title: PsoriaticSkin_OCT_020

city: Hellerup

first: Marianne

middle: Bengtson

last: Løvendorf

address: Niels Andersens Vej 65

department: Dermato-Allergology

country: Denmark

institute: Gentofte Hospital

description:
X4,40,PP,OCT
raw data file (Hy3): 1_Exiqon_14201628_S01.txt
raw data file (Hy5): 0_Exiqon_14201628_S01.txt

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 15.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Grödig, Austria).

scan_protocol: Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the resulting TIFF images segmented using the ImaGene 8.0 software on standard settings (BioDiscovery, Inc., USA).

data_processing:
Data were imported into the R working environment (http://www.r-project.org) using the LIMMA package of the Bioconductor project. Probe signals were background corrected by fitting a convolution of normal and exponential distributions to the foreground intensities using the background intensities as a covariate. Four technical replicate spots for each probe were combined to produce one signal by taking the logarithmic base-2 mean of reliable spots. If all four replicates for a given probe were judged unreliable (weight = 0) the probe was excluded from further analysis. The data were quantile normalized to make the arrays comparable. Only human miRNAs reported in the miRBASE version 15.0 were included in the further analysis.

Final, processed data are normalized, log2 Cy3 signals.  The reference channel Hy5 data (though made available as raw data files) were not used in calculating the Cy3 signals.

source_name: psoriatic skin, OCT

label_protocol: miRCURY Hy3/Hy5 LNA Array power labelling kit (Exiqon)

extract_protocol: FFPE and OCT samples were cut in 8 x 10 µm sections with a microtome and the RNA was extracted from the tissue sections using the RecoverAll(TM) Total Nucleic Acid Isolation kit (Applied Biosystems, Naerum, Denmark) and the mirVanaTM miRNA Isolation Kit (Applied Biosystems), respectively. Frozen skin biopsies (FS) were ground in liquid nitrogen and transferred to 600 µl lysis/binding buffer (Applied Biosystems) and homogenized with a rotor stator (Polytron PT3000, Kinamatica AG, Buch & Holm A/S, Denmark). MicroRNAs were then isolated using the mirVanaTM miRNA Isolation Kit (Applied Biosystems) following the manufacturer’s instructions. RNA concentration was determined using a NanoDrop™ 1000 Spectrophotometer (Thermo Fisher Scientific, Copenhagen, Denmark) and the quality assessed using the Agilent RNA 6000 nano kit and the Agilent 2100 Bioanalyzer (Agilent Technologies, Naerum, Denmark). The RNA samples were stored at -80˚C.

tag: patient

value: psoriatic skin

tag: preservation method

value: OCT

source_name: [reference] FirstChoice® Human total RNA survey Panel (AM6000, Ambion)

tag: sample type

value: reference RNA


title: PsoriaticSkin_OCT_024

status: Public on Mar 22 2012

type: RNA

description:
X5,39,PP,OCT
raw data file (Hy3): 1_Exiqon_14201710_S01.txt
raw data file (Hy5): 0_Exiqon_14201710_S01.txt

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: PsoriaticSkin_OCT_025

description:
X5,35,PP,OCT
raw data file (Hy3): 1_Exiqon_14201742_S01.txt
raw data file (Hy5): 0_Exiqon_14201742_S01.txt


title: PsoriaticSkin_OCT_014

description:
X3,37,PP,OCT
raw data file (Hy3): 1_Exiqon_14201558_S01.txt
raw data file (Hy5): 0_Exiqon_14201558_S01.txt


title: PsoriaticSkin_OCT_018

description:
X4,38,PP,OCT
raw data file (Hy3): 1_Exiqon_14201626_S01.txt
raw data file (Hy5): 0_Exiqon_14201626_S01.txt


title: PsoriaticSkin_OCT_016

description:
X4,36,PP,OCT
raw data file (Hy3): 1_Exiqon_14201624_S01.txt
raw data file (Hy5): 0_Exiqon_14201624_S01.txt


title: PsoriaticSkin_OCT_019

description:
X4,39,PP,OCT
raw data file (Hy3): 1_Exiqon_14201627_S01.txt
raw data file (Hy5): 0_Exiqon_14201627_S01.txt


title: BXD62_F

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

country: USA

institute: University of Tennessee Health Science Center

description: Gene expression data from adult hypothalamus

hyb_protocol: The wash and staining are done on a Affymetrix Fluidics Station 450 and hybed and scanned using Affymetrix manufactures protocols for the Mouse Gene ST 1.0

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000

data_processing: Probe intensity values were extracted using the Affymetrix GeneChip Operating Software and RMA normalized

label: biotin

organism: Mus musculus

source_name: Hypothalamus, BXD62, F

label_protocol: 100ng of total RNA were amplified and labeled according to Affymetrix manufactures protocols for the Mouse Gene ST 1.0. Samples were amplified using the Ambion Whole Transcriptome Amplification Kit using manufactures protocols and the fragmentation and labeling was done according to Affymetrix manufactures protocols.

extract_protocol: RNA was purified using the RNAeasy micro kit on the QIAcube system (Qiagen, www.qiagen.com).

value: Hypothalamus

tag: strain

tag: Sex

value: F

tag: age (days)


title: BXD34_F

source_name: Hypothalamus, BXD34, F


title: PsoriaticSkin_OCT_017

description:
X4,37,PP,OCT
raw data file (Hy3): 1_Exiqon_14201625_S01.txt
raw data file (Hy5): 0_Exiqon_14201625_S01.txt


title: BXD32_M

source_name: Hypothalamus, BXD32, M

value: M


title: BXD100_M

source_name: Hypothalamus, BXD100, M


title: BXD75_M

source_name: Hypothalamus, BXD75, M


title: BXD42_F

source_name: Hypothalamus, BXD42, F


title: BXD31_F

source_name: Hypothalamus, BXD31, F


title: PsoriaticSkin_OCT_022

description:
X5,37,PP,OCT
raw data file (Hy3): 1_Exiqon_14201708_S01.txt
raw data file (Hy5): 0_Exiqon_14201708_S01.txt


title: BXD84_M

source_name: Hypothalamus, BXD84, M


title: BXD34_M

source_name: Hypothalamus, BXD34, M


title: PsoriaticSkin_OCT_023

description:
X5,38,PP,OCT
raw data file (Hy3): 1_Exiqon_14201709_S01.txt
raw data file (Hy5): 0_Exiqon_14201709_S01.txt


title: BXD14_F

source_name: Hypothalamus, BXD14, F


title: BXD24_F

source_name: Hypothalamus, BXD24, F


title: BXD31_M

source_name: Hypothalamus, BXD31, M


title: BXD1_F

source_name: Hypothalamus, BXD1, F


title: PsoriaticSkin_OCT_015

description:
X3,38,PP,OCT
raw data file (Hy3): 1_Exiqon_14201564_S01.txt
raw data file (Hy5): 0_Exiqon_14201564_S01.txt


title: BXD75_F

source_name: Hypothalamus, BXD75, F


title: PsoriaticSkin_OCT_013

description:
X3,36,PP,OCT
raw data file (Hy3): 1_Exiqon_14201557_S01.txt
raw data file (Hy5): 0_Exiqon_14201557_S01.txt


title: PsoriaticSkin_OCT_021

description:
X5,36,PP,OCT
raw data file (Hy3): 1_Exiqon_14201706_S01.txt
raw data file (Hy5): 0_Exiqon_14201706_S01.txt


title: PsoriaticSkin_OCT_011

description:
X3,34,PP,OCT
raw data file (Hy3): 1_Exiqon_14201554_S01.txt
raw data file (Hy5): 0_Exiqon_14201554_S01.txt


title: PsoriaticSkin_OCT_012

description:
X3,35,PP,OCT
raw data file (Hy3): 1_Exiqon_14201555_S01.txt
raw data file (Hy5): 0_Exiqon_14201555_S01.txt


title: PsoriaticSkin_OCT_010

description:
X2,38,PP,OCT
raw data file (Hy3): 1_Exiqon_14201478_S01.txt
raw data file (Hy5): 0_Exiqon_14201478_S01.txt


title: PsoriaticSkin_OCT_009

description:
X2,37,PP,OCT
raw data file (Hy3): 1_Exiqon_14201477_S01.txt
raw data file (Hy5): 0_Exiqon_14201477_S01.txt


title: PsoriaticSkin_OCT_007

description:
X2,35,PP,OCT
raw data file (Hy3): 1_Exiqon_14201475_S01.txt
raw data file (Hy5): 0_Exiqon_14201475_S01.txt


title: PsoriaticSkin_OCT_008

description:
X2,36,PP,OCT
raw data file (Hy3): 1_Exiqon_14201476_S01.txt
raw data file (Hy5): 0_Exiqon_14201476_S01.txt


title: PsoriaticSkin_OCT_006

description:
X2,34,PP,OCT
raw data file (Hy3): 1_Exiqon_14201474_S01.txt
raw data file (Hy5): 0_Exiqon_14201474_S01.txt


title: BXD29_F

source_name: Hypothalamus, BXD29, F


title: PsoriaticSkin_OCT_005

description:
X1,38,PP,OCT
raw data file (Hy3): 1_Exiqon_14201416_S01.txt
raw data file (Hy5): 0_Exiqon_14201416_S01.txt

source_name: psoriatic skin, OCT


title: BXD39_M

source_name: Hypothalamus, BXD39, M


title: BXD12_M

source_name: Hypothalamus, BXD12, M


title: PsoriaticSkin_OCT_004

description:
X1,37,PP,OCT
raw data file (Hy3): 1_Exiqon_14201415_S01.txt
raw data file (Hy5): 0_Exiqon_14201415_S01.txt

source_name: [reference] FirstChoice® Human total RNA survey Panel (AM6000, Ambion)


title: BXD1_M

source_name: Hypothalamus, BXD1, M


title: PsoriaticSkin_OCT_001

description:
X1,34,PP,OCT
raw data file (Hy3): 1_Exiqon_14201412_S01.txt
raw data file (Hy5): 0_Exiqon_14201412_S01.txt


title: PsoriaticSkin_OCT_002

description:
X1,35,PP,OCT
raw data file (Hy3): 1_Exiqon_14201413_S01.txt
raw data file (Hy5): 0_Exiqon_14201413_S01.txt


title: PsoriaticSkin_OCT_003

description:
X1,36,PP,OCT
raw data file (Hy3): 1_Exiqon_14201414_S01.txt
raw data file (Hy5): 0_Exiqon_14201414_S01.txt


title: BXD73_F

description: Gene expression data from adult hypothalamus

source_name: Hypothalamus, BXD73, F


title: BXD27_F

source_name: Hypothalamus, BXD27, F


title: BXD29_M

source_name: Hypothalamus, BXD29, M


title: BXD11_M

source_name: Hypothalamus, BXD11, M


title: PsoriaticSkin_FS_025

description:
X5,48,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201725_S01.txt
raw data file (Hy5): 0_Exiqon_14201725_S01.txt

