title: Ls174T-L8 con2

description: Ls174T-L8 cells carry a doxycyclin-inducible dominant-negative Tcf4 transgene. Cells were untreated (con) or trangene expression was induced for 24 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.

source_name: Ls174T, dominant-negative Tcf4, uninduced


title: Ls174T-pTER-β-catenin con2

status: Public on Nov 29 2011

type: RNA

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.

hyb_protocol: 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ls174T, β-catenin siRNA, uninduced

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.

tag: cell line

tag: cell type

value: intestinal colorectal carcinoma cells

tag: induction

tag: time


title: Ls174T-L8 con1


title: Ls174T-L8 dox1

source_name: Ls174T, dominant-negative Tcf4, induced

value: dominant-negative Tcf4 transgene


title: Ventricularis_Oscillatory_4_miRNA

city: Atlanta

first: Hanjoong

last: Jo

state: GA

department: Biomedical Engineering

country: USA

institute: Emory University

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Because of low background, no normalization was used for data analysis. GenomeStudio V2010.1 was used to generate values.

source_name: Ventricularis HAVEC, Oscillatory Shear, 24h

label_protocol: Using suggested labelling protocol by Illumina.

growth_protocol: Side-specific human aortic valvular endothelial cells (fHAVEC and vHAVEC) were grown in MCDB 131 supplemented with FBS, ECGS, IGF, EGF, FGF, VEGF, ascorbic acid, and hydrocortisone

extract_protocol: Total RNA was extracted using Qiazol and Qiagen's miRNeasy kit.

treatment_protocol: fHAVEC and vHAVEC were sheared under oscillatory and laminar shear for 24h.

value: Aortic Valve, Endothelial Cells, Shear

tag: group


title: Ls174T-pTER-β-catenin dox2

source_name: Ls174T, β-catenin siRNA, induced

value: shRNA against β-catenin


title: Mouse_Peripheral_6M_HF diet_01

city: Palo Alto

first: Li Fen

last: Liu

state: CA

address: 3801 Miranda AVE

department: Medicine

institute: Stanford University

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit.  Affymetrix GeneChip Hybridization Oven 640  Three heating blocks are required: one at 65°C, one at 99°C, and the third one at 45°C.  1. Prepare the Hybridization Cocktail in a 1.5 mL RNase-free microfuge tube as shown  in Table 5.1.  2. Flick or gently vortex the tubes and spin down.  3. Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes,  and centrifuge at maximum speed for 1 minute.  4. Equilibrate the GeneChip ST Array to room temperature immediately before use.  Label the array with the name of the sample that will be hybridized.  5. Inject the appropriate amount (see Table 5.2) of the specific sample into the array  through one of the septa (see Figure 5.1 for location of the septa on the array).  6. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 17 hours ± 1 hour.  During the latter part of the array hybridization, commence preparation of the  reagents required immediately after completion of hybridization.

scan_protocol: the GeneChip Expression Wash, Stain and Scan User Manual (P/N702731) for the washing and staining steps required immediately after completion of hybridization. Please refer to Appendix C for fluidics protocols and fluidics script information for GeneChip ST Arrays. Scan model are Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip Scanner 3000 7G.

data_processing: The raw data from microarrays were analyzed using Partek Genome Suite software, version 6.3 Copyright  2008 (Partek Inc., St. Louis, MO, USA).  Briefly, Affymetrix .CEL files were processed to generate gcRMA (robust multi-array average) values.  This step was followed by quantile normalization and log2 transformation to represent gene expression levels.

organism: Mus musculus

source_name: Peripheral

label_protocol: Whole Transcript Sense Target Labeling Assay using AmbionWT expression Kit P/N 702808.

growth_protocol: Bone marrow adipocytes and peripheral white adipocytes (n=6-10 animals per group) were isolated from obese mice Obob, male C57BL/6J mice (6-months, 14-months and 18-months of age) fed either with standard chow or high fat diet.  All mice were housed in temperature-controlled conditions on a 12-h light, 12-h dark cycle.

extract_protocol: Total RNA was extracted using Trizol (Life Technologies, Grand Island, NY, USA) and chloroform followed by purification on an RNeasy MinElute column (QIAGEN, Valencia, CA. USA).  Three pooled RNA preparations were generated from 6-10 animals due to the low yield of bone marrow adipocytes during isolation.

treatment_protocol: Briefly, both femurs and tibias were collected after mice were sacrificed.  Bones were cleaned and rinsed with 75% ethanol and DEPC water to eliminate surrounding fat and muscle cells.  Fresh bone marrows were flushed out with PBS containing 1% fatty acid-free BSA and 1% RNAase and DNAase-free water using a 25-gauge needle from femurs and tibias.  Red blood cells were lysed using red cell lysis buffer.  After centrifugation at 3000 RPM for 5 min, floating adipocytes were collected from bone marrow stromal cells and then were washed with PBS buffer three times.

tag: sample type

value: C57BL/6J Male, 6 month old

tag: genetic background

tag: genotype

value: wild type

tag: age

value: 6 month old

tag: gender

value: male

value: Peripheral white adipocyte

tag: diet

value: high fat


title: Ls174T-L8 dox3


title: Ls174T-pTER-β-catenin dox1


title: CDC7_KD

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

country: Japan

institute: Kyushu University

hyb_protocol: 10 µg biotin incorporated cRNA was fragmented and then denatured. The denatured cRNA was slowly loaded into the bioarray flex chamber without the introduction of air bubbles. All samples were loaded within 30 minutes of cRNA denaturation. The sealed bioarrays were left to hybridise in a 37°C shaker-incubator for 18 hours. The slides were washed and placed in a solution of Cy5-streptavidin for 30 minutes, before stringent washes were used to remove any unbound dye.

scan_protocol: The arrays were scanned with Agilnet DNA Microarray Scanner model G2565BA.

data_processing: The scanned images were quantified with CodeLink Expression Array Software (Applied Microarrays, formally supplied by GE Healthcare), where the intensity of each spot was divided by the spot’s signal median.

source_name: HUVEC

label_protocol: Biotin-labelled complex cRNAs were prepared to according to the manufacturer's protocols (Applied Microarrays, formally supplied by GE Healthcare)

growth_protocol: HUVECs were isolated from umbilical cords by collagenase digestion and cultured at 37ºC/5%CO2 in basal culture medium supplemented with a proprietary mixture of heparin, hydrocortisone, epidermal growth factor, 2% foetal calf serum (FCS; EGM-2, Cambrex, Workingham, UK).

extract_protocol: Cell cultures were washed with 1 x PBS and lysed using TRIzol® reagent. Total RNA was extracted using phenol chloroform, with the precipitated RNA washed in 70% ethanol and resuspended in Rnase free water. RNA concentration and quality was assess by spectrophotometer and Agilent BioAnalyser.

treatment_protocol: HUVEC pools consisting of 10 biological isolates were transfected with siRNA smartpools from Dharmacon Inc. (Lafayette, Colorado, USA) using the siFectamine transfection reagent (ICVEC, London, UK) used according to the manufacturer’s instructions. Transfection was carried out when HUVEC pools were 60-80% confluent, with siRNA smartpools at a final concentration of 100nm per treatment and RNA was extracted 24hrs after transfection.

tag: tissue

value: HUVEC

tag: sirna knocked down

value: CDC7 siRNA knocked down


title: CDH12_KD

value: CDH12 siRNA knocked down


title: Ventricularis_Oscillatory_2_miRNA

description: replicate 2


title: Ventricularis_Oscillatory_3_miRNA

description: replicate 3


title: Ventricularis_Oscillatory_1_miRNA

description: replicate 1


title: Mouse_BM_6M_HF diet_02

source_name: Bone marrow

value: Bone marrow adipocyte


title: Ls174T-L8 con3


title: Mouse_BM_6M_HF diet_01


title: CDC45L_KD

value: CDC45L siRNA knocked down


title: Mouse_BM_6M_HF diet_03


title: Mouse_Peripheral_6M_03

value: control


title: CDC6_KD

value: CDC6 siRNA knocked down


title: cb_ips_HCB_3

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description: Gene expression data from CB iPSC HCB 3

hyb_protocol: According to manufacturer's instructions.

scan_protocol: scanner model: GCS3000

data_processing: RMA quantile summarization and normalization by R/BioConductor

source_name: CB iPSC

label_protocol: GeneChip One- Cycle labeling kit (Affymetrix)

extract_protocol: RNA was purified by an RNeasy kit (Qiagen, Cat# 74106)

value: iPSC


title: Fibrosa_Oscillatory_6_miRNA

description: replicate 6

source_name: Fibrosa HAVEC, Oscillatory Shear, 24h


title: Ls174T-pTER-β-catenin con1

value: intestinal colorectal carcinoma cells


title: CDC42EP4_KD

value: CDC42EP4 siRNA knocked down


title: Fibrosa_Oscillatory_5_miRNA

description: replicate 5

value: Aortic Valve, Endothelial Cells, Shear


title: Ls174T-L8 dox2

value: dominant-negative Tcf4 transgene


title: Mouse_Peripheral_6M_02

value: C57BL/6J Male, 6 month old

value: wild type


title: LB vs 7d in vivo#3

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

description: Biological replicate 3 of 3

hyb_protocol: TIGR SOP#M008

scan_protocol: Slides were scanned using a ScanArray Express microarray scanner (Perkin Elmer) at 10 um resolution and quantified using ScanArray Express software.

data_processing: Total normalization using MIDAS (TIGR) and analysis using MeV (TIGR).

organism: Proteus mirabilis

source_name: log phase LB (OD600 = 1.0)

label_protocol: cDNA was generated and labeled with CyDye according to TIGR SOP#M007

extract_protocol: RNA was stabilized using RNA Protect (Qiagen) and isolated using the RNeasy kit (Qiagen).

