title: t0_fluc_end_rep2

hyb_protocol: Custom gene expression SurePrint G3 microarrays (eArray accession number Candida_albicans_2007_1244213353206) were hybridized with CY3 labeled cRNA of growth duplicates according to manufacturer’s instructions (Agilent, Low Input Quick Amp Labelling kit).

scan_protocol: Arrays were scanned on an Agilent G2505C microarray scanner and microarray scan data was extracted using Agilent feature extraction software.

data_processing: Gene expression microarray raw data were normalized using limmaGUI software (R/ Bioconductor, Boston, MA, USA).

source_name: candida albicans, t0, fluconazole, end, replicate2

label_protocol: Same amounts of RNA extract (500 ng) from each replicate were amplified and Cy-3-labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies)

growth_protocol: Candida albicans strains used in this study were engineered to exhibit different levels of Leucine misincorporation at Serine CUG codons. T0: control strain 3,2% Leu misincorporation (natural mistranslation); T1: 24,9% Leu misincorporation. These highly ambiguous strains were constructed on the basis of the strain SN148 (arg4  /arg4   leu2  /leu2   his1  /his1 ura3  ::imm43/ura3  ::imm43 iro1  ::imm43/iro1  ::imm43) using homologous recombination methodologies as described in Bezerra et al PNAS 2013.

extract_protocol: RNA was extracted from strains at the beginning (T0, T1), middle (T0FM, T1FM) and end (T0FH, T1FH) of the evolution experiment. Additionally,clones were evolved for an equal number of total passages without the drug to study effects caused by mistranslation and by the antifungal fluconazole (T0NF, T1NF). RNA was extracted from mid-exponential phase cells using the hot phenol method. DNase I (Invitrogen) treated RNA was resuspended in RNAse free water and RNA quantity and integrity was assessed using UV/Vis spectrometry (Nanodrop) and the 2100 Agilent Bioanalyzer respectively.

treatment_protocol: Resistance to antifungal drugs was monitored using the E-test assay method (AB biodisk, Biomerieux). Therefore, cells were grown to mid-log phase, washed in 1xPBS, and diluted to an OD600 of 0.015. 150μl of cells were plated on SD minus uracil agar plates (pH7) using glass beads and allowed to dry for 15-30 minutes before applying a fluconazole E-test strip (0.016– 256 μg/ml, AB Biodisk). Plates were incubated at 30°C and the MIC was determined after 48 hours. Each passage the Fluconazole (Sigma Aldrich) concentration of the liquid (SD minus uracil) growth medium was adjusted to a concentration corresponding to twice the last measured MIC. Passages were pursued until strains were growing in liquid media containing a Fluconazole concentration of 256 μg/ml.

value: end


title: t1_fluc_mid_rep1

status: Public on Jul 18 2017

type: RNA

city: S. Michele all'Adige (TN)

first: Tobias

last: Weil

address: Via E. Mach, 1

country: Italy

institute: Fondazione Edmund Mach

molecule: total RNA

organism: Candida albicans

source_name: candida albicans, t1, fluconazole, mid, replicate1

tag: strain

tag: treatment

value: Fluconazole

tag: time

value: middle


title: t1_fluc_mid_rep2

source_name: candida albicans, t1, fluconazole, mid, replicate2


title: 19_id_BayTubes

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: raw data file: US11263921_252800520993_S01_GE2_1105_Oct12_2_3.txt

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays, , according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing:
These are dual-channel arrays that have been analyzed as single-channel arrays. All raw data files are available in a tar archive on the series record.
Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.

organism: Mus musculus

source_name: BayTubes

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: Female C57BL/6 mice (7-8 weeks old) were housed in groups of four in stainless steel cages, bedded with aspen chip and were provided with standard mouse chow diet and tab water ad lib. 12 h dark/light cycle was used in the animal room temperature being 20-21 degree celcius and humidity of 40-45 %.

extract_protocol: RNA isolation from the lung samples was done with TRIsure (phenol-chloroform extraction) and the quantity and purity was determined by NanoDrop spectrophotometer. Further quality check of the total RNA was performed with the Agilent BioAnalyzer, according to the manufacturer's recommendations.

treatment_protocol: mice lung tissue samples collected 24h after final exposure. Tissue samples stored in RNAlater in -80ºC

tag: tissue

value: lung

tag: gender

value: female

tag: exposure

value: 10 ug of CNM in 50 ul of PBS

tag: exposure method

value: oropharyngeal aspiration


title: 20_id_BayTubes

description: raw data file: US11263921_252800520994_S01_GE2_1105_Oct12_1_1.txt


title: 11_id_SES

description: raw data file: US11263921_252800520993_S01_GE2_1105_Oct12_2_1.txt

source_name: SES


title: t1_fluc_end_rep2

source_name: candida albicans, t1, fluconazole, end, replicate2


title: t1_fluc_end_rep1

source_name: candida albicans, t1, fluconazole, end, replicate1


title: 2_id_Ctrl

description: raw data file: US11263921_252800520993_S01_GE2_1105_Oct12_2_4.txt

source_name: Ctrl

value: 50 ul of PBS


title: 15_id_Graphite

description: raw data file: US11263921_252800520993_S01_GE2_1105_Oct12_1_1.txt

source_name: Graphite


title: 4_id_rCNT

description: raw data file: US11263921_252800520993_S01_GE2_1105_Oct12_1_2.txt

source_name: rCNT


title: 7_id_tCNT

description: raw data file: US11263921_252800520993_S01_GE2_1105_Oct12_1_3.txt

source_name: tCNT


title: t0_fluc_end_rep1

source_name: candida albicans, t0, fluconazole, end, replicate1


title: t0_fluc_mid_rep1

source_name: candida albicans, t0, fluconazole, mid, replicate1


title: t1_control_end_rep2

source_name: candida albicans, t1, end, replicate2

value: not treated


title: t0_fluc_mid_rep2

source_name: candida albicans, t0, fluconazole, mid, replicate2


title: 10µM STATTIC IFNγ+LPS rep1

city: Poznan

first: Martyna

last: Plens Gałąska

state: Wielkopolska

address: Umultowska 89

department: Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz Univerity

description:
replicate 1
SAMPLE 9
200536980060_H_Grn

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina Genome Studio

label: biotin

organism: Homo sapiens

source_name: 10µM STATTIC IFNγ+LPS, Human Endothelial Microvascular Cell Line

label_protocol: Biotinylated cRNA were prepared with the Illumina®TotalPrep™ RNA Amplification Kit

extract_protocol: RNA was isolated from harvested cells with GeneMATRIX Universal RNA Purification Kit (EURx, Gdansk, Poland). Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: 10µM STATTIC IFNγ+LPS


title: 24_id_fullerene

description: raw data file: US11263921_252800520995_S01_GE2_1105_Oct12_2_3.txt

source_name: fullerene


title: 25µM STX-0119 IFNγ+LPS rep1

description:
replicate 1
SAMPLE 7
200536980060_A_Grn

source_name: 25µM STX-0119 IFNγ+LPS, Human Endothelial Microvascular Cell Line

value: 25µM STX-0119 IFNγ+LPS


title: 10µM STATTIC IFNγ+LPS rep2

description:
replicate 2
SAMPLE 10
200536980060_J_Grn

value: Human Endothelial Microvascular Cell Line


title: 1_id_Ctrl

description: raw data file: US11263921_252800520994_S01_GE2_1105_Oct12_2_1.txt


title: 25µM STX-0119 IFNγ+LPS rep2

description:
replicate 2
SAMPLE 8
200536980060_E_Grn


title: 5_id_rCNT

description: raw data file: US11263921_252800520995_S01_GE2_1105_Oct12_1_1.txt


title: 50µM C01L_F03 IFNγ+LPS rep1

description:
replicate 1
SAMPLE 5
200536980060_G_Grn

source_name: 50µM C01L_F03 IFNγ+LPS, Human Endothelial Microvascular Cell Line

value: 50µM C01L_F03 IFNγ+LPS


title: t1_control_end_rep1

source_name: candida albicans, t1, end, replicate1


title: 50µM C01L_F03 IFNγ+LPS rep2

description:
replicate 2
SAMPLE 6
200536980060_K_Grn


title: 14_id_Graphite

description: raw data file: US11263921_252800520994_S01_GE2_1105_Oct12_1_4.txt


title: IFNγ+LPS rep2

description:
replicate 2
SAMPLE 4
200536980060_C_Grn

source_name: IFNγ+LPS, Human Endothelial Microvascular Cell Line

value: IFNγ+LPS


title: IFNγ+LPS rep1

description:
replicate 1
SAMPLE 3
200536980060_L_Grn


title: t1_fluc_beg_rep1

source_name: candida albicans, t1, beginning, replicate1

value: beginning


title: t0_control_end_rep2

source_name: candida albicans, t0, end, replicate2


title: t1_fluc_beg_rep2

source_name: candida albicans, t1, beginning, replicate2


title: 10_id_SES

description: raw data file: US11263921_252800520994_S01_GE2_1105_Oct12_1_2.txt

source_name: SES


title: Untreated rep2

description:
replicate 2
SAMPLE 2
200536980060_I_Grn

source_name: Untreated, Human Endothelial Microvascular Cell Line

value: Untreated


title: 3_id_Ctrl

source_name: Ctrl


title: LNCaP_Torin 1+R1881_rep2

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

country: Canada

institute: Université Laval

hyb_protocol: RNA was hybridized to Illumina HumanHT-12 Expression Beachip v4 and quantified at Génome Québec Innovation Centre (McGill University)

scan_protocol: Scan of the microarrays was performed by the Génome Québec Innovation Centre (McGill University)

data_processing:
The expression data were analyzed using FlexArray10 software.
FlexArray10 software was using for data normalization and expression comparison between groups.