source_name: psoriatic skin, Frozen

value: Frozen


title: BXD69_F

source_name: Hypothalamus, BXD69, F


title: BXD80_M

source_name: Hypothalamus, BXD80, M


title: BXD11_F

source_name: Hypothalamus, BXD11, F


title: BXD80_F

source_name: Hypothalamus, BXD80, F


title: BXD27_M

source_name: Hypothalamus, BXD27, M


title: PsoriaticSkin_FS_024

description:
X5,46,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201721_S01.txt
raw data file (Hy5): 0_Exiqon_14201721_S01.txt


title: BXD69_M

source_name: Hypothalamus, BXD69, M


title: PsoriaticSkin_FS_022

description:
X5,42,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201715_S01.txt
raw data file (Hy5): 0_Exiqon_14201715_S01.txt


title: PsoriaticSkin_FS_021

description:
X5,40,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201713_S01.txt
raw data file (Hy5): 0_Exiqon_14201713_S01.txt


title: BXD60_M

source_name: Hypothalamus, BXD60, M


title: BXD103_F

source_name: Hypothalamus, BXD103, F


title: BXD73_M

source_name: Hypothalamus, BXD73, M


title: PsoriaticSkin_FS_020

description:
X4,49,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201637_S01.txt
raw data file (Hy5): 0_Exiqon_14201637_S01.txt


title: PsoriaticSkin_FS_018

description:
X4,45,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201633_S01.txt
raw data file (Hy5): 0_Exiqon_14201633_S01.txt


title: PsoriaticSkin_FS_019

description:
X4,47,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201635_S01.txt
raw data file (Hy5): 0_Exiqon_14201635_S01.txt


title: PsoriaticSkin_FS_023

description:
X5,44,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201718_S01.txt
raw data file (Hy5): 0_Exiqon_14201718_S01.txt


title: PsoriaticSkin_FS_016

description:
X4,41,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201629_S01.txt
raw data file (Hy5): 0_Exiqon_14201629_S01.txt


title: BXD103_M

source_name: Hypothalamus, BXD103, M


title: PsoriaticSkin_FS_014

description:
X3,45,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201572_S01.txt
raw data file (Hy5): 0_Exiqon_14201572_S01.txt

source_name: [reference] FirstChoice® Human total RNA survey Panel (AM6000, Ambion)


title: PsoriaticSkin_FS_017

description:
X4,43,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201631_S01.txt
raw data file (Hy5): 0_Exiqon_14201631_S01.txt


title: BXD49_M

source_name: Hypothalamus, BXD49, M


title: BXD44_F

source_name: Hypothalamus, BXD44, F


title: BXD45_F

source_name: Hypothalamus, BXD45, F


title: BXD43_M

source_name: Hypothalamus, BXD43, M


title: PsoriaticSkin_FS_013

description:
X3,43,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201569_S01.txt
raw data file (Hy5): 0_Exiqon_14201569_S01.txt


title: PsoriaticSkin_FS_015

description:
X3,47,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201574_S01.txt
raw data file (Hy5): 0_Exiqon_14201574_S01.txt


title: PsoriaticSkin_FS_011

description:
X3,39,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201565_S01.txt
raw data file (Hy5): 0_Exiqon_14201565_S01.txt


title: PsoriaticSkin_FS_010

description:
X2,47,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201487_S01.txt
raw data file (Hy5): 0_Exiqon_14201487_S01.txt


title: BXD44_M

source_name: Hypothalamus, BXD44, M


title: BXD60_F

source_name: Hypothalamus, BXD60, F


title: PsoriaticSkin_FS_009

description:
X2,45,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201485_S01.txt
raw data file (Hy5): 0_Exiqon_14201485_S01.txt

source_name: psoriatic skin, Frozen


title: PsoriaticSkin_FS_008

description:
X2,43,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201483_S01.txt
raw data file (Hy5): 0_Exiqon_14201483_S01.txt


title: PsoriaticSkin_FS_007

description:
X2,41,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201481_S01.txt
raw data file (Hy5): 0_Exiqon_14201481_S01.txt


title: PsoriaticSkin_FS_012

description:
X3,41,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201567_S01.txt
raw data file (Hy5): 0_Exiqon_14201567_S01.txt


title: PsoriaticSkin_FS_006

description:
X2,39,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201479_S01.txt
raw data file (Hy5): 0_Exiqon_14201479_S01.txt


title: PsoriaticSkin_FS_004

description:
X1,45,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201424_S01.txt
raw data file (Hy5): 0_Exiqon_14201424_S01.txt


title: BXD102_M

description: Gene expression data from adult hypothalamus

source_name: Hypothalamus, BXD102, M


title: PsoriaticSkin_FS_005

description:
X1,47,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201426_S01.txt
raw data file (Hy5): 0_Exiqon_14201426_S01.txt


title: BXD45_M

source_name: Hypothalamus, BXD45, M


title: OBOB_16_weeks_2

city: Valencia

first: David

last: Montaner

address: C/ Eduardo Primo Yufera, 3

department: Bioinformatics

country: Spain

institute: CIPF

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: Affymetrix Power Tools

label_protocol: Affymetrix GeneChip whole-transcript sense target–labeling assay (Affymetrix, High Wycombe, U.K.)

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

tag: cell type

value: isolated ATMs and adipocytes

tag: genotype

value: OBOB

tag: weeks


title: WT_16_weeks_2

value: WT


title: OBOB_16_weeks_4


title: OBOB_16_weeks_3


title: OBOB_16_weeks_1


title: WT_16_weeks_3


title: PsoriaticSkin_FS_001

description:
X1,39,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201417_S01.txt
raw data file (Hy5): 0_Exiqon_14201417_S01.txt


title: WT_16_weeks_4


title: OBOB_5_weeks_2


title: PsoriaticSkin_FS_003

description:
X1,43,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201422_S01.txt
raw data file (Hy5): 0_Exiqon_14201422_S01.txt


title: WT_16_weeks_1


title: PsoriaticSkin_FS_002

description:
X1,41,PP,Frozen
raw data file (Hy3): 1_Exiqon_14201419_S01.txt
raw data file (Hy5): 0_Exiqon_14201419_S01.txt


title: PsoriaticSkin_FFPE_025

description:
X5,34,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201703_S01.txt
raw data file (Hy5): 0_Exiqon_14201703_S01.txt

source_name: psoriatic skin, FFPE

value: FFPE


title: PsoriaticSkin_FFPE_024

description:
X5,33,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201702_S01.txt
raw data file (Hy5): 0_Exiqon_14201702_S01.txt


title: PsoriaticSkin_FFPE_023

description:
X5,32,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201701_S01.txt
raw data file (Hy5): 0_Exiqon_14201701_S01.txt


title: OBOB_5_weeks_1


title: WT_5_weeks_3


title: OBOB_5_weeks_3


title: WT_5_weeks_2


title: WT_5_weeks_4


title: WT_5_weeks_1


title: PsoriaticSkin_FFPE_021

description:
X5,30,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201699_S01.txt
raw data file (Hy5): 0_Exiqon_14201699_S01.txt


title: Fe-sufficient 1

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: Four micrograms of labelled aRNA was hybridized to the array according to the manufacturer’s recommendations (http://www.combimatrix.com/support_docs.htm). Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C. Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS) using 4 μg of labelled aRNA. Hybridization washings were performed as following: wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20), wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20), 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).

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

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

organism: Solanum lycopersicum

source_name: 27-d-old plants, 1-wk Fe-sufficiency

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

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

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

treatment_protocol:
21-old-plants were transferred for a further week to a Fe-free nutrient solution (Fe-deficient) and as control few tomato plants were transferred for a week to a nutrient solution containing 100 μM Fe-EDTA  (Fe-sufficient plants).
The nutrient solutions were renewed every three days. The controlled climatic conditions were the following: day/night photoperiod, 16/8 h; light intensity, 220 μE m-2s-1; temperature (day/night) 25/20 °C; RH 70 to 80 %.
24 hours before harvesting, all nutrient solutions were renewed and the pH was adjusted at 7.5 with 10 mM Hepes-KOH. Roots of Fe-deficient and Fe-sufficient tomato plants (27-d-old) were harvested five hours after the beginning of light phase.

tag: cultivar

value: Marmande superprecoce

tag: age

value: 27 days old

value: roots


title: Fe-sufficient 3


title: Fe-deficient 3

source_name: 27-d-old plants, 1-wk Fe-deficiency


title: Fe-deficient 2


title: Fe-sufficient 2


title: PsoriaticSkin_FFPE_022

description:
X5,31,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201700_S01.txt
raw data file (Hy5): 0_Exiqon_14201700_S01.txt


title: PsoriaticSkin_FFPE_020

description:
X4,35,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201623_S01.txt
raw data file (Hy5): 0_Exiqon_14201623_S01.txt


title: Fe-deficient 1


title: PsoriaticSkin_FFPE_019

description:
X4,34,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201622_S01.txt
raw data file (Hy5): 0_Exiqon_14201622_S01.txt


title: PsoriaticSkin_FFPE_018

description:
X4,33,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201621_S01.txt
raw data file (Hy5): 0_Exiqon_14201621_S01.txt


title: normal breast DFHCC 04-183 reference FFPE sample7

type: genomic

city: Lyngby

first: Nicolai

middle: Juul

last: Birkbak

address: Kemitorvet, Build. 208

department: Center for Biological Sequence Analysis

institute: Technical University of Denmark

description: Two chips were used per sample. For SNP A/B, one (xxxA.CEL) chip give signal / copy number of A allele, the other chip (xxxC.CEL) give that of B allele.  Copy number assessment of a given SNP is the sum of allele A and B. We used normals as the reference for the test samples.  The copy number is a relative value between the test and normal references.

hyb_protocol: Hybridization was performed by Affymetrix according to the platform protocol

scan_protocol: Scanning was performed by Affymetrix

data_processing:
Data processing was performed by Affymetrix
Tables contain genotypes, copynumber, signal A intensity and signal B intensity, as provided by Affymetrix.

molecule: genomic DNA

source_name: FFPE negative lymph node

label_protocol: Labeling was performed by Affymetrix according to the platform protocol

extract_protocol: genomic DNA was extracted with phenolchloroform followed by ethanol precipitation. Normal reference were from blood, FFPE normal reference were from negative lymph nodes.

value: FFPE negative lymph node

tag: disease state

value: normal


title: normal breast DFHCC 04-183 reference sample27

source_name: Blood

value: Blood


title: PsoriaticSkin_FFPE_017

description:
X4,32,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201620_S01.txt
raw data file (Hy5): 0_Exiqon_14201620_S01.txt

value: psoriatic skin


title: normal breast DFHCC 04-183 reference sample29


title: normal breast DFHCC 04-183 reference sample26


title: normal breast DFHCC 04-183 reference sample28


title: PsoriaticSkin_FFPE_016

description:
X4,31,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201619_S01.txt
raw data file (Hy5): 0_Exiqon_14201619_S01.txt


title: normal breast DFHCC 04-183 reference sample23


title: normal breast DFHCC 04-183 reference FFPE sample8


title: normal breast DFHCC 04-183 reference sample21


title: normal breast DFHCC 04-183 reference sample25


title: normal breast DFHCC 04-183 reference sample20


title: normal breast DFHCC 04-183 reference FFPE sample6


title: normal breast DFHCC 06-202 reference sample7

description: Copy number assessment of a given SNP is the sum of allele A and B. We used normals as the reference for the test samples. The copy number is a relative value between the test and normal references.


