom R scripts

organism: Drosophila melanogaster

source_name: Drosophila wing imaginal disc

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit (ambion)

growth_protocol: Larvae for each genotype were grown in bottles, and late third instar larvae were collected, sexed, and the wing imaginal discs were dissected out.

extract_protocol: RNA extraction was performed using a modified protocol for the RNAeasy kit (Qiagen), with DNase I treatment. We Used ~ 40-50 imaginal discs for each biological replicate

tag: strain

value: Oregon-R

tag: line number

tag: allele

value: Third instar larvae

value: Wing imaginal disc

tag: biological replicate

tag: technical (labeling) replicate

value: a

tag: sentrix_id (slide)

tag: sentrix position (array)


title: Control 9


title: Oregon-R_sd[E3]_2_b (1631824019-H2)

tag: developmental stage

value: b


title: GBM15


title: GBM19


title: GBM14


title: GBM34


title: GBM24


title: Samarkand_sd[E3]_2_b (1631824019-G2)

value: Samarkand


title: Samarkand_wt_2_b (1631824019-E2)


title: GBM8


title: Oregon-R_sd[E3]_1_b (1631824019-G1)


title: GBM29


title: Samarkand_wt_1_b (1631824019-F1)


title: Oregon-R_wt_2_b (1631824019-F2)


title: GBM10


title: Samarkand_sd[E3]_1_b (1631824019-H1)


title: Samarkand_wt_1_a (1631824019-B1)


title: GBM1


title: GBM3


title: Control 8


title: GBM17


title: Oregon-R_wt_2_a (1631824019-B2)


title: GBM12


title: Oregon-R_sd[E3]_1_a (1631824019-C1)


title: Samarkand_sd[E3]_1_a (1631824019-D1)


title: Oregon-R_sd[E3]_2_a (1631824019-D2)


title: Samarkand_sd[E3]_2_a (1631824019-C2)


title: Oregon-R_wt_1_b (1631824019-E1)


title: Samarkand_7_2 (1926673003-H2)

tag: hybridization date


title: S[k09530]_2_1 (1926673003-G2)


title: Samarkand_wt_2_a (1631824019-A2)


title: Control 7_2

description: Technical replicate


title: GBM20


title: babo[k16912]_1_2 (1926673003-H1)


title: aos[W11]_2_2 (1926673003-E2)


title: mam[kg02641]_2_2 (1926673003-G1)


title: sbb[BG01610]_2_2 (1926673003-F1)


title: tkv[kg01923]_1_2 (1926673003-F2)


title: pnt[kg04968]_1_2 (1926673003-E1)


title: Control 7


title: GBM16


title: GBM11


title: mam[kg02641]_1_2 (1926673003-C2)


title: ast[kg07563]_1_1 (1926673003-D2)


title: sax[kg07525]_2_3 (1926673003-D1)


title: rho[kg07115]_2_2 (1926673003-A2)


title: spi[s3457]_2_3 (1926673003-C1)


title: babo[k16912]_1_3 (1926673003-B1)


title: tkv[k19713]_2_1 (1926673002-H2)


title: aos[W11]_1_2 (1926673003-B2)


title: ed[k01102]_2_1 (1926673003-A1)


title: mad[kg00581]_2_3 (1926673001-C1)


title: ksr[J5E2]_1_3 (1926673001-C2)


title: mam[BG02477]_2_1 (1926673001-D1)


title: Mad[k00237]_2_3 (1926673001-D2)


title: ed[k01102]_2_2 (1926673001-F1)


title: rho[kg07115]_1_2 (1926673001-F2)


title: mad[kg00581]_1_2 (1926673002-A2)


title: Samarkand_6_1 (1926673001-E2)


title: mad[kg00581]_1_3 (1926673001-G1)


title: Dpp[kg08191]_1_2 (1926673001-E1)


title: sbb[BG01610]_1_1 (1926673001-G2)


title: Ptc[k02507]_2_3 (1926673002-A1)


title: ed[k01102]_1_2 (1926673002-B1)


title: dad[J1E4]_2_2 (1926673001-H1)


title: Bs[k07909]_1_2 (1926673001-H2)


title: Gap1[mip-w+]_1_3 (1926673002-H1)


title: babo[k16912]_2_1 (1926673002-B2)


title: Samarkand_4_1 (1926673002-C1)


title: ksr[J5E2]_1_1 (1926673002-D1)


title: Egfr[k05115]_2_1 (1926673002-D2)


title: tkv[kg01923]_2_3 (1926673002-C2)


title: mam[BG02477]_1_2 (1926673002-E2)


