title: Genomic DNA from normal human Kidney 88

city: Jefferson

first: Stancy

last: Joseph

state: Ar

address: 3900 NCTR Road

department: Biochemical Toxicology

institute: FDA/NCTR

description:
SAMPLE 88
Location 1, idat file 1: 9407201121_R02C02_Grn.idat
Location 1, idat file 2: 9407201121_R02C02_Red.idat
Location 2, idat file 1: 9407201102_R06C02_Grn.idat
Location 2, idat file 2: 9407201102_R06C02_Red.idat
Location 3, idat file 1: 9407201121_R01C02_Grn.idat
Location 3, idat file 2: 9407201121_R01C02_Red.idat
Normal human kidney

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader

data_processing: BeadStudio Software

label: Cy3 and Cy5

source_name: normal human Kidney 88

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from normal human kidney tissue samples using Qiagen DNeasy Kit according to standard instructions

tag: Sex

value: Female

tag: ethnicity

value: African American

value: normal kidney


title: Genomic DNA from normal human Kidney 89

status: Public on Mar 10 2017

type: genomic

country: USA

description:
SAMPLE 89
Location 1, idat file 1: 9407201065_R02C01_Grn.idat
Location 1, idat file 2: 9407201065_R02C01_Red.idat
Location 2, idat file 1: 9406922120_R03C01_Grn.idat
Location 2, idat file 2: 9406922120_R03C01_Red.idat
Location 3, idat file 1: 9407201065_R01C01_Grn.idat
Location 3, idat file 2: 9407201065_R01C01_Red.idat
Normal human kidney

molecule: genomic DNA

organism: Homo sapiens

source_name: normal human Kidney 89

value: Male

tag: age

tag: tissue


title: ST-1 embryonic stem cells [3-3]

type: RNA

city: Shanghai

first: Hongying

last: Sha

state: Shanghai

address: 220 Handan Rd, WuJiaoChang, Yangpu Qu

country: China

institute: Fudan University

hyb_protocol: The pre-hybridization of HOA v7 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

molecule: total RNA

source_name: ST-1 embryonic stem cells [3-3]

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: In vitro culture at  5% CO2,37℃

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: All embryonic stem cells were cultured onto inactived feeder cells  and classical media for humanembryonic stem cells.  Human embryonic fibroblast cells were cultured under 10% fetal  bovine serum  in DMEM/f12.

value: from inner cell mass of ST blastocyst


title: PB1T-2 embryonic stem cells [2-2]

source_name: PB1T-2 embryonic stem cells [2-2]

value: from inner cell mass of PB1T blastocyst


title: ST-2 embryonic stem cells [4-2]

source_name: ST-2 embryonic stem cells [4-2]


title: ST-1 embryonic stem cells [3-1]

source_name: ST-1 embryonic stem cells [3-1]


title: PB1T-2 embryonic stem cells [2-1]

source_name: PB1T-2 embryonic stem cells [2-1]


title: Genomic DNA from normal human Kidney 92

description:
SAMPLE 92
Location 1, idat file 1: 9407201102_R02C01_Grn.idat
Location 1, idat file 2: 9407201102_R02C01_Red.idat
Location 2, idat file 1: 9407201095_R05C02_Grn.idat
Location 2, idat file 2: 9407201095_R05C02_Red.idat
Location 3, idat file 1: 9407201095_R06C02_Grn.idat
Location 3, idat file 2: 9407201095_R06C02_Red.idat
Normal human kidney

source_name: normal human Kidney 92

value: European American


title: ST-1 embryonic stem cells [3-2]

source_name: ST-1 embryonic stem cells [3-2]


title: PB1T-2 embryonic stem cells [2-3]

source_name: PB1T-2 embryonic stem cells [2-3]


title: PB1T-1 embryonic stem cells [1-3]

source_name: PB1T-1 embryonic stem cells [1-3]


title: Genomic DNA from normal human Kidney 95

description:
SAMPLE 95
Location 1, idat file 1: 9407201102_R04C01_Grn.idat
Location 1, idat file 2: 9407201102_R04C01_Red.idat
Location 2, idat file 1: 9407201041_R03C01_Grn.idat
Location 2, idat file 2: 9407201041_R03C01_Red.idat
Location 3, idat file 1: 9407201041_R04C01_Grn.idat
Location 3, idat file 2: 9407201041_R04C01_Red.idat
Normal human kidney

source_name: normal human Kidney 95


title: Genomic DNA from normal human Kidney 78

description:
SAMPLE 78
Location 1, idat file 1: 9407201102_R01C01_Grn.idat
Location 1, idat file 2: 9407201102_R01C01_Red.idat
Location 2, idat file 1: 9407201095_R03C02_Grn.idat
Location 2, idat file 2: 9407201095_R03C02_Red.idat
Location 3, idat file 1: 9407201095_R04C02_Grn.idat
Location 3, idat file 2: 9407201095_R04C02_Red.idat
Normal human kidney

source_name: normal human Kidney 78


title: Genomic DNA from normal human Kidney 75

description:
SAMPLE 75
Location 1, idat file 1: 9407201051_R02C02_Grn.idat
Location 1, idat file 2: 9407201051_R02C02_Red.idat
Location 2, idat file 1: 9406922032_R06C02_Grn.idat
Location 2, idat file 2: 9406922032_R06C02_Red.idat
Location 3, idat file 1: 9407201051_R01C02_Grn.idat
Location 3, idat file 2: 9407201051_R01C02_Red.idat
Normal human kidney

source_name: normal human Kidney 75


title: Genomic DNA from normal human Kidney 86

description:
SAMPLE 86
Location 1, idat file 1: 9407201051_R06C02_Grn.idat
Location 1, idat file 2: 9407201051_R06C02_Red.idat
Location 2, idat file 1: 9406922120_R02C01_Grn.idat
Location 2, idat file 2: 9406922120_R02C01_Red.idat
Location 3, idat file 1: 9407201051_R05C02_Grn.idat
Location 3, idat file 2: 9407201051_R05C02_Red.idat
Normal human kidney

source_name: normal human Kidney 86


title: human embryonic fibroblast [HF-2]

source_name: human embryonic fibroblast [HF-2]

value: skin cells from aborted fetus at 3 months of pregnancy


title: PB1T-1 embryonic stem cells [1-2]

source_name: PB1T-1 embryonic stem cells [1-2]


title: Genomic DNA from normal human Kidney 83

description:
SAMPLE 83
Location 1, idat file 1: 9407201121_R06C01_Grn.idat
Location 1, idat file 2: 9407201121_R06C01_Red.idat
Location 2, idat file 1: 9407201102_R05C02_Grn.idat
Location 2, idat file 2: 9407201102_R05C02_Red.idat
Location 3, idat file 1: 9407201121_R05C01_Grn.idat
Location 3, idat file 2: 9407201121_R05C01_Red.idat
Normal human kidney

source_name: normal human Kidney 83


title: Genomic DNA from normal human Kidney 93

description:
SAMPLE 93
Location 1, idat file 1: 9407201102_R03C01_Grn.idat
Location 1, idat file 2: 9407201102_R03C01_Red.idat
Location 2, idat file 1: 9407201041_R01C01_Grn.idat
Location 2, idat file 2: 9407201041_R01C01_Red.idat
Location 3, idat file 1: 9407201041_R02C01_Grn.idat
Location 3, idat file 2: 9407201041_R02C01_Red.idat
Normal human kidney

source_name: normal human Kidney 93


title: human embryonic fibroblast [HF-1]

source_name: human embryonic fibroblast [HF-1]


title: Genomic DNA from normal human Kidney 73

description:
SAMPLE 73
Location 1, idat file 1: 9407201121_R04C01_Grn.idat
Location 1, idat file 2: 9407201121_R04C01_Red.idat
Location 2, idat file 1: 9407201102_R04C02_Grn.idat
Location 2, idat file 2: 9407201102_R04C02_Red.idat
Location 3, idat file 1: 9407201121_R03C01_Grn.idat
Location 3, idat file 2: 9407201121_R03C01_Red.idat
Normal human kidney

source_name: normal human Kidney 73


title: Genomic DNA from normal human Kidney 70

description:
SAMPLE 70
Location 1, idat file 1: 9407201065_R04C02_Grn.idat
Location 1, idat file 2: 9407201065_R04C02_Red.idat
Location 2, idat file 1: 9406922120_R01C02_Grn.idat
Location 2, idat file 2: 9406922120_R01C02_Red.idat
Location 3, idat file 1: 9407201065_R03C02_Grn.idat
Location 3, idat file 2: 9407201065_R03C02_Red.idat
Normal human kidney

source_name: normal human Kidney 70


title: 254706910130_b2 - Colwounding_2 vs Colmock_2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Is MKK3 involved in the transcriptional regulation of wounding-induced genes ?

