title: 43-MDD-L5-4

description: Gene expression data for subject 43, diagnosis MDD, layer 5, replicate 2

value: dorsolateral prefrontal cortex


title: PCA29

status: Public on Apr 04 2017

type: RNA

city: Vancouver

first: Elai

last: Davicioni

state: British Columbia

address: 1038 Homer st

country: Canada

institute: GenomeDx Biosciences Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using SCAN software package (Bioconductor)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary prostate cancer FFPE tissue sample

label_protocol: RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 3.0 (NuGEN)

extract_protocol: RNA was extracted using the Qiagen RNeasy FFPE Kit .

tag: tissue

value: prostate cancer


title: CD43neg C11.P0

city: Lund

first: Carolina

last: Guibentif

country: Sweden

institute: Lund University

description: 1 cell

data_processing: Following the Biomark run, data was first analysed with Fluidigm Real-Time PCR Analysis Software, for evaluation of the amplification curves, and Ct thresholds were set automatically using the auto detector function.  Reactions with Ct>30 were considered negative. In assays where amplification was detected in no-RT controls, all reactions displaying Ct > [min(CtnoRTcontrols) – 2] were considered negative. The data was then analysed using the SCexV online tool http://stemsysbio.bmc.lu.se/SCexV/  (Lang et al., 2015) together with the Index-sort data, for performing principal component analysis (PCA) and hierarchical clustering based on the gene expression data. Cells displaying a Ct value >25 in the housekeeping gene GAPDH were excluded from the analysis, as well as the positive control samples. Subsequent analysis was then performed for the remaining cells (representing over 90% of the total sorted cells), using all assays and surface phenotype data excluding the housekeeping gene GAPDH.

label: FAM-MGB

source_name: plate 1

label_protocol: Pre-amplification mastermix (6.25 µl of 2X Reaction Buffer, 1 µl of SuperScript III RT/ Platinum Taq mix, and 1.5 µl of Taqman assays equal volume pool) was then added to each sample and reverse transcription was performed followed by pre-amplification in a Biorad T100 thermal cycler using the following program: 1h at 50ºC, 2 min at 95ºC and 25 cycles of 15 sec at 95ºC and 4 min at 60ºC. Pre-amplified samples were diluted 1:5 and run in Fluidigm 96.96 arrays on a Biomark device (Fluidigm), with Taqman universal MasterMix (Life Technologies) and the Taqman assays using the appropriate loading reagents according to manufacturer’s instructions.

growth_protocol: The iPS line was maintained in co-culture with irradiated murine embryonic fibroblasts in Dulbecco’s Modified Eagle Medium Nutrient Mixture F-12 supplemented with 20% KnockOut-serum replacement, Glutamax, Non-Essential Amino Acids, 50 µM beta-mercaptoethanol and 10 ng/mL Fgf2 (all from Life Technologies) in a humidified incubator at 37ºC, 5% CO2. Cells were passaged every six days using 1mg/ml Collagenase IV (Life Technologies). During two days preceding initiation of the blood differentiation protocol, the cultures were treated with 3 µM CHIR99021 (R&D Systems Europe).

extract_protocol: Single CD34+ cells were sorted directly into 96-well PCR plates (Sarstedt), using the Index-Sorting function of the Diva Software, into 4 µl of lysis buffer [65 µM of dNTP mix (Takara), 0.4% of NP40 Cell Lysis Buffer, 2.4 mM dithiothreitol, 0.5 U/µl RNAseOUT (Life Technologies) in nuclease-free water]. Target-specific pre-amplification was then performed using CellsDirect One-Step qRT-PCR Kit (Life Technologies).

treatment_protocol: Differentiation towards the blood lineage was performed as follows: the iPS colonies were incubated in 500 µg/ml Dispase (Life Technologies) for 40 minutes at 37ºC and resulting embryoid bodies (EBs) were transferred into ultra-low attachment culture dishes (Corning) in Mesototal medium (Primorigen Biosciences, Wisconsin). At day eight the EBs were plated on Matrigel-coated dishes (8 µg/cm2, Corning) in order to attach and spread a monolayer. Fresh Mesototal medium was added every second day throughout the protocol.

tag: cell type

value: human iPS-derived CD34+

tag: cd43 phenotype

value: negative


title: PCA26


title: 5-UC-L5-3

city: Pittsburgh

first: David

last: Lewis

state: PA

address: 3811 O'Hara St

department: Psychiatry and Neuroscience

country: USA

institute: University of Pittsburgh

description: Gene expression data for subject 5, diagnosis UC, layer 5, replicate 1

hyb_protocol: CDNA was synthesized and amplified using the Ovation Pico WTA System.

scan_protocol: Loaded on an Affymetrix GeneChip® U219.

data_processing: Expression intensities were extracted from Affymetrix Expression Console and normalized using Robust Multi-array Average Express.

label: Encore Biotin module (Nugen)

source_name: dorsolateral prefrontal cortex

label_protocol: Labeled using the Encore Biotin module (Nugen).

growth_protocol: Brain specimens were obtained during autopsies conducted at the Allegheny County Office of the Medical Examiner (Pittsburgh, PA) after consent was obtained from the next-of-kin.

extract_protocol: For each sample, RNA was extracted using the QIAGEN® RNeasy Plus Micro kit (QIAGEN, Valencia).

treatment_protocol: An independent committee of experienced research clinicians made consensus DSM-IV diagnoses for each subject using information obtained from medical records and structured diagnostic interviews conducted with the decedent’s family members.

value: pyramidal neuron cell

tag: shape

value: characteristic triangular shape and prominent apical dendrite

tag: genotype

value: Unaffected Comparison subject

tag: dsm-iv diagnoses

value: Unaffected Comparison


title: PCA27


title: PCA25


title: 43-MDD-L3-2

description: Gene expression data for subject 43, diagnosis MDD, layer 3, replicate 2

value: Major Depressive Disorder

value: MDD; ADR


title: 5-UC-L5-4

description: Gene expression data for subject 5, diagnosis UC, layer 5, replicate 2


title: CD43neg C11.P1

description: 1 cell

source_name: plate 2


title: CD43neg C11.P2

description: 1 cell

source_name: plate 3


title: 5-UC-L3-1

description: Gene expression data for subject 5, diagnosis UC, layer 3, replicate 1


title: 43-MDD-L3-1

description: Gene expression data for subject 43, diagnosis MDD, layer 3, replicate 1


title: CD43neg C10.P3

description: 1 cell

source_name: plate 4


title: 24-BP-L5-4

description: Gene expression data for subject 24, diagnosis BP, layer 5, replicate 2

value: Bipolar

value: Bipolar I, PF; ADC; ODC


title: 24-BP-L5-3

description: Gene expression data for subject 24, diagnosis BP, layer 5, replicate 1


title: 24-BP-L3-2

description: Gene expression data for subject 24, diagnosis BP, layer 3, replicate 2


title: 24-BP-L3-1

description: Gene expression data for subject 24, diagnosis BP, layer 3, replicate 1


title: 5-UC-L3-2

description: Gene expression data for subject 5, diagnosis UC, layer 3, replicate 2


title: PCA21


title: 61-SZ-L5-4

description: Gene expression data for subject 61, diagnosis SZ, layer 5, replicate 2

value: Schizophrenia

value: SA; ADC; ODR


title: PCA32


title: CD43neg C10.P2

description: 1 cell


title: PCA28


title: PCA22


title: CD43neg C10.P1

description: 1 cell


title: PCA20


title: PCA19


title: PCA18


title: CD43neg C10.P0

description: 1 cell


title: PCA23


title: CD43neg B9.P4

description: 1 cell

source_name: plate 5


title: 61-SZ-L5-3

description: Gene expression data for subject 61, diagnosis SZ, layer 5, replicate 1


title: 42-MDD-L5-4

description: Gene expression data for subject 42, diagnosis MDD, layer 5, replicate 2

value: MDD


title: CD43neg B9.P3

description: 1 cell


title: 61-SZ-L3-2

description: Gene expression data for subject 61, diagnosis SZ, layer 3, replicate 2


title: PCA15


title: 42-MDD-L3-1

description: Gene expression data for subject 42, diagnosis MDD, layer 3, replicate 1


title: 61-SZ-L3-1

description: Gene expression data for subject 61, diagnosis SZ, layer 3, replicate 1


title: 42-MDD-L3-2

description: Gene expression data for subject 42, diagnosis MDD, layer 3, replicate 2


title: 42-MDD-L5-3

description: Gene expression data for subject 42, diagnosis MDD, layer 5, replicate 1


title: PCA14


title: CD43neg B9.P2

description: 1 cell


title: PCA24


title: CD43neg B9.P1

description: 1 cell


title: 4-UC-L5-3

description: Gene expression data for subject 4, diagnosis UC, layer 5, replicate 1


title: 4-UC-L3-2

description: Gene expression data for subject 4, diagnosis UC, layer 3, replicate 2


title: PCA17


title: CD43neg C10.P4

description: 1 cell


title: 23-BP-L5-3

description: Gene expression data for subject 23, diagnosis BP, layer 5, replicate 1

value: Bipolar I; ADC


title: 4-UC-L3-1

description: Gene expression data for subject 4, diagnosis UC, layer 3, replicate 1


title: CD43neg B9.P0

description: 1 cell


title: CD43neg B8.P4

description: 1 cell


title: 23-BP-L3-2

description: Gene expression data for subject 23, diagnosis BP, layer 3, replicate 2


title: 60-SZ-L5-3

description: Gene expression data for subject 60, diagnosis SZ, layer 5, replicate 1

value: SA


title: 60-SZ-L3-2

description: Gene expression data for subject 60, diagnosis SZ, layer 3, replicate 2

value: dorsolateral prefrontal cortex


title: 23-BP-L5-4

description: Gene expression data for subject 23, diagnosis BP, layer 5, replicate 2


title: 23-BP-L3-1

description: Gene expression data for subject 23, diagnosis BP, layer 3, replicate 1


title: CD43neg B8.P3

description: 1 cell


title: 4-UC-L5-4

description: Gene expression data for subject 4, diagnosis UC, layer 5, replicate 2


title: PCA13

value: prostate cancer


title: CD43neg B8.P2

description: 1 cell

value: human iPS-derived CD34+


title: 60-SZ-L3-1

description: Gene expression data for subject 60, diagnosis SZ, layer 3, replicate 1


title: 41-MDD-L5-3

description: Gene expression data for subject 41, diagnosis MDD, layer 5, replicate 1

value: MDD, recurrent; ADC


title: 41-MDD-L5-4

description: Gene expression data for subject 41, diagnosis MDD, layer 5, replicate 2

value: pyramidal neuron cell


title: CD43neg B8.P1

description: 1 cell

value: negative


title: 22-BP-L5-4

description: Gene expression data for subject 22, diagnosis BP, layer 5, replicate 2

value: characteristic triangular shape and prominent apical dendrite

value: Bipolar I


title: PCA12


title: 3-UC-L5-3

description: Gene expression data for subject 3, diagnosis UC, layer 5, replicate 1

value: Unaffected Comparison subject

value: Unaffected Comparison


title: 41-MDD-L3-1

description: Gene expression data for subject 41, diagnosis MDD, layer 3, replicate 1

value: Major Depressive Disorder


title: 3-UC-L3-1

description: Gene expression data for subject 3, diagnosis UC, layer 3, replicate 1


title: 3-UC-L3-2

description: Gene expression data for subject 3, diagnosis UC, layer 3, replicate 2


title: CD43neg B7.P3

description: 1 cell


title: PCA16


title: CD43neg B7.P4

description: 1 cell


title: CD43neg B7.P2

description: 1 cell


title: CD43neg B8.P0

description: 1 cell


title: CD43neg B7.P1

description: 1 cell


title: 22-BP-L3-2

description: Gene expression data for subject 22, diagnosis BP, layer 3, replicate 2

