title: A.thaliana 35S:GFP (Col) vs  35S:IYO-GFP (Col-0) Rep 4

city: MADRID

first: MAITE

last: SANMARTIN

address: CALLE DARWIN 3

institute: CNB-CSIC

description: Biological replicate 4 of 4. Gene expression of 35S:IYO-GFP (Col-0) vs 35S:GFP (Col-0)

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

source_name: shoot apices from 35S:GFP

label_protocol: 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5  and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Arabidopsis seeds were vernalized for two days in soil and transferred to a growth chamber for 22 days under a photoperiod of 14h light/10h dark with a temperature range 20ºC/22ºC. Shoot apices were separated and immediately frozen in liquid nitrogen.

extract_protocol: The frozen plant tissue (~100 mg) was ground in tiny mortars dipped in liquid nitrogen. The frozen powder was carefully transfered into 1.5 ml microcentrifuge tubes using small funnels and rubber spatulas also cooled with liquid nitrogen. Total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with an RNeasy mini kit (Qiagen, 74104).1 ug of total RNA was amplified via the aRNA MessageAmp II kit (Ambion, 1751)

treatment_protocol: Shoot apices of 35S:IYO-GFP compared to shoot apices of 35S:GFP plants

tag: ecotype

value: Columbia

tag: transgenic line

value: shoot apices

source_name: shoot apices from 35S:IYO-GFP


title: 20051221_07_05-206_NP

status: Public on Jul 09 2011

type: RNA

city: Seattle

first: Alvin

middle: Y

last: Liu

state: WA

address: 815 Mercer Street Box 358056

department: Urology

country: USA

institute: University of Washington

description: bulk tissue

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Normal prostate tissue

label_protocol: GeneChip® One-Cycle Target Labeling Kit

growth_protocol: Cells were isolated after overnight tissue digestion with collagenase in serum-free RPMI1640 media.

extract_protocol: Sorted cell populations were lysed in RLT buffer for RNA isolation.

treatment_protocol: Cells were labeled with dye conjugated-antiCD monoclonal antibodies and sorted by MACS

tag: tissue/origin

value: normal prostate

tag: cell type

value: Normal prostate tissue


title: 20061218_02_06-125_NB_CD13posi

description: CD13+ stromal cells

source_name: Normal bladder stromal cells

label_protocol: GeneChip® Two-Cycle Target Labeling Kit

value: normal urinary bladder

value: Normal bladder stromal cells


title: 20070619_05_07-015_NB_epi_CD9posi

description: CD9+ urothelial cells

source_name: Normal bladder urothelial cells

value: Normal bladder urothelial cells


title: VvCBF4 overexpressor, biological rep1

city: Reno

first: Richard

middle: Leonard

last: Tillett

state: NV

address: University of Nevada Reno Mailstop 330

department: Department of Biochemistry & Molecular Biology

institute: University of Nevada Reno

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 h at 45C on Affymetrix GeneChip® 16K Vitis vinifera (Grape) Genome Arrays ver. 1.0. GeneChips were washed and stained in the Affymetrix® 3000 7G Scanner, Hybridization, and Fluidics System.

scan_protocol: GeneChips were scanned using the Affymetrix® 3000 7G Scanner, Hybridization, and Fluidics System.

data_processing: Raw hybridization intensity values were processed by Robust Multi-Array Average (RMA), using the R package affy. Specifically, expression values were extracted from raw CEL files by first applying the RMA model of probe-specific correction to PM (perfect match) probes. Corrected probe values were then normalized via quantile normalization, and a median value computed for the PM probeset. Resulting RMA expression values were log2-transformed.

organism: Vitis vinifera

source_name: 35S::VvCBF4 overexpressor '9-12'

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 µg total RNA (Affymetrix GeneChip Expression Analysis Technical Manual, 2009).

growth_protocol: Vines were clonally propagated in sterile Magenta GA-7 boxes and transferred to soil. Specifically, green cuttings (2-3 internodes) were rooted in boxes containing 80 ml of 0.8% (w/v) Plant Tissue Culture Agar (#A111, Phytotechnology Laboratories, Shawnee Mission, KS) with Murashige and Skoog modified Basal Medium w/ Gamborg Vitamins (#M404, Phytotechnology Laboratories), 1.5% sucrose, pH 5.6-5.7 and 300 mM Indoleacetic Acid (IAA) for 14 days. Rooted cuttings were transferred to media lacking IAA for 10 further days. Lastly, the young vines were transferred to soil and grown for 14 days in a Percival Scientific growth chamber (model# AR75L).

extract_protocol: Total RNA was extracted using RNeasy Midi column (Qiagen, Inc., Valencia, CA) with 2% Polyethylene Glycol (PEG, mw = 20,000, Sigma Aldrich, Inc., St. Louis, MO) added to the RLT buffer, on-column DNase digestion, phenol:chloroform:isoamyl-alcohol (25:24:1) extraction and final clean-up on RNeasy Mini column (Qiagen) with 2% PEG (Tattersall et al., 2005).

treatment_protocol: Grapevines of the Vitis hybrid rootstock cv. ‘Freedom’ were transformed with a 35S::VvCBF4 construct or an empty vector control. Clones of the regenerated plantlets (grown as above) were collected under well-watered conditions.

tag: cultivar

value: Freedom

tag: tissue

value: whole aerial tissues (stem + 5 leaves)

tag: genotype

value: 35S::VvCBF4 overexpressor '9-12'

tag: age

value: young cuttings


title: A.thaliana 35S:GFP (Col) vs  35S:IYO-GFP (Col-0) Rep 3

country: Spain

description: Biological replicate 3 of 4. Gene expression of 35S:IYO-GFP (Col-0) vs 35S:GFP (Col-0)

organism: Arabidopsis thaliana


title: Wt edt_25

status: Public on Jul 08 2011

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Labelled RNA samples were hybridised onto Affymetrix GeneChip Mouse Genome 430 2.0 Arrays according to the AGRFs protocol. Samples were prepared for hybridisation to the GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that included 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul was prepared for each sample and 200ul loaded into a GeneChip.  The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip was washed and stained with SAPE using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using a GeneChip scanner 3000 with the scanner operating software, GCOS.

data_processing: Expression data were pre-processed and normalized using the gcRMA algorithm (Bioconductor package gcrma).

organism: Mus musculus

source_name: Dorsal telencephalon

label_protocol: RNA was processed according to the Australian Genome Research Facility (AGRF) protocol using the Two-Cycle Target cDNA synthesis kit (Millenium Sciences cat no. 900432), GeneChip Eukaryotic poly-A RNA spikes (Millenium Sciences cat no. 900433), Affymetrix GeneChip Sample CLeanup kit (Millenium Sciences cat no. 900371) and Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted by preferentially precipitating RNA from an aqueous guanidine hydrochloride solution using the method described by Chirgwin et. al., 1979 (Biochemistry 18:5294-5299)

tag: strain

tag: gender

tag: genotype/variation

value: wild type

tag: developmental stage

value: embryo

tag: age (days)

value: Dorsal telencephalon

tag: mouse number


title: Qkf edt_30

value: Qkf gt/gt mutant


title: A.thaliana 35S:GFP (Col) vs  35S:IYO-GFP (Col-0) Rep 2

description: Biological replicate 2 of 4. Gene expression of 35S:IYO-GFP (Col-0) vs 35S:GFP (Col-0)


title: Wt adult dc_13

source_name: Dorsal cerebral cortex

value: Male

value: adult

value: Dorsal cerebral cortex


title: Qkf edt_26r


title: Wt edt_29


title: A.thaliana 35S:GFP (Col) vs  35S:IYO-GFP (Col-0) Rep 1

description: Biological replicate 1 of 4. Gene expression of 35S:IYO-GFP (Col-0) vs 35S:GFP (Col-0)

value: Columbia

value: shoot apices


title: Wt edt_28


title: Qkf edt_27


title: Wt adult dc_2


title: Qkf adult dc_14


title: PBMC4

city: New York

first: Erin

middle: L.

last: Heinzen

state: NY

department: Institute for Genomic Medicine

institute: Columbia University

description:
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps and HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

hyb_protocol: A hybridization cocktail was prepared, including the fragmented target, and probe array controls (Affymetrix). It then was hybridized to the probe array  during a 16-hour incubation.  Immediately following hybridization, the probe array underwent anautomated washing and staining protocol on the fluidics station.

scan_protocol: Samples were scanned using an Affymetrix Gene ChIP Scanner 3000

data_processing: Expression values are calculated based on the difference of the PM signal and MM signal at each of the probe pairs using the Affymetrix GeneChip Operating System (GCOS).  Expression data then was processed in Affymetrix Expression Console using the PLIER protocol with a sketch-quantile normalization procedure.

source_name: peripheral blood mononucleated cells collected from healthy controls

label_protocol: Samples were fragmented and biotinylated using the Affymetrix WT Terminal Labeling Kit.

extract_protocol: RNA from frozen brain tissue specimen or PBMCs was extracting using RNeasy kit (Qiagen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

value: female

tag: postmortem interval (brain specimens only)

tag: site of specimen collection

tag: position along eigenstrat axis 1 (ethnicity correction)

tag: position along eigenstrat axis 2 (ethnicity correction)

tag: position along eigenstrat axis 3 (ethnicity correction)