hyb_protocol: Colmock_2 Cy5 / Colwounding_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - Media: soil hygrometry: 65% Temperature: 22 day/18 night Light: 12h/12h

treatment_protocol: no treatment

tag: genotype

value: wild type

value: 15.9 days

tag: developmental stage (boyes et al. plant cell 2001)

value: leaves

treatment_protocol: Name:Wounding - environmental treatment - injury,wounding:. Col and mkk3 KO plants were wounded with a forceps. Leaves were harvested 2h after the stress.


title: Genomic DNA from normal human Kidney 48

description:
SAMPLE 48
Location 1, idat file 1: 9407201051_R06C01_Grn.idat
Location 1, idat file 2: 9407201051_R06C01_Red.idat
Location 2, idat file 1: 9406922032_R05C02_Grn.idat
Location 2, idat file 2: 9406922032_R05C02_Red.idat
Location 3, idat file 1: 9407201051_R05C01_Grn.idat
Location 3, idat file 2: 9407201051_R05C01_Red.idat
Normal human kidney

source_name: normal human Kidney 48


title: human embryonic fibroblast [HF-3]

source_name: human embryonic fibroblast [HF-3]


title: Genomic DNA from normal human Kidney 67

description:
SAMPLE 67
Location 1, idat file 1: 9407201121_R02C01_Grn.idat
Location 1, idat file 2: 9407201121_R02C01_Red.idat
Location 2, idat file 1: 9407201102_R03C02_Grn.idat
Location 2, idat file 2: 9407201102_R03C02_Red.idat
Location 3, idat file 1: 9407201121_R01C01_Grn.idat
Location 3, idat file 2: 9407201121_R01C01_Red.idat
Normal human kidney

source_name: normal human Kidney 67


title: Genomic DNA from normal human Kidney 51

description:
SAMPLE 51
Location 1, idat file 1: 9407201121_R06C02_Grn.idat
Location 1, idat file 2: 9407201121_R06C02_Red.idat
Location 2, idat file 1: 9407201095_R01C02_Grn.idat
Location 2, idat file 2: 9407201095_R01C02_Red.idat
Location 3, idat file 1: 9407201095_R02C02_Grn.idat
Location 3, idat file 2: 9407201095_R02C02_Red.idat
Normal human kidney

source_name: normal human Kidney 51


title: Genomic DNA from normal human Kidney 44

description:
SAMPLE 44
Location 1, idat file 1: 9407201121_R05C02_Grn.idat
Location 1, idat file 2: 9407201121_R05C02_Red.idat
Location 2, idat file 1: 9407201095_R05C01_Grn.idat
Location 2, idat file 2: 9407201095_R05C01_Red.idat
Location 3, idat file 1: 9407201095_R06C01_Grn.idat
Location 3, idat file 2: 9407201095_R06C01_Red.idat
Normal human kidney

source_name: normal human Kidney 44


title: Genomic DNA from normal human Kidney 53

description:
SAMPLE 53
Location 1, idat file 1: 9407201102_R02C02_Grn.idat
Location 1, idat file 2: 9407201102_R02C02_Red.idat
Location 2, idat file 1: 9407201041_R05C02_Grn.idat
Location 2, idat file 2: 9407201041_R05C02_Red.idat
Location 3, idat file 1: 9407201041_R06C02_Grn.idat
Location 3, idat file 2: 9407201041_R06C02_Red.idat
Normal human kidney

source_name: normal human Kidney 53


title: PB1T-1 embryonic stem cells [1-1]

source_name: PB1T-1 embryonic stem cells [1-1]


title: 254706910130_b4 - Colwounding_3 vs Colmock_3

hyb_protocol: Colmock_3 Cy5 / Colwounding_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Genomic DNA from normal human Kidney 40

description:
SAMPLE 40
Location 1, idat file 1: 9407201121_R04C02_Grn.idat
Location 1, idat file 2: 9407201121_R04C02_Red.idat
Location 2, idat file 1: 9407201095_R03C01_Grn.idat
Location 2, idat file 2: 9407201095_R03C01_Red.idat
Location 3, idat file 1: 9407201095_R04C01_Grn.idat
Location 3, idat file 2: 9407201095_R04C01_Red.idat
Normal human kidney

source_name: normal human Kidney 40


title: PC3 cells miR-130a transfected 2

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing: Gene-level expression signals were obtained from raw data CEL files by the RMA procedure implemented in the Affymetrix Expression Console software.

label: biotin

source_name: Human prostate cancer cell line

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip WT PLUS Reagent Kit User Guide.

growth_protocol: PC3 cell lines were cultured using recommended medium supplemented with 10% of fetal bovine serum and 1% of penicillin-streptomycin (FBS; GIBCO, Invitrogen, Carlsbad, CA, USA) and maintained at 37°C and 5% CO2 in a humidified chamber.

extract_protocol: Total RNA was obtained by suspension in TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) and, after adding chloroform, total RNA was purified from the aqueous phase of TRIzol® extract using PureLink™ RNA Mini Kit (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s recommendations.

treatment_protocol: MiR-130a was transiently transfected in PC3 cells with a Pre-miR™ miRNA precursor or negative control (pre-miR-130a, PM10506; miR-NC, AM17010, Applied Biosystems, Foster City, CA, USA).

tag: cell line

tag: transfection


title: Genomic DNA from normal human Kidney 39

description:
SAMPLE 39
Location 1, idat file 1: 9407201102_R06C01_Grn.idat
Location 1, idat file 2: 9407201102_R06C01_Red.idat
Location 2, idat file 1: 9407201041_R01C02_Grn.idat
Location 2, idat file 2: 9407201041_R01C02_Red.idat
Location 3, idat file 1: 9407201041_R02C02_Grn.idat
Location 3, idat file 2: 9407201041_R02C02_Red.idat
Normal human kidney

source_name: normal human Kidney 39


title: PC3 cells miR-130a transfected 3


title: 254706910130_b1 - Colmock_2 vs Colwounding_2

hyb_protocol: Colwounding_2 Cy5 / Colmock_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910129_b3 - Colmock_1 vs Colwounding_1

hyb_protocol: Colwounding_1 Cy5 / Colmock_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC3 cells miR-130a transfected 1


title: PC3 cells negative control 3

value: negative control


title: Genomic DNA from normal human Kidney 54

description:
SAMPLE 54
Location 1, idat file 1: 9407201051_R04C02_Grn.idat
Location 1, idat file 2: 9407201051_R04C02_Red.idat
Location 2, idat file 1: 9406922120_R01C01_Grn.idat
Location 2, idat file 2: 9406922120_R01C01_Red.idat
Location 3, idat file 1: 9407201051_R03C02_Grn.idat
Location 3, idat file 2: 9407201051_R03C02_Red.idat
Normal human kidney

source_name: normal human Kidney 54


title: 254706910129_b4 - Colwounding_1 vs Colmock_1

hyb_protocol: Colmock_1 Cy5 / Colwounding_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910129_b2 - mkk3wounding_3 vs mkk3mock_3

hyb_protocol: mkk3mock_3 Cy5 / mkk3wounding_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: MKK3 mutant


title: 254706910130_b3 - Colmock_3 vs Colwounding_3

hyb_protocol: Colwounding_3 Cy5 / Colmock_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910129_b1 - mkk3mock_3 vs mkk3wounding_3

hyb_protocol: mkk3wounding_3 Cy5 / mkk3mock_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PC3 cells negative control 1


title: Genomic DNA from normal human Kidney 45

description:
SAMPLE 45
Location 1, idat file 1: 9407201102_R01C02_Grn.idat
Location 1, idat file 2: 9407201102_R01C02_Red.idat
Location 2, idat file 1: 9407201041_R03C02_Grn.idat
Location 2, idat file 2: 9407201041_R03C02_Red.idat
Location 3, idat file 1: 9407201041_R04C02_Grn.idat
Location 3, idat file 2: 9407201041_R04C02_Red.idat
Normal human kidney