value: Bipolar


title: 22-BP-L5-3

description: Gene expression data for subject 22, diagnosis BP, layer 5, replicate 1


title: 59-SZ-L5-4

description: Gene expression data for subject 59, diagnosis SZ, layer 5, replicate 2

value: Schizophrenia


title: CD43neg B7.P0

description: 1 cell


title: CD43neg B6.P4

description: 1 cell


title: 59-SZ-L3-2

description: Gene expression data for subject 59, diagnosis SZ, layer 3, replicate 2


title: PCA11


title: CD43neg B6.P3

description: 1 cell


title: CD43neg B6.P2

description: 1 cell


title: 59-SZ-L5-3

description: Gene expression data for subject 59, diagnosis SZ, layer 5, replicate 1


title: CD43neg B6.P1

description: 1 cell


title: 40-MDD-L5-3

description: Gene expression data for subject 40, diagnosis MDD, layer 5, replicate 1

value: MDD, recurrent; ODC; ODR; OAC; OAR


title: CD43neg B6.P0

description: 1 cell


title: 40-MDD-L5-4

description: Gene expression data for subject 40, diagnosis MDD, layer 5, replicate 2


title: 40-MDD-L3-2

description: Gene expression data for subject 40, diagnosis MDD, layer 3, replicate 2


title: 59-SZ-L3-1

description: Gene expression data for subject 59, diagnosis SZ, layer 3, replicate 1


title: 2-UC-L3-2

description: Gene expression data for subject 2, diagnosis UC, layer 3, replicate 2


title: 22-BP-L3-1

description: Gene expression data for subject 22, diagnosis BP, layer 3, replicate 1


title: 2-UC-L5-3

description: Gene expression data for subject 2, diagnosis UC, layer 5, replicate 1


title: CD43neg B5.P4

description: 1 cell


title: 41-MDD-L3-2

description: Gene expression data for subject 41, diagnosis MDD, layer 3, replicate 2


title: CD43neg B5.P2

description: 1 cell


title: CD43neg B5.P1

description: 1 cell


title: CD43neg B5.P0

description: 1 cell


title: 21-BP-L3-2

description: Gene expression data for subject 21, diagnosis BP, layer 3, replicate 2

value: Bipolar I, PF; ADR


title: PCA7


title: CD43neg B4.P3

description: 1 cell


title: CD43neg B4.P4

description: 1 cell


title: 40-MDD-L3-1

description: Gene expression data for subject 40, diagnosis MDD, layer 3, replicate 1


title: 58-SZ-L5-4

description: Gene expression data for subject 58, diagnosis SZ, layer 5, replicate 2

value: US


title: PCA3


title: CD43neg B4.P0

description: 1 cell


title: PCA4


title: CD43neg B5.P3

description: 1 cell


title: CD43neg B4.P2

description: 1 cell


title: PCA1


title: 21-BP-L3-1

description: Gene expression data for subject 21, diagnosis BP, layer 3, replicate 1


title: PCA10


title: 39-MDD-L5-3

description: Gene expression data for subject 39, diagnosis MDD, layer 5, replicate 1

value: MDD, recurrent, PF; AAR


title: 39-MDD-L5-4

description: Gene expression data for subject 39, diagnosis MDD, layer 5, replicate 2

value: dorsolateral prefrontal cortex


title: 58-SZ-L3-1

description: Gene expression data for subject 58, diagnosis SZ, layer 3, replicate 1


title: CD43neg B4.P1

description: 1 cell


title: CD43neg B3.P3

description: 1 cell


title: PCA2

value: prostate cancer


title: CD43neg B3.P2

description: 1 cell

value: human iPS-derived CD34+


title: CD43neg B2.P4

description: 1 cell


title: 39-MDD-L3-1

description: Gene expression data for subject 39, diagnosis MDD, layer 3, replicate 1


title: CD43neg B3.P0

description: 1 cell


title: PCA6


title: 2-UC-L3-1

description: Gene expression data for subject 2, diagnosis UC, layer 3, replicate 1


title: CD43neg B3.P4

description: 1 cell


title: 21-BP-L5-4

description: Gene expression data for subject 21, diagnosis BP, layer 5, replicate 2


title: CD43neg B2.P3

description: 1 cell


title: CD43neg B2.P2

description: 1 cell


title: PCA9


title: CD43neg B2.P1

description: 1 cell


title: PCA8


title: CD43neg B2.P0

description: 1 cell


title: 58-SZ-L5-3

description: Gene expression data for subject 58, diagnosis SZ, layer 5, replicate 1


title: 1-UC-L5-3

description: Gene expression data for subject 1, diagnosis UC, layer 5, replicate 1


title: 1-UC-L5-4

description: Gene expression data for subject 1, diagnosis UC, layer 5, replicate 2


title: 21-BP-L5-3

description: Gene expression data for subject 21, diagnosis BP, layer 5, replicate 1


title: 1-UC-L3-2

description: Gene expression data for subject 1, diagnosis UC, layer 3, replicate 2


title: 1-UC-L3-1

description: Gene expression data for subject 1, diagnosis UC, layer 3, replicate 1


title: 20-BP-L5-3

description: Gene expression data for subject 20, diagnosis BP, layer 5, replicate 1

value: Bipolar NOS; ADR; ODC; OAC; OAR


title: CD43neg B12.P3

description: 1 cell


title: 20-BP-L5-4

description: Gene expression data for subject 20, diagnosis BP, layer 5, replicate 2

value: pyramidal neuron cell


title: CD43neg B12.P1

description: 1 cell

value: negative


title: CD43neg B11.P4

description: 1 cell


title: CD43neg B12.P2

description: 1 cell


title: CD43neg B12.P0

description: 1 cell


title: 20-BP-L3-1

description: Gene expression data for subject 20, diagnosis BP, layer 3, replicate 1

value: characteristic triangular shape and prominent apical dendrite


title: 20-BP-L3-2

description: Gene expression data for subject 20, diagnosis BP, layer 3, replicate 2


title: CD43neg B12.P4

description: 1 cell


title: 39-MDD-L3-2

description: Gene expression data for subject 39, diagnosis MDD, layer 3, replicate 2


title: CD43neg B11.P2

description: 1 cell


title: CD43neg B3.P1

description: 1 cell


title: CD43neg B11.P1

description: 1 cell


title: CD43neg B10.P4

description: 1 cell


title: CD43neg B11.P0

description: 1 cell


title: PCA5


title: CD43neg B10.P2

description: 1 cell


title: BTSC233 transduced with ZBTB18-expressing lentiviral vector 2

city: Freiburg

first: Maria Stella

last: Carro

address: Breisacherstraße 64

country: Germany

institute: Freiburg University Medical Center

description:
BTSC233-ZBTB18-2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: Glioblastoma

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

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

tag: gbm subtype

value: mesenchymal

tag: cell line

value: brain tumor stem cell-like BTSC233

tag: genotype/variation


title: BTSC233 transduced with ZBTB18-expressing lentiviral vector 3

description:
BTSC233-ZBTB18-3
replicate 3


title: CD43neg B10.P3

description: 1 cell


title: BTSC233 transduced with ZBTB18-expressing lentiviral vector 1

description:
BTSC233-ZBTB18-1
replicate 1


title: 58-SZ-L3-2

description: Gene expression data for subject 58, diagnosis SZ, layer 3, replicate 2


title: JX6 transduced with ZBTB18-expressing lentiviral vector 1

description:
JX6-ZBTB18-1
replicate 1

value: brain tumor xenoline JX6


title: JX6 transduced with control lentiviral vector 3

description:
JX6-Ctr3
replicate 3

value: control


title: JX6 transduced with control lentiviral vector 2

description:
JX6-Ctr2
replicate 2


title: JX6 transduced with ZBTB18-expressing lentiviral vector 3

description:
JX6-ZBTB18-3
replicate 3


title: BTSC233 transduced with control lentiviral vector 1

description:
BTSC233-Ctr1
replicate 1


title: CD43neg B10.P0

description: 1 cell


title: JX6 transduced with control lentiviral vector 1

description:
JX6-Ctr1
replicate 1


title: JX6 transduced with ZBTB18-expressing lentiviral vector 2

description:
JX6-ZBTB18-2
replicate 2


title: CD43neg A9.P2

description: 1 cell


title: CD43neg A8.P1

description: 1 cell


title: BTSC233 transduced with control lentiviral vector 3

description:
BTSC233-Ctr3
replicate 3


title: CD43neg B11.P3

description: 1 cell


title: CD43neg B10.P1

description: 1 cell


title: CD43neg A9.P3

description: 1 cell


title: CD43neg A7.P1

description: 1 cell


title: CD43neg A9.P1

description: 1 cell


title: CD43neg A8.P3

description: 1 cell


title: CD43neg A9.P0

description: 1 cell


title: CD43neg A7.P2

description: 1 cell


title: CD43neg A6.P3

description: 1 cell


title: CD43neg A8.P2

description: 1 cell


title: CD43neg A7.P3

description: 1 cell


title: CD43neg A7.P4

description: 1 cell


title: CD43neg A6.P1

description: 1 cell


title: CD43neg A8.P0

description: 1 cell


title: CD43neg A5.P2

description: 1 cell


title: CD43neg A5.P1

description: 1 cell


title: BTSC233 transduced with control lentiviral vector 2

description:
BTSC233-Ctr2
replicate 2


title: CD43neg A6.P4

description: 1 cell


title: CD43neg A7.P0

description: 1 cell


title: CD43neg A3.P3

description: 1 cell


title: CD43neg A9.P4

description: 1 cell


title: CD43neg A4.P0

description: 1 cell


title: CD43neg A5.P4

description: 1 cell


title: CD43neg A3.P4

description: 1 cell


title: CD43neg A4.P4

description: 1 cell


title: CD43neg A4.P2

description: 1 cell


title: CD43neg A5.P0

description: 1 cell


title: CD43neg A5.P3

description: 1 cell


title: CD43neg A4.P3

description: 1 cell


title: ELT (epiairway) filtered air 3

status: Public on Apr 03 2017

city: Cardiff

first: Iain

middle: A

last: Perry

state: South Glamorgan

address: Longwood Drive

department: Wales Gene Park

country: United Kingdom

institute: Cardiff University

description:
US84300231_251485054887_S01_GE1_105_Jan09_1_3.txt
Biological replicate 3 of 4. Bronchial epithelial cells, exposed to filtered air.

hyb_protocol: For each hybridisation, 1ug experimental and 1ug reference cRNA were mixed, fragmented and hybridized at 65 Celsius for 17hrs onto Agilent Whole human genome 4x44K 60mer Oligo Microarrays.

scan_protocol: Post wash, arrays were scanned using Agilent Array scanner (G2505C) (Agilent Technologies).

data_processing: Data was normalized and extracted using Agilent feature extraction software (version 9.5.3) and the GE2-v5_95_Feb07 protocol.

source_name: Female Bronchial epithelial cells, MatTek's human 3D in vitro respiratory tissue model, exposed to filtered air

label_protocol: 500ng total RNA from each sample and universal human reference RNA (Stratagene, USA) was used for amplification of RNA and labelling with Cy5 (experimental) or Cy3 (reference) using Agilent's low RNA input linear amplification kit (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: MatTek's human 3D in vitro respiratory tissue model.

extract_protocol: RNA was extracted and purified using RNeasy Mini Kits (Qiagen UK) and integrity assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies, USA).

treatment_protocol: Mainstream cigarette smoke generated through the burning of 3R4F referenced filtered cigarettes was drawn under ISO standard conditions and diluted 1/50 (smoke:air) in filtered air using an RM20s smoke engine (Borgwaldt Technik GmbH, Germany), and delivered continually to exposure chambers for a period of 1hr.

