title: 143

description:
gene expression data
MM_0_24h_143_IL16188_Liver_.HT_MG.430_PM._G03_2.CEL


title: 193

status: Public on Jun 25 2017

type: RNA

city: chapel hill

first: Yunjung

last: Kim

state: North Carolina

address: 120 Mason farm road

country: USA

institute: UNC at Chapel Hill

description:
gene expression data
MM_0_24h_193_IL16912_Liver_.HT_MG.430_PM._D07.CEL

hyb_protocol: Total RNA was isolated from the median lobe liver tissue of all animals using Trizol reagent (Invitrogen) according to manufacturer’s instructions. The isolated RNA was further purified using the QIAcube automated system (Qiagen). Following purification, the quantity of RNA was determined spectrophotometrically and the integrity of the RNA was evaluated with the Agilent 2100 Bioanalyzer. Double-stranded cDNA was synthesized from 50-150 ng (dependent on RNA yield) of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix). Fifteen (15) µg of labeled cRNA was fragmented and prepared for hybridization on HT MG430 PM peg arrays. The Gene Titan robotic instrumentation (Affymetrix) was used to perform the hybridization, washing and scanning of the peg arrays.

scan_protocol: standar Affymetrix protocol

data_processing: Robust multiarray average method (RMA) implemented in the Affymetrix gene expression console with default settings (median polish and sketch-quantile normalization) to estimate normalized expression levels of transcripts

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: standar Affymetrix protocol

extract_protocol: The liver of each animal was excised and weighed. A section of the left and median liver lobes was fixed in 10% neutral buffered formalin and processed for histological analysis. A section of liver tissue encompassing all regions of the median lobe was diced, placed in RNAlater (Ambion), and processed for gene expression analysis.

treatment_protocol: Eight male mice from each 45 genetically different inbred strains of the CC were purchased from the University of North Carolina, Chapel Hill (UNC). Animals were housed in polycarbonate cages, kept on a 12-h light-dark cycle and provided Pelleted PicoLab Rodent Diet 20 (Lab Diet) ad libitum, except during an approximate 18-h period of fasting prior to necropsy. Animals were acclimated for approximately 7 days prior to dosing. At the initiation of dosing, mice were approximately 8-10 weeks of age. Care of mice followed institutional guidelines under a protocol approved by Mispro Biotech Services Institutional Animal Care and Use Committee.

tag: treatment

value: Control


title: 14

description:
gene expression data
MM_0_24h_14_OR867_Liver_.HT_MG.430_PM._A01.CEL


title: 13

description:
gene expression data
MM_0_24h_13_OR867_Liver_.HT_MG.430_PM._A03.CEL


title: 161

description:
gene expression data
MM_0_24h_161_IL16441_Liver_.HT_MG.430_PM._H01.CEL


title: 12

description:
gene expression data
MM_0_24h_12_OR867_Liver_.HT_MG.430_PM._A02.CEL


title: 131

description:
gene expression data
MM_0_24h_131_OR15155_Liver_.HT_MG.430_PM._F07.CEL


title: 152

description:
gene expression data
MM_0_24h_152_OR13140_Liver_.HT_MG.430_PM._G08.CEL


title: 133

description:
gene expression data
MM_0_24h_133_OR15155_Liver_.HT_MG.430_PM._F09.CEL


title: 122

description:
gene expression data
MM_0_24h_122_IL16750_Liver_.HT_MG.430_PM._F02.CEL


title: 153

description:
gene expression data
MM_0_24h_153_OR13140_Liver_.HT_MG.430_PM._G09.CEL


title: YFV2012008 PBMC Day 14

city: Beijing

first: Yiming

last: Shao

state: Beijing

address: No. 155 Changbai Road, Changping District

department: National Center for AIDS/STD Control and Prevention

country: China

institute: Chinese Center for Disease Control and Prevention

hyb_protocol: After hybridization on Human PrimeView Arrays for 16 h at 45℃ and 60 rpm in Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA), slides were washed and stained with a Fluidics Station 450 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Scanning was performed on a seventh-generation GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, USA). Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.

data_processing: Initially, data quality was assessed by background level, 3’ labeling bias, RNA quality and pair-wise correlation among samples. For the PrimeView chip, the customized CDF (version 17, ENTREZG) downloaded from the BrainArray website was performed in probe set mapping. IQR was applied for raw data filtering using the genefilter package, and the threshold was set to remove probes/genes with IQR less than the 20th percentile of the IQR’s across all probes/genes. . Normalization was performed with RMA algorithm that includes global background adjustment and quantile normalization. The resulting matrix showed genes as rows and samples as columns was log2 transformed and used as input for linear modeling using the limma package.The limma package was performed to identify differentially expressed genes (DEG) at any time point post immunization, compared with baseline (Day 0). Empirical Bayes moderation of the standard error and Benjamini and Hochberg false-discovery rate (FDR) correction for multiple testing were employed, and the criteria for differentially expressed genes (DEG) were threshold fold change more than 1.5 and BH adjusted FDR less than 0.01.

organism: Homo sapiens

source_name: human Day 14

label_protocol: Total RNA were amplified, labeled and purified by using the GeneChip 3’IVT Express Kit (Affymetrix, Santa Clara, CA, USA) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: After PMBC isolation, 1 × 10^6 PBMC cells were lysed in 1 ml of TRIzol (Life technologies, Carlsbad, CA, USA) immediately and stored at -80℃. The samples were thawed and RNA extracted following the manufacturer’s instructions. The quality of the RNA was assessed by using Nanodrop 2000 Spectrometer (Thermo Scientific, MA, USA) as well as by visualization of the integrity of the 28S and 18S band on Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, USA).  Qualified total RNA was further purified by RNeasy micro kit (QIAGEN, GmBH, Germany) and removed genomic contamination by RNase-Free DNase Set (QIAGEN, GmBH, Germany).  The purified RNA was stored at -80℃.

tag: subject id

tag: time points

value: Day 14

tag: groups

tag: gender

value: Male


title: YFV2012008 PBMC Day 5

source_name: human Day 5

value: Day 5


title: 123

description:
gene expression data
MM_0_24h_123_IL16750_Liver_.HT_MG.430_PM._F03.CEL


title: 104

description:
gene expression data
MM_0_24h_104_OR13067_Liver_.HT_MG.430_PM._B05.CEL


title: YFV2012008 PBMC Day 3

source_name: human Day 3

value: Day 3


title: 113

description:
gene expression data
MM_0_24h_113_OR13421_Liver_.HT_MG.430_PM._E09.CEL


title: 114

description:
gene expression data
MM_0_24h_114_OR13421_Liver_.HT_MG.430_PM._B07.CEL


title: YFV2012006 PBMC Day 5

value: Female


title: 111

description:
gene expression data
MM_0_24h_111_OR13421_Liver_.HT_MG.430_PM._E07.CEL


title: YFV2012006 PBMC Day 14


title: 124

description:
gene expression data
MM_0_24h_124_IL6750_Liver_.HT_MG.430_PM._B09.CEL


title: YFV2012006 PBMC Day 3


title: 112

description:
gene expression data
MM_0_24h_112_OR13421_Liver_.HT_MG.430_PM._E08.CEL


title: 102

description:
gene expression data
MM_0_24h_102_OR13067_Liver_.HT_MG.430_PM._E02.CEL


title: 11

description:
gene expression data
MM_0_24h_11_OR867_Liver_.HT_MG.430_PM._A01.CEL


title: YFV2012008 PBMC Day 1

source_name: human Day 1

value: Day 1


title: YFV2012007 PBMC Day 14


title: YFV2012008 PBMC Day 2

source_name: human Day 2

value: Day 2


title: YFV2012007 PBMC Day 2


title: 103

description:
gene expression data
MM_0_24h_103_OR13067_Liver_.HT_MG.430_PM._E03.CEL


title: YFV2012006 PBMC Day 2


title: YFV2012007 PBMC Day 5


title: YFV2012007 PBMC Day 1


title: YFV2012007 PBMC Day 3


title: YFV2012006 PBMC Day 1


title: 101

description:
gene expression data
MM_0_24h_101_OR13067_Liver_.HT_MG.430_PM._E01.CEL


title: YFV2012004 PBMC Day 14


title: YFV2012002 PBMC Day 5


title: YFV2012002 PBMC Day 2


title: YFV2012004 PBMC Day 3


title: YFV2012002 PBMC Day 1


title: YFV2012023 PBMC Hour 4

source_name: human Hour 4

value: Hour 4


title: YFV2012004 PBMC Day 5


title: YFV2012023 PBMC Day 28

source_name: human Day 28

value: Day 28


title: YFV2012002 PBMC Day 3


title: YFV2012002 PBMC Day 14


title: YFV2012023 PBMC Day 7

source_name: human Day 7

value: Day 7


title: YFV2012024 PBMC Day 0

source_name: human Day 0

value: Day 0


title: YFV2012022 PBMC Day 0


title: Patient Ps17

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

hyb_protocol: Labeled cRNA products were randomly fragmented and hybridized onto Affymetrix GeneChips.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: CEL files were preprocessed into Partek GS with default partek options.

source_name: Patient Ps17

label_protocol: 250 ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs and labeled into biotinylated cRNA using the GeneChip WT PLUS Reagent kit (Affymetrix) according to the manufacturer’s standard protocols (P/N 4425209 Rev.B 05/2009 and P/N 702808 Rev.6)

extract_protocol: Total RNAs were extracted from 21 AML patient samples using the NucleoSpin® RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.

tag: tissue

value: Peripheral blood

tag: disease

value: Acute myeloid leukemia

tag: total tumor burden fold reduction

tag: ic50 arac um


title: YFV2012024 PBMC Hour 4


title: YFV2012022 PBMC Hour 4


title: Patient Ps18

source_name: Patient Ps18


title: Patient Ps14

source_name: Patient Ps14


title: Patient Ps22

source_name: Patient Ps22


title: YFV2012004 PBMC Day 1


title: YFV2012004 PBMC Day 2


title: YFV2012022 PBMC Day 7


title: YFV2012023 PBMC Day 0


title: YFV2012022 PBMC Day 28


title: YFV2012024 PBMC Day 28


title: Patient Ps13

source_name: Patient Ps13


title: YFV2012024 PBMC Day 7


title: Patient Ps12

source_name: Patient Ps12


title: Patient Ps15

source_name: Patient Ps15


title: YFV2012021 PBMC Day 28


title: YFV2012021 PBMC Day 7


title: YFV2012020 PBMC Day 7


title: YFV2012021 PBMC Day 0


title: YFV2012021 PBMC Hour 4


title: YFV2012020 PBMC Day 28


title: Patient Ps10

source_name: Patient Ps10


title: Patient Ps09

source_name: Patient Ps09


title: YFV2012020 PBMC Hour 4


title: Patient Ps06

source_name: Patient Ps06


title: YFV2012019 PBMC Day 7


title: YFV2012019 PBMC Hour 4


title: YFV2012019 PBMC Day 0


title: YFV2012019 PBMC Day 28


title: Patient Ps11

source_name: Patient Ps11


title: YFV2012020 PBMC Day 0


title: Patient Ps05

source_name: Patient Ps05


title: Patient Ps07

source_name: Patient Ps07


title: YFV2012017 PBMC Day 28


title: YFV2012017 PBMC Day 7


title: YFV2012018 PBMC Day 0


title: YFV2012018 PBMC Day 7


title: YFV2012017 PBMC Hour 4

source_name: human Hour 4


title: YFV2012018 PBMC Hour 4


title: YFV2012017 PBMC Day 0


title: Patient 1956

source_name: Patient 1956


title: Patient Ps04

source_name: Patient Ps04


title: Patient Ps02

source_name: Patient Ps02


title: Patient Ps01

source_name: Patient Ps01


title: YFV2012018 PBMC Day 28

source_name: human Day 28


title: YFV2012016 PBMC Day 28


title: 121

description:
gene expression data
MM_0_24h_121_IL16750_Liver_.HT_MG.430_PM._F01.CEL


title: YFV2012016 PBMC Day 7

source_name: human Day 7


title: YFV2012016 PBMC Day 0

source_name: human Day 0


title: YFV2012015 PBMC Day 7


title: YFV2012016 PBMC Hour 4


title: Patient 325

source_name: Patient 325


title: YFV2012014 PBMC Day 0


title: YFV2012015 PBMC Day 28


title: Patient 262

source_name: Patient 262


title: YFV2012014 PBMC Day 28


title: YFV2012014 PBMC Hour 4


title: YFV2012015 PBMC Day 0


title: YFV2012013 PBMC Hour 4


title: YFV2012015 PBMC Hour 4


title: U937, Met, repA

source_name: U937, treated with 10mM metformin, replicate A

label_protocol: 250 ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs and labeled into biotinylated cRNA using the GeneChip WT PLUS Reagent kit (Affymetrix) according to the manufacturer’s standard protocols (P/N 4425209 Rev.B 05/2009 and P/N 702808 Rev.6).