title: PBMC9

value: male


title: Qkf adult dc_3


title: Wt adult dc_1


title: Qkf adult dc_4


title: PBMC46


title: PBMC5


title: PBMC42


title: PBMC41


title: PBMC8


title: PBMC6


title: PBMC39


title: PBMC47


title: PBMC43


title: PBMC48


title: PBMC38


title: PBMC7


title: PBMC27


title: PBMC29


title: PBMC45


title: PBMC3


title: PBMC33


title: PBMC31


title: PBMC30


title: PBMC24


title: PBMC44


title: PBMC26


title: PBMC32


title: PBMC25


title: PBMC37


title: PBMC22


title: PBMC2


title: PBMC23


title: PBMC20


title: PBMC18


title: PBMC16


title: PBMC17


title: PBMC13


title: PBMC12


title: PBMC19


title: PBMC14


title: PBMC78


title: PBMC79


title: PBMC80


title: PBMC11


title: PBMC70


title: PBMC10


title: PBMC77


title: PBMC15


title: PBMC67


title: PBMC64


title: PBMC65


title: PBMC71


title: PBMC68


title: PBMC75


title: PBMC73


title: PBMC1


title: PBMC72


title: PBMC61


title: PBMC66


title: PBMC62


title: PBMC55


title: PBMC59


title: PBMC54


title: PBMC69


title: PBMC60


title: PBMC56


title: PBMC40


title: PBMC53


title: PBMC51


title: PBMC52


title: PBMC57


title: PBMC58


title: PBMC34


title: PBMC36


title: PBMC50


title: PBMC63


title: BRAIN90

source_name: autopsy collected cortical brain tissue specimen


title: PBMC49


title: PBMC35


title: BRAIN91


title: BRAIN93


title: BRAIN89


title: PBMC74


title: BRAIN87


title: PBMC28


title: BRAIN85


title: BRAIN92


title: BRAIN82


title: PBMC76


title: BRAIN80


title: BRAIN88


title: BRAIN83


title: PBMC21


title: BRAIN86


title: BRAIN75


title: BRAIN73


title: BRAIN68


title: BRAIN78


title: BRAIN79


title: BRAIN74


title: BRAIN84


title: BRAIN71


title: BRAIN63


title: BRAIN66


title: BRAIN69


title: BRAIN77


title: BRAIN65


title: BRAIN70


title: BRAIN55


title: BRAIN62


title: BRAIN57


title: BRAIN58


title: BRAIN59


title: BRAIN54


title: BRAIN61


title: BRAIN50


title: BRAIN52


title: BRAIN51


title: BRAIN53


title: BRAIN72


title: BRAIN60


title: BRAIN45


title: BRAIN48


title: BRAIN44


title: BRAIN46


title: BRAIN43


title: BRAIN47


title: BRAIN39


title: BRAIN76


title: BRAIN49


title: BRAIN81


title: BRAIN40


title: BRAIN38


title: BRAIN64


title: BRAIN34


title: BRAIN41


title: BRAIN33


title: BRAIN35


title: BRAIN32


title: BRAIN42


title: BRAIN37


title: BRAIN27


title: BRAIN36


title: BRAIN25


title: BRAIN28


title: BRAIN29


title: BRAIN30


title: BRAIN31


title: BRAIN26


title: BRAIN24


title: BRAIN20


title: BRAIN22


title: BRAIN17


title: BRAIN16


title: BRAIN56


title: PBMC9


title: BRAIN23


title: BRAIN14


title: BRAIN13


title: BRAIN11


title: PBMC8


title: BRAIN12


title: BRAIN9


title: BRAIN15


title: BRAIN8


title: BRAIN18


title: BRAIN21


title: BRAIN67


title: BRAIN19


title: PBMC7


title: PBMC48


title: PBMC6


title: PBMC46


title: PBMC47


title: PBMC45


title: BRAIN4


title: BRAIN2


title: BCmicroRNA 210

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Breast Cancer

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Local background subtraction (BeadStudio version 3.2.7) and quantile normalization (www.bioconductor.org, Bio/C version 2.4).

source_name: breast

label_protocol: Manufacturer’s instructions

extract_protocol: Total RNA was isolated by Trizol method (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions

value: Breast Cancer

tag: patient age

tag: tumour size

tag: nodes involved

tag: er status

tag: tumour grade

tag: distant-relapse event

tag: distant-relapse free survival


title: BCmicroRNA 209

description: Breast Cancer

tag: tissue


title: BCmicroRNA 207

description: Breast Cancer


title: BRAIN6

tag: gender

tag: age


title: BRAIN3


title: BRAIN10


title: BRAIN7


title: BCmicroRNA 205

description: Breast Cancer


title: BCmicroRNA 206

description: Breast Cancer


title: BCmicroRNA 202

description: Breast Cancer


title: BCmicroRNA 201

description: Breast Cancer


title: PBMC44


title: BCmicroRNA 204

description: Breast Cancer


title: PBMC43


title: PBMC39


title: PBMC38


title: PBMC41


title: PBMC33


title: PBMC4


title: BCmicroRNA 198

description: Breast Cancer


title: BCmicroRNA 199

description: Breast Cancer


title: BCmicroRNA 208

description: Breast Cancer


title: PBMC37


title: PBMC32


title: PBMC42


title: BRAIN5


title: BCmicroRNA 203

description: Breast Cancer


title: Treated_2b

city: Barcelona

first: Sergi

middle: Pelayo

last: Martinez

state: Barcelona

address: Jordi Girona n.18

department: IDAEA

institute: CSIC

description:
Gene expression after 72hr in 50nM T3
T2B-M

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 55 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 Agilent-015064 D. rerio (Zebrafish) Oligo Microarray 4x44K G2519F (Platform GPL7302)  for 17 hours at 65Â°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 37Â°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 (G2505BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, 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_95 and Grid: 019161_D_F_20080131) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Danio rerio

source_name: Treated Embryo Sample 2B (Treated Embryo sample 2 Replicate)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: Zebrafish embryos were obtained by natural mating and raised at 28.5ºC with 12l:12D photoperiode in embryo water [90mg/l of instant ocean (aquarium systems, sorreburg,France), 0,58 CaSO4·2H2O, dissolved in reverse osmosis purified water].

extract_protocol: Total RNA was isolated from 100 embryos per replicate using Trizol reagent protocol (Invitrogen. Rna concentration was measured by spectrophotometric absorption at 260nm in nanodrop ND-800 (nanodrop technologies, Wilmington, DE) and their quality checked by Agilent 2100 bioanalyzer (agilent technologies, Santa Clara CA).

treatment_protocol: Three treated embryo replicates and three control replicates with 100 newwly-hatched larvae (48 hpf) were exposed for 72h in a 100ml glass. Treated solutions were prepared with 50nM of 3.3',5-triiodo-L-throixine (T3) dissoved in DMSO and the control solutions were prepared with the same final concentration of DMSO (0,1%) and directly prepared in embryo water. All the solutions were prepared on the same day of the experiment.

tag: agent

value: 50nM thyroid hormone

tag: development stage

value: 5 dpf's embryo


title: BRAIN1

tag: postmortem interval (brain specimens only)


title: Treated_2

description:
Gene expression after 72hr in 50nM T3
T2-M

source_name: Treated Embryo Sample 2


title: Treated_3

description:
Gene expression after 72hr in 50nM T3
T3

source_name: Treated Embryo Sample 4


title: BCmicroRNA 200

description: Breast Cancer


title: PBMC30

tag: site of specimen collection


title: BCmicroRNA 196

description: Breast Cancer


title: BCmicroRNA 197

description: Breast Cancer


title: BCmicroRNA 194

description: Breast Cancer


title: BCmicroRNA 195

description: Breast Cancer


title: BCmicroRNA 192

description: Breast Cancer


title: PRC3

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description: 786-0: vector control, grown under standard conditions, triplicate #3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v3 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: human established renal cancer cells 786-0: vector control, grown under standard conditions.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA using MessageAmp™ II aRNA Kit from Ambion

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

tag: cell line

tag: cell type

value: renal cancer

tag: genotype/variation

value: transfected with vector control


title: WHT1

description: RCC4: Grown under standard conditions, triplicate #1

source_name: human established renal cancer cells RCC4: transfected with the wild-type VHL gene.

value: transfected with the wild-type VHL gene


title: RCC2

description: RCC4: vector control grown under standard conditions, triplicate #2

source_name: human established renal cancer cells RCC4: vector control, grown under standard conditions.


title: RCC1

description: RCC4: vector control grown under standard conditions, triplicate #1


title: RCC3

description: RCC4: vector control grown under standard conditions, triplicate #3


title: PRC1

description: 786-0: vector control, grown under standard conditions, triplicate #1


title: WHT3

description: RCC4: Grown under standard conditions, triplicate #3


title: WHT2

description: RCC4: Grown under standard conditions, triplicate #2


title: PRC2

description: 786-0: vector control, grown under standard conditions, triplicate #2


title: PBMC31

tag: position along eigenstrat axis 1 (ethnicity correction)

tag: position along eigenstrat axis 2 (ethnicity correction)

tag: position along eigenstrat axis 3 (ethnicity correction)


title: 0WT3

description: 786-0: transfected with the wild-type VHL gene, triplicate #3

source_name: human established renal cancer cell line 786-0: transfected with the wild-type VHL gene.


title: PBMC5


title: 0WT2

description: 786-0: transfected with the wild-type VHL gene, triplicate #2


title: Ctrl_2B

description:
Gene expression after 72hr
C2B-M

source_name: Control Sample 2B (Control 2 replicate)


title: PBMC29


title: Ctrl_1

description:
Gene expression after 72hr
C1-M

source_name: Control Sample 1


title: PBMC3


title: Treated_1

description:
Gene expression after 72hr in 50nM T3
T1-M

source_name: Treated Embryo Sample 1


title: Ctrl_2

description:
Gene expression after 72hr
C2-M

source_name: Control Sample 2


title: BCmicroRNA 193

description: Breast Cancer

tag: patient age

tag: tumour size

tag: nodes involved

tag: er status


title: PBMC27


title: 0WT1

description: 786-0: transfected with the wild-type VHL gene, triplicate #1


title: BCmicroRNA 191

description: Breast Cancer

tag: tissue

tag: tumour grade

tag: distant-relapse event

tag: distant-relapse free survival


title: Ctrl_3

description:
Gene expression after 72hr
C3-M

source_name: Control Sample 3

tag: agent

tag: development stage


title: BCmicroRNA 190

description: Breast Cancer


title: PBMC24

description:
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps and HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

tag: gender

tag: age

tag: postmortem interval (brain specimens only)

tag: site of specimen collection


title: PBMC25

tag: position along eigenstrat axis 1 (ethnicity correction)


title: PBMC23

tag: position along eigenstrat axis 2 (ethnicity correction)


title: PBMC26

tag: position along eigenstrat axis 3 (ethnicity correction)


title: UMR1

description: UMRC2: vector control, grown under standard conditions, triplicate #1

source_name: human established renal cancer cells UMRC2: vector control, grown under standard conditions.

tag: cell line

tag: cell type

tag: genotype/variation


title: UMR2

description: UMRC2: vector control, grown under standard conditions, triplicate #2


title: VHL2

description: UMRC2: transfected with the wild-type VHL gene, triplicate #2

source_name: human established renal cancer cells UMRC2: transfected with the wild-type VHL gene.