source_name: normal human Kidney 45


title: Genomic DNA from normal human Kidney 38

description:
SAMPLE 38
Location 1, idat file 1: 9407201051_R04C01_Grn.idat
Location 1, idat file 2: 9407201051_R04C01_Red.idat
Location 2, idat file 1: 9406922032_R04C02_Grn.idat
Location 2, idat file 2: 9406922032_R04C02_Red.idat
Location 3, idat file 1: 9407201051_R03C01_Grn.idat
Location 3, idat file 2: 9407201051_R03C01_Red.idat
Normal human kidney

source_name: normal human Kidney 38


title: Genomic DNA from normal human Kidney 28

description:
SAMPLE 28
Location 1, idat file 1: 9407201102_R05C01_Grn.idat
Location 1, idat file 2: 9407201102_R05C01_Red.idat
Location 2, idat file 1: 9407201041_R05C01_Grn.idat
Location 2, idat file 2: 9407201041_R05C01_Red.idat
Location 3, idat file 1: 9407201041_R06C01_Grn.idat
Location 3, idat file 2: 9407201041_R06C01_Red.idat
Normal human kidney

source_name: normal human Kidney 28


title: TS616_sparse_rep4

city: Bethesda

first: Jayne

middle: M

last: Stommel

state: MD

address: 10 Center Drive

institute: National Cancer Institute

description: TS616 glioma cells sparse

hyb_protocol: 10 ug of fragmented, labeled, antisense RNA, hyb'ed overnight at 45 degrees on PrimeView Affymetrix Human Gene Expression Array

scan_protocol: Scanned on Affymetrix GeneChip Scanner

data_processing: In Partek Genomics Suite, normalization was performed using RMA background correction with the following settings: adjust for GC content, quantile normalization, probeset summarization = mean.  Batch removal was performed across experimental replicates.

source_name: TS616 glioma cells sparse

label_protocol: Affymetrix GeneChip 3'IVT Express Kit, as in manufacturer's instructions.

growth_protocol: Primary glioma cells were splated at either sparse plating density (5x104 cells/mL) or dense (3x105 cell/mL).  NHAs were plated at either sparse plating density (3.5x105 cells/55cm2 dish) or dense (5.2x106/55cm2 dish) at a final conc of 5x104 cells/mL and 3x105 cell/mL.  Cells were incubated for 5 days prior to RNA harvest.

extract_protocol: Qiagen Rneasy Mini

tag: group

value: cancer

tag: density

value: sparse


title: Genomic DNA from normal human Kidney 36

description:
SAMPLE 36
Location 1, idat file 1: 9406922120_R06C02_Grn.idat
Location 1, idat file 2: 9406922120_R06C02_Red.idat
Location 2, idat file 1: 9406922032_R01C02_Grn.idat
Location 2, idat file 2: 9406922032_R01C02_Red.idat
Location 3, idat file 1: 9406922032_R02C02_Grn.idat
Location 3, idat file 2: 9406922032_R02C02_Red.idat
Normal human kidney

source_name: normal human Kidney 36


title: Genomic DNA from normal human Kidney 25

description:
SAMPLE 25
Location 1, idat file 1: 9407201121_R03C02_Grn.idat
Location 1, idat file 2: 9407201121_R03C02_Red.idat
Location 2, idat file 1: 9407201095_R01C01_Grn.idat
Location 2, idat file 2: 9407201095_R01C01_Red.idat
Location 3, idat file 1: 9407201095_R02C01_Grn.idat
Location 3, idat file 2: 9407201095_R02C01_Red.idat
Normal human kidney

source_name: normal human Kidney 25


title: Genomic DNA from normal human Kidney 30

description:
SAMPLE 30
Location 1, idat file 1: 9407201065_R02C02_Grn.idat
Location 1, idat file 2: 9407201065_R02C02_Red.idat
Location 2, idat file 1: 9406922120_R06C01_Grn.idat
Location 2, idat file 2: 9406922120_R06C01_Red.idat
Location 3, idat file 1: 9407201065_R01C02_Grn.idat
Location 3, idat file 2: 9407201065_R01C02_Red.idat
Normal human kidney

source_name: normal human Kidney 30


title: 254706910128_b4 - mkk3wounding_2 vs mkk3mock_2

hyb_protocol: mkk3mock_2 Cy5 / mkk3wounding_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910128_b3 - mkk3mock_2 vs mkk3wounding_2

hyb_protocol: mkk3wounding_2 Cy5 / mkk3mock_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: TS616_sparse_rep3

description: TS616 glioma cells sparse


title: PC3 cells negative control 2


title: 254706910128_b2 - mkk3wounding_1 vs mkk3mock_1

hyb_protocol: mkk3mock_1 Cy5 / mkk3wounding_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Genomic DNA from normal human Kidney 26

description:
SAMPLE 26
Location 1, idat file 1: 9407201065_R06C01_Grn.idat
Location 1, idat file 2: 9407201065_R06C01_Red.idat
Location 2, idat file 1: 9406922120_R05C01_Grn.idat
Location 2, idat file 2: 9406922120_R05C01_Red.idat
Location 3, idat file 1: 9407201065_R05C01_Grn.idat
Location 3, idat file 2: 9407201065_R05C01_Red.idat
Normal human kidney

source_name: normal human Kidney 26


title: TS616_dense_rep4

description: TS616 glioma cells dense

source_name: TS616 glioma cells dense

value: dense


title: Genomic DNA from normal human Kidney 23

description:
SAMPLE 23
Location 1, idat file 1: 9407201051_R02C01_Grn.idat
Location 1, idat file 2: 9407201051_R02C01_Red.idat
Location 2, idat file 1: 9406922032_R03C02_Grn.idat
Location 2, idat file 2: 9406922032_R03C02_Red.idat
Location 3, idat file 1: 9407201051_R01C01_Grn.idat
Location 3, idat file 2: 9407201051_R01C01_Red.idat
Normal human kidney

source_name: normal human Kidney 23


title: TS616_sparse_rep2

description: TS616 glioma cells sparse


title: 254706910126_b2 - mkk3mock_3 vs Colmock_3

description: Is MKK3 involved in the transcriptional regulation of wounding-induced genes ?

hyb_protocol: Colmock_3 Cy5 / mkk3mock_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Genomic DNA from normal human Kidney 15

description:
SAMPLE 15
Location 1, idat file 1: 9406922120_R04C02_Grn.idat
Location 1, idat file 2: 9406922120_R04C02_Red.idat
Location 2, idat file 1: 9406922032_R03C01_Grn.idat
Location 2, idat file 2: 9406922032_R03C01_Red.idat
Location 3, idat file 1: 9406922032_R04C01_Grn.idat
Location 3, idat file 2: 9406922032_R04C01_Red.idat
Normal human kidney

source_name: normal human Kidney 15


title: 254706910126_b1 - Colmock_3 vs mkk3mock_3

hyb_protocol: mkk3mock_3 Cy5 / Colmock_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910125_b4 - mkk3mock_2 vs Colmock_2

hyb_protocol: Colmock_2 Cy5 / mkk3mock_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: TS576_sparse_rep2

description: TS576 glioma cells sparse

source_name: TS576 glioma cells sparse


title: TS616_dense_rep3

description: TS616 glioma cells dense


title: Genomic DNA from normal human Kidney 5

description:
SAMPLE 5
Location 1, idat file 1: 9406922120_R02C02_Grn.idat
Location 1, idat file 2: 9406922120_R02C02_Red.idat
Location 2, idat file 1: 9407201065_R05C02_Grn.idat
Location 2, idat file 2: 9407201065_R05C02_Red.idat
Location 3, idat file 1: 9407201065_R06C02_Grn.idat
Location 3, idat file 2: 9407201065_R06C02_Red.idat
Normal human kidney