tag: strain

tag: growth condition

value: log phase LB (OD600 = 1.0)

source_name: 7d in vivo

value: 7d in vivo


title: Fibrosa_Oscillatory_4_miRNA

description: replicate 4


title: LB vs 7d in vivo#2

description: Biological replicate 2 of 3


title: LB vs 3d in vivo#3

description: Biological replicate 3 of 3

source_name: 3d in vivo

value: 3d in vivo


title: LB vs 7d in vivo#1

description: Biological replicate 1 of 3


title: Mouse_BM_6M_03

value: 6 month old

value: male


title: CDC37_KD

value: HUVEC

value: CDC37 siRNA knocked down


title: Fibrosa_Oscillatory_3_miRNA

description: replicate 3


title: LB vs 3d in vivo#2

description: Biological replicate 2 of 3


title: Mouse_Peripheral_6M_01

value: Peripheral white adipocyte


title: Ventricularis_Laminar_6_miRNA

description: replicate 6

source_name: Ventricularis HAVEC, Laminar Shear, 24h


title: Fibrosa_Oscillatory_2_miRNA

description: replicate 2


title: Fibrosa_Oscillatory_1_miRNA

description: replicate 1


title: Mouse_BM_6M_02

value: Bone marrow adipocyte

value: control


title: CDC34_KD

value: CDC34 siRNA knocked down


title: LB vs 1d in vivo#2

description: Biological replicate 2 of 3

source_name: 1d in vivo

value: 1d in vivo


title: CDC2_KD

value: CDC2 siRNA knocked down


title: Mouse_BM_6M_01


title: LB vs 1d in vivo#3

description: Biological replicate 3 of 3


title: Ventricularis_Laminar_5_miRNA

description: replicate 5

value: Aortic Valve, Endothelial Cells, Shear


title: LB vs 3d in vivo#1

description: Biological replicate 1 of 3


title: Ventricularis_Laminar_4_miRNA

description: replicate 4


title: LB vs 1d in vivo#1

description: Biological replicate 1 of 3


title: CDC25B_KD

value: CDC25B siRNA knocked down


title: Ventricularis_Laminar_3_miRNA

description: replicate 3


title: CDC25A_KD

value: CDC25A siRNA knocked down


title: CDC25C_KD

value: CDC25C siRNA knocked down


title: Mouse bone marrow adipocyte, 18 month old, biological rep 3

hyb_protocol: The GeneChip® Hybridization, Wash and Stain Kit.  Affymetrix GeneChip Hybridization Oven 640 Three heating blocks are required: one at 65°C, one at 99°C, and the third one at 45°C. 1. Prepare the Hybridization Cocktail in a 1.5 mL RNase-free microfuge tube 2. Flick or gently vortex the tubes and spin down. 3. Heat the Hybridization Cocktail at 99°C for 5 minutes. Cool to 45°C for 5 minutes, and centrifuge at maximum speed for 1 minute. 4. Equilibrate the GeneChip ST Array to room temperature immediately before use. Label the array with the name of the sample that will be hybridized. 5. Inject the appropriate amount (see Table 5.2) of the specific sample into the array through one of the septa (see Figure 5.1 for location of the septa on the array). 6. Place array in 45°C hybridization oven, at 60 rpm, and incubate for 17 hours ± 1 hour. During the latter part of the array hybridization, commence preparation of the reagents required immediately after completion of hybridization.

scan_protocol: Scan model are Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip Scanner 3000 7G.

data_processing: The raw data from microarrays were analyzed using Partek® Genome Suite software, version 6.3 Copyright © 2008 (Partek Inc., St. Louis, MO, USA).  Briefly, Affymetrix .CEL files were processed to generate gcRMA (robust multi-array average) values.  This step was followed by quantile normalization and log2 transformation to represent gene expression levels.

growth_protocol: Bone marrow adipocytes and peripheral white adipocytes (n=6-10 animals per group) were isolated from male C57BL/6J mice (6-months, 14-months and 18-months of age).  All mice were housed in temperature-controlled conditions on a 12-h light, 12-h dark cycle, and were fed standard chow.

value: Male

value: 18 month old

value: bone marrow adipocyte


title: Mouse Peripheral adipocyte, 18 month old, biological rep 2

value: Peripheral adipocyte


title: Mouse Peripheral adipocyte, 18 month old, biological rep 3


title: CDC27_KD

value: CDC27 siRNA knocked down


title: Ventricularis_Laminar_2_miRNA

description: replicate 2


title: TKO_num2_rep2

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

description:
TKO2.2nd
Stanford SFGF

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Quantile normalization was applied to control for the technical variations between arrays.

source_name: cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: RPMI1640 supplied with 10% fetal bovine serum

extract_protocol: RNeasy Plus Mini Kit (QIAGEN)

treatment_protocol: No treatment

value: blood

value: Female


title: Mouse bone marrow adipocyte, 18 month old, biological rep 1


title: Ventricularis_Laminar_1_miRNA

description: replicate 1


title: CDC42EP1_KD

value: HUVEC

value: CDC42EP1 siRNA knocked down


title: Mouse bone marrow adipocyte, 18 month old, biological rep 2


title: CDC16_KD

value: CDC16 siRNA knocked down


title: Fibrosa_Laminar_6_miRNA

description: replicate 6

source_name: Fibrosa HAVEC, Laminar Shear, 24h


title: CCNT1_KD

value: CCNT1 siRNA knocked down


title: Mouse Peripheral adipocyte, 18 month old, biological rep 1


title: CCNT2_KD

value: CCNT2 siRNA knocked down


title: TKO_num2_rep3

description:
TKO2.3rd
Stanford SFGF


title: Fibrosa_Laminar_5_miRNA

description: replicate 5


title: TKO_num2_rep1

description:
TKO2.1st
Stanford SFGF


title: Mouse Peripheral adipocyte, 14 month old, biological rep 3

value: 14 month old


title: TKO_num1_rep3

description:
TKO1.3rd
Stanford SFGF


title: Mouse Peripheral adipocyte, 14 month old, biological rep 1


title: TKO_num1_rep2

description:
TKO1.2nd
Stanford SFGF


title: CCNI_KD

value: CCNI siRNA knocked down


title: Fibrosa_Laminar_2_miRNA

description: replicate 2

value: Aortic Valve, Endothelial Cells, Shear


title: CCNG2_KD

value: CCNG2 siRNA knocked down


title: CCNH_KD

value: CCNH siRNA knocked down


title: KMS11_control_rep3

description:
KM11.3rd
Stanford SFGF


title: Fibrosa_Laminar_1_miRNA

description: replicate 1


title: Fibrosa_Laminar_3_miRNA

description: replicate 3


title: Mouse bone marrow adipocyte, 14 month old, biological rep 2

value: Male


title: CCNG1_KD

value: CCNG1 siRNA knocked down


title: Fibrosa_Laminar_4_miRNA

description: replicate 4


title: Mouse bone marrow adipocyte, 14 month old, biological rep 3

value: bone marrow adipocyte


title: KMS11_control_rep2

description:
KM11.2nd
Stanford SFGF


title: TKO_num1_rep1

description:
TKO1.1st
Stanford SFGF


title: KMS11_control_rep1

description:
KM11.1st
Stanford SFGF


title: Mouse bone marrow adipocyte, 14 month old, biological rep 1


title: CCNF_KD

value: CCNF siRNA knocked down


title: Mouse Peripheral adipocyte, 6 month old, biological rep 3

value: 6 month old

value: Peripheral adipocyte


title: CDC20_KD

value: CDC20 siRNA knocked down


title: Mouse Peripheral adipocyte, 14 month old, biological rep 2


title: RNAi_num2_rep2

description:
RNAi_2_2
Stanford SFGF

value: blood cells

tag: RNAi transfection

value: KMS11-NSD2 RNAi#2

value: Female


title: CCND3_KD

value: HUVEC

value: CCND3 siRNA knocked down


title: CCNE1_KD

value: CCNE1 siRNA knocked down


title: CCND2_KD

value: CCND2 siRNA knocked down


title: RNAi_num1_rep2

description:
RNAi_1_2
Stanford SFGF

value: KMS11-NSD2 RNAi#1


title: Mouse bone marrow adipocyte, 6 month old, biological rep 2


title: Mouse bone marrow adipocyte, 6 month old, biological rep 3


title: CCNE2_KD

value: CCNE2 siRNA knocked down


title: Mouse Peripheral adipocyte, 6 month old, biological rep 1


title: CCND1_KD

value: CCND1 siRNA knocked down


title: Mouse bone marrow adipocyte, 6 month old, biological rep 1

value: Male


title: Mouse Peripheral adipocyte, 6 month old, biological rep 2


title: CCNC_KD

value: CCNC siRNA knocked down


title: CCNB3_KD

value: CCNB3 siRNA knocked down


title: RNAi_num1_rep1

description:
RNAi_1_1
Stanford SFGF


title: RNAi_control_rep2

description:
control_2
Stanford SFGF


title: RNAi_control_rep1

description:
control_1
Stanford SFGF


title: CCNB2_KD

value: CCNB2 siRNA knocked down


title: RNAi_num2_rep1

description:
RNAi_2_1
Stanford SFGF


title: CCNB1_KD

value: CCNB1 siRNA knocked down


title: Ventricularis_Oscillatory_6_mRNA

description: replicate 6

data_processing: Because of low background, no normalization was used for data analysis.  GenomeStudio V2010.1 was used to generate values.

value: Aortic Valve, Endothelial Cells, Shear


title: Ventricularis_Oscillatory_4_mRNA

description: replicate 4


title: Ventricularis_Oscillatory_5_mRNA

description: replicate 5


title: Ventricularis_Oscillatory_2_mRNA

description: replicate 2


title: 5312759006_A

city: New York

first: Mariano

middle: Javier

last: Alvarez

state: NY

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

description: Murine Xen-eyfp cell line treated for 96h with the Alk4 inhibitor SB431542. 200 ng of total RNA were profiled on Illumina mouseWG6v2 expression arrays.

hyb_protocol: According to Illumina whole-genome gene expression direct hybridization assay guide

scan_protocol: The arrays were scanned using an iScan (Illumina). Images were segmented and quantified by BeadStudio (Illumina).

data_processing: BeadStudio-acquisition (version is 3.2); followed by variance stabilization transformation and robust spline normalization as implemented in lumi R package (Bioconductor)

label_protocol: 200 ng total RNA were processed according to Illumina TotalPrep RNA amplification kit (Ambion)

extract_protocol: TRIZOL followed by MagMAX96 for microarrays total RNA isolation kit (Ambion)

value: Xen-eyfp

tag: treatment


title: 5038753033_C

description: Murine Xen-eyfp cell line treated for 96h with 100 ng/ml recombinant Cripto protein. 200 ng of total RNA were profiled on Illumina mouseWG6v2 expression arrays.

value: 100 ng/ml Cripto


title: CCNA2_KD

value: CCNA2 siRNA knocked down


title: E14.5 Tgfbr2 Wildtype Mouse Model Palate 5

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description:
strain: C57B6
genotype: Tgfbr2fl/fl
tissue: Secondary palate
age: E14.5
gender: Not determined

hyb_protocol: Standard Affymetrix hybridization protocol was used.

scan_protocol: Standard Affymetrix scanning protocol was used.

data_processing: We used the RMA normalization protocol as implemented by the following website:  http://www.webarraydb.org/webarray/index.html

source_name: E14.5 Tgfbr2fl/fl Wildtype Mouse Model Palate

label_protocol: Standard Affymetrix cRNA labeling protocol was used.

growth_protocol: Standard IACUC protocols were used.

extract_protocol: Embryo was harvested at the designated time point.  Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from the secondary palate.

treatment_protocol: Mice were maintained under standard IACUC protocols.

value: Secondary palate

value: Not determined


title: 5312759006_C

description: Murine Xen-eyfp cell line treated for 96h with 100 ng/ml recombinant Cripto protein plus the Alk4 inhibitor SB431542. 200 ng of total RNA were profiled on Illumina mouseWG6v2 expression arrays.

value: 100 ng/ml Cripto and SB431542


title: 5312759005_A


title: E14.5 Tgfbr2 Wildtype Mouse Model Palate 3


title: CASP1_KD

value: HUVEC

value: CASP1 siRNA knocked down


title: Fibrosa_Oscillatory_6_mRNA

description: replicate 6


title: 5312759005_D

description: Murine Xen-eyfp cell line treated for 96h with 50 ng/ml recombinant Nodal protein. 200 ng of total RNA were profiled on Illumina mouseWG6v2 expression arrays.