source_name: LNCaP cells, 48h Torin 1 + R1881 treatment

label_protocol: Labeling was performed using standard Illumina protocol at Génome Québec Innovation Centre (McGill University)

growth_protocol: Cells were seeded in RPMI media with no phenol red and with charcoal-stripped serum (no steroids) . 48h later, cell were treated with 10nM R1881, Torin 1 (100nM) or vehicles (EtOH and DMSO) for 48h. Triplicate samples were sent for each conditions.

extract_protocol: RNA was purified using RNeasy mini kit from QIAGEN

treatment_protocol: Cells were treated for 48h with R1881 (10nM), Torin 1 (100nM), or  vehicles (EtOH+DMSO).

value: human LNCaP prostate cancer cells (immortalized cell line)

value: Torin 1 + R1881


title: Untreated rep1

description:
replicate 1
SAMPLE 1
200536980060_D_Grn


title: 18_id_BayTubes

source_name: BayTubes


title: 12_id_SES


title: 8_id_tCNT

source_name: tCNT


title: LNCaP_vehicle+Torin 1_rep3

source_name: LNCaP cells, 48h Torin 1 treatment

value: Torin 1


title: 17_id_BayTubes


title: LNCaP_Torin 1+R1881_rep3


title: t0_fluc_beg_rep2

source_name: candida albicans, t0, beginning, replicate2


title: t0_fluc_beg_rep1

source_name: candida albicans, t0, beginning, replicate1


title: 23_id_fullerene

source_name: fullerene


title: 16_id_Graphite

source_name: Graphite


title: t0_control_end_rep1

source_name: candida albicans, t0, end, replicate1

value: end


title: LNCaP_Torin 1+R1881_rep1


title: 0h_RNA_withDNase_0.67URNase_rep3

status: Public on Jul 17 2017

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

description:
9 Rneasy 0.026 U
Total RNA depleted of small RNAs.

hyb_protocol: The expression profile of 1881 mouse miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were vsn normalized and logarithmized.

label: Cyanine 3-pcp

source_name: liver, 0h, with DNase, 0.67U RNase

label_protocol: miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456).

extract_protocol: Tissue stored for 0 hours, isolated with RNeasy Kit with optional DNase digestion to isolate undegraded total RNA depleted of small RNAs without potential DNA contamination, 3µg RNA were treated with 0.026 U RNase (Roche) and incubated for 30 min at 37°C, RNA was reisolated with miRNeasy Kit without DNase digestion to generate partially degraded total RNA.

value: liver

tag: dnase

value: with

tag: rnase

tag: rna integrity (rin)


title: 0h_RNA_withDNase_0URNase_rep3

description:
9 Rneasy 0U
Total RNA depleted of small RNAs.

source_name: liver, 0h, with DNase, 0U RNase

extract_protocol: Tissue stored for 0 hours, isolated with RNeasy Kit with optional DNase digestion to isolate undegraded total RNA depleted of small RNAs without potential DNA contamination, 3µg RNA were treated with 0U RNase (Roche) and incubated for 30 min at 37°C, RNA was reisolated with miRNeasy Kit without DNase digestion.

value: 0 U


title: LNCaP_vehicle+Torin 1_rep1


title: 96h_miRNA_withoutDNase_rep3

description:
9 96h mi -
Total RNA including miRNA.

source_name: liver, 96h, without DNase

extract_protocol: Tissue stored for 96 hours, isolated with miRNeasy Kit without optional DNase digestion to isolate degraded total RNA including small RNAs with potential DNA contamination.

value: without


title: 0h_RNA_withDNase_rep3

description:
9 Rneasy
Total RNA depleted of small RNAs.

source_name: liver, 0h, with DNase

extract_protocol: Tissue stored for 0 hours, isolated with RNeasy Kit with optional DNase digestion to isolate undegraded total RNA depleted of small RNAs without potential DNA contamination.


title: 96h_miRNA_withDNase_rep3

description:
9 96h mi +
Total RNA including miRNA.

source_name: liver, 96h, with DNase

extract_protocol: Tissue stored for 96 hours, isolated with miRNeasy Kit with optional DNase digestion to isolate degraded total RNA including small RNAs without potential DNA contamination.


title: 0h_miRNA_withoutDNase_rep3

description:
9 0h mi -
Total RNA including miRNA.

source_name: liver, 0h, without DNase

extract_protocol: Tissue stored for 0 hours, isolated with miRNeasy Kit without optional DNase digestion to isolate undegraded total RNA including small RNAs with potential DNA contamination.


title: 0h_RNA_withDNase_0.026URNAse_rep3

description:
9 Rneasy 0.67 U
Total RNA depleted of small RNAs.

source_name: liver, 0h, with DNase, 0.026U RNase

extract_protocol: Tissue stored for 0 hours, isolated with RNeasy Kit with optional DNase digestion to isolate undegraded total RNA depleted of small RNAs without potential DNA contamination, 3µg RNA were treated with 0.67U RNase (Roche) and incubated for 30 min at 37°C, RNA was reisolated with miRNeasy Kit without DNase digestion to generate fully degraded total RNA.


title: LNCaP_vehicle+R1881_rep2

source_name: LNCaP cells, 48h R1881 treatment


title: LNCaP_vehicle+Torin 1_rep2


title: A549_shGFP_rep1

city: Charlestown

first: Robert

last: Morris

state: Massachusetts

address: 149 13th Street

country: USA

institute: Mass. General Hospital Cancer Center

description: This sample is of shGFP in A549 cells replicates 1.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Arrays were scanned on Nimblegen MS200 at 2um resolution

data_processing: Array data was background corrected and normalized as suggested using the Roche NimbleScan 2.6 software

source_name: A549 shGFP

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Human breast (MDA-MB-231) and lung (A549) cancer cell lines (American Type Culture Collection, Manassas, VA, USA) were grown in Dulbeccco’s modified medium, which supplemented with 10% fetal bovine serum and penicillin/streptomycin (Pen/Strep). Both cell lines were maintained in 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was isolated 72 hr after lentiviral shRNA infection.

treatment_protocol: Lentiviral shRNA constructs were obtained from the RNAi Consortium shRNA Library at the Broad Institute. Conditioned medium containing infective lentiviral particles was generated by cotransfecting 3µg of each lentiviral vector, 3µg of pCMV d8.91 and 1µg pHCMV-G into 1×10*6 293T human embryonic kidney cells using FuGENE 6 transfection reagent (Roche Applied Science). Supernatants were collected 48 hr after transfection and filtered through a 0.45 µM membrane (Millipore). Cells were infected with each supernatants using 8µg/mL polybrene and selected with 2µg/mL puromycin. RNA was isolated 72 hr after lentiviral shRNA infection.

value: Lung cancer cell line A549

tag: genotype/variation

value: control


title: MDA-MB-231_shSETD1A_rep1

description: This sample is of shSETD1A in MDA-MB-231 cells replicates 1.

source_name: MDA-MB-231 shSETD1A

value: Breast cancer cell line MDA-MB-231

value: SETD1A depletion


title: MDA-MB-231_shGFP_rep1

description: This sample is of shGFP in MDA-MB-231 cells replicates 1.

source_name: MDA-MB-231 shGFP


title: LNCaP_vehicle+R1881_rep1


title: 0h_miRNA_withDNase_rep3

description:
9 0h mi +
Total RNA including miRNA.

extract_protocol: Tissue stored for 0 hours, isolated with miRNeasy Kit with optional DNase digestion to isolate undegraded total RNA including small RNAs without potential DNA contamination.


title: 0h_RNA_withDNase_0.67URNase_rep2

description:
10 Rneasy 0.67 U
Total RNA depleted of small RNAs.


title: 0h_RNA_withDNase_0.026URNAse_rep2

description:
10 Rneasy 0.026 U
Total RNA depleted of small RNAs.


title: MDA-MB-231_shSETD1A_rep2

description: This sample is of shSETD1A in MDA-MB-231 cells replicates 2.


title: 0h_RNA_withDNase_0URNase_rep2

description:
10 Rneasy 0U
Total RNA depleted of small RNAs.


title: LNCaP_vehicle+R1881_rep3


title: A549_shSETD1A_rep1

description: This sample is of shSETD1A in A549 cells replicates 1.

source_name: A549 shSETD1A


title: A549_shSETD1A_rep2

description: This sample is of shSETD1A in A549 cells replicates 2.


title: LNCaP_vehicle_rep1

source_name: LNCaP cells, vehicle treatment

value: vehicle


title: 0h_RNA_withDNase_rep2

description:
10 Rneasy
Total RNA depleted of small RNAs.


title: 96h_miRNA_withoutDNase_rep2

description:
10 96h mi -
Total RNA including miRNA.


title: LNCaP_vehicle_rep2


title: 0h_miRNA_withoutDNase_rep2

description:
10 0h mi -
Total RNA including miRNA.


title: 96h_miRNA_withDNase_rep2

description:
10 96h mi +
Total RNA including miRNA.


title: 0h_RNA_withDNase_rep1

description:
7 Rneasy
Total RNA depleted of small RNAs.