title: Ptc[k02507]_2_1 (1926673002-F2)


title: aos[W11]_2_3 (1926673002-F1)


title: Samarkand_7_1 (1926673002-G2)


title: Mad[k00237]_1_1 (1926673002-E1)


title: rho-6[kg05638]_1_1 (1926673002-G1)


title: brk[kg08470]_2_3 (1926673001-B2)


title: Ptc[k02507]_2_2 (1926673001-A2)


title: S[k09530]_1_1 (1926673001-B1)


title: Egfr[k05115]_1_1 (1631824009-H1)


title: Samarkand_2_2 (1926673001-A1)


title: ed[k01102]_1_2 (1631824009-H2)


title: S[k09530]_2_1 (1631824009-G2)


title: Samarkand_1_1 (1631824009-C1)


title: mam[BG02477]_1_3 (1631824009-C2)


title: brk[kg08470]_2_2 (1631824009-D2)


title: Bs[k07909]_2_3 (1631824009-E1)


title: mad[kg00581]_1_2 (1631824009-F2)


title: Egfr[k05115]_1_3 (1631824017-A1)


title: babo[k16912]_2_1 (1631824009-F1)


title: sbb[BG01610]_1_1 (1631824009-D1)


title: Dpp[kg08191]_2_2 (1631824017-D2)


title: Samarkand_7_2 (1631824009-E2)


title: rho-6[kg05638]_1_1 (1631824017-C2)


title: Samarkand_3_2 (1631824017-B1)


title: rho[kg07115]_1_1s (1631824017-A2)


title: pnt[kg04968]_2_3 (1631824017-C1)


title: tkv[k19713]_3_2 (1631824017-D1)


title: sax[kg07525]_1_1 (1631824017-B2)


title: aos[W11]_1_3 (1631824005-F1)


title: brk[kg08470]_2_1 (1631824005-G2)


title: mam[BG02477]_2_3 (1631824005-D2)


title: spi[s3457]_2_2 (1631824005-H2)


title: pnt[kg04968]_2_2 (1631824005-H1)


title: Bs[k07909]_1_2 (1631824005-F2)


title: S[k09530]_2_2 (1631824005-G1)


title: ksr[J5E2]_2_1 (1631824005-D1)


title: cbl[kg03080]_1_3 (1631824005-E2)


title: Samarkand_4_1 (1631824017-F1)


title: spi[s3457]_2_1 (1631824017-G2)


title: mam[kg02641]_1_2 (1631824017-F2)


title: cbl[kg03080]_1_2 (1631824009-A2)


title: tkv[kg01923]_1_1 (1631824009-B1)


title: aos[W11]_2_1 (1631824009-B2)


title: aos[W11]_1_1 (1631824017-E1)


title: rho-6[kg05638]_2_2 (1631824009-A1)


title: cbl[kg03080]_2_2 (1631824017-E2)


title: drk[k02401]_2_2 (1631824017-H2)


title: Ptc[k02507]_1_1 (1631824017-H1)


title: ed[k01102]_2_2 (1631824017-G1)


title: drk[k02401]_2_3 (1631824009-G1)


title: dad[J1E4]_2_3 (1631824011-H2)


title: drk[k02401]_1_3 (1631824005-A1)


title: Samarkand_6_1 (1631824005-B1)


title: mad[kg00581]_1_1s (1631824005-A2)


title: Mad[k00237]_2_2 (1631824005-C1)


title: tkv[kg01923]_2_3 (1631824005-B2)


title: rho[kg07115]_1_3 (1631824005-C2)


title: mam[kg02641]_2_1s (1631824005-E1)


title: sax[kg07525]_1_3 (1631824011-F1)


title: cbl[kg03080]_2_1 (1631824011-E2)


title: Samarkand_2_2 (1631824011-F2)


title: mad[kg00581]_2_1 (1631824011-G2)


title: tkv[kg01923]_1_2 (1631824011-G1)


title: mam[BG02477]_2_1 (1631824011-H1)


title: Mad[k00237]_2_1 (1631824011-D2)


title: MouseLiver_0.2ugSe_rep1

city: Madison

first: Roger

middle: A

last: Sunde

state: WI

address: 1415 Linden Dr

department: Nutritional Sciences

institute: University of Wisconsin

description: Gene expression from liver of a mouse fed 0.2 ug Se/g diet for 35 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Genome 230 2.0 or Mouse Genome 430 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following the EukGE_WS2v5_450 fluidics protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GC 3000 G7 Scanner and image data was extracted using the AFX Expression Console software.