value: 50 ng/ml Nodal


title: 5038753033_E


title: E14.5 Tgfbr2 Wildtype Mouse Model Palate 4


title: CCNA1_KD

value: CCNA1 siRNA knocked down


title: Fibrosa_Oscillatory_5_mRNA

description: replicate 5


title: C3orf26_KD

value: C3orf26 siRNA knocked down


title: E14.5 Tgfbr2 Wildtype Mouse Model Palate 2


title: Ventricularis_Oscillatory_1_mRNA

description: replicate 1


title: 5038753033_B


title: 5312759005_E


title: E14.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Palate 5

description:
strain: C57B6
genotype: Tgfbr2fl/fl;Wnt1-Cre
tissue: Secondary palate
age: E14.5
gender: Not determined


title: E14.5 Tgfbr2 Wildtype Mouse Model Palate 1


title: 5312759005_C

description: Murine Xen-eyfp cell line. 200 ng of total RNA were profiled on Illumina mouseWG6v2 expression arrays.

source_name: Xen-eyfp

value: Media


title: C17orf62_KD

value: C17orf62 siRNA knocked down


title: 5038753033_A


title: Fibrosa_Oscillatory_4_mRNA

description: replicate 4


title: Fibrosa_Oscillatory_2_mRNA

description: replicate 2


title: Ventricularis_Oscillatory_3_mRNA

description: replicate 3


title: Fibrosa_Oscillatory_3_mRNA

description: replicate 3


title: BIRC6_KD

value: BIRC6 siRNA knocked down


title: Ventricularis_Laminar_6_mRNA

description: replicate 6


title: Fibrosa_Oscillatory_1_mRNA

description: replicate 1


title: 5038753032_E


title: 5038753080_C


title: E14.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Palate 1


title: E14.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Palate 3


title: BCOR_KD

value: BCOR siRNA knocked down


title: BDNF_KD

value: BDNF siRNA knocked down


title: Ventricularis_Laminar_4_mRNA

description: replicate 4

value: Aortic Valve, Endothelial Cells, Shear


title: AURKB_KD

value: AURKB siRNA knocked down


title: 5038753032_D

description: Murine Xen-eyfp cell line treated for 96h with 50 ng/ml recombinant Nodal protein plus the Alk4 inhibitor SB431542. 200 ng of total RNA were profiled on Illumina mouseWG6v2 expression arrays.

value: Xen-eyfp

value: 50 ng/ml Nodal and SB431542


title: Ventricularis_Laminar_2_mRNA

description: replicate 2


title: BCAP31_KD

value: BCAP31 siRNA knocked down


title: Ventricularis_Laminar_5_mRNA

description: replicate 5


title: 5038753049_A


title: BCL6_KD

value: BCL6 siRNA knocked down


title: Fibrosa_Laminar_6_mRNA

description: replicate 6


title: E14.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Palate 4

value: Secondary palate

value: Not determined


title: Ventricularis_Laminar_1_mRNA

description: replicate 1


title: Ventricularis_Laminar_3_mRNA

description: replicate 3


title: 5038753080_B


title: DEN-PB tumor-39W vs. DEN-PB CAR-KO-39W

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression comparison of DEN-PB treated CAR-KO mouse liver vs WT mouse liver tumor at 39 weeks

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

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

data_processing: Data was obtained using the Agilent Feature Extraction software (v7.5), using the 2-color defaults for all parameters.

source_name: DEN-PB tumor

label_protocol: Starting with 0.5µg of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.

extract_protocol: Total liver RNA was isolated using RNeasy Kit (QIAGEN, Valencia, CA, USA), according to the manufacturers’ protocols.

treatment_protocol: Both WT and CAR-KO mice were treated with PB in drinking water after initiation of liver tumor with DEN.

tag: background strain

value: 39 weeks

value: Liver Tumor

source_name: DEN-PB CAR-KO

value: Liver


title: AURKA_KD

value: HUVEC

value: AURKA siRNA knocked down


title: E14.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Palate 2


title: DEN-CAR-KO 39W vs. DEN-PB CAR-KO-39W

description: Gene expression comparison of DEN-PB treated and DEN treated CAR-KO mouse livers at 39 weeks

source_name: DEN-CAR-KO


title: 5038753065_F


title: ATR_KD

value: ATR siRNA knocked down


title: DEN-PB CAR-KO-39W vs. DEN-PB tumor-39W


title: ATP13A3_KD

value: ATP13A3 siRNA knocked down


title: DEN-PB CAR-KO-39W vs. DEN-CAR-KO 39W


title: ASNS_KD

value: ASNS siRNA knocked down


title: CCL2_KD

value: CCL2 siRNA knocked down


title: 5038753065_E


title: 5038753080_A


title: ATM_KD

value: ATM siRNA knocked down


title: Fibrosa_Laminar_4_mRNA

description: replicate 4

tag: cell type

value: Aortic Valve, Endothelial Cells, Shear


title: 5038753032_A

value: Xen-eyfp

value: 100 ng/ml Cripto


title: ARHGEF1_KD

value: ARHGEF1 siRNA knocked down


title: DEN-PB CAR-KO-39W vs. DEN-PB WT-39W

description: Gene expression comparison of DEN-PB treated WT mouse liver vs CAR-KO mouse liver at 39 weeks

source_name: DEN-PB WT


title: 5038753049_E


title: 5038753032_C


title: Fibrosa_Laminar_2_mRNA

description: replicate 2


title: Fibrosa_Laminar_3_mRNA

description: replicate 3


title: Fibrosa_Laminar_5_mRNA

description: replicate 5


title: 5038753065_C


title: DEN-PB WT-39W vs. DEN-PB CAR-KO-39W


title: Salmonella typhi 1

city: Grand Rapids

first: Mrutyunjaya

last: Parida

address: 333 Bostwick Ave N.E.

department: Research

institute: Van Andel Institute

hyb_protocol: Standard Agilent hybridization protocol 65C 10 rpm 17 hr

scan_protocol: Agilent scanner G2505B Red&Green resolution 5um with XDR

data_processing: Agilent Feature Extraction software

source_name: convalescent phase

label_protocol: Standard Agilent gene expression 2-color Cy3 and Cy5

extract_protocol: Paxgene blood RNA kit

tag: infection

value: Salmonella typhi

tag: disease stage

value: convalescent phase

value: peripheral blood

source_name: acute phase

value: acute phase


title: 5038753080_F

value: 50 ng/ml Nodal

tag: time


title: ATBF1_KD

source_name: HUVEC

value: ATBF1 siRNA knocked down


title: Salmonella typhi 2


title: Salmonella typhi 3


title: 5038753049_D


title: ANGPT2_KD

value: HUVEC

value: ANGPT2 siRNA knocked down


title: ANAPC2_KD

value: ANAPC2 siRNA knocked down


title: ANGPT1_KD

value: ANGPT1 siRNA knocked down


title: Klebsiella

value: Klebsiella


title: Fibrosa_Laminar_1_mRNA

description: replicate 1

tag: group


title: SVZ cells_MCAo2_7d

type: other

city: Detroit

first: Xian Shuang

address: 2799 West Grand BLVD

institute: Henry Ford Hospital

description: Gene expression data from ischemic cultured SVZ neural progenitor cells

hyb_protocol: Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Taq RNA labeling Kit manual.

scan_protocol: The microarrays were scanned on an Axon Genepix 4000B scanner (Affymetrix Inc),

data_processing: Data were extracted from images using GenePix V4.1 software. miRNA QC Tool (Affymetrix Inc), a software for data summarization, Log2 transformation, normalization and quality control, was used.

molecule: other

organism: Rattus norvegicus

source_name: total RNA from MCAo SVZ neural progenitor cells

label_protocol: The RNA samples were 3’-end labeled with biotin dye using the FlashTagTM Biotin RNA Labeling Kits

extract_protocol: miRNeasy Mini Kit

value: 3-4 months

tag: cells

value: cultured neural progenitor cells in subventricular zone of the brain

value: middle cerebral artery occlusion


title: SVZ cells_MCAo1_7d


title: ARHGAP1_KD

value: ARHGAP1 siRNA knocked down


title: 5038753080_E

value: Xen-eyfp

value: Media


title: Colorectal carcinoma 9

city: Shanghai

first: Sun

last: Y

address: 180 Fenglin Road

country: China

institute: Fudan University

hyb_protocol: Agilent’s miRNA Complete Labeling and Hybridization Kit V2 was utilized for processing the samples.

scan_protocol: The hybridized array was then washed and scanned according to Agilent specifications and data was extracted from the scanned image using Feature Extraction version 10.5 (Agilent,USA).

data_processing: The results were analyzed using GeneSpring GX 10.0 software (Agilent,USA).

label_protocol: Standard Agilent protocol

extract_protocol: Total RNA extraction was performed by High Pure miRNA Isolation Kit (Roche, USA) according to the manufacturer's protocol.

tag: disease state

value: CRC

value: Colorectal carcinoma

tag: survival group

value: short time (S)survival (<5 years)


title: SVZ cells_MCAo3_7d

tag: age


title: 5038753065_A


title: Non-typhoid S. typhi

value: Non-typhoid S. typhi

value: convalescent phase

value: peripheral blood

value: acute phase


title: ARHGAP4_KD

value: HUVEC

value: ARHGAP4 siRNA knocked down


title: AKT1_KD

value: AKT1 siRNA knocked down


title: ABL1_KD

value: ABL1 siRNA knocked down


title: Colorectal carcinoma 10


title: Acinetobacter

value: Acinetobacter


title: Colorectal carcinoma 7


title: Colorectal carcinoma 11


title: Colorectal carcinoma 8


title: Colorectal carcinoma 12


title: 5038753065_B

value: 50 ng/ml Nodal


title: AFF1_KD

value: AFF1 siRNA knocked down


title: 5038753049_C


title: Colorectal carcinoma 6

value: long time (L)survival (≥5 years)


title: Colorectal carcinoma 5


title: SVZ cells_non-MCAo2

description: Gene expression data from non-MCAo cultured SVZ neural progenitor cells

source_name: total RNA from non-MCAo SVZ neural progenitor cells

value: 3-4 months

value: cultured neural progenitor cells in subventricular zone of the brain

value: control


title: Colorectal carcinoma 4

value: CRC

value: Colorectal carcinoma


title: SVZ cells_non-MCAo1


title: SVZ cells_non-MCAo3


title: E. coli MG1655 and P. aeruginosa culture rep2

city: San Marcos

first: Robert

middle: JC

last: McLean

state: TX

address: 601 University Drive

department: Biology

institute: Texas State University-San Marcos

description: Gene expression data from mixed culture

hyb_protocol: Following fragmentation, 4-6ug cDNA was hybridized to E coli or P aeruginosa gene chips

scan_protocol: Gene chips were scanned using an Affymetrix Model 3000 GeneArray scanner

data_processing: Microarray .cel files were analyzed by multiarray analysis method using the Affy package (version 1.18.2, Affymetrix) using default options.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli and P. aer. Mixed culture

label_protocol: Enzo Bioarray Terminal Labeling Kit (Affymetrix cat # 900181) according to manufacturer's instructions

growth_protocol: E coli and P aeruginosa cells were grown aerobically at 37C in pure and mixed culture in a MOPS-buffered medium containing N-acetyl glucosamine

extract_protocol: Qiagen RNA extraction following manufacturer's protocol

treatment_protocol: Following incubation samples were stabilized with RNA later (Ambion) and stored at 4C prior to RNA extraction

tag: culture

value: E. coli and P. aeruginosa culture


title: Colorectal carcinoma 3

tag: tissue


title: E. coli MG1655 and P. aeruginosa culture rep1

description: Gene expression data from mixed culture


title: Colorectal carcinoma 2

extract_protocol: Total RNA extraction was performed by the miRVana miRNA Isolation Kit (Ambion,USA) according to the manufacturer's protocol.