title: 0h_RNA_withDNase_0.026URNAse_rep1

description:
7 Rneasy 0.026 U
Total RNA depleted of small RNAs.


title: 0h_RNA_withDNase_0.67URNase_rep1

description:
7 Rneasy 0.67 U
Total RNA depleted of small RNAs.


title: 96h_miRNA_withDNase_rep1

description:
7 96h mi +
Total RNA including miRNA.


title: 0h_miRNA_withDNase_rep2

description:
10 0h mi +
Total RNA including miRNA.


title: 0h_miRNA_withoutDNase_rep1

description:
7 0h mi -
Total RNA including miRNA.


title: brain_12h_RT_rep1

description:
RT_brain_12h
Total RNA including miRNA.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were vsn normalized and logarithmized using R package.

source_name: brain, 12h, RT

extract_protocol: Total RNA including miRNAs was isolated using miRNeasy Kit (Qiagen) after manufacturer's recommendations.

value: brain

tag: temperature

value: RT


title: brain_48h_RT_rep1

description:
RT_brain_48h
Total RNA including miRNA.

source_name: brain, 48h, RT


title: brain_6h_RT_rep1

description:
RT_brain_6h
Total RNA including miRNA.

source_name: brain, 6h, RT


title: brain_24h_RT_rep1

description:
RT_brain_24h
Total RNA including miRNA.

source_name: brain, 24h, RT


title: 96h_miRNA_withoutDNase_rep1

description:
7 96h mi -
Total RNA including miRNA.


title: brain_6h_4°C_rep1

description:
4C_brain_6h
Total RNA including miRNA.

source_name: brain, 6h, 4°C

value: 4 degrees Celsius


title: brain_1h_RT_rep1

description:
RT_brain_1h
Total RNA including miRNA.

source_name: brain, 1h, RT


title: brain_12h_4°C_rep1

description:
4C_brain_12h
Total RNA including miRNA.

source_name: brain, 12h, 4°C


title: brain_0h_RT_rep1

description:
RT_brain_0h
Total RNA including miRNA.

source_name: brain, 0h, RT


title: brain_24h_4°C_rep1

description:
4C_brain_24h
Total RNA including miRNA.

source_name: brain, 24h, 4°C


title: brain_96h_4°C_rep1

description:
4C_brain_96h
Total RNA including miRNA.

source_name: brain, 96h, 4°C


title: brain_48h_4°C_rep1

description:
4C_brain_48h
Total RNA including miRNA.

source_name: brain, 48h, 4°C


title: 0h_RNA_withDNase_0URNase_rep1

description:
7 Rneasy 0U
Total RNA depleted of small RNAs.

source_name: liver, 0h, with DNase, 0U RNase


title: brain_3h_RT_rep1

description:
RT_brain_3h
Total RNA including miRNA.

source_name: brain, 3h, RT


title: brain_3h_4°C_rep1

description:
4C_brain_3h
Total RNA including miRNA.

source_name: brain, 3h, 4°C


title: brain_1h_4°C_rep1

description:
4C_brain_1h
Total RNA including miRNA.

source_name: brain, 1h, 4°C


title: 0h_miRNA_withDNase_rep1

description:
7 0h mi +
Total RNA including miRNA.

source_name: liver, 0h, with DNase


title: brain_96h_RT_rep1

description:
RT_brain_96h
Total RNA including miRNA.

source_name: brain, 96h, RT


title: LNCaP_vehicle_rep3

source_name: LNCaP cells, vehicle treatment


title: liver_96h_RT_rep1

description:
RT_liver_96h
Total RNA including miRNA.

source_name: liver, 96h, RT


title: liver_48h_RT_rep1

description:
RT_liver_48h
Total RNA including miRNA.

source_name: liver, 48h, RT


title: liver_6h_RT_rep1

description:
RT_liver_6h
Total RNA including miRNA.

source_name: liver, 6h, RT


title: liver_12h_RT_rep1

description:
RT_liver_12h
Total RNA including miRNA.

source_name: liver, 12h, RT


title: brain_0h_4°C_rep1

description:
4C_brain_0h
Total RNA including miRNA.

source_name: brain, 0h, 4°C


title: liver_24h_RT_rep1

description:
RT_liver_24h
Total RNA including miRNA.

source_name: liver, 24h, RT


title: liver_3h_RT_rep1

description:
RT_liver_3h
Total RNA including miRNA.

source_name: liver, 3h, RT


title: liver_48h_4°C_rep1

description:
4C_liver_48h
Total RNA including miRNA.

source_name: liver, 48h, 4°C


title: liver_0h_RT_rep1

description:
RT_liver_0h
Total RNA including miRNA.

source_name: liver, 0h, RT


title: liver_24h_4°C_rep1

description:
4C_liver_24h
Total RNA including miRNA.

source_name: liver, 24h, 4°C


title: liver_12h_4°C_rep1

description:
4C_liver_12h
Total RNA including miRNA.

source_name: liver, 12h, 4°C


title: liver_1h_4°C_rep1

description:
4C_liver_1h
Total RNA including miRNA.

source_name: liver, 1h, 4°C


title: liver_3h_4°C_rep1

description:
4C_liver_3h
Total RNA including miRNA.

source_name: liver, 3h, 4°C


title: liver_0h_4°C_rep1

description:
4C_liver_0h
Total RNA including miRNA.

source_name: liver, 0h, 4°C


title: heart_96h_RT_rep1

description:
RT_heart_96h
Total RNA including miRNA.

source_name: heart, 96h, RT

value: heart


title: heart_6h_RT_rep1

description:
RT_heart_6h
Total RNA including miRNA.

source_name: heart, 6h, RT


title: heart_12h_RT_rep1

description:
RT_heart_12h
Total RNA including miRNA.

source_name: heart, 12h, RT


title: heart_48h_RT_rep1

description:
RT_heart_48h
Total RNA including miRNA.

source_name: heart, 48h, RT


title: heart_3h_RT_rep1

description:
RT_heart_3h
Total RNA including miRNA.

source_name: heart, 3h, RT


title: heart_24h_RT_rep1

description:
RT_heart_24h
Total RNA including miRNA.

source_name: heart, 24h, RT


title: liver_1h_RT_rep1

description:
RT_liver_1h
Total RNA including miRNA.

source_name: liver, 1h, RT


title: heart_48h_4°C_rep1

description:
4C_heart_48h
Total RNA including miRNA.

source_name: heart, 48h, 4°C


title: heart_24h_4°C_rep1

description:
4C_heart_24h
Total RNA including miRNA.

source_name: heart, 24h, 4°C


title: heart_96h_4°C_rep1

description:
4C_heart_96h
Total RNA including miRNA.

source_name: heart, 96h, 4°C


title: heart_6h_4°C_rep1

description:
4C_heart_6h
Total RNA including miRNA.

source_name: heart, 6h, 4°C


title: heart_1h_RT_rep1

description:
RT_heart_1h
Total RNA including miRNA.

source_name: heart, 1h, RT


title: heart_12h_4°C_rep1

description:
4C_heart_12h
Total RNA including miRNA.

source_name: heart, 12h, 4°C


title: heart_0h_RT_rep1

description:
RT_heart_0h
Total RNA including miRNA.

source_name: heart, 0h, RT


title: heart_0h_4°C_rep1

description:
4C_heart_0h
Total RNA including miRNA.

source_name: heart, 0h, 4°C


title: heart_1h_4°C_rep1

description:
4C_heart_1h
Total RNA including miRNA.

source_name: heart, 1h, 4°C


title: heart_3h_4°C_rep1

description:
4C_heart_3h
Total RNA including miRNA.

source_name: heart, 3h, 4°C


title: input_for_CPEB1

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: oocyte lysate before IP

hyb_protocol: Hybridization, washing, staining and scanning of Affymetrix GeneChip Xenopus laevis Genome 2.0 arrays were performed following the manufacturer’s recommendations

scan_protocol: Scanned images (DAT files) were transformed into intensities (CEL files) by AGCC software (Affymetrix).

data_processing: GeneChip Xenopus laevis Genome 2.0 Array were processed with Bioconductor, using RMA background correction, quantile normalization and RMA summarization. Significantly enriched target genes in CPEB1 vs. preserum and HA-MSI vs. HA samples were detected with the phenoTest package, using a fold-change threshold of 1.5 times or more and a Benjamini-Hogberg adjusted p-value < 0.05.

molecule: cytoplasmic RNA

organism: Xenopus laevis

source_name: oocyte lysate before IP

label_protocol: Amplified cDNA was purified and quantified on a Nanodrop ND-1000 spectrophotometer (Thermo-Fischer). 8 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 250K Nsp Assay Kit (Affymetrix).

growth_protocol: α IPs and western blot were performed with αCPEB1 rabbit polyclonal antibodies21, αHA (Roche, 1867431). For IP, antibodies were covalently cross-linked to protein A-Dynabeads or protein G dynabeads (Invitrogen). 25 oocytes per condition were lysed (20 mM Tris–HCl pH 8.0, 1 mM EDTA, 0.5% NP-40, 1 mM MgCl2, 100 mM NaCl) and incubated with RNAse A, when indicated, for 20 min at 37°C (100 μg.mL-1). Oocyte extracts were precleared with 25 μL dynabeads for 1 h at 4ºC, then incubated for 2 h at 4ºC with the antibody crosslinked to the beads.