title: normal breast DFHCC 06-202 reference sample3


title: normal breast DFHCC 04-183 reference sample22


title: normal breast DFHCC 04-183 reference FFPE sample18


title: normal breast DFHCC 06-202 reference sample49


title: normal breast DFHCC 06-202 reference sample13


title: normal breast DFHCC 06-202 reference sample28


title: normal breast DFHCC 06-202 reference sample15


title: normal breast DFHCC 04-183 reference sample16


title: PsoriaticSkin_FFPE_013

description:
X3,31,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201546_S01.txt
raw data file (Hy5): 0_Exiqon_14201546_S01.txt


title: normal breast DFHCC 06-202 reference sample41


title: PsoriaticSkin_FFPE_012

description:
X3,30,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201544_S01.txt
raw data file (Hy5): 0_Exiqon_14201544_S01.txt


title: PsoriaticSkin_FFPE_011

description:
X3,29,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201543_S01.txt
raw data file (Hy5): 0_Exiqon_14201543_S01.txt


title: PsoriaticSkin_FFPE_014

description:
X3,32,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201549_S01.txt
raw data file (Hy5): 0_Exiqon_14201549_S01.txt


title: normal breast DFHCC 06-202 reference sample14


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample33

source_name: Primary frozen breast cancer tumor tissue

tag: er

value: negative

tag: pr

tag: neoadjuvant therapy

value: cisplatin + bevacizumab

value: breast cancer


title: normal breast DFHCC 04-183 reference FFPE sample13


title: normal breast DFHCC 04-183 reference sample14


title: normal breast DFHCC 04-183 reference FFPE sample9


title: normal breast DFHCC 04-183 reference sample10


title: normal breast DFHCC 04-183 reference sample11


title: PsoriaticSkin_FFPE_010

description:
X2,32,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201472_S01.txt
raw data file (Hy5): 0_Exiqon_14201472_S01.txt

value: reference RNA


title: normal breast DFHCC 06-202 reference sample19


title: normal breast DFHCC 04-183 reference sample15


title: normal breast DFHCC 04-183 reference sample12


title: normal breast DFHCC 06-202 reference sample20


title: normal breast DFHCC 04-183 reference sample7


title: normal breast DFHCC 04-183 reference sample24


title: PsoriaticSkin_FFPE_015

description:
X3,33,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201553_S01.txt
raw data file (Hy5): 0_Exiqon_14201553_S01.txt


title: PsoriaticSkin_FFPE_009

description:
X2,31,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201471_S01.txt
raw data file (Hy5): 0_Exiqon_14201471_S01.txt


title: PsoriaticSkin_FFPE_008

description:
X2,30,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201470_S01.txt
raw data file (Hy5): 0_Exiqon_14201470_S01.txt


title: normal breast DFHCC 04-183 reference sample5


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample51

tag: miller-payne response

value: Primary frozen breast cancer tumor tissue


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample24


title: normal breast DFHCC 04-183 reference sample8


title: PsoriaticSkin_FFPE_007

description:
X2,29,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201469_S01.txt
raw data file (Hy5): 0_Exiqon_14201469_S01.txt

tag: patient


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample46


title: PsoriaticSkin_FFPE_006

description:
X2,28,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201468_S01.txt
raw data file (Hy5): 0_Exiqon_14201468_S01.txt

tag: preservation method


title: normal breast DFHCC 04-183 reference sample6


title: normal breast DFHCC 04-183 reference sample4


title: normal breast DFHCC 04-183 reference sample17


title: breast tumor DFHCC 04-183 cisplatin sample27

value: P

value: Cisplatin

tag: brca1 methylation

value: neg

tag: brca1 mutation

value: N

tag: grade

value: III


title: breast tumor DFHCC 04-183 cisplatin sample26

value: pos

tag: tissue


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample21


title: PsoriaticSkin_FFPE_004

description:
X1,31,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201408_S01.txt
raw data file (Hy5): 0_Exiqon_14201408_S01.txt

value: FFPE

tag: sample type


title: normal breast DFHCC 04-183 reference sample1


title: breast tumor DFHCC 04-183 cisplatin sample28

tag: p53 status

value: WT


title: normal breast DFHCC 04-183 reference sample3


title: breast tumor DFHCC 04-183 cisplatin sample24

value: MSM


title: breast tumor DFHCC 04-183 cisplatin sample29

value: NSM


title: PsoriaticSkin_FFPE_005

description:
X1,32,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201409_S01.txt
raw data file (Hy5): 0_Exiqon_14201409_S01.txt


title: breast tumor DFHCC 04-183 cisplatin sample25


title: PsoriaticSkin_FFPE_003

description:
X1,30,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201407_S01.txt
raw data file (Hy5): 0_Exiqon_14201407_S01.txt


title: PsoriaticSkin_FFPE_002

description:
X1,29,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201404_S01.txt
raw data file (Hy5): 0_Exiqon_14201404_S01.txt


title: PsoriaticSkin_FFPE_001

description:
X1,28,PP,FFPE
raw data file (Hy3): 1_Exiqon_14201403_S01.txt
raw data file (Hy5): 0_Exiqon_14201403_S01.txt


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample29


title: breast tumor DFHCC 04-183 cisplatin FFPE sample18

description: Two chips were used per sample. For SNP A/B, one (xxxA.CEL) chip give signal / copy number of A allele, the other chip (xxxC.CEL) give that of B allele.  Copy number assessment of a given SNP is the sum of allele A and B. We used normals as the reference for the test samples.  The copy number is a relative value between the test and normal references.

source_name: Primary FFPE breast cancer tumor tissue

value: Y

value: Primary FFPE breast cancer tumor tissue


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample18

description: Copy number assessment of a given SNP is the sum of allele A and B. We used normals as the reference for the test samples. The copy number is a relative value between the test and normal references.

value: negative


title: breast tumor DFHCC 04-183 cisplatin sample22


title: breast tumor DFHCC 04-183 cisplatin sample23


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample40

value: cisplatin + bevacizumab


title: breast tumor DFHCC 04-183 cisplatin sample21

value: breast cancer


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample17


title: breast tumor DFHCC 04-183 cisplatin sample16


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample4


title: breast tumor DFHCC 04-183 cisplatin FFPE sample13


title: breast tumor DFHCC 04-183 cisplatin sample14


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample39


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample43


title: breast tumor DFHCC 04-183 cisplatin sample11


title: breast tumor DFHCC 04-183 cisplatin sample12


title: control vehicle-treated PCK rat kidney

city: Toyoake

first: Kugita

last: Masanori

state: Aichi

address: kutsukake-cho Denngakugakubo 1-98

department: Center of Animal Models for Human Diseases

country: Japan

institute: Fujita Health University

hyb_protocol: 1.65 μg aliquots of Cy3-labeled RNA were hybridized using the Gene Expression hybridization kit (Agilent Technologies) onto Rat Oligo Microarrays (Agilent Technologies, product no. G4130A) according to the manufacturer’s hybridization protocol.

scan_protocol: The microarray slides were examined with an Agilent microarray scanner and software.

data_processing: Data analysis was performed with Agilent Feature Extraction software (version 10.7.3.1).

organism: Rattus norvegicus

source_name: control vehicle-treated PCK rat kidney

label_protocol: 500 ng aliquots of total RNA obtained from kidneys of three rats were labeled using an Quick Amp Labeling Kit, one-color (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions.  The pooled renal RNA of PIO- or vehicle-treated rats were labeled with the Cy3-fluorescence dye.

growth_protocol: PCK rats were allowed free access to water and food throughout the study.

extract_protocol: RNA was extracted from kidneys of rats with or without PIO treatment using a monophasic solution of phenol/guanidine isothiocyanate and TRIzol® reagent (Invitrogen Co., Carlsbad, CA, USA) in accordance with their manual, and the samples were incubated with RNase-free DNase I (Ambion, TX, USA).  The quality and concentration of each sample was confirmed by spectrophotometry (NanoDropTM ND-1000; Asahi glass Co. Ltd., Tokyo, Japan).

treatment_protocol: Female PCK and +/+ rats (n = 10 per gender) were randomly assigned to one of two groups: treatment with 10 mg/kg pioglitazone (PIO) (Takeda Pharmaceutical Company Limited, Osaka, Japan) or vehicle control (0.5% DMSO) by gavage every day from 4 to 20 weeks of age.

tag: agent

value: vehicle control (0.5% DMSO)

tag: strain

value: PCK

tag: gender

value: female


title: pioglitazone-treated PCK rat kidney

source_name: pioglitazone-treated PCK rat kidney

value: 10 mg/kg pioglitazone


title: breast tumor DFHCC 04-183 cisplatin sample10

value: Cisplatin

value: neg

tag: age

value: Primary frozen breast cancer tumor tissue


title: HHUA treated with telmisartan_4

city: Yufu-shi

first: Noriyuki

last: Takai

state: Oita

address: 1-1 Idaigaoka, Hasama-machi

department: Obstetrics and Gynecology

institute: Oita University Faculty of Medicine

description: Gene expression of HHUA treated with telmisartan

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HHUA treated with telmisartan

label_protocol: Cyanine-3 (Cy3)-labeled cRNA targets were generated using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies).

growth_protocol: HHUA cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from telmisartan-treated and untreated HHUA cells using an RNeasy mini kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.

treatment_protocol: HHUA cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2, and treated with or without telmisartan for 48 hours.

tag: cell line

value: HHUA

value: telmisartan


title: breast tumor DFHCC 04-183 cisplatin FFPE sample9

tag: er

value: N

value: III

tag: disease state


title: HHUA treated with telmisartan_3


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample19

tag: pr

tag: neoadjuvant therapy


title: breast tumor DFHCC 04-183 cisplatin sample20

tag: miller-payne response


title: breast tumor DFHCC 04-183 cisplatin sample6

value: MSM


title: HHUA control_1

description: Gene expression of HHUA

source_name: HHUA control

value: control


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample9


title: breast tumor DFHCC 04-183 cisplatin sample4


title: breast tumor DFHCC 04-183 cisplatin sample5

value: Y


title: breast tumor DFHCC 04-183 cisplatin sample7

value: negative

value: pos

value: NSM


title: breast tumor DFHCC 04-183 cisplatin sample3

value: breast cancer


title: breast tumor DFHCC 04-183 cisplatin sample8


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample36

value: cisplatin + bevacizumab


title: breast tumor DFHCC 04-183 cisplatin sample1


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample5


title: 23DD, Liposarcoma (Slide 19)

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: 23DD, Liposarcoma (Slide 19)

hyb_protocol: The samples are hybridized on the miRCURY LNA Array (v.11.0)

scan_protocol: Scanned on an Axon GenePix 4000B.  Images were quantified using GenePix pro V6.0.

data_processing: Within-slide normalisation of Hy3/Hy5 ratios (log2 transformed) by background subtraction and with a global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Liposarcoma

label_protocol: The samples are labeled using the miRCURY Hy3/Hy5Power labeling kit