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450K Beadchip using standard Illumina protocol

source_name: normal human Kidney 5


title: 254706910125_b1 - Colmock_1 vs mkk3mock_1

hyb_protocol: mkk3mock_1 Cy5 / Colmock_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: TS576_sparse_rep1

description: TS576 glioma cells sparse


title: Genomic DNA from normal human Kidney 13

description:
SAMPLE 13
Location 1, idat file 1: 9406922120_R03C02_Grn.idat
Location 1, idat file 2: 9406922120_R03C02_Red.idat
Location 2, idat file 1: 9406922032_R01C01_Grn.idat
Location 2, idat file 2: 9406922032_R01C01_Red.idat
Location 3, idat file 1: 9406922032_R02C01_Grn.idat
Location 3, idat file 2: 9406922032_R02C01_Red.idat
Normal human kidney

source_name: normal human Kidney 13


title: TS616_sparse_rep1

description: TS616 glioma cells sparse


title: TS576_sparse_rep3

description: TS576 glioma cells sparse


title: 254706910125_b3 - Colmock_2 vs mkk3mock_2

hyb_protocol: mkk3mock_2 Cy5 / Colmock_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910127_b3 - Colwounding_3 vs mkk3wounding_3

hyb_protocol: mkk3wounding_3 Cy5 / Colwounding_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910127_b4 - mkk3wounding_3 vs Colwounding_3

hyb_protocol: Colwounding_3 Cy5 / mkk3wounding_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: TS576_dense_rep3

description: TS576 glioma cells dense

source_name: TS576 glioma cells dense


title: 254706910127_b2 - mkk3wounding_2 vs Colwounding_2

hyb_protocol: Colwounding_2 Cy5 / mkk3wounding_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910127_b1 - Colwounding_2 vs mkk3wounding_2

hyb_protocol: mkk3wounding_2 Cy5 / Colwounding_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910126_b4 - mkk3wounding_1 vs Colwounding_1

hyb_protocol: Colwounding_1 Cy5 / mkk3wounding_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: TS576_dense_rep2

description: TS576 glioma cells dense


title: TS576_dense_rep1

description: TS576 glioma cells dense


title: TS543_sparse_rep3

description: TS543 glioma cells sparse

source_name: TS543 glioma cells sparse


title: TS543_sparse_rep2

description: TS543 glioma cells sparse


title: 254706910128_b1 - mkk3mock_1 vs mkk3wounding_1

hyb_protocol: mkk3wounding_1 Cy5 / mkk3mock_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910125_b2 - mkk3mock_1 vs Colmock_1

hyb_protocol: Colmock_1 Cy5 / mkk3mock_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910126_b3 - Colwounding_1 vs mkk3wounding_1

hyb_protocol: mkk3wounding_1 Cy5 / Colwounding_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Genomic DNA from normal human Kidney 18

description:
SAMPLE 18
Location 1, idat file 1: 9406922120_R05C02_Grn.idat
Location 1, idat file 2: 9406922120_R05C02_Red.idat
Location 2, idat file 1: 9406922032_R05C01_Grn.idat
Location 2, idat file 2: 9406922032_R05C01_Red.idat
Location 3, idat file 1: 9406922032_R06C01_Grn.idat
Location 3, idat file 2: 9406922032_R06C01_Red.idat
Normal human kidney

source_name: normal human Kidney 18


title: Fin-cut-rep5

city: Stanford

first: James

last: Chen

state: CA

address: 269 W. Campus Drive, CCSR 3150

department: Chemical and Systems Biology

institute: Stanford University

description: Total RNA isolated from posterior tissues in 3 dpf larvae previously cut at 2 dpf

hyb_protocol: Hybridization was performed by the Stanford Functional Genomics Center (Stanford, CA) according to guidelines established by Roche Nimblegen (see www.nimblegen.com)

scan_protocol: Scanning was performed by the Stanford Functional Genomics Center (Stanford, CA) according to guidelines established by Roche Nimblegen (see www.nimblegen.com)

data_processing: Alignment was performed on raw images (.tif files) and the raw data (.pair file) was extracted using NimbleScan (ver 2.6) software.  The raw .pair files was then preprocessed (RMA background correction with quartile normalization) using ArraySta 12r software (DNASTAR) and differentially expressed genes were called using 90% confidence (Bonferroni-Hochberg adjusted P-values obtained from a moderated T-test) and 1.5 fold-change as thresholds.

organism: Danio rerio

source_name: Posterior tissue

label_protocol: Labeling was performed by the Stanford Functional Genomics Center (Stanford, CA) according to guidelines established by Roche Nimblegen (see www.nimblegen.com)

growth_protocol: Embryos were raised in E3 medium in a 28.5 degree Celsius incubator until the specified stages

extract_protocol: Total RNA was extracted from approximately 150 amputations per condition using the Rneasy Mini Kit (Invitrogen) and genomic DNA was removed using a DNA-free Kit (Applied Biosystems).

treatment_protocol: In cut samples, tail fins were amputated just posterior to the notochord using a fine surgical blade (Fine Science Tools, 10318-14) at 2 dpf and posterior tissues were collected on ice at 3 dpf.  In uncut samples, posterior tissues were isolated at 3 dpf.

tag: strain

value: WT AB

tag: Stage

value: 3 dpf

value: posterior tissue

tag: condition

value: Previously cut at 2 dpf


title: TS543_dense_rep4

description: TS543 glioma cells dense

hyb_protocol: 10 ug of fragmented, labeled, antisense RNA, hyb'ed overnight at 45 degrees on PrimeView Affymetrix Human Gene Expression Array

source_name: TS543 glioma cells dense


title: control 3

city: London

first: Pradeepa

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

description: Biological replicate 3 of 3. Control gRNA transfected embryonic stem cells,

hyb_protocol: 1.6ugs of labeled RNA was hybridized to a Mouse GE 4x44K microarray (Agilent; G4122F-014868) according to manufacturer's instructions. Microarrays were hybridized for 17 hours and washed according to manufacturer’s instructions.

scan_protocol: Washed arrays were scanned on a NimbleGen scanner at 5mm resolution and the resulting single channel TIFF images were processed using feature extraction software (Agilent).

data_processing:
The resulting single channel TIFF images were processed using feature extraction software (Array-Pro Analyzer) to generate a single output table containing the intensity values for all 4 samples hybrisised to the microarray
These raw background subtracted intensity values were quantile normalised using the limma package in R.

organism: Mus musculus

source_name: embryonic stem cells

label_protocol: 1ug of purified RNA was mixed with RNA standards (One Colour RNA Spike-In Kit; Agilent - 5188-5282) and the mixture labelled with Cyanine 3 (Cy3) using the Amino Allyl MessageAmp™ II with Cy™3 kit (Ambion; AM1795) according to manufacturer’s instructions. RNA quantification and integrity were monitored throughout using the total RNA Nano Chip measured on an Agilent Bioanalyzer.

growth_protocol: E14 ESCs (129/Ola background) were cultured on 0.1% gelatin (Sigma G1890) coated Corning flasks in ESC medium (GMEM (Sigma G5154) supplemented with 10% fetal calf serum (FCS), 1x MEM non-essential amino acids (Life Technologies 11140-036), 0.1 ?M 2-Mercaptoethanol (Sigma M6250), 2 mM L-Glutamine (Life Technologies 25030-024), 1 mM Sodium Pyruvate (Life Technologies 11360-039), and 1,000 U/ml of Lif.

extract_protocol: RNA was extracted from 90% confleuent 6 well plate using an RNeasy Mini kit according to manufacturer’s instructions (Qiagen).

treatment_protocol: Five guide RNA plasmid pools targeting the promoters of Hottip and Hoxa13  were designed as above and cloned into pSLQ1371. These gRNA plasmids encoding mCherry and puromycin resistance were co-transfected with a plasmid encoding dCas9-VP160 (pAC94-pmax-dCas9VP160-2A-puro, Addgene plasmid number 48226). 24hrs after transfection, transfected mES cells were selected by addition of 2ug/ml puromycin for another 24 hrs. RNA was extracted 48hrs after transfection, Microarray gene expression analysis performed according to the manufacturer’s protocol (Agilent Technologies). Plasmids containing non-targeting guide RNAs and dCas9 alone?served as controls.