extract_protocol: RNA was then extracted by phenol chloroform followed by isopropanol precipitation.

treatment_protocol: Stage VI oocytes were lysed and IPs were performed as described above with the indicated antibody. Co-Immunoprecipitated RNAs were eluted in proteinase K buffer (200 mM Tris pH7.5, 100M NaCl, 10 mM EDTA, 1%SDS) with 100 µg of proteinase K (30 min at 37ºC).

value: oocytes

tag: antibody

value: none (input)


title: preSerum

description: control IP ofCPEB1

source_name: control IP of CPEB1

value: PreSerum from Rabbit


title: IP Msi1_replicate

description: RIP against Mushashi1 tagget with HA

source_name: RIP against Mushashi1 tagged with HA

value: Anti -HA (Roche 1867431)


title: CPEB

description: RIP against endogenous CPEB1

source_name: RIP against endogenous CPEB1

value: Anti-CPEB1(Xenopus Laevis)


title: HA

description: control IP of HA-msi1

source_name: control IP of HA-msi1


title: HA-Msi1

description: RIP against HA-Msi1

source_name: RIP against HA-Msi1


title: input_for_Msi1

description: oocyte lysate before IP


title: IP HA_replicate

description: Control IP of HA-Msi1 (no HA-msi2 overexpression

source_name: Control IP of HA-Msi1


title: Bone_marrow_erythroblast_rep11_genotype

type: genomic

city: Montreal

first: Guillaume

last: Lettre

state: Québec

address: 5000 rue Bélanger

institute: Montreal Heart Institute

description:
Sample name: BA000LET8271
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).

hyb_protocol: Resuspended DNA was hybridized to locus-specific probes bound to the surface of each BeadChip. Unhybridized or non-specifically hybridized DNA was removed by gentle washing of BeadChips. DNA that remained specifically bound to the BeadChip was then genotyped using a fluorescently labeled single base extension assay

scan_protocol: Each BeadChip was scanned and analyzed using the Illumina iScan Reader.

data_processing:
Genomic DNA extracted from erythroblasts was genotyped using Infinium nfinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina). Scanned images were analyzed using Illumina’s GenomeStudio2011.1, with the following  parameters: A) cluster algorithm GenTrain 2.0, B) No-Call threshold of 0.15 checked. The data analysis process was performed using the standard Illumina HumanOmniExpress-12v1-1_B cluster file.
Processed data include: Genotype: A,B,or - (no call), Theta, R, B Allele frequency and Log R Ratio.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Erythroblast differentiated from human bone marrow CD34+ hematopoietic stem cells

label_protocol: 4 μL of genomics DNA at 50ng/μL (approximately 200ng of genomic DNA) was whole  genome amplified and fragmented.

growth_protocol: Fetal and adult erythroblasts were generated from CD34+ hematopoietic stem cells using a two-phase serum-free culture as described previously (Sankaran VG et al. Science 2008).

extract_protocol: We extracted genomic DNA with the Gentra Puregene Cell Kit (Qiagen)

tag: developmental stage

value: adult

value: Bone marrow


title: Bone_marrow_erythroblast_rep9_genotype

description:
Sample name: BA000LET8267
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep3_genotype

description:
Sample name: BA000LET8256
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep0_genotype

description:
Sample name: BA000LET8249
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep4_genotype

description:
Sample name: BA000LET8258
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep12_genotype

description:
Sample name: BA000LET8260
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep5_genotype

description:
Sample name: BA000LET8273
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep6_genotype

description:
Sample name: BA000LET8262
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep2_genotype

description:
Sample name: BA000LET8253
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep10_genotype

description:
Sample name: BA000LET8269
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep11_genotype

description:
Sample name: BA000LET8272
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).

source_name: Erythroblast differentiated from human fetal liver CD34+ hematopoietic stem cells

value: fetal

value: Fetal liver


title: Fetal_liver_erythroblast_rep12_genotype

description:
Sample name: BA000LET8274
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep7_genotype

description:
Sample name: BA000LET8264
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Bone_marrow_erythroblast_rep8_genotype

description:
Sample name: BA000LET8266
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep10_genotype

description:
Sample name: BA000LET8270
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: IP CPEB_replicate

description: RIP against endogenous CPEB1


title: Bone_marrow_erythroblast_rep1_genotype

description:
Sample name: BA000LET8251
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep8_genotype

description:
Sample name: BA000LET8265
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep9_genotype

description:
Sample name: BA000LET8268
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep7_genotype

description:
Sample name: BA000LET8263
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep6_genotype

description:
Sample name: BA000LET8261
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: IP preserum_replicate

description: control IP of CPEB1


title: Fetal_liver_erythroblast_rep5_genotype

description:
Sample name: BA000LET8259
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: input_replicate

description: oocyte lysate before IP


title: Fetal_liver_erythroblast_rep4_genotype

description:
Sample name: BA000LET8257
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep3_genotype

description:
Sample name: BA000LET8255
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep2_genotype

description:
Sample name: BA000LET8254
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep0_genotype

description:
Sample name: BA000LET8250
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: Fetal_liver_erythroblast_rep1_genotype

description:
Sample name: BA000LET8252
Genomic DNA extracted from erythroblasts was genotyped using Infinium HumanOmniExpress-12 v1.1 Genotyping BeadChips (Illumina).


title: genomic DNA from UCWBC 132

city: Cincinnati

first: Shuk-mei

last: Ho

state: OH

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing:
R software
processed values: 0 samples having 10 % of sites with a detection p-value greater than 0.05 were removed; 367 sites were removed as beadcount <3 in 5 % of samples; 11592 sites having 1 % of samples with a detection p-value greater than 0.05 were removed; dasen from wateRmelon package
signal.txt includes unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: cord blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from umblical cord blood using Qiagen DNeasy Kit according to standard instructions

tag: Sex

value: male

value: normal cord blood


title: genomic DNA from UCWBC 131


title: genomic DNA from UCWBC 133


title: genomic DNA from UCWBC 129


title: genomic DNA from UCWBC 138


title: genomic DNA from UCWBC 144


title: genomic DNA from UCWBC 135


title: genomic DNA from UCWBC 151


title: genomic DNA from UCWBC 148


title: genomic DNA from UCWBC 127


title: genomic DNA from UCWBC 123

value: female


title: genomic DNA from UCWBC 141


title: genomic DNA from UCWBC 152


title: genomic DNA from UCWBC 146


title: genomic DNA from UCWBC 140


title: genomic DNA from UCWBC 147


title: genomic DNA from UCWBC 142


title: genomic DNA from UCWBC 139


title: genomic DNA from UCWBC 137


title: genomic DNA from UCWBC 126


title: genomic DNA from UCWBC 150


title: genomic DNA from UCWBC 128


title: genomic DNA from UCWBC 125


title: genomic DNA from UCWBC 149


title: genomic DNA from UCWBC 136


title: genomic DNA from UCWBC 145


title: genomic DNA from UCWBC 124


title: genomic DNA from UCWBC 121


title: genomic DNA from UCWBC 130


title: genomic DNA from UCWBC 143


title: genomic DNA from UCWBC 134


title: genomic DNA from UCWBC 120


title: genomic DNA from UCWBC 122


title: genomic DNA from UCWBC 118


title: genomic DNA from UCWBC 101


title: genomic DNA from UCWBC 115


title: genomic DNA from UCWBC 109


title: genomic DNA from UCWBC 111


title: genomic DNA from UCWBC 113


title: genomic DNA from UCWBC 98


title: genomic DNA from UCWBC 110


title: genomic DNA from UCWBC 104


title: genomic DNA from UCWBC 112


title: genomic DNA from UCWBC 102


title: genomic DNA from UCWBC 96


title: genomic DNA from UCWBC 108


title: genomic DNA from UCWBC 93


title: genomic DNA from UCWBC 105


title: genomic DNA from UCWBC 106


title: genomic DNA from UCWBC 103


title: genomic DNA from UCWBC 95


title: genomic DNA from UCWBC 100


title: genomic DNA from UCWBC 119


title: genomic DNA from UCWBC 107


title: genomic DNA from UCWBC 92


title: genomic DNA from UCWBC 97


title: genomic DNA from UCWBC 94


title: genomic DNA from UCWBC 99


title: genomic DNA from UCWBC 114


title: biological replicate to Olaparib 1

city: Frankfurt

first: Dorothea

last: Schulte

address: Heinrich Hoffmann Str. 7

department: Neurology (Edinger Institute)

institute: Goethe University Hospital, Frankfurt

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) were hybridized with 2.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe_group_file: Unsupported Mouse Gene 1.0 ST Array CDF Files
meta-probeset_file: MoGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 32 (7.8 MB, 10/7/11)

source_name: primary adult neurospheres

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Sphere-forming cells were isolated from the lateral walls of the lateral ventricle of 9-12 week old C57BL/6 mice and propagated under non-adherent conditions in DMEM/F-12 containing 3.5 mM glucose, B-27 supplement, 20 ng/ml fibroblast growth factor-2 and 20 ng/ml epidermal growth factor, L-Glutamine, and penicillin / streptomycin. Primary neurospheres were used for further treatment.