data_processing: The data were analyzed in R/Bioconductor using the GCRMA algorithm.

source_name: liver, 0.2 ug Se/g diet

label_protocol: Biotinylated cRNA were prepared with ENZO IVT kits from 5 ug cDNA for mouse samples and with MessageAmp Biotin-Enhanced IVT kits from 3 ug total RNA for rat samples

growth_protocol: Weanling mice or rats were housed in hanging wire cages and fed Se-deficient diets supplemented with up to 5 ug Se/g diet for 35 or 28 days, respectively

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

treatment_protocol: Animals were anesthetized with ether and livers were perfused in situ with ice-cold 0.15 M potassium chloride.  Liver and kidney were removed and snap-frozen in liquid nitrogen for later RNA analysis.

value: liver

value: 0.2 ug Se/g diet


title: MouseKidney_0.2ugSe_rep1

description: Gene expression from kidney of a mouse fed 0.2 ug Se/g diet for 35 days

source_name: kidney, 0.2 ug Se/g diet

value: kidney


title: MouseKidney_0.05ugSe_rep1

description: Gene expression from kidney of a mouse fed 0.05 ug Se/g diet for 35 days

source_name: kidney, 0.05 ug Se/g diet

value: 0.05 ug Se/g diet


title: pnt[kg04968]_1_3 (1631824011-E1)


title: MouseKidney_0.05ugSe_rep3


title: MouseKidney_SeDef_rep1

description: Gene expression from kidney of a mouse fed a Se-deficient diet for 35 days

source_name: kidney, Se deficient

value: Se deficient


title: MouseKidney_0.2ugSe_rep3


title: brk[kg08470]_1_1 (1631824016-G2)


title: Dpp[kg08191]_1_3 (1631824011-B1)


title: tkv[k19713]_2_2 (1631824011-C2)


title: ksr[J5E2]_1_1 (1631824011-A2)


title: Egfr[k05115]_1_2 (1631824011-B2)


title: Gap1[mip-w+]_2_2 (1631824011-D1)


title: ast[kg07563]_2_2 (1631824016-G1)


title: ksr[J5E2]_2_3 (1631824016-H1)


title: Bs[k07909]_2_2 (1631824011-A1)


title: tkv[k19713]_2_3 (1631824016-H2)


title: MouseKidney_SeDef_rep2


title: MouseLiver_0.2ugSe_rep2


title: MouseKidney_0.05ugSe_rep2


title: MouseLiver_0.05ugSe_rep2

description: Gene expression from liver of a mouse fed 0.05 ug Se/g diet for 35 days

source_name: liver, 0.05 ug Se/g diet


title: MouseKidney_0.2ugSe_rep2


title: MouseLiver_SeDef_rep1

description: Gene expression from liver of a mouse fed a Se-deficient diet for 35 days

source_name: liver, Se deficient


title: dad[J1E4]_2_1 (1631824016-D2)


title: Samarkand_2_1 (1631824016-E1)


title: babo[k16912]_1_1 (1631824016-D1)


title: spi[s3457]_1_2 (1631824016-F1)


title: aos[W11]_1_2 (1631824016-E2)


title: ed[k01102]_2_3 (1631824016-F2)


title: MouseLiver_0.05ugSe_rep1


title: GBM40

description: serie 2

hyb_protocol: Hybridizations were performed following the manufacturer's recommendations (protocol version 5.7)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters

source_name: brain

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 350 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using NucleoSpin RNAII Kit (Macherey-Nagel)

value: DNA methylation data available


title: tkv[kg01923]_2_2 (1631824016-C2)


title: GBM37

description: serie 2


title: GBM39

description: serie 2


title: sax[kg07525]_2_1 (1631824016-C1)


title: MouseLiver_0.05ugSe_rep3


title: Control 5

description: serie 2


title: Ptc[k02507]_2_3 (1631824016-B2)


title: GBM32

description: serie 2


title: MouseLiver_SeDef_rep2


title: MouseLiver_0.2ugSe_rep3


title: GBM38

description: serie 2


title: Control 6

description: serie 2


title: GBM35

description: serie 2


title: Control 4

description: serie 2


title: edr1, 36 hrs, bio rep 3

city: Bloomington

last: Innes

state: IN

address: 915 East Third Street

department: Biology

institute: Indiana University

hyb_protocol: Fifteen µg of biotinylated cRNA is added to a total hybridization cocktail of 300 µl, and 200 µl is hybridized to a GeneChip® after adding control oligonucleotides. Hybridization is at 45°C for 17 h with constant rotation. The hybridization mixture is then removed and the GeneChips® are washed, stained with phycoerythrin-labeled Streptavidin, washed, incubated with biotinylated anti-streptavidin, and then restained with phycoerythrin-labeled Streptavidin to amplify the signals; these steps are carried out using the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the dedicated scanner, controlled by Affymetrix GCOS software.  The data was analyzed with Affymetrix MAS5 and the average intensity on each array is normalized by global scaling to a target intensity of 1000.