tag: tissue type

value: Lung epithelium

tag: gender

value: Female

tag: treatment

value: Filtered air


title: C. carboxidivorans Syngas 4

city: Bunkyo-ku

first: Tatsuya

last: Inoue

state: Tokyo

address: Yayoi 1-1-1

department: Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

description: SG14484453_258414610002_S001_GE1_1105_Oct12_2_4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarray, 8×15K (Design ID : 084146, Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Sure Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Clostridium carboxidivorans

source_name: Log phase cells of C. carboxidivorans grown on syngas

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent One-color Microarray-Based Exon Analysis Low Input Quick Amp WT Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: C. carboxidivorans was inoculated to 30 ml of inorganic medium (Rajagopalan, S et al., 2002) containing 1 g/10 ml of iron granule in serum bottles . As controls, inoculated serum bottles without iron granule but with syngas were prepared. All procedures were done in anaerobic chamber (COY LABORATORY PRODUCTS AIR LOCK).

extract_protocol: RNA was prepared using the PowerSoil Total RNA Isolation Kit (MO BIO).  The protocol includes cell disruption by bead beating, and an on-column DNase digestion.  RNA was quantified using a UV-700 series (Nihon Bunkou) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: medium

value: Inorganic

tag: electron donor

value: syngas


title: CD43neg A6.P2

description: 1 cell


title: C. carboxidivorans Fe 4

description: SG14484453_258414610002_S001_GE1_1105_Oct12_1_4

source_name: Log phase cells of C. carboxidivorans corroding iron granule

value: iron granule


title: CD43neg A4.P1

description: 1 cell


title: C. carboxidivorans Syngas 2

description: SG14484453_258414610002_S001_GE1_1105_Oct12_2_2


title: C. carboxidivorans Fe 3

description: SG14484453_258414610002_S001_GE1_1105_Oct12_1_3


title: ELT (epiairway) smoke 2

description:
US84300231_251485054887_S01_GE1_105_Jan09_1_2.txt
Biological replicate 2 of 4. Bronchial epithelial cells, exposed to smoke.

source_name: Female Bronchial epithelial cells, MatTek's human 3D in vitro respiratory tissue model, exposed to cigarette smoke

value: Cigarette smoke


title: ELT (epiairway) smoke 3

description:
US84300231_251485054888_S01_GE1_105_Jan09_1_3.txt
Biological replicate 3 of 4. Bronchial epithelial cells, exposed to smoke.


title: C. carboxidivorans Syngas 1

description: SG14484453_258414610002_S001_GE1_1105_Oct12_2_1


title: ELT (epiairway) filtered air 1

description:
US84300231_251485054887_S01_GE1_105_Jan09_1_1.txt
Biological replicate 1 of 4. Bronchial epithelial cells, exposed to filtered air.


title: C. carboxidivorans Fe 2

description: SG14484453_258414610002_S001_GE1_1105_Oct12_1_2


title: ELT (epiairway) filtered air 2

description:
US84300231_251485054888_S01_GE1_105_Jan09_1_2.txt
Biological replicate 2 of 4. Bronchial epithelial cells, exposed to filtered air.


title: ELT (epiairway) smoke 4

description:
US84300231_251485054888_S01_GE1_105_Jan09_1_4.txt
Biological replicate 4 of 4. Bronchial epithelial cells, exposed to smoke.


title: C. carboxidivorans Syngas 3

description: SG14484453_258414610002_S001_GE1_1105_Oct12_2_3


title: C. carboxidivorans Fe 1

description: SG14484453_258414610002_S001_GE1_1105_Oct12_1_1


title: ELT (epiairway) filtered air 4

description:
US84300231_251485054887_S01_GE1_105_Jan09_1_4.txt
Biological replicate 4 of 4. Bronchial epithelial cells, exposed to filtered air.


title: ELT (epiairway) smoke 1

description:
US84300231_251485054888_S01_GE1_105_Jan09_1_1.txt
Biological replicate 1 of 4. Bronchial epithelial cells, exposed to smoke.


title: neutrophils_supernatant_rep3

city: Sheffield

first: Ian

last: Sabroe

address: Beech Hill Rd

department: Infection, Immunity and Cardiovascular Disease

institute: University of Sheffield

description: Neutrophils were pooled from 5 donors and kept in RPMI media supplemented with 1% penicillin and streptomycin and 10% low endotoxin FCS.

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus 2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: RMA normalisation procedure

source_name: human neutrophils after 4h incubation under LPS supernatant

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

growth_protocol: Human neutrophils were isolated by dextran sedimentation followed by plasma-Percoll gradient centrifugation from whole blood of healthy volunteers with written informed consent and ethical approval from the South Sheffield Research Ethics Committee. Neutrophils were kept at a concentration of 5 million cells per mL in RPMI media supplemented with  1% penicillin and streptomycin and 10% low endotoxin FCS

extract_protocol: After incubation,  pooled human neutrophils from 5 donors were taken from each condition and extracted using a TRI-Reagent

treatment_protocol: Human neutrophils were incubated under each treatment for 4h prior extraction.

value: Peripheral blood human neutrophils


title: neutrophils_mediaControl_rep3

source_name: human neutrophils after 4h incubation under LPS media (neg control)


title: neutrophils_supernatant_rep2


title: Control

city: Chuo-ku

first: Mitsuhiro

last: Machitani

address: 5-1-1 Tsukiji

institute: National Cancer Center Research Institute

hyb_protocol: The labeled samples were hybridized and washed using the Agilent Gene Expression Hybridization Kit and Wash Buffers Kit (Agilent Technologies).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using an Agilent SureScan microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software was used to read out and to process the microarray image files. Background subtraction and lowess normalization were performed in the analysis.

source_name: HeLa cells transfected with an control mimic

label_protocol: One hundred ng of each total RNA sample was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Hela-shDicer cells, which inducibly express shDicer by Dox treatment, were cultured in Dox-containing medium.

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

treatment_protocol: The cells were transfected with siControl or siAgp2. After 48 h incubation, total RNA was extracted using Isogen (Nippongen).

value: HeLa cells

tag: transfection


title: neutrophils_mediaControl_rep1


title: miR-27b

source_name: HeLa cells transfected with an miR-27b mimic


title: neutrophils_supernatant_rep1


title: neutrophils_PKAagonist_rep3

source_name: human neutrophils after 4h incubation under PKA agonist


title: neutrophils_PKAagonist_rep1


title: miR-27a

source_name: HeLa cells transfected with an miR-27a mimic


title: neutrophils_hypoxia_rep2

source_name: human neutrophils after 4h incubation under hypoxia


title: Offspring air 3

description:
US84300231_251486828199_S01_GE1_105_Jan09_1_2.txt
Biological replicate 3 of 3. Offspring, exposed to filtered air.

hyb_protocol: For each hybridisation, 1ug experimental and 1ug reference cRNA were mixed, fragmented and hybridized at 65 Celsius for 17hrs onto Agilent Whole mouse genome 4x44K 60mer Oligo Microarrays.

organism: Mus musculus

source_name: Female B6C6F1 mice, prenatal offspring, lung tissue, exposed to filtered air

label_protocol: 500ng total RNA from each sample and universal mouse reference RNA (Stratagene, USA) was used for amplification of RNA and labelling with Cy5 (experimental) or Cy3 (reference) using Agilent's low RNA input linear amplification kit (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: Female B6C6F1 mice.

treatment_protocol: Mainstream cigarette smoke generated through the burning of 3R4F referenced filtered cigarettes was drawn under ISO standard conditions and diluted 1/50 (smoke:air) in filtered air using an RM20s smoke engine (Borgwaldt Technik GmbH, Germany), and delivered continually to exposure chambers 4hrs/day, 5days/week during gestation until parturition (18 days) before sacrifice and lungs extracted for RNA extraction.

tag: strain/background

tag: developmental stage

value: Prenatal mice

value: Lung


title: neutrophils_TLR4agonist_rep2

source_name: human neutrophils after 4h incubation under TLR4 agonist


title: Striatum_5%O2_2h

city: Tokyo

first: Shuichi

last: Hara

address: 6-1-1 Shinjuku, Shinjuku-ku

department: Forensic Medicine

institute: Tokyo Medical University

description: Gene expression in striatum 2h after exposure to 5% O2 for 40 min.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (Cy3-CTP incorporation > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent Fragmentation Buffer and 2x Agilent Blocking Agent according to the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays 4x44k (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash Buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green, Green PMT is set to 100% and TIFF file dynamic range is 20bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Striatum, 5% O2 Exposure for 40min, 2h after Exposure

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Lipid Tissue Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male Sprague-Dawley rats (235 to 265 g; Charles River Laboratories, Kanagawa, Japan) were acclimated in the facility for at least 1 week before the experiments. The rat was anesthetized with sodium pentobarbital (50 mg/kg, i.p.) at 0, 2, 6 or 12 hours after the 40-minute exposure to air, 1000 ppm CO, 3000 ppm CO, or 5% O2. The brain was removed after perfusion with chilled saline via a cannula inserted into the carotid artery through the left ventricle. Both striata were dissected on ice, weighed, immersed in the RNAlater solution (Ambion, USA) overnight at 4ºC, and stored at -80ºC until analyzed. The experimental protocol for this study was approved by the Institutional Animal Care and Use Committee (IACUC) of Tokyo Medical University, and all experiments were performed in accordance with the Fundamental Guidelines for the Proper Conduct of Animal Experiments and Related Activities in Academic Research Institutions under the jurisdiction of the Ministry of Education, Culture, Sports, Science, and Technology, Japan.

tag: tissue

value: Striatum on both sides of the brain

value: male


title: neutrophils_hypoxia_rep3

tag: cell type


title: Striatum_5%O2_0h

description: Gene expression in striatum 0h after exposure to 5% O2 for 40 min.

source_name: Striatum, 5% O2 Exposure for 40min, 0h after Exposure


title: neutrophils_TLR4agonist_rep1


title: neutrophils_GMCSF_rep3

source_name: human neutrophils after 4h incubation under GMCSF


title: neutrophils_mediaControl_rep2


title: neutrophils_GMCSF_rep2


title: neutrophils_TLR4agonist_rep3


title: neutrophils_PKAagonist_rep2


title: neutrophils_hypoxia_rep1


title: Offspring smoke 1

description:
US84300231_251486828197_S01_GE1_105_Jan09_1_1.txt
Biological replicate 1 of 3. Offspring, exposed to smoke.

source_name: Female B6C6F1 mice, prenatal offspring, lung tissue, exposed to cigarette smoke


title: Dams air 3

description:
US84300231_251486828199_S01_GE1_105_Jan09_1_4.txt
Biological replicate 3 of 3. Dam mice, exposed to filtered air.

source_name: Female B6C6F1 mice, dam, lung tissue, exposed to filtered air

value: Mature pregnant mice


title: Offspring air 2

description:
US84300231_251486828199_S01_GE1_105_Jan09_1_1.txt
Biological replicate 2 of 3. Offspring, exposed to filtered air.


title: neutrophils_GMCSF_rep1


title: Striatum_5%O2_6h

description: Gene expression in striatum 6h after exposure to 5% O2 for 40 min.

source_name: Striatum, 5% O2 Exposure for 40min, 6h after Exposure


title: 20073368 Adipose 1 High Gain

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

hyb_protocol: Following fragmentation, cRNA was hybridized for 20 hr at 45C on Bovine 1.1ST Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned with the Affymetrix GeneAtlas Imager.