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen.RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 40ng total RNA

treatment_protocol: 3 million aNS per replicate were transfected with 75pmol Silencer Select control siRNAs (cat# 4390846; Life Technologies). 4 hours later, cells were dissociated for 5 minutes at 37 °C in 500  µl Accutase, washed once in culture medium and incubated for 5 hours in medium containing pCLIG-Pax6 viral particles and either 100nM Olaparib in 0.01% DMSO or 0.01% DMSO alone as control. Cells were collected by centrifugation, washed in culture medium, cultured for 36h under non-adherent conditions and in the continuing presence of 100nM Olaparib and / or 0.01% DMSO. Differentiation was induced by growth factor withdrawal and plating on laminin 10 hours prior to RNA isolation.

tag: transduction

tag: transfection

value: non-targeting siRNAs

value: differentiated for 10 hours in the presence of 100nM Olaparib in 0.01% DMSO


title: genomic DNA from UCWBC 90


title: genomic DNA from UCWBC 91


title: primary adult neurospheres of the SVZ (aNS),  Pax6,  non-targeting siRNAs,  0.01% DMSO

tag: strain

tag: treatment

value: differentiated for 10 hours in the presence of 0.01% DMSO


title: genomic DNA from UCWBC 116

tag: tissue


title: genomic DNA from UCWBC 89


title: genomic DNA from UCWBC 88


title: genomic DNA from UCWBC 117


title: genomic DNA from UCWBC 86


title: genomic DNA from UCWBC 87


title: Right testis, short sperm line male 2011.M.777

city: Sheffield

first: Kang-Wook

last: Kim

address: Western Bank

department: Animal and Plant Sciences

country: United Kingdom

institute: The University of Sheffield

description: Gene expression data from right testis of a short sperm line male

hyb_protocol: Following fragmentation, cRNA were hybridized on Zebra finch Gene 1.1 ST Array according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan.

data_processing: The data were analyzed with Affymetrix Expression Console ver 1.3 using default analysis settings and RMA (robust multi-array average) as normalization method.

organism: Taeniopygia guttata

source_name: Zebra finch right testis, short sperm line male 2011.M.777

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

growth_protocol: Male zebra finches were euthanized and dissected. Testes were extracted from both sides and washed with PBS.

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

treatment_protocol: Testes were treated with RNAlater and stored at -80C until RNA extraction

value: testis

tag: gender

tag: age


title: biological replicate to Control1


title: primary adult neurospheres of the SVZ (aNS),  Pax6,  non-targeting siRNAs, 100nM Olaparib in 0.01% DMSO