data_processing: MAS5.0, GCRMA

organism: Arabidopsis thaliana

source_name: edr1 rosettes, 36 hpi with Golovinomyces cichoracearum

label_protocol: Biotinlylated cRNA was made using the Affymetrix IVT kit.

growth_protocol: Arabidopsis thaliana Col-0 and edr1 seeds were sown on Metromix soil and placed at 4ºC for three days.  Plants were then transferred to a growth room and grown under 9 hour days at a temperature of 23ºC for four weeks.

extract_protocol: Tissue was collected for each time point (0, 18, 36, and 96 hours) by harvesting four full rosettes per genotype per biological replicate.  Four biological replicates were collected and placed in liquid nitrogen.  Tissue was ground with a mortar and pestle and used for RNA preparations.  High quality RNA was prepared using the Spectrum Plant Total RNA Kit (Sigma) and concentrated to >0.75 μg/μl with the RNEasy MinElute Cleanup Kit (Qiagen). A total of 6 µg RNA was used.

treatment_protocol: Plants were inoculated with Golovinomyces cichoracearum using a settling tower ~1 meter tall.  Plants to be inoculated were placed at the bottom of the tower, which contained a Nytex mesh screen at the top.  Four pad4 mutants with heavy powder growth were passed over the mesh 20 times each to transfer the spores to the plants below.  Spores were allowed to settle for 30 minutes and the plants were transferred to growth chambers.

tag: genotype


title: MouseKidney_SeDef_rep3


title: babo[k16912]_2_3 (1631824015-H2)


title: Dpp[kg08191]_1_2 (1631824016-A1)


title: S[k09530]_1_1 (1631824016-B1)


title: mam[kg02641]_1_1s (1631824016-A2)


title: GBM34

description: serie 2


title: GBM33

description: serie 2


title: GBM31

description: serie 2


title: MouseLiver_SeDef_rep3


title: GBM30

description: serie 2


title: Gap1[mip-w+]_2_2 (1631824015-G2)


title: Dpp[kg08191]_2_3 (1631824015-H1)


title: S[k09530]_1_3 (1631824015-G1)


title: dad[J1E4]_1_3 (1631824015-F2)


title: GBM28

description: serie 2


title: sbb[BG01610]_2_3 (1631824015-F1)


title: edr1, 36 hrs, bio rep 1


title: BdkrB2 null/wt replicate 2 duplicate

city: NEW ORLEANS

first: Lei

last: Yan

state: LA

address: 1430 Tulane Ave #SL37

department: Pediatrics

institute: Tulane University

description: BdkrB2 null/WT replicate 2 duplicate

hyb_protocol: Hybridization was performed following Agilent’s oligonucleotide microarray hybridization User’s Manual and Agilent’s in situ Hybridization Plus kit. The labeled cDNA was hybridized to Agilent 44K Whole Mouse Genome Oligonucleotide Microarray (containing ~41,000 genes).

scan_protocol: The arrays were scanned using a dual-laser DNA microarray scanner (Agilent).

data_processing: The data was then extracted from images by the Feature Extraction software 6.1 (Agilent). Lowess normalization was applied to correct for artifacts caused by non-linear rates of dye incorporation, as well as inconsistencies in the relative fluorescence intensity between some red and green dyes.

source_name: BdkrB2 null embryonic day 14.5 kidney

label_protocol: The quality of RNA samples was assessed by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Fluorescently labeled cDNA was generated from 0.5 μg of total RNA in each reaction using the Agilent Fluorescent Direct Label Kit and 1.0 mM Cyanine 3- or 5- labeled  dCTP (PerkinElmer, Boston, MA), and following  the User’s Manual.

growth_protocol: BdkrB2 heterzygous female mice on high salt food feeding were paired to BdkrB2 heterzygous mice. Embryonic kidney of the progenies were harvested at embryonic day 14.5 stage. Embryonic kidneys were stored in RNA later solution(Ambion Inc, TX).

extract_protocol: Total RNA extracted with Rneasy Mini kit according to manufacturer's protocol.

treatment_protocol: BdkrB2 heterzygous females were put on 5% Sodium high salt food feeding.

