title: Cerebellum Oxidative Bisulfite Treated, LBB5H.OXCE

status: Public on Nov 30 2015

type: genomic

city: Exeter

first: Rebecca

middle: Georgina

last: Smith

state: Devon

address: RILD, RD and E

department: Medical School

country: United Kingdom

institute: University of Exeter

description: Sample name: LBB5H.OXCE

hyb_protocol: Illumina Infinium protocol.

scan_protocol: Illumina Infinium protocol. Scanned using Illumina HiScan System.

data_processing: Data loaded into R using methylumi, quantile normalised using Dasen function within wateRmelon (version 1.4.0).

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Cerebellum, oxidative bisulfite

label_protocol: Illumina Infinium protocol.

extract_protocol: Phenol chloroform DNA extraction.

treatment_protocol: Prefrontal cortex and cerebellum samples were sulfite treated or oxidative bisulfite treated.

tag: disease state

value: no evidence of neurological impairment

tag: tissue

value: cerebellum

tag: gender

value: female

tag: treatment

value: oxidative bisulfite

tag: donor id

tag: sentrixid


title: Cerebellum Oxidative Bisulfite Treated, LBB6H.OXCE

description: Sample name: LBB6H.OXCE

value: male


title: Cerebellum Bisulfite Treated, LBB6H.BSCE

description: Sample name: LBB6H.BSCE

source_name: Cerebellum, bisulfite

value: bisulfite


title: Prefrontal Cortex Bisulfite Treated, LBB6A.BSCE

description: Sample name: LBB6A.BSCE

source_name: Prefrontal cortex, bisulfite

value: prefrontal cortex


title: Cerebellum Bisulfite Treated, LBB4H.BSCE

description: Sample name: LBB4H.BSCE


title: Cerebellum Oxidative Bisulfite Treated, LBB1H.OXCE

description: Sample name: LBB1H.OXCE


title: Prefrontal Cortex Oxidative Bisulfite Treated, LBB5A.OXCE

description: Sample name: LBB5A.OXCE

source_name: Prefrontal cortex, oxidative bisulfite


title: Prefrontal Cortex Oxidative Bisulfite Treated, LBB47A.OXCE

description: Sample name: LBB47A.OXCE


title: Cerebellum Oxidative Bisulfite Treated, CEGX CTL.2.OXCE

description: Sample name: CEGX CTL.2.OXCE

value: CEGX control


title: Cerebellum Bisulfite Treated, CEGX CTL.1.BSCE

description: Sample name: CEGX CTL.1.BSCE


title: Cerebellum Bisulfite Treated, CEGX CTL.2.BSCE

description: Sample name: CEGX CTL.2.BSCE


title: Cerebellum Bisulfite Treated, LBB44H.BSCE

description: Sample name: LBB44H.BSCE


title: Prefrontal Cortex Bisulfite Treated, LBB5A.BSCE

description: Sample name: LBB5A.BSCE


title: Cerebellum Oxidative Bisulfite Treated, CEGX CTL.1.OXCE

description: Sample name: CEGX CTL.1.OXCE


title: Cerebellum Bisulfite Treated, LBB5H.BSCE

description: Sample name: LBB5H.BSCE


title: Prefrontal Cortex Oxidative Bisulfite Treated, LBB1A.OXCE

description: Sample name: LBB1A.OXCE


title: Cerebellum Oxidative Bisulfite Treated, LBB47H.OXCE

description: Sample name: LBB47H.OXCE


title: Prefrontal Cortex Oxidative Bisulfite Treated, LBB6A.OXCE

description: Sample name: LBB6A.OXCE


title: Cerebellum Oxidative Bisulfite Treated, LBB44H.OXCE

description: Sample name: LBB44H.OXCE


title: Cerebellum Bisulfite Treated, LBB1H.BSCE

description: Sample name: LBB1H.BSCE


title: Cerebellum Oxidative Bisulfite Treated, LBB4H.OXCE

description: Sample name: LBB4H.OXCE


title: Prefrontal Cortex Oxidative Bisulfite Treated, LBB44A.OXCE

description: Sample name: LBB44A.OXCE


title: Prefrontal Cortex Bisulfite Treated, LBB47A.BSCE

description: Sample name: LBB47A.BSCE


title: Cerebellum Bisulfite Treated, LBB47H.BSZY

description: Sample name: LBB47H.BSZY


title: Cerebellum Bisulfite Treated, LBB47H.BSCE

description: Sample name: LBB47H.BSCE


title: Prefrontal Cortex Bisulfite Treated, LBB44A.BSCE

description: Sample name: LBB44A.BSCE


title: Prefrontal Cortex Bisulfite Treated, LBB1A.BSCE