title: genomic DNA from UCWBC 85


title: Right testis, short sperm line male 2011.M.808

source_name: Zebra finch right testis, short sperm line male 2011.M.808


title: genomic DNA from UCWBC 80


title: Right testis, short sperm line male 2011.M.771

source_name: Zebra finch right testis, short sperm line male 2011.M.771


title: Right testis, short sperm line male 2011.M.744

source_name: Zebra finch right testis, short sperm line male 2011.M.744


title: genomic DNA from UCWBC 81


title: Right testis, short sperm line male 2011.M.684

source_name: Zebra finch right testis, short sperm line male 2011.M.684


title: genomic DNA from UCWBC 77


title: genomic DNA from UCWBC 82


title: genomic DNA from UCWBC 76


title: genomic DNA from UCWBC 75


title: genomic DNA from UCWBC 79


title: Right testis, short sperm line male 2011.M.657

source_name: Zebra finch right testis, short sperm line male 2011.M.657


title: genomic DNA from UCWBC 78


title: genomic DNA from UCWBC 73


title: genomic DNA from UCWBC 71


title: genomic DNA from UCWBC 69


title: Right testis, short sperm line male 2011.M.605

source_name: Zebra finch right testis, short sperm line male 2011.M.605


title: Right testis, short sperm line male 2011.M.580

source_name: Zebra finch right testis, short sperm line male 2011.M.580


title: Right testis, short sperm line male 2011.M.565

source_name: Zebra finch right testis, short sperm line male 2011.M.565


title: genomic DNA from UCWBC 72


title: genomic DNA from UCWBC 68


title: genomic DNA from UCWBC 70


title: Right testis, short sperm line male 2011.M.563

source_name: Zebra finch right testis, short sperm line male 2011.M.563


title: genomic DNA from UCWBC 67


title: genomic DNA from UCWBC 74


title: Right testis, short sperm line male 2011.M.556

source_name: Zebra finch right testis, short sperm line male 2011.M.556


title: Right testis, short sperm line male 2011.M.549

source_name: Zebra finch right testis, short sperm line male 2011.M.549


title: genomic DNA from UCWBC 66


title: genomic DNA from UCWBC 84


title: Right testis, short sperm line male 2011.M.508

source_name: Zebra finch right testis, short sperm line male 2011.M.508


title: Right testis, short sperm line male 2011.M.548

source_name: Zebra finch right testis, short sperm line male 2011.M.548


title: genomic DNA from UCWBC 65


title: genomic DNA from UCWBC 64


title: Right testis, short sperm line male 2011.M.465

source_name: Zebra finch right testis, short sperm line male 2011.M.465


title: genomic DNA from UCWBC 62

source_name: cord blood


title: genomic DNA from UCWBC 63


title: Right testis, short sperm line male 2011.M.388

source_name: Zebra finch right testis, short sperm line male 2011.M.388


title: Right testis, short sperm line male 2011.M.437

source_name: Zebra finch right testis, short sperm line male 2011.M.437


title: genomic DNA from UCWBC 61


title: Left testis, short sperm line male 2011.M.777

description: Gene expression data from left testis of a short sperm line male

source_name: Zebra finch left testis, short sperm line male 2011.M.777


title: Left testis, short sperm line male 2011.M.857

source_name: Zebra finch left testis, short sperm line male 2011.M.857


title: genomic DNA from UCWBC 60


title: Left testis, short sperm line male 2011.M.771

source_name: Zebra finch left testis, short sperm line male 2011.M.771


title: Left testis, short sperm line male 2011.M.657

source_name: Zebra finch left testis, short sperm line male 2011.M.657


title: Left testis, short sperm line male 2011.M.565

source_name: Zebra finch left testis, short sperm line male 2011.M.565


title: genomic DNA from UCWBC 54


title: Left testis, short sperm line male 2011.M.605

source_name: Zebra finch left testis, short sperm line male 2011.M.605


title: Left testis, short sperm line male 2011.M.563

source_name: Zebra finch left testis, short sperm line male 2011.M.563


title: genomic DNA from UCWBC 58


title: Left testis, short sperm line male 2011.M.549

source_name: Zebra finch left testis, short sperm line male 2011.M.549


title: genomic DNA from UCWBC 57


title: genomic DNA from UCWBC 59


title: genomic DNA from UCWBC 51


title: genomic DNA from UCWBC 56


title: Left testis, short sperm line male 2011.M.537

source_name: Zebra finch left testis, short sperm line male 2011.M.537


title: genomic DNA from UCWBC 83


title: Left testis, short sperm line male 2011.M.508

source_name: Zebra finch left testis, short sperm line male 2011.M.508


title: Left testis, short sperm line male 2011.M.388

source_name: Zebra finch left testis, short sperm line male 2011.M.388


title: genomic DNA from UCWBC 53


title: Left testis, short sperm line male 2011.M.438

source_name: Zebra finch left testis, short sperm line male 2011.M.438


title: genomic DNA from UCWBC 47


title: Left testis, short sperm line male 2011.M.437

source_name: Zebra finch left testis, short sperm line male 2011.M.437


title: genomic DNA from UCWBC 48


title: Right testis, long sperm line male 2011.M.853

description: Gene expression data from right testis of a long sperm line male

source_name: Zebra finch right testis, long sperm line male 2011.M.853


title: genomic DNA from UCWBC 55

source_name: cord blood


title: Left testis, short sperm line male 2011.M.548

source_name: Zebra finch left testis, short sperm line male 2011.M.548


title: Right testis, long sperm line male 2011.M.838

source_name: Zebra finch right testis, long sperm line male 2011.M.838


title: genomic DNA from UCWBC 49


title: Right testis, long sperm line male 2011.M.774

source_name: Zebra finch right testis, long sperm line male 2011.M.774


title: genomic DNA from UCWBC 44


title: genomic DNA from UCWBC 52


title: genomic DNA from UCWBC 42


title: Right testis, long sperm line male 2011.M.761

source_name: Zebra finch right testis, long sperm line male 2011.M.761


title: genomic DNA from UCWBC 43


title: Right testis, long sperm line male 2011.M.720

source_name: Zebra finch right testis, long sperm line male 2011.M.720


title: Right testis, long sperm line male 2011.M.752

source_name: Zebra finch right testis, long sperm line male 2011.M.752


title: genomic DNA from UCWBC 45


title: genomic DNA from UCWBC 39


title: Right testis, long sperm line male 2011.M.717

source_name: Zebra finch right testis, long sperm line male 2011.M.717


title: genomic DNA from UCWBC 41


title: Right testis, long sperm line male 2011.M.628

source_name: Zebra finch right testis, long sperm line male 2011.M.628


title: Right testis, long sperm line male 2011.M.596

source_name: Zebra finch right testis, long sperm line male 2011.M.596


title: genomic DNA from UCWBC 35


title: genomic DNA from UCWBC 36


title: Right testis, long sperm line male 2011.M.555

source_name: Zebra finch right testis, long sperm line male 2011.M.555


title: genomic DNA from UCWBC 37


title: Right testis, long sperm line male 2011.M.798

source_name: Zebra finch right testis, long sperm line male 2011.M.798


title: genomic DNA from UCWBC 38


title: Right testis, long sperm line male 2011.M.562

source_name: Zebra finch right testis, long sperm line male 2011.M.562


title: Right testis, long sperm line male 2011.M.522

source_name: Zebra finch right testis, long sperm line male 2011.M.522


title: genomic DNA from UCWBC 40


title: genomic DNA from UCWBC 50


title: genomic DNA from UCWBC 46


title: Right testis, long sperm line male 2011.M.432

source_name: Zebra finch right testis, long sperm line male 2011.M.432


title: Right testis, long sperm line male 2011.M.521

source_name: Zebra finch right testis, long sperm line male 2011.M.521


title: genomic DNA from UCWBC 33


title: genomic DNA from UCWBC 30


title: genomic DNA from UCWBC 28


title: Left testis, long sperm line male 2011.M.853

description: Gene expression data from left testis of a long sperm line male

source_name: Zebra finch left testis, long sperm line male 2011.M.853


title: Right testis, long sperm line male 2011.M.417

source_name: Zebra finch right testis, long sperm line male 2011.M.417


title: genomic DNA from UCWBC 31

source_name: cord blood


title: Left testis, long sperm line male 2011.M.852

source_name: Zebra finch left testis, long sperm line male 2011.M.852


title: genomic DNA from UCWBC 34


title: genomic DNA from UCWBC 29


title: Left testis, long sperm line male 2011.M.838

source_name: Zebra finch left testis, long sperm line male 2011.M.838


title: genomic DNA from UCWBC 24


title: genomic DNA from UCWBC 32


title: Left testis, long sperm line male 2011.M.798

source_name: Zebra finch left testis, long sperm line male 2011.M.798


title: genomic DNA from UCWBC 26


title: genomic DNA from UCWBC 25


title: Left testis, long sperm line male 2011.M.832

source_name: Zebra finch left testis, long sperm line male 2011.M.832


title: Left testis, long sperm line male 2011.M.752

source_name: Zebra finch left testis, long sperm line male 2011.M.752


title: Left testis, long sperm line male 2011.M.774

source_name: Zebra finch left testis, long sperm line male 2011.M.774


title: genomic DNA from UCWBC 20


title: genomic DNA from UCWBC 22


title: Left testis, long sperm line male 2011.M.717

source_name: Zebra finch left testis, long sperm line male 2011.M.717


title: genomic DNA from UCWBC 23


title: Left testis, long sperm line male 2011.M.720

source_name: Zebra finch left testis, long sperm line male 2011.M.720


title: Right testis, long sperm line male 2011.M.058

source_name: Zebra finch right testis, long sperm line male 2011.M.058


title: Left testis, long sperm line male 2011.M.761

source_name: Zebra finch left testis, long sperm line male 2011.M.761


title: Left testis, long sperm line male 2011.M.628

source_name: Zebra finch left testis, long sperm line male 2011.M.628


title: Left testis, long sperm line male 2011.M.562

source_name: Zebra finch left testis, long sperm line male 2011.M.562


title: genomic DNA from UCWBC 19


title: Left testis, long sperm line male 2011.M.555

source_name: Zebra finch left testis, long sperm line male 2011.M.555


title: genomic DNA from UCWBC 21


title: Left testis, long sperm line male 2011.M.468

source_name: Zebra finch left testis, long sperm line male 2011.M.468


title: Left testis, long sperm line male 2011.M.521

source_name: Zebra finch left testis, long sperm line male 2011.M.521


title: Left testis, long sperm line male 2011.M.432

source_name: Zebra finch left testis, long sperm line male 2011.M.432


title: genomic DNA from UCWBC 16

source_name: cord blood


title: genomic DNA from UCWBC 17


title: genomic DNA from UCWBC 18


title: genomic DNA from UCWBC 14


title: Left testis, long sperm line male 2011.M.419

source_name: Zebra finch left testis, long sperm line male 2011.M.419


title: Left testis, long sperm line male 2011.M.522

source_name: Zebra finch left testis, long sperm line male 2011.M.522


title: Left testis, long sperm line male 2011.M.417

source_name: Zebra finch left testis, long sperm line male 2011.M.417


title: Left testis, long sperm line male 2011.M.403

source_name: Zebra finch left testis, long sperm line male 2011.M.403


title: Left testis, long sperm line male 2011.M.058

source_name: Zebra finch left testis, long sperm line male 2011.M.058


title: genomic DNA from UCWBC 13


title: genomic DNA from UCWBC 8


title: genomic DNA from UCWBC 11


title: genomic DNA from UCWBC 27


title: genomic DNA from UCWBC 10


title: genomic DNA from UCWBC 12


title: genomic DNA from UCWBC 5


title: genomic DNA from UCWBC 15


title: genomic DNA from UCWBC 9


title: genomic DNA from UCWBC 4


title: genomic DNA from UCWBC 3


title: genomic DNA from UCWBC 2


title: genomic DNA from UCWBC 7


title: Breast tumor from TOP Cohort patient P_58

status: Public on Jul 16 2017

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description:
SAMPLE 295
Breast tumor from Cohort TOP (methylation)

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

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

data_processing: .idat files were loaded using methylumi R-package. High-detection p-value, SNP-containing, Cross-reactive and heterochromosomic probes were filtered out (replaced by null) and data were peak-based normalized using in-house R-scripts.

source_name: Breast tumor

label_protocol: Standard Infinium HD Methylation Assay protocol

extract_protocol: Genomic DNA was extracted with the Qiagen-DNeasy Blood &Tissue Kit (Qiagen, Hilden, Germany) or the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany)

value: breast tumor

tag: cohort id

tag: grade

tag: t

tag: n

tag: os_time (days)

tag: dmfs_time (days)

tag: pcr


title: Breast tumor from TOP Cohort patient P_55

description:
SAMPLE 292
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_56

description:
SAMPLE 293
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_50

description:
SAMPLE 287
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_44

description:
SAMPLE 281
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_51

description:
SAMPLE 288
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_53

description:
SAMPLE 290
Breast tumor from Cohort TOP (methylation)


title: genomic DNA from UCWBC 1


title: Breast tumor from TOP Cohort patient P_42

description:
SAMPLE 279
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_47

description:
SAMPLE 284
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_52

description:
SAMPLE 289
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_39

description:
SAMPLE 276
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_43

description:
SAMPLE 280
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_37

description:
SAMPLE 274
Breast tumor from Cohort TOP (methylation)


title: genomic DNA from UCWBC 6


title: Breast tumor from TOP Cohort patient P_41

description:
SAMPLE 278
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_54

description:
SAMPLE 291
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_49

description:
SAMPLE 286
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_48

description:
SAMPLE 285
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_36

description:
SAMPLE 273
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_34

description:
SAMPLE 271
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_33

description:
SAMPLE 270
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_32

description:
SAMPLE 269
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_35

description:
SAMPLE 272
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_45

description:
SAMPLE 282
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_57

description:
SAMPLE 294
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_31

description:
SAMPLE 268
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_38

description:
SAMPLE 275
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_29

description:
SAMPLE 266
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_28

description:
SAMPLE 265
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_30

description:
SAMPLE 267
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_40

description:
SAMPLE 277
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_25

description:
SAMPLE 262
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_24

description:
SAMPLE 261
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_22

description:
SAMPLE 259
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_27

description:
SAMPLE 264
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_21

description:
SAMPLE 258
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_19

description:
SAMPLE 256
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_46

description:
SAMPLE 283
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_12

description:
SAMPLE 249
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_17

description:
SAMPLE 254
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_10

description:
SAMPLE 247
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_16

description:
SAMPLE 253
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_18

description:
SAMPLE 255
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_26

description:
SAMPLE 263
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_11

description:
SAMPLE 248
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_15

description:
SAMPLE 252
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_9

description:
SAMPLE 246
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_20

description:
SAMPLE 257
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_7

description:
SAMPLE 244
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_8

description:
SAMPLE 245
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_23

description:
SAMPLE 260
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_14

description:
SAMPLE 251
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_3

description:
SAMPLE 240
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from Cohort 2 patient P_118

description:
SAMPLE 236
Breast tumor from Cohort 2 (methylation)

value: Basal

tag: itu-ly

tag: str-ly

tag: idfs_time (years)

tag: ddfs_time (years)

tag: os_time (years)


title: Breast tumor from TOP Cohort patient P_13

description:
SAMPLE 250
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_6

description:
SAMPLE 243
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_2

description:
SAMPLE 239
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from Cohort 2 patient P_114

description:
SAMPLE 232
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_119

description:
SAMPLE 237
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_115

description:
SAMPLE 233
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_117

description:
SAMPLE 235
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_116

description:
SAMPLE 234
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_110

description:
SAMPLE 228
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from TOP Cohort patient P_1

description:
SAMPLE 238
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from TOP Cohort patient P_4

description:
SAMPLE 241
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from Cohort 2 patient P_104

description:
SAMPLE 222
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_103

description:
SAMPLE 221
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_113

description:
SAMPLE 231
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_106

description:
SAMPLE 224
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_108

description:
SAMPLE 226
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_109

description:
SAMPLE 227
Breast tumor from Cohort 2 (methylation)

value: LumB


title: Breast tumor from Cohort 2 patient P_112

description:
SAMPLE 230
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from TOP Cohort patient P_5

description:
SAMPLE 242
Breast tumor from Cohort TOP (methylation)