tag: gestational salt status

value: High salt

value: C57BL/6 genetic background

value: BdkrB2 null

source_name: BdkrB2 WT embryonic day 14.5 kidney

value: BdkrB2 WT


title: BdkrB2 null/wt replicate 2

description: BdkrB2 null/WT replicate 2


title: GBM36

description: serie 2

tag: tissue

value: brain


title: GBM24

description: serie 2


title: BdkrB2 null/wt replicate 3 duplicate

description: BdkrB2 null/WT replicate 3 duplicate

tag: genotype/variation


title: BdkrB2 null/wt replicate 3

description: BdkrB2 null/WT replicate 3


title: GBM27

description: serie 2


title: BdkrB2 null/wt replicate 1 duplicate

description: BdkrB2 null/WT replicate 1 duplicate


title: GBM21

description: serie 2


title: BdkrB2 null/wt replicate 1

description: BdkrB2 null/WT replicate 1


title: GBM23

description: serie 2


title: GBM26

description: serie 2


title: spi[s3457]_1_3 (1631824015-C2)


title: non-SP-002

city: shanghai

first: m

middle: jing

last: zi

address: libing Rd

country: China

institute: southgene

description: non-SP cells

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio

source_name: non-SP cells

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPre RNA Amplification kit (IL1791) for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: MCF-7 cells were detached by trypsinization and washed with ice-cold PBS.Cells (1×106) were labeled in the growth medium with 5.0 µg/mL Hoechst33342 dye, either alone or in combination with 50 µg/mL verapamil at 37°C for 90 minutes. Then, the cells were incubated with 2 μg/mL PI to exclude dead cells. SP analysis and sorting were done using a FACSVantage SE.The breast cancer cells were sorted into SP and non-SP cells.Total RNA was isolated from the FACS-sorted SP or non-SP cells.

tag: cell line

tag: facs-sorted type

value: non-SP cells


title: Samarkand_2_2 (1631824015-D1)

value: Third instar larvae


title: rho[kg07115]_2_3 (1631824015-E2)

value: Wing imaginal disc


title: Ptc[k02507]_2_1 (1631824015-D2)


title: sax[kg07525]_2_2s (1631824015-E1)


title: Col-0, 18 hrs, bio rep 2

source_name: Col-0 rosettes, 18 hpi with Golovinomyces cichoracearum


title: brk[kg08470]_1_2 (1631824015-C1)


title: GBM25

description: serie 2


title: Control 3

description: serie 1


title: ksr[J5E2]_1_2 (1631824015-B2)


title: BdkrB2 wt/null replicate 2 duplicate

description: BdkrB2 WT/null replicate 2 duplicate


title: GBM22

description: serie 2


title: drk[k02401]_1_2 (1631824015-A2)


title: Bs[k07909]_1_3 (1631824015-B1)


title: SP-001

description: breast cancer stem cells (SP cells)

source_name: breast cancer stem cells (SP cells)

value: breast cancer stem cells (SP cells)


title: BdkrB2 wt/null replicate 2

description: BdkrB2 WT/null replicate 2


title: BdkrB2 wt/null replicate 3 duplicate

description: BdkrB2 WT/null replicate 3 duplicate


title: GBM9

description: serie 1


title: GBM29

description: serie 2


title: BdkrB2 wt/null replicate 3

description: BdkrB2 WT/null replicate 3


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #334

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: A total of 825 ng of amplified amino-allyl aRNA from each experimental sample was hybridized to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2565BA (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used to grid, extract, and normalize data. Spots of poor quality or average intensity levels <300 were removed from further analysis.

label_protocol: A total of 825 ng of amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set. Total RNA was amplified two rounds using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), incorporating amino-allyl UTP into amplified antisense RNA.  Sample quality and quantity were assessed by agarose gel electrophoresis and absorbance at A260 using the Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific Wilmington, DE.)

tag: gender

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Total RNA from laser-capture microdissected experimental samples was isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA.) Total RNA was amplified two rounds using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), incorporating amino-allyl UTP into amplified antisense RNA.  Sample quality and quantity were assessed by agarose gel electrophoresis and absorbance at A260 using the Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific Wilmington, DE.)