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

value: Liposarcoma

source_name: common reference

value: common reference


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample20


title: WB, biological rep4

city: Yokohama

first: Michio

last: Shibata

address: 2-12-1 Fukuura, Kanazawa-ku

institute: Shiseido Research Center

description: Gene expression data from mouse dorsal skin with tape stripping and oral administration of winged bean extract

hyb_protocol: Then the cRNA was fragmented and hybridized to an Affymetrix Mouse Genome 430 2.0 Array. Following hybridization at 45°C for 16h, the array was washed and labeled with phycoerythrin. Fluorescence signals were scanned by the Affymetrix GeneChip System.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix GeneChip Command Console software was used to reduce array images to the intensity of each probe. The raw microarray data (CEL files) were quantified by Factor Analysis for Robust Microarray Summarization (FARMS) without any background correction and quantile normalization using statistical language R and Bioconductor. To extract differentially expressed genes between NT and TS groups, as well as between TS and TS/WB, Rank products methods was applied to the FARMS quantified data.

label: phycoerythrin

source_name: Mouse skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: 6 weeks old male albino hairless HOS: HR-1 mice (Hoshino Laboratory Animals Co., Ltd., Saitama, Japan) were fed water and a commercial diet CRF-1 (Oriental Yeast Co., Ltd., Tokyo, Japan) ad libitum.

extract_protocol: Total RNA extracted using Isogen. They were further purified using a RNeasy Fibrous Tissue Mini Kit (QIAGEN, Valencia, CA) following manufacturer's instructions.

treatment_protocol: Winged bean extract was solved in 0.3% (w/v) carboxymethylcellulose at concentrations of 20 mg/ml, and administered orally to mice 5 times per week for 5 weeks at 200 mg/kg weight/day. Barrier disruption was achieved by repeated application and removal (tape stripping; TS) of cellophane tape (Nichiban, Hidaka, Japan) on the dorsal skin of the left side. TS was terminated when transepidermal water loss (TEWL) reached 70-100 g/m2/h, when monitored with an electrolytic water analyzer Vapometer (Delfin Technologies, Ltd., Kuopio, Finland). This procedure was started after 1 week-administration of the extract, and was conducted 3 times per week for 4 weeks.

value: dorsal skin

value: 6 weeks

value: male

tag: treatment


title: 8DD, Liposarcoma (Slide 35)

description: 8DD, Liposarcoma (Slide 35)


title: WB, biological rep6

value: mouse dorsal skin with tape stripping and oral administration of winged bean extract


title: WB, biological rep5


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample42

value: Primary frozen breast cancer tumor tissue


title: 7DD, Liposarcoma (Slide 33)

description: 7DD, Liposarcoma (Slide 33)


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample34


title: breast tumor DFHCC 04-183 cisplatin sample17

value: Cisplatin

tag: brca1 methylation

value: N

value: WT


title: 4DD, Liposarcoma (Slide 30)

description: 4DD, Liposarcoma (Slide 30)


title: 21DD, Liposarcoma (Slide 17)

description: 21DD, Liposarcoma (Slide 17)


title: 10DD, Liposarcoma (Slide 1)

description: 10DD, Liposarcoma (Slide 1)


title: breast tumor DFHCC 04-183 cisplatin sample15

value: P

tag: brca1 mutation

value: III


title: 26WD, Liposarcoma (Slide 21)

description: 26WD, Liposarcoma (Slide 21)


title: 25WD, Liposarcoma (Slide 20)

description: 25WD, Liposarcoma (Slide 20)


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample49

value: negative


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample48


title: 13WD, Liposarcoma (Slide 7)

description: 13WD, Liposarcoma (Slide 7)


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample50


title: 10WD, Liposarcoma (Slide 4)

description: 10WD, Liposarcoma (Slide 4)


title: WB, biological rep2


title: WB, biological rep1


title: TS, biological rep6

description: Gene expression data from mouse dorsal skin with tape stripping

value: mouse dorsal skin with tape stripping


title: 7WD, Liposarcoma (Slide 34)

description: 7WD, Liposarcoma (Slide 34)


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample45L


title: 10 uM 48h, biological rep 4

city: Barcelona

first: Sergi

last: Mas Herrero

state: Catalunya

address: Casanova 143

department: Pharmacology, School of Medicine

institute: University of Barcelona

data_processing: RMA processing algorithm. Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)

source_name: SK-N-SH cells treated with Risperidone 10uM for 48h

growth_protocol: SK-N-SH cell line was grown at 37ºC in a humidified incubator with 5% of CO2 in MEM supplemented with 10% FBS, 2 mM L-glutamine, sodium pyruvate, 50 U/mL penicillin and 50 µg/mL streptomycin. Cells were seeded at 3x105 cells/well in 6-well culture plates. The cells were allowed to grow for 48 h to reach 95% confluence.

treatment_protocol: the cells were incubated for increasing times, up to 48 h, with 0.1, 1 and 10 µM risperidone. Gene expression was assessed by microarray in cells treated with risperidone 10 µM at 6, 24 and 48 h. Each condition was assessed in quadruplicate. Risperidone was resuspended in DMSO. In each experiment, controls were treated with the vehicle (DMSO) only. The vehicle did not exhibit cytotoxic effects at the concentrations used in the experiments (maximum concentration 1% of total volume).

value: SK-N-SH

value: treated with Risperidone 10uM for 48h


title: 10 uM 48h, biological rep 3

hyb_protocol: Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)


title: 3WD, Liposarcoma (Slide 29)

description: 3WD, Liposarcoma (Slide 29)


title: HHUA control_2

description: Gene expression of HHUA

value: HHUA

value: control


title: TS, biological rep3


title: TS, biological rep5


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample41

value: cisplatin + bevacizumab

value: breast cancer


title: 10 uM 48h, biological rep 2

scan_protocol: Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)


title: 2WD, Liposarcoma (Slide 26)

description: 2WD, Liposarcoma (Slide 26)

value: Liposarcoma

value: common reference


title: TS, biological rep4

value: dorsal skin

value: 6 weeks

value: male


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample30

value: Primary frozen breast cancer tumor tissue


title: TS, biological rep2


title: 11EF, Liposarcoma (Slide 5)

description: 11EF, Liposarcoma (Slide 5)


title: 10EF, Liposarcoma (Slide 2)

description: 10EF, Liposarcoma (Slide 2)


title: 10 uM 48h, biological rep 1

label_protocol: Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample35


title: 2EF, Liposarcoma (Slide 25)

description: 2EF, Liposarcoma (Slide 25)


title: TS, biological rep1


title: 10 uM 24h, biological rep 4

source_name: SK-N-SH cells treated with Risperidone 10uM for24h

value: treated with Risperidone 10uM for24h


title: 10 uM 24h, biological rep 2


title: 1EF, Liposarcoma (Slide 15)

description: 1EF, Liposarcoma (Slide 15)


title: NT, biological rep5

description: Gene expression data from mouse dorsal skin without tape stripping


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample26


title: 10 uM 24h, biological rep 1


title: 20NF, Normal Fat (Slide 16)

description: 20NF, Normal Fat (Slide 16)

source_name: Normal Fat

value: Normal Fat


title: NT, biological rep6

value: mouse dorsal skin without tape stripping


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample27

value: negative


title: NT, biological rep3


title: NT, biological rep4


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample32


title: 10 uM 6h, biological rep 4

source_name: SK-N-SH cells treated with Risperidone 10uM for 6h

value: treated with Risperidone 10uM for 6h


title: 19NF, Normal Fat (Slide 14)

description: 19NF, Normal Fat (Slide 14)


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample15


title: 10 uM 6h, biological rep 3

value: SK-N-SH


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample14


title: NT, biological rep2


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample28

value: P


title: 10 uM 6h, biological rep 2


title: 10 uM 24h, biological rep 3


title: NT, biological rep1


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample13


title: BCL11A-/- ko mouse 3

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description: FACS-sorted CD71+Ter119+ erythroid progenitors from knockout (Bcl11a fl/fl EpoR-Cre) mouse

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed by dchip and arrays were normalized against the baseline array that has the median brightness.

source_name: CD71+Ter119+ erythroid progenitors from 6-week old bone marrow

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

growth_protocol: Primary erythroid progenitors (CD71+Ter119+) were FACS-sorted from 6-week old bone marrows

value: Bcl11a fl/fl EpoR-Cre+

tag: genotype/variation

value: BCL11A knockout

value: bone marrow erythoid progenitors

value: female

tag: developmental stage

value: 6-week old adult


title: BCL11A-/- ko mouse 2

tag: tissue


title: 18NF, Normal Fat (Slide 13)

description: 18NF, Normal Fat (Slide 13)

tag: sample type

value: common reference


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample10

value: cisplatin + bevacizumab

value: breast cancer


title: untreated cells, biological rep 4

source_name: Untreated SK-N-SH cells

value: untreated


title: BCL11A+/+ control mouse 3

description: FACS-sorted CD71+Ter119+ erythroid progenitors from control (Bcl11a+/+) mouse

value: wildtype


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample12

value: Primary frozen breast cancer tumor tissue


title: 10 uM 6h, biological rep 1


title: 15NF, Normal Fat (Slide 9)

description: 15NF, Normal Fat (Slide 9)

value: Normal Fat


title: untreated cells, biological rep 3


title: untreated cells, biological rep 2


title: 14NF, Normal Fat (Slide 8)

description: 14NF, Normal Fat (Slide 8)


title: 10NF, Normal Fat (Slide 3)

description: 10NF, Normal Fat (Slide 3)


title: 17NF, Normal Fat (Slide 12)

description: 17NF, Normal Fat (Slide 12)


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample6


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample7


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample3


title: untreated cells, biological rep 1


title: 9NF, Normal Fat (Slide 37)

description: 9NF, Normal Fat (Slide 37)


title: WB, biological rep3

value: dorsal skin

value: 6 weeks

value: male

value: mouse dorsal skin with tape stripping and oral administration of winged bean extract


title: BCL11A+/+ control mouse 1


title: BCL11A+/+ control mouse 2


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample45R

value: negative


title: BCL11A-/- ko mouse 1

value: Bcl11a fl/fl EpoR-Cre+


title: genomic DNA from frozen squamous carcinoma 2

status: Public on Mar 21 2012

city: LIEGE

first: Samuel

last: GUENIN

address: CHU Sart Tilman, B23+4

department: GIGA CANCER

country: Belgium

institute: Université de Liège

description: genomic DNA

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: squamous cell carcinoma of the cervix

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from frozen tissue samples using QIAamp DNA micro kit (Qiagen, Valencia, CA) according to manufacturer’s instructions

value: Female

value: frozen tissue

value: cancer


title: genomic DNA from frozen squamous carcinoma 4

description: genomic DNA


title: genomic DNA from frozen squamous carcinoma 1

description: genomic DNA


title: Lung adenocarcinoma LTH45427FF

city: Los Angeles

first: Ite

last: Laird-Offringa

state: CA

address: 1441 Eastlake Avenue, Suite 6420

department: Biochemistry

institute: University of Southern California

hyb_protocol: Standard Illumina protocol performed at the USC Epigenome Center

scan_protocol: Standard Illumina scan protocol performed at the USC Epigenome Center

data_processing: DNA methylation levels are reported as  β-values, calculated from mean non-background corrected methylated (M) and unmethylated (U) signal intensities for each locus for each sample using the formula (β=M/(M+U)) and the Illumina BeadStudio software v3.2. Probes with detection p-values of >0.05 as described previously (Noushemehr et al., 2010) were deemed not significantly different from background noise and were labeled “NA”.