title: Breast tumor from Cohort 2 patient P_101

description:
SAMPLE 219
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_111

description:
SAMPLE 229
Breast tumor from Cohort 2 (methylation)

value: 25 September 2009

value: cancer


title: Breast tumor from Cohort 2 patient P_107

description:
SAMPLE 225
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_99

description:
SAMPLE 217
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_100

description:
SAMPLE 218
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_96

description:
SAMPLE 214
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_98

description:
SAMPLE 216
Breast tumor from Cohort 2 (methylation)

value: 14 February 2007


title: Breast tumor from Cohort 2 patient P_105

description:
SAMPLE 223
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_94

description:
SAMPLE 212
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_95

description:
SAMPLE 213
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_93

description:
SAMPLE 211
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_92

description:
SAMPLE 210
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_102

description:
SAMPLE 220
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_86

description:
SAMPLE 204
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_97

description:
SAMPLE 215
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_87

description:
SAMPLE 205
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_88

description:
SAMPLE 206
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_85

description:
SAMPLE 203
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_89

description:
SAMPLE 207
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_77

description:
SAMPLE 195
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_82

description:
SAMPLE 200
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_83

description:
SAMPLE 201
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_90

description:
SAMPLE 208
Breast tumor from Cohort 2 (methylation)

value: 01 October 2005


title: Breast tumor from Cohort 2 patient P_78

description:
SAMPLE 196
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_91

description:
SAMPLE 209
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_71

description:
SAMPLE 189
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_76

description:
SAMPLE 194
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_81

description:
SAMPLE 199
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_75

description:
SAMPLE 193
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_70

description:
SAMPLE 188
Breast tumor from Cohort 2 (methylation)

value: NK


title: Breast tumor from Cohort 2 patient P_79

description:
SAMPLE 197
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_73

description:
SAMPLE 191
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_74

description:
SAMPLE 192
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_67

description:
SAMPLE 185
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_80

description:
SAMPLE 198
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_65

description:
SAMPLE 183
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_69

description:
SAMPLE 187
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_64

description:
SAMPLE 182
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_84

description:
SAMPLE 202
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_68

description:
SAMPLE 186
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_63

description:
SAMPLE 181
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_62

description:
SAMPLE 180
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_61

description:
SAMPLE 179
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_66

description:
SAMPLE 184
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_59

description:
SAMPLE 177
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_60

description:
SAMPLE 178
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_55

description:
SAMPLE 173
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_58

description:
SAMPLE 176
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_46

description:
SAMPLE 164
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_72

description:
SAMPLE 190
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_51

description:
SAMPLE 169
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_47

description:
SAMPLE 165
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_56

description:
SAMPLE 174
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_54

description:
SAMPLE 172
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_49

description:
SAMPLE 167
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_41

description:
SAMPLE 159
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_57

description:
SAMPLE 175
Breast tumor from Cohort 2 (methylation)

value: 14 December 2011

value: general conditions


title: Breast tumor from Cohort 2 patient P_43

description:
SAMPLE 161
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_52

description:
SAMPLE 170
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_42

description:
SAMPLE 160
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_48

description:
SAMPLE 166
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_50

description:
SAMPLE 168
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_40

description:
SAMPLE 158
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_44

description:
SAMPLE 162
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_35

description:
SAMPLE 153
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_53

description:
SAMPLE 171
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_38

description:
SAMPLE 156
Breast tumor from Cohort 2 (methylation)

value: cancer+general conditions (alcoholist)


title: Breast tumor from Cohort 2 patient P_37

description:
SAMPLE 155
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_34

description:
SAMPLE 152
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_32

description:
SAMPLE 150
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_33

description:
SAMPLE 151
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_36

description:
SAMPLE 154
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_28

description:
SAMPLE 146
Breast tumor from Cohort 2 (methylation)

value: LumA


title: Breast tumor from Cohort 2 patient P_29

description:
SAMPLE 147
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_25

description:
SAMPLE 143
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_45

description:
SAMPLE 163
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_26

description:
SAMPLE 144
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_21

description:
SAMPLE 139
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_20

description:
SAMPLE 138
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_17

description:
SAMPLE 135
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_27

description:
SAMPLE 145
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_24

description:
SAMPLE 142
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_19

description:
SAMPLE 137
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_39

description:
SAMPLE 157
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_22

description:
SAMPLE 140
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_18

description:
SAMPLE 136
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_31

description:
SAMPLE 149
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_11

description:
SAMPLE 129
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_30

description:
SAMPLE 148
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_23

description:
SAMPLE 141
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_16

description:
SAMPLE 134
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_14

description:
SAMPLE 132
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_9

description:
SAMPLE 127
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_13

description:
SAMPLE 131
Breast tumor from Cohort 2 (methylation)

value: 11 September 2005


title: Breast tumor from Cohort 2 patient P_15

description:
SAMPLE 133
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_7

description:
SAMPLE 125
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_10

description:
SAMPLE 128
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_6

description:
SAMPLE 124
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_5

description:
SAMPLE 123
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_12

description:
SAMPLE 130
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_4

description:
SAMPLE 122
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_3

description:
SAMPLE 121
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 2 patient P_8

description:
SAMPLE 126
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 1 patient P_117

description:
SAMPLE 117
Breast tumor from Cohort 1 (methylation)

tag: rfs_time (years)

tag: rfs_time_censored (years)


title: Breast tumor from Cohort 1 patient P_114

description:
SAMPLE 114
Breast tumor from Cohort 1 (methylation)

tag: tissue


title: Breast tumor from Cohort 1 patient P_115

description:
SAMPLE 115
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 2 patient P_2

description:
SAMPLE 120
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 1 patient P_104

description:
SAMPLE 104
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_107

description:
SAMPLE 107
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 2 patient P_1

description:
SAMPLE 119
Breast tumor from Cohort 2 (methylation)


title: Breast tumor from Cohort 1 patient P_118

description:
SAMPLE 118
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_111

description:
SAMPLE 111
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_116

description:
SAMPLE 116
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_113

description:
SAMPLE 113
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_100

description:
SAMPLE 100
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_99

description:
SAMPLE 99
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_98

description:
SAMPLE 98
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_103

description:
SAMPLE 103
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_106

description:
SAMPLE 106
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_110

description:
SAMPLE 110
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_96

description:
SAMPLE 96
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_102

description:
SAMPLE 102
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_112

description:
SAMPLE 112
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_105

description:
SAMPLE 105
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_97

description:
SAMPLE 97
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_95

description:
SAMPLE 95
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_93

description:
SAMPLE 93
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_94

description:
SAMPLE 94
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_101

description:
SAMPLE 101
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_109

description:
SAMPLE 109
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_92

description:
SAMPLE 92
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_90

description:
SAMPLE 90
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_89

description:
SAMPLE 89
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_82

description:
SAMPLE 82
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_91

description:
SAMPLE 91
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_108

description:
SAMPLE 108
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_80

description:
SAMPLE 80
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_87

description:
SAMPLE 87
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_83

description:
SAMPLE 83
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_88

description:
SAMPLE 88
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_84

description:
SAMPLE 84
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_73

description:
SAMPLE 73
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_75

description:
SAMPLE 75
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_79

description:
SAMPLE 79
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_74

description:
SAMPLE 74
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_78

description:
SAMPLE 78
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_76

description:
SAMPLE 76
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_86

description:
SAMPLE 86
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_77

description:
SAMPLE 77
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_71

description:
SAMPLE 71
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_68

description:
SAMPLE 68
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_85

description:
SAMPLE 85
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_65

description:
SAMPLE 65
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_64

description:
SAMPLE 64
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_66

description:
SAMPLE 66
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_69

description:
SAMPLE 69
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_70

description:
SAMPLE 70
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_67

description:
SAMPLE 67
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_63

description:
SAMPLE 63
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_81

description:
SAMPLE 81
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_61

description:
SAMPLE 61
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_57

description:
SAMPLE 57
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_56

description:
SAMPLE 56
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_58

description:
SAMPLE 58
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_60

description:
SAMPLE 60
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_59

description:
SAMPLE 59
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_55

description:
SAMPLE 55
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_62

description:
SAMPLE 62
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_54

description:
SAMPLE 54
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_47

description:
SAMPLE 47
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_50

description:
SAMPLE 50
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_52

description:
SAMPLE 52
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_43

description:
SAMPLE 43
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_48

description:
SAMPLE 48
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_53

description:
SAMPLE 53
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_45

description:
SAMPLE 45
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_72

description:
SAMPLE 72
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_49

description:
SAMPLE 49
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_42

description:
SAMPLE 42
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_38

description:
SAMPLE 38
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_37

description:
SAMPLE 37
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_46

description:
SAMPLE 46
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_36

description:
SAMPLE 36
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_39

description:
SAMPLE 39
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_44

description:
SAMPLE 44
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_51

description:
SAMPLE 51
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_33

description:
SAMPLE 33
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_34

description:
SAMPLE 34
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_41

description:
SAMPLE 41
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_32

description:
SAMPLE 32
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_31

description:
SAMPLE 31
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_29

description:
SAMPLE 29
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_40

description:
SAMPLE 40
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_27

description:
SAMPLE 27
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_25

description:
SAMPLE 25
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_26

description:
SAMPLE 26
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_24

description:
SAMPLE 24
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_30

description:
SAMPLE 30
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_23

description:
SAMPLE 23
Breast tumor from Cohort 1 (methylation)


title: Rice suspension cells treated with 100 µM rapamycin for 24 h Replicate 3

status: Public on Jul 15 2017

city: Ghent

first: Osvaldo

last: Filipe

address: Coupure Links 653

department: Crop Protection

institute: Ghent University

description:
Rapa3
Gene expression after 24hr in Kitaake rice suspension cells.