tag: sample type

value: 5000 cells laser-capture microdissected from frozen OCT tissue block


title: GBM6

description: serie 1

tag: integrative analysis


title: GBM8

description: serie 1


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #302


title: Control 1

description: serie 1


title: Control 2

description: serie 1


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #316


title: aos[W11]_2_3 (1631824015-A1)

tag: strain

value: Samarkand

tag: line number


title: GBM7

description: serie 1


title: Ptc[k02507]_2_2 (1631824012-H2)

tag: allele

tag: biological replicate


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #324


title: spi[s3457]_1_1 (1631824012-H1)

tag: technical (labeling) replicate

tag: sentrix_id (slide)


title: Gap1[mip-w+]_2_1 (1631824012-G2)

tag: developmental stage

tag: sentrix position (array)


title: GBM20

description: serie 1


title: BdkrB2 wt/null replicate 1 duplicate

description: BdkrB2 WT/null replicate 1 dupllicate


title: BdkrB2 wt/null replicate 1

description: BdkrB2 WT/null replicate 1


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #307


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #317


title: GBM4

description: serie 1


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #339


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #332


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #327


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #308


title: GBM5

description: serie 1


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #305


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #311


title: GBM2

description: serie 1


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #329


title: sbb[BG01610]_1_2 (1631824012-G1)

tag: hybridization date


title: GBM19

description: serie 1


title: rho-6[kg05638]_1_3 (1631824012-F2)


title: GBM18

description: serie 1


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #323


title: Egfr[k05115]_2_3 (1631824012-F1)


title: GBM3

description: serie 1


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #318


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #309


title: LCM benign prostate epithelium from patient treated with daily transdermal DHT #343


title: brk[kg08470]_1_1 (1631824012-D2)


title: ast[kg07563]_1_3 (1631824012-E1)


title: tkv[kg01923]_1_3 (1631824012-E2)


title: tkv[k19713]_3_3 (1631824012-D1)


title: Samarkand_1_2 (1631824012-C2)


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #326


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #336


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #335


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #301


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #315


title: GBM14

description: serie 1


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #306


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #312


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #338


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #341


title: GBM17

description: serie 1


title: GBM15

description: serie 1


title: S[k09530]_1_2s (1631824012-B1)


title: pnt[kg04968]_2_1 (1631824012-C1)


title: babo[k16912]_2_2 (1631824012-B2)


title: Mad[k00237]_1_3 (1631824012-A2)


title: Parent S288C1

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

institute: INRA

hyb_protocol: Hybridization was carried out in a hybridization chamber (Corning) and using Pronto Universal Hybridization Kit Quick

scan_protocol: The hybridization signal was detected with a GenePix 4000B laser Scanner (Axon Instruments), and the signal was transformed to numerical values using the integrated GenePix software version 3.0

data_processing: initial filtering:mean red signal must be greater than 3 times the mean red background signal  print-tip-loess within-array normalization, quantile between-array normalization. R 2.9.2 software and limma bioconductor package used. All gpr files are Cy3 (test) to Cy5 (pool of 30)

organism: Saccharomyces cerevisiae

source_name: Parent S288C1

label_protocol: Fluorescent-labelled cDNA was synthesized from 5µg of total RNA using the CleanUP System (Pronto). Labelled cDNA was purified using the Pronto Purification kit (Pronto)

growth_protocol: Fermentation experiments and precultures were carried out at 28°C on a 1L synthetic medium MS300 (BELY et al. 1990). Extraction time at 50% of fermentation advancement (45g of released CO2).

extract_protocol: Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies) (Chomczynski et Sacchi, 1987) and purified using a “RNA Cleanup kit” from Qiagen

value: Parent S288C

tag: genetic background

tag: rmax

tag: fd

tag: cp

tag: nass

tag: suc

tag: gly

tag: ace

tag: pyr

source_name: Pool of the 30 segregants

value: Pool of the 30 segregants


title: Parent 59A4

source_name: Parent 59A4

tag: strain

value: Parent 59A


title: Parent S288C2

source_name: Parent S288C2


title: GBM10

description: serie 1

tag: tissue

tag: integrative analysis

value: DNA methylation data available


title: Parent 59A3

source_name: Parent 59A3


title: Segregant 25a

source_name: Segregant 25a

value: Segregant 25a


title: Segregant 28b

source_name: Segregant 28b

value: Segregant 28b


title: Segregant 31b

source_name: Segregant 31b

value: Segregant 31b


title: Segregant 29c

source_name: Segregant 29c

value: Segregant 29c


title: Parent S288C3

source_name: Parent S288C3


title: mam[kg02641]_1_3 (1631824018-H1)

hyb_protocol: Standard Illumina hybridization protocol

source_name: Drosophila wing imaginal disc

tag: line number

tag: allele

tag: biological replicate

tag: technical (labeling) replicate


title: Parent 59A5

source_name: Parent 59A5


title: Parent 59A2

source_name: Parent 59A2


title: Bs[k07909]_1_2 (1631824012-A1)

tag: developmental stage

tag: sentrix_id (slide)

tag: sentrix position (array)

tag: hybridization date


title: Parent S288C5

source_name: Parent S288C5

tag: genetic background

tag: rmax

tag: fd

tag: cp


title: Parent 59A1

source_name: Parent 59A1

tag: nass

tag: suc

tag: gly

tag: ace


title: Parent S288C4

source_name: Parent S288C4

tag: strain

tag: pyr


title: tkv[kg01923]_2_1 (1631824018-G2)

tag: line number

tag: allele

tag: tissue


title: GBM11

description: serie 1

source_name: brain

value: brain

tag: integrative analysis


title: S[k09530]_2_3 (1631824018-G1)

tag: developmental stage

tag: biological replicate

tag: technical (labeling) replicate

tag: sentrix_id (slide)


title: Ptc[k02507]_1_3 (1631824018-F2)

tag: sentrix position (array)

tag: hybridization date


title: Segregant 19c

source_name: Segregant 19c

value: Segregant 19c

tag: genetic background

tag: rmax

tag: fd

tag: cp


title: Segregant 19b

source_name: Segregant 19b

value: Segregant 19b

tag: nass

tag: suc

tag: gly

tag: ace

source_name: Pool of the 30 segregants


title: Segregant 24a

source_name: Segregant 24a

tag: strain

value: Segregant 24a

tag: pyr


title: Segregant 23b

source_name: Segregant 23b

value: Segregant 23b


title: LCM benign prostate epithelium from patient treated with daily transdermal placebo gel #346

tag: gender

value: male

tag: tissue

tag: sample type


title: GBM16

description: serie 1

tag: integrative analysis


title: Gap1[mip-w+]_1_1 (1631824018-E2)

tag: line number

tag: allele

tag: developmental stage

value: Third instar larvae

value: Wing imaginal disc

tag: biological replicate

tag: technical (labeling) replicate

tag: sentrix_id (slide)


title: Dpp[kg08191]_2_1 (1631824018-F1)

value: Samarkand

tag: sentrix position (array)

tag: hybridization date


title: GBM13

description: serie 1


title: Segregant 22c

source_name: Segregant 22c

value: Segregant 22c

tag: genetic background

tag: rmax

tag: fd

tag: cp

tag: nass

tag: suc


title: Segregant 18b

source_name: Segregant 18b

tag: strain

value: Segregant 18b

tag: gly

tag: ace

tag: pyr

value: Pool of the 30 segregants


title: Segregant 16b

source_name: Segregant 16b

value: Segregant 16b


title: Segregant 16c

source_name: Segregant 16c

value: Segregant 16c


title: Segregant 17a

source_name: Segregant 17a

value: Segregant 17a


title: Segregant 16d

source_name: Segregant 16d

value: Segregant 16d


title: Segregant 22a

source_name: Segregant 22a

value: Segregant 22a


title: Segregant 20b

source_name: Segregant 20b

value: Segregant 20b


title: Segregant 20a

source_name: Segregant 20a

value: Segregant 20a


title: drk[k02401]_2_1s (1631824018-E1)

source_name: Drosophila wing imaginal disc

tag: line number

tag: allele

tag: tissue


title: GBM12

description: serie 1

value: brain

tag: integrative analysis

value: DNA methylation data available


title: Segregant 16a

source_name: Segregant 16a

value: Segregant 16a


title: Segregant 14b

source_name: Segregant 14b

value: Segregant 14b


title: ast[kg07563]_1_2 (1631824018-C1)

tag: developmental stage

value: Third instar larvae

tag: biological replicate

tag: technical (labeling) replicate

tag: sentrix_id (slide)


title: Samarkand_6_1 (1631824018-D2)

value: Wing imaginal disc

tag: sentrix position (array)

tag: hybridization date


title: cbl[kg03080]_2_2 (1631824018-C2)

value: Samarkand


title: Segregant 9a

source_name: Segregant 9a

value: Segregant 9a

tag: genetic background

tag: rmax

tag: fd

tag: cp


title: skeletal muscle sample at T2, pig 1

first: Giuliano

last: Galimberti

address: Via delle Belle Arti, 41

institute: Università di Bologna

description: Gene expression data from porcine skeletal muscle at 6 hours after death

hyb_protocol: labeled cRNA was fractionated and hybridized with the GeneChip® Porcine Genome Array according to the standard procedures provided by the manufacturer. Affymetrix Fluidics Station 450 was used to wash and stain the chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA

scan_protocol: Fluorescent images were captured using Affymetrix Gene Chip® Scanner 3000 7G (Affymetrix)

data_processing: Raw CEL files were background-subtracted, normalized and summarized with the Robust Multi-array Average (RMA) algorithm (Irizarry et al., 2003) contained in the affy package (Bioconductor)

organism: Sus scrofa

source_name: Porcine skeletal muscle (3-5 g portion), sampled from the left leg, at 6 hours after death

label_protocol: biotin-labeled cRNA was syntethized using the GeneChip IVT labeling kit (Afffimetrix) from 5 mg of total RNA

growth_protocol: 3-5 g portions of semimebranosus muscle from 3 commercial hybrid pigs of female sex ( of about 160 kg each) raised in the same commercial farm

extract_protocol: total RNA was extracted with RNeasy Midi kit (Qiagen, Hamburg, Germany) following the protocol for animal tissue

treatment_protocol: portions were collected at 20 minutes, 2, 6 and 24 hours after slaughtering under normal conditions at the same abattoir

tag: gender

value: female

value: semimembranosus muscle

tag: time

value: 6 hours after death


title: Segregant 7a

source_name: Segregant 7a

tag: strain

value: Segregant 7a

tag: nass

tag: suc

tag: gly

tag: ace

tag: pyr

source_name: Pool of the 30 segregants

value: Pool of the 30 segregants


title: skeletal muscle sample at T1, pig 3

description: Gene expression data from porcine skeletal muscle at 2 hours after death

source_name: Porcine skeletal muscle (3-5 g portion), sampled from the left leg, at 2 hours after death

tag: tissue

value: 2 hours after death


title: Segregant 14a

source_name: Segregant 14a

value: Segregant 14a


title: Mad[k00237]_1_2 (1631824018-B2)

tag: line number

tag: allele

tag: developmental stage

tag: biological replicate

tag: technical (labeling) replicate


title: Segregant 18c

source_name: Segregant 18c

value: Segregant 18c

tag: genetic background

tag: rmax


title: skeletal muscle sample at T2, pig 2


title: Segregant 6b

source_name: Segregant 6b

value: Segregant 6b

tag: fd

tag: cp


title: Segregant 5a

source_name: Segregant 5a

value: Segregant 5a


title: Segregant 4c

source_name: Segregant 4c

value: Segregant 4c


title: Segregant 10b

source_name: Segregant 10b

value: Segregant 10b


title: pnt[kg04968]_1_2 (1631824013-G1)

tag: sentrix_id (slide)

tag: sentrix position (array)

tag: hybridization date


title: Egfr[k05115]_2_2 (1631824018-B1)

tag: strain


title: ed[k01102]_1_1 (1631824013-H2)


title: mam[BG02477]_2_2 (1631824018-A1)


title: Muscle_NormalFood_Swimming

city: Kyoto

first: Toru

last: Mizoguchi

state: Kyoto

address: 369, Karasuma-dori, Gojo, Shimogyo-ku

department: Research and Development Department

country: Japan

institute: Sun Chlorella Corp.

description: Gene expression after 14days in swimming mouse muscle

hyb_protocol: We used One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) v5.5 and according to the manufacturer’s instructions.

scan_protocol: Microarray was scanned by DNA Microarray Scanner G2565BA (Agilent Technologies, Palo Alto, CA, USA).

data_processing: The intensities were measured using Agilent Feature Extraction Software 9.5 (Agilent Technologies). A global normalization was performed for the inter-chip normalization. In order to define the expression level of the gene/probe, the signal intensity of each gene on a chip was divided by the median value of the signal intensities of the entire genes on the chip.

source_name: Muscle, 14days, normal food, swimming

label_protocol: The total RNA of each group was pooled (n = 10 for each group) and labeled with Cyanine 3 (Perkin Elmer, Boston, MA, USA) using 500 ng of total RNA, according to the manufacturer’s instructions, which generated one-color labeled cRNAs.

extract_protocol: A part of the muscle tissue was then placed in RNAlater RNA Stabilization Reagent (Qiagen, Inc., Valencia, CA, USA) and was kept overnight at 4°C and subsequently stored at  20°C. RNA was isolated using an RNeasy Mini Kit (Qiagen) and was purified according to the manufacturer’s instructions. RNA purity and concentration were evaluated with a spectrophotometer using an absorbance ratio of 260/280 nm.

tag: gender

value: male

tag: age

value: Six-week-old

value: swimming muscle


title: rho[kg07115]_2_2 (1631824013-F2)

value: Samarkand

value: Third instar larvae

value: Wing imaginal disc