description: Sample name: LBB1A.BSCE


title: Cerebellum Bisulfite Treated, LBB4H.BSZY

description: Sample name: LBB4H.BSZY


title: Cerebellum Bisulfite Treated, LBB5H.BSZY

description: Sample name: LBB5H.BSZY


title: Cerebellum Bisulfite Treated, LBB1H.BSZY

description: Sample name: LBB1H.BSZY


title: Cerebellum Bisulfite Treated, LBB44H.BSZY

description: Sample name: LBB44H.BSZY


title: Prefrontal Cortex Bisulfite Treated, LBB44A.BSZY

description: Sample name: LBB44A.BSZY


title: Prefrontal Cortex Bisulfite Treated, LBB5A.BSZY

description: Sample name: LBB5A.BSZY


title: Prefrontal Cortex Bisulfite Treated, LBB6A.BSZY

description: Sample name: LBB6A.BSZY


title: Prefrontal Cortex Bisulfite Treated, LBB47A.BSZY

description: Sample name: LBB47A.BSZY


title: Cell Line_SF_268

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

description: cell line

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

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

data_processing:
Genome Studio V2011.2
Average Beta, Detection P-value, Unmethylated and Methylated Signal Intensities
The NCI60_DataMatrix.txt contains both processed and raw data (Average Beta, Detection P-value, Unmethylated and Methylated Signal Intensities).

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: cell line

tag: cell type

value: Glioma

tag: -log(ic50) cisplatin (m)

tag: -log(ic50) carboplatin (m)


title: Cerebellum Bisulfite Treated, LBB6H.BSZY

description: Sample name: LBB6H.BSZY


title: Prefrontal Cortex Bisulfite Treated, LBB4A.BSZY

description: Sample name: LBB4A.BSZY


title: Sample2_NPC_4F

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

country: USA

institute: UCSD

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting

data_processing: Samples were normalized and filtered using the statistical programming language R (http://www.r-project.org/) (v.3.0.1) and the R package minfi (v.1.6.0). Briefly, samples were first control-normalized using Illumina’s internal bead controls and probes with a detection P value > 0.01 in at least one sample were discarded. The samples were then SWAN normalized using the minfi package and β values (Methylated allele intensity/ Unmethylated allele intensity + Methylated allele intensity) were exported. Probes with less than a max β – min β of 0.5 were removed

label: Cy5 and Cy3

source_name: iPSC-derived human Neural Progenitor Cell, inhibition of the PI3K and MAPK signaling pathways

label_protocol: Standard Illumina Protocol

growth_protocol: Neurobasal media (Invitrogen) supplemented with N2 (Invitrogen), B27 (Invitrogen), and FGF2 (10 ng/ml; preprotech)

extract_protocol: DNA was isolated using the DNeasy kit (69504, Qiagen), quantified (Qubit dsDNA BR Assay Kits, Life Technologies, Inc.) and bisulfite converted (EZDNA Methylation Kit, Zymo Research) according to the manufacturer’s protocol.

value: Neural Progenitor Cell

value: Inhibitionition of PI3K and MAPK signaling pathways

value: iPSC derived


title: Cell Line_BT_549

description: cell line

value: Breast Ductal Carcinoma


title: Sample4_NS27Z_B_AB0789

source_name: human Glioma Tumor Initiating Cells

value: Glioma Stem Cell

value: No Treatment

value: Derived by Pollard et al., 2009 Cell Stem Cell, GNS G179. Deposited by Steve Pollard, Austin Smith, Peter Dirks and Ian Clarke at the biorep S.r.l. Catalog number NS00011*B


title: Cell Line_RXF393

description: cell line

value: Renal Cell Carcinoma


title: Cell Line_NCI_H460

description: cell line

value: Lung Large Cell Carcinoma


title: Sample3_NPC_wt

source_name: iPSC-derived human Neural Progenitor Cell


title: Sample1_NPC_4FP53

source_name: iPSC-derived human Neural Progenitor Cell, P53 knockdown and inhibition of the PI3K and MAPK signaling pathways