tag: cell type

value: embryonic stem cells


title: TS543_sparse_rep4

description: TS543 glioma cells sparse


title: hottip activation 3

description: Biological replicate 3 of 4. Hottip  gRNA transfected embryonic stem cells,


title: hottip activation 1

description: Biological replicate 1 of 4. Hottip gRNA transfected embryonic stem cells,


title: hottip activation 4

description: Biological replicate 4 of 4. Hottip  gRNA transfected embryonic stem cells,


title: control 1

description: Biological replicate 1 of 3. Control gRNA transfected embryonic stem cells,


title: TS616_dense_rep2

description: TS616 glioma cells dense


title: TS543_sparse_rep1

description: TS543 glioma cells sparse


title: Fin-cut-rep4


title: TS543_dense_rep2

description: TS543 glioma cells dense


title: Fin-cut-rep3


title: TS616_dense_rep1

description: TS616 glioma cells dense


title: TS543_dense_rep1

description: TS543 glioma cells dense


title: Fin-cut-rep1


title: TS543_dense_rep3

description: TS543 glioma cells dense


title: NHA_sparse_rep2

description: normal astrocytes sparse

source_name: normal astrocytes sparse

value: normal

value: NHA


title: hottip activation 2

description: Biological replicate 2 of 4. Hottip  gRNA transfected embryonic stem cells,


title: Hoxa13 activation 2

description: Biological replicate 2 of 3. Hoxa13 gRNA transfected embryonic stem cells,


title: Fin-uncut-rep4

description: Total RNA isolated from posterior tissues in 3 dpf larvae

value: Uncut


title: Fin-cut-rep2


title: Fin-uncut-rep2


title: Hoxa13 activation 1

description: Biological replicate 1 of 3. Hoxa13 gRNA transfected embryonic stem cells,


title: NHA_sparse_rep1

description: normal astrocytes sparse


title: Hoxa13 activation 3

description: Biological replicate 3 of 3. Hoxa13 gRNA transfected embryonic stem cells,


title: Fin-uncut-rep3


title: NHA_sparse_rep3

description: normal astrocytes sparse


title: NHA_dense_rep2

description: normal astrocytes dense

source_name: normal astrocytes dense


title: Fin-uncut-rep1


title: NHA_dense_rep3

description: normal astrocytes dense


title: WT_1

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Partek Genomics Suite using RMA algorithm.

source_name: Microglia, control

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

extract_protocol: RNeasy Mini Kit (Qiagen, Maryland, USA), including DNase treatment.

tag: genotype/variation

value: WT

tag: model

value: Control

value: Microglia


title: WT_3


title: gill collected from control Branchiostoma belcheri

city: Beihai

first: Xin

last: Liao

state: Guangxi

address: 2# JinHaian Road

department: School of Life Sciences

institute: Nanjing University

description: Gill Control

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

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

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).
Averages are derived from LOWESS normalized data from all probes per miRNA.

organism: Branchiostoma belcheri

label_protocol: The assay started from 2 to 5 µg total RNA sample were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag(Cy3) was then ligated to the poly(A) tail for later fluorescent dye staining.

growth_protocol: The adults of amphioxus (B. belcheri) were obtained from Zhanjiang, Guangdong Province, China, and cultured at 24-25°C with air-pumped circulating artificial seawater, and fed with Chlorella.

extract_protocol: Total RNA was extracted using miRNeasy Kit(Qiagen, 217004), following the manufacturer's recommended protocol.

treatment_protocol: Fifteen microliters of LPS in PBS suspension (1 mg/ml) were injected into the cavum of amphioxus, and the same dosage of PBS was injected as the negative control. After that, the injected amphioxuses were cultured at 25 °C and were separately collected at different time points after injection (i.e. 2, 6, 12, 24, 48, and 72h). The gills were rapidly removed and frozen by liquid nitrogen for RNA extraction.

tag: agent

value: control

value: gill


title: P9CTRL-Biological Replica 3

city: Barcelona

first: Renuka

last: Kadhaya Pillai

state: Barcelona

address: Passeig Vall d’Hebron

department: Aging Basic Research Group, Molecular Biology and Biochemistry Research Center for Nanomedicine

country: Spain

institute: CIBBIM-Nanomedicine

description: Control Passage 9

hyb_protocol: The labeled samples were hybridized to Human Gene ST 1.0 Arrays (Affymetrix)

scan_protocol: The arrays were scanned in a GeneChip Scanner 3000 (Affymetrix). CEL files were generated from DAT files using GCOS software (Affymetrix).

data_processing: To generate the log2 expression estimates, overall array intensity was normalized between arrays and the probe intensity of all probes in a probeset summarized to a single value using RMA (Robust Multichip Average) algorithm.

source_name: Control or untreated cells

label_protocol: Briefly, cDNA library preparation and amplification were performed from 50ng total RNA using WTA2 (Sigma-Aldrich) with 17cycles of amplification. 10 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

growth_protocol: Human umbilical vein endothelial cells (HUVECs) purchased from Clonetics/Lonza (Bazel, Switzerland) were grown in EGM-2 medium supplemented with growth factors (EGM-2 bullet kit; Clonetics/Lonza).

extract_protocol: RNA was collected using TRIzol.

treatment_protocol: Human umbilical vein endothelial cells (HUVECs) were untreated or treated with TNF (5ng/ml) for 26 days (or Passged until senecence with TNF α).

value: HUVEC

tag: phenotype

value: Non-senescent Cells


title: P8CTRL- Biological Replica 2

description: Control Passage 8


title: P9TNFα-Biological Replica 1

description: TNFα Passage 9

source_name: senescent cells or cells treated with TNFα

value: Senescent Cells (upon TNFα treatment)


title: SOD_3

source_name: Microglia, ALS

value: SOD1 G93A

value: Amyotrophic lateral sclerosis (ALS)


title: SOD_1


title: P8TNFα-Biological Replica 2

description: TNFα Passage 8


title: SOD_2


title: gill collected from Branchiostoma belcheri treated with LPS at 12h

description: Gill LPS

value: LPS


title: P9CTRL-Biological Replica 1

description: Control Passage 9


title: WT_2


title: NHA_dense_rep1

description: normal astrocytes dense

value: dense


title: OSKM mouse iPSCs biological rep3

status: Public on Mar 09 2017

city: Taipei

first: I-I

last: KUAN

address: 128 Sec.2 ﹐Academia Rd ﹐

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Acdamic Sinica

description:
Gene expression data from OSKM miPSCs  biological rep3
OSKM3

hyb_protocol: After aRNA fragmentation, 12.5 ug of fragmented aRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip mouse genome 430 2.0 arrays. Affymetrix Fluidics Station 450 was used for gene chips washing and staining.

scan_protocol: Affymetrix GeneChip mouse genome 430 2.0 arrays were scanned by GeneChip@Scanner 3000 G7.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and use Gene Spring Software 11 to normalize data (RMA mode).  The up & down data were generated by comparing normalized experiment samples (ESC1, ESC2, ESC3, KEE1, KEE2, KEE3, KEE4, OEE1, OEE2, OEE3, OEE4, OSKM1,OSKM2, OSKM3, OSKM4) to normalized control samples (MEF1+ MEF2 + MEF3 average value , labled as MEF). The up & down data were showed which fold change were more than 10 fold.

source_name: iPSCs (MEFs were overexpressed Oct4, Sox2, Klf4 and c-Myc.)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip® 3’ IVT Express Kit, Affymetrix).

growth_protocol: MEFs isolated from E13.5 mice (B6.Cg-Gt (ROSA) 26Sortm1 (rtTA*M2) Jae/J; B6.129S4-POU5f1tm2Jae/J) were used to generate iPSCs. We used MEFs within four passages. The iPSC medium consisted of Dulbecco's modified Eagle's medium/F-12 (Invitrogen, Carlsbad, CA, USA) with 20% knock-out serum replacer, 1 µM LIF (Millipore, MA, USA), 1 mM β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA), 10 mM nonessential amino acids (Invitrogen), and 1 mM L-glutamine (Invitrogen). MEF medium contains high-glucose DMEM, 10% FBS, 1 mM L-glutamine, 10 mM nonessential amino acids (Invitrogen), 10 mM penicillin/streptomycin (Invitrogen), and 10 mM HEPES (Invitrogen).