growth_protocol: Cell lines were grown in the presence of 100 units per ml of penicillin and 100 μg/ml of streptomycin, and were incubated at 37 °C with 5% CO2.   The cultured cells were split every 2–3 days and maintained in an exponential growth phase.

extract_protocol: Total RNAs were extracted from cells using the Qiagen kit according to the manufacturer’s instructions.

treatment_protocol: For treated samples, cell lines were incubated with 10 mM Metformin for 24 hours

tag: cell line

value: Met

tag: cell line oxidative phosphorylation and energetic status

value: low oxphos

tag: replicate

value: A


title: YFV2012012 PBMC Day 0


title: YFV2012014 PBMC Day 7


title: YFV2012013 PBMC Day 28


title: YFV2012012 PBMC Hour 4


title: U937, Ctrl, repB

source_name: U937, untreated, replicate B

value: Ctrl

tag: oxidative phosphorylation and energetic status

value: B


title: U937, Met, repC

source_name: U937, treated with 10mM metformin, replicate C

value: C


title: YFV2012012 PBMC Day 7


title: YFV2012013 PBMC Day 0


title: U937, Met, repB

source_name: U937, treated with 10mM metformin, replicate B


title: YFV2012011 PBMC Day 28

value: Male


title: YFV2012013 PBMC Day 7


title: YFV2012012 PBMC Day 28


title: Patient 973

source_name: Patient 973


title: Patient 53

source_name: Patient 53


title: U937, Ctrl, repC

source_name: U937, untreated, replicate C


title: YFV2012011 PBMC Day 7


title: YFV2012010 PBMC Day 28


title: YFV2012010 PBMC Hour 4

source_name: human Hour 4


title: YFV2012011 PBMC Day 0


title: U937, Ctrl, repA

source_name: U937, untreated, replicate A


title: YFV2012010 PBMC Day 7


title: MOLM14, Met, repC

source_name: MOLM14, treated with 10mM metformin, replicate C

value: high oxphos


title: MOLM14, Ctrl, repC

source_name: MOLM14, untreated, replicate C


title: YFV2012009 PBMC Day 0


title: YFV2012009 PBMC Day 28


title: MOLM14, Met, repA

source_name: MOLM14, treated with 10mM metformin, replicate A


title: YFV2012008 PBMC Day 0


title: YFV2012009 PBMC Day 7


title: KG1a, Met, repC

source_name: KG1a, treated with 10mM metformin, replicate C


title: YFV2012008 PBMC Day 7

source_name: human Day 7


title: MOLM14, Ctrl, repA

source_name: MOLM14, untreated, replicate A


title: YFV2012011 PBMC Hour 4


title: MOLM14, Ctrl, repB

source_name: MOLM14, untreated, replicate B


title: YFV2012008 PBMC Hour 4


title: YFV2012009 PBMC Hour 4


title: YFV2012007 PBMC Day 7

value: Female


title: YFV2012007 PBMC Hour 4


title: KG1a, Met, repB

source_name: KG1a, treated with 10mM metformin, replicate B


title: YFV2012008 PBMC Day 28

source_name: human Day 28


title: KG1a, Met, repA

source_name: KG1a, treated with 10mM metformin, replicate A


title: YFV2012007 PBMC Day 28


title: MOLM14, Met, repB

source_name: MOLM14, treated with 10mM metformin, replicate B


title: YFV2012007 PBMC Day 0

source_name: human Day 0


title: KG1a, Ctrl, repC

source_name: KG1a, untreated, replicate C


title: YFV2012006 PBMC Day 0


title: YFV2012004 PBMC Day 7


title: YFV2012006 PBMC Day 7


title: YFV2012006 PBMC Hour 4


title: YFV2012004 PBMC Hour 4


title: YFV2012006 PBMC Day 28


title: KG1a, Ctrl, repA

source_name: KG1a, untreated, replicate A


title: HL60, Met, repC

source_name: HL60, treated with 10mM metformin, replicate C


title: KG1a, Ctrl, repB

source_name: KG1a, untreated, replicate B


title: YFV2012004 PBMC Day 28


title: YFV2012004 PBMC Day 0


title: YFV2012002 PBMC Day 28


title: YFV2012002 PBMC Day 7


title: Patient 262_PDX_PBS

hyb_protocol: protocol not available

scan_protocol: protocol not available

data_processing: Data were normalized by RMA (GeneSpring GX)

source_name: Patient 262, PDX, PBS

label_protocol: protocol not available

extract_protocol: RNA was extracted using Trizol (Invitrogen) or RNeasy (Qiagen). RNA was amplified before array analysis (NuGEN Technologies).

tag: tumor  type

value: xenograft model of human AML

tag: host strain

tag: patient

value: PBS


title: Patient 53_PDX_AraC

source_name: Patient 53, PDX, AraC

value: AraC


title: HL60, Met, repA

source_name: HL60, treated with 10mM metformin, replicate A


title: Patient 325_PDX_PBS

source_name: Patient 325, PDX, PBS


title: Patient 325_PDX_AraC

source_name: Patient 325, PDX, AraC


title: HL60, Met, repB

source_name: HL60, treated with 10mM metformin, replicate B


title: HL60, Ctrl, repC

source_name: HL60, untreated, replicate C


title: Patient 262_PDX_AraC

source_name: Patient 262, PDX, AraC


title: HL60, Ctrl, repB

source_name: HL60, untreated, replicate B


title: YFV2012002 PBMC Hour 4

source_name: human Hour 4

value: Hour 4


title: HL60, Ctrl, repA

source_name: HL60, untreated, replicate A


title: YFV2012002 PBMC Day 0


title: control_mouse_2

status: Public on Jun 24 2017

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

hyb_protocol: 130µl hybridization mix prepared from labeled ssDNA was hybridized for 17h at 45°C to GeneChip Mouse Gene 2.0 ST arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed with the Expression Console v1.2.1.20 software (Affymetrix); background correction, nomalization and gene-level probeset summary were performed with the RMA sketch workflow using default parameter settings.

source_name: small intestine of HEL-immunized mouse

label_protocol: 100ng total RNA from each sample was processed with the WT PLUS reagent kit (Affymetrix, Santa Clara, CA) following the manufacturer's protocol.

growth_protocol: Mice were immunized subcutaneously in both sides of the flank with 200 μg MP4 (Alexion Pharmaceuticals) or hen-egg lysozyme (HEL) (Sigma) in complete Freund's adjuvant (CFA; Difco) that contained 5 mg/ml M. tuberculosis H37Ra. On the day of immunization and 48 h later, 200 ng pertussis toxin (List Biological Laboratories) were injected intraperitoneally in 250 μl sterile phosphate-buffered saline (PBS).

extract_protocol: n = 2 MP4-immunized and n = 2 HEL-immunized mice were sacrificed 14 days after immunization. The small intestine was removed and placed in liquid nitrogen for freezing. The frozen tissue was grinded using mortar and pestle. RNA was extracted with tritzol.

treatment_protocol: After immunization there was no further treatment. The development of EAE was evaluated daily according to the standard scoring system: (0), no disease; (1), floppy tail; (2), hind leg weakness; (3), full hind leg paralysis; (4), quadriplegia; (5), death.

tag: group

value: control

tag: rin


title: Patient 53_PDX_PBS

source_name: Patient 53, PDX, PBS

tag: treatment


title: YFV2012010 PBMC Day 0

source_name: human Day 0

tag: subject id

tag: time points

value: Day 0


title: control_mouse_1


title: acute_mouse_1

source_name: small intestine of MP4-immunized mouse

value: acute


title: acute_mouse_2


title: 34A

status: Public on Jun 23 2017

type: genomic

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

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:
Minfi v1.12.0
matrix signal intensities value definition: Unmethylated and methylated signal intensities normalized using preprocessIllumina function of Minfi package

label: Cy3, Cy5

molecule: genomic DNA

source_name: Primary melanoma

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: disease state

value: Primary melanoma


title: 32_MEL


title: 33_MEL_2


title: 4_MEL


title: 27_I_MEL_2


title: 28A


title: 20_MEL


title: 6I_MEL_2


title: 24A


title: 30_MEL


title: 35_MEL


title: 40B


title: 26


title: 21


title: 13_MEL


title: 12_I


title: 23_I


title: 22_MEL


title: 11


title: 14


title: 18_MEL_2


title: 19_MEL


title: 1MelO


title: 15


title: 10


title: 9


title: 8


title: 7


title: 31


title: 39


title: 5


title: 2


title: 3


title: 98_MEL_2

source_name: Metastatic melanoma

value: Metastatic melanoma


title: 56C


title: 97_MEL_2


title: 58_MEL


title: 55_MEL_2


title: 36A


title: 95_MEL_2


title: 44_MEL_2


title: 61_I_MEL


title: 48_MEL_2


title: 45


title: 87


title: 105


title: 49


title: 93


title: 54


title: 64


title: 59


title: 46


title: 96


title: 86


title: 99


title: 82

source_name: Nevi

value: Nevi


title: 89


title: 106


title: 50


title: 84


title: 81


title: 102


title: 37


title: 42


title: 80


title: 77


title: 73


title: 75


title: 74


title: 67


title: 76


title: 72


title: Mock at 24H, biological rep 3

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Gene expression data from mock infected mouse macrophage 24 hpi rep 3

hyb_protocol: Following fragmentation, 15 ug of aRNA were hydridized for 16hrs at 45 0C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analysed with GeneChip operating software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intesity of each array on a given time point, which then further calculated in fold change up- or down-regulation with respect to the signal intesity in Mock infected cells, after analyzed by ANOVA with p value < 0.05

source_name: Mock infected mouse macropahges 24 hpi, rep 3

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: The cells were grown in DMEM L929 (30%) cell condition media (Gibco) and 100 units/ml of penicillin/Streptomycin (Gibco), at 37 0C, 5% CO2

extract_protocol: RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's directions at 4 0C

treatment_protocol: The cells were infected with either of Influenza A viruses (H1N1/WSN, H5N2/F118 and H5N3) MOI=4 in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of penicillin/Streptomycin (Gibco), at 37 0C, 5% CO2

tag: tissue

value: macrophage CD11b+


title: Mock at 24H, biological rep 2

description: Gene expression data from mock infected mouse macrophage 24 hpi rep 2

source_name: Mock infected mouse macropahges 24 hpi, rep 2


title: Mock at 24H, biological rep 1

description: Gene expression data from mock infected mouse macrophage 24 hpi rep 1

source_name: Mock infected mouse macropahges 24 hpi, rep 1


title: Placebo_Normal_Patient_35

city: Atlanta

first: Carlos

middle: S.