data_processing: The data were transformed by Affymetrix and analyzed with Affymetrix Expression Console and Affymetrix Transcriptome Analysis Console using the one-way between-Subject ANOVA (Unpaired) algorithm was (Linear Fold Change cutoff of 2 and ANOVA p-value (Condition pair) <0.05).

label: Biotin

organism: Bos taurus

source_name: Subcutaneous adipose tissue biopsied from the lumbo-sacral fat pad

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Cows (n=121) were placed on a diet to provide 120 kcal ME/kg BW0.75 for 112 days. Adipose was sampled on the 105th day of this trial. Cows were then offered feed ad libitum for 112 days. Adipose tissue was sampled at day 49.

extract_protocol: TriPure Reagent was used to extract total RNA according to manufacturer's instructions, except that a 20 minute centrifugation (rather than 15 min) was used following the addition of chloroform.

treatment_protocol: Animals most divergent for gain (6 highes gaining animals, and 6 lowest gaining animals) calculated using data from the ad libitum study, were selected and adipose tissue samples were collected. The adipose transcriptome was evaluated by microarray.

tag: group

value: High Gain

value: Subcutaneous adipose


title: Striatum_3000ppmCO_12h

description: Gene expression in striatum 12h after exposure to 3000ppm CO for 40 min.

source_name: Striatum, 3000ppm CO Exposure for 40min, 12h after Exposure


title: Offspring air 1

description:
US84300231_251486828197_S01_GE1_105_Jan09_1_3.txt
Biological replicate 1 of 3. Offspring, exposed to filtered air.


title: Striatum_3000ppmCO_6h

description: Gene expression in striatum 6h after exposure to 3000ppm CO for 40 min.

source_name: Striatum, 3000ppm CO Exposure for 40min, 6h after Exposure


title: Striatum_3000ppmCO_0h

description: Gene expression in striatum 0h after exposure to 3000ppm CO for 40 min.

source_name: Striatum, 3000ppm CO Exposure for 40min, 0h after Exposure


title: 20073368 Adipose 2 High Gain


title: Striatum_1000ppmCO_12h

description: Gene expression in striatum 12h after exposure to 1000ppm CO for 40 min.

source_name: Striatum, 1000ppm CO Exposure for 40min, 12h after Exposure


title: Offspring smoke 3

description:
US84300231_251486828198_S01_GE1_105_Jan09_1_4.txt
Biological replicate 3 of 3. Offspring, exposed to smoke.


title: Offspring smoke 2

description:
US84300231_251486828198_S01_GE1_105_Jan09_1_2.txt
Biological replicate 2 of 3. Offspring, exposed to smoke.


title: Dams air 2

description:
US84300231_251486828198_S01_GE1_105_Jan09_1_3.txt
Biological replicate 2 of 3. Dam mice, exposed to filtered air.


title: Striatum_3000ppmCO_2h

description: Gene expression in striatum 2h after exposure to 3000ppm CO for 40 min.

source_name: Striatum, 3000ppm CO Exposure for 40min, 2h after Exposure


title: Dams air 1

description:
US84300231_251486828198_S01_GE1_105_Jan09_1_1.txt
Biological replicate 1 of 3. Dam mice, exposed to filtered air.


title: 20073292 Adipose 2 Low Gain

value: Low Gain


title: Dams smoke 3

description:
US84300231_251486828199_S01_GE1_105_Jan09_1_3.txt
Biological replicate 3 of 3. Dam mice, exposed to smoke.

source_name: Female B6C6F1 mice, dam, lung tissue, exposed to cigarette smoke


title: Dams smoke 1

description:
US84300231_251486828197_S01_GE1_105_Jan09_1_2.txt
Biological replicate 1 of 3. Dam mice, exposed to smoke.


title: 20073271 Adipose 2 High Gain


title: Dams smoke 2

description:
US84300231_251486828197_S01_GE1_105_Jan09_1_4.txt
Biological replicate 2 of 3. Dam mice, exposed to smoke.


title: Striatum_1000ppmCO_2h

description: Gene expression in striatum 2h after exposure to 1000ppm CO for 40 min.

source_name: Striatum, 1000ppm CO Exposure for 40min, 2h after Exposure


title: Striatum_1000ppmCO_6h

description: Gene expression in striatum 6h after exposure to 1000ppm CO for 40 min.

source_name: Striatum, 1000ppm CO Exposure for 40min, 6h after Exposure


title: Striatum_Air_0h

description: Gene expression in striatum 0h after exposure to air for 40 min.

source_name: Striatum, Air Exposure for 40min, 0h after Exposure


title: 20073271 Adipose 1 High Gain


title: Striatum_1000ppmCO_0h

description: Gene expression in striatum 0h after exposure to 1000ppm CO for 40 min.

source_name: Striatum, 1000ppm CO Exposure for 40min, 0h after Exposure


title: 20073292 Adipose 1 Low Gain


title: 20073167 Adipose 2 Low Gain


title: 20073228 Adipose 1 Low Gain


title: 20073167 Adipose 1 Low Gain


title: 20073240 Adipose 2 Low Gain


title: 20073228 Adipose 2 Low Gain


title: 20073093 Adipose 2 High Gain


title: 20073070 Adipose 1 High Gain


title: 20073048 Adipose 2 High Gain


title: 20073070 Adipose 2 High Gain


title: 20073240 Adipose 1 Low Gain


title: 20073093 Adipose 1 High Gain


title: 20073017 Adipose 1 Low Gain


title: 20073017 Adipose 2 Low Gain


title: 20073048 Adipose 1 High Gain


title: 20073011 Adipose 2 Low Gain


title: 20073011 Adipose 1 Low Gain


title: 20073007 Adipose 2 High Gain


title: 1928z-hIL18-3-Day8

city: NEW YORK

first: Mauro

middle: Pellegrino

last: Avanzi

state: NY

address: 427 east 73rd street apt 5B

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: nCounter XT CodeSet Gene Expression  Assays, July-2016.

scan_protocol: Data Collection is carried out in the nCounter® Digital Analyzer. At the highest standard data resolution, 555–1155 fields of view (FOV) are  collected per flow cell using a microscope objective and a CCD camera yielding data of hundreds of thousands of target molecule counts.  Digital images are processed on the nCounter Digital Analyzer and the barcode counts are tabulated in a comma separated value (CSV)  format.

data_processing: nCounter®  Expression Data Analysis Guide-MAN-C0011-03, using nSolver Analysis Software v2.5.

label: Nanostring

source_name: Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Nanostring protocol from 2 ug total RNA.

growth_protocol: RPMI media in 37 degree and 5% CO2 incubator

extract_protocol: Total RNA was extracted with Ambion RNA extraction kit

value: blood

value: CAR T cells


title: 1928z-hIL18-3-Day1


title: 20073007 Adipose 1 High Gain


title: genomic DNA from HB38T

type: genomic

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

description: tumor

hyb_protocol: 250ng of bisulfite converted DNA was hybridized in the 450K Illumina Beadchip arrays using standard Illumina protocol

scan_protocol: The Illumina iScan SQ scanner was used to obtain images of the microarrays.

data_processing: The fluorescence signals were interpreted with the GenomeStudio software (v.2011.1) with the methylation module v.1.9.0 (Illumina).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Hepatoblastoma 38

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted  using phenol:chloroform method

value: female

tag: morphology

value: Mixed


title: 1928z-hIL18-1-Day8


title: genomic DNA from HB45T

description: tumor

source_name: Hepatoblastoma 45

value: Fetal


title: genomic DNA from HB40T

description: tumor

source_name: Hepatoblastoma 40


title: genomic DNA from HB42T

description: tumor

source_name: Hepatoblastoma 42


title: genomic DNA from HB44T

description: tumor

source_name: Hepatoblastoma 44


title: 1928z-hIL18-2-Day8


title: genomic DNA from HB43T

description: tumor

source_name: Hepatoblastoma 43


title: genomic DNA from HB39T

description: tumor

source_name: Hepatoblastoma 39


title: 1928z-3-Day8


title: genomic DNA from HB37T

description: tumor

source_name: Hepatoblastoma 37


title: 1928z-hIL18-1-Day1


title: 1928z-hIL18-2-Day1


title: genomic DNA from HB30T

description: tumor

source_name: Hepatoblastoma 30


title: genomic DNA from HB35T

description: tumor

source_name: Hepatoblastoma 35


title: genomic DNA from HB31T

description: tumor

source_name: Hepatoblastoma 31


title: genomic DNA from HB16T

description: tumor

source_name: Hepatoblastoma 16


title: 1928z-3-Day1


title: 1928z-2-Day8


title: 1928z-2-Day1


title: 1928z-1-Day1


title: genomic DNA from HB33T

description: tumor

source_name: Hepatoblastoma 33


title: genomic DNA from HB17T

description: tumor

source_name: Hepatoblastoma 17


title: genomic DNA from HB28T

description: tumor

source_name: Hepatoblastoma 28

value: Embryonal


title: genomic DNA from FIG32N

description: normal

source_name: Differentiated liver 32

value: normal differentiated liver


title: genomic DNA from HB18T

description: tumor

source_name: Hepatoblastoma 18


title: genomic DNA from HB32T

description: tumor

source_name: Hepatoblastoma 32


title: genomic DNA from HB41T

description: tumor

source_name: Hepatoblastoma 41


title: 1928z-1-Day8

source_name: Blood


title: genomic DNA from FIG31N

description: normal

source_name: Differentiated liver 31


title: genomic DNA from FIG30N

description: normal

source_name: Differentiated liver 30


title: genomic DNA from FIG19N

description: normal

source_name: Differentiated liver 19


title: genomic DNA from saliva of 73SA_S60M15016

status: Public on Apr 02 2017

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University College of Medicine

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

source_name: saliva of 73SA_S60M15016

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using QIAamp DNA Investigator Kit and Mini Kit

tag: age

value: Male

tag: ethnicity

value: Korean-Asian

value: Saliva


title: genomic DNA from FIG17N

description: normal

source_name: Differentiated liver 17


title: genomic DNA from saliva of 53SA_S50M15002

source_name: saliva of 53SA_S50M15002


title: genomic DNA from saliva of 48SA_40M15013

source_name: saliva of 48SA_40M15013


title: genomic DNA from HB15T

description: tumor

source_name: Hepatoblastoma 15


title: genomic DNA from saliva of 70SA_S60M15009

source_name: saliva of 70SA_S60M15009


title: genomic DNA from saliva of 42SA_S40M15020

source_name: saliva of 42SA_S40M15020


title: genomic DNA from saliva of 28SA_20M15014

source_name: saliva of 28SA_20M15014


title: genomic DNA from FIG20N

description: normal

source_name: Differentiated liver 20


title: genomic DNA from saliva of 45SA_40M15028

source_name: saliva of 45SA_40M15028


title: genomic DNA from saliva of 47SA_40M15021

source_name: saliva of 47SA_40M15021


title: genomic DNA from saliva of 49SA_S40M15006

source_name: saliva of 49SA_S40M15006


title: genomic DNA from FIG16N

description: normal

source_name: Differentiated liver 16


title: genomic DNA from saliva of 29SA_20M15038

source_name: saliva of 29SA_20M15038


title: genomic DNA from FIG15N

description: normal

source_name: Differentiated liver 15


title: genomic DNA from saliva of 52SA_S50M15016

source_name: saliva of 52SA_S50M15016


title: genomic DNA from saliva of 64SA_60M15005

source_name: saliva of 64SA_60M15005


title: genomic DNA from saliva of 69SA_S60M15003

source_name: saliva of 69SA_S60M15003


title: genomic DNA from saliva of 44SA_40M15023

source_name: saliva of 44SA_40M15023


title: genomic DNA from saliva of 52SA_50M15004

source_name: saliva of 52SA_50M15004


title: genomic DNA from saliva of 70SA_60M15006

source_name: saliva of 70SA_60M15006


title: genomic DNA from saliva of 50SA_50M15001

source_name: saliva of 50SA_50M15001


title: genomic DNA from saliva of 36SA_S30M15024

source_name: saliva of 36SA_S30M15024


title: genomic DNA from FIG33N

description: normal

source_name: Differentiated liver 33


title: genomic DNA from saliva of 65SA_S60M15004

source_name: saliva of 65SA_S60M15004


title: genomic DNA from saliva of 65SA_S60M15006

source_name: saliva of 65SA_S60M15006


title: genomic DNA from saliva of 62SA_S60M15013

source_name: saliva of 62SA_S60M15013


title: genomic DNA from FIG09N

description: normal

source_name: Differentiated liver 09


title: genomic DNA from saliva of 30SA_30M15040

source_name: saliva of 30SA_30M15040


title: genomic DNA from saliva of 56SA_S50M15001

source_name: saliva of 56SA_S50M15001


title: genomic DNA from saliva of 58SA_S50M15008

source_name: saliva of 58SA_S50M15008


title: genomic DNA from saliva of 54SA_S50M15019

source_name: saliva of 54SA_S50M15019


title: genomic DNA from saliva of 55SA_S50M15010

source_name: saliva of 55SA_S50M15010


title: KO(cy3) vs EV(cy5) biological replicate 2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

hyb_protocol: After washing in GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2505C.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: HEC1B harboring the empty vector (EV) cells

label_protocol: Differentially labeled 825 ng of each cRNA samples were hybridized on microarray slides. Samples were then hybridized on Agilent 4 × 44KWhole Human Genome Oligo Microarray ver. 2 (G4845A) at 65 °C for 17 h with rotation in the dark. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions.