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

treatment_protocol: MEFs (1 × 10^6) were nucleo-transfected with 2.5 µg of PiggyBac helper plasmids and 2.5 µg of PB-TET-OSKM, PB-TET-Oct4, PB-TET-Sox2, or PB-TET-Klf4, with or without PB-TET-EpCAM. The cells were plated in a 6 well plate with feeder cells in iPSC media. After 24 h, doxycycline (1.5 µg/mL) was added to induce the expression of reprogramming factors for 21 days. The culture medium was changed daily after nucleo-transfection.

tag: protocol

value: MEFs were transfected to overexpress Oct4, Sox2, Klf4 and c-Myc, in order to generate iPSCs.

value: miPSCs


title: OSKM mouse iPSCs biological rep4

description:
Gene expression data from OSKM miPSCs  biological rep4
OSKM4

value: B6.Cg-Gt (ROSA) 26Sortm1 (rtTA*M2) Jae/J; B6.129S4-POU5f1tm2Jae/J


title: OSKM mouse iPSCs biological rep1

description:
Gene expression data from OSKM miPSCs biological rep1
OSKM1


title: OEE mouse iPSCs biological rep2

description:
Gene expression data from OE + E miPSCs  biological rep2
OEE2

source_name: iPSCs (MEFs were overexpressed Oct4 and EpCAM, and treated with EpEx.)

value: MEFs were transfected to overexpress Oct4 and EpCAM, and treated with EpEx, in order to generate iPSCs.


title: OEE mouse iPSCs biological rep1

description:
Gene expression data from OE + E miPSCs biological rep1
OEE1


title: KEE mouse iPSCs biological rep2

description:
Gene expression data from KE + E miPSCs  biological rep2
KEE2

source_name: iPSCs (MEFs were overexpressed Klf4 and EpCAM, and treated with EpEx.)

value: MEFs were transfected to overexpress Klf4 and EpCAM, and treated with EpEx, in order to generate iPSCs.


title: OEE mouse iPSCs biological rep4

description:
Gene expression data from OE + E miPSCs  biological rep4
OEE4


title: KEE mouse iPSCs biological rep3

description:
Gene expression data from KE + E miPSCs  biological rep3
KEE3


title: OSKM mouse iPSCs biological rep2

description:
Gene expression data from OSKM miPSCs  biological rep2
OSKM2


title: Mouse embryonic stem cells biological rep3

description:
Gene expression data from mESCs biological rep3
ESC3

source_name: Mouse embryonic stem cell

value: mESCs


title: OEE mouse iPSCs biological rep3

description:
Gene expression data from OE + E miPSCs  biological rep3
OEE3


title: KEE mouse iPSCs biological rep4

description:
Gene expression data from KE + E miPSCs  biological rep4
KEE4


title: Mouse embryonic stem cells biological rep2

description:
Gene expression data from mESCs biological rep2
ESC2


title: Mouse embryonic stem cells biological rep1

description:
Gene expression data from mESCs biological rep1
ESC1


title: KEE mouse iPSCs biological rep1

description:
Gene expression data from KE + E miPSCs biological rep1
KEE1


title: Mouse embryonic fibroblasts biological rep2

description:
Gene expression data from MEF biological rep2
MEF2

source_name: MEFs isolated from E13.5 mice

value: MEFs isolated from E13.5 mice

value: MEFs


title: B2

city: FuZhou

first: Guo

last: Zheng

state: FuJian

address: No.1 Xue Yuan Road

department: Department of Bioinformatics

institute: Fujian Medical University

description: non-tumor

hyb_protocol: Total RNAs were hybridized using mRNA + lncRNA Human Gene Expression Microarray V4.0 (4×180K format,  CapitalBio Corp, Beijing, China)

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

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

source_name: non-tumor

label_protocol: The purity and concentration of RNA was determined by Nano Drop ND-1000 spectrophotometer according to OD260/280 reading.

extract_protocol: Tumor samples were microdissected to ensure the purity of the tumor. From the same patient, adjacent normal tissue samples were collected from resected, located approximately 3.5-5 cm away from the tumor site.

treatment_protocol: Samples were fresh frozen and were shipped on ice for subsequent RNA extraction

value: non-tumor


title: B4

description: non-tumor


title: D4

description: non-tumor


title: B1

description: non-tumor


title: D3

description: non-tumor


title: Mouse embryonic fibroblasts biological rep3

description:
Gene expression data from MEF biological rep3
MEF3


title: C4

description: lung adenocarcinoma

source_name: lung adenocarcinoma

value: lung adenocarcinoma


title: Mouse embryonic fibroblasts biological rep1

description:
Gene expression data from MEF biological rep1
MEF1


title: C2

description: lung adenocarcinoma


title: B3

description: non-tumor


title: C3

description: lung adenocarcinoma


title: A2

description: lung adenocarcinoma


title: D2

description: non-tumor


title: P9TNFα-Biological Replica 3

description: TNFα Passage 9

value: HUVEC


title: C1

description: lung adenocarcinoma


title: D1

description: non-tumor


title: A1

description: lung adenocarcinoma


title: control 2

description: Biological replicate 2 of 3. Control gRNA transfected embryonic stem cells,

value: embryonic stem cells


title: A3

description: lung adenocarcinoma


title: HUVEC EV biological rep5

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from EV-transduced HUVEC

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human HG-U133_Plus_2 type from Affymetrix. A Custom CDF Version 14 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: HUVEC transduced with empty vector

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

growth_protocol: Human GATA4 cDNA (IMAGE:8144111) was cloned into pBabePuro vector (Addgene). To obtain recombinant retroviral particles, Phoenix producer cells [ATCC CRL-3213] were lipofected with vector DNA as described by Viemann D et al, 2007.

extract_protocol: Total was RNA from GATA4- or empty vector-transduced HUVEC was extracted with EZNA TM Total-RNA-Kit according to the manufacturer's protocol (OMEGA Biotec).

treatment_protocol: Filtered supernatants from Phoenix cells containing retroviral particles were applied to HUVEC at three consecutive days. Before harvesting the cells (day 7) puromycin (Invitrogen) was added (day 5) at a concentration of 1 μg/ml to GATA4- or empty vector-transduced HUVEC.

tag: transduction

value: empty Vector


title: Stab2Cre;Gata4 knockout biological rep3

description: Gene expression data from Gata4-deficient fetal liver

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 18 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Gata4-deficient fetal liver

growth_protocol: Stab2-Cre mice were crossed to mouse lines bearing floxed alleles of Gata4 (B6;129-Gata4tm1.1Sad/J; Jax#008194]. To obtain loss-of-function and control genotypes Stab2-Cretg/wt;Gata4fl/wt were crossed to Gata4fl/fl mice.

extract_protocol: Total was RNA from Stab2-Cre;Gata4fl/fl or control fetal liver was extracted with High Pure RNA isolation Kit according to the manufacturer's protocol (Roche).

treatment_protocol: Timed matings were performed, the embryos were harvested at embryonic day 11.5 and the fetal liver was dissected.

tag: tissue

value: fetal liver

value: Stab2Cre;Gata4 knockout


title: HUVEC EV biological rep4


title: Stab2Cre;Gata4 knockout biological rep1


title: Stab2Cre;Gata4 heterozygous biological rep3

description: Gene expression data from control fetal liver

source_name: control fetal liver

value: Stab2Cre;Gata4 heterozygous


title: HUVEC GATA4 biological rep5

description: Gene expression data from GATA4-transduced HUVEC

source_name: HUVEC transduced with Gata4 vector


title: HUVEC GATA4 biological rep4


title: A4

description: lung adenocarcinoma


title: Stab2Cre;Gata4 heterozygous biological rep2


title: Stab2Cre;Gata4 heterozygous biological rep1


title: Stab2Cre;Gata4 knockout biological rep2


title: HUVEC GATA4 biological rep3


title: HUVEC GATA4 biological rep2


title: HUVEC EV biological rep1


title: HUVEC GATA4 biological rep1


title: HUVEC EV biological rep2


title: HUVEC EV biological rep3


title: H37Rv anti-AM sera stimulon replicate 3

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: Biological replicate 3 of 3

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol.

scan_protocol: Scanned with PMT voltage adjusted for maximum dynamic range on Axon Genepix 4000B scanner

data_processing: Spots were gridded and quantitated in TIGR Spotfinder, data were processed in TIGR MIDAS with lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis H37Rv

source_name: H37Rv anti-AM/PA sera-exposed

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix. After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers. cDNA concentration and purity were measured by Nanodrop. Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit. Probe concentration, purity, and dye incorporation were measured by Nanodrop.