last: Moreno

state: GA

address: Michael Street

department: Pathology & Laboratory Medicine

institute: Emory University

hyb_protocol: Hybridization was performed using standard Illumina protocol for Illumina HumanMethylation450 BeadChip Microarrays.

scan_protocol: BeadChip Microarrays were imaged using Illumina iScan system.

data_processing: Signal intensities were extracted using GenomeStudio Methylation Module.

label: Cy5 and Cy3

source_name: Human prostate

label_protocol: Labeling was performed using standard Illumina protocol for Illumina HumanMethylation450 BeadChip Microarrays.

extract_protocol: Genomic DNA was isolated from frozen prostate tissues using DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions.

tag: gender

tag: age


title: Placebo_Tumor_Patient_38


title: Placebo_Tumor_Patient_39


title: Genistein_Tumor_Patient_7


title: Placebo_Tumor_Patient_24


title: Genistein_Tumor_Patient_17


title: Placebo_Tumor_Patient_25


title: 70


title: 41


title: Genistein_Normal_Patient_10


title: Placebo_Tumor_Patient_27


title: Genistein_Tumor_Patient_14


title: Placebo_Normal_Patient_38


title: Genistein_Tumor_Patient_1


title: Placebo_Tumor_Patient_33


title: Genistein_Tumor_Patient_8


title: Genistein_Tumor_Patient_20


title: Genistein_Tumor_Patient_10


title: PorcineSerum_P20_biorep4

city: Olsztyn

first: Monika

middle: M

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description: microRNA detection in serum samples from Day 20 pregnant pigs

hyb_protocol: Dried (MiVac DNA Concentrator, Genevac, USA) samples were resuspended in nuclease free water with addition of 10x GE Blocking Agent and 2x Hi-RPM Hybridization Buffer, and incubated at 100°C for 5 minutes. Afterwards cooled mixtures were hybridized to Agilent miRNA microarrays for 20 h at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x15 K array slides (Scan resolution 5 µm, Dye channel set to Green and Green PMT set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent Technologies) using default parameters (protocol miRNA_107_Sep09 and Grid: 031147_D_F_20101114) to obtain background subtracted and spatially detrended Processed Signal intensities. Baseline transformation to the median of all samples was applied, and then data were normalized among the samples by quantile method. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies for miRNA arrays and using the standard Flag criteria in the GeneSpring GX 12 Software (Agilent).

organism: Sus scrofa

source_name: Porcine serum, Day 20 of pregnancy, biological replicate 4

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 2 µl of sample (dilution 1:2) fallowing the manufacturer’s instructions supplied with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Waldbronn, Germany). First sample was dephosphorylated in 37°C for 30 minutes in a reaction volume of 7 µl containing 1x Calf Intestinal Phosphatase Buffer and 0.7 µl of Calf Intestinal Phosphatase. On completion of the dephosphorylation 5 µl of 100% DMSO was added and incubated at 100°C for 10 minutes. Labelling was accomplished by addition of 10x T4 RNA Ligase Buffer, Cyanine3-pCp, and T4 RNA ligase to the abovementioned mixture and incubation at 16°C for 2 hours, followed by Micro BioSpin 6 column (Bio-Rad, USA) purification.

growth_protocol: Hampshire x Duroc crossbred gilts of similar age (7-8 months) and genetic background from one commercial herd were inseminated 12 and 24 hours after detection of the third estrus.

extract_protocol: Total RNA was isolated with the miRVana miRNA isolation kit (Ambion, Life Technologies, USA) according to the manufacturer’s instructions. The protocol includes sample disruption in lysis buffer, acid phenol:chloroform extraction and an on-column RNA isolation. Quality and quantity of RNA was determined using UV spectrophotometry (NanoDrop 1000). RNA with RNA Integrity number higher than 7 (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA) was used for microarray analysis of each individual sample.

treatment_protocol: Blood samples were collected post mortem on day (D) 12 (n=4/status), 16 (n=4/status) and 20 (n=4/status) of either the estrous cycle or pregnancy. After centrifugation (1,800 x g for 10 min, 4°C; 10,000 x g for 15 min, 4°C) serum samples were stored at - 80 °C for further use.

value: serum

tag: breed

value: Hampshire x Duroc

tag: day

value: Day 20

tag: status

value: pregnant


title: PorcineSerum_P20_biorep3

source_name: Porcine serum, Day 20 of pregnancy, biological replicate 3


title: H5N2 at 24H, biological rep 1

description: Gene expression data from H5N2 infected mouse macrophage 24 hpi rep 1

source_name: H5N2 infected mouse macropahges 24 hpi, rep 1


title: H5N2 at 2H, biological rep 1

description: Gene expression data from H5N2 infected mouse macrophage 2 hpi rep 1

source_name: H5N2 infected mouse macropahges 2 hpi, rep 1


title: H1N1 at 24H, biological rep 3

description: Gene expression data from H1N1 infected mouse macrophage 24 hpi rep 3

source_name: H1N1 infected mouse macropahges 24 hpi, rep 3


title: PorcineSerum_P20_biorep2

source_name: Porcine serum, Day 20 of pregnancy, biological replicate 2


title: Genistein_Normal_Patient_17

value: Male


title: Ymac-1

city: Kaohsiung

first: Chih-Chung

last: Lai

address: 100,Shih-Chuan 1st Road

country: Taiwan

institute: Kaohsiung Medical University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 500 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.  532nm scanning values considered chip control values.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: Ymac-1 cell line

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Ymac-1 mouse liver cancer were cultured in DMEM in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

tag: cell line

value: Ymac-1 liver cell line


title: H5N2 at 24H, biological rep 2

description: Gene expression data from H5N2 infected mouse macrophage 24 hpi rep 2

source_name: H5N2 infected mouse macropahges 24 hpi, rep 2


title: H5N2 at 2H, biological rep 2

description: Gene expression data from H5N2 infected mouse macrophage 2 hpi rep 2

source_name: H5N2 infected mouse macropahges 2 hpi, rep 2


title: H5N2 at 2H, biological rep 3

description: Gene expression data from H5N2 infected mouse macrophage 2 hpi rep 3

source_name: H5N2 infected mouse macropahges 2 hpi, rep 3


title: Placebo_Tumor_Patient_35


title: Placebo_Tumor_Patient_30


title: H5N3 at 24H, biological rep 3

description: Gene expression data from H5N3 infected mouse macrophage 24 hpi rep 3

source_name: H5N3 infected mouse macropahges 24 hpi, rep 3


title: 60


title: Gnmt-/- HCC

description: Gnmt-ko-female tumor

source_name: Gnmt-/- mouse liver tumor

value: female

value: liver tumor

tag: genotype/variation

value: Gnmt-/-


title: H1N1 at 24H, biological rep 1

description: Gene expression data from H1N1 infected mouse macrophage 24 hpi rep 1

source_name: H1N1 infected mouse macropahges 24 hpi, rep 1


title: PorcineSerum_P20_biorep1

source_name: Porcine serum, Day 20 of pregnancy, biological replicate 1


title: Genistein_Tumor_Patient_13


title: Normal liver

description: WT-female

source_name: Normal mouse liver tissue

value: liver tissue

value: wild type


title: Placebo_Tumor_Patient_34


title: H5N3 at 24H, biological rep 2

description: Gene expression data from H5N3 infected mouse macrophage 24 hpi rep 2

source_name: H5N3 infected mouse macropahges 24 hpi, rep 2


title: PorcineSerum_C20_biorep4

description: microRNA detection in serum samples from Day 20 cyclic pigs

source_name: Porcine serum, Day 20 of the estrous cycle, biological replicate 4

value: cyclic


title: Placebo_Tumor_Patient_26

source_name: Human prostate


title: H5N3 at 24H, biological rep 1

description: Gene expression data from H5N3 infected mouse macrophage 24 hpi rep 1

source_name: H5N3 infected mouse macropahges 24 hpi, rep 1


title: Genistein_Tumor_Patient_18


title: H1N1 at 2H, biological rep 3

description: Gene expression data from H1N1 infected mouse macrophage 2 hpi rep 3

source_name: H1N1 infected mouse macropahges 2 hpi, rep 3


title: H1N1 at 24H, biological rep 2

description: Gene expression data from H1N1 infected mouse macrophage 24 hpi rep 2

source_name: H1N1 infected mouse macropahges 24 hpi, rep 2


title: 430063_2_4_H675

city: Diepenbeek

first: Tim

middle: S

last: Nawrot

address: Campus Diepenbeek Agoralaan Gebouw D

department: Centre for Environmental Sciences

country: Belgium

institute: Hasselt University

description: Gene expression in cord blood

hyb_protocol: Cyanine-3 labelled cRNA was hybridized onto Agilent Whole Human Genome 8 x 60K microarrays.

scan_protocol: Microarray signals were detected using the Agilent DNA Microarray Scanner (Agilent Technologies).

data_processing: An in-house developed quality control pipeline in R software was used to preprocess raw data as follows: local background correction, omission of controls, bad spots, and spots with too low intensity, log2 transformation and quantile normalization. Further preprocessing included removal of genes with more than 30% missing data, merging of replicates based on the median, imputation of missing values by means of K-nearest neighbor imputation (K=15) and correction for batch effects using an empirical Bayes method (Johnson et al., Biostatistics, 2007). For genes represented by multiple probes, only the probe with the largest interquartile range was considered. The final dataset used for statistical analyses contained 16,844 genes.

source_name: Cord blood

label_protocol: An aliquot of 0.2 µg total RNA was reverse-transcribed into cDNA, labeled with cyanine-3 following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies).

extract_protocol: Total RNA was isolated from whole blood collected in Tempus tubes (ThermoFisher Scientific, Waltham, MA, USA) using the Tempus Spin RNA Isolation kit (Life Technologies, Paisley, UK) according to the manufacturer’s instructions. RNA yields were determined using the NanoDrop Spectrophotometer (Isogen Life Sciences, De Meern, the Netherlands) and the quality was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands). Samples with RNA Integrity Number below 6 were excluded from further analysis.