value: Inhibition of P53 and PI3K and MAPK signaling pathways


title: Cell Line_DU_145

description: cell line

value: Prostate Adenocarcinoma


title: Cell Line_LOXIMVI

description: cell line

source_name: LOXIMVI

value: LOXIMVI

value: Malignant Melanoma


title: Cell Line_A549

description: cell line

value: Lung Non Small Cell Carcinoma


title: Cell Line_SK_MEL_5

description: cell line


title: Cell Line_SF_539

description: cell line


title: Cell Line_HOP_92

description: cell line


title: Cell Line_NCI_H226

description: cell line

value: Lung Squamous Cell Carcinoma


title: Cell Line_786_0

description: cell line

value: Renal Tumor Clear Cell


title: Cell Line_KM12

description: cell line

value: Colon Adenocarcinoma


title: Cell Line_HOP_62

description: cell line

value: Lung Adenocarcinoma


title: Cell Line_MDA_MB_468

description: cell line

value: Breast Carcinoma


title: Cell Line_ACHN

description: cell line

source_name: ACHN

value: ACHN


title: Cell Line_SN12C

description: cell line


title: Cell Line_SF_295

description: cell line

value: Glioma


title: Cell Line_T47D

description: cell line

value: Breast Ductal Carcinoma


title: Cell Line_SNB_75

description: cell line


title: Cell Line_SK_MEL_2

description: cell line


title: Cell Line_RPMI_8226

description: cell line

value: Plasma Cell Myeloma


title: Prefrontal Cortex Bisulfite Treated, LBB1A.BSZY

description: Sample name: LBB1A.BSZY

value: no evidence of neurological impairment

value: prefrontal cortex

value: female

value: bisulfite


title: Cell Line_UO_31

description: cell line

value: Renal Cell Carcinoma


title: Cell Line_TK_10

description: cell line


title: Cell Line_OVCAR_8

description: cell line

value: Ovary Carcinoma


title: Cell Line_IGROV1

description: cell line


title: Cell Line_NCI_H522

description: cell line


title: Cell Line_SNB_19

description: cell line

value: Astrocytoma


title: Cell Line_SK_MEL_28

description: cell line

value: Malignant Melanoma


title: Cell Line_OVCAR_4

description: cell line


title: Cell Line_MDA_MB_231

description: cell line


title: Cell Line_HCT_15

description: cell line

value: Colorectal Carcinoma


title: Cell Line_MOLT_4

description: cell line

value: Acute Lymphoblastic Leukemia


title: Cell Line_COLO205

description: cell line

value: Colon Adenocarcinoma


title: Cell Line_CAKI_1

description: cell line

value: Renal Tumor Clear Cell


title: Cell Line_NCI_H322M

description: cell line

value: Lung Bronchioloalveolar Adenocarcinoma


title: Cell Line_MDA_MB_435

description: cell line


title: Cell Line_MCF7

description: cell line

value: Breast Carcinoma


title: Cell Line_OVCAR 3

description: cell line

source_name: OVCAR 3

value: OVCAR 3

value: Ovary Adenocarcinoma


title: Cell Line_U251

description: cell line

value: Glioma


title: Cell Line_UACC_62

description: cell line


title: Cell Line_SW_620

description: cell line


title: Cell Line_NCI_H23

description: cell line

value: Lung Non Small Cell Carcinoma


title: Cell Line_HCT_116

description: cell line


title: Cell Line_M14

description: cell line


title: Cell Line_OVCAR_5

description: cell line


title: Cell Line_EKVX

description: cell line

source_name: EKVX

value: EKVX

value: Lung Adenocarcinoma


title: Cell Line_NCI_ADR_RES

description: cell line


title: Cell Line_A498

description: cell line

value: Renal Carcinoma


title: Cell Line_CCRF_CEM

description: cell line


title: Cell Line_PC_3

description: cell line

value: Prostate Adenocarcinoma


title: Cell Line_HL_60

description: cell line

value: Acute Leukemia


title: Cell Line_HT29

description: cell line


title: Cell Line_SK_OV_3

description: cell line


title: genomic DNA from lung tissue123

city: Vienna

first: Matthias

last: Wielscher

address: Muthgasse 11

department: Health and Enviroment

country: Austria

institute: Austrian Institute of Technology

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
The Avrg_Beta.txt contains Average Beta values.
The non_normalized.txt contains Unmethylated and methylated signal intensities.

source_name: diseased lung tissue

extract_protocol: genomic DNA was extracted and purified from snap frozen lung tissue biopsy samples using Qiagen All-Prep Kit according to standard instructions