label: Cy3 and Cy5

source_name: Fresh frozen macrodissected tissue

growth_protocol: Fresh-frozen tissue

extract_protocol: Genomic DNA was extracted after macrodissection and a proteinase K digstion by  phenol-chloroform

treatment_protocol: Bisulfite treatment

tag: tissue source

value: USC (University of Southern California)

value: Lung tumor

tag: bisulfite plate

tag: beadchip

tag: strip

value: A

tag: bisulfite well

tag: ethnicity

tag: smoking status

tag: histology

value: Lung adenocarcinoma

tag: Stage

tag: subject


title: Lung adenocarcinoma LTH15307FF

label_protocol: Standard Illumina protocol performed at the USC Epigenome Center

value: C

tag: gender

value: Caucasian

value: Former


title: genomic DNA from frozen squamous carcinoma 3

description: genomic DNA

tag: disease state


title: genomic DNA from frozen squamous carcinoma 5

description: genomic DNA


title: breast tumor DFHCC 06-202 cisplatin bevacizumab sample37

source_name: Primary frozen breast cancer tumor tissue

tag: er

tag: pr

tag: miller-payne response

tag: neoadjuvant therapy

value: cisplatin + bevacizumab

value: breast cancer


title: Lung adenocarcinoma LTH63896FF

tag: tissue

value: Male

value: Asian

value: Never


title: Lung adenocarcinoma LTH46058FF

tag: tissue source

value: I


title: Lung adenocarcinoma LTH00549FF

tag: bisulfite plate

value: H


title: genomic DNA from frozen normal ectocervix 4

description: genomic DNA

source_name: normal ectocervix

value: Female

tag: sample type

value: normal


title: genomic DNA from frozen normal ectocervix 3

description: genomic DNA

value: frozen tissue


title: Lung adenocarcinoma LTH12472FF

value: USC (University of Southern California)

tag: beadchip

tag: strip

value: G


title: Lung adenocarcinoma LTH59808FF

value: Lung tumor

value: B

tag: bisulfite well

tag: ethnicity


title: Lung adenocarcinoma D690T

value: OTB (Ontario Tumor Bank)

tag: smoking status

value: Current

tag: histology

value: Lung adenocarcinoma

value: Stage IA


title: Lung adenocarcinoma D532T

value: K

tag: Stage

value: Stage IB

tag: subject


title: genomic DNA from frozen normal ectocervix 2

description: genomic DNA

tag: gender

tag: disease state


title: Lung adenocarcinoma D693T

value: A

value: Male


title: Lung adenocarcinoma D192T

value: C

value: Former

value: Stage IIB


title: Lung adenocarcinoma D134T

value: F


title: Lung adenocarcinoma D216T

value: L

value: Female

value: Stage IV


title: Lung adenocarcinoma D860T

value: Lung tumor


title: Lung adenocarcinoma B785T

value: J

value: Stage IIIA


title: Lung adenocarcinoma D1186T

value: OTB (Ontario Tumor Bank)

value: H


title: Lung adenocarcinoma B573T

value: Lung adenocarcinoma


title: Lung adenocarcinoma D483T

value: Stage IA


title: Lung adenocarcinoma B467T

value: Stage IB


title: Lung adenocarcinoma B527T


title: genomic DNA from frozen normal ectocervix 1

description: genomic DNA

value: frozen tissue

value: normal


title: Lung adenocarcinoma B393T

value: C

value: Male


title: Lung adenocarcinoma B1102T

value: Never


title: Lung adenocarcinoma B347T

value: F

value: Former


title: Adjacent non-tumor lung LNH15307FF

value: USC (University of Southern California)

value: Normal lung

value: E

value: Female

value: Caucasian

value: Histologically Normal Lung


title: Lung adenocarcinoma B420T

value: OTB (Ontario Tumor Bank)

value: Lung tumor

value: Stage IIB


title: Lung adenocarcinoma B178T

value: H

value: Lung adenocarcinoma


title: Adjacent non-tumor lung LNH45427FF

value: G


title: Lung adenocarcinoma B1023T

value: L

value: Current


title: Adjacent non-tumor lung B467N

value: C


title: Adjacent non-tumor lung D134N


title: Adjacent non-tumor lung B507N

value: Male


title: Adjacent non-tumor lung LNH63896FF

value: I

value: Asian

value: Never


title: Adjacent non-tumor lung LNH00549FF

value: USC (University of Southern California)

value: Normal lung

value: D


title: Adjacent non-tumor lung LNH46058FF

value: B

value: Former

value: Histologically Normal Lung


title: Adjacent non-tumor lung D532N

value: OTB (Ontario Tumor Bank)

value: Female


title: Adjacent non-tumor lung LNH12472FF

value: E

value: Caucasian


title: Lung adenocarcinoma B389T

value: Lung tumor

value: G

value: Lung adenocarcinoma

value: Stage IIIA


title: Adjacent non-tumor lung D1186N

value: Male


title: Adjacent non-tumor lung D693N

value: I


title: Adjacent non-tumor lung D690N

value: J

value: Current


title: Lung adenocarcinoma B1015T

value: A

value: Never

value: Stage IA


title: Adjacent non-tumor lung D192N

value: Normal lung

value: D

value: Former


title: Adjacent non-tumor lung D860N

value: OTB (Ontario Tumor Bank)

value: F

value: Female

value: Histologically Normal Lung


title: Adjacent non-tumor lung D216N


title: Adjacent non-tumor lung B785N

value: K


title: Adjacent non-tumor lung B420N

value: G


title: Adjacent non-tumor lung LNH59808FF

value: USC (University of Southern California)

value: H

value: Caucasian


title: Adjacent non-tumor lung B393N

value: L

value: Male


title: Adjacent non-tumor lung B389N

value: Current


title: Adjacent non-tumor lung B178N


title: Adjacent non-tumor lung B260N

value: Never


title: Lung adenocarcinoma L2_T (methylation)

source_name: Lung adenocarcinoma

label_protocol: Standard Illumina protocol

tag: sample id

value: nci-edrn

tag: beadstrip

value: I

tag: bisulfite alu

tag: age

value: Lung tumor

value: Asian

tag: pack years

value: Stage IIIA

tag: recurrence

value: No

tag: kras mutation status

value: WT

tag: egfr mutation status

value: MUT

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung B347N

tag: tissue source

value: OTB (Ontario Tumor Bank)

tag: tissue

value: Normal lung

tag: bisulfite plate

tag: beadchip

tag: strip

value: D

tag: bisulfite well

value: Female

tag: ethnicity

value: Former

value: Histologically Normal Lung


title: Adjacent non-tumor lung B573N

value: A

tag: gender

tag: smoking status

tag: histology

tag: Stage

tag: subject


title: Adjacent non-tumor lung L15_N (methylation)

source_name: Adjacent non-tumor

tag: sample id

tag: beadstrip

value: H

tag: bisulfite alu

tag: age

tag: pack years

value: Stage IB

tag: recurrence

value: Yes


title: Adjacent non-tumor lung B1015N

tag: tissue source

tag: tissue

value: Never


title: Adjacent non-tumor lung L2_N (methylation)

value: nci-edrn

tag: bisulfite plate

tag: beadchip


title: Lung adenocarcinoma 3035_T (methylation)

value: ttr-data

value: K

value: Lung tumor

value: Male

value: White

value: Stage IA

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Lung adenocarcinoma L15_T (methylation)

value: J

tag: gender

tag: ethnicity

value: Asian

tag: smoking status

value: WT

value: MUT


title: Adjacent non-tumor lung B1023N

value: OTB (Ontario Tumor Bank)

value: Normal lung

tag: strip

tag: bisulfite well

value: Female

value: Current

tag: histology

value: Histologically Normal Lung

tag: Stage

tag: subject


title: Adjacent non-tumor lung 3036_N (methylation)

tag: sample id

tag: beadstrip

value: I

tag: bisulfite alu

tag: age

tag: pack years

value: Never

value: Stage IIA


title: Lung adenocarcinoma 3036_T (methylation)

tag: tissue source

value: ttr-data

tag: bisulfite plate

tag: beadchip

value: E

tag: tissue

tag: kras mutation status


title: Adjacent non-tumor lung 3030_N (methylation)

value: A

tag: gender

tag: ethnicity

value: Stage IB


title: Adjacent non-tumor lung 3033_N (methylation)

value: White

tag: smoking status

value: Stage IIIA


title: Adjacent non-tumor lung 3039_N (methylation)

value: C

value: Stage IIB


title: Lung adenocarcinoma 3039_T (methylation)

value: Lung tumor

value: WT

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Lung adenocarcinoma 3024_T (methylation)

value: Male

tag: Stage

value: MUT

tag: subject


title: Lung adenocarcinoma 3022_T (methylation)

tag: sample id

tag: beadstrip

value: Current

value: Stage IA


title: Adjacent non-tumor lung 3031_N (methylation)

tag: bisulfite alu

tag: age

value: Normal lung

value: Female


title: Lung adenocarcinoma 3032_T (methylation)

tag: tissue source

value: I

tag: pack years

value: Never


title: Adjacent non-tumor lung 3032_N (methylation)

value: ttr-data

tag: bisulfite plate

tag: beadchip


title: Lung adenocarcinoma 3023_T (methylation)

tag: tissue

tag: kras mutation status


title: Adjacent non-tumor lung 3024_N (methylation)

value: H

tag: gender

tag: ethnicity


title: Lung adenocarcinoma 3030_T (methylation)

tag: smoking status

value: Stage IB

tag: egfr mutation status


title: Lung adenocarcinoma 3031_T (methylation)

value: J

value: White

value: Stage IIA

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung 3035_N (methylation)

value: F

tag: Stage

tag: subject


title: Adjacent non-tumor lung 3023_N (methylation)

tag: sample id

tag: beadstrip

value: L


title: Lung adenocarcinoma 3021_T (methylation)

value: B

tag: bisulfite alu

tag: age

value: Lung tumor

value: WT


title: Adjacent non-tumor lung 3022_N (methylation)

tag: tissue source

value: Male

tag: pack years

value: Current


title: Lung adenocarcinoma 3014_T (methylation)

tag: bisulfite plate

tag: beadchip

value: C

value: Stage IIIA

value: MUT


title: Lung adenocarcinoma 3033_T (methylation)

tag: tissue

value: Female

value: Never

tag: kras mutation status


title: Adjacent non-tumor lung 3014_N (methylation)

value: ttr-data

value: I

value: Normal lung

tag: gender

tag: ethnicity


title: Lung adenocarcinoma 07L6_T (methylation)