tag: Sex

value: boys

tag: long-term pm2.5 exposure  (µg/m3)

tag: short-term pm2.5 exposure (µg/m3)


title: Genistein_Tumor_Patient_19


title: PorcineSerum_C20_biorep3

source_name: Porcine serum, Day 20 of the estrous cycle, biological replicate 3


title: 430063_2_3_H672

description: Gene expression in cord blood

value: girls


title: PorcineSerum_C20_biorep2

source_name: Porcine serum, Day 20 of the estrous cycle, biological replicate 2


title: 430063_2_2_H671

description: Gene expression in cord blood


title: 430063_2_1_H670

description: Gene expression in cord blood


title: 430063_1_4_H668

description: Gene expression in cord blood


title: 430063_1_2_H666

description: Gene expression in cord blood


title: 430063_1_1_H664

description: Gene expression in cord blood


title: 422232_2_4_H663

description: Gene expression in cord blood


title: PorcineSerum_C20_biorep1

source_name: Porcine serum, Day 20 of the estrous cycle, biological replicate 1


title: H1N1 at 2H, biological rep 2

description: Gene expression data from H1N1 infected mouse macrophage 2 hpi rep 2

source_name: H1N1 infected mouse macropahges 2 hpi, rep 2


title: 422232_2_2_H661

description: Gene expression in cord blood


title: H1N1 at 2H, biological rep 1

description: Gene expression data from H1N1 infected mouse macrophage 2 hpi rep 1

source_name: H1N1 infected mouse macropahges 2 hpi, rep 1


title: PorcineSerum_P16_biorep4

description: microRNA detection in serum samples from Day 16 pregnant pigs

source_name: Porcine serum, Day 16 of pregnancy, biological replicate 4

value: Day 16


title: 422232_2_3_H662

description: Gene expression in cord blood


title: PorcineSerum_P16_biorep3

source_name: Porcine serum, Day 16 of pregnancy, biological replicate 3


title: 422232_2_1_H660

description: Gene expression in cord blood


title: PorcineSerum_P16_biorep1

source_name: Porcine serum, Day 16 of pregnancy, biological replicate 1


title: 430063_1_3_H667

description: Gene expression in cord blood


title: 422232_1_4_H659

description: Gene expression in cord blood

value: none provided by submitter


title: 422232_1_3_H658

description: Gene expression in cord blood


title: Fabp7 KO 2

city: Sendai

first: Jun

last: Suzuki

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Department of Otorhinolaryngology-Head and Neck Surgery

country: Japan

institute: Tohoku University School of Medicine

hyb_protocol: Microarray analysis (one-color assay) was performed using a SurePrint G3 Mouse GE 8x60K Microarray Kit (Agilent) according to the manufacturer's instructions. The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent). A total of 600 ng of Cy3-labeled cRNA in hybridization buffer was hybridized for microarray.

scan_protocol: The array was washed in Agilent GE Wash Buffer 1 and Agilent GE Wash Buffer 2 and was scanned with Agilent’s Microarray Scanner System.

data_processing: The image data were processed using Agilent Feature Extraction software, version 10.7. All of the data were subsequently uploaded into GeneSpring GX software, version 12.5 (Agilent Technologies) for quantile normalization and data analysis.

source_name: cochlea

label_protocol: Nort provided

extract_protocol: Female Fabp7 (+/+) and Fabp7(-/-) mice were sacrificed at 7 months of age, and their cochlear tissues, including the otic capsule but excluding vestibular tissues, were dissected. Total RNA was isolated from 4 cochleae from 2 mice for 1 sample using an RNA isolation reagent (TRIzol, Life Technologies) according to the manufacturer’s protocol. Three samples (6 mice) per group were collected.

tag: genotype

value: 7 months


title: Fabp7 KO 3


title: Fabp7 KO 1


title: Wild-type 2


title: Wild-type 1


title: 422232_1_2_H657

description: Gene expression in cord blood


title: 422232_1_1_H656

description: Gene expression in cord blood


title: Wild-type 3


title: PorcineSerum_C16_biorep4

description: microRNA detection in serum samples from Day 16 cyclic pigs

source_name: Porcine serum, Day 16 of the estrous cycle, biological replicate 4

value: serum


title: PorcineSerum_C16_biorep2

source_name: Porcine serum, Day 16 of the estrous cycle, biological replicate 2

value: Hampshire x Duroc


title: PorcineSerum_C16_biorep3

source_name: Porcine serum, Day 16 of the estrous cycle, biological replicate 3


title: 422231_1_4_H649

description: Gene expression in cord blood


title: PorcineSerum_C16_biorep1

source_name: Porcine serum, Day 16 of the estrous cycle, biological replicate 1


title: 422231_2_1_H650

description: Gene expression in cord blood


title: 422231_1_2_H646

description: Gene expression in cord blood


title: 422231_2_2_H651

description: Gene expression in cord blood


title: PorcineSerum_P12_biorep4

description: microRNA detection in serum samples from Day 12 pregnant pigs

source_name: Porcine serum, Day 12 of pregnancy, biological replicate 4

value: Day 12


title: 422230_2_4_H644

description: Gene expression in cord blood


title: 422231_2_3_H652

description: Gene expression in cord blood


title: PorcineSerum_P16_biorep2

source_name: Porcine serum, Day 16 of pregnancy, biological replicate 2

value: pregnant


title: 422231_2_4_H655

description: Gene expression in cord blood


title: PorcineSerum_P12_biorep2

source_name: Porcine serum, Day 12 of pregnancy, biological replicate 2


title: 422230_2_2_H640

description: Gene expression in cord blood

source_name: Cord blood


title: PorcineSerum_P12_biorep3

source_name: Porcine serum, Day 12 of pregnancy, biological replicate 3


title: 422230_2_1_H639

description: Gene expression in cord blood


title: 422230_2_3_H641

description: Gene expression in cord blood


title: PorcineSerum_P12_biorep1

source_name: Porcine serum, Day 12 of pregnancy, biological replicate 1


title: 422231_1_3_H647

description: Gene expression in cord blood


title: 422230_1_4_H559

description: Gene expression in cord blood


title: 422231_1_1_H645

description: Gene expression in cord blood


title: PorcineSerum_C12_biorep4

description: microRNA detection in serum samples from Day 12 cyclic pigs

source_name: Porcine serum, Day 12 of the estrous cycle, biological replicate 4


title: 422230_1_2_H543

description: Gene expression in cord blood


title: 422229_2_2_H636

description: Gene expression in cord blood


title: PorcineSerum_C12_biorep3

source_name: Porcine serum, Day 12 of the estrous cycle, biological replicate 3


title: 422229_2_3_H637

description: Gene expression in cord blood


title: 422229_2_4_H638

description: Gene expression in cord blood


title: 422230_1_3_H547

description: Gene expression in cord blood


title: 422229_2_1_H635

description: Gene expression in cord blood


title: 422230_1_1_H424

description: Gene expression in cord blood


title: PorcineSerum_C12_biorep2

source_name: Porcine serum, Day 12 of the estrous cycle, biological replicate 2


title: 422228_2_2_H628

description: Gene expression in cord blood


title: PorcineSerum_C12_biorep1

source_name: Porcine serum, Day 12 of the estrous cycle, biological replicate 1


title: 422229_1_1_H631

description: Gene expression in cord blood


title: 422228_2_4_H630

description: Gene expression in cord blood


title: 422229_1_3_H633

description: Gene expression in cord blood


title: 422229_1_4_H634

description: Gene expression in cord blood


title: 422228_2_3_H629

description: Gene expression in cord blood


title: 422229_1_2_H632

description: Gene expression in cord blood


title: 422228_1_1_H623

description: Gene expression in cord blood


title: 422228_1_2_H624

description: Gene expression in cord blood


title: 422228_1_3_H625

description: Gene expression in cord blood


title: 422227_2_4_H622

description: Gene expression in cord blood


title: 422227_1_3_H609

description: Gene expression in cord blood


title: 422227_1_4_H612

description: Gene expression in cord blood


title: 422228_1_4_H626

description: Gene expression in cord blood


title: 422228_2_1_H627

description: Gene expression in cord blood


title: aorta_vascular smooth muscle cells_KO_rep4

city: Heidelberg

first: Stephanie

middle: Sarah

last: Kapel

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Division of Vascular Oncology and Metastasis

institute: German Cancer Research Center (DKFZ)

description:
18618\/17\/15 (1)_9482914024_F.mean
Sample 8
replicate 4_KO

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

organism: Mus

source_name: mouse aortic vascular smooth muscle cells

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

growth_protocol: Cells were cultured and passaged in DMEM+15%FCS+1% P/S

extract_protocol: RNA was extracted and cleaned-up with DNase I treatment and QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Male

tag: strain

value: C57 black 6

value: KO

value: 8 weeks

value: Aorta

tag: cell type

value: smooth muscle

tag: passage

value: passage 1


title: aorta_vascular smooth muscle cells_KO_rep2

description:
18593\/92\/91 (1)_9853741053_F.mean
Sample 6
replicate 2_KO


title: 432719_2_4_H554

description: Gene expression in cord blood


title: 422227_1_1_H605

description: Gene expression in cord blood


title: 432719_2_3_H679

description: Gene expression in cord blood


title: 422227_2_2_H617

description: Gene expression in cord blood


title: aorta_vascular smooth muscle cells_WT_rep4

description:
18625\/24\/23 (1)_9853741053_D.mean
Sample 4
replicate 4_WT

value: WT


title: 426916_2_4_H542

description: Gene expression in cord blood


title: 426916_2_2_H539

description: Gene expression in cord blood


title: 426916_2_3_H540

description: Gene expression in cord blood


title: aorta_vascular smooth muscle cells_WT_rep3

description:
57\/58_9853741053_C.mean
Sample 3
replicate 3_WT


title: 422227_1_2_H606

description: Gene expression in cord blood


title: 426916_1_4_H537

description: Gene expression in cord blood

value: boys


title: 422227_2_1_H614

description: Gene expression in cord blood

value: girls


title: aorta_vascular smooth muscle cells_WT_rep1

description:
18670\/71(2)_9853741053_A.mean
Sample 1
replicate 1_WT


title: aorta_vascular smooth muscle cells_WT_rep2

description:
18555\/56_9853741053_B.mean
Sample 2
replicate 2_WT


title: aorta_vascular smooth muscle cells_KO_rep3

description:
18567\/66\/63_9482914024_E.mean
Sample 7
replicate 3_KO


title: aorta_vascular smooth muscle cells_KO_rep1

description:
18663\/62 (1)_9853741053_E.mean
Sample 5
replicate 1_KO


title: 432719_2_2_H618

description: Gene expression in cord blood


title: 426916_2_1_H538

description: Gene expression in cord blood


title: 426916_1_2_H531

description: Gene expression in cord blood


title: 426916_1_3_H535

description: Gene expression in cord blood


title: 426916_1_1_H435

description: Gene expression in cord blood


title: 425647_2_4_H433

description: Gene expression in cord blood


title: 425647_1_4_H427

description: Gene expression in cord blood


title: 425647_2_2_H429

description: Gene expression in cord blood


title: Shoot_PminusTreated_rep1

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix AraGene-1_0-st arrays according to the GeneChip WT Terminal Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 4.0 (Affymetrix)

data_processing: Arabidopsis Gene Array 1.0 ST .cel files were imported into Partek Genomics Suite 6.6 (6.13.0731) and normalized on a gene level using the standard RMA algorithm for normalization and background correction.

organism: Arabidopsis thaliana

source_name: shoot_absence of phosphorus

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix' GeneChip® WT PLUS Reagent Kit from 250 ng total RNA

growth_protocol: Mature seeds of the Arabidopsis thaliana cv. Col-0 were surface sterilized and grown hydroponically in 0.5X MS + 1.5% (w/v) Suc medium for 5 days.