title: BCmicroRNA 188

description: Breast Cancer

tag: patient age

tag: tumour size

tag: nodes involved

tag: er status


title: BCmicroRNA 189

description: Breast Cancer

tag: tissue

tag: tumour grade

tag: distant-relapse event

tag: distant-relapse free survival


title: VHL1

description: UMRC2: transfected with the wild-type VHL gene, triplicate #1


title: BCmicroRNA 186

description: Breast Cancer


title: BCmicroRNA 185

description: Breast Cancer


title: VHL3

description: UMRC2: transfected with the wild-type VHL gene, triplicate #3


title: BCmicroRNA 187

description: Breast Cancer


title: BCmicroRNA 184

description: Breast Cancer


title: BCmicroRNA 183

description: Breast Cancer


title: UMR3

description: UMRC2: vector control, grown under standard conditions, triplicate #3


title: PBMC20

source_name: peripheral blood mononucleated cells collected from healthy controls

tag: gender

tag: age


title: PBMC2

tag: postmortem interval (brain specimens only)

tag: site of specimen collection


title: PBMC19

tag: position along eigenstrat axis 1 (ethnicity correction)

tag: position along eigenstrat axis 2 (ethnicity correction)


title: BCmicroRNA 182

description: Breast Cancer


title: Day 8 glp-1 ash-2 #1

city: Palo Alto

first: Eric

middle: Lieberman

last: Greer

address: Alway M314 300 Pasteur Drive

department: Genetics

institute: Stanford University

hyb_protocol: Affymetrix protocol was followed by Stanford Protein and Nucleic Acid facility

scan_protocol: Again scanning was performed according to affymetrix protocol by Stanford Protein and Nucleic Acid facility

data_processing: Background adjustment and normalization was performed with RMA (Robust Multiarray Analysis) in R

organism: Caenorhabditis elegans

source_name: whole worm Day 8 lysates

label_protocol: Labeling was performed at the Stanford Protein and Nucleic Acid facility using biotin

growth_protocol: Worms were grown at 20 degrees

extract_protocol: RNAqueous kit (Ambion) was used

treatment_protocol: Worms were washed several times with M9 buffer prior to extraction

value: Day 8

value: glp-1(e2141ts) mutant

tag: treatment

value: ash-2 RNAi


title: PBMC21

tag: position along eigenstrat axis 3 (ethnicity correction)


title: PBMC22


title: Day 8 glp-1 E.V. #2

tag: genotype/variation

value: empty vector (EV)


title: Day 8 glp-1 ash-2 #2


title: Day 8 glp-1 E.V. #3


title: Day 8 glp-1 ash-2 #3


title: PBMC18


title: PBMC16


title: PBMC17


title: Day 8 N2 (WT) ash-2 #3

value: WT


title: BCmicroRNA 181

description: Breast Cancer

source_name: breast

tag: patient age


title: Day 8 N2 (WT) ash-2 #2


title: Day 8 N2 (WT) ash-2 #1


title: BCmicroRNA 180

description: Breast Cancer

tag: tumour size


title: PBMC15


title: Day 8 glp-1 E.V. #1


title: Day 8 N2 (WT) E.V. #1


title: PBMC14


title: BCmicroRNA 179

description: Breast Cancer

tag: nodes involved


title: BCmicroRNA 178

description: Breast Cancer

tag: er status


title: PBMC13


title: BCmicroRNA 177

description: Breast Cancer

tag: tissue


title: BCmicroRNA 176

description: Breast Cancer

tag: tumour grade


title: L3 glp-1 E.V. #3

source_name: whole worm L3 lysates


title: L3 glp-1 ash-2 #3


title: BCmicroRNA 175

description: Breast Cancer

tag: distant-relapse event


title: PBMC11


title: L3 glp-1 ash-2 #2


title: L3 glp-1 E.V. #1


title: BCmicroRNA 174

description: Breast Cancer

tag: distant-relapse free survival


title: L3 N2 (WT) ash-2 #2


title: Day 8 N2 (WT) E.V. #2


title: L3 glp-1 E.V. #2


title: PBMC12

tag: gender


title: L3 N2 (WT) E.V. #2

tag: age


title: BCmicroRNA 173

description: Breast Cancer


title: PBMC80

tag: postmortem interval (brain specimens only)


title: L3 N2 (WT) E.V. #3


title: PBMC1

tag: site of specimen collection


title: L3 N2 (WT) E.V. #1


title: L3 N2 (WT) ash-2 #3


title: PBMC79

tag: position along eigenstrat axis 1 (ethnicity correction)


title: BCmRNA 214

description: Breast Cancer


title: L3 N2 (WT) ash-2 #1


title: PBMC10

tag: position along eigenstrat axis 2 (ethnicity correction)