growth_protocol: For culture in standard conditions (arginine-replete), cell lines were cultured in DMEM supplemented with 10% FBS, penicillin (100 IU/mL), and streptomycin (100 μg/mL) and maintained at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using miRNeasy following manufacturer's instructions

treatment_protocol: In arginine or lysine depletion experiments, cells were cultured in arginine- or lysine-depleted DMEM supplemented with 10% dialyzed FBS, penicillin (100 IU/mL), and streptomycin (100 μg/mL) and maintained at 37°C in 5% CO2.

tag: genotype

value: ASS1 wild-type

source_name: ASS1-KO HEC1B cells


title: genomic DNA from saliva of 53SA_50M15005

source_name: saliva of 53SA_50M15005


title: genomic DNA from saliva of 60SA_S60M15012

source_name: saliva of 60SA_S60M15012


title: genomic DNA from saliva of 50SA_S50M15018

source_name: saliva of 50SA_S50M15018


title: EV(cy3) vs KO(cy5) biological eplicate 2 dyeswap


title: genomic DNA from saliva of 49SA_40M15018

source_name: saliva of 49SA_40M15018


title: genomic DNA from saliva of 31SA_30M15027

source_name: saliva of 31SA_30M15027


title: genomic DNA from saliva of 44SA_40M15008

source_name: saliva of 44SA_40M15008


title: genomic DNA from saliva of 27SA_20M15039

source_name: saliva of 27SA_20M15039


title: genomic DNA from saliva of 57SA_50M15009

source_name: saliva of 57SA_50M15009


title: genomic DNA from saliva of 42SA_40M15026

source_name: saliva of 42SA_40M15026


title: KO(cy3) vs EV(cy5) biological replicate 1


title: genomic DNA from saliva of 38SA_30M15011

source_name: saliva of 38SA_30M15011


title: genomic DNA from saliva of 47SA_40M15020

source_name: saliva of 47SA_40M15020


title: genomic DNA from saliva of 34SA_30M15005

source_name: saliva of 34SA_30M15005


title: genomic DNA from saliva of 35SA_S30M15031

source_name: saliva of 35SA_S30M15031


title: genomic DNA from saliva of 32SA_30M15008

source_name: saliva of 32SA_30M15008


title: genomic DNA from saliva of 39SA_30M15001

source_name: saliva of 39SA_30M15001


title: genomic DNA from saliva of 47SA_40M15001

source_name: saliva of 47SA_40M15001


title: genomic DNA from saliva of 25SA_20M15041

source_name: saliva of 25SA_20M15041


title: genomic DNA from saliva of 26SA_20M15032

source_name: saliva of 26SA_20M15032


title: genomic DNA from saliva of 37SA_S30M15011

source_name: saliva of 37SA_S30M15011


title: Liver_D_rep1

status: Public on Apr 01 2017

city: Dalian

first: Zhou

last: Zhang

state: Liaoning

address: Linggong Road 2

department: Environmental Science and Technology

country: China

institute: Dalian University of Technology

description: Gene expression after 96h exposure of surface water from site D

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

organism: Danio rerio

source_name: liver, 97h, site D

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: Zebrafish were raised at 27±1℃ with a 14:10 h light/dark cycle.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Adult zebrafish were treated with surface water from several sites of the Hun River for 96h.

value: liver

value: 3 month


title: EV(cy3) vs KO(cy5) biological replicate 1 dyeswap

source_name: ASS1-KO HEC1B cells

source_name: HEC1B harboring the empty vector (EV) cells


title: genomic DNA from saliva of 24SA_20M15007

source_name: saliva of 24SA_20M15007


title: Liver_H4_rep1

description: Gene expression after 96h exposure of surface water from site H4

source_name: liver, 96h, site H4

value: male


title: genomic DNA from saliva of 52SA_50M15011

source_name: saliva of 52SA_50M15011


title: genomic DNA from saliva of 33SA_30M15044

source_name: saliva of 33SA_30M15044


title: genomic DNA from saliva of 22SA_20M15029

source_name: saliva of 22SA_20M15029


title: genomic DNA from saliva of 23SA_20M15013

source_name: saliva of 23SA_20M15013


title: Leaf gDNA_Carignan white berry variant_rep1

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

country: Spain

institute: CSIC

description:
CB1
Vitis vinifera L.
Berry colour variant Carignan Blanc.

hyb_protocol: 7.5 µg of labelled DNA was used for hybridization of microarrays according to the Affymetrix GeneChip® Expression Analysis Technical Manual.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 as recommended by manufacturer.

data_processing: CEL files were normalized using RMA and differential probe set hybridization between black/white cultivars evaluated with the RankProd package from Bioconductor (Breitling et al. 2004). Copy number along the genome was analyzed by searching differential hybridization signal between black- and white-skinned berry lines using a cut-off value white/colored line ratio of -1.8 fold-change and P <0.001 to detect genes with decreased copy number in the white line genome.

organism: Vitis vinifera

source_name: young leaves, Carignan white berry variant

label_protocol: gDNA samples (10 µg each) were fragmented to an average size of 0.5 kb with a sonicator Labsonic U set at 50% intensity and repeating duty cycle 0.5, 4 pulses of 10 seconds each. Labelling of DNA was performed as recommended in GeneChip® Whole Transcript Double-Stranded Target Assay (Affymetrix). Briefly, fragmented DNA was amplified, purified and biotin terminal labelled with Double-Stranded DNA Terminal Labeling Kit (Affymetrix), following recommendations.

growth_protocol: Grapevine plants used were all grafted in Richter-110 rootstock, trellised in double cordon Royat system and cultured under vineyard conditions.

extract_protocol: Total gDNA was isolated from young leaves using the DNeasy Plant Mini Kit (Qiagen, Germany) according to the protocol described by the manufacturer.

treatment_protocol: White berry variants were compared to original black berry cultivars.

tag: cultivar

value: Carignan Blanc

tag: berry color

value: white

value: young leaves


title: genomic DNA from saliva of 21SA_20M15035

source_name: saliva of 21SA_20M15035


title: Leaf gDNA_Carignan white berry variant_rep2

description:
CB2
Vitis vinifera L.
Berry colour variant Carignan Blanc.


title: Liver_H5_rep1

description: Gene expression after 96h exposure of surface water from site H5

source_name: liver, 96h, site H5


title: Liver_control_rep1

description: Gene expression after 96h untreated

source_name: liver, 96h, control


title: Leaf gDNA_Granacha white berry variant_rep2

description:
GB2
Vitis vinifera L.
Berry colour variant Garnacha Blanca.

source_name: young leaves, Granacha white berry variant

value: Garnacha Blanca


title: Liver_H2_rep1

description: Gene expression after 96h exposure of surface water from site H2

source_name: liver, 96h, site H2


title: genomic DNA from saliva of 19SA_20M15009

source_name: saliva of 19SA_20M15009


title: Liver_H1_rep1

description: Gene expression after 96h exposure of surface water from site H1

source_name: liver, 96h, site H1


title: Leaf gDNA_Tempranillo original berry colour line_rep2

description:
TT2
Vitis vinifera L.
Original berry colour Tempranillo Tinto.

source_name: young leaves, Tempranillo original berry colour line

value: Tempranillo Tinto

value: black


title: Leaf gDNA_Granacha original berry colour line_rep1

description:
GT1
Vitis vinifera L.
Original berry colour Garnacha Tinta.

source_name: young leaves, Granacha original berry colour line

value: Garnacha Tinta


title: genomic DNA from saliva of 20SA_20M15015

source_name: saliva of 20SA_20M15015


title: Leaf gDNA_Granacha white berry variant_rep1

description:
GB1
Vitis vinifera L.
Berry colour variant Garnacha Blanca.


title: Leaf gDNA_Tempranillo white berry variant_rep2

description:
TB2
Vitis vinifera L.
Berry colour variant Tempranillo Blanco.

source_name: young leaves, Tempranillo white berry variant

value: Tempranillo Blanco


title: Liver_X_rep1

description: Gene expression after 96h exposure of surface water from site X

source_name: liver, 97h, site X


title: Leaf gDNA_Granacha original berry colour line_rep2

description:
GT2
Vitis vinifera L.
Original berry colour Garnacha Tinta.


title: Leaf gDNA_Tempranillo white berry variant_rep1

description:
TB1
Vitis vinifera L.
Berry colour variant Tempranillo Blanco.


title: Leaf gDNA_Tempranillo original berry colour line_rep1

description:
TT1
Vitis vinifera L.
Original berry colour Tempranillo Tinto.


title: genomic DNA from saliva of 18SA_20M15020

source_name: saliva of 18SA_20M15020


title: E13.5 TH-MYCN_passage sphere_rep.1-1

city: Nagoya

first: Shoma

last: Tsubota

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Molecular Biology

institute: Nagoya University Graduate School of Medicine

description:
Gene expression of  E13.5 TH-MYCN_primary sphere_rep.1-1
SAMPLE 8

hyb_protocol: Purified labelled total RNAs were hybridized to SurePrint G3 Mouse Gene Expression 8x60K Microarray (G4852A, Agilent Technologies).

scan_protocol: Hybridization, scanning of microarrays, and data extraction from scanned images were conducted using the SureScan Microarray Scanner (G4900DA, Agilent Technologies) according to the Agilent protocol version 6.9 and Feature Extraction (version 13.1) software.

data_processing: Scanned signals were analyzed using Subio Platform (Subio inc., Japan). Low signal cutoff was set to 1.0. Log transformation was applied with base 2. Global normalization was cunducted at percentage 75. Centering was applied by Mean. The normalized data (included in the sample table) was further filtered out (1) if Entrez gene ID is not annotated, (2) if Refseq number starts from either XM or XR (which is predicted gene), and (3) if the gene name contains "Predicted gene". It was further filtered out if 50% of gIsWellAboveBGs flag is zero at all sample groups (which signals are lower than background signal), and if standard deviation of normalized signals are over 2 at one of each sample group (which signals are fluctuating within a sample group). The resulting data (with 20403 data rows) was used for comparing differentially expressed probes.