extract_protocol: Total RNA was isolated from frozen root and shoot tissues separately using RNeasy Plant Mini Kit with on column DNase digestion (Qiagen, USA), according to the manufacturer’s instructions. The integrity of RNA was checked on agarose gel and concentrations were determined using Nanodrop (Wilmington, DE, USA).

treatment_protocol: Seedlings was grown for 5 days as described in growth protocol, thereafter seedlings were transferred into varying Pi concentration such as no Pi (0 mM), control Pi (1.25 mM) and excess Pi (20.0 mM) for 7 days. Plants were grown under standard growth condition i.e. 16h light /8h dark photoperiod, 120 µmol m-2 s-1 light intensity, 60-70% humidity, at 230C.

tag: ecotype

value: cv. Col-0

value: shoot

tag: treated with

value: absence of phosphorus (P-)


title: Root_PminusTreated_rep3

source_name: root_absence of phosphorus

tag: tissue

value: root


title: 425647_2_3_H431

description: Gene expression in cord blood


title: Root_PminusTreated_rep1


title: 425646_2_1_H415

description: Gene expression in cord blood


title: 425647_1_2_H425

description: Gene expression in cord blood


title: Shoot_PminusTreated_rep3


title: Shoot_20mMTreated_rep2

source_name: shoot_20mM of phosphorus

value: 20mM of phosphorus


title: 425646_2_2_H420

description: Gene expression in cord blood


title: 425646_2_3_H421

description: Gene expression in cord blood


title: 425647_1_3_H426

description: Gene expression in cord blood


title: Shoot_PminusTreated_rep2


title: Root_PminusTreated_rep2


title: Shoot_20mMTreated_rep1


title: 425646_2_4_H422

description: Gene expression in cord blood


title: 425647_2_1_H428

description: Gene expression in cord blood


title: 425646_1_4_H411

description: Gene expression in cord blood


title: Shoot_20mMTreated_rep3


title: Root_20mMTreated_rep3

source_name: root_20mM of phosphorus


title: 425646_1_3_H410

description: Gene expression in cord blood


title: Root_20mMTreated_rep2


title: 425646_1_2_H405

description: Gene expression in cord blood


title: Root_20mMTreated_rep1


title: Shoot_1.25mMTreated_rep3

source_name: shoot_1.25mM of phosphorus

value: 1.25mM of phosphorus


title: 425645_1_4_H363

description: Gene expression in cord blood


title: 425645_1_3_H361

description: Gene expression in cord blood


title: 425645_2_4_H395

description: Gene expression in cord blood


title: 425613_1_3_H195

description: Gene expression in cord blood


title: 425645_2_1_H364

description: Gene expression in cord blood


title: 425646_1_1_H404

description: Gene expression in cord blood


title: 425645_2_3_H367

description: Gene expression in cord blood


title: Shoot_1.25mMTreated_rep2


title: Root_1.25mMTreated_rep3

source_name: root_1.25mM of phosphorus


title: 425645_1_2_H359

description: Gene expression in cord blood


title: 425613_2_3_H282

description: Gene expression in cord blood


title: 425612_2_1_H388

description: Gene expression in cord blood


title: 425613_1_2_H106

description: Gene expression in cord blood


title: 425612_1_1_H380

description: Gene expression in cord blood


title: 425613_2_2_H241

description: Gene expression in cord blood


title: 425612_1_4_H387

description: Gene expression in cord blood


title: 425645_2_2_H365

description: Gene expression in cord blood


title: 425612_2_2_H391

description: Gene expression in cord blood


title: 425613_2_4_H321

description: Gene expression in cord blood


title: 425645_1_1_H353

description: Gene expression in cord blood


title: Shoot_1.25mMTreated_rep1


title: 425613_1_4_H220

description: Gene expression in cord blood


title: Root_1.25mMTreated_rep2


title: 425612_2_3_H392

description: Gene expression in cord blood


title: 425613_2_1_H228

description: Gene expression in cord blood


title: 425612_1_3_H384

description: Gene expression in cord blood


title: 425612_2_4_H394

description: Gene expression in cord blood


title: 425613_1_1_H69

description: Gene expression in cord blood


title: Root_1.25mMTreated_rep1


title: 425600_2_4_H378

description: Gene expression in cord blood


title: 425600_2_2_H376

description: Gene expression in cord blood


title: 425600_2_1_H373

description: Gene expression in cord blood


title: 425600_2_3_H377

description: Gene expression in cord blood


title: 425600_1_2_H370

description: Gene expression in cord blood


title: 425600_1_4_H214

description: Gene expression in cord blood


title: 411096_2_1_H413

description: Gene expression in cord blood


title: 411082_2_4_H406

description: Gene expression in cord blood


title: 411096_1_1_H408

description: Gene expression in cord blood


title: 411082_2_1_H402

description: Gene expression in cord blood


title: 425600_1_1_H369

description: Gene expression in cord blood


title: 411096_2_2_H414

description: Gene expression in cord blood


title: 411082_1_4_H401

description: Gene expression in cord blood


title: 411096_1_4_H412

description: Gene expression in cord blood


title: 410982_2_2_H226

description: Gene expression in cord blood


title: 410982_2_4_H231

description: Gene expression in cord blood


title: 410982_2_1_H225

description: Gene expression in cord blood


title: 411096_2_4_H417

description: Gene expression in cord blood


title: 411082_1_2_H397

description: Gene expression in cord blood


title: 425600_1_3_H371

description: Gene expression in cord blood


title: 410982_1_3_H215

description: Gene expression in cord blood


title: testis_stageI_pool2, P36

city: Barcelona

first: Mercedes

last: Blazquez

address: Passeig Maritim 37-49

institute: Institut de Ciencies del Mar (ICM-CSIC)

hyb_protocol: Amplified samples (1.65 μg per sample) were hybridized to a custom oligonucleotide high-density seabass microarray (Agilent-024502 4 × 44 K design format) containing 60-mer oligonucleotides with a linker directly spotted on glass slides using the Agilent's SurePrint Technology. Hybridizations were performed at 65 °C for 17 h using Agilent's GE Hybridization Kit. Washes were conducted as recommended by the manufacturer using Agilent's Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner model G2505B using one color scan setting for 1x44k array slides. Spot intensities and other quality control features were extracted with Agilent's Feature Extraction software version 10.4.

data_processing: Agilent's Feature Extraction software version 10.4 performs an initial lowess normalization. Finally, microarray feature extracted data were analyzed using GeneSpring software version 10.1. Percentile shift normalization was used to adjust all spot intensities in the array (percentile target = 75). Principal Component Analysis (PCA) was used as means of quality control on samples and allowed to decrease the number of false positives before the statistical analysis. After normalization, all data were filtered by comparison of the standard deviation expression among groups (filter by expression). Only entities with values equal to or greater than the standard deviation were retained, allowing for the identification of outliers (genes with a low variation in expression across samples). Statistical analysis was performed on filtered data using an unpaired t-test. Significant differences in the transcriptomic profile between early stages of spermatogenesis were set at p < 0.01.

organism: Dicentrarchus labrax

source_name: testicular tissue, stage I

label_protocol: Denatured total RNA samples (100 ng) were reverse transcribed, amplified and labelled with a single dye, Cy3. RNA labelling was performed according to Agilent Quick Amp Labelling kit instructions.

extract_protocol: Tissues (approx. 50-100 mg) were homogenized in Trizol (Invitrogen, Carlsbad, CA) using the FastPrep® Instrument (Qbiogene, Inc., Carlsbad, CA), a tissue homogenizer using ceramic spheres (1.4 mm diameter) as a lysing matrix. Total RNA was subsequently extracted from the lysate using the PureLinkTM RNA mini Kit (Invitrogen) following the manufacturer's instructions. Briefly, RNA was phase separated and washed using the spin cartridges provided in the kit, to be finally eluted in DEPC water.

treatment_protocol: By the time of sea bass normal puberty, a sampling procedure was designed to obtain testis during early stages of maturation, including Stage I and Stage II. With that purpose, samplings (15 fish at each sampling point) were performed every 10 days starting in mid-August and finishing at the end of October.

tag: gender

value: male

value: testis

tag: spermatogenic stage

value: I


title: testis_stageII_pool2, P37

source_name: testicular tissue, stage II

value: II


title: testis_stageII_pool3, P37


title: testis_stageI_pool3, P36


title: testis_stageII_pool1, P37


title: testis_stageI_pool3, P37


title: testis_stageI_pool1, P36


title: testis_stageII_pool3, P36


title: 410982_1_1_H200

description: Gene expression in cord blood


title: 410981_2_2_H186

description: Gene expression in cord blood


title: 410981_2_1_H179

description: Gene expression in cord blood


title: 410981_2_3_H191

description: Gene expression in cord blood


title: 411082_1_3_H399

description: Gene expression in cord blood


title: 410981_1_4_H177

description: Gene expression in cord blood


title: 410967_1_3_H360

description: Gene expression in cord blood


title: 410981_1_1_H39

description: Gene expression in cord blood


title: 410966_1_4_H309

description: Gene expression in cord blood


title: 410966_1_3_H294

description: Gene expression in cord blood


title: 410966_2_4_H328

description: Gene expression in cord blood


title: 410966_2_3_H324

description: Gene expression in cord blood


title: 410966_2_1_H310

description: Gene expression in cord blood


title: 410966_1_2_H288

description: Gene expression in cord blood


title: 410965_2_3_H253

description: Gene expression in cord blood


title: 410965_2_2_H250

description: Gene expression in cord blood


title: 410965_2_1_H246

description: Gene expression in cord blood


title: 410965_1_2_H236

description: Gene expression in cord blood


title: 410965_2_4_H259

description: Gene expression in cord blood


title: 410965_1_1_H233

description: Gene expression in cord blood


title: Plasma Cell 4

city: Montpellier

first: Jerome

last: Moreaux

address: 80 Av. Augustin Fliche

department: Biological Hematology

country: France

institute: CHRU Montpellier

description: microRNA expression data from plasma cell

hyb_protocol: The labelled RNA was then hybridized to Affymetrix GeneChip® microRNA arrays v1.0 following Affymetrix recommended protocol.

scan_protocol: Genechips were scanned on an Affymetrix GeneChip 3000 7G scanner.

data_processing: The data were extracted using Affymetrix miRNA QC tool software using default analysis settings for normalization and summarization methods.

source_name: Plasma Cell, in vitro day 10

label_protocol: small RNA was processed using the FlashTag labeling kit, which uses a tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

growth_protocol: All cultures were performed in Iscoves modified Dulbecco medium (IMDM) and 10%FCS, supplemented with 50 ﾵg/ml human transferrin and 5 ug/ml human insulin. Purified memory B-cells were activated with 10 ug/ml of CpG oligodeoxynucleotide 2006 and histidine tagged soluble recombinant human CD40L (50 ng/ml) and anti-poly-histidine mAb (5 ug/ml) (R&D Systems) in presence of IL-2 (20 U/ml), IL-10(50 ng/ml) and IL-15 (10 ng/ml. At day 4 cells were harvested and cultured with IL-2, IL-6 (50ng/ml), IL-10 and IL-15 until day 7. At day 7 cells were washed and cultured with IL-6, IL-15 and IFN-alpha (500 U/ml)until day 10. Cell samples: Peripheral blood Memory B cells were obtained from healthy volunteers. After removal of CD2+ cells using anti-CD2 magnetic beads (Invitrogen), CD19+ CD27+ cells were sorted by FACS Aria. Day 4 preplasmablasts CD20- CD38-, day 7 Plasmablasts CD20- CD38+ and day 10 Plasma cells CD20- CD138+ were sorted from cell culture using FACS Aria.