title: BCmicroRNA 172

description: Breast Cancer


title: L3 glp-1 ash-2 #1

tag: treatment


title: PBMC78

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BCmicroRNA 171

description: Breast Cancer


title: BCmRNA 213

description: Breast Cancer


title: BCmRNA 211

description: Breast Cancer


title: BCmRNA 212

description: Breast Cancer


title: BCmRNA 215

description: Breast Cancer


title: BCmicroRNA 170

description: Breast Cancer


title: PBMC77


title: BCmRNA 216

description: Breast Cancer


title: BCmicroRNA 169

description: Breast Cancer


title: BCmicroRNA 168

description: Breast Cancer


title: BCmRNA 208

description: Breast Cancer


title: BCmRNA 210

description: Breast Cancer


title: BCmRNA 209

description: Breast Cancer


title: BCmRNA 207

description: Breast Cancer


title: BCmicroRNA 167

description: Breast Cancer


title: BCmRNA 205

description: Breast Cancer


title: PBMC76


title: PBMC75


title: PBMC74


title: BCmRNA 203

description: Breast Cancer


title: BCmicroRNA 164

description: Breast Cancer


title: BCmicroRNA 166

description: Breast Cancer


title: BCmRNA 204

description: Breast Cancer


title: BCmicroRNA 165

description: Breast Cancer


title: BCmRNA 200

description: Breast Cancer


title: BCmRNA 202

description: Breast Cancer


title: BCmRNA 206

description: Breast Cancer


title: PBMC72


title: PBMC71


title: PBMC73


title: BCmRNA 199

description: Breast Cancer


title: BCmRNA 201

description: Breast Cancer


title: BCmRNA 195

description: Breast Cancer


title: BCmicroRNA 162

description: Breast Cancer


title: BCmRNA 198

description: Breast Cancer


title: BCmRNA 197

description: Breast Cancer


title: BCmRNA 191

description: Breast Cancer


title: PBMC70


title: BCmRNA 192

description: Breast Cancer


title: BCmRNA 196

description: Breast Cancer


title: BCmicroRNA 161

description: Breast Cancer


title: BCmRNA 194

description: Breast Cancer


title: BCmicroRNA 163

description: Breast Cancer


title: PBMC67


title: BCmRNA 190

description: Breast Cancer


title: PBMC69


title: BCmRNA 193

description: Breast Cancer


title: PBMC68


title: PBMC65


title: BCmRNA 187

description: Breast Cancer


title: BCmRNA 188

description: Breast Cancer


title: BCmicroRNA 158

description: Breast Cancer


title: BCmicroRNA 157

description: Breast Cancer


title: BCmicroRNA 160

description: Breast Cancer


title: BCmRNA 189

description: Breast Cancer


title: PBMC66


title: BCmRNA 185

description: Breast Cancer


title: BCmicroRNA 156

description: Breast Cancer


title: BCmicroRNA 159

description: Breast Cancer


title: BCmRNA 186

description: Breast Cancer


title: BCmicroRNA 155

description: Breast Cancer


title: BCmRNA 183

description: Breast Cancer


title: BCmRNA 184

description: Breast Cancer


title: PBMC61


title: BCmRNA 181

description: Breast Cancer


title: BCmicroRNA 153

description: Breast Cancer


title: BCmicroRNA 154

description: Breast Cancer


title: PBMC62


title: PBMC63


title: PBMC64


title: BCmRNA 179

description: Breast Cancer


title: BCmicroRNA 152

description: Breast Cancer


title: BCmRNA 180

description: Breast Cancer


title: PBMC60


title: BCmRNA 182

description: Breast Cancer


title: PBMC58


title: BCmicroRNA 151

description: Breast Cancer


title: PBMC59


title: BCmRNA 175

description: Breast Cancer


title: PBMC57


title: BCmRNA 174

description: Breast Cancer


title: BCmRNA 170

description: Breast Cancer


title: BCmRNA 172

description: Breast Cancer


title: BCmRNA 169

description: Breast Cancer


title: BCmRNA 168

description: Breast Cancer


title: BCmRNA 178

description: Breast Cancer


title: BCmRNA 176

description: Breast Cancer


title: BCmRNA 177

description: Breast Cancer


title: BCmRNA 171

description: Breast Cancer


title: BCmRNA 173

description: Breast Cancer


title: PBMC56


title: BCmicroRNA 148

description: Breast Cancer


title: BCmicroRNA 149

description: Breast Cancer


title: BCmRNA 165

description: Breast Cancer


title: BCmicroRNA 147

description: Breast Cancer


title: BCmicroRNA 146

description: Breast Cancer


title: BCmicroRNA 150

description: Breast Cancer


title: BCmRNA 164

description: Breast Cancer


title: BCmRNA 162

description: Breast Cancer


title: PBMC51


title: BCmRNA 167

description: Breast Cancer


title: BCmicroRNA 144

description: Breast Cancer


title: PBMC53


title: PBMC54


title: BCmRNA 161

description: Breast Cancer


title: BCmRNA 158

description: Breast Cancer


title: BCmicroRNA 145

description: Breast Cancer


title: PBMC55


title: PBMC52


title: BCmRNA 154

description: Breast Cancer


title: BCmRNA 155

description: Breast Cancer


title: BCmRNA 160

description: Breast Cancer


title: BCmRNA 152

description: Breast Cancer


title: BCmRNA 156

description: Breast Cancer


title: BCmRNA 157

description: Breast Cancer


title: BCmicroRNA 143

description: Breast Cancer


title: BCmicroRNA 142

description: Breast Cancer


title: PBMC50


title: PBMC49


title: BCmicroRNA 141

description: Breast Cancer


title: BCmRNA 159

description: Breast Cancer


title: PBMC40


title: BCmRNA 166

description: Breast Cancer


title: BCmicroRNA 140

description: Breast Cancer


title: PBMC35


title: BCmRNA 149

description: Breast Cancer


title: BCmicroRNA 139

description: Breast Cancer


title: BCmicroRNA 138

description: Breast Cancer


title: PBMC36


title: BCmRNA 151

description: Breast Cancer


title: PBMC34


title: BCmRNA 150

description: Breast Cancer


title: BCmRNA 148

description: Breast Cancer


title: BCmRNA 147

description: Breast Cancer


title: BCmRNA 153

description: Breast Cancer


title: BCmicroRNA 137

description: Breast Cancer


title: BCmRNA 145

description: Breast Cancer


title: BCmRNA 163

description: Breast Cancer


title: BRAIN93

source_name: autopsy collected cortical brain tissue specimen


title: BCmicroRNA 136

description: Breast Cancer


title: BCmicroRNA 135

description: Breast Cancer


title: BCmRNA 144

description: Breast Cancer


title: BCmRNA 142

description: Breast Cancer


title: BRAIN92


title: BCmRNA 139

description: Breast Cancer


title: BCmRNA 138

description: Breast Cancer


title: BCmRNA 140

description: Breast Cancer


title: BCmicroRNA 133

description: Breast Cancer


title: BCmicroRNA 134

description: Breast Cancer


title: BRAIN91


title: BCmRNA 141

description: Breast Cancer


title: BCmRNA 146

description: Breast Cancer


title: BCmRNA 143

description: Breast Cancer


title: BCmicroRNA 132

description: Breast Cancer


title: BCmRNA 136

description: Breast Cancer


title: BRAIN90


title: PBMC28


title: BCmicroRNA 131

description: Breast Cancer


title: BCmRNA 133

description: Breast Cancer


title: BCmRNA 134

description: Breast Cancer


title: BRAIN89


title: BCmRNA 132

description: Breast Cancer


title: BCmRNA 137

description: Breast Cancer


title: BCmRNA 135

description: Breast Cancer


title: BCmRNA 130

description: Breast Cancer


title: BRAIN87


title: BCmRNA 129

description: Breast Cancer


title: BCmicroRNA 129

description: Breast Cancer


title: BCmRNA 131

description: Breast Cancer


title: BCmicroRNA 130

description: Breast Cancer


title: BCmicroRNA 128

description: Breast Cancer


title: BRAIN88


title: BRAIN86


title: BRAIN85


title: BCmRNA 127

description: Breast Cancer


title: BCmRNA 128

description: Breast Cancer


title: BCmRNA 126

description: Breast Cancer


title: BCmRNA 123

description: Breast Cancer


title: BCmRNA 124

description: Breast Cancer


title: BCmRNA 125

description: Breast Cancer


title: BRAIN84


title: BCmicroRNA 127

description: Breast Cancer


title: BCmRNA 120

description: Breast Cancer


title: BCmRNA 121

description: Breast Cancer


title: BCmicroRNA 126

description: Breast Cancer


title: BRAIN83


title: BRAIN81


title: BRAIN82


title: BCmRNA 118

description: Breast Cancer


title: BCmRNA 116

description: Breast Cancer


title: BCmRNA 117

description: Breast Cancer


title: BCmicroRNA 124

description: Breast Cancer


title: BCmicroRNA 122

description: Breast Cancer


title: BCmRNA 119

description: Breast Cancer


title: BCmicroRNA 125

description: Breast Cancer


title: BCmicroRNA 121

description: Breast Cancer


title: BRAIN78


title: BRAIN77


title: BCmicroRNA 120

description: Breast Cancer


title: BCmicroRNA 123

description: Breast Cancer


title: BCmRNA 114

description: Breast Cancer


title: BCmRNA 115

description: Breast Cancer


title: BCmRNA 111

description: Breast Cancer


title: BCmRNA 110

description: Breast Cancer


title: BRAIN79


title: BCmRNA 109

description: Breast Cancer


title: BCmRNA 107

description: Breast Cancer


title: BCmRNA 112

description: Breast Cancer


title: BRAIN80


title: BCmRNA 108

description: Breast Cancer


title: BRAIN76


title: BCmRNA 113

description: Breast Cancer


title: BCmicroRNA 119

description: Breast Cancer


title: BCmicroRNA 118

description: Breast Cancer


title: BRAIN75


title: BCmicroRNA 117

description: Breast Cancer


title: BCmicroRNA 116

description: Breast Cancer


title: BCmRNA 104

description: Breast Cancer


title: BCmRNA 122

description: Breast Cancer


title: BCmRNA 103

description: Breast Cancer


title: BRAIN73


title: BRAIN74


title: BCmicroRNA 113

description: Breast Cancer


title: BRAIN72


title: BCmRNA 101

description: Breast Cancer


title: BRAIN71


title: BCmRNA 99

description: Breast Cancer


title: BCmRNA 106

description: Breast Cancer


title: BCmicroRNA 115

description: Breast Cancer


title: BCmicroRNA 114

description: Breast Cancer


title: BCmRNA 95

description: Breast Cancer


title: BRAIN70


title: BCmRNA 97

description: Breast Cancer


title: BCmRNA 105

description: Breast Cancer


title: BRAIN69


title: BCmRNA 92

description: Breast Cancer


title: BCmRNA 100

description: Breast Cancer


title: BCmRNA 94

description: Breast Cancer


title: BCmRNA 102

description: Breast Cancer


title: BCmRNA 98

description: Breast Cancer


title: BCmRNA 91

description: Breast Cancer


title: BCmRNA 96

description: Breast Cancer


title: BCmicroRNA 112

description: Breast Cancer


title: BCmicroRNA 111

description: Breast Cancer


title: BRAIN68


title: BCmicroRNA 110

description: Breast Cancer


title: BCmRNA 93

description: Breast Cancer


title: BCmicroRNA 107

description: Breast Cancer


title: BCmicroRNA 109

description: Breast Cancer


title: BCmicroRNA 108

description: Breast Cancer


title: BRAIN65


title: BRAIN66


title: BCmRNA 90

description: Breast Cancer


title: BCmRNA 88

description: Breast Cancer


title: BCmRNA 87

description: Breast Cancer


title: BRAIN64


title: BCmRNA 89

description: Breast Cancer


title: BCmRNA 81

description: Breast Cancer


title: BRAIN67


title: BCmRNA 86

description: Breast Cancer


title: BCmRNA 83

description: Breast Cancer


title: BCmRNA 79

description: Breast Cancer


title: BRAIN61


title: BCmicroRNA 105

description: Breast Cancer


title: BCmicroRNA 106

description: Breast Cancer


title: BCmRNA 80

description: Breast Cancer


title: BCmRNA 78

description: Breast Cancer


title: BCmRNA 85

description: Breast Cancer


title: BCmRNA 82

description: Breast Cancer


title: BCmRNA 84

description: Breast Cancer


title: BCmRNA 76

description: Breast Cancer


title: BCmRNA 77

description: Breast Cancer


title: BRAIN62


title: BCmicroRNA 104

description: Breast Cancer


title: BCmicroRNA 102

description: Breast Cancer


title: BRAIN59


title: BRAIN58


title: Treated mouse 5

first: Ramil

last: Nurtdinov

address: Dr. Aiguader 88

department: Bioinformatics and Genomics

institute: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Chips were processed on an Affymetrix Expression Console. Background adjustment by Robust Multi-Array (RMA) algorithm was applied to probes intensities. Raw probes gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: Treated mouse

label_protocol: Samples were chemically fragmented and biotinylated using the WT Terminal labeling kit (Affymetrix)

extract_protocol: Total RNA was extracted from brain and spinal cord samples using T9424-TRI Reagent® Sigma

treatment_protocol: Mice were treated with MOG-DNA or pCi at 28 and 14 days alter EAE induction

value: brain and spinal cord

value: MOG-DNA

tag: strain


title: BRAIN60


title: BCmicroRNA 101

description: Breast Cancer

tag: patient age


title: BCmicroRNA 100

description: Breast Cancer

tag: tumour size


title: BCmicroRNA 103

description: Breast Cancer

tag: nodes involved


title: Treated mouse 3


title: BCmicroRNA 99

description: Breast Cancer

tag: er status


title: BRAIN57


title: BCmRNA 73

description: Breast Cancer

tag: tissue


title: BCmicroRNA 98

description: Breast Cancer

tag: tumour grade


title: Treated mouse 4


title: BCmRNA 72

description: Breast Cancer

tag: distant-relapse event


title: BCmRNA 75

description: Breast Cancer

tag: distant-relapse free survival


title: BCmRNA 74

description: Breast Cancer


title: BRAIN63

tag: gender


title: Treated mouse 2


title: BRAIN55

tag: age


title: Treated mouse 1


title: BRAIN56

tag: postmortem interval (brain specimens only)


title: Control mouse 6

source_name: Control mouse

value: control


title: BCmicroRNA 97

description: Breast Cancer


title: BCmRNA 71

description: Breast Cancer


title: BCmicroRNA 96

description: Breast Cancer


title: Control mouse 3


title: Control mouse 4


title: BRAIN54

tag: site of specimen collection


title: BCmRNA 69

description: Breast Cancer


title: BCmicroRNA 95

description: Breast Cancer


title: BRAIN53

tag: position along eigenstrat axis 1 (ethnicity correction)


title: BCmicroRNA 93

description: Breast Cancer


title: BRAIN51

tag: position along eigenstrat axis 2 (ethnicity correction)


title: BCmRNA 70

description: Breast Cancer


title: Control mouse 2

tag: treatment


title: BCmRNA 68

description: Breast Cancer


title: BRAIN50

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BCmicroRNA 92

description: Breast Cancer


title: BRAIN49


title: BCmRNA 67

description: Breast Cancer


title: Control mouse 1

tag: strain


title: BCmRNA 65

description: Breast Cancer

tag: patient age


title: BCmRNA 66

description: Breast Cancer

tag: tumour size


title: BCmRNA 64

description: Breast Cancer

tag: nodes involved


title: Cbt 36, rep4

first: Laura

last: Buttitta

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

description:
3L
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.

hyb_protocol: Hybridization was performed by the FHCRC microarray facility, following NimbleGen standard hybridization protocol (see www.nimblegen.com).

scan_protocol: Scanning was performed by the FHCRC microarray facility, following NimbleGen standard scanning protocol (see www.nimblegen.com).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package.

organism: Drosophila melanogaster

source_name: dissected wing, 36h post-pupa, Cabut

label_protocol: Labeling was performed by the FHCRC microarray facility, following NimbleGen standard operating protocol (see www.nimblegen.com).

growth_protocol: Drosophila were grown on standard cornmeal, molasses media at 18oC until transgene induction.

extract_protocol: 10 wings of the indicated stages were dissected, and total RNA was extracted using a Qiagen RNeasy kit.

treatment_protocol: Gal4/UAS transgene expression (or mock controls) were shifted to 28oC, permissive for Gal4/UAS driven expression without excessive cell death.

tag: genotype

value: wing

tag: developmental stage

value: 36 hours after pupa formation

tag: transgene

value: Cabut


title: BRAIN52

value: female


title: BCmicroRNA 94

description: Breast Cancer

tag: tissue

value: Breast Cancer

tag: er status

tag: tumour grade

tag: distant-relapse event


title: BRAIN47

tag: gender

value: male

tag: age

tag: postmortem interval (brain specimens only)


title: Cbt 36, rep1

description:
3I
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.


title: BCmRNA 63

description: Breast Cancer

tag: distant-relapse free survival


title: BRAIN46

tag: site of specimen collection

tag: position along eigenstrat axis 1 (ethnicity correction)

tag: position along eigenstrat axis 2 (ethnicity correction)


title: BRAIN48

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BCmicroRNA 89

description: Breast Cancer

tag: patient age

tag: tumour size


title: BCmicroRNA 91

description: Breast Cancer

tag: nodes involved


title: Cbt 36, rep2

description:
3J
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.

tag: genotype

tag: developmental stage


title: BRAIN45


title: Cbt 36, rep3

description:
3K
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.

tag: tissue

tag: transgene


title: BCmicroRNA 88

description: Breast Cancer

tag: er status

tag: tumour grade


title: Cbt 24, rep3

description:
3G
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.

source_name: dissected wing, 24h post-pupa, Cabut

value: 24 hours after pupa formation


title: BCmRNA 61

description: Breast Cancer

tag: distant-relapse event


title: Cbt 24, rep2

description:
3F
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.


title: BCmicroRNA 90

description: Breast Cancer


title: BRAIN44

tag: gender

tag: age


title: Cbt 24, rep4

description:
3H
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.


title: Cbt 24, rep1

description:
3E
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.