title: msh1, stunt, biological rep 2

city: Lincoln

first: Ying-Zhi

last: Xu

state: NE

address: 1901 Vine St.

department: Center for Plant Science Innovation

institute: University of Nebraska

description:
msh1_stunt-2
Gene expression data from stunted msh1 transgenic line

hyb_protocol: RNA was hybridized to individual Affymetrix GeneChip oligonucleotide ATH1 array using manufacturers instructions

scan_protocol: According to Affymetrix instructions

data_processing: Expression data from Affymetrix genechips were normalized using the Robust Multichip Average (RMA) method using ioconductor’s affy package in the R language

organism: Glycine max

source_name: msh1 RNAi stunted line

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

growth_protocol: green house grown

extract_protocol: total RNA was extracted from each plant using TRIzol (Invitrogen) extraction procedure followed by purification on RNeasy columns (Qiagen).

treatment_protocol: 6 weeks old plants

value: above ground part

value: 6-week-old old plant

tag: genotype/variation

value: msh1 RNAi stunted line


title: E. coli MG1655 pure culture rep1

description: Gene expression data from pure culture

source_name: E. coli pure culture

value: E. coli pure culture


title: msh1, stunt, biological rep 3

description:
msh1_stunt-3
Gene expression data from stunted msh1 transgenic line


title: Colorectal carcinoma 1


title: msh1, stunt, biological rep 1

description:
msh1_stunt-1
Gene expression data from stunted msh1 transgenic line


title: msh1, variegation, biological rep 2

description:
msh1_var-2
Gene expression data from variegation msh1 transgenic line

source_name: msh1 RNAi variegated line

value: msh1 RNAi variegated line


title: msh1, variegation, biological rep 3

description:
msh1_var-3
Gene expression data from variegation msh1 transgenic line


title: msh1, variegation, biological rep 1

description:
msh1_var-1
Gene expression data from variegation msh1 transgenic line


title: wild type, biological rep 4

description:
thorn-4
Gene expression data from wild type

source_name: wild type

value: wild type


title: Trans_NSD2_rep2

description:
trans_rep2
Stanford SFGF

data_processing: Raw data were normalized by rank invariant gene sets and differential genes were identified by dChip software

source_name: cell line

growth_protocol: DMEM supplied with 10% fetal bovine serum

tag: cell line

value: embryonic fibroblasts (derived from p19ARF-/- micderived from p19ARF-/- micee)

value: blood

tag: transduction

value: wild-type NSD2

tag: gender

value: Female


title: Trans_control_rep2

description:
control_rep2
Stanford SFGF


title: wild type, biological rep 1

description:
thorn-1
Gene expression data from wild type


title: DSiPS4factor_8942-3_D12

city: Minato-ku

first: Yasuhiro

last: Ebihara

state: Tokyo

address: 4-6-1, Shirokanedai

institute: The Institute of Medical Science, The University of Tokyo

hyb_protocol: 600 ng of Cy3-labeled RNA was hybridized to Agilent Whole Human Genome Oligo Microarray

scan_protocol: The signals were detected by DNA microarray scanner.

data_processing: The scanned images were extracted with Feature Extraction Software 10.7.3.1 (Agilent Technologies)  using default parameters. Subsequent data processing was performed using the GeneSpringGX11.5 software package (Agilent Technologies) and IPA 8.5 (Tomy digital biology).

label_protocol: 100 ng aliquots of total RNA were amplified and labeled using a Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturers’ instructions.

growth_protocol: hiPS cells were maintained and passaged weekly on mitomycin C-treated SNL or irradiated MEF feeder cells. To induce hiPS cells to differentiate into hematopoietic cells, we used a coculture system with murine stromal cell line, AGM-S3 cells. Briefly, 10 undifferentiated hiPS cell colonies (each consisting of approximately 1 x 10^3 cells) were picked up, transferred onto each well of 6-well plates (Sumitomo Bakelite Co), which were coated with 25 Gy-irradiated confluent AGM-S3 cells (approximately 1-2 x 10^5 cells), and cultured in hiPS cell maintenance medium for 3 days. Then culture medium was changed to hematopoietic differentiation medium (IMDM, 10% FBS, 3 mM L-glutamine, 5.5 mg ml-1 human transferrin, 50 mg ml-1 ascorbic acid, 1x10^-4 M 2-ME, 1x10^-4 M nonessential amino acids and 100 ng ml^-1 human vascular endothelial growth factor) and replaced everyday for 12 days.

extract_protocol: Total RNA was extracted with SV total RNA isolation system (Promega) and RNA integrity was assessed by a 2100 Bioanalyzer (Agilent Technologies).

tag: days after induction of differentiation

tag: factors using in making ips cells

value: OCT3/4, SOX2, KLF4, c-MYC


title: Mut vs. WT biological repeat3

city: Tel-Aviv

first: Nir

last: Osherov

address: Ramat Aviv Campus

department: Medical Microbiology and Immunology

country: Israel

institute: Tel-Aviv University

description: Biological replicate 3 of 3

hyb_protocol: The probe was heated for two cycles of 5 min at 95°C and then applied to the slide and incubated at 42°C for 18 h. After post-incubation washes (two cycles of 55°C in 2X SSC, 0.1% SDS; room temperature (RT) in 0.1X SSC, 0.1% SDS and RT 0.1X SSC)

scan_protocol: slides were scanned with a Genepix 6000B scanner (Molecular Devices LLC, Sunnyvale, CA) to generate images that were then analyzed with the Spotfinder program

data_processing: Exported fluorescence intensities were normalized in MIDAS (29) using LOWESS (Locally Weighted Scatterplot Smoothing), followed by flip-dye consistency check and in-slide-replicate analysis.  The expression profiles were analyzed using EXPANDER, a general microarray analysis software. Please see 'readme.txt' file on the Series record for raw data file - label associations.

organism: Aspergillus fumigatus

source_name: mutant delta-PrtT A

label_protocol: cDNA was generated from 2 µg of total RNA by incubating for 18 h at 42°C with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA), a dNTP mixture containing amino-allyl dTTP and primed with random hexamers. Unincorporated dNTPs and hexamers were removed by purification with a Qiagen PCR purification column. Samples were then incubated for 18 h at room temperature with either Cy-3 or Cy-5 dye. After labeling, unincorporated dye was removed by purification with a Qiagen PCR purification column. Dye-coupled cDNA probes were evaporated and resuspended in hybridization buffer (40% formamide, 5X SSC, 0.1% SDS, 0.1 mM DTT and 6% salmon sperm DNA). The probe was heated for two cycles of 5 min at 95°C and then applied to the slide

growth_protocol: 1x107 wild type (Af293 strain) and mutant delta-PrtT A. fumigatus conidia were grown in 50 ml of 1% skim milk medium for 24 h at 37°C in an orbital incubator at 180 rpm

extract_protocol: The mycelium (wild type or delta PrtT) was subsequently freeze-dried. Total RNA from three independent biological repeats was extracted. Total RNA was isolated from each strain using the Qiagen RNeasy plant kit (Qiagen, Valencia, CA) following the filamentous fungus protocol.

treatment_protocol: growth on skim-milk medium of mutant and wild-type strains and subsequent analysis of transcriptional profiles

tag: strain

value: mutant delta-PrtT A

source_name: wild type (Af293 strain)

value: wild type Af293


title: DSiPS3factor_5397-33_D12

tag: cell type

value: OCT3/4, SOX2, and KLF4


title: Trans_NSD2_rep1

description:
trans_rep1
Stanford SFGF


title: DSiPS3factor_5397-32_D12


title: DSiPS3factor_8942-32_D12


title: wild type, biological rep 2

description:
thorn-2
Gene expression data from wild type


title: NORMALiPS_A31_D12

value: control hiPS


title: DSiPS4factor_6872-12_D12

value: DS-iPS4factor 6872-12


title: wild type, biological rep 3

description:
thorn-3
Gene expression data from wild type


title: Mut vs. WT biological repeat2

description: Biological replicate 2 of 3


title: Mut vs. WT biological repeat1

description: Biological replicate 1 of 3.


title: Trans_control_rep1

description:
control_rep1
Stanford SFGF

value: control


title: NORMALiPS_253G1_D12


title: NORMALiPS_253G4_D12


title: F2-2347-M

status: Public on Nov 28 2011

city: Bar Harbor

first: Ricardo

middle: Alejandro

last: Verdugo

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Transcript expression data from a male (MRL/MpJ x SM/J)F2 mouse.

hyb_protocol: 2.3µg of biotin-labeled and fragmented cDNA was then hybridized onto GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) for 16 hours at 45°C.  Post-hybridization staining and washing were performed according to manufacturer’s protocols using the Fludics Station 450 instrument (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.

data_processing: Data were imported into R (v2.11) and processed using the affy package from Bioconductor (v2.6). The data were normalized using robust multi-array average (rma) expression with no background correction. A custom cdf file MoGene10stvMmENST cdf V11.0.1 was obtained from Brainarray (http://brainarray.mbni.med.umich.edu).

source_name: liver, F2, male

label_protocol: Following reverse transcription with random primers-T7 primers (Affymetrix, Santa Clara, Ca), double stranded cDNA was synthesized with the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara, Ca).  In an in vitro trancription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified to generate cRNA.  In the second cycle of cDNA synthesis, random primers are used to generate single-stranded DNA in the sense orientation.  Incorporation of dUTP in the cDNA synthesis step allows for the fragmentation of the cDNA strand utilizing uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the dUTP and allows for breakage at these residues. Labeling occurs by terminal deoxynucleotidyl transferase (TdT) where biotin is added by a Affymetrix Labeling Reagent.

growth_protocol: Mice were housed in a climate-controlled facility with a 14-hour:10-hour light-dark cycle with free access to food and water throughout the experiment. After weaning, mice were maintained on a chow diet (5K52 LabDiet, St. Louis, MO). F2 mice were tail-tipped at 2 weeks of age.

extract_protocol: Tissue samples were stored in RNAlater (Ambion, Austin TX) following dissection and later homogenized in TRIzolTM (Invitrogen, Carlsbad, CA).  Total RNA was isolated by TRIzolPlus TM methods according to the manufacturer’s protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA).

treatment_protocol: The mice were housed individually for 3 days prior to the tissue collection and fasted for 4-5 hours on the day of the collection. There was no treatment group, all mice were in the same conditions.

value: MRL/MpJ x SM/J

tag: generation

tag: Sex

value: male

value: 13 weeks

value: liver

tag: batch


title: F2-2069-F

description: Transcript expression data from a female (MRL/MpJ x SM/J)F2 mouse.

source_name: liver, F2, female

value: female


title: F2-2272-F


title: F2-2059-M


title: F2-2115-F


title: F2-2041-F


title: F2-2081-F


title: F2-2013-F


title: F2-2168-F


title: F2-2186-M


title: F2-2014-M


title: ESC-H1OGN input

type: genomic

first: Akiko

last: Doi

address: 855 N Wolfe St, Rangos 580

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner per manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan v2.5 software.