value: nci-edrn

value: J

value: Asian

tag: smoking status

tag: recurrence

value: Yes

tag: egfr mutation status


title: Lung adenocarcinoma 07L66_T (methylation)

value: H

value: White

tag: Stage

value: Stage IA

value: No

tag: lkb1 mutation status

tag: kras mutation type


title: Lung adenocarcinoma 3012_T (methylation)

tag: sample id

tag: beadstrip

value: K

value: Lung tumor

value: Current

value: WT

tag: subject


title: Lung adenocarcinoma 3003_T (methylation)

tag: tissue source

value: B

tag: bisulfite alu

tag: age

value: Female

value: Stage IIA

value: MUT


title: Adjacent non-tumor lung 3012_N (methylation)

value: ttr-data

tag: bisulfite plate

tag: beadchip

value: Normal lung

tag: pack years

value: Stage IIIA


title: Adjacent non-tumor lung 07L66_N (methylation)

value: nci-edrn

value: D

tag: tissue

tag: gender


title: Adjacent non-tumor lung 07L6_N (methylation)

value: C

value: Male

tag: ethnicity

value: Asian

tag: smoking status

value: Never

value: Yes


title: Adjacent non-tumor lung 07L5_N (methylation)

value: White

value: Stage IB

tag: recurrence

value: No


title: Adjacent non-tumor lung 07L51_N (methylation)

value: I

value: Current

tag: Stage

value: Stage IA


title: Lung adenocarcinoma 07L5_T (methylation)

value: Lung tumor

value: Female

tag: kras mutation status

value: MUT

tag: egfr mutation status

value: WT

tag: lkb1 mutation status


title: Adjacent non-tumor lung 3003_N (methylation)

tag: sample id

value: ttr-data

tag: beadstrip

value: E

value: Normal lung

value: Stage IIA


title: Lung adenocarcinoma 3013_T (methylation)

tag: tissue source

value: G

value: Stage IIIA

tag: kras mutation type

tag: subject


title: Adjacent non-tumor lung 07L32_N (methylation)

value: nci-edrn

tag: bisulfite plate

tag: bisulfite alu

tag: age


title: Lung adenocarcinoma 07L32_T (methylation)

tag: beadchip

value: B

tag: tissue

value: White

tag: pack years


title: Adjacent non-tumor lung 07L28_N (methylation)

tag: gender

tag: ethnicity

tag: smoking status

value: Never

value: No


title: Adjacent non-tumor lung 3021_N (methylation)

value: K

value: Male

value: Current

tag: Stage

value: Stage IB


title: Lung adenocarcinoma 07L51_T (methylation)

value: I

value: Lung tumor

value: Female

value: Stage IA

tag: recurrence

value: Yes

tag: kras mutation status

value: MUT

tag: egfr mutation status


title: Adjacent non-tumor lung 07L38_N (methylation)

tag: sample id

tag: beadstrip

value: F

value: Normal lung

value: Asian


title: Adjacent non-tumor lung 3013_N (methylation)

tag: tissue source

value: ttr-data

value: G

value: Stage IIIA


title: Lung adenocarcinoma 07L25_T (methylation)

value: nci-edrn

value: J

value: White

value: No

value: WT

tag: lkb1 mutation status

tag: kras mutation type

tag: subject


title: Lung adenocarcinoma 07L38_T (methylation)

tag: bisulfite plate

value: I

tag: bisulfite alu

tag: age

value: Never


title: Lung adenocarcinoma 07L28_T (methylation)

tag: beadchip

tag: tissue

value: Lung tumor

value: Female

tag: pack years


title: Adjacent non-tumor lung 07L31_N (methylation)

value: A

tag: gender

tag: ethnicity

tag: smoking status

value: Current

value: Stage IA


title: Lung adenocarcinoma 07L21_T (methylation)

value: D

value: Male

tag: Stage

value: Stage IB

tag: recurrence

tag: kras mutation status

value: MUT


title: Lung adenocarcinoma 07L22_T (methylation)

tag: sample id

tag: beadstrip

value: Asian

tag: egfr mutation status


title: Adjacent non-tumor lung 07L25_N (methylation)

tag: tissue source

value: nci-edrn

value: B

value: Normal lung


title: Lung adenocarcinoma 06L64_T (methylation)

value: K

value: White

value: No

tag: lkb1 mutation status

tag: kras mutation type

tag: subject


title: Lung adenocarcinoma 07L16_T (methylation)

tag: bisulfite plate

value: H

tag: bisulfite alu

tag: age

value: Never

value: WT


title: Lung adenocarcinoma 06L71_T (methylation)

tag: beadchip

value: L

tag: tissue

value: Lung tumor

value: Female

tag: pack years


title: Lung adenocarcinoma 07L31_T (methylation)

tag: gender

tag: ethnicity

tag: smoking status

value: Current

value: Stage IA


title: Adjacent non-tumor lung 06L71_N (methylation)

value: J

tag: Stage

tag: recurrence


title: Lung adenocarcinoma 06L54_T (methylation)

tag: sample id

tag: beadstrip

value: E

value: Male

tag: kras mutation status


title: Adjacent non-tumor lung 06L64_N (methylation)

tag: tissue source

value: nci-edrn

value: I


title: Adjacent non-tumor lung 06L29_N (methylation)

value: Normal lung

value: Asian

value: Stage IB


title: Lung adenocarcinoma 07L19_T (methylation)

value: No

tag: egfr mutation status

value: MUT

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung 07L21_N (methylation)

tag: bisulfite plate

value: D

tag: bisulfite alu

value: White

tag: subject


title: Adjacent non-tumor lung 07L22_N (methylation)

tag: beadchip

tag: age

tag: tissue

value: Never


title: Lung adenocarcinoma 06L20_T (methylation)

value: K

value: Lung tumor

tag: gender

tag: ethnicity

tag: pack years

value: WT


title: Lung adenocarcinoma 06L50_T (methylation)

value: A

value: Female

tag: smoking status

value: Current

tag: Stage

value: Stage IA

tag: recurrence

value: Yes


title: Adjacent non-tumor lung 06L50_N (methylation)

tag: sample id

value: nci-edrn

tag: beadstrip

value: J


title: Lung adenocarcinoma 06L57_T (methylation)

tag: tissue source

value: F

value: Stage IIIA

tag: kras mutation status

tag: egfr mutation status


title: Lung adenocarcinoma 06L3_T (methylation)

tag: bisulfite plate

value: Stage IIA

tag: lkb1 mutation status

tag: kras mutation type


title: Lung adenocarcinoma 06L29_T (methylation)

tag: beadchip

value: G

tag: bisulfite alu

value: Asian

value: Stage IB

value: No

tag: subject


title: Adjacent non-tumor lung 06L57_N (methylation)

value: K

tag: age

tag: tissue

value: Normal lung

tag: gender

value: White


title: Adjacent non-tumor lung 06L54_N (methylation)

value: Male

tag: ethnicity

tag: pack years

tag: smoking status


title: Adjacent non-tumor lung 06L3_N (methylation)

tag: sample id

value: E

value: Female

tag: Stage

tag: recurrence


title: Lung adenocarcinoma 06L46_T (methylation)

tag: tissue source

tag: beadstrip

value: B

value: Lung tumor

value: Current

tag: kras mutation status

value: MUT

value: WT


title: Adjacent non-tumor lung 06L46_N (methylation)

value: nci-edrn

tag: bisulfite plate

value: L

value: Yes


title: Adjacent non-tumor lung 06L20_N (methylation)

value: F


title: Adjacent non-tumor lung 07L19_N (methylation)

value: C

value: Asian

value: Never

value: Stage IB


title: Adjacent non-tumor lung 07L16_N (methylation)

value: K

value: Normal lung

value: White

value: Stage IA

value: No


title: Lung adenocarcinoma 06L11_T (methylation)

value: Lung tumor

value: Female

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung 06L11_N (methylation)

tag: beadchip

value: J

tag: bisulfite alu

value: Current

tag: subject


title: Lung adenocarcinoma 06L14_T (methylation)

value: nci-edrn

tag: age

tag: tissue

tag: gender

value: Stage IIA

value: MUT

value: WT


title: Lung adenocarcinoma 06L10_T (methylation)

value: A

tag: ethnicity

tag: pack years

tag: smoking status


title: Adjacent non-tumor lung 06L14_N (methylation)

tag: sample id

value: H

tag: Stage

tag: recurrence

value: Yes


title: Lung adenocarcinoma 05L9_T (methylation)

tag: tissue source

tag: beadstrip

value: D

tag: kras mutation status


title: Lung adenocarcinoma 05L47_T (methylation)

tag: bisulfite plate

value: Asian

value: Never

tag: egfr mutation status

tag: lkb1 mutation status


title: Adjacent non-tumor lung 05L9_N (methylation)

tag: beadchip

tag: bisulfite alu

value: Normal lung

value: White


title: Lung adenocarcinoma 05L45_T (methylation)

value: G

tag: age

value: Stage IA

value: No

tag: kras mutation type

tag: subject


title: Adjacent non-tumor lung 05L43_N (methylation)

value: J

tag: tissue

tag: gender

value: Female

tag: ethnicity

value: Stage IB


title: Lung adenocarcinoma 05L40_T (methylation)

tag: sample id

value: nci-edrn

value: B

value: Lung tumor

tag: pack years

tag: smoking status


title: Lung adenocarcinoma 05L6_T (methylation)

tag: tissue source

value: F

tag: Stage

tag: recurrence

value: WT

value: MUT


title: Adjacent non-tumor lung 05L40_N (methylation)

tag: bisulfite plate

tag: beadstrip


title: Lung adenocarcinoma 05L7_T (methylation)

value: I

value: Male

value: Yes

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status


title: Lung adenocarcinoma 05L54_T (methylation)

tag: beadchip

value: L

tag: bisulfite alu

tag: age

value: Asian

value: Never


title: Adjacent non-tumor lung 05L45_N (methylation)

tag: tissue

value: Normal lung

value: Stage IA

tag: subject


title: Adjacent non-tumor lung 05L6_N (methylation)

value: C

tag: gender

tag: ethnicity


title: Lung adenocarcinoma 05L49_T (methylation)

tag: sample id

value: Female

tag: pack years

tag: kras mutation type


title: Adjacent non-tumor lung 05L54_N (methylation)

tag: tissue source

tag: smoking status

tag: Stage


title: Lung adenocarcinoma 05L4_T (methylation)

tag: bisulfite plate

tag: beadstrip

value: A

value: Stage IIB

tag: recurrence

value: No


title: Adjacent non-tumor lung 05L4_N (methylation)

value: nci-edrn


title: Lung adenocarcinoma 05L43_T (methylation)

value: H

value: Lung tumor

value: White

value: Current

value: Stage IB

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status


title: Lung adenocarcinoma 05L39_T (methylation)

tag: beadchip

value: E

tag: bisulfite alu

tag: age

value: MUT

value: WT


title: Adjacent non-tumor lung 05L49_N (methylation)

value: I

tag: tissue

tag: gender

value: Asian

value: Never

value: Yes

tag: subject


title: Adjacent non-tumor lung 05L34_N (methylation)

tag: sample id

value: B

value: Normal lung

value: Female

tag: ethnicity

tag: pack years


title: Lung adenocarcinoma 05L34_T (methylation)

tag: tissue source

tag: smoking status

value: No

tag: kras mutation type


title: Adjacent non-tumor lung 05L7_N (methylation)

value: nci-edrn

tag: bisulfite plate

tag: beadstrip

value: F

value: Male

tag: Stage


title: Adjacent non-tumor lung 05L39_N (methylation)

value: G

tag: recurrence


title: Adjacent non-tumor lung 06L10_N (methylation)

value: White

value: Current


title: Adjacent non-tumor lung 05L32_N (methylation)

value: Stage IIA


title: Lung adenocarcinoma 05L27_T (methylation)

value: D

value: Lung tumor

tag: kras mutation status

tag: egfr mutation status

value: MUT

tag: lkb1 mutation status


title: Adjacent non-tumor lung 05L19_N (methylation)

tag: beadchip

value: A

tag: bisulfite alu

tag: age

value: Stage IV


title: Adjacent non-tumor lung 05L47_N (methylation)

value: H

tag: tissue

tag: gender

value: Asian

value: Never

tag: subject


title: Lung adenocarcinoma 05L19_T (methylation)

tag: sample id

value: C

value: Female

tag: ethnicity

tag: pack years

value: Yes

value: WT


title: Adjacent non-tumor lung 05L27_N (methylation)

tag: tissue source

value: nci-edrn

value: K

value: Normal lung

tag: smoking status


title: MCF7 breast cancer cell line - 10nM DAC treated - day 3 [CH3'n profiling]