title: BCmRNA 60

description: Breast Cancer

tag: distant-relapse free survival


title: BCmRNA 62

description: Breast Cancer


title: BCmicroRNA 86

description: Breast Cancer


title: BCmicroRNA 87

description: Breast Cancer


title: BCmicroRNA 85

description: Breast Cancer


title: BRAIN43

tag: postmortem interval (brain specimens only)

tag: site of specimen collection


title: BRAIN42

tag: position along eigenstrat axis 1 (ethnicity correction)

tag: position along eigenstrat axis 2 (ethnicity correction)


title: BCmicroRNA 84

description: Breast Cancer

tag: patient age


title: BCmRNA 59

description: Breast Cancer

tag: tumour size


title: BCmicroRNA 83

description: Breast Cancer

tag: nodes involved


title: BCmRNA 58

description: Breast Cancer


title: BRAIN39

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BCmRNA 57

description: Breast Cancer


title: BCmRNA 56

description: Breast Cancer


title: Cbt L3, rep3

description:
3C
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.

source_name: dissected wing, L3, Cabut

tag: genotype

tag: developmental stage

value: wandering 3rd larval instar


title: BRAIN40


title: BRAIN38


title: Cbt L3, rep1

description:
3A
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.

tag: tissue

tag: transgene


title: BCmRNA 55

description: Breast Cancer

tag: er status

tag: tumour grade


title: Cbt L3, rep4

description:
3D
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.


title: BCmicroRNA 81

description: Breast Cancer

tag: distant-relapse event


title: BCmRNA 54

description: Breast Cancer


title: dE2F1+dDP 36, rep4

description:
2L
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.

source_name: dissected wing, 36h post-pupa, dE2F1+dDP


title: BRAIN41

description:
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps and HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

tag: gender

tag: age


title: BRAIN36

tag: postmortem interval (brain specimens only)


title: dE2F1+dDP 36, rep3

description:
2K
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.


title: BCmicroRNA 82

description: Breast Cancer

tag: distant-relapse free survival


title: BRAIN35

tag: site of specimen collection

tag: position along eigenstrat axis 1 (ethnicity correction)


title: BCmicroRNA 79

description: Breast Cancer

tag: patient age


title: Cbt L3, rep2

description:
3B
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-Cabut.


title: BCmRNA 51

description: Breast Cancer

tag: tumour size


title: BCmRNA 53

description: Breast Cancer

tag: nodes involved


title: BRAIN37

tag: position along eigenstrat axis 2 (ethnicity correction)

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BCmRNA 52

description: Breast Cancer


title: dE2F1+dDP 36, rep1

description:
2I
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.

tag: genotype

tag: developmental stage


title: BCmRNA 50

description: Breast Cancer

tag: tissue


title: dE2F1+dDP 36, rep2

description:
2J
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.

tag: transgene


title: BCmicroRNA 77

description: Breast Cancer

tag: er status

tag: tumour grade


title: BCmicroRNA 80

description: Breast Cancer

tag: distant-relapse event


title: BCmicroRNA 78

description: Breast Cancer


title: BCmicroRNA 76

description: Breast Cancer


title: BRAIN33

tag: gender

tag: age


title: BRAIN34

tag: postmortem interval (brain specimens only)


title: BCmRNA 49

description: Breast Cancer

tag: distant-relapse free survival


title: dE2F1+dDP 24, rep1

description:
2E
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.

source_name: dissected wing, 24h post-pupa, dE2F1+dDP


title: dE2F1+dDP 24, rep2

description:
2F
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.


title: BCmRNA 48

description: Breast Cancer


title: dE2F1+dDP 24, rep4

description:
2H
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.


title: BCmRNA 47

description: Breast Cancer


title: dE2F1+dDP 24, rep3

description:
2G
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.


title: BCmicroRNA 74

description: Breast Cancer


title: BCmicroRNA 75

description: Breast Cancer


title: BRAIN31

tag: site of specimen collection

tag: position along eigenstrat axis 1 (ethnicity correction)


title: BCmicroRNA 72

description: Breast Cancer

tag: patient age

tag: tumour size


title: BRAIN30

tag: position along eigenstrat axis 2 (ethnicity correction)


title: BCmRNA 46

description: Breast Cancer

tag: nodes involved


title: BCmicroRNA 73

description: Breast Cancer


title: BCmicroRNA 71

description: Breast Cancer


title: BRAIN32

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BRAIN28


title: dE2F1+dDP L3, rep2

description:
2B
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.

source_name: dissected wing, L3, dE2F1+dDP

tag: genotype

tag: developmental stage


title: BRAIN27


title: BCmRNA 45

description: Breast Cancer

tag: tissue


title: dE2F1+dDP L3, rep1

description:
2A
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.

tag: transgene


title: BRAIN29


title: BCmicroRNA 70

description: Breast Cancer

tag: er status

tag: tumour grade


title: dE2F1+dDP L3, rep3

description:
2C
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens., UAS-dE2F1, UASdDP. One replicate (2d) did not pass quality control and was not included in the analysis.


title: control 36, rep4

description:
1L
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.

source_name: dissected wing, 36h post-pupa, control


title: BCmRNA 43

description: Breast Cancer

tag: distant-relapse event


title: BRAIN26

tag: gender

tag: age


title: BCmicroRNA 69

description: Breast Cancer

tag: distant-relapse free survival


title: BCmRNA 44

description: Breast Cancer


title: BCmicroRNA 68

description: Breast Cancer


title: BCmicroRNA 67

description: Breast Cancer


title: control 36, rep2

description:
1J
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.


title: BCmRNA 41

description: Breast Cancer


title: BCmRNA 42

description: Breast Cancer


title: control 36, rep1

description:
1I
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.


title: BRAIN24

tag: postmortem interval (brain specimens only)

tag: site of specimen collection


title: control 24, rep4

description:
1H
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.

source_name: dissected wing, 24h post-pupa, control


title: BRAIN23

tag: position along eigenstrat axis 1 (ethnicity correction)


title: control 24, rep3

description:
1G
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.


title: BCmRNA 38

description: Breast Cancer

tag: patient age

tag: tumour size


title: control 36, rep3

description:
1K
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.


title: BCmicroRNA 65

description: Breast Cancer

tag: nodes involved


title: BRAIN21

description:
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps and HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

tag: position along eigenstrat axis 2 (ethnicity correction)

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BRAIN22


title: BCmRNA 40

description: Breast Cancer


title: BRAIN25


title: BCmicroRNA 64

description: Breast Cancer


title: BCmicroRNA 63

description: Breast Cancer


title: control 24, rep1

description:
1E
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.

tag: genotype

tag: developmental stage


title: BRAIN20


title: BCmicroRNA 66

description: Breast Cancer

tag: tissue


title: BCmRNA 37

description: Breast Cancer

tag: er status


title: BCmicroRNA 62

description: Breast Cancer

tag: tumour grade


title: control 24, rep2

description:
1F
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.

tag: transgene


title: control L3, rep4

description:
1D
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.

source_name: dissected wing, L3, control


title: BCmicroRNA 61

description: Breast Cancer

tag: distant-relapse event


title: BCmRNA 39

description: Breast Cancer


title: BCmicroRNA 60

description: Breast Cancer


title: BRAIN18

tag: gender

tag: age


title: BCmRNA 36

description: Breast Cancer

tag: distant-relapse free survival


title: BRAIN19

tag: postmortem interval (brain specimens only)

tag: site of specimen collection


title: BCmicroRNA 59

description: Breast Cancer

tag: patient age


title: BRAIN17

tag: position along eigenstrat axis 1 (ethnicity correction)


title: BCmRNA 33

description: Breast Cancer

tag: tumour size

tag: nodes involved


title: Fetal_liver_sample 2

city: Evry

first: stefano

last: cairo

address: 4 rue Pierre Fontaine

country: France

institute: Xentech

hyb_protocol: The chips were hybridized on Tecan HS 4800 hybridization station. Chips were pre-hybridized at 25C for 30 min in the buffer of 6x SSPE/ 30% formamide/ 1x Denhardt's solution. The chips were further hybridized with labeled target in 6x SSPE/ 30% formamide at 25C for 18 hr. Hybridization, post-hybridization washing in 0.75x TNT (Tris, sodium, Tween 20) (see PNAS) at 37C for 40 mins. The chips were stained by streptavidin-alexa647 (1:500) dilution in TNT for 30 mins. Post-staining washing in 1x TNT FOR 40 min. Rinse with water and spin dry.

scan_protocol: Arrays were scanned on the GenePix scanner and analyzed using the GenePix Pro software package.

data_processing: Raw data were normalized by the print-tip loess method (Hua YJ, Genomics 2008)

source_name: fetal liver

label_protocol: Refer to Liu et al (PNAS 101: 9740-9744 (2004)). 5 ug of total RNA was labeled in reverse transcription at 37C for 90 mins by using biotin-labeled rand-octomer oligo primer. The RT reaction mix was further denatured by using 0.5 N NaOH / 1 mM EDTA at 65C for 15 mins and neutralized by 1 M Tris HCl pH 7.6. Biotin signal was detected with an Alexa 647-Streptavidin conjugate.

extract_protocol: On average, 30 ug of tissue was homogenized in trizol buffer, and RNA extraction was performed according to maunfacturer's instructions.

value: fetal liver


title: BCmicroRNA 58

description: Breast Cancer


title: control L3, rep2

description:
1B
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.


title: BCmRNA 35

description: Breast Cancer


title: BCmRNA 34

description: Breast Cancer


title: BCmicroRNA 57

description: Breast Cancer


title: Fetal_liver_sample 1


title: Patient_49

source_name: primary hepatoblastoma

value: primary hepatoblastoma

tag: histology

value: Mixed

tag: main epithelial component

value: Well differentiated

tag: 16-gene classifier

tag: sex

value: M

tag: chemotheraphy

value: Yes


title: BCmRNA 32

description: Breast Cancer

tag: tissue

tag: er status

tag: tumour grade


title: control L3, rep1

description:
1A
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.

tag: genotype

tag: developmental stage

tag: transgene


title: BRAIN16

tag: gender

tag: age

tag: postmortem interval (brain specimens only)

tag: position along eigenstrat axis 2 (ethnicity correction)

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BRAIN15

tag: site of specimen collection

tag: position along eigenstrat axis 1 (ethnicity correction)


title: control L3, rep3

description:
1C
This sample is one of four independent replicates of apterous-gal4, UAS-GFP, tubulin-Gal80temp.sens.


title: BCmicroRNA 56

description: Breast Cancer

tag: patient age

tag: tumour size

tag: nodes involved

tag: distant-relapse event

tag: distant-relapse free survival


title: Patient_48

tag: tissue

tag: histology

value: Epithelial

tag: main epithelial component

tag: 16-gene classifier

tag: sex

tag: chemotheraphy


title: SN250PK/SN250BF biological replicate 2

city: Merced

first: Clarissa

middle: Jane

last: Nobile

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California - Merced

scan_protocol: Slides were scanned on a Genepix 4000B Axon Instrument Scanner, and processed using GenePix Pro version 5.1 [see Lohse and Johnson, 2010 (PMCID: PMC3057202)].