molecule: genomic DNA

source_name: Input fraction from ESC-H1OGN

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

value: human ES cells

source_name: Methyl-depleted fraction from ESC-H1OGN


title: F2-2284-F


title: F2-2184-M


title: F2-2329-M


title: F2-2263-M


title: F2-2283-F


title: F2-2239-F


title: F2-2056-M


title: F2-2049-M


title: ESC-CHB8 input

source_name: Input fraction from ESC-CHB8

source_name: Methyl-depleted fraction from ESC-CHB8


title: F2-2225-M


title: F2-2320-F


title: F2-2120-M


title: F2-2206-F


title: F2-2349-M


title: ESC-H9 input

source_name: Input fraction from ESC-H9

source_name: Methyl-depleted fraction from ESC-H9


title: ESC-Hue2 input

source_name: Input fraction from ESC-Hue2

source_name: Methyl-depleted fraction from ESC-Hue2


title: ESC-H1 input

source_name: Input fraction from ESC-H1

source_name: Methyl-depleted fraction from ESC-H1


title: F2-2121-M


title: F2-2182-F


title: F2-2291-F


title: F2-2085-F


title: F2-2343-M


title: F2-2253-M


title: K-iPSC-N9-p34 input

source_name: Input fraction from K-iPSC-N9-p34

value: human keratinocyte-derived iPS cells-N9

tag: passage

source_name: Methyl-depleted fraction from K-iPSC-N9-p34


title: F2-2346-M


title: F2-2259-F


title: ESC-BG03 input

source_name: Input fraction from ESC-BG03

source_name: Methyl-depleted fraction from ESC-BG03


title: K-iPSC-N9-p30 input

source_name: Input fraction from K-iPSC-N9-p30

source_name: Methyl-depleted fraction from K-iPSC-N9-p30


title: F2-2044-F

source_name: liver, F2, female


title: F1-1146-M

description: Transcript expression data from a male (MRL/MpJ x SM/J)F1 mouse.

source_name: liver, F1, male


title: F2-2074-M

source_name: liver, F2, male


title: F2-2026-M


title: K-iPSC-N9-p9 input

source_name: Input fraction from K-iPSC-N9-p9

source_name: Methyl-depleted fraction from K-iPSC-N9-p9


title: F2-2254-M


title: F2-2114-F


title: K-iPSC-N9-p33-c2 input

source_name: Input fraction from K-iPSC-N9-p33-c2

source_name: Methyl-depleted fraction from K-iPSC-N9-p33-c2


title: F2-2019-F


title: F2-2318-M


title: K-iPSC-N9-p8-c2 input

source_name: Input fraction from K-iPSC-N9-p8-c2

source_name: Methyl-depleted fraction from K-iPSC-N9-p8-c2


title: K-iPSC-N9-p25 input

source_name: Input fraction from K-iPSC-N9-p25

source_name: Methyl-depleted fraction from K-iPSC-N9-p25


title: K-iPSC-N9-p8-c3 input

source_name: Input fraction from K-iPSC-N9-p8-c3

source_name: Methyl-depleted fraction from K-iPSC-N9-p8-c3


title: F2-2027-M


title: K-iPSC-N9-p7 input

source_name: Input fraction from K-iPSC-N9-p7

source_name: Methyl-depleted fraction from K-iPSC-N9-p7


title: F2-2213-F


title: F2-2008-M


title: F2-2324-F


title: F2-2328-M


title: F2-2122-F


title: F2-2048-M


title: MRL-1-F

description: Transcript expression data from a female MRL/MpJ mouse.

source_name: liver, parental, female

value: MRL/MpJ

value: parental


title: K-iPSC-N9-p10 input

source_name: Input fraction from K-iPSC-N9-p10

source_name: Methyl-depleted fraction from K-iPSC-N9-p10


title: F2-2173-M


title: F2-2282-F

source_name: liver, F2, female


title: F2-2201-F


title: F2-2322-F


title: F2-2280-F


title: K-iPSC-N9-p12 input

source_name: Input fraction from K-iPSC-N9-p12

source_name: Methyl-depleted fraction from K-iPSC-N9-p12


title: F2-2211-M

source_name: liver, F2, male


title: F2-2249-F


title: F2-2344-M


title: F2-2199-M


title: F2-2325-F


title: F2-2227-M


title: F1-1145-F

description: Transcript expression data from a female (MRL/MpJ x SM/J)F1 mouse.

source_name: liver, F1, female


title: F2-2303-F


title: F2-2165-M


title: F2-2295-F


title: F2-2009-F


title: K-iPSC-N9-p33-c3 input

source_name: Input fraction from K-iPSC-N9-p33-c3

source_name: Methyl-depleted fraction from K-iPSC-N9-p33-c3


title: F2-2116-F


title: F2-2166-M


title: F2-2308-M


title: F2-2052-F


title: F2-2311-F


title: F2-2217-M


title: F2-2157-F


title: F2-2065-M


title: F2-2241-M


title: F2-2061-M


title: F2-2191-F


title: F2-2223-M


title: F2-2232-M


title: SM-1-F

description: Transcript expression data from a female SM/J mouse.

value: SM/J


title: F2-2310-M


title: F2-2156-F


title: F2-2270-F


title: F2-2287-M


title: F2-2306-M


title: F2-2331-M


title: F2-2010-F


title: F2-2294-F


title: F2-2188-M


title: F2-2002-F


title: F2-2237-M


title: F2-2075-M


title: F2-2251-M


title: F2-2202-F


title: F2-2190-F


title: F2-2163-M


title: F2-2063-F


title: F2-2015-M


title: F2-2236-M


title: F2-2248-F


title: F2-2268-F


title: F2-2066-M


title: F2-2035-M


title: F2-2016-M


title: F2-2012-F


title: F2-2158-F


title: F2-2266-M


title: F2-2238-M


title: F2-2264-M


title: F2-2235-M


title: F2-2185-M


title: F2-2036-M


title: F2-2351-M


title: F2-2106-M


title: F2-2132-M


title: F2-2245-M


title: F2-2087-M


title: F2-2281-F


title: F2-2300-F


title: F2-2256-F


title: F2-2110-F


title: F2-2112-F


title: F2-2118-M


title: F2-2257-F


title: F2-2124-F


title: F2-2172-M


title: F2-2204-F


title: F1-1149-F


title: F2-2267-F


title: F2-2073-F


title: F2-2231-F


title: F2-2055-M


title: F2-2064-M


title: F2-2233-M


title: F2-2269-F


title: MRL-3-F


title: F2-2169-M


title: F2-2258-F


title: F2-2290-F


title: F2-2162-M


title: F2-2032-F


title: F2-2180-F


title: SM-2-F


title: F2-2289-F


title: F2-2296-M


title: F2-2006-F


title: Clinical sample, B-T6 133-

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

description: Clinical sample

scan_protocol: ABI Prism 7900 HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA)

data_processing: SDS files were processed in RQ manager software and raw data were then exported in XLS file

label: FAM

source_name: Breast cancer

label_protocol:
cDNA was prepared using the High Capacity cDNA kit with RNAse inhibitor (Applied Biosystems, Foster City, CA) as per the manufacturer’s instructions,
but no labelling was performed as TaqMan-based qRT-PCR was performed subsequently.

growth_protocol: Clinical samples were fresh frozen. Cell lines were grown either as monolayer or in 3-D (see Gillet et al. Manuscript in submission)

extract_protocol: Total RNA was prepared using the Trizol method (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: All the CP-r cells were maintained in the presence of cisplatin, but cisplatin was removed from the medium 3 days prior to preparation of RNA. See Gillet et al. (Manuscript in in submision)

value: breast

tag: sample type

value: CD133- sorted cells

tag: percentage of tumor cells


title: Clinical sample, B-T7

description: Clinical sample

value: Bulk sample


title: F2-2348-M

tag: age


title: Clinical sample, B-T6 133+

description: Clinical sample

value: CD133+ sorted cells


title: Clinical sample, B-T6

description: Clinical sample


title: F2-2271-F


title: Clinical sample, B-T5 r2

description: Clinical sample


title: F2-2183-M


title: Clinical sample, B-T5 r1 133+

description: Clinical sample


title: Clinical sample, B-T5 r2 133+

description: Clinical sample


title: F2-2046-M


title: SM-6-M

description: Transcript expression data from a male SM/J mouse.

source_name: liver, parental, male


title: F2-2133-M


title: F2-2104-F


title: F2-2214-F


title: F2-2265-M


title: F2-2208-M


title: F2-2218-M


title: Clinical sample, B-T5 r1

description: Clinical sample


title: F2-2210-M


title: Clinical sample, B-T4

description: Clinical sample


title: Clinical sample, B-T3

description: Clinical sample


title: F2-2292-F


title: Clinical sample, B-T3 133+

description: Clinical sample


title: Clinical sample, B-T2

description: Clinical sample


title: Clinical sample, B-T2 133+

description: Clinical sample


title: Clinical sample, B-T1

description: Clinical sample


title: F2-2198-M


title: Clinical sample, B-T1 133+

description: Clinical sample


title: Clinical sample, B-N4 r1 133+

description: Clinical sample

source_name: Normal breast tissue


title: Clinical sample, B-N4

description: Clinical sample


title: Clinical sample, B-N3 133+

description: Clinical sample


title: Clinical sample, B-N4 r1 133-

description: Clinical sample


title: F2-2080-F


title: Clinical sample, B-N3

description: Clinical sample


title: F2-2247-F


title: Clinical sample, B-N2 133-

description: Clinical sample


title: F2-2181-F


title: F2-2017-M


title: Clinical sample, B-N2 133+

description: Clinical sample


title: F2-2179-F


title: F2-2278-M


title: Clinical sample, B-N2

description: Clinical sample


title: F2-2038-M


title: F2-2246-M


title: F2-2312-F


title: F2-2332-M


title: Clinical sample, B-N1 r1 133+

description: Clinical sample


title: Clinical sample, B-N1 r2 133-

description: Clinical sample


title: Clinical sample, B-N1 r1 133-

description: Clinical sample


title: F2-2305-M


title: F2-2319-M


title: Clinical sample, B-N1

description: Clinical sample


title: F2-2103-F


title: F2-2018-M


title: F2-2126-F


title: Cell line, MCF7-ADR

description: Cell line

value: NCI-60 panel


title: Cell line, MCF7 (ADR-sensitive)

description: Cell line


title: F2-2209-M


title: F2-2174-M


title: F2-2234-M


title: Cell line, Non CSC-R1

description: Cell line

value: NCI-60 panel CD44+/CD24+


title: Cell line, CSC-R1

description: Cell line

value: NCI-60 panel CD44+/CD24-


title: Clinical sample, B-N1 r2 133+

description: Clinical sample


title: Cell line, CSC-R2

description: Cell line


title: Cell line, Non CSC-R2

description: Cell line


title: Cell line, T-47D

description: Cell line


title: F2-2057-M

value: MRL/MpJ x SM/J


title: Cell line, MDA-MB-231

description: Cell line


title: Cell line, MCF7

description: Cell line


title: F2-2130-M

value: male


title: Cell line, BT-549

description: Cell line


title: F2-2315-M

value: 13 weeks


title: SNT16

first: Paul

middle: D

last: Ling

state: Texas

address: One Baylor Plaza

department: Molecular Virology and Microbiology

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

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

data_processing:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system-related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
A t-test is performed between SNK6 and “SNT16” samples using the probe repeats as individual samples. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: SNT16 cell line

label_protocol: The microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore), and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: Cells were cultured in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, 250 ng/ml Fungizone (Amphotericin B; Invitrogen) and 600 IU of IL-2.  Every three days, the cells were fed with fresh media supplemented with 600 IU of IL-2.