hyb_protocol: Hybridized to commercially available 60-mer 44K Agilent rice arrays according to the manufacturer’s protocols (Agilent Technologies). A full list of the expressed sequence tags (ESTs) represented on the array can be found at http://ricexpro.dna.affrc.go.jp/rice-44k-microarray.html

scan_protocol: Following washing, slide image files were generated using a DNA microarray scanner (Agilent Technologies).

data_processing: Signal intensities were extracted and normalized within each array using Feature Extraction version 9.5 (Agilent Technologies). Signal intensities among all arrays were normalized according to the quantile method for standardization (global scaling) using EXPANDER version 6.

organism: Oryza sativa

source_name: Kitaake rice suspension cells, rapamycin

label_protocol: 200 ng of total RNA were primed with 1.8 µl of T7 primer mix + 2 µl spike A/B 1:16 at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in cDNA master mix (500 µM dNTP mix, 10 µM DTT, 1xRT buffer and 1.2 µl Affinity script (violet)), + 6 µl Cy3 or Cy5.

growth_protocol: Rice suspension cells (cultivar Kitaake) were grown in modified AA medium on a rotary shaker (120 rpm) at 28°C in the dark. The cells were subcultured in fresh medium every week (10 ml old culture to 40 ml new AA), and all experiments were performed 3 or 4 days after transfer.

extract_protocol: Total RNA was extracted using TRIZOL reagent according to the manufacturer’s protocol (Invitrogen).

treatment_protocol: Kitaake rice suspension cells were treated with 100 µM rapamycin for 24 h and subjected to genome-wide transcriptome analysis using 44k rice GeneChips.

tag: cultivar

value: Kitaake

value: Rice suspension

value: Day 4

tag: treatment

value: Rapamycin

tag: duration

value: 24 hours


title: Breast tumor from Cohort 1 patient P_28

description:
SAMPLE 28
Breast tumor from Cohort 1 (methylation)

value: breast tumor

tag: cohort id

tag: grade


title: Breast tumor from Cohort 1 patient P_35

description:
SAMPLE 35
Breast tumor from Cohort 1 (methylation)

value: LumB


title: Rice suspension cells treated with DMSO for 24 h Replicate 3

description:
DMSO3
Gene expression after 24hr in Kitaake rice suspension cells.

source_name: Kitaake rice suspension cells, DMSO

tag: age

value: DMSO


title: Rice suspension cells treated with 100 µM rapamycin for 24 h Replicate 2

description:
Rapa2
Gene expression after 24hr in Kitaake rice suspension cells.


title: Breast tumor from Cohort 1 patient P_9

description:
SAMPLE 9
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_10

description:
SAMPLE 10
Breast tumor from Cohort 1 (methylation)

value: Basal


title: Breast tumor from Cohort 1 patient P_18

description:
SAMPLE 18
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_22

description:
SAMPLE 22
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_14

description:
SAMPLE 14
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_12

description:
SAMPLE 12
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_21

description:
SAMPLE 21
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_17

description:
SAMPLE 17
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_13

description:
SAMPLE 13
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_16

description:
SAMPLE 16
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_11

description:
SAMPLE 11
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_7

description:
SAMPLE 7
Breast tumor from Cohort 1 (methylation)


title: SKN 3

status: Public on Jul 14 2017

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

description: Gene expression from skin cell culture

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Canine Gene ST 1.0 GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Interrogating probes were imported, RMA normalized and RMA background corrected, Quantile normalization, Log probes using base 2 and Probeset summarization is Median Polish (Partek Genome Suite v6.6 (6.151022)

organism: Canis lupus familiaris

source_name: Skin cell culture

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: Community-based dogs that underwent routine surgery at Struggletown Veterinary Clinic, Sydney had excess waste tissue (1-2 cm3) opportunistically harvested and donated by consenting owners. The use of canine tissue was approved by the Animal Care and Ethics Committee of The University of New South Wales.  Skin biopsies were immediately transferred in Phosphate-buffered saline (PBS; Thermo Fisher Scientific) and processed within 6 hours. The specimen was washed in PBS (Thermo Fisher Scientific) containing 1% Penicillin Streptomycin (Thermo Fisher Scientific), divided into 1-2 mm2 pieces and washed again. The tissue was digested with 0.1% Trypsin (Thermo Fisher Scientific) for 40 minutes at 37°C, followed by 0.1% DNAse (Roche Applied Science) digestion for 1 minute at room temperature. Then mechanically dissociated and passed through a 40 µm cell strainer (BD Bioscience).  The dissociated cells were then centrifuged at 180G for 5 minutes.     For fibroblast cell culture, the cells were re-suspended in 3:1 DMEM/F12 (Dulbecco's Modified Eagle Medium/Ham's F-12 Nutrient Mixture; Thermo Fisher Scientific) medium, containing 10% FBS (Thermo Fisher Scientific), 1% Glutamax (Thermo Fisher Scientific), and 1% Penicillin Streptomycin (Thermo Fisher Scientific). The cells were then plated onto non-tissue culture treated dishes at a density of 100,000 cells/cm2.    For SKN cell culture, following centrifugation, the cells were re-suspended in serum free complete medium containing 3:1 DMEM/F12 (Dulbecco's Modified Eagle Medium/Ham's F-12 Nutrient Mixture; Thermo Fisher Scientific) medium, 1% Penicillin Streptomycin (Thermo Fisher Scientific), 20 ng/mL Epidermal growth factor (EGF; BD Bioscience), 40 ng/mL β-Fibroblast growth factor (β-FGF; Thermo Fisher Scientific), and 2% B-27 (Thermo Fisher Scientific).  The cells were then plated non-tissue culture treated dishes at a density of 100,000 cells/cm2.    SKNs were initially cultured as neurospheres, which formed within 1-5 days after isolation. When most neurospheres reached >50 µm in diameter, they were collected and dissociated using TrypLE Select (Thermo Fisher Scientific) for 5 minutes at 37°C. The single cells suspension, diluted in complete medium, was then centrifuged at 180G for 5 minutes, re-suspended in complete medium and grown as an adherent monolayer by seeding at a density of 10,000 cells/cm2 on 0.1% gelatin coated flasks. SKNs were passaged when 80% confluent using TrypLE Select (Thermo Fisher Scientific).    For brain derived neural precursor cell culture, three recently euthanized dogs obtained from a local pound for use, as permissible under New South Wales law. Deceased animals were obtained within 4 hours post mortem and prior to routine cremation. The age of the subjects was not known, however all were mature adults. Tissue samples from the subventricular zone brain regions were diced then digested enzymatically with 0.1% Trypsin EDTA (Thermo Fisher Scientific) for 7 minutes at 37°C/5% CO2, washed with DMEM (Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (FBS: Thermo Fisher Scientific) – hereafter known as FDMEM, and then further mechanically dissociated. Cells were then washed again with FDMEM, centrifuged at 100rcf, and seeded in NeuroCult complete medium consisting of NeuroCult basal medium (Rat; Stem Cell Technologies) with the addition of NeuroCult NS-A proliferation supplements (Stem Cell Technologies), 2% FBS (Thermo Fisher Scientific), 2 µg/mL heparin (Sigma-Aldrich), 20 ng/mL EGF (BD Bioscience) and 10 ng/mL βFGF (Thermo Fisher Scientific). Neurospheres were collected after 14-21 days by centrifugation at 100rcf for 7 minutes. Following 0.1% trypsin EDTA (Thermo Fisher Scientific) for 2 minutes and repeated centrifugation, the single cell were re-suspended in complete medium and seeded at 10,000 cells/cm2 in 0.1% gelatin coated flasks.

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

treatment_protocol: The skin (SKN) cells, fibroblasts and brain derived neural precursor cells underwent no treatments prior to RNA extraction.

tag: primary cell culture type

value: Skin (SKN)


title: SKN 2

description: Gene expression from skin cell culture


title: Breast tumor from Cohort 1 patient P_15

description:
SAMPLE 15
Breast tumor from Cohort 1 (methylation)

value: 1.7+0.7 BIFOCAL


title: Brain 1

description: Gene expression from brain cell culture

source_name: Brain cell culture

value: Brain


title: Breast tumor from Cohort 1 patient P_4

description:
SAMPLE 4
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_20

description:
SAMPLE 20
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_19

description:
SAMPLE 19
Breast tumor from Cohort 1 (methylation)


title: Rice suspension cells treated with DMSO for 24 h Replicate 1

description:
DMSO1
Gene expression after 24hr in Kitaake rice suspension cells.


title: Breast tumor from Cohort 1 patient P_6

description:
SAMPLE 6
Breast tumor from Cohort 1 (methylation)


title: Rice suspension cells treated with DMSO for 24 h Replicate 2

description:
DMSO2
Gene expression after 24hr in Kitaake rice suspension cells.


title: Rice suspension cells treated with 100 µM rapamycin for 24 h Replicate 1

description:
Rapa1
Gene expression after 24hr in Kitaake rice suspension cells.


title: Breast tumor from Cohort 1 patient P_8

description:
SAMPLE 8
Breast tumor from Cohort 1 (methylation)