source_name: E13.5 TH-MYCN_passage sphere

label_protocol: 40 or 200 ng of total RNAs were labeled with Cyanine3 using Low Input Quick-Amp Labeling Kit (one color, 5190-2305, Agilent technologies) according to the manufacture’s instruction, followed by probe purification with RNeasy Mini Kit (74104, QIAGEN).

extract_protocol: Total RNAs from spheres were isolated using ISOGEN II (317-07363, Nippon Gene) according to the manufacture’s instruction. Total RNA quantity and quality was examined by Agilent RNA6000 Nano Kit (5067-1511, Agilent Technologies) and Agilent 2100 Bioanalyzer (Agilent Technologies)　according to the manufacture’s instruction. Total RNA samples with over RNA Integrity Number 8 were subjected to microarray analysis.

tag: strain background

tag: genotype/variation

value: TH-MYCN (hemizygote)

value: primary sphere


title: E13.5 TH-MYCN_passage sphere_rep.2-2

description:
Gene expression of  E13.5 TH-MYCN_primary sphere_rep.2-2
SAMPLE 11


title: E13.5 TH-MYCN_passage sphere_rep.3-2

description:
Gene expression of  E13.5 TH-MYCN_primary sphere_rep.3-2
SAMPLE 13


title: E13.5 WT_primary sphere_rep.4-1

description:
Gene expression of  E13.5 WT_primary sphere_rep.4-1
SAMPLE 6

source_name: E13.5 WT_primary sphere

value: wild-type


title: E13.5 TH-MYCN_passage sphere_rep.4-1

description:
Gene expression of  E13.5 TH-MYCN_primary sphere_rep.4-1
SAMPLE 14


title: E13.5 TH-MYCN_passage sphere_rep.4-2

description:
Gene expression of  E13.5 TH-MYCN_primary sphere_rep.4-2
SAMPLE 15


title: E13.5 TH-MYCN_passage sphere_rep.2-1

description:
Gene expression of  E13.5 TH-MYCN_primary sphere_rep.2-1
SAMPLE 10


title: E13.5 TH-MYCN_passage sphere_rep.1-2

description:
Gene expression of  E13.5 TH-MYCN_primary sphere_rep.1-2
SAMPLE 9


title: E13.5 WT_primary sphere_rep.3-1

description:
Gene expression of  E13.5 WT_primary sphere_rep.3-1
SAMPLE 5


title: E13.5 WT_primary sphere_rep.2-2

description:
Gene expression of  E13.5 WT_primary sphere_rep.2-2
SAMPLE 4


title: Liver_H3_rep1

description: Gene expression after 96h exposure of surface water from site H3

source_name: liver, 96h, site H3

tag: gender


title: E13.5 TH-MYCN_passage sphere_rep.3-1

description:
Gene expression of  E13.5 TH-MYCN_primary sphere_rep.3-1
SAMPLE 12


title: E13.5 WT_primary sphere_rep.4-2

description:
Gene expression of  E13.5 WT_primary sphere_rep.4-2
SAMPLE 7


title: E13.5 WT_primary sphere_rep.1-2

description:
Gene expression of  E13.5 WT_primary sphere_rep.1-2
SAMPLE 2


title: Leaf gDNA_Carignan original berry colour line_rep1

description:
CN1
Vitis vinifera L.
Original berry colour Carignan Noir.

source_name: young leaves, Carignan original berry colour line

value: Carignan Noir


title: 3w TH-MYCN_Passage sphere_rep.4-2

description:
Gene expression of  3-week-old TH-MYCN passage sphere rep.4-2 passaged 5 times
SAMPLE 32

data_processing: Scanned signals were analyzed using Subio Platform (Subio inc., Japan). Low signal cutoff was set to 1.0. Log transformation was applied with base 2. Global normalization was cunducted at percentage 75. Centering was applied by Mean. The normalized data (included in the sample table) was further filtered out (1) if Entrez gene ID is not annotated, (2) if Refseq number starts from either XM or XR (which is predicted gene), and (3) if the gene name contains "Predicted gene". It was further filtered out if 50% of gIsWellAboveBGs flag is zero at all sample groups (which signals are lower than background signal). The resulting data (with 23330 data rows) was considered as reliable probes. In the analysis, the normalized data was further filtered out if mean of normalized signals are between -1 to 1 at all sample groups (which signals are not varying), and filtered out if standard deviation of normalized signals are over 2 at one of each sample group (which signals are fluctuating within a sample group). The resulting data (with 7232 data rows) was considered as differentially expressed probes among four groups.

source_name: 3-week-old TH-MYCN_Passage sphere

value: TH-MYCN hemizygote (TH-MYCN+/-)

value: 3 weeks

tag: tissue/cell type

value: passage sphere


title: 3w TH-MYCN_Passage sphere_rep.4-1

description:
Gene expression of  3-week-old TH-MYCN passage sphere rep.4-1 passaged 5 times
SAMPLE 31


title: 3w TH-MYCN_Passage sphere_rep.3-1

description:
Gene expression of  3-week-old TH-MYCN passage sphere rep.3-1 passaged 5 times
SAMPLE 29


title: 3w TH-MYCN_Passage sphere_rep.2-1

description:
Gene expression of  3-week-old TH-MYCN passage sphere rep.2-1 passaged 5 times
SAMPLE 27


title: 3w TH-MYCN_Passage sphere_rep.3-2

description:
Gene expression of  3-week-old TH-MYCN passage sphere rep.3-2 passaged 5 times
SAMPLE 30


title: 3w TH-MYCN_Passage sphere_rep.1-1

description:
Gene expression of  3-week-old TH-MYCN passage sphere rep.1-1 passaged 5 times
SAMPLE 25


title: 3w TH-MYCN_Passage sphere_rep.2-2

description:
Gene expression of  3-week-old TH-MYCN passage sphere rep.2-2 passaged 5 times
SAMPLE 28


title: 3w TH-MYCN_Passage sphere_rep.1-2

description:
Gene expression of  3-week-old TH-MYCN passage sphere rep.1-2 passaged 5 times
SAMPLE 26


title: 3w TH-MYCN_Primary sphere_rep.7

description:
Gene expression of  3-week-old TH-MYCN primary sphere rep.7 cultured for 8 days
SAMPLE 23

source_name: 3-week-old TH-MYCN_Primary sphere


title: E13.5 WT_primary sphere_rep.1-1

description:
Gene expression of  E13.5 WT_primary sphere_rep.1-1
SAMPLE 1


title: 3w TH-MYCN_Primary sphere_rep.4

description:
Gene expression of  3-week-old TH-MYCN primary sphere rep.4 cultured for 8 days
SAMPLE 20


title: E13.5 WT_primary sphere_rep.2-1

description:
Gene expression of  E13.5 WT_primary sphere_rep.2-1
SAMPLE 3


title: 3w TH-MYCN_Primary sphere_rep.5

description:
Gene expression of  3-week-old TH-MYCN primary sphere rep.5 cultured for 8 days
SAMPLE 21


title: 3w TH-MYCN_Primary sphere_rep.8

description:
Gene expression of  3-week-old TH-MYCN primary sphere rep.8 cultured for 8 days
SAMPLE 24


title: 3w TH-MYCN_Primary sphere_rep.2

description:
Gene expression of  3-week-old TH-MYCN primary sphere rep.2 cultured for 8 days
SAMPLE 18


title: 3w TH-MYCN_Primary sphere_rep.6

description:
Gene expression of  3-week-old TH-MYCN primary sphere rep.6 cultured for 8 days
SAMPLE 22


title: 3w TH-MYCN_SMG_rep.8

description:
Gene expression of  3-week-old TH-MYCN SMG rep.8
SAMPLE 16

source_name: 3-week-old TH-MYCN_SMG

value: superior mesenteric ganglion (SMG)


title: 3w TH-MYCN_Primary sphere_rep.1

description:
Gene expression of  3-week-old TH-MYCN primary sphere rep.1 cultured for 8 days
SAMPLE 17


title: 3w TH-MYCN_SMG_rep.2

description:
Gene expression of  3-week-old TH-MYCN SMG rep.2
SAMPLE 10


title: 3w WT_SMG_rep.5

description:
Gene expression of  3-week-old WT SMG rep.5
SAMPLE 5

source_name: 3-week-old WT_SMG

value: wild type


title: Leaf gDNA_Carignan original berry colour line_rep2

description:
CN2
Vitis vinifera L.
Original berry colour Carignan Noir.


title: 3w TH-MYCN_Primary sphere_rep.3

description:
Gene expression of  3-week-old TH-MYCN primary sphere rep.3 cultured for 8 days
SAMPLE 19


title: 3w TH-MYCN_SMG_rep.5

description:
Gene expression of  3-week-old TH-MYCN SMG rep.5
SAMPLE 13


title: 3w TH-MYCN_SMG_rep.1

description:
Gene expression of  3-week-old TH-MYCN SMG rep.1
SAMPLE 9


title: 3w WT_SMG_rep.4

description:
Gene expression of  3-week-old WT SMG rep.4
SAMPLE 4


title: 3w WT_SMG_rep.3

description:
Gene expression of  3-week-old WT SMG rep.3
SAMPLE 3


title: 3w TH-MYCN_SMG_rep.4

description:
Gene expression of  3-week-old TH-MYCN SMG rep.4
SAMPLE 12


title: 3w TH-MYCN_SMG_rep.7

description:
Gene expression of  3-week-old TH-MYCN SMG rep.7
SAMPLE 15


title: 3w WT_SMG_rep.7

description:
Gene expression of  3-week-old WT SMG rep.7
SAMPLE 7


title: 3w WT_SMG_rep.1

description:
Gene expression of  3-week-old WT SMG rep.1
SAMPLE 1


title: 3w TH-MYCN_SMG_rep.3

description:
Gene expression of  3-week-old TH-MYCN SMG rep.3
SAMPLE 11


title: 3w WT_SMG_rep.8

description:
Gene expression of  3-week-old WT SMG rep.8
SAMPLE 8


title: 3w TH-MYCN_rep.1_RA (-) sphere

description: Gene expression of  3-week-old TH-MYCN rep.1 primary spheres cultured in RA (-) medium for 8 days

data_processing: Scanned signals were analyzed using Subio Platform (Subio inc., Japan). Low signal cutoff was set to 1.0. Log transformation was applied with base 2. Global normalization was cunducted at percentage 75. Centering was applied by Mean. The normalized data (included in the sample table) was further filtered out if 50% of gIsWellAboveBGs flag is zero at one of the sample groups (which signals are lower than background signal), and further filtered if 100% of gIsFeatNonUnifOLs flag is zero at all samples (which signals are reliable). The resulting data (with 26,452 data rows) was used for comparing differentially expressed probes.