growth_protocol: Cultures were grown in minimal medium (MM) [KH2PO4 1 g/l, Na2HPO4 2.5 g/l, asparagine 0.5 g/l, ferric ammonium citrate 50 mg/l, MgSO4×7 H2O 0.5 g/l, CaCl2 0.5 mg/l, ZnSO4 0.1 mg/l, 0.1% (v/v) glycerol, and with or without Tyloxapol 0.05% (v/v; Sigma), pH 7.0] for 6 days then subcultured in MM without Tyloxapol for 5 days. Cultures were harvested and submitted to a syringe and gentle sonication to breakdown clumps.

extract_protocol: Cultures were pelleted and resuspended in 1ml Trizol and transferred to a Fast-Prep lysing matrix B tube. Tubes were processed in Fast-Prep apparatus for 45 seconds at 6.5 M per second then cooled on ice for 1 minute before debris was pelleted by centrifugation. RNA was then purified and sample was DNase-treated following Direct-zol kit manufacturer instructions.

treatment_protocol: Cultures were then incubated with immune sera from C57/BL6 mice immunized with an arabinomannan-protective antigen conjugate or protective antigen alone at 1:200 for 4 hours.

value: H37Rv anti-AM/PA sera-exposed

source_name: H37Rv anti-PA sera-exposed

value: H37Rv anti-PA sera-exposed


title: Fkh1-Myc_fkh2Δ_G1_anti_Myc_rep_2

city: Los Angeles

first: Andrew

middle: Zachary

last: Ostrow

state: California

address: 1050 Childs Way

department: Biological Sciences

institute: University of Southern California

description: ChIP-chip FKH1-MYC9 G1-Phase cells

hyb_protocol: Nimblegen standard protocol

scan_protocol: Genepix Personal 4100A Scanner (Axon Instruments).

data_processing: We used MA2C to perform normalization.

organism: Saccharomyces cerevisiae

label_protocol: Nimblegen standard protocol

growth_protocol: cells were grown in YEPD

extract_protocol: Genomic DNA was extracted as described in as described in Viggiani CJ, Aparicio JG, Aparicio OM (2009) ChIP-chip to analyze the binding of replication proteins to chromatin using oligonucleotide DNA microarrays. Methods Mol Biol 521: 255-278.

treatment_protocol: incubated with α-factor for 3hrs

value: FKH1-MYC9 (TRP1) bar1Δ::hisG fkh2Δ::HIS3MX

tag: chip antibody

value: 9E10 monoclonal


title: Fkh1-dsm-Myc_fkh2Δ_G1_anti_Myc_rep_3

description: ChIP-chip fkh1-dsm-MYC9 G1-Phase cells

value: fkh1Δ::KanMX::fkh1-dsm (LEU2)::MYC9 (TRP1) bar1Δ::hisG fkh2Δ::HIS3MX


title: Fkh1-dsm-Myc_fkh2Δ_G1_anti_Myc_rep_1

description: ChIP-chip fkh1-dsm-MYC9 G1-Phase cells


title: Fkh1-Myc_fkh2Δ_G1_anti_Myc_rep_1

description: ChIP-chip FKH1-MYC9 G1-Phase cells


title: Fkh1-dsm-Myc_fkh2Δ_G1_anti_Myc_rep_2

description: ChIP-chip fkh1-dsm-MYC9 G1-Phase cells


title: Fkh1-Myc_fkh2Δ_G1_anti_Myc_rep_3

description: ChIP-chip FKH1-MYC9 G1-Phase cells


title: ShCtrl_2

city: Boston

first: Koen

last: Dreijerink

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data in cells expressing control small hairpin RNA's

hyb_protocol: The fragmented cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cDNA that has not hybridized to its complementary oligonucleotide probe. The bound cDNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing:
Affymetrix Power Tools; APT script: probeset-summarize
Transformed count

source_name: Mammary luminal progenitor cells

label_protocol: Control RNA's - the Core spikes in four in vitro synthesized, polyadenylated B. subtilis mRNA's into each submitted sample. cDNA synthesis I - double-stranded cDNA is synthesized from the RNA sample starting with T7 promoter-tailed random hexamers. cRNA synthesis - cRNA is synthesized in a T7 polymerase catalyzed reaction containing unmodified ribonucleoside triphosphates. cDNA synthesis II - single-stranded cDNA is synthesized from the cRNA template using random primers and dUTP, dTTP, dATP, dCTP and dGTP. cRNA hydrolysis - the cRNA is hydrolyzed by RNase H, and the single-stranded cDNA is purified. Fragmentation of a single-stranded cDNA - Uracil DNA glycosylase and Apurine/Apyrimidinic Endonuclease I are used to fragment the cDNA at Uracil-containing positions. Biotinylation - The fragmented cDNA is end-labeled with a biotinylated nucleotide analog.

growth_protocol: Mammary luminal progenitor cells were isolated from patient-derived breast tissue after tissue digestion and FACS-sorting using anitibodies directed at CD49f+ and EpCAM. After harvesting and cell sorting, Cells were maintained in DMEM F12 medium containing 10% FBS and cholera toxin 20 μg/mL (Sigma), EGF 10 mg/mL (Sigma), Glutamine (Gibco), hydrocortisone 0.5 μg/mL (Sigma), Insulin 5 μg/mL Sigma). The medium was changed every three days.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, Venlo, Netherlands).

treatment_protocol: For lentiviral infections in LP cells pre-synthesized virus particles were used expressing non-inducible shRNA’s directed at MEN1 (sc-35922-V) or non specific sequences (sc-108080)(Santa Cruz Biotechnology). After the cells had settled in 12 well plates plates, cells were subjected to two rounds of lentiviral infection using 10 μl of viral particles in the presence of 5 μg/mL polybrene. After 24 hours, shRNA expressing cells were selected by culturing in medium with 2 μg/mL puromycin for 5-8 days.

tag: treatment

value: control


title: ShMEN1_1

description: Gene expression data in cells expressing small hairpin RNA's directed at the MEN1 mRNA


title: H37Rv anti-AM sera stimulon replicate 2

description: Biological replicate 2 of 3


title: H37Rv anti-AM sera stimulon replicate 1

description: Biological replicate 1 of 3


title: PDGFRb-TK treated with control IgG rep2

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

description:
603
GCV injected

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: GenomeStudio

source_name: 4T1 breast tumor

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

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

value: control IgG

tag: pdgfrb tk

value: Positive

value: 4T1 breast tumor

tag: genotype

value: PDGFRb-TK


title: PDGFRb-TK treated with control IgG rep3

description:
191
GCV injected


title: PDGFRb-TK treated with anti-Ang2 antibody rep2

description:
173
GCV injected

value: anti-Ang2 antibody


title: SET33_CTL_(miRNA-4_0)

city: Seoul

first: Hyeong-Gon

last: Moon

address: 101, Daehak-ro Jongno-gu

department: Surgery

country: South Korea

institute: Seoul National University Hospital

description: in-direct co-culture method

hyb_protocol: RNA-array hybridization was performed with agitation at 60 rotations per minute for 16–18 hours at 48°C on an Affymetrix® 450 Fluidics Station.

scan_protocol: The chips were then scanned with an Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software. The CEL files import, miRNA level RMA+DABG-All analysis and result export using Affymetrix® Expression Console™ Software.

source_name: adipocyte cell line

label_protocol: 1µg RNA samples were labeled with the FlashTag™ Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

growth_protocol: 3T3-L1 cells were cultured in DMEM supplemented with 10% bovine serum at 37°C in 5% CO2. 3T3-L1 cells were grown to confluency and induced with adipogenesis media (DMEM with 10% FBS, 10μg/ml insulin, 0.5mM IBMX and 1μM dexamethasone). After 2 days, the media was changed with DMEM with 10% FBS and 10μg/ml insulin and maintained for 4 days. After 8 days of differentiation with DMEM with 10% FBS, the cells were used for further experiments.