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

institute: Ghent University

description:
MCF7DAC
DAC treated cell line

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

data_processing: Raw methylated and unmethylated signals are used to recalculate beta values without background subtraction. Probes with a detection p-value equal to or greater than .05 are set to NA. Data handling and processing done in R.

source_name: Breast cancer cell line, DAC treated

growth_protocol: Obtained from ATCC and cultured according to instructions

extract_protocol: Phenol-chloroform extraction

treatment_protocol: 10nM DAC for 72h, renewing the medium every 24h

tag: cell line

value: MCF7 breast cancer cell line

tag: agent

value: DAC

tag: time point

value: day 3


title: MCF7 breast cancer cell line - Untreated [CH3'n profiling]

description:
MCF7
Untreated cell line control

source_name: Breast cancer cell line

treatment_protocol: 1x PBS for 72h

value: Untreated


title: Kasumi-1 leukemia cell line - Untreated - rep2 [CH3'n profiling]

description:
kasumi_rep
Untreated cell line control

source_name: Kasumi-1 leukemia cell line

value: Kasumi-1 leukemia cell line


title: Lung adenocarcinoma 05L13_T (methylation)

tag: bisulfite plate

tag: beadstrip

value: G

value: Lung tumor

value: Male

tag: Stage

value: Stage IB

tag: recurrence

tag: kras mutation status

value: MUT

tag: kras mutation type


title: Adjacent non-tumor lung 05L13_N (methylation)

tag: beadchip

value: L

tag: bisulfite alu

tag: age

tag: tissue

value: Asian

value: Never


title: KG1 leukemia cell line - 10nM DAC treated - day 3 [CH3'n profiling]

description:
KG1DAC
DAC treated cell line

source_name: KG1 leukemia cell line, DAC treated, day 3

value: KG1 leukemia cell line


title: Primary Leukemia - DAC treated - Patient 6347 [CH3'n profiling]

description:
X6347DAC
DAC treated primary leukemia

source_name: Primary leukemia, DAC treated

growth_protocol: Cultured short term in STEMLINE II Medium

tag: general control

value: Primary Leukemia (Patient 6347)


title: Kasumi-1 leukemia cell line - 10nM DAC treated - day 3, rep2 [CH3'n profiling]

description:
DAC10
DAC treated cell line

source_name: Kasumi-1 leukemia cell line, DAC treated


title: Kasumi-1 leukemia cell line - TSA treated [CH3'n profiling]

description:
TSA
TSA treated cell line

source_name: Kasumi-1 leukemia cell line, TSA treated

treatment_protocol: 300nM DAC for 18h, renewing the medium every 24h untill 72h

value: TSA


title: KG1 leukemia cell line - Untreated [CH3'n profiling]

description:
KG1
Untreated cell line control

source_name: KG1 leukemia cell line


title: Kasumi-1 leukemia cell line - ARA-C treated [CH3'n profiling]

description:
ARAC
ARA-C treated cell line

source_name: Kasumi-1 leukemia cell line, ARA-C treated

treatment_protocol: 100nM ARA-C for 72h, renewing the medium every 24h

value: ARA-C


title: Primary Leukemia - Untreated - Patient 6347 [CH3'n profiling]

description:
X6347
Untreated Primary leukemia control

source_name: Primary leukemia


title: Lung adenocarcinoma 05L32_T (methylation)

tag: sample id

value: nci-edrn

tag: gender

tag: ethnicity

value: White

tag: pack years

value: Current

value: Stage IIA

value: Yes

value: WT

tag: egfr mutation status

tag: lkb1 mutation status

tag: subject


title: Kasumi-1 leukemia cell line - 10nM DAC treated - day 3, rep1 [CH3'n profiling]

description:
kasumid3DAC
DAC treated cell line

source_name: Kasumi-1 leukemia cell line, DAC treated, day 3

tag: cell line

value: Kasumi-1 leukemia cell line

tag: agent

value: DAC

tag: time point

value: day 3


title: Adjacent non-tumor lung 05L12_N (methylation)

tag: tissue source

tag: bisulfite plate

tag: beadstrip

value: E

value: Normal lung

value: Male

tag: smoking status

tag: Stage

value: Stage IIIA

tag: recurrence


title: Kasumi-1 leukemia cell line - 10nM DAC treated - day 28 [CH3'n profiling]

description:
kasumid28DAC
DAC treated cell line

source_name: Kasumi-1 leukemia cell line, DAC treated, day 28

value: day 28


title: KG1A leukemia cell line - 10nM DAC treated - day 3 [CH3'n profiling]

description:
KG1ADAC
DAC treated cell line

source_name: KG1A leukemia cell line, DAC treated, day 3

value: KG1A leukemia cell line


title: KG1A leukemia cell line - Untreated [CH3'n profiling]

description:
KG1A
Untreated cell line control

source_name: KG1A leukemia cell line

value: Untreated


title: Kasumi-1 leukemia cell line - 10nM DAC treated - day 21 [CH3'n profiling]

description:
kasumid21DAC
DAC treated cell line

source_name: Kasumi-1 leukemia cell line, DAC treated, day 21

value: day 21


title: Kasumi-1 leukemia cell line - 10nM DAC treated - day 7 [CH3'n profiling]

description:
kasumid7DAC
DAC treated cell line

source_name: Kasumi-1 leukemia cell line, DAC treated, day 7

value: day 7


title: Lung adenocarcinoma 05L12_T (methylation)

source_name: Lung adenocarcinoma

value: nci-edrn

tag: beadchip

value: D

tag: bisulfite alu

tag: age

tag: tissue

value: Lung tumor

value: Asian

value: Never

tag: kras mutation status

value: MUT

tag: kras mutation type


title: Kasumi-1 leukemia cell line - Untreated - rep1 [CH3'n profiling]

description:
kasumi
Untreated cell line control

value: Kasumi-1 leukemia cell line


title: Primary Leukemia - Untreated - Patient 2 [CH3'n profiling]

description:
PL2
Primary leukemia control

tag: general control

value: Primary Leukemia (Patient 2)


title: Primary Leukemia - Untreated - Patient 5 [CH3'n profiling]

description:
PL5
Primary leukemia control

value: Primary Leukemia (Patient 5)


title: Primary Leukemia - Untreated - Patient 4 [CH3'n profiling]

description:
PL4
Primary leukemia control

value: Primary Leukemia (Patient 4)


title: Primary Leukemia - Untreated - Patient 1 [CH3'n profiling]

description:
PL1
Primary leukemia control

value: Primary Leukemia (Patient 1)


title: whole rhesus brain RNA pool_17

city: Seattle

first: Susan

last: Sunkin

address: 551 N. 34th Street

institute: Allen Institute for Brain Science

description:
Gene expression data from whole rhesus brain.
@52031700647947061408403392032075

hyb_protocol: Following fragmentation, 10 ug of cDNA was hybridized for 18 hr at 45C on the GeneChip Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were normalized using Matlab2007b. Each batch was normalized within itself by RMA. Batch effects were subsequently removed by normalizing each probe based on common whole brain control samples across batches. Data is reported as Log10 normalized intensity.

organism: Macaca mulatta

source_name: whole rhesus brain RNA pool (Biochain)

label_protocol: Biotinylated cDNA was prepared using 5ng total RNA input and 2 cycles of the GeneChip HT One-Cylce cDNA Synthesis Kit from Affymetrix.

extract_protocol: RNA was isolated from each brain region following the manufacturer's directions for the RNeasy Micro kit. Whole rhesus brain RNA pool obtained from Biochain.

tag: sample type

value: common RNA pool control sample

value: whole brain


title: whole rhesus brain RNA pool_22

description:
Gene expression data from whole rhesus brain.
@52031700647947061408403392032092


title: whole rhesus brain RNA pool_10

description:
Gene expression data from whole rhesus brain.
@52031700647910061408403391923054


title: whole rhesus brain RNA pool_32

description:
Gene expression data from whole rhesus brain.
@52031700789764081009405808017311


title: whole rhesus brain RNA pool_24

description:
Gene expression data from whole rhesus brain.
@52031700647949061408403392032183


title: whole rhesus brain RNA pool_12

description:
Gene expression data from whole rhesus brain.
@52031700647911061408403391930715


title: whole rhesus brain RNA pool_33

description:
Gene expression data from whole rhesus brain.
@52031700789764081009405808017310


title: whole rhesus brain RNA pool_9

description:
Gene expression data from whole rhesus brain.
@52031700684828061008403361515206


title: whole rhesus brain RNA pool_31

description:
Gene expression data from whole rhesus brain.
@52031700789764081009405808017315


title: whole rhesus brain RNA pool_11

description:
Gene expression data from whole rhesus brain.
@52031700647909061408403391923011


title: whole rhesus brain RNA pool_18

description:
Gene expression data from whole rhesus brain.
@52031700647947061408403392032067


title: whole rhesus brain RNA pool_23

description:
Gene expression data from whole rhesus brain.
@52031700647949061408403392032200


title: whole rhesus brain RNA pool_16

description:
Gene expression data from whole rhesus brain.
@52031700647950061408403392032257


title: whole rhesus brain RNA pool_7

description:
Gene expression data from whole rhesus brain.
@52031700647909061408403391923006


title: whole rhesus brain RNA pool_8

description:
Gene expression data from whole rhesus brain.
@52031700647911061408403391930698


title: Dorsal Lateral Geniculate Nucleus: Koniocellular; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Dorsal_Lateral_Geniculate_Nucleus_Koniocellular

tag: gender

value: Male

value: Dorsal Lateral Geniculate Nucleus

tag: tissue region

value: Koniocellular


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 5;  Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Dorsolateral_Prefrontal_Cortex_Layer 5