tag: patient group

value: Cancer

tag: sample type

value: tissue biopsy

value: AdenoCa


title: Cell Line_MALME_3M

description: cell line

value: Malignant Melanoma


title: genomic DNA from lung tissue129


title: genomic DNA from lung tissue124


title: Cell Line_HCC_2998

description: cell line

value: Colon Adenocarcinoma


title: genomic DNA from lung tissue121

value: SqCCL


title: genomic DNA from lung tissue127

source_name: heatlhy matched tissue for sample_102

value: healthy


title: genomic DNA from lung tissue118

source_name: heatlhy matched tissue for sample_114


title: genomic DNA from lung tissue125


title: Cell Line_UACC_257

description: cell line


title: genomic DNA from lung tissue126

source_name: heatlhy matched tissue for sample_110


title: Cell Line_K_562

description: cell line

value: Chronic Myeloid Leukemia


title: genomic DNA from lung tissue128


title: genomic DNA from lung tissue117

source_name: heatlhy matched tissue for sample_129


title: genomic DNA from lung tissue112

source_name: heatlhy matched tissue for sample_107


title: Cell Line_HS578T

description: cell line

value: Breast Carcinoma


title: genomic DNA from lung tissue116


title: genomic DNA from lung tissue115


title: genomic DNA from lung tissue119

source_name: heatlhy matched tissue for sample_124


title: genomic DNA from lung tissue111

source_name: heatlhy matched tissue for sample_109


title: genomic DNA from lung tissue108

source_name: heatlhy matched tissue for sample_100


title: genomic DNA from lung tissue107


title: genomic DNA from lung tissue114


title: genomic DNA from lung tissue120

source_name: heatlhy matched tissue for sample_106


title: genomic DNA from lung tissue109


title: genomic DNA from lung tissue113


title: genomic DNA from lung tissue110


title: genomic DNA from lung tissue103

source_name: heatlhy matched tissue for sample_125


title: genomic DNA from lung tissue104

source_name: heatlhy matched tissue for sample_96


title: genomic DNA from lung tissue99

source_name: heatlhy matched tissue for sample_115


title: Cell Line_SR

description: cell line

source_name: SR

value: SR

value: Lymphoid Neoplasm


title: genomic DNA from lung tissue102


title: genomic DNA from lung tissue122

source_name: heatlhy matched tissue for sample_121


title: genomic DNA from lung tissue105

source_name: heatlhy matched tissue for sample_123


title: genomic DNA from lung tissue92

value: COPD


title: genomic DNA from lung tissue94


title: genomic DNA from lung tissue101

source_name: heatlhy matched tissue for sample_116


title: genomic DNA from lung tissue90

source_name: diseased lung tissue


title: genomic DNA from lung tissue100


title: genomic DNA from lung tissue91

source_name: nomal lung tissue


title: genomic DNA from lung tissue86


title: genomic DNA from lung tissue106


title: genomic DNA from lung tissue88


title: genomic DNA from lung tissue85


title: genomic DNA from lung tissue87


title: genomic DNA from lung tissue82


title: genomic DNA from lung tissue84


title: genomic DNA from lung tissue83


title: genomic DNA from lung tissue98

source_name: heatlhy matched tissue for sample_113


title: genomic DNA from lung tissue81


title: genomic DNA from lung tissue89


title: genomic DNA from lung tissue76


title: genomic DNA from lung tissue93


title: genomic DNA from lung tissue77


title: genomic DNA from lung tissue78


title: genomic DNA from lung tissue79


title: genomic DNA from lung tissue75


title: genomic DNA from lung tissue65


title: H3 X E3- DYE-SWAP ARRAY 5

type: RNA

city: Rio de Janeiro

first: Leandra

middle: Linhares

last: Lacerda

state: RJ

address: Av. Brasil 4365 pav 26 sala 506 Manguinhos

department: Oswaldo Cruz Institution

country: Brazil

institute: Oswaldo Cruz Foundation

description: Biological replicate 3 of 3, technical replicate 2 of 2. TEC without supernatant/TEC + T cell non-infected supernatant (CEM)

hyb_protocol: Hybridization and washing were performed according to the manufacturer's instructions (Agilent Technologies).

scan_protocol: Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA).

data_processing: Intensities were extracted using the Agilent Feature Extraction software (AFE, version A.9.5.3) with standard protocols and options. The pre-processing and differential expression analysis of gene expression data were performed in the R programming environment and processed using Bioconductor (http://www.bioconductor.com) Agi4x44PreProcess library. Normalized data were scaled by the quantile method and filtered to 1) maintain intensities within the dynamic range of the scanner (elimination of saturated points); and 2) retain genetic data of good quality. The library of the Bioconductor hgug4112a.db was used to assign the access code for the gene (ENTREZ ID) corresponding to each probe Agilent. Differential expression was analyzed with the limma library in empirical Bayesian methods.

molecule: total RNA

source_name: TEC without supernatant-replicate 3

label_protocol: We used 400 ng of total RNA of three independent samples for each condition, using two-color hybridizations with dye-swap in a 4 X 44K Agilent Whole Human Gene Microarray (G4112F, Agilent Technologies). Labeling was performed according to the manufacturer's instructions (Agilent Technologies).

growth_protocol: All cells were cultivated in RPMI (Sigma) supplemented with 10% of fetal bovine serum (FBS) (GIBCO) in 5% of CO2, 37°C in humidity and for CIB we supplemented the medium with 50 units/mL of IL-2 (Sigma).

extract_protocol: Total RNA from TECs was extracted with TRIreagent (Sigma-Aldrich) according to the manufacturer’s protocol. Total RNA concentration and quality was measured using NanoDrop (Thermo Scientific) and 2100 Bioanalyzer (Agilent Technologies), respectively.

treatment_protocol: Thymic Epithelial Cell (TEC) were in contact with the supernatant from CEM, CIB or C91PL for 