treatment_protocol: 3T3-L1 cells were cultured in a indirect co-culture wells with breast cancer cells

tag: cell line

value: adipocyte cell line

tag: cocultured with

value: none (control)


title: ShCtrl_1


title: SET33_231_(miRNA-4_0)

description: in-direct co-culture method


title: SET36_231_(miRNA-4_0)

description: in-direct co-culture method


title: set35_Adipo_231_140424_(miRNA-4_0)

description: in-direct co-culture method


title: WT treated with control IgG rep1

description:
180
GCV injected

value: WT


title: PDGFRb-TK treated with anti-Ang2 antibody rep1

description:
172
GCV injected


title: WT treated with control IgG rep2

description:
186
GCV injected


title: set35_Adipo_CTL_140424_(miRNA-4_0)

description: in-direct co-culture method


title: PDGFRb-TK treated with control IgG rep1

description:
166
GCV injected


title: ShMEN1_2


title: PDGFRb-TK treated with anti-Ang2 antibody rep3

description:
176
GCV injected


title: WT treated with control IgG rep3

description:
188
GCV injected


title: SET36_CTL_(miRNA-4_0)

description: in-direct co-culture method


title: SET33_7_(miRNA-4_0)

description: in-direct co-culture method


title: SET36_7_(miRNA-4_0)

description: in-direct co-culture method


title: set35_Adipo_7_140424_(miRNA-4_0)

description: in-direct co-culture method


title: bEnd3 EV biological rep5

description: Gene expression data from EV-transduced bEnd3

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: bEnd3, EV

growth_protocol: Synthetic codon optimized cDNA (GeneArt) referring to murine Gata4 (GenBank: AB075549.1) amino acid sequence was cloned in combination with IRES, mCherry, T2A, and puromycin into pLenti-EF1α vector. To obtain mGata4-IRES-mCherry-puromycin and control (IRES-mCherry-puromycin only) expressing lentiviral particles HEK293T cells were co-transfected with vector DNA, pMD2.G L1 (Addgene), pMDLg/pRRE L3 (Addgene), and pRSV rev L2 (Addgene) plasmids using X-tremeGENE 9 (Roche) transfection reagent.

extract_protocol: Total was RNA from Gata4- or empty vector-transduced bEnd3 cells was extracted with EZNA TM Total-RNA-Kit according to the manufacturer's protocol (OMEGA Biotec).

treatment_protocol: Conditioned supernatants were harvested 48 h, 60 h and 72 h after transfection, filtered (0.45 μm, Carl Roth) and concentrated using Vivaspin 20 MWCO 100000 columns (Sartorius). Concentrated supernatants were applied to bEnd3 cells. Selection was carried out with 2 μg/ml Puromycin (Invivogen).

value: empty vector


title: bEnd3 EV biological rep3


title: bEnd3 EV biological rep2


title: bEnd3 EV biological rep4


title: bEnd3 Gata4 biological rep5

description: Gene expression data from Gata4-transduced bEnd3

source_name: bEnd3, Gata4


title: PCa_N34

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

description: Prostate adenocarcinoma from Caucasian men.

hyb_protocol: Samples were hybridized to oligonucleotide glass arrays with sequences representing probes for 866 human and 89 human viral miRNAs from the Sanger miRBase (release 12.0) (Human miRNA Microarray V3, Agilent Technologies). After 20 hours, slides were washed and scanned.

scan_protocol: Slides were scanned with the dual-laser Agilent scanner G2505B.

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to analyze miRNA expression profiles in normal prostates and prostate cancer tissues. Raw intensity values were background subtracted (method = subtract with an offset of 20) and normalized using the quantile method. Duplicated probes were averaged.

source_name: Prostate cancer

label_protocol: MiRNA expression profiling was carried out using the one-colour labelling method. Labelling, hybridization, washing and slide scanning were performed following the manufacturer's protocol (Agilent Technologies). Briefly, 100 ng of total RNA were dephosphorylated and denaturated; then a ligation and labeling step with Cy3 was performed.

extract_protocol: Total RNA was isolated following standard TriReagent protocol (Sigma-Aldrich) and DNase treatment was performed (TURBO DNase-free, Life Technologies). Total RNA quality and quantity were checked by means of Bioanalyzer (Agilent Technologies) and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific), respectively.

value: prostate adenocarcinoma

tag: gender

value: male

tag: population

value: Caucasian


title: PCa_O47


title: PCa_P53


title: bEnd3 Gata4 biological rep4


title: bEnd3 EV biological rep1


title: bEnd3 Gata4 biological rep3


title: bEnd3 Gata4 biological rep1


title: bEnd3 Gata4 biological rep2


title: A375-iPCCs_3

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

institute: German Cancer Research Center

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

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol.

data_processing: The data were normalised for red and green channel seperately using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore. Three-step preprocessing: (1) removal of probes that are SNP-enriched, are cross-reactive or contain bad detection p-values; (2) BMIQ normalization; (3) removal of probes not in CpG context

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol: Infinium® HD Assay Methylation Protocol Guide

extract_protocol: Genomic DNA was isolated using the QIAGEN DNeasy Blood & Tissue Kit according to the manufacturer’s instructions.

value: female

value: A375-iPCCs, reprogrammed daughter cells

tag: volume

tag: input


title: HT-144-iPCCS_6

value: HT-144-iPCCs, reprogrammed daughter cells


title: HT-144-dFLCs I b

source_name: HT-144-dFLCs I b


title: HT-144-iPCCS_5


title: PCa_M21


title: iPSC_2

value: iPSCs, stem cells


title: iPSC_3


title: PCa_F55


title: HT-144-dFLCs III c

source_name: HT-144-dFLCs III c


title: HT-144-iPCCS_1


title: A375-iPCCs_2


title: HT-144-dFLCs III b

source_name: HT-144-dFLCs III b


title: iPSC_1


title: A375-iPCCs_1


title: HT-144-iPCCS_2


title: HT-144-dFLCs II c

source_name: HT-144-dFLCs II c


title: HT-144-iPCCS_4


title: HT-144-dFLCs II b

source_name: HT-144-dFLCs II b


title: HT-144-dFLCs II a

source_name: HT-144-dFLCs II a


title: HT-144-dFLCs I c

source_name: HT-144-dFLCs I c


title: HT-144-dFLCs III a

source_name: HT-144-dFLCs III a


title: PCa_Q65


title: A375_3

value: A375, melanoma cells


title: HT-144-dFLCs I a

source_name: HT-144-dFLCs I a


title: HT-144_1

value: HT-144, melanoma cells


title: HT-144_3


title: HT-144_4


title: NHF

source_name: NHF

value: fibroblast


title: A375_1


title: genomic DNA from OSCC lesion 9

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450Beadchip using standard Illumina protocol

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

data_processing: IDAT files were processed using RnBeads for data processing. We used SWAN normailzation. After normalization and quality control checking, the signal intesities along with the detection P-values are calculated for each CpG probes. Normalized average beta values are calculated using RnBead software implemented in R software.

source_name: Disease OSCC

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from OSCC samples using Qiagen Tissue & Blood DNA Kit according to standard instructions

tag: subject status

value: oral squamous cell carcinoma (OSCC) patient

value: Male

tag: tissue type

value: OSCC lesion

tag: disease state

value: Disease

tag: hpv status


title: genomic DNA from Adjacent Normal 11

source_name: Adjacent Normal

value: Adjacent Normal

value: Normal


title: genomic DNA from Adjacent Normal 10

value: Female


title: HT-144_2


title: genomic DNA from Adjacent Normal 9


title: PCa_E45

value: prostate adenocarcinoma


title: genomic DNA from OSCC lesion 8


title: genomic DNA from Adjacent Normal 8


title: genomic DNA from OSCC lesion 11


title: PCa_D40

value: male


title: genomic DNA from Adjacent Normal 2


title: HT-144-iPCCS_3


title: genomic DNA from Adjacent Normal 3


title: genomic DNA from OSCC lesion 5


title: genomic DNA from Adjacent Normal 6


title: genomic DNA from OSCC lesion 7


title: genomic DNA from OSCC lesion 10


title: genomic DNA from OSCC lesion3


title: genomic DNA from Adjacent Normal 1


title: genomic DNA from OSCC lesion 6


title: A375_2


title: genomic DNA from Adjacent Normal 7


title: PCa_CC83

value: Caucasian


title: genomic DNA from OSCC lesion 1


title: PCa_AA62


title: PCa_D37


title: genomic DNA from OSCC lesion2


title: P195

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2; the 'complete_data.txt' contains unmethylated and methylated signal intensities along with average beta and Pval.

label: Cy3, Cy5

source_name: Prostate Tumor

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

value: Tumor sample

value: Prostate Tumor

tag: sample type

value: fresh frozen tissue


title: PCa_A9