extract_protocol: miRNeasy

value: nasal natural killer T cell lymphoma (NKTCL) cells


title: SNK6

source_name: SNK6 cell line


title: F2-2034-M

value: liver


title: F2-2164-M


title: F2-2054-F

value: female


title: F2-2031-F


title: F2-2323-F


title: F1-1152-M

source_name: liver, F1, male


title: F2-2277-M


title: F2-2252-M


title: Cell line, HS578T

description: Cell line


title: F2-2309-M


title: F2-2024-M


title: F2-2108-M


title: F2-2205-F


title: F2-2089-M


title: F2-2326-F


title: xenograft_control_time48_rep3

city: Randwick

first: Vivek

middle: A

last: Bhadri

state: NSW

address: Lowy Cancer Research Centre

department: Leukaemia Biology Program

country: Australia

institute: Children's Cancer Institute Australia for Medical Research

description: tumour derived from vehicle-treated mouse, at 48 hr post treatment, replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The sample probe profiles with no normalisation or background correction were exported from BeadStudio (version 3.0.14, Illumina, San Diego, CA). The data were pre-processed using variance stabilising transformation and robust spline normalisation in lumi, from R/Bioconductor

source_name: xenograft tumour

label_protocol: Biotinylated cRNA were prepared with the TotalPrep RNA Amplification kit for Illumina arrays (Ambion, Austin, TX)

growth_protocol: Cells from ALL-3, a glucocorticoid-sensitive xenograft, were inoculated by tail-vein injection into 28 NOD/SCID mice.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany) and the RNA integrity verified (Agilent Bioanalyzer, Santa Clara, CA).

treatment_protocol: When high level engraftment was achieved the mice were randomised to receive either dexamethasone 15 mg/kg or vehicle control IP. Mice were culled at 0 hours, 8 hours, 24 hours or 48 hours following treatment. The mice in the 48 hour groups received a second dose of dexamethasone or vehicle control at 24 hours.

tag: xenograft

tag: mouse strain

value: NOD/SCID

tag: sentrix id

tag: time

tag: treatment

value: vehicle

tag: replicate


title: F2-2079-F

tag: tissue


title: F2-2321-F


title: xenograft_dex-treated_time48_rep1

description: tumour derived from dex-treated mouse, at 48 hr post treatment, replicate 1

value: dexamethasone


title: xenograft_dex-treated_time48_rep2

description: tumour derived from dex-treated mouse, at 48 hr post treatment, replicate 2


title: F2-2298-M


title: xenograft_dex-treated_time48_rep3

description: tumour derived from dex-treated mouse, at 48 hr post treatment, replicate 3


title: F2-2250-F


title: xenograft_control_time48_rep1

description: tumour derived from vehicle-treated mouse, at 48 hr post treatment, replicate 1


title: F2-2293-F


title: xenograft_dex-treated_time24_rep4

description: tumour derived from dex-treated mouse, at 24 hr post treatment, replicate 4


title: xenograft_control_time48_rep2

description: tumour derived from vehicle-treated mouse, at 48 hr post treatment, replicate 2


title: F2-2307-M


title: xenograft_dex-treated_time24_rep3

description: tumour derived from dex-treated mouse, at 24 hr post treatment, replicate 3


title: F2-2047-M


title: F2-2279-M


title: F2-2220-M


title: xenograft_dex-treated_time8_rep4

description: tumour derived from dex-treated mouse, at 8 hr post treatment, replicate 4


title: xenograft_control_time24_rep3

description: tumour derived from vehicle-treated mouse, at 24 hr post treatment, replicate 3


title: xenograft_control_time24_rep4

description: tumour derived from vehicle-treated mouse, at 24 hr post treatment, replicate 4


title: F2-2200-F

description: Transcript expression data from a female (MRL/MpJ x SM/J)F2 mouse.


title: xenograft_control_time24_rep2

description: tumour derived from vehicle-treated mouse, at 24 hr post treatment, replicate 2


title: xenograft_dex-treated_time24_rep1

description: tumour derived from dex-treated mouse, at 24 hr post treatment, replicate 1


title: F2-2314-F


title: xenograft_dex-treated_time8_rep3

description: tumour derived from dex-treated mouse, at 8 hr post treatment, replicate 3


title: F2-2117-M

description: Transcript expression data from a male (MRL/MpJ x SM/J)F2 mouse.


title: F2-2161-M


title: F2-2212-M


title: F2-2261-M


title: xenograft_control_time8_rep3

description: tumour derived from vehicle-treated mouse, at 8 hr post treatment, replicate 3


title: F2-2330-M


title: F2-2170-M


title: MRL-2-F

description: Transcript expression data from a female MRL/MpJ mouse.

source_name: liver, parental, female

value: MRL/MpJ

value: parental


title: xenograft_dex-treated_time8_rep1

description: tumour derived from dex-treated mouse, at 8 hr post treatment, replicate 1


title: xenograft_control_time24_rep1

description: tumour derived from vehicle-treated mouse, at 24 hr post treatment, replicate 1


title: xenograft_dex-treated_time8_rep2

description: tumour derived from dex-treated mouse, at 8 hr post treatment, replicate 2


title: xenograft_control_time8_rep2

description: tumour derived from vehicle-treated mouse, at 8 hr post treatment, replicate 2


title: F2-2060-M


title: xenograft_control_time8_rep4

description: tumour derived from vehicle-treated mouse, at 8 hr post treatment, replicate 4


title: F2-2127-F


title: xenograft_dex-treated_time24_rep2

description: tumour derived from dex-treated mouse, at 24 hr post treatment, replicate 2


title: xenograft_control_time8_rep1

description: tumour derived from vehicle-treated mouse, at 8 hr post treatment, replicate 1


title: F2-2037-M


title: xenograft_control_time0_rep4

description: tumour derived from mice prior to treatment, replicate 4

value: control


title: xenograft_control_time0_rep3

description: tumour derived from mice prior to treatment, replicate 3


title: sample collected from patient MM 40 weeks after transplantation

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

description: RNA was extracted using the PAXgene Blood RNA Kit (QIAgen)

hyb_protocol: The hybridization procedure was performed after control of RNA quality and integrity and according to the “One-Colour Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 0.6 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to RISET 1.0 microarrays using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated (37°C) Agilent Gene Expression Wash Buffer 2 containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies, Inc.). The Agilent Feature Extraction Software (FES v. 10.2.1.3/10.5.1.1) was used to read out and process the microarray image files.

data_processing: In order to determine differential gene expression, FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (v. 7.2.2.0.0., Rosetta Inpharmatics LLC).

source_name: peripheral vein blood

label_protocol: Sample labeling was performed as detailed in the “One-Colour Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040). Briefly, 0.5 µg of each total RNA sample was used for the amplification and labelling step using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) in the presence of cyanine 3-CTP. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.).

extract_protocol: Peripheral vein blood was drawn directly into PAXgene Blood RNA tubes (QIAgen, Crawley UK). Whole-blood RNA was extracted using the PAXgene Blood RNA Kit including DNAse I treatment (QIAgen). Quality and integrity of PAXgene purified RNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring A260nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: Seven days prior to transplantation, donor-derived M regs were administered to two recipients (CA and MM) of living donor kidney transplants. To reduce the risk of M regs sensitising the patients, treatment with 2 mg/ kg/ day azathioprine was commenced three days prior to the infusion and was continued for 8 weeks postoperatively. From the day of transplantation onwards, the patients were immunosuppressed with tacrolimus and steroids; steroids were weaned over the first ten weeks postoperatively, leaving the patients with maintenance tacrolimus monotherapy, aiming for trough serum levels between 4 and 8 ng/ml.

tag: patient

value: MM

tag: time post transplantation [weeks]

tag: medication

value: tacrolimus


title: F2-2111-F

description: Transcript expression data from a female (MRL/MpJ x SM/J)F2 mouse.

tag: strain

tag: generation


title: F2-2053-F

tag: Sex

tag: batch


title: sample collected from patient MM 52 weeks after transplantation


title: sample collected from patient MM 45 weeks after transplantation


title: F2-2178-F


title: F2-2229-F


title: F2-2189-F


title: sample collected from patient MM 36 weeks after transplantation


title: F2-2316-M


title: F2-2226-M


title: xenograft_control_time0_rep1

description: tumour derived from mice prior to treatment, replicate 1


title: sample collected from patient MM 25 weeks after transplantation


title: F2-2176-F


title: sample collected from patient MM 32 weeks after transplantation


title: sample collected from patient MM 20 weeks after transplantation


title: F2-2113-F


title: xenograft_control_time0_rep2

description: tumour derived from mice prior to treatment, replicate 2


title: sample collected from patient MM 28 weeks after transplantation


title: sample collected from patient MM 16 weeks after transplantation


title: F2-2260-M


title: F2-2123-F


title: sample collected from patient MM two weeks after transplantation

value: tacrolimus/steroids/azathioprine


title: sample collected from patient MM four weeks after transplantation


title: sample collected from patient MM three weeks after transplantation


title: F2-2255-F


title: F2-2301-F


title: sample collected from patient MM one week after transplantation


title: F2-2352-M


title: F2-2224-M


title: sample collected from patient MM one week before transplantation and before M reg application

value: azathioprine


title: sample collected from patient MM one day before transplantation and after M reg application

value: preTx


title: F2-2109-M

value: MRL/MpJ x SM/J


title: F2-2273-F


title: F2-2196-M

value: male


title: F2-2242-M

value: 13 weeks


title: F2-2187-M


title: sample collected from patient CA 63 weeks after transplantation

value: CA


title: F2-2327-F

value: liver


title: sample collected from patient CA 36 weeks after transplantation


title: sample collected from patient CA 43 weeks after transplantation


title: sample collected from patient CA 51 weeks after transplantation


title: sample collected from patient CA 47 weeks after transplantation


title: F1-1151-M

description: Transcript expression data from a male (MRL/MpJ x SM/J)F1 mouse.


title: sample collected from patient CA 32 weeks after transplantation


title: F2-2107-M

description: Transcript expression data from a male (MRL/MpJ x SM/J)F2 mouse.


title: Pou2/3 Kd d21 rep2

city: Cambridge

first: Mansi

last: Srivastava

address: 9 Cambridge Center

institute: Whitehead Institutue

hyb_protocol: Agilent custom planarian 4x44,000 expression arrays were hybridized according manufacturer instructions and scanned using an Agilent DNA microarray scanner.

scan_protocol: Array images were quantified and statistical significance of differential expression was calculated using Agilent’s Feature Extraction Image Analysis software with the default two-color gene expression protocol.

data_processing: Agilent two-color arrays were within-array normalized by loess, followed by between-array quantile normalization of average intensities across channels (Aquantile).

organism: Schmidtea mediterranea

source_name: control animals, day 21

label_protocol: Cy3 and Cy5-labeled cRNA was prepared using a QuickAmp labeling kit (Agilent) starting with 1μg total RNA

growth_protocol: Animals were maintained at 20 degrees celsius.

extract_protocol: RNA was extracted using the standard Trizol method.