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 5;  Male CR5C1

value: Layer 5


title: Hippocampus: CA2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Hippocampus_CA2

source_name: Hippocampus: CA2; Female 99C018

value: Female

value: Hippocampus


title: Orbitofrontal cortex, layer 3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Orbitofrontal_cortex_Layer 3

value: Orbitofrontal cortex

value: Layer 3


title: Hippocampus: CA3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Hippocampus_CA3

source_name: Hippocampus: CA3; Female 99C018


title: V1 (area 17), layer 2; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V1_Layer 2

source_name: V1 (area 17), layer 2; Male CR5C1

value: V1 (area 17)

value: Layer 2


title: Middle temporal area (MT), layer 4; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Medial_Temporal_area_ of_vis_ctx_Layer 4

value: Middle temporal area (MT)

value: Layer 4


title: Dorsal Lateral Geniculate Nucleus: Magnocellular; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Dorsal_Lateral_Geniculate_Nucleus_Magnocellular

value: Magnocellular


title: Middle temporal area (MT), layer 4; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Medial_Temporal_area_ of_vis_ctx_Layer 4


title: V2 (area 18), layer 6; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V2_Layer 6

source_name: V2 (area 18), layer 6; Male CR5C1

value: V2 (area 18)

value: Layer 6


title: V1 (area 17), layer 6; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V1_Layer 6

source_name: V1 (area 17), layer 6; Female 98C096


title: Primary motor cortex, Layer 3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_motor_cortexLayer 3

value: Primary motor cortex


title: V1 (area 17), layer 5; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V1_Layer 5

source_name: V1 (area 17), layer 5; Female 98C096


title: Dorsal Lateral Geniculate Nucleus: Koniocellular; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Dorsal_Lateral_Geniculate_Nucleus_Koniocellular


title: Middle temporal area (MT), layer 3; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Medial_Temporal_area_ of_vis_ctx_Layer 3


title: Dorsal Lateral Geniculate Nucleus: Magnocellular; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Dorsal_Lateral_Geniculate_Nucleus_Magnocellular


title: Middle temporal area (MT), layer 6; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Medial_Temporal_area_ of_vis_ctx_Layer 6


title: V2 (area 18), layer 5; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V2_Layer 5

source_name: V2 (area 18), layer 5; Male CR5C1


title: Orbitofrontal cortex, layer 5; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Orbitofrontal_cortex_Layer 5


title: V1 (area 17), layer 4a; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V1_Layer 4a

source_name: V1 (area 17), layer 4a; Female 99C018

value: Layer 4a


title: V1 (area 17), layer 2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V1_Layer 2

source_name: V1 (area 17), layer 2; Female 98C096


title: Middle temporal area (MT), layer 2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Medial_Temporal_area_ of_vis_ctx_Layer 2


title: V1 (area 17), layer 4ca; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V1_Layer 4ca

source_name: V1 (area 17), layer 4ca; Female 99C018

value: Layer 4ca


title: Primary somatosensory cortex, layer 2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_somatosensory_cortex_Layer 2

value: Primary somatosensory cortex


title: V1 (area 17), layer 4ca; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V1_Layer 4ca

source_name: V1 (area 17), layer 4ca; Female 98C096


title: Primary auditory ctx, layer 6; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_ auditory_ctx_Layer 6

value: Primary auditory ctx


title: V1 (area 17), layer 3; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V1_Layer 3

source_name: V1 (area 17), layer 3; Male CR5C1

value: Male


title: Primary somatosensory cortex, layer 2; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_somatosensory_cortex_Layer 2


title: Anterior cingulate gyrus, layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Anterior_cingulate_gyrusLayer 5

value: Female

value: Anterior cingulate gyrus

value: Layer 5


title: Hippocampus: CA1; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Hippocampus_CA1

source_name: Hippocampus: CA1; Male 018G

value: Hippocampus


title: Orbitofrontal cortex, layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Orbitofrontal_cortex_Layer 3

value: Orbitofrontal cortex

value: Layer 3


title: Primary motor cortex, Layer 3; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_motor_cortexLayer 3


title: Primary auditory ctx, layer 4; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_ auditory_ctx_Layer 4


title: Primary auditory ctx, layer 5; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_ auditory_ctx_Layer 5


title: Primary motor cortex, Layer 6; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_motor_cortexLayer 6


title: V1 (area 17), layer 3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V1_Layer 3

source_name: V1 (area 17), layer 3; Female 98C096

value: V1 (area 17)


title: V1 (area 17), layer 4ca; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V1_Layer 4ca

source_name: V1 (area 17), layer 4ca; Male 018G


title: Temporal area, layer 4; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Temporal_area_Layer 4

source_name: Temporal area, layer 4; Male CR5C1

value: Temporal area

value: Layer 4


title: Anterior cingulate gyrus, layer 2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Anterior_cingulate_gyrusLayer 2

value: Layer 2


title: Anterior cingulate gyrus, layer 2; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Anterior_cingulate_gyrusLayer 2


title: Primary somatosensory cortex, layer 5; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_somatosensory_cortex_Layer 5


title: Primary auditory ctx, layer 2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_ auditory_ctx_Layer 2


title: Primary somatosensory cortex, layer 2; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_somatosensory_cortex_Layer 2


title: Kasumi-1 leukemia cell line - 10nM DAC treated - day 14 [CH3'n profiling]

description:
kasumid14DAC
DAC treated cell line

source_name: Kasumi-1 leukemia cell line, DAC treated, day 14

tag: cell line

value: Kasumi-1 leukemia cell line

tag: agent

value: DAC

tag: time point

value: day 14


title: Primary somatosensory cortex, layer 3; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_somatosensory_cortex_Layer 3


title: V1 (area 17), layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V1_Layer 3

source_name: V1 (area 17), layer 3; Female 99C018


title: Anterior cingulate gyrus, layer 3; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Anterior_cingulate_gyrusLayer 3


title: Primary motor cortex, Layer 6; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_motor_cortexLayer 6

value: Primary motor cortex

value: Layer 6


title: Temporal area, layer 2; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Temporal_area_Layer 2

source_name: Temporal area, layer 2; Male CR5C1


title: V1 (area 17), layer 4a; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V1_Layer 4a

source_name: V1 (area 17), layer 4a; Female 98C096

value: Layer 4a


title: Primary somatosensory cortex, layer 3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_somatosensory_cortex_Layer 3

value: Primary somatosensory cortex


title: Temporal area, layer 2; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Temporal_area_Layer 2

source_name: Temporal area, layer 2; Male 018G

value: Male


title: Primary auditory ctx, layer 6; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_ auditory_ctx_Layer 6

value: Female

value: Primary auditory ctx


title: Temporal area, layer 3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Temporal_area_Layer 3

source_name: Temporal area, layer 3; Female 98C096


title: Primary somatosensory cortex, layer 4; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_somatosensory_cortex_Layer 4


title: Primary somatosensory cortex, layer 4; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_somatosensory_cortex_Layer 4


title: Primary somatosensory cortex, layer 5; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_somatosensory_cortex_Layer 5

value: Layer 5


title: Primary somatosensory cortex, layer 4; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_somatosensory_cortex_Layer 4


title: Primary motor cortex, Layer 3; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_motor_cortexLayer 3


title: Anterior cingulate gyrus, layer 2; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Anterior_cingulate_gyrusLayer 2

value: Anterior cingulate gyrus


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Dorsolateral_Prefrontal_Cortex_Layer 3

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 3; Female 98C096

value: Layer 3


title: Primary motor cortex, Layer 5; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_motor_cortexLayer 5


title: Primary motor cortex, Layer 2; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_motor_cortexLayer 2


title: Primary motor cortex, Layer 2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_motor_cortexLayer 2


title: Orbitofrontal cortex, layer 2;  Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Orbitofrontal_cortex_Layer 2

value: Orbitofrontal cortex


title: V1 (area 17), layer 4cb; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V1_Layer 4cb

source_name: V1 (area 17), layer 4cb; Male 018G

value: V1 (area 17)

value: Layer 4cb


title: Primary auditory ctx, layer 4; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_ auditory_ctx_Layer 4

value: Layer 4


title: Temporal area, layer 2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Temporal_area_Layer 2

source_name: Temporal area, layer 2; Female 99C018

value: Temporal area

value: Layer 2


title: Orbitofrontal cortex, layer 5;  Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Orbitofrontal_cortex_Layer 5


title: Primary motor cortex, Layer 6; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_motor_cortexLayer 6


title: Primary motor cortex, Layer 2; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_motor_cortexLayer 2


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 6; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Dorsolateral_Prefrontal_Cortex_Layer 6

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 6; Female 98C096


title: Primary auditory ctx, layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_ auditory_ctx_Layer 5


title: Middle temporal area (MT), layer 6; Female 99C039

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C039_Medial_Temporal_area_ of_vis_ctx_Layer 6

value: Middle temporal area (MT)


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 4; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Dorsolateral_Prefrontal_Cortex_Layer 4

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 4; Male 01D150


title: Temporal area, layer 3; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Temporal_area_Layer 3

source_name: Temporal area, layer 3; Male 018G


title: V2 (area 18), layer 6; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V2_Layer 6

source_name: V2 (area 18), layer 6; Male 018G

value: V2 (area 18)


title: Primary somatosensory cortex, layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_somatosensory_cortex_Layer 5


title: Primary auditory ctx, layer 2; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_ auditory_ctx_Layer 2


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 3; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Dorsolateral_Prefrontal_Cortex_Layer 3

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 3; Male 01D150


title: Anterior cingulate gyrus, layer 6; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Anterior_cingulate_gyrusLayer 6

value: Layer 6


title: Primary motor cortex, Layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_motor_cortexLayer 3

value: Primary motor cortex


title: Anterior cingulate gyrus, layer 5; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Anterior_cingulate_gyrusLayer 5


title: Temporal area, layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Temporal_area_Layer 5

source_name: Temporal area, layer 5; Female 99C018


title: V1 (area 17), layer 4b; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V1_Layer 4b

source_name: V1 (area 17), layer 4b; Male CR5C1

value: Layer 4b


title: V1 (area 17), layer 2; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V1_Layer 2

source_name: V1 (area 17), layer 2; Male 018G

value: Male


title: Orbitofrontal cortex, layer 3; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Orbitofrontal_cortex_Layer 3


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 3;  Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Dorsolateral_Prefrontal_Cortex_Layer 3

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 3;  Male CR5C1


title: V1 (area 17), layer 6; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V1_Layer 6

source_name: V1 (area 17), layer 6; Male CR5C1


title: V1 (area 17), layer 6; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V1_Layer 6

source_name: V1 (area 17), layer 6; Female 99C018

value: Female


title: Temporal area, layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Temporal_area_Layer 3

source_name: Temporal area, layer 3; Female 99C018


title: Primary motor cortex, Layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_motor_cortexLayer 5


title: Temporal area, layer 6; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Temporal_area_Layer 6

source_name: Temporal area, layer 6; Male CR5C1


title: V1 (area 17), layer 4a; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V1_Layer 4a

source_name: V1 (area 17), layer 4a; Male 018G

value: Layer 4a