source_name: 3w TH-MYCN_RA (-) sphere

tag: cell type source

tag: medium

value: RA (-) medium

value: primary spheres


title: 3w TH-MYCN_rep.4_RA (-) sphere

description: Gene expression of  3-week-old TH-MYCN rep.4 primary spheres cultured in RA (-) medium for 8 days


title: 3w TH-MYCN_rep.2_RA (-) sphere

description: Gene expression of  3-week-old TH-MYCN rep.2 primary spheres cultured in RA (-) medium for 8 days


title: 3w TH-MYCN_rep.2_RA (+) sphere

description: Gene expression of  3-week-old TH-MYCN rep.2 primary spheres cultured in RA (+) medium for 8 days

source_name: 3w TH-MYCN_RA (+) sphere

value: RA (+) medium


title: 3w WT_SMG_rep.2

description:
Gene expression of  3-week-old WT SMG rep.2
SAMPLE 2


title: 3w TH-MYCN_rep.3_RA (-) sphere

description: Gene expression of  3-week-old TH-MYCN rep.3 primary spheres cultured in RA (-) medium for 8 days


title: 3w TH-MYCN_rep.3_RA (+) sphere

description: Gene expression of  3-week-old TH-MYCN rep.3 primary spheres cultured in RA (+) medium for 8 days


title: 3w TH-MYCN_rep.4_RA (+) sphere

description: Gene expression of  3-week-old TH-MYCN rep.4 primary spheres cultured in RA (+) medium for 8 days


title: 3w TH-MYCN_rep.1_RA (+) sphere

description: Gene expression of  3-week-old TH-MYCN rep.1 primary spheres cultured in RA (+) medium for 8 days


title: 3w WT_SMG_rep.6

description:
Gene expression of  3-week-old WT SMG rep.6
SAMPLE 6


title: 3w TH-MYCN_SMG_rep.6

description:
Gene expression of  3-week-old TH-MYCN SMG rep.6
SAMPLE 14


title: H_101A

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Amplified and labelled samples were added to hybridization buffer (Agilent In Situ Hybridization Kit Plus), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially and dried with acetonitrile according to the Agilent protocol.

scan_protocol: Scanned on an Genepix A4100 scanner.

data_processing: Images were quantified using GenePix v. 5.1.

label_protocol: RNA was isolated using the RNeasy kit (Qiagen) and the total RNA was reverse-transcribed, preamplified, and labeled using the BD Atlas SMART Fluorescent Probe Amplification Kit (Clontech Laboratories). RNA was subjected to reverse transcription. cDNA obtained from the reverse transcription was amplified with 22 SMART PCR cycles. The dsDNA products were labeled by four additional PCR cycles in the presence of aminoallylated UTP, and then coupled with monofunctional reactive Cy3- and Cy5-dyes (Amersham). The labeled dsDNA was purified with the Qiaquick PCR Purification Kit (Qiagen) following the kit instructions

extract_protocol: Lung tissues were collected from patients with IPF undergoing lung transplantation at the University of Giessen (Germany) or Vienna (Austria). All patients were accessed, diagnosed, and treated in expert centers for interstitial lung disease. Nontransplanted donor lung tissue showing no evidence of interstitial lung disease served as healthy controls. Laser-Microdissection of donor and patient lungs was performed as described previously (Kwapiszewska G. et al. (2005) Respir Res 6:109107). Cryosections from lung tissue were mounted on glass slides, subjected to haemalaun staining and septa were microdissected under optical control using the Laser Microbeam System (P.A.L.M.).

value: fibrotic lung, non-fibrotic tissue

source_name: Donor

value: healty lung


title: H_130A


title: H_105B


title: H_52B


title: H_24A


title: H_86A


title: F_86A

value: fibrotic lung, fibrotic tissue


title: H_88B


title: H_45B


title: KCNQ mutant heart biological rep 3

city: Claremont

first: Alexander

middle: C

last: Zambon

state: CA

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

description: Gene expression data from drosophila heart tubes

hyb_protocol: Hybridization of the RNA to the Affymetrix GeneChips, washing and scanning were done according to protocols recommended by Affymetrix using an Affymetrix GeneChip fluidic station and scanner (Affymetrix, Santa Clara, CA).

scan_protocol: Affymetrix GeneChip Scanner 3000 was used to scan arrays

data_processing: Raw cell files were normalized using RMA using AltAnalyze

organism: Drosophila melanogaster

source_name: Drosophila heart tubes

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

growth_protocol: Adult flies were collected upon eclosion, separated by sex and aged in vials containing 20-30 flies on standard cornmeal medium. Flies were maintained at 25oC, 30-50% humidity for 3 weeks with food changes every 3 days.

extract_protocol: For each sample, 30 flies were dissected to expose the heart and attached fat and tracheols  glass micropipets were used to suction away attached fat and tracheols. Hearts were manually extracted and placed in  Trizol (Invitrogen, Carlsbad, CA) followed by purification with RNeasy Kit (Qiagen, Carlsbad, CA)


title: KCNQ control heart biological rep 1


title: KCNQ mutant heart biological rep 2


title: Sei mutant heart biological rep 2


title: F_101A


title: F_130A


title: KCNQ control heart biological rep 3


title: F_105B


title: H_43B


title: Sei mutant heart biological rep 5


title: KCNQ control heart biological rep 2


title: Sei mutant heart biological rep 3


title: F_43B


title: H_21A


title: F_73A


title: F_52B


title: F_45B


title: F_24A


title: KCNQ mutant heart biological rep 1


title: F_88B


title: Sei mutant heart biological rep 1


title: Canton-S control heart biological rep 5

value: Canton-S


title: Sei mutant heart biological rep 4


title: Canton-S control heart biological rep 4


title: Canton-S control heart biological rep 2


title: Canton-S control heart biological rep 3


title: Canton-S control heart biological rep 1


title: EOC Primary 17

city: Boston

first: Ilya

last: Korsunsky

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

description:
Primary Ovarian Tissue, Subject 17
Sample 23

hyb_protocol: As per manufacturer instruction

scan_protocol: As per manufacturer instruction

data_processing: The raw data were processed using Bioconductor lumi's implementation of background correction, log2 transformation, and quantile normalization

source_name: Ovarian Tissue

label_protocol: As per manufacturer instruction

extract_protocol: As per manufacturer instruction

tag: survival time (months)

tag: survival status

value: ALIVE

tag: tumor stage

value: IIa


title: EOC Primary 16

description:
Primary Ovarian Tissue, Subject 16
Sample 22

value: DECEASED

value: IIIc


title: EOC Primary 12

description:
Primary Ovarian Tissue, Subject 12
Sample 18


title: EOC Primary 15

description:
Primary Ovarian Tissue, Subject 15
Sample 21


title: EOC Primary 4

description:
Primary Ovarian Tissue, Subject 4
Sample 10

value: IIIb


title: EOC Primary 18

description:
Primary Ovarian Tissue, Subject 18
Sample 24


title: EOC Primary 2

description:
Primary Ovarian Tissue, Subject 2
Sample 8


title: EOC Primary 19

description:
Primary Ovarian Tissue, Subject 19
Sample 25


title: EOC Primary 5

description:
Primary Ovarian Tissue, Subject 5
Sample 11


title: EOC Primary 13

description:
Primary Ovarian Tissue, Subject 13
Sample 19


title: EOC Primary 9

description:
Primary Ovarian Tissue, Subject 9
Sample 15


title: Benign 2

description:
Benign Ovarian Mass, Subject 2
SAMPLE 3


title: EOC Primary 1

description:
Primary Ovarian Tissue, Subject 1
Sample 7


title: Benign 4

description:
Benign Ovarian Mass, Subject 4
SAMPLE 5


title: EOC Primary 10

description:
Primary Ovarian Tissue, Subject 10
Sample 16


title: Benign 1

description:
Benign Ovarian Mass, Subject 1
SAMPLE 1


title: EOC Primary 3

description:
Primary Ovarian Tissue, Subject 3
Sample 9


title: Benign 5

description:
Benign Ovarian Mass, Subject 5
SAMPLE 6


title: Benign 3

description:
Benign Ovarian Mass, Subject 3
SAMPLE 4


title: EOC Primary 11

description:
Primary Ovarian Tissue, Subject 11
Sample 17

value: IIc


title: EOC Primary 7

description:
Primary Ovarian Tissue, Subject 7
Sample 13


title: EOC Primary 6

description:
Primary Ovarian Tissue, Subject 6
Sample 12

value: LIVING


title: EOC Primary 8

description:
Primary Ovarian Tissue, Subject 8
Sample 14


title: control mouse 67

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description:
untreated control mouse
PXB302-67

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: human hepatocytes extracted from chimeric mouse liver_control

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Human hepatocyte chimeric mice were prepared as described previously (Tateno et al, 2004). Mice were inoculated via the mouse tail vein with 100 µl of human serum containing 4×10^5 copies of HCV genotype 1b. SIL-treated mice were sacrificed under ether anesthesia at day 3 or 14 after treatment. Human hepatocytes were finely dissected from chimeric mouse livers for RNA extraction.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: Chimeric mice with established HCV infection were treated with daily intravenous SIL doses of 469 mg/kg or 246 mg/kg. A bottle of Legalon SIL was dissolved in 35 ml of physiological solution with a total of 500 µL infused each day for 5min.

tag: mouse model

value: Chronically HCV-infected mice

tag: treated with

value: none (control)


title: control mouse 8

description:
untreated control mouse
PXB303-8

value: human hepatocytes extracted from chimeric mouse liver


title: SIL mouse 76

description:
high dose SIL-treated mouse sacrificed at day 14
CSB0069-0076

source_name: human hepatocytes extracted from chimeric mouse liver_SIL_14days

value: SIL 469 mg/kg

tag: days after treatment

value: 14 days


title: control mouse 80

description:
untreated control mouse
PXB302-80


title: EOC Primary 14

description:
Primary Ovarian Tissue, Subject 14
Sample 20


title: TH-MYCN tumor tissue replicate 6

description: Biological replicate 6 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.

hyb_protocol: Hybridization, scanning of arrays, and data extraction from scanned immages were conducted using the Agilent Micoroarray Scanner System (G2505B, Agilente Technologies) and Feature Extraction software.

data_processing:
Scanned signals were analyzed using Agilent Genomic Workbench (7.0.4.0) software. Normalized log2 ratio (Cy5/Cy3) was calcurated using Preprocessing function in the software with default settings.
Normalized log2 ratio (Cy5/Cy3)

source_name: TH-MYCN derived tumor tissue

label_protocol: 500 ng of DNA was digested, labeled, purified, and hybridized to the SurePrint G3 Mouse CGH Microarray 4x180K (G4839A, Agilent Technologies) according to the manufacturers instructions (Agilent Technologies).

extract_protocol: Genomic DNAs from spheres and tissue samples were isolated using Dneasy Blood & Tissue Kit (69504, QIAGEN).

value: TH-MYCN (hemizygote)

tag: strain

tag: age

value: 10- to 15-week-old

tag: tissue

value: Tumor in abdomen

source_name: TH-MYCN spleen

value: spleen


title: TH-MYCN tumor tissue replicate 5

description: Biological replicate 5 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.

scan_protocol: Hybridization, scanning of arrays, and data extraction from scanned immages were conducted using the Agilent Micoroarray Scanner System (G2505B, Agilente Technologies) and Feature Extraction software.

tag: genotype


title: TH-MYCN tumor tissue replicate 7

description: Biological replicate 7 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.


title: TH-MYCN tumor tissue replicate 4

description: Biological replicate 4 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.


title: TH-MYCN tumor tissue replicate 10

description: Biological replicate 10 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.


title: TH-MYCN tumor tissue replicate 3

description: Biological replicate 3 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.


title: TH-MYCN tumor tissue replicate 1

description: Biological replicate 1 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.


title: TH-MYCN tumor tissue replicate 9

description: Biological replicate 9 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.


title: TH-MYCN tumor tissue replicate 2

description: Biological replicate 2 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.


title: SIL mouse 89

description:
high dose SIL-treated mouse sacrificed at day 14
CSB0069-0089


title: SIL mouse 117

description:
low dose SIL-treated mouse sacrificed at day 14
CSB0069-0117

value: SIL 246 mg/kg


title: SIL mouse 24

description:
high dose SIL-treated mouse sacrificed at day 3
CSB0069-0024

source_name: human hepatocytes extracted from chimeric mouse liver_SIL_3days

value: 3 days


title: U266 shKDM3A#C normoxia

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

hyb_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).

scan_protocol: Agilent G2600A SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent), computed normalized signal intencity with 75%tile normalization.

source_name: U266 shKDM3A#C normoxia

growth_protocol: RPMI1640 plus 10% FCS.