extract_protocol: Total RNA containing miRNAs were extracted using Qiagen RNeasy Plus Mini Kit.

value: plasma cell


title: Plasma Cell 5


title: Plasma Cell 3


title: Plasmablast 5

description: microRNA expression data from plasmablast

source_name: Plasmablast, in vitro day 7

value: plasmablast


title: Plasmablast 6


title: Plasma Cell 2


title: 410965_1_3_H237

description: Gene expression in cord blood

source_name: Cord blood


title: DMD DNA sample 139

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis version 7.4

scan_protocol: Images were quantified using Agilent Feature Extraction Software version 12

data_processing:
Agilent Genomic Workbench version 7.0
Standard set-up of the ADM-2 statistical analysis provided by Genomic Workbench software

source_name: DNA from blood

extract_protocol: DNA extraction from blood

tag: subject status

value: Duchenne Muscular Dystrophy (DMD) patient

value: blood

source_name: Reference Human Male DNA Promega

tag: sample type

value: reference


title: Plasma Cell 1


title: Plasmablast 4


title: DMD DNA sample 515

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis version 7.4


title: DMD DNA sample 994


title: Plasmablast 2


title: Memory B Cell 4

description: microRNA expression data from memory B cell

source_name: Memory B cells

value: memory B cell


title: Preplasmablast 5

description: microRNA expression data from preplasmablasts

source_name: Preplasmablast, in vitro day 4

value: preplasmablasts


title: Preplasmablast 1


title: Preplasmablast 6


title: DMD DNA sample 214


title: Preplasmablast 4


title: Plasmablast 3


title: DMD DNA sample 728


title: DMD DNA sample 561


title: DMD DNA sample 176


title: DMD DNA sample 894


title: Memory B Cell 3


title: Memory B Cell 2


title: Memory B Cell 1


title: Plasmablast 1


title: Preplasmablast 3


title: Preplasmablast 2


title: Placebo_Tumor_Patient_24

hyb_protocol: Standard hybridization protocol for Illumina Expression BeadChip.

scan_protocol: Standard scanning protocol for Illumina Expression BeadChip.

data_processing: Gene expression analysis was performed using GenePattern Comparative Marker Selection module.

label: Biotin

source_name: Human prostate

label_protocol: Biotin-labeled cRNA samples were prepared using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip.

extract_protocol: Total RNA was extracted from frozen prostate tissues using the mirVana miRNA Isolation Kit, followed by RNA clean-up using the RNeasy Mini Kit according to the manufacurer's instructions. RNA quality control was performed using Agilent 2100 Bioanalyzer.

value: Male

tag: age


title: Genistein_Tumor_Patient_1


title: Placebo_Tumor_Patient_25


title: Placebo_Tumor_Patient_27


title: Genistein_Tumor_Patient_13


title: Genistein_Normal_Patient_17


title: Placebo_Tumor_Patient_26


title: Placebo_Tumor_Patient_39


title: Placebo_Normal_Patient_35


title: Placebo_Normal_Patient_38


title: Placebo_Tumor_Patient_30


title: Placebo_Tumor_Patient_33


title: Genistein_Normal_Patient_10


title: Genistein_Tumor_Patient_7


title: Placebo_Tumor_Patient_35


title: Genistein_Tumor_Patient_14


title: Genistein_Tumor_Patient_17


title: Genistein_Tumor_Patient_20


title: Placebo_Tumor_Patient_38


title: Genistein_Tumor_Patient_18


title: Genistein_Tumor_Patient_10


title: Genistein_Tumor_Patient_8


title: Genistein_Tumor_Patient_19


title: T-cell_control_rep7

city: Leicester

first: David

middle: John

last: Cousins

address: NIHR BRC Respiratory, Glenfield Hospital

department: Respiratory Sciences

country: United Kingdom

institute: University of Leicester

description: control

hyb_protocol: Standard Illumina hybridization protocol except hyb performed at 48 degrees C

data_processing: The data were normalised using quantile normalisation within Genome Studio without background correction. Data was submitted using Illumina's GEO Data Submission Report Plug-in for Gene Expression

source_name: Skin, control

label_protocol: cDNA synthesis and amplification was performed with the Ovation PicoSL WTA system V2 kit (NuGEN, Leek, Netherlands) as per the manufacturer’s instructions. Purity and yield was then analyzed using the Bioanalyzer platform (Agilent, Stockport, UK) and NanoDrop 2000 spectrophotometer (Thermo Scientific, Loughborough, UK) respectively before amplified cDNA was biotin-labeled with the NuGEN Encore BiotinIL module according to the manufacturer’s instructions

growth_protocol: Skin biopsy was dissected and resuspended in complete medium. Samples were cultured at 37°C, 5% CO2 in the presence of rIL-2 (50 U/ml). After 3-4 days, cells were passed through a 0.2 μm cell strainer to obtain single cell suspensions and restimulated by culturing on anti-CD3/28 antibody coated plates. Cells were cultured for a further 7 days with removal from stimulation after 3-4 days.

extract_protocol: RNA was isolated from cell pellets using the miRNeasy mini kit and RNeasy MinElute cleanup kit (Qiagen, Manchester, UK) according to the manufacturer’s instructions.

treatment_protocol: Cells were activated with PMA/Ionomycin for 4hrs.

value: T-cells

tag: treatment

value: control


title: T-cell_IDIT_rep7

description: IDIT

source_name: Skin, IDIT

value: IDIT


title: T-cell_control_rep6

description: control


title: T-cell_IDIT_rep6

description: IDIT


title: T-cell_IDIT_rep5

description: IDIT


title: T-cell_control_rep3

description: control


title: T-cell_IDIT_rep4

description: IDIT


title: T-cell_control_rep8

description: control


title: Placebo_Tumor_Patient_34


title: HGEC_NIC14_rep2

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: Micoarray expression analysis was performed on a Microarray Analysis Suite instrument system (Affymetrix, Santa Clara, CA) using Affymetrix HG-U133A v2 arrays. Sample preparations, labeling, hybridizations, and scanning were done according to the established Affymetrix protocols.

scan_protocol: Affymetrix protocol

data_processing: All sample data were scaled to a uniform target intensity of 500 to allow quantitative comparisons across experiments. RMA normalization was applied to raw data across all treatment and control samples to normalize data at the probe set level. Probe sets with too small or large variation across all samples were filtered out and control adjustment within treatment was applied using treatment specific control samples. The differences in logarithmic intensities between each treatment and its own control were calculated.

source_name: normal primary human gingival epithelial cells, Treated with NIC14, Replicate 2

label_protocol: The purity and integrity of each RNA preparation was evaluated by using RNA Nano Chips on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

growth_protocol: Human oral squamous cell carcinoma cell lines 101A (UM-SCC-101A, primary tonsil tumor) and 101B (UM-SCC-101B, lymph node metastasis) were obtained from Dr. T. Carey (Univ. of Michigan) [20,21]. Both cells were grown in DMEM with 10% fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA), 100 U/ml of penicillin-streptomycin, 2 mM Glutamine, and 100 nM nonessential amino acids. Primary human gingival epithelial cells (HGEC) were obtained from the University of Louisville School of Dentistry (Dr. D. Kinane) [22,23]. HGECs were grown in keratinocyte-serum-free medium (Invitrogen, Carlsbad, CA) containing 10 mg/ml of insulin, 5 mg/ml of transferrin, 10 mM of 2-mercaptoethanol, 10 mM of 2-aminoethanol, 10 mM of sodium selenite, 50 mg/ml of bovine pituitary extract, 100 U/ml of penicillin-streptomycin, and 50 ng/ml of Fungizone. All cells were grown at 37ºC in a humidified atmosphere with 5% CO2

extract_protocol: Cells were grown to approximately 75% confluence in 6-well plates, treated for 24 hours, and total RNA was subsequently isolated with TriZolTM reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: Target cells were exposed for 24 hours to different TPPs or solvent only as vehicle controls. Doses were chosen based on previous systematic dose- and time-dependent cytotoxicity studies [13]. For TPM and WS-CM, EC-30 doses were applied; for ST/CAS, the dose with the same amount of NIC as that in TPM at EC-30 was applied since no EC-30 could be determined. In addition, low and high doses of NIC alone were used as controls. The low dose (14 ug/ml) represented the levels of nicotine in the combustible TPP exposures, while the high dose (474 ug/ml) was used to reach exposure levels nearing the cytotoxic response in the TPP exposures. The high NIC dose was chosen in this range because it was previously shown that NIC at close to millimolar doses had some cytotoxic effects on other cell types [12] and since we had determined such range yielded 20% cytotoxicity in oral cells [13]. NIC vs DMSO was done mainly as control exposure and was not included for microarray expression profiling in the 101B cell line

tag: cell line

value: HGEC


title: HGEC_WZ-DMSO_rep2

source_name: normal primary human gingival epithelial cells, Treated by WZ with DMSO, Replicate 2


title: HGEC_WZ-CAS_rep1

source_name: normal primary human gingival epithelial cells, Treated by WZ with CAS, Replicate 1


title: T-cell_control_rep1

description: control


title: HGEC_NIC474_rep1

source_name: normal primary human gingival epithelial cells, Treated with NIC474, Replicate 1


title: HGEC_NIC474_rep3

source_name: normal primary human gingival epithelial cells, Treated with NIC474, Replicate 3


title: HGEC_WZ-DMSO_rep3

source_name: normal primary human gingival epithelial cells, Treated by WZ with DMSO, Replicate 3


title: HGEC_WZ-DMSO_rep1

source_name: normal primary human gingival epithelial cells, Treated by WZ with DMSO, Replicate 1


title: HGEC_NIC14_rep1

source_name: normal primary human gingival epithelial cells, Treated with NIC14, Replicate 1


title: HGEC_WZ-CAS_rep2

source_name: normal primary human gingival epithelial cells, Treated by WZ with CAS, Replicate 2


title: T-cell_control_rep4

description: control


title: HGEC_NIC474_rep2

source_name: normal primary human gingival epithelial cells, Treated with NIC474, Replicate 2


title: T-cell_IDIT_rep2

description: IDIT


title: HGEC_WZ-CAS_rep3

source_name: normal primary human gingival epithelial cells, Treated by WZ with CAS, Replicate 3


title: T-cell_IDIT_rep3

description: IDIT


title: T-cell_control_rep5

description: control


title: HGEC_NIC14_rep3

source_name: normal primary human gingival epithelial cells, Treated with NIC14, Replicate 3


title: T-cell_IDIT_rep1

description: IDIT


title: T-cell_control_rep2

description: control


title: HGEC_STE474_rep3

source_name: normal primary human gingival epithelial cells, Treated with STE474, Replicate 3


title: HGEC_STE474_rep2

source_name: normal primary human gingival epithelial cells, Treated with STE474, Replicate 2


title: HGEC_CAS_rep3

source_name: normal primary human gingival epithelial cells, Treated with CAS, Replicate 3


title: HGEC_STE474_rep1

source_name: normal primary human gingival epithelial cells, Treated with STE474, Replicate 1


title: HGEC_CAS_rep2

source_name: normal primary human gingival epithelial cells, Treated with CAS, Replicate 2


title: HGEC_CAS_rep1

source_name: normal primary human gingival epithelial cells, Treated with CAS, Replicate 1


title: HGEC_STE14_rep3

source_name: normal primary human gingival epithelial cells, Treated with STE14, Replicate 3


title: HGEC_STE14_rep2

source_name: normal primary human gingival epithelial cells, Treated with STE14, Replicate 2


title: HGEC_WS-CM_rep2

source_name: normal primary human gingival epithelial cells, Treated with WS-CM, Replicate 2


title: HGEC_WS-CM_rep1

source_name: normal primary human gingival epithelial cells, Treated with WS-CM, Replicate 1


title: HGEC_MEDIUM_rep2

source_name: normal primary human gingival epithelial cells, Treated with MEDIUM, Replicate 2


title: HGEC_DMSO_rep3

source_name: normal primary human gingival epithelial cells, Treated with DMSO, Replicate 3


title: HGEC_DMSO_rep2

source_name: normal primary human gingival epithelial cells, Treated with DMSO, Replicate 2


title: HGEC_TPM_rep2

source_name: normal primary human gingival epithelial cells, Treated with TPM, Replicate 2


title: NOD1-deficient zebrafish

city: Wuhan

first: M

middle: X

last: Chang

address: Luojiaashan

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions
For the normalization it uses the average of three housekeeping genes: hprt1,nono and rpl13a
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., NOD1-1IS-/-/WT) ratios.