data_processing: Global Lowess normalization analysis was performed for each array using a Goulphar script (Lemoine et al., 2006) for R (The R Foundation for Statistical Computing) [see Lohse and Johnson, 2010 (PMCID: PMC3057202)].

organism: Candida albicans

source_name: Candida albicans planktonic a/alpha cells

growth_protocol: planktonic, Spider medium, 37 degrees

extract_protocol: RNA Extract protocol is using the Ambion Yeast RNeasy Kit following the manufacturer's protocol [see Nobile et al. 2009 (PMCID: PMC2688839)].

tag: strain type

value: planktonic

source_name: Candida albicans biofilm a/alpha cells

growth_protocol: biofilm, 48 hours, Spider medium, 37 degrees

value: biofilm


title: BCmicroRNA 55

description: Breast Cancer

source_name: breast

tag: er status

tag: tumour grade


title: BCmicroRNA 54

description: Breast Cancer


title: BRAIN12

source_name: autopsy collected cortical brain tissue specimen

tag: gender

tag: age

tag: postmortem interval (brain specimens only)

tag: position along eigenstrat axis 2 (ethnicity correction)

tag: position along eigenstrat axis 3 (ethnicity correction)


title: SN250PK/SN250BF biological replicate 1

description: 252016610007 block F 530 540

hyb_protocol: see Lohse and Johnson, 2010 (PMCID: PMC3057202)


title: BCmRNA 31

description: Breast Cancer

tag: patient age

tag: tumour size

tag: nodes involved


title: Patient_47

tag: tissue

value: Poorly differentiated


title: BCmRNA 30

description: Breast Cancer

tag: distant-relapse event

tag: distant-relapse free survival


title: BCmicroRNA 53

description: Breast Cancer


title: Normal_control_7

source_name: normal liver

value: normal liver


title: BRAIN14

tag: site of specimen collection

tag: position along eigenstrat axis 1 (ethnicity correction)


title: BRAIN13


title: BRAIN11


title: Patient_46

tag: histology

tag: main epithelial component

tag: 16-gene classifier

tag: sex

tag: chemotheraphy


title: BCmicroRNA 52

description: Breast Cancer

tag: er status

tag: tumour grade


title: BRAIN10

tag: gender

tag: age

tag: postmortem interval (brain specimens only)

tag: position along eigenstrat axis 2 (ethnicity correction)


title: BCmRNA 29

description: Breast Cancer

tag: patient age

tag: tumour size

tag: nodes involved


title: BCmRNA 28

description: Breast Cancer

tag: tissue

tag: distant-relapse event

tag: distant-relapse free survival


title: Patient_45

tag: histology

value: F

value: No


title: BRAIN8

value: female

tag: site of specimen collection

tag: position along eigenstrat axis 1 (ethnicity correction)

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BRAIN9


title: BCmRNA 27

description: Breast Cancer

value: Breast Cancer


title: BCmRNA 26

description: Breast Cancer


title: BCmRNA 25

description: Breast Cancer


title: BCmRNA 23

description: Breast Cancer


title: BCmicroRNA 51

description: Breast Cancer


title: Patient_44

tag: main epithelial component

tag: 16-gene classifier

tag: sex

tag: chemotheraphy


title: BCmicroRNA 49

description: Breast Cancer

tag: er status

tag: tumour grade


title: Normal_control_6


title: BCmicroRNA 50

description: Breast Cancer


title: Patient_43


title: BCmicroRNA 48

description: Breast Cancer


title: Normal_control_5


title: BRAIN7

tag: gender

tag: age

tag: postmortem interval (brain specimens only)

tag: position along eigenstrat axis 2 (ethnicity correction)


title: BCmicroRNA 46

description: Breast Cancer

tag: tissue

tag: patient age

tag: tumour size

tag: nodes involved


title: BRAIN5

tag: site of specimen collection


title: BRAIN6

tag: position along eigenstrat axis 1 (ethnicity correction)


title: BCmRNA 22

description: Breast Cancer

tag: distant-relapse event

tag: distant-relapse free survival


title: BCmicroRNA 45

description: Breast Cancer


title: Patient_42

tag: histology

tag: main epithelial component

tag: 16-gene classifier


title: Patient_41

tag: sex

tag: chemotheraphy


title: BCmRNA 20

description: Breast Cancer

tag: er status

tag: tumour grade


title: Patient_40


title: BRAIN4

tag: gender

tag: age

tag: postmortem interval (brain specimens only)

tag: position along eigenstrat axis 3 (ethnicity correction)


title: BCmRNA 21

description: Breast Cancer

tag: tissue

tag: patient age

tag: tumour size


title: BCmRNA 24

description: Breast Cancer

tag: nodes involved


title: BCmicroRNA 44

description: Breast Cancer

tag: distant-relapse event


title: BRAIN2

tag: site of specimen collection

tag: position along eigenstrat axis 1 (ethnicity correction)

tag: position along eigenstrat axis 2 (ethnicity correction)


title: BCmRNA 19

description: Breast Cancer

tag: distant-relapse free survival


title: BRAIN1


title: BCmicroRNA 43

description: Breast Cancer


title: BRAIN3


title: Patient_39

tag: histology

tag: main epithelial component

tag: 16-gene classifier

tag: sex


title: BCmicroRNA 47

description: Breast Cancer

tag: er status

tag: tumour grade


title: Normal_control_4


title: BCmicroRNA 42

description: Breast Cancer


title: Patient_38

tag: chemotheraphy


title: BCmicroRNA 41

description: Breast Cancer


title: BCmRNA 17

description: Breast Cancer


title: BCmicroRNA 40

description: Breast Cancer


title: BCmicroRNA 39

description: Breast Cancer


title: Patient_36


title: Patient_37


title: BCmRNA 15

description: Breast Cancer


title: U2OS_shRent1_Upf1_4.5hr

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, with shUpf1/Rent1 treated with 100 ug/ml of DRB for 4.5 hr.

hyb_protocol: Labeled and fragmented cRNA was hybridized to HG-U133 Plus 2.0 Affymetrix GeneChips using standard techniques recommended by the manufacturer.

scan_protocol: Affymetrix 7G GeneArray scanner.

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using the Agilent Genespring GX11 program. No further adjustments were made to the data in the table.

source_name: U2OScells, shRent1, 4.5 hrs

label_protocol: Labeled target cRNA population was generated with the Affymetrix 3’-IVT Express kit.

growth_protocol: U2OS cells (osteosarcoma) were grown in DMEM (4.5 g/dl glucose) with 10% FCS.

extract_protocol: Trizol was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the ABI cDNA kit.

treatment_protocol: Cells were treated with the specific stresses for three hours, and then with the pol II elongation inhibitor DRB.  RNA was collected at 0 hrs or the indicated time points after DRB addition.

tag: cell line

tag: cell type

value: osteosarcoma cells

tag: treatment

tag: treatment duration

value: 3 hrs

tag: sampling time point

value: 4.5 hrs


title: U2OS_shRent1_Upf1_3hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, with shUpf1/Rent1 treated with 100 ug/ml of DRB for 3 hr.

source_name: U2OScells, shRent1, 3 hrs


title: BCmicroRNA 38

description: Breast Cancer

tag: tissue

tag: patient age

tag: tumour size

tag: nodes involved

tag: distant-relapse event


title: Patient_35

value: primary hepatoblastoma

tag: histology


title: BCmRNA 16

description: Breast Cancer

tag: distant-relapse free survival


title: BCmRNA 14

description: Breast Cancer


title: Patient_34

value: Mixed

tag: main epithelial component

tag: 16-gene classifier


title: BCmicroRNA 37

description: Breast Cancer

tag: er status


title: BCmRNA 18

description: Breast Cancer

tag: tumour grade


title: U2OS_shRent1_Upf1_1.5hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, with shUpf1/Rent1 treated with 100 ug/ml of DRB for 1.5 hr.

source_name: U2OScells, shRent1, 1.5 hrs

value: 1.5 hrs


title: BCmRNA 13

description: Breast Cancer


title: Patient_33

tag: sex

tag: chemotheraphy


title: BCmicroRNA 36

description: Breast Cancer


title: BCmRNA 12

description: Breast Cancer


title: U2OS_emetine_3hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 100 ug/ml emetine for 3 hrs, treated with 100 ug/ml of DRB for 3 hr.

source_name: U2OScells, emetine, 3 hrs

tag: cell line

tag: cell type

value: emetine


title: BCmRNA 10

description: Breast Cancer


title: U2OS_shRent1_Upf1_0hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, with shUpf1/Rent1.

source_name: U2OScells, shRent1, 0 hr

tag: treatment

tag: treatment duration

value: 0 hr


title: U2OS_emetine_4.5hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 100 ug/ml emetine for 3 hrs, treated with 100 ug/ml of DRB for 4.5 hr.

source_name: U2OScells, emetine, 4.5 hrs

tag: sampling time point


title: BCmRNA 11

description: Breast Cancer

tag: tissue

tag: patient age


title: BCmRNA 8

description: Breast Cancer

tag: tumour size

tag: nodes involved


title: U2OS_emetine_1.5hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 100 ug/ml emetine for 3 hrs, treated with 100 ug/ml of DRB for 1.5 hr.

source_name: U2OScells, emetine, 1.5 hrs


title: U2OS_Tunicamycin_4.5hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 2.5 ug/ml tunicamycin for 3 hrs treated with 100 ug/ml of DRB for 4.5 hr.

source_name: U2OScells, tunicamycin, 4.5 hrs

value: tunicamycin


title: BCmRNA 9

description: Breast Cancer

tag: distant-relapse event


title: Patient_32

tag: histology

value: Yes


title: U2OS_emetine_0hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 100 ug/ml emetine for 3 hrs.

source_name: U2OScells, emetine, 0 hr


title: U2OS_Tunicamycin_3hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 2.5 ug/ml tunicamycin for 3 hrs treated with 100 ug/ml of DRB for 3 hr.

source_name: U2OScells, tunicamycin, 3 hrs


title: BCmicroRNA 35

description: Breast Cancer

tag: distant-relapse free survival


title: Patient_31

tag: main epithelial component

value: Well differentiated

tag: 16-gene classifier


title: BCmicroRNA 33

description: Breast Cancer

tag: er status

tag: tumour grade


title: Patient_30

value: Epithelial

tag: sex

tag: chemotheraphy


title: BCmicroRNA 34

description: Breast Cancer


title: Patient_29

value: M


title: BCmicroRNA 32

description: Breast Cancer


title: U2OS_Tunicamycin_1.5hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 2.5 ug/ml tunicamycin for 3 hrs treated with 100 ug/ml of DRB for 1.5 hr.