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: normoxia: 21%O2, hypoxia: 1%O2.

tag: cell line

tag: cell type

value: myeloma

tag: oxygen status

value: normoxia

tag: shRNA


title: SIL mouse 61

description:
high dose SIL-treated mouse sacrificed at day 3
CSB0069-0061

tag: tissue/cell type


title: U266 normal hypoxia

source_name: U266 normal hypoxia

label_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).

value: hypoxia


title: U266 normal normoxia

source_name: U266 normal normoxia


title: U266 Scr hypoxia

source_name: U266 Scr hypoxia

value: Scr


title: TH-MYCN tumor tissue replicate 8

description: Biological replicate 8 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.


title: U6 human term placenta from IUGR pregnancy

city: Los Angeles

first: Alison

last: Chu

address: 10833 LeConte Avenue

institute: UCLA

description: miRNA expression data from whole term human placenta

hyb_protocol: Hybridization was performed per the manufacturer's protocol (Affymetrix). Briefly, the hybridization cocktail mix is prepared as per the appropriate starting volume, denature the hybridization cocktail and centrifuge with cocktail and transfer into the appropriate well of the hybridization tray.

scan_protocol: The scanner used is the GeneChip Scanner 3000 7G, scanner type M10, software version Express console 1.4.1.46

data_processing: Microarray analysis was performed by the Clinical Microarray Core facility at UCLA, using the Affymetrix GeneChip miRNA 4.0 Array. The data obtained was initially analyzed using the Express Console Software version 1.4.1.46 (Affymetrix).

source_name: whole human placenta isolated from the fetal aspect

label_protocol: The RNA was labeled using the FlashTag Biotin HSR RNA labeling Kit (Affymetrix), per the manufacturer's protocol starting with 8ug of RNA. Briefly, starting with total RNA, the process involved a brief tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

extract_protocol: total miRNA from human placentas was purified using the Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA) per manufacturer's protocol. Tissue was prepared by adding 700uL QIAzol lysis reagent to 50 mg of placental tissue and homogenized for one minute using the Omni tissue homogenizer. After elution of the miRNA, the Qiagen RNeasy MinElute Cleanup Kit was used to remove contaminating DNA and to concentrate the samples. RNA concentration and quality were measured using NonoDrop 2000c spectrophotometer (ThermoFisher Scientific).

value: 40+2 weeks

tag: gender

value: M infant

tag: delivery

value: C/section

tag: birth weight


title: U4 human term placenta from IUGR pregnancy

value: 38+4 weeks


title: U3 human term placenta from IUGR pregnancy

value: NSVD


title: SIL mouse 54

description:
high dose SIL-treated mouse sacrificed at day 3
CSB0069-0054

value: Chronically HCV-infected mice

value: SIL 469 mg/kg

value: human hepatocytes extracted from chimeric mouse liver


title: U2 human term placenta from IUGR pregnancy

value: 37+6 weeks

value: F infant


title: U266 shKDM3A#C hypoxia

source_name: U266 shKDM3A#C hypoxia


title: U266 Scr normoxia

source_name: U266 Scr normoxia


title: YL66

city: Yokohama

first: Taishi

last: Nakamura

address: 3-9, Fukuura, Kanazawa-ku

department: Department of Neurosurgery

institute: Yokohama city university

description: * Tumor (clinical diagnosis) WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues, Fourth Edition

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy3, Cy5

source_name: primary CNS lymphoma

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.

tag: public id

tag: pcnsl/ metastatic dlbcl in cns

value: PCNSL

value: Male

tag: ebv infection


title: MYL002

source_name: metastatic DLBCL in CNS

value: metastatic DLBCL in CNS


title: U11 human term placenta from IUGR pregnancy

value: 39 wks


title: C4 human term placenta from AGA pregnancy

value: M newborn


title: YL65

value: Female


title: ML001


title: C19 human term placenta from AGA pregnancy


title: YL64


title: C27 human term placenta from AGA pregnancy

value: 37 wks


title: C2 human term placenta from AGA pregnancy

value: 38 wks


title: YL62


title: C9 human term placenta from AGA pregnancy


title: U15 human term placenta from IUGR pregnancy

value: M infant


title: YL49


title: YL63


title: YL60


title: C1 human term placenta from AGA pregnancy

value: 41+5 wk gestation


title: YL59


title: YL48


title: YL57


title: YL45


title: YL02


title: C14 human term placenta from AGA pregnancy

value: F newborn

value: C/section


title: YL43


title: YL33


title: L536


title: L534


title: L530


title: L529


title: L533


title: L514


title: L532


title: TH-MYCN tumor tissue replicate 11

description: Biological replicate 11 of 11. A tumor tissue developed in the abdomen of TH-MYCN (hemizygote) mouse.

value: TH-MYCN (hemizygote)

value: 10- to 15-week-old

value: Tumor in abdomen

value: spleen


title: L526


title: L528


title: L531


title: L521


title: L512


title: L510


title: L511


title: L505


title: L507


title: L504


title: L503


title: L502


title: L409


title: L412


title: L411


title: L513


title: L406


title: L405


title: L501


title: L404


title: L410


title: L408


title: L403


title: L402


title: L401


title: L322


title: L321


title: L317


title: L319


title: L320


title: L315


title: L313


title: L311


title: L310


title: L314


title: L316


title: L309


title: L308


title: L306


title: L302


title: L304


title: L301


title: L215


title: L216


title: L213


title: L305


title: Pediatric brain tumor 5  - FFPE_REPLI-g

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

institute: Gothenburg University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchips using standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Raw methylation data was normalized using ssNoob-normalization with the R minfi package.  CpG-sites with detection p-value >0.01 were regarded as failed and were assigned as missing.

source_name: Pediatric brain tumor 5  - FFPE_REPLI-g

label_protocol: 500 ng FF DNA, 1 µg REPLI-g restored FFPE DNA and 1 µg unrestored FFPE DNA (for restoration with the Infinium kit after bisulfite conversion) was used for bisulfite conversion with the EZ DNA methylation kit (D5001, Zymo Research, Orange, CA) according to the manufacturer’s instructions using the alternative incubation conditions recommended for the Illumina Infinium methylation arrays. Successful conversion was verified by control PCR reactions with a primer set specific for bisulfite converted DNA and a primer set for unconverted DNA.

extract_protocol: DNA from FF tumours was extracted with the DNeasy Blood & Tissue Kit (69504, Qiagen, Hilden, Germany) according to the manufacturer’s instructions with the addition of lysing the samples with the QIAGEN TissueLyser. FFPE samples (1-3 years old) were sectioned and DNA was isolated using QIAamp DNA FFPE Tissue Kit (56404, Qiagen) according to manufacturer’s recommendations except de-waxing steps with Xylene was repeated twice and the tissue was digested overnight. DNA concentration was determined with the Qubit® Fluorometer (Life technologies). The quality of the DNA extracted from FFPE samples was assessed in triplicates with the real-time PCR-based Illumina FFPE QC kit (WG-321-1001, Illumina, Inc., San Diego, CA) according to the provided protocol.

value: brain tumor

tag: dna restoration

value: 1µg FFPE DNA was used for REPLI-g restoration, Thirwell 2010.


title: L214

value: PCNSL


title: L210

value: Male


title: L212


title: Pediatric brain tumor 9  - FFPE_REPLI-g

source_name: Pediatric brain tumor 9  - FFPE_REPLI-g


title: Pediatric brain tumor 7  - FFPE_REPLI-g

source_name: Pediatric brain tumor 2  - FFPE_REPLI-g


title: L208


title: L209


title: L207


title: L307


title: Pediatric brain tumor 9  - FFPE Infinium

source_name: Pediatric brain tumor 9  - FFPE Infinium

value: All of eluate 1 of the bisulfite converted unrestored FFPE DNA was used for restoration with the Infinium HD FFPE DNA Restore Kit (WG-321-1002, Illumina) using the Infinium HD FFPE Restore Protocol supplied by the manufacturer.


title: L206


title: Pediatric brain tumor 8  - FF

source_name: Pediatric brain tumor 8  - FF


title: Pediatric brain tumor 8  - FFPE_REPLI-g

source_name: Pediatric brain tumor 8  - FFPE_REPLI-g


title: L205


title: Pediatric brain tumor 2  - FF

source_name: Pediatric brain tumor 2  - FF


title: Pediatric brain tumor 6  - FFPE Infinium

source_name: Pediatric brain tumor 6  - FFPE Infinium


title: L204


title: Pediatric brain tumor 8  - FFPE Infinium

source_name: Pediatric brain tumor 8  - FFPE Infinium


title: L203


title: Pediatric brain tumor 11  - FFPE_REPLI-g

source_name: Pediatric brain tumor 11  - FFPE_REPLI-g


title: Pediatric brain tumor 9  - FF

source_name: Pediatric brain tumor 9  - FF


title: EOC Primary 18

description:
Primary Ovarian Tissue, Subject 18
microRNA

data_processing:
The raw data were processed using Bioconductor htqpcr package, and normalized using Delta-CT with RNU44 and U6, followed by quantile normalization. MicroRNAs absent in more than 25% of samples were discarded.
Data were processed using the OpenArray Real-Time qPCR Analysis software and exported for analysis using the Applied Biosystems DataAssist Software

label: FAMTP

source_name: Ovarian Tissue

tag: survival time (months)

tag: survival status

value: DECEASED

tag: tumor stage

value: IIIc


title: EOC Primary 17

description:
Primary Ovarian Tissue, Subject 17
microRNA

value: ALIVE

value: IIa


title: Pediatric brain tumor 1  - FFPE_REPLI-g

source_name: Pediatric brain tumor 1  - FFPE_REPLI-g

tag: tissue


title: EOC Primary 16

description:
Primary Ovarian Tissue, Subject 16
microRNA


title: Pediatric brain tumor 6  - FFPE_REPLI-g

source_name: Pediatric brain tumor 6  - FFPE_REPLI-g


title: Pediatric brain tumor 10  - FFPE_REPLI-g

source_name: Pediatric brain tumor 10  - FFPE_REPLI-g


title: L112

source_name: primary CNS lymphoma

tag: age


title: EOC Primary 15

description:
Primary Ovarian Tissue, Subject 15
microRNA


title: EOC Primary 19

description:
Primary Ovarian Tissue, Subject 19
microRNA


title: L102

value: Female


title: Pediatric brain tumor 3  - FFPE_REPLI-g

source_name: Pediatric brain tumor 3  - FFPE_REPLI-g


title: EOC Primary 14

description:
Primary Ovarian Tissue, Subject 14
microRNA


title: L097


title: EOC Primary 13

description:
Primary Ovarian Tissue, Subject 13
microRNA

value: IIIb


title: L110


title: EOC Primary 11

description:
Primary Ovarian Tissue, Subject 11
microRNA

value: IIc


title: Pediatric brain tumor 3  - FF

source_name: Pediatric brain tumor 3  - FF


title: EOC Primary 12

description:
Primary Ovarian Tissue, Subject 12
microRNA


title: L088


title: Pediatric brain tumor 2  - FFPE_REPLI-g


title: Pediatric brain tumor 4  - FFPE_REPLI-g

source_name: Pediatric brain tumor 4  - FFPE_REPLI-g


title: L082


title: L202


title: Pediatric brain tumor 12  - FFPE_REPLI-g

source_name: Pediatric brain tumor 12  - FFPE_REPLI-g


title: EOC Primary 10

description:
Primary Ovarian Tissue, Subject 10
microRNA


title: L076


title: EOC Primary 9

description:
Primary Ovarian Tissue, Subject 9
microRNA


title: Pediatric brain tumor 5  - FF

source_name: Pediatric brain tumor 5  - FF