label: SYBR Green

organism: Danio rerio

source_name: larvae

label_protocol: PCR assays were performed using the zebrafish larvae-zebrafish mTOR Signaling RT² Profiler™ PCR Array (Qiagen) following the Manufacturer’s instructions.  Reverse transcription was performed from 1000 ng total RNA using SuperScript. III Reverse Transcriptase (invitrogen). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 40 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted using TRIZOL® Reagent (Invitrogen)

tag: developmental stage

value: 10 dpf


title: Wild type zebrafish

description: control


title: HGEC_MEDIUM_rep3

source_name: normal primary human gingival epithelial cells, Treated with MEDIUM, Replicate 3


title: HGEC_DMSO_rep1

source_name: normal primary human gingival epithelial cells, Treated with DMSO, Replicate 1


title: 101B_WZ-CAS_rep1

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated by WZ with DMSO, Replicate 1


title: HGEC_TPM_rep3

source_name: normal primary human gingival epithelial cells, Treated with TPM, Replicate 3


title: 101B_STE14_rep3

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with STE14, Replicate 3


title: 101B_CAS_rep2

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with CAS, Replicate 2


title: SE_15

city: Dublin

last: Henshall

address: 123 St Stephens Green

country: Ireland

institute: Royal College of Surgeons in Ireland

description: NCSE

data_processing:
OpenArray profiling data were analysed in two steps. First, to ensure good quality detection and to avoid false-positives the data were filtered according to “AmpScore” or “CqConf” values provided by the ExpressionSuite software (ThermoFisher Scientific). Cutoff thresholds were set to 35. This gave us a general idea about microRNA expression in CSF. Second, more in depth data analysis was performed in R/Bioconductor (R Core Team, 2016; Huber et al., 2015) and a more stringent “present”/“absent” filtering step was included whereby a microRNA was considered “present” in a set of samples if the Ct was < 28 in 60% of the samples. A microRNA was considered “absent” if the Ct was > 28 in 80% of the same samples. MicroRNA were removed unless they were either present in both control/TLE or control/SE samples, or if they were absent from one set of samples and present in the other. Missing data points were imputed (Bioconductor package “Non-detects” (McCall et al., 2014)), the data was normalised to the geometric mean as implemented in Bioconductor package “HTqPCR” (Dvinge and Bertone, 2009) and corrected for batch effects due to sample origin (Bioconductor package “ComBat” (Johnson et al., 2007)). Differential expression analysis was performed using the limma package (Ritchie et al., 2015). P-values were adjusted for multiple testing by controlling the false discovery rate (FDR) according to the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995).
Matrix normalized worksheet reports geometric mean normalized signal.
Fold Change worksheet reports log2FC, p.value and adj.p.value. FC was calculated as 2^-ΔΔCt, where -ΔΔCt = -[ΔCt_test -Δct_control]. Differential expression analysis was performed using the limma package (Ritchie et al., 2015). P-values were adjusted for multiple testing by controlling the false discovery rate (FDR) according to the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995).

source_name: CSF

label_protocol: 3 µl of total RNA was processed by reverse transcriptase and pre-amplification steps following the manufacturer’s protocol (Applied Biosystems). The pre-amplification reaction was mixed with TaqMan OpenArray Real-Time PCR Master mix (1:1). The mix was loaded onto the OpenArray human panel (755 human miRNAs) using the Accufill System and ran using a QuantStudio 12K Flex PCR (Life Technologies).

extract_protocol: Total RNA was extracted from 200 μl of CSF or plasma using the miRCURY RNA isolation kit-biofluid (Exiqon) according to the manufacturer’s protocol

tag: diagnosis

value: Status epilepticus

value: f

value: cerebral spinal fluid


title: SE_14

description: FSE


title: SE_13

description: FSE

value: m


title: HGEC_MEDIUM_rep1

source_name: normal primary human gingival epithelial cells, Treated with MEDIUM, Replicate 1


title: 101B_STE14_rep2

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with STE14, Replicate 2


title: 101B_WZ-CAS_rep2

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated by WZ with DMSO, Replicate 2


title: HGEC_WS-CM_rep3

source_name: normal primary human gingival epithelial cells, Treated with WS-CM, Replicate 3


title: 101B_CAS_rep3

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with CAS, Replicate 3


title: 101B_STE474_rep2

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with STE474, Replicate 2


title: HGEC_TPM_rep1

source_name: normal primary human gingival epithelial cells, Treated with TPM, Replicate 1


title: SE_12

description: NCSE


title: 101B_STE474_rep3

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with STE474, Replicate 3


title: 101B_STE474_rep1

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with STE474, Replicate 1


title: 101B_WZ-CAS_rep3

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated by WZ with DMSO, Replicate 3


title: HGEC_STE14_rep1

source_name: normal primary human gingival epithelial cells, Treated with STE14, Replicate 1


title: 101B_CAS_rep1

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with CAS, Replicate 1


title: 101B_MEDIUM_rep3

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with MEDIUM, Replicate 3


title: SE_11

description: FSE


title: 101B_MEDIUM_rep2

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with MEDIUM, Replicate 2


title: 101B_MEDIUM_rep1

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with MEDIUM, Replicate 1


title: 101B_WS-CM_rep3

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with WS-CM, Replicate 3


title: SE_8

description: NCSE

source_name: CSF


title: SE_10

description: FSE


title: SE_7

description: FSE


title: SE_6

description: GTC


title: 101B_WS-CM_rep2

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with WS-CM, Replicate 2


title: 101B_STE14_rep1

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with STE14, Replicate 1


title: SE_3

description: FSE


title: SE_4

description: GTC


title: SE_2

description: NCSE


title: SE_1

description: FSE


title: T_15

description: epilepsy

value: Temporal lobe epilepsy


title: T_14

description: epilepsy


title: SE_9

description: GTC


title: T_12

description: epilepsy


title: T_13

description: epilepsy


title: T_11

description: epilepsy


title: SE_5

description: FSE


title: 101B_DMSO_rep3

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with DMSO, Replicate 3


title: 101B_TPM_rep3

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with TPM, Replicate 3


title: T_10

description: epilepsy


title: 101A_NIC474_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with NIC474, Replicate 1


title: 101B_DMSO_rep1

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with DMSO, Replicate 1


title: 101B_WS-CM_rep1

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with WS-CM, Replicate 1


title: T_8

description: epilepsy


title: T_9

description: epilepsy


title: 101A_WZ-DMSO_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated by WZ with DMSO, Replicate 3


title: 101B_TPM_rep1

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with TPM, Replicate 1


title: 101A_NIC474_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with NIC474, Replicate 3


title: 101B_TPM_rep2

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with TPM, Replicate 2


title: 101B_DMSO_rep2

source_name: human oral squamous cell carcinoma Cell Line 101B, Treated with DMSO, Replicate 2


title: 101A_NIC474_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with NIC474, Replicate 2


title: 101A_WZ-DMSO_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated by WZ with DMSO, Replicate 1


title: T_6

description: epilepsy


title: 101A_WZ-DMSO_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated by WZ with DMSO, Replicate 2


title: 101A_NIC14_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with NIC14, Replicate 3


title: T_5

description: epilepsy

source_name: CSF


title: T_4

description: epilepsy


title: T_2

description: epilepsy


title: T_7

description: epilepsy


title: 101A_WZ-CAS_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated by WZ with CAS Replicate 3


title: 101A_NIC14_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with NIC14, Replicate 1


title: 101A_NIC14_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with NIC14, Replicate 2


title: 101A_WZ-CAS_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated by WZ with CAS Replicate 2


title: 101A_STE474_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with STE474, Replicate 2


title: 101A_WZ-CAS_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated by WZ with CAS Replicate 1


title: 101A_STE474_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with STE474, Replicate 1


title: 101A_STE474_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with STE474, Replicate 3


title: T_1

description: epilepsy


title: CH_15

description: Control

value: Control headache


title: CH_12

description: Control


title: CH_9

description: Control


title: CH_13

description: Control


title: 101A_CAS_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with CAS, Replicate 3


title: CH_14

description: Control


title: CH_11

description: Control


title: CH_10

description: Control


title: T_3

description: epilepsy


title: CH_8

description: Control


title: 101A_STE14_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with STE14, Replicate 3


title: CH_7

description: Control


title: CH_5

description: Control


title: 101A_MEDIUM_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with MEDIUM, Replicate 2


title: 101A_MEDIUM_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with MEDIUM, Replicate 3


title: 101A_STE14_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with STE14, Replicate 2


title: 101A_CAS_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with CAS, Replicate 2


title: 101A_STE14_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with STE14, Replicate 1


title: 101A_WS-CM_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with WS-CM, Replicate 3


title: CH_4

description: Control

source_name: CSF


title: CH_3

description: Control


title: CH_1

description: Control


title: 101A_MEDIUM_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with MEDIUM, Replicate 1


title: CH_6

description: Control


title: Wild type zebrafish

description: control

source_name: larvae

label_protocol: PCR assays were performed using the zebrafish larvae-zebrafish PI3K-AKT Signaling Pathway RT2 Profiler PCR Array (Qiagen) following the Manufacturer’s instructions.  Reverse transcription was performed from 1000 ng total RNA using SuperScript. III Reverse Transcriptase (invitrogen). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.


title: NOD1-deficient zebrafish

description: Test


title: 101A_WS-CM_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with WS-CM, Replicate 2


title: 101A_CAS_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with CAS, Replicate 1


title: 101A_WS-CM_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with WS-CM, Replicate 1


title: CH_2

description: Control


title: Foreskin Dermal fibroblasts from 1 year old patient

city: Iowa City

first: Kranti

middle: A

last: Mapuskar

state: Iowa

address: 500 Newton Road

department: Radiation Oncology

institute: University of Iowa

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes: 2^-deltaCt, where deltaCt = (Ct_Target - Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control ratios: normalized gene expression (2^(- Delta Ct)) in the Test Sample divided the normalized gene expression (2^(- Delta Ct)) in the Control Sample
Fold-Regulation represents fold-change results in a biologically meaningful way. Fold-change values greater than one indicate a positive- or an up-regulation, and the fold-regulation is equal to the fold-change for values > 1. For Fold-change values < 1, values have been transformed to -1/VALUE.