source_name: U2OScells, tunicamycin, 1.5 hrs

tag: cell line

tag: cell type


title: BCmRNA 5

description: Breast Cancer


title: BCmRNA 4

description: Breast Cancer


title: BCmRNA 7

description: Breast Cancer


title: BCmRNA 6

description: Breast Cancer


title: U2OS_Tunicamycin_0hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 2.5 ug/ml tunicamycin for 3 hrs.

source_name: U2OScells, tunicamycin, 0 hr

tag: treatment

tag: treatment duration


title: Patient_28

source_name: primary hepatoblastoma

tag: tissue

value: Poorly differentiated

value: F


title: BCmicroRNA 31

description: Breast Cancer

tag: patient age


title: BCmRNA 3

description: Breast Cancer

tag: tumour size


title: BCmicroRNA 30

description: Breast Cancer

tag: nodes involved


title: Patient_27


title: BCmRNA 2

description: Breast Cancer

tag: distant-relapse event


title: U2OS_Hypoxia_4.5hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, rendered hypoxic (<0.1% Oxygen for 3 hrs), treated with 100 ug/ml of DRB for 4.5 hr.

source_name: U2OScells, hypoxia, 4.5 hrs

value: hypoxia

tag: sampling time point


title: Patient_25

tag: histology

value: No


title: U2OS_Hypoxia_3hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, rendered hypoxic (<0.1% Oxygen for 3 hrs), treated with 100 ug/ml of DRB for 3 hr.

source_name: U2OScells, hypoxia, 3 hrs

value: osteosarcoma cells


title: Patient_26

tag: main epithelial component


title: BCmicroRNA 28

description: Breast Cancer

source_name: breast

value: Breast Cancer

tag: distant-relapse free survival


title: BCmRNA 1

description: Breast Cancer

tag: er status


title: U2OS_Control_4.5hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 100 ug/ml of DRB for 4.5 hr.

source_name: U2OScells, control, 4.5 hrs

value: control

value: 3 hrs

value: 4.5 hrs


title: BCmicroRNA 27

description: Breast Cancer

tag: tumour grade


title: U2OS_Hypoxia_1.5hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, rendered hypoxic (<0.1% Oxygen for 3 hrs), treated with 100 ug/ml of DRB for 1.5 hr.

source_name: U2OScells, hypoxia, 1.5 hrs

value: 1.5 hrs


title: U2OS_Hypoxia_0hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, rendered hypoxic (<0.1% Oxygen for 3 hrs).

source_name: U2OScells, hypoxia, 0 hr


title: Patient_24

value: primary hepatoblastoma

value: Mixed

tag: 16-gene classifier

tag: sex


title: BCmicroRNA 29

description: Breast Cancer


title: BCmicroRNA 26

description: Breast Cancer


title: Patient_23

tag: chemotheraphy


title: Patient_22


title: BCmicroRNA 25

description: Breast Cancer


title: Patient_21


title: Patient_20


title: BCmicroRNA 23

description: Breast Cancer


title: BCmicroRNA 24

description: Breast Cancer


title: U2OS_Control_1.5hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 100 ug/ml of DRB for 1.5 hr.

source_name: U2OScells, control, 1.5 hrs

tag: cell line

tag: cell type


title: Normal_control_3

source_name: normal liver

value: normal liver


title: H9-b

city: Berlin

first: Alessandro

last: Prigione

state: Berlin

address: Robert-Roessle-Str. 10

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

description: replicate 2

data_processing: Illumina BeadStudio software version 3

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

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

tag: age

value: Passage 56

value: hESCs


title: BCmicroRNA 22

description: Breast Cancer

tag: tissue


title: H9-a

description: replicate 1

value: Passage 55


title: BCmicroRNA 21

description: Breast Cancer

tag: patient age


title: H1-a

description: replicate 1


title: Patient_18

value: Yes


title: BCmicroRNA 20

description: Breast Cancer

tag: tumour size


title: Patient_17

value: Well differentiated


title: iPS4-b

description: replicate 2

value: Passage 15

value: iPSCs from HFF1 fibroblasts


title: U2OS_Control_3hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS, treated with 100 ug/ml of DRB for 3 hr.

source_name: U2OScells, control, 3 hrs

tag: treatment

tag: treatment duration


title: U2OS_Control_0hr

description: Gene expression data of U2OS cells grown in DMEM/10% FCS.

source_name: U2OS cells, control, 0 hr

tag: sampling time point

value: 0 hr


title: Patient_19

tag: histology

value: F


title: SW780-siFFluc-2

city: Tokyo

first: Hyun-soo

last: Cho

address: 4-6-1, shirokanedai, minatoku

country: Japan

institute: University of Tokyo

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: A549 (RPMI1640) / SW780 (Leibovitz’s L-15) cell lines supplemented with 10% fetal bovine serum and 1% antibiotic/antimycotic solution and maintained at 37 degree in humid air with/ without  5% CO2 condition.

extract_protocol: Total RNA was performed according to the manufacturer's instructions.

treatment_protocol: siRNA duplexes (100 nM final concentration) were transfected in cancer cell lines with lipofectamine 2000 (Invitrogen) for 24 h

tag: transfector

value: siFFluc


title: BCmicroRNA 19

description: Breast Cancer

value: Breast Cancer

tag: nodes involved

tag: distant-relapse event

tag: distant-relapse free survival


title: iPS4-a

description: replicate 1


title: H1-b

description: replicate 2


title: SW780-siKDM3A-1


title: Patient_16

value: Epithelial

tag: main epithelial component

tag: 16-gene classifier

value: M


title: iPS2-b

description: replicate 2


title: SW780-siKDM3A-2


title: SW780-siFFluc-1


title: iB5-b

description: replicate 2

value: iPSCs from BJ fibroblasts


title: iPS2-a

description: replicate 1


title: iB4-b

description: replicate 2


title: iB5-a

description: replicate 1


title: SW780-siEGFP-2

value: siEGFP


title: SW780-siEGFP-1


title: A549-siKDM3A-2


title: BCmicroRNA 18

description: Breast Cancer

tag: er status

tag: tumour grade


title: Normal_control_2

tag: sex


title: Patient_15

value: primary hepatoblastoma

tag: chemotheraphy


title: BCmicroRNA 17

description: Breast Cancer

tag: tissue


title: BCmicroRNA 16

description: Breast Cancer

tag: patient age


title: BCmicroRNA 14

description: Breast Cancer

tag: tumour size


title: Patient_14


title: Normal_control_1

value: normal liver


title: A549-siKDM3A-1

tag: cell line


title: Patient_13

value: Mixed


title: BCmicroRNA 13

description: Breast Cancer


title: BCmicroRNA 12

description: Breast Cancer


title: BCmicroRNA 11

description: Breast Cancer


title: BCmicroRNA 15

description: Breast Cancer


title: Patient_11


title: iB4-a

description: replicate 1

tag: age

tag: cell type


title: BCmicroRNA 10

description: Breast Cancer


title: A549-siFFluc-1


title: A549-siFFluc-2


title: BJ-b

description: replicate 2

source_name: BJ

value: BJ

value: Neonatal, Passage 4

value: fetal foreskin fibroblasts


title: A549-siEGFP-1


title: HFF1-b

description: replicate 2


title: A549-siEGFP-2


title: HFF1-a

description: replicate 1


title: Patient_12

tag: histology

value: Poorly differentiated

value: Yes


title: BCmicroRNA 9

description: Breast Cancer


title: BJ-a

description: replicate 1


title: Patient_8


title: BCmicroRNA 8

description: Breast Cancer


title: Activated tolerogenic DCs, technical replicate 3

city: Nijmegen

first: Bastiaan

last: Jansen

address: PO Box 9101

department: Tumor Immunology

country: Netherlands

institute: Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Center Nijmegen

description: Gene expression data from monocyte-derived DCs stimulated with IL10/dexamethason 24hr, LPS 6hr

hyb_protocol: 17 hours at 45 degrees Celsius in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using using Stain cocktails included in the Affymetrix 3' IVT Express Kit

scan_protocol: GeneChip scanner 3000 7G

data_processing: GCRMA (in Bioconductor version 2.6.1) using R version 2.10.1 on Mac OS X 10.4.11 (PPC), and the Bioconductor packages gcrma (version 2.18.1) and affy (version 1.24.2).

source_name: DCs derived from CD14+ monocytes from adult human blood, stimulated with IL10/dexamethason for 24 hr, and for an additional 6 hr with LPS

label_protocol: Biotin labeling using Affymetrix 3' IVT Express Kit, following manufacturer's directions

extract_protocol: RNeasy column purification

value: DCs derived from CD14+ blood monocytes cultured for 6 days in the presence of IL4 and GGM-CSF

tag: stimulus

value: IL10/dexamethasone 24 hr, then LPS 6hr


title: Activated tolerogenic DCs, technical replicate 2


title: Activated tolerogenic DCs, technical replicate 1


title: Patient_10

value: Well differentiated

value: F


title: T3359 iNOS shRNA2 replicate2

city: Cleveland

first: Jeremy

last: Rich

state: OH

address: NE3-30 Lerner Reseach Institute, 9500 Euclid Avenue

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic

description:
JR11-3359-5B
gene expression data from T3359 glioma stem cells exposed to lentivirus expressing NOS2 directed shRNA

hyb_protocol: according to manufacturer's instructions

data_processing: quantile normalization (Illumina Genome Studio software, version 3.0)

source_name: glioma stem cells isolated from human glioma xenograft T3359

growth_protocol: glioma stem cells were cultured in Neurobasal media with supplements (EGF, FGF, B27, sodium pyruvate, glutamine, and penicillin/streptomycin)

extract_protocol: RNA was harvested using Qiagen RNAeasy kits

treatment_protocol: glioma stem cells were treated with lentivirus expressing the indicated shRNAs

value: human glioma xenograft

tag: xenograft

tag: lentivirus infection

value: iNOS shRNA2


title: T3359 iNOS shRNA1 replicate2

description:
JR9-3359-4B
gene expression data from T3359 glioma stem cells exposed to lentivirus expressing NOS2 directed shRNA

scan_protocol: according to manufacturer's instructions

value: iNOS shRNA1


title: T3691 iNOS shRNA1 replicate2

description:
JR10-3691-4B
gene expression data from T3691 glioma stem cells exposed to lentivirus expressing NOS2 directed shRNA

source_name: glioma stem cells isolated from human glioma xenograft T3691

label_protocol: according to manufacturer's instructions


title: T3691 iNOS shRNA2 replicate2

description:
JR12-3691-5B
gene expression data from T3691 glioma stem cells exposed to lentivirus expressing NOS2 directed shRNA