treatment_protocol: RNA from Six1/2(RNAi) and POU2/3(RNAi) animals was harvested at days 8 and 15 after RNAi initiation for the former and days 15 and 21 for the latter. RNA from control RNAi animals was harvested at days 8, 15, and 21.

tag: knockdown

value: whole organism

source_name: POU2/3 RNAi animals, day 21


title: Pou2/3 Kd d21 rep3


title: Pou2/3 Kd d15 rep3

source_name: control animals, day 15

source_name: POU2/3 RNAi animals, day 15


title: sample collected from patient CA 24 weeks after transplantation


title: sample collected from patient CA 19 weeks after transplantation


title: sample collected from patient CA eight weeks after transplantation


title: sample collected from patient CA 40 weeks after transplantation


title: Six1/2 Kd d15 rep3

source_name: Six1/2 RNAi animals, day 15


title: Pou2/3 Kd d21 rep1


title: F2-2228-F

source_name: liver, F2, female

value: female


title: Six1/2 Kd d15 rep2


title: F2-2285-F


title: F2-2077-M

source_name: liver, F2, male


title: Pou2/3 Kd d15 rep2


title: F2-2129-F


title: F2-2101-F


title: F2-2045-M


title: F2-2222-M


title: F2-2042-F


title: Pou2/3 Kd d15 rep1


title: F2-2240-F


title: sample collected from patient CA 16 weeks after transplantation


title: SM-3-F

description: Transcript expression data from a female SM/J mouse.

value: SM/J


title: F2-2304-F


title: F2-2317-M


title: sample collected from patient CA four weeks after transplantation


title: F2-2128-F


title: F2-2022-F


title: F2-2067-M


title: Six1/2 Kd d8 rep3

source_name: control animals, day 8

value: 8 d

source_name: Six1/2 RNAi animals, day 8


title: F2-2216-F


title: F2-2345-M


title: sample collected from patient CA one day before transplantation and after M reg application


title: F2-2070-F


title: F2-2219-M


title: sample collected from patient CA one week after transplantation


title: sample collected from patient CA one week before transplantation and before M reg application


title: Six1/2 Kd d15 rep1


title: F2-2082-F


title: F1-1150-F

description: Transcript expression data from a female (MRL/MpJ x SM/J)F1 mouse.

source_name: liver, F1, female


title: Six1/2 Kd d8 rep2


title: SM-7-M

description: Transcript expression data from a male SM/J mouse.

source_name: liver, parental, male


title: Six1/2 Kd d8 rep1


title: F2-2177-F


title: sample collected from patient CA two weeks after transplantation


title: MRL-8-M

description: Transcript expression data from a male MRL/MpJ mouse.

value: MRL/MpJ


title: F2-2286-M


title: whole heart, P1, rep 2 [MoGene[exon_level]]

city: Bad Nauheim

first: Pascal

last: Gellert

address: Ludwigstr. 43

department: Cardiac Development and Remodelling

institute: Max Planck Institut for Heart and Lung Research

description: whole heart – P1

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.  Heat cocktails at 99C for 5 minutes, then 42C for 5 minutes centrifuge at max speed for 1 minute, Transfer 200ul of hyb solution to each array, then tape holes, Hybridize 17 hours at 45C at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalized, gene and exon level expression values from Affymetrix Power Tools
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps and MoGene-1_0-st-v1.r4.all.ps

source_name: whole heart – P1

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse embryonic stem cells are differentiated into cardiomyocytes with DMEM based culture media supplied with 10% serum. Mouse hearts dissected from E17.5 and P1 mice.

extract_protocol: RNA was extracted from each samples (culture cells and tissues) with TRIzol reagent (Invitrogen).  Isolated RNAs were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

tag: tissue/cell  type

value: whole heart


title: F2-2299-M

tag: age


title: F2-2011-F


title: whole heart, adult, rep 1 [MoGene[exon_level]]

description: whole heart – adult

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 200μl of hyb solution to each array, then tape holes. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

source_name: whole heart – adult

treatment_protocol: not applicable

value: Adult


title: F2-2021-F


title: F2-2275-M


title: whole heart, adult, rep 2 [MoGene[exon_level]]

description: whole heart – adult


title: undifferentiated ES cells, rep 2 [MoEx[gene_level]]

description:
undifferentiated ES cells
probe_group_file: MoEx-1_0-st-v1.r2.pgf
meta-probeset_file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps and MoEx-1_0-st-v1.r2.dt1.mm9.core.ps

data_processing: RMA normalized, gene and exon level expression values from Affymetrix Power Tools

source_name: undifferentiated ES cells

growth_protocol: Mouse embryonic stem cells are differentiated into cardiomyocytes with DMEM based culture media supplied with 10% serum.

extract_protocol: RNA was extracted from each samples with TRIzol reagent (Invitrogen). Isolated RNAs were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

value: 0 days

value: undifferentiated ES (cell culture)


title: embryonic bodies, rep 1 [MoEx[gene_level]]

description:
embryonic bodies
probe_group_file: MoEx-1_0-st-v1.r2.pgf
meta-probeset_file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps and MoEx-1_0-st-v1.r2.dt1.mm9.core.ps

source_name: embryonic bodies

value: 7 days

value: embryonic bodies (cell culture)


title: F2-2243-M


title: F2-2105-F


title: cardiac bodies, rep 2 [MoEx[gene_level]]

description:
cardiac bodies
probe_group_file: MoEx-1_0-st-v1.r2.pgf
meta-probeset_file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps and MoEx-1_0-st-v1.r2.dt1.mm9.core.ps

source_name: cardiac bodies

value: 14 day

value: cardiac bodies (cell culture)


title: whole heart, P1, rep 1  [MoGene[exon_level]]

description: whole heart – P1


title: embryonic bodie, rep 2 [MoEx[gene_level]]


title: whole heart, E17.5, rep 2 [MoGene[exon_level]]

description: whole heart – E17.5

source_name: whole heart – E17.5


title: MRL-7-M

value: parental

value: male


title: F2-2043-F

value: MRL/MpJ x SM/J

value: 13 weeks


title: F2-2068-F

value: liver


title: F2-2007-M


title: cardiac bodies, rep 1 [MoEx[gene_level]]


title: undifferentiated ES cells, rep 1 [MoEx[gene_level]]


title: F2-2119-M


title: whole heart, E17.5, rep 1 [MoGene[exon_level]]

description: whole heart – E17.5


title: embryonic bodie, rep 2 [MoGene[exon_level]]

description: embryonic bodies


title: cardiac bodies, rep 2 [MoGene[exon_level]]

description: cardiac bodies


title: F2-2171-M


title: cardiac bodies, rep 1 [MoGene[exon_level]]

description: cardiac bodies


title: embryonic bodies, rep 1 [MoGene[exon_level]]

description: embryonic bodies


title: F2-2020-F

value: female


title: F2-2230-F


title: undifferentiated ES cells, rep 2 [MoGene[exon_level]]

description: undifferentiated ES cells


title: F2-2288-M


title: BL41_control_2

city: Berlin

first: Volkhard

last: Seitz

address: Hindenburgdamm 30

department: Institute of Pathology

institute: Charité Universitätsmedizin

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
For analysis of Affymetrix data the expression levels were normalized using VSN. Limma was used to fit a model for the effect of treatment, the cell type and the experiment batch.   Probe sets were tested for differential expression in cell lines with and without MYC siRNA treatment using an empirical Bayesian method. P-values were corrected for multiple testing by the method proposed by Benjamini and Hochberg.
Probe sets were tested for differential expression in cell lines with and without MYC siRNA treatment using an empirical Bayesian method. P-values were corrected for multiple testing by the method proposed by Benjamini and Hochberg.
A corrected p-value of < 0.05 and a fold-change >1.2 was used as threshold.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Five human Burkitt lymphoma (BL) cell lines (Raji, CA46, Blue1, BL41, Ramos), were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) and supplemented with 10% Sera Plus (PAN Biotech, Aidenbach, Germany) at 37°C.

extract_protocol: Total RNA of MYC siRNA-treated and control-treated cells was extracted employing the RNeasy Midi kit according to standard protocols (Qiagen, Hilden, Germany).

treatment_protocol: siRNA-mediated knock-down of MYC was done employing the BL cell lines Raji, BL41 and Blue1 in order to detect MYC-driven gene expression changes. For this purpose, the cells were Amaxa-transfected using MYC smart pool siRNA and control siRNA (Thermo Scientific/Dharmacon, Erembodegem, Belgium), respectively.

tag: cell line

value: B-cell lymphoma cell line


title: F2-2274-M


title: F2-2131-M


title: pathogen isolates: Hawaii 94-1 (avir) - time: 288 hai - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: PI462312  Hawaii 94-1 treatment 288 hours

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

source_name: leaf (pathogen isolates: Hawaii 94-1 (avir) - time: 288 hai)

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: TRIzol-Qiagen

tag: pathogen isolates

value: Hawaii 94-1 (avir)

tag: germplasm name

tag: organism part

tag: development stage

value: PO:0007134 A vegetative growth

tag: growth media

value: soil mix


title: pathogen isolates: Hawaii 94-1 (avir) - time: 216 hai - rep3

description: PI462312  Hawaii 94-1 treatment 216 hours

source_name: leaf (pathogen isolates: Hawaii 94-1 (avir) - time: 216 hai)

tag: time


title: pathogen isolates: Hawaii 94-1 (avir) - time: 288 hai - rep2


title: F2-2262-M

tag: tissue


title: pathogen isolates: Hawaii 94-1 (avir) - time: 216 hai - rep2


title: pathogen isolates: Hawaii 94-1 (avir) - time: 288 hai - rep1


title: BL41_control_1


title: BL41_MYC_siRNA_2


title: MRL-6-M

value: MRL/MpJ


title: F2-2175-M


title: F2-2160-F


title: F2-2192-F


title: F2-2276-M


title: BL41_MYC_siRNA_1


title: F2-2030-F


title: F2-2005-F


title: undifferentiated ES cells, rep 1 [MoGene[exon_level]]

description: undifferentiated ES cells

value: 0 days


title: SM-8-M

value: SM/J


title: F2-2001-F


title: F2-2051-F


title: Blue1_MYC_control_2


title: pathogen isolates: Hawaii 94-1 (avir) - time: 216 hai - rep1


title: pathogen isolates: Hawaii 94-1 (avir) - time: 144 hai - rep3

description: PI462312  Hawaii 94-1 treatment 144 hours

source_name: leaf (pathogen isolates: Hawaii 94-1 (avir) - time: 144 hai)


title: Blue1_MYC_control_1


title: F2-2350-M


title: Blue1_MYC_siRNA_2


title: F2-2004-F


title: pathogen isolates: Hawaii 94-1 (avir) - time: 144 hai - rep1


title: F2-2302-F


title: pathogen isolates: Hawaii 94-1 (avir) - time: 144 hai - rep2


title: F2-2203-F


title: F2-2125-F


title: pathogen isolates: Hawaii 94-1 (avir) - time: 72 hai - rep3

description: PI462312  Hawaii 94-1 treatment 72 hours

source_name: leaf (pathogen isolates: Hawaii 94-1 (avir) - time: 72 hai)

value: 72 hr


title: F2-2215-F


title: pathogen isolates: Hawaii 94-1 (avir) - time: 72 hai - rep1


title: Raji_Myc_control_1

source_name: Raji


title: Raji_Myc_control_2


title: F2-2159-F

source_name: liver, F2, female


title: 20th hybridization susceptible vs. Resistant tree

city: Vancouver

first: Sébastien

last: Verne

state: BC

address: 2424, Main Mall

department: Forest Sciences

country: Canada

institute: University of British Columbia

hyb_protocol: The slide was prewashed twice in 0.1% SDS at room temperature for 5 min., followed by two 2 min. washes in MilliQ-H2O, 3 min. at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat-denatured at 80ºC for 10 min, maintained at 65ºC prior to adding to a microarray slide that heated to 55ºC, and covered with a 22 x 60 mm glass coverslip.  First hybridization (cDNA hybdridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS Buffer; LNA dT blocker; nuclease-free water together with 2 ug of salmon testes DNA (Invitrogen).  The incubation condition for cDNA hybridization was 16h at 60ºC. The slide was washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, and three washes (5 min. each) in 2x SSC at room temperature, and three washes (5 min. each) in 0.2x SSC at room temperature, and dried by centrifugation.  Second hybridization (3DNA hybridization) used the ingredients of Genisphere Array350 kit (Genisphere, Hatfield, USA): 2X SDS buffer; Cy3 3DNA dendrimer; Cy5 3DNA dendrimer; and nuclease-free water.  Incubation condition for 3DNA hybridization was 3 h at 60ºC, followed by washing and drying as described for the first hybridization.