source_name: Foreskin

label_protocol: PCR assays were performed using the Mitochondria Energy Metabolism PCR array panel from Qiagen (PAHS008Z) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: foreskin

value: primary dermal fibroblasts

value: 1 year old


title: Foreskin Dermal fibroblasts from 5 month old patient

description: Control

value: 5 months old


title: 101A_DMSO_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with DMSO, Replicate 3


title: 101A_DMSO_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with DMSO, Replicate 1


title: 101A_DMSO_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with DMSO, Replicate 2


title: 101A_TPM_rep2

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with TPM, Replicate 2


title: 101A_TPM_rep3

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with TPM, Replicate 3


title: 101A_TPM_rep1

source_name: human oral squamous cell carcinoma Cell Line 101A, Treated with TPM, Replicate 1


title: 5004: Diagnosis AML

status: Public on Jun 22 2017

city: Rotterdam

first: Nicole

last: Larmonie

address: Wytemaweg

country: Netherlands

institute: ErasmusMC

description:
CpG island array screening
Reference: Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)

hyb_protocol: The Oligo aCGH/ChiP-on-chip Hybridization Kit was used according the protocol to hybridize the labeled gDNA onto the microarrays enclosed in the Agilent SureHyb-enabled hybridization chambers. After o/n hybridization, slides were washed according to protocol o/n.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (V10.5.1.1) for data extraction. The R and Bioconductor statistical environment (version 2.10.0) were used for quality control and LOESS normalization (limma package). No background correction was performed.

source_name: Peripheral Blood

label_protocol: 500ng genomic DNA was cut with MseI, generating 200-800bp fragments. These fragments were ligated to linkers and cut with two methylation-sensitive restriction enzymes (BstuI and HpaII), cutting all the unmethylated fragments. Methylated CpG-island fragments were afterwards amplified by linker-PCR. Amplicons were labeled with Cy5 (patient samples) and Cy3 (common reference samples) fluorescent dye using the BioPrime Array-CGH Genomic Labeling kit (Invitrogen, Carlsbad, USA).

extract_protocol: Genomic DNA  was extracted using Trizol reagent according to manufacturer's instructions.

value: Female

tag: diagniosis

value: AML

tag: fab

tag: type 2 molecular aberration

source_name: Common Reference Samples

value: Normal


title: 5154: Diagnosis AML

source_name: Unknown

value: Male


title: 3444: Diagnosis AML

value: unknown


title: 3455: Diagnosis AML

source_name: Bone Marrow


title: 7556: Diagnosis AML


title: 5177: Diagnosis AML


title: 3411: Diagnosis AML


title: 1311: Diagnosis AML


title: 7153: Diagnosis AML


title: 8386: Diagnosis AML


title: 8357: Diagnosis AML

value: Unknown


title: 7328: Diagnosis AML


title: 3437: Diagnosis AML

value: NPM1 mutations


title: 4734: Diagnosis AML


title: 4740: Diagnosis AML


title: 5127: Diagnosis AML


title: 7325: Diagnosis AML


title: 8658: Diagnosis AML


title: 7321: Diagnosis AML


title: 7812: Diagnosis AML


title: 4745: Diagnosis AML


title: 3435: Diagnosis AML


title: 4805: Diagnosis AML


title: 5057: Diagnosis AML


title: 4744: Diagnosis AML


title: 8320: Diagnosis AML


title: 6328: Diagnosis AML


title: 8322: Diagnosis AML

value: s-AML


title: 4394: Diagnosis AML


title: 4370: Diagnosis AML


title: 4730: Diagnosis AML


title: 4559: Diagnosis AML


title: 5120: Diagnosis AML


title: 7515: Diagnosis AML


title: 3495: Diagnosis AML


title: 4297: Diagnosis AML


title: 4936: Diagnosis AML

value: C/EPBα (double mutation)


title: 3450: Diagnosis AML


title: 4128: Diagnosis AML


title: 3439: Diagnosis AML


title: 7912: Diagnosis AML


title: 4451: Diagnosis AML


title: 4432: Diagnosis AML


title: 4392: Diagnosis AML


title: 4098: Diagnosis AML


title: 3434: Diagnosis AML


title: 8723: Diagnosis AML


title: 4412: Diagnosis AML


title: 4742: Diagnosis AML


title: 4418: Diagnosis AML


title: 4445: Diagnosis AML


title: 5064: Diagnosis AML


title: 3494: Diagnosis AML


title: 5032: Diagnosis AML


title: 7961: Diagnosis AML


title: 8356: Diagnosis AML


title: 4373: Diagnosis AML


title: 3443: Diagnosis AML


title: 3399: Diagnosis AML


title: 4712: Diagnosis AML


title: 3410: Diagnosis AML


title: 8281: Diagnosis AML


title: 8355: Diagnosis AML


title: 4089: Diagnosis AML


title: 5061: Diagnosis AML


title: 3828: Diagnosis AML


title: 4217: Diagnosis AML


title: 3471: Diagnosis AML


title: 4737: Diagnosis AML


title: 3398: Diagnosis AML


title: 3442: Diagnosis AML


title: 4450: Diagnosis AML


title: 3465: Diagnosis AML


title: 7339: Diagnosis AML


title: 4087: Diagnosis AML


title: 7514: Diagnosis AML


title: 7332: Diagnosis AML


title: 5236: Diagnosis AML

value: PML-RARA


title: 5185: Diagnosis AML


title: 7180: Diagnosis AML


title: 5178: Diagnosis AML


title: 5170: Diagnosis AML


title: 5169: Diagnosis AML


title: 5157: Diagnosis AML


title: 5166: Diagnosis AML


title: 5119: Diagnosis AML


title: 5143: Diagnosis AML


title: 5160: Diagnosis AML


title: 5145: Diagnosis AML


title: 7327: Diagnosis AML


title: 5144: Diagnosis AML


title: 5048: Diagnosis AML


title: 5148: Diagnosis AML


title: 5036: Diagnosis AML


title: 5130: Diagnosis AML


title: 5065: Diagnosis AML


title: 5031: Diagnosis AML


title: 5013: Diagnosis AML


title: 5033: Diagnosis AML


title: 4770: Diagnosis AML


title: 5056: Diagnosis AML


title: 506: Diagnosis AML


title: 5012: Diagnosis AML


title: 5005: Diagnosis AML


title: 4728: Diagnosis AML


title: 4905: Diagnosis AML


title: 4714: Diagnosis AML


title: 4715: Diagnosis AML


title: 4713: Diagnosis AML


title: 4710: Diagnosis AML


title: 4746: Diagnosis AML


title: 4720: Diagnosis AML


title: 4704: Diagnosis AML


title: 4701: Diagnosis AML


title: 4700: Diagnosis AML


title: 4557: Diagnosis AML


title: 4560: Diagnosis AML


title: 4549: Diagnosis AML


title: 4395: Diagnosis AML


title: 4409: Diagnosis AML


title: 4448: Diagnosis AML


title: 4425: Diagnosis AML


title: 4382: Diagnosis AML


title: 4416: Diagnosis AML


title: 4576: Diagnosis AML


title: 4533: Diagnosis AML


title: 4400: Diagnosis AML


title: 4536: Diagnosis AML


title: 4102: Diagnosis AML


title: 4396: Diagnosis AML


title: 4082: Diagnosis AML


title: 3446: Diagnosis AML


title: 3470: Diagnosis AML


title: 4096: Diagnosis AML


title: 4405: Diagnosis AML


title: 3451: Diagnosis AML


title: set1DDam.mst2_2239_2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: data column in DamID_results.txt file: set1DDam.mst2_2239_2_vs_Damonly_spb492_2

hyb_protocol: Hybridization was performed for 16h at 45°C and 60rpm in an Affymetrix hybridization oven; washing steps were done in an Affymetrix Fluidics station with the Affymetrix protocol FS450_0002

scan_protocol: GeneChips were scanned with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing:
Oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R. Contrasts were computed on the oligo level by subtracting respective columns of expression. Differential expression values for individual features in the file sPombegenomicelementsV02_ALL.txt were calculated by averaging enrichment values for all the oligos overlapping the individual features, considering only features covered by at least 50 oligos. This produces the DamID_results.txt file [contains all 8014 features for which DamID enrichment was calculated, with a separate column for each of the 4 contrasts].
All results file are summarised in DamID_results.txt file
DamID_results.txt is a table containing all 17910 features for which DamID enrichment was calculated with a separate column for each of the 14 contrasts

organism: Schizosaccharomyces pombe

source_name: Dam fused to Mst2 in set1D cells

label_protocol: The DNA was fragmented and labeled using the Affymetrix GeneChip® GeneChip Hybridization, Wash, and Stain Kit according to the manufactuer's instructions

growth_protocol: Cells were grown to early exponential phase (OD=0.4) and harvested.

extract_protocol: Genomic DNA isolated using Dneasy Blood and Tissue Kit (Qiagen)

treatment_protocol: Harvested cells were spheroplasted to remove cell wall

tag: expression

tag: genotype

tag: strain number


title: set1DDam.mst2_2239_1

description: data column in DamID_results.txt file: set1DDam.mst2_2239_1_vs_Damonly_spb492_1


title: set2DDam.mst2_2220_2

description: data column in DamID_results.txt file: set2DDam.mst2_2220_2_vs_Damonly_spb492_2

source_name: Dam fused to Mst2 in set2D cells


title: set2DDam.mst2_2220_1

description: data column in DamID_results.txt file: set2DDam.mst2_2220_1_vs_Damonly_spb492_1


title: 4216: Diagnosis AML


title: pdp3DDam.mst2_2212_2

description: data column in DamID_results.txt file: pdp3DDam.mst2_2212_2_vs_Damonly_spb492_2

source_name: Dam fused to Mst2 in pdp3D cells


title: 4601: Diagnosis AML


title: 3441: Diagnosis AML


title: 4084: Diagnosis AML


title: 3438: Diagnosis AML


title: 4733: Diagnosis AML


title: pdp3DDam.mst2_2212_1

description: data column in DamID_results.txt file: pdp3DDam.mst2_2212_1_vs_Damonly_spb492_1


title: 4079: Diagnosis AML


title: Dam.mst2_spb2104_1

description: data column in DamID_results.txt file: Dam.mst2_spb2104_1_vs_Damonly_spb492_1

source_name: Dam fused to Mst2 in WT cells

value: WT


title: Dam.mst2pdp3D_spb2212.3

description: data column in DamID_results.txt file: Dam.mst2pdp3D_spb2212.3_vs_Damonly_492.1


title: Dam.mst2pdp3D_spb2212.2

description: data column in DamID_results.txt file: Dam.mst2pdp3D_spb2212.2_vs_Damonly_492.2


title: Dam.mst2_2104.3

description: data column in DamID_results.txt file: Dam.mst2_2104.3_vs_Damonly_492.2


title: Dam.mst2pdp3D_spb2212.1

description: data column in DamID_results.txt file: Dam.mst2pdp3D_spb2212.1_vs_Damonly_492.1