title: Patient_7

value: Epithelial

value: M


title: Patient_9

value: primary hepatoblastoma


title: BCmicroRNA 6

description: Breast Cancer

value: Breast Cancer

tag: nodes involved

tag: distant-relapse event

tag: distant-relapse free survival


title: BCmicroRNA 5

description: Breast Cancer

tag: er status


title: BCmicroRNA 7

description: Breast Cancer

tag: tumour grade


title: Patient_2

tag: main epithelial component

tag: 16-gene classifier

tag: sex


title: Patient_6

tag: tissue

value: Mixed

tag: chemotheraphy


title: Patient_4


title: Patient_5


title: Patient_1


title: BCmicroRNA 1

description: Breast Cancer

tag: patient age

tag: tumour size


title: BCmicroRNA 4

description: Breast Cancer


title: Patient_3


title: T3359 non-targeting control replicate2

description:
JR7-3359-NB
gene expression data from T3359 glioma stem cells exposed to lentivirus expressing non-targeting shRNA

value: non-targeting control


title: BCmicroRNA 3

description: Breast Cancer


title: BCmicroRNA 2

description: Breast Cancer


title: T3359 iNOS shRNA2 replicate1

description:
JR5-3359-5A
gene expression data from T3359 glioma stem cells exposed to lentivirus expressing NOS2 directed shRNA


title: Tolerogenic DCs, technical replicate 3

description: Gene expression data from monocyte-derived DCs stimulated with IL10/dexamethason 24hr

source_name: DCs derived from CD14+ monocytes from adult human blood, stimulated with IL10/dexamethason for 24 hr

tag: cell type

value: IL10/dexamethasone 24 hr


title: T3691 non-targeting control replicate2

description:
JR8-3691-NB
gene expression data from T3691 glioma stem cells exposed to lentivirus expressing non-targeting shRNA


title: Tolerogenic DCs, technical replicate 2


title: Tolerogenic DCs, technical replicate 1


title: Immature DCs, technical replicate 2

description: Gene expression data from immature monocyte-derived DCs

source_name: DCs derived from CD14+ monocytes from adult human blood


title: T3691 iNOS shRNA1 replicate1

description:
JR4-3691-4A
gene expression data from T3691 glioma stem cells exposed to lentivirus expressing NOS2 directed shRNA


title: T3691 non-targeting control replicate1

description:
JR2-3691-NA
gene expression data from T3691 glioma stem cells exposed to lentivirus expressing non-targeting shRNA


title: Immature DCs, technical replicate 3


title: Maturing DCs, technical replicate 3

description: Gene expression data from monocyte-derived DCs stimulated with LPS 6hr

source_name: DCs derived from CD14+ monocytes from adult human blood, stimulated with LPS for 6 hr

value: LPS 6 hr


title: Immature DCs, technical replicate 1


title: T3691 iNOS shRNA2 replicate1

description:
JR6-3691-5A
gene expression data from T3691 glioma stem cells exposed to lentivirus expressing NOS2 directed shRNA


title: T3359 non-targeting control replicate1

description:
JR1-3359-NA
gene expression data from T3359 glioma stem cells exposed to lentivirus expressing non-targeting shRNA


title: Maturing DCs, technical replicate 1


title: T3359 iNOS shRNA1 replicate1

description:
JR3-3359-4A
gene expression data from T3359 glioma stem cells exposed to lentivirus expressing NOS2 directed shRNA


title: ΔRaf1 activation and MEK inhibition, Replicate 1

status: Public on Jul 07 2011

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

description: Biological replicate 1 of 3. ΔRaf1 activated and MEK inhibited.

hyb_protocol: The dual colour hybridization of the microarray chips was performed at ServiceXS (ServiceXS, Leiden, The Netherlands) according to Agilent protocol G4140-90050 v.5.7 (www.Agilent.com) for Two-Color Microarray-Based Gene Expression Analysis.

scan_protocol: Microarray data were processed from raw data image files with Feature Extraction Software 9.5.3 (Agilent Technologies). The arrays were scanned twice with 10% PMT and 100% PMT laser power and the XDR function was used to extend the dynamic range with 10-fold.

data_processing: The feature extraction software version 9.5, protocol ge2_V5_95 from Agilent was used to generate the feature extraction data. For the background subtraction the option 'No background substraction and spatial detrend' was used. For analysis, microarray data was imported into Rosetta Resolver 7.0 (Rosetta Biosoftware) and subjected to default ratio error modeling.

source_name: ZFL-ΔRaf1-ER cells

label_protocol: Amino-allyl-modified amplified RNA (aRNA) was synthesized in one amplification round from 1µg of total RNA using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion). Subsequently, 6µg of amino-allyl-modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dyes (GE Healthcare) and column purified.

growth_protocol: The ZFL-ΔRaf1-ER cell line was cultured in complete growth medium (CGM; 50% Leibovitz's L-15 medium, 35% Dulbecco's modified Eagle's medium, 15% Ham's F12 medium, supplemented with 15mM HEPES, 0.01mg/ml insulin, 50ng/ml EGF and 5% fetal bovine serum; all purchased from Invitrogen) supplemented with 0.5mg/ml G418, at 28°C without additional CO2.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37°C with 10 U of DNaseI (Roche Applied Science) to remove residual genomic DNA before purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean-up protocol. The integrity of the RNA was confirmed by lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies). Samples used for microarray analysis had an average RNA integrity number value of 9 and a minimum RNA integrity number value of 8.

treatment_protocol: The ZFL-ΔRaf1-ER cells were cultured in 12-well plates till confluence. Cell were starved for 4h in plain medium and susequently treated with or without 1µM 4HT and/or 30µM U0126 for 12h.

tag: cell line

value: ZFL-ΔRaf1-ER cell line

tag: treatment


title: ΔRaf1 activation and MEK inhibition, Replicate 2

description: Biological replicate 2 of 3. ΔRaf1 activated and MEK inhibited.


title: healthy liver tissue, replicate 3

description: Biological replicate 3 of 6. Healthy liver tissue.

source_name: healthy and tumor liver tissues, mixed as common reference

treatment_protocol: Three-week-old zebrafish fry were treated with 0.75ppm 7,12-dimethylbenz(α)anthracene (DMBA) or DMSO (vehicle) for 24h. The treatment was repeated once at 5-week-old for another 24h with 1.25ppm DMBA or DMSO. Treated fish were rinsed three times in fresh water and transferred into new tanks for maintenance. Fish were sampled during 6-10 months after the onset of DMBA exposure. Tumor samples > 3mm in diameter were histopathologically diagnosed before RNA extraction.

value: liver

tag: common reference

value: A mixture of the 11 total RNA samples

source_name: healthy liver tissue

tag: disease state

value: healthy

tag: biological replicate


title: healthy liver tissue, replicate 6

description: Biological replicate 6 of 6. Healthy liver tissue.


title: ΔRaf1 activation, Replicate 1

description: Biological replicate 1 of 3. ΔRaf1 activated.

value: no 4HT, no U0126

value: 1µM 4HT, no U0126


title: Liver tumor, replicate 3

description: Biological replicate 3 of 5. Liver tumor.

source_name: liver tumor

value: tumor


title: Liver tumor, replicate 5

description: Biological replicate 5 of 5. Liver tumor.


title: ΔRaf1 activation, Replicate 3

description: Biological replicate 3 of 3. ΔRaf1 activated.


title: Liver tumor, replicate 2

description: Biological replicate 2 of 5. Liver tumor.


title: ΔRaf1 activation and MEK inhibition, Replicate 3

description: Biological replicate 3 of 3. ΔRaf1 activated and MEK inhibited.


title: healthy liver tissue, replicate 2

description: Biological replicate 2 of 6. Healthy liver tissue.


title: Liver tumor, replicate 1

description: Biological replicate 1 of 5. Liver tumor.


title: healthy liver tissue, replicate 4

description: Biological replicate 4 of 6. Healthy liver tissue.


title: ΔRaf1 activation, Replicate 2

description: Biological replicate 2 of 3. ΔRaf1 activated.


title: healthy liver tissue, replicate 5

description: Biological replicate 5 of 6. Healthy liver tissue.


title: Liver tumor, replicate 4

description: Biological replicate 4 of 5. Liver tumor.


title: Sézary patient 3 (BAC array)

type: genomic

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: Array CGH analysis of a female patient with Sézary syndrome.

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics).

scan_protocol: Slides were scanned at 10 µm resolution using an Agilent scanner (G2565BA). PMT settings: 100/100

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not subtracted. Signal intensities were normalized by subgridd LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.2 and -0.2, respectively.

label: Alexa Fluor 3

molecule: genomic DNA

source_name: DNA isolated from living peripheral blood mononuclear cells (PBMC) of patient

label_protocol: DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime® Total Genomic Labeling System). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics).

extract_protocol: Living PBMCs were digested with proteinase K followed by phenol/chloroform/isopropanol DNA purification.

treatment_protocol: Whole genome amplification by GenomePlex (Sigma)

tag: patient

tag: gender

value: female

value: Sézary syndrome

tag: age

tag: time point of blood sample (mm/yy)

label: Alexa Fluor 5

source_name: DNA pool isolated from living peripheral blood mononuclear cells (PBMC) of healthy donors

extract_protocol: DNA of MeOH/Hac fixated PBMCs were isolated with phenol/chloroform/ isopropanol.

value: healthy control


title: Sézary patient 16 (BAC array)

scan_protocol: Slides were scanned at 10 um resolution using an Agilent scanner (G2565BA). PMT settings: 100/100

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005).Background intensities were not subtracted. Signal intensities were normalized by subgridd LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.2 and -0.2, respectively.

source_name: DNA pool isolated from fixed peripheral blood mononuclear cells (PBMC) of healty donors

extract_protocol: DNA of MeOH/Hac fixated PBMCs were isolated with phenol/chloroform/ isopropanol


title: Sézary patient 17 (BAC array)

extract_protocol: Living PBMCs were digested with proteinase K followed by phenol/chloroform/isopropanol DNA purification


title: Sézary patient 5 (BAC array)

source_name: DNA isolated from fixed peripheral blood mononuclear cells (PBMC) of patient


title: Sézary patient 18 (BAC array)

description: Array CGH analysis of a female patient with Sézary syndrome

source_name: DNA isolated form living peripheral blood mononuclear cells (PBMC) of patient

label_protocol: DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime? Total Genomic Labeling System). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics).

extract_protocol: Living PBMCs were digested with proteinase K followed by phenol/chloroform/QIAamp DNA purification.

value: male

source_name: DNA pool isolated from living peripheral blood mononuclear cells (PBMC) of healty donors

extract_protocol: Living PBMCs were digested with proteinase K followed by QIAamp DNA purification.


title: Sézary patient 11 (BAC array)

extract_protocol: DNA of MeOH/Hac fixed PBMCs were isolated with phenol/chloroform extraction followed by DNA precipitation using isopropanol.


title: Sézary patient 6 (BAC array)

label_protocol: DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime Total Genomic Labeling System). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics).


title: Sézary patient 13 (BAC array)


title: healthy liver tissue, replicate 1

description: Biological replicate 1 of 6. Healthy liver tissue.


title: Sézary patient 12 (BAC array)

description: Array CGH analysis of a male patient with Sézary syndrome.


title: Sézary patient 1 (BAC array)


title: Sézary patient 8 (BAC array)