scan_protocol: The slide was scanned using ScanArray Express (Perkin Elmer, Foster City, USA).The Cy3 and Cy5 cyanine fluors were excited with laser at 543 nm and 633 nm respectively. Scanning was consistently done with 90% laser power. The optimal photomultiplier tube (PMT) gain was set at the dynamic range of 60%<PMT<80% to minimize background intensity, and maximize the signal intensity while the number of saturated spots, excluding human positive spikes and GFP orientation marker, not exceeding 5% of each subgird. Fluorescent intensity data were quantified using the ImaGene 6 software (Biodiscovery, El Segundo, USA).

data_processing: Within subgrids, subtraction of the lowest 10% of median foreground intensities was used for background correction. Data gained from the 20 microarray hybridizations were normalized by variance stabilizing normalization (VSN) to compensate for non-linearity of intensity distributions (Huber et al., 2002) within arrays to arrive at the expression levels ratio between resistant and susceptible trees. A linear mixed-effects model was used to fit to the normalized intensities of the Cy3 and Cy5 channels related to the 20 microarray slides. The model contained a fixed effect for resistance phenotype and random effect for individuals within resistance phenotype. P-values were computed and Q-values were calculated to adjust for the false discovery rate (FDR) (Storey & Tibshirani, 2003). Analyses of the data were done using the R statistical package (www.r-project.org/).

organism: Picea engelmannii x Picea glauca

label_protocol: Used Genisphere Array350 kit (Genisphere, Hatfield, USA) following the manufacturer protocol: 40 micrograms of total RNA for reverse transcription; Superscript II reverse transcriptase (Invitrogen); 5.0 pmole/ul RT Primer for Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647; Cy5/Alexa Fluor 647 dye-labeled; hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min; and neutralized in 1 M Tris-HCl (pH 7.5).

extract_protocol: Total RNA extraction used a modified version of the protocol described by Kolosova et al. (2004) Biotechniques 36: 821-824. The extracted RNA was quantified and quality checked using spectrophotometry and agarose gel electrophoresis; in respect to the wavelength of maximum absorption at 260 nm and 280 nm and the presence of sharp bright bands of 28s and 18s ribosomal subunits at ~4.5 kb and ~1.9 kb on 1% agarose gel.

treatment_protocol: Specimen (bark/phloem sources of tissue) collected from one lateral shoot of the individual tree was flash-frozen on the field by liquid nitrogen and kept in -80 ºC freezer until extraction.

value: bark tissue sampled from the shoots of mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC (collection established 1972-1973).

tag: phenotype


title: pathogen isolates: Hawaii 94-1 (avir) - time: 72 hai - rep2


title: Blue1_MYC_siRNA_1


title: F2-2040-F


title: Raji_MYC_siRNA_2


title: F2-2207-M

source_name: liver, F2, male


title: 17th hybridization susceptible vs. Resistant tree


title: pathogen isolates: Hawaii 94-1 (avir) - time: 24 hai - rep3

description: PI462312  Hawaii 94-1 treatment 24 hours

source_name: leaf (pathogen isolates: Hawaii 94-1 (avir) - time: 24 hai)

value: 24 hr


title: F2-2313-F

description: Transcript expression data from a female (MRL/MpJ x SM/J)F2 mouse.


title: Raji_MYC_siRNA_1


title: pathogen isolates: Hawaii 94-1 (avir) - time: 24 hai - rep1


title: 18th hybridization susceptible vs. Resistant tree


title: pathogen isolates: Hawaii 94-1 (avir) - time: 12 hai - rep2

description: PI462312  Hawaii 94-1 treatment 12 hours

source_name: leaf (pathogen isolates: Hawaii 94-1 (avir) - time: 12 hai)

value: 12 hr


title: 13th hybridization susceptible vs. Resistant tree


title: 11th hybridization susceptible vs. Resistant tree


title: 12th hybridization susceptible vs. Resistant tree


title: 15th hybridization susceptible vs. Resistant tree


title: D4 patient

city: Sao Paulo

first: Patricia

middle: Locosque

last: Ramos

state: SP

address: Av Dr Arnaldo 455

department: Pediatria

country: Brazil

institute: Universidade de Sao Paulo

hyb_protocol: In order to determine gene expression profiles, 44K DNA microarrrays (Agilent Technologies, cat no. G4845A Santa Clara, CA) were used. The procedures for hybridization followed the protocols provided by the manufacturer´s instructions (One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling).

scan_protocol: The images were captured by the Agilent High-Resolution Microarray Scanner Bundle (catalog #G2565CA) reader according to the parameters recommended for bioarrays and extracted by Agilent Feature Extraction software version 9.5.3.

data_processing: Among the 45,015 spots present in each array, only those with none or only one flag (i.e. low intensity, saturation, controls, etc.) were selected for analysis using the R software version 2.9.2 (R Development Core Team, 2009). Fold change was calculated using the following formulae: =sign(group A mean - group B mean)*2^ABS(group A mean - group B mean). Group mean was calculated by the summation of each group component divided by number of group components. We selected as differentially expressed transcripts those presenting a p-value Â£ 0.05 (Student's t test and adjusted Bonferroni correction) and fold variation of ±2. Hierarchical clustering was based on Pearson correlation and complete linkage.

source_name: thymus, DS

label_protocol: The RNA was labeled using the Cyanine CTP Dye Pack, one color, Agilent technologies, Part no. 5188-1169-P.

extract_protocol: Tissue samples (20-30mg) were homogenized with TissueRupter (QIagen, cat. no. 9001272 Valencia, CA) and total RNA was extracted from the homogenates using the RNeasy Mini Kit (QIagen cat. no. 74104, Valencia, CA) according to the manufacturer's instructions.

tag: disease

value: Down syndrome

tag: gender

value: 1 year and 2 months

value: thymus


title: C1 patient

source_name: thymus, control

value: cardiopathy

value: 200 days


title: 16th hybridization susceptible vs. Resistant tree


title: pathogen isolates: Taiwan 80-2 (vir) - time: 288 hai - rep2

description: PI462312  Taiwan 80-2 treatment 288 hours

source_name: leaf (pathogen isolates: Taiwan 80-2 (vir) - time: 288 hai)

value: Taiwan 80-2 (vir)


title: 9th hybridization susceptible vs. Resistant tree


title: D3 patient

value: female

value: 1 year and 6 months


title: D2 patient

value: male


title: 14th hybridization susceptible vs. Resistant tree


title: pathogen isolates: Hawaii 94-1 (avir) - time: 12 hai - rep1

value: Hawaii 94-1 (avir)

value: PO:0007134 A vegetative growth

value: soil mix


title: pathogen isolates: Taiwan 80-2 (vir) - time: 288 hai - rep1


title: 5th hybridization susceptible vs. Resistant tree

value: bark tissue sampled from the shoots of mature trees grown under the same environment at the clones bank of Barnes Creek, BC (collection established 1972-1973).


title: 7th hybridization susceptible vs. Resistant tree


title: pathogen isolates: Hawaii 94-1 (avir) - time: 12 hai - rep3


title: 8th hybridization susceptible vs. Resistant tree


title: 6th hybridization susceptible vs. Resistant tree


title: D1 patient

value: 6 months


title: 3rd hybridization susceptible vs. Resistant tree

value: bark tissue sampled from the shoots of mature trees grown under the same environment at the Picearetum of Kalamalka Research Station, Vernon, BC (collection established 1972-1973).


title: 2nd hybridization susceptible vs. Resistant tree


title: 10th hybridization susceptible vs. Resistant tree


title: pathogen isolates: Taiwan 80-2 (vir) - time: 288 hai - rep3


title: 4th hybridization susceptible vs. Resistant tree


title: pathogen isolates: Hawaii 94-1 (avir) - time: 24 hai - rep2

value: 24 hr


title: pathogen isolates: Taiwan 80-2 (vir) - time: 216 hai - rep2

description: PI462312  Taiwan 80-2 treatment 216 hours

source_name: leaf (pathogen isolates: Taiwan 80-2 (vir) - time: 216 hai)


title: pathogen isolates: Taiwan 80-2 (vir) - time: 216 hai - rep3


title: pathogen isolates: Taiwan 80-2 (vir) - time: 144 hai - rep2

description: PI462312  Taiwan 80-2 treatment 144 hours

source_name: leaf (pathogen isolates: Taiwan 80-2 (vir) - time: 144 hai)


title: C4 patient

value: 2 years


title: Effects of dexamethasone on human adipose tissue MA rep

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

description: Labeling and hybridization qualities were verified with Agilent’s spike in kit.

hyb_protocol: 850 ng of Cy5 labelled probe was cohybridized the same amount of Cy3 labelled probe. We used the whole human genome oligo microarray from Agilent with the gene expression hybridization kit according to the manufacturer's protocol.

scan_protocol: Micro-arrays were scanned on a InnoScan 700 scanner (Innopsys, Carbonne, France, EU) and data were extracted with Mapix software (Innopsys).

data_processing: The data extracted with Mapix software (Innopsys) were normalized with the Lowess procedure without background subtraction by use of R. Features with a signal to background ratio strictly below 2 in both color as well as control spots were discarded. Value is the Log2 of normalized Red/Green value ratio.

source_name: Human adipose tissue, control

label_protocol: Total RNA quality was checked by capillary electrophoresis (Agilent 2100 bioanalyzer and RNA 6000 labChip Kit) and good quality RNA extracts only were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 500ng of RNA with the low RNA input linear amplification kit (Agilent).

extract_protocol: Total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer instructions.

tag: agent

value: control

value: subcutaneous abdominal adipose tissue

source_name: Human adipose tissue, 4-d dexamethasone treatment

value: 4-d dexamethasone


title: C3 patient

value: cardiopathy

value: 9 years and 10 months

value: thymus


title: C2 patient

value: 30 days


title: Effects of dexamethasone on human adipose tissue BS rep


title: pathogen isolates: Taiwan 80-2 (vir) - time: 144 hai - rep3

value: Taiwan 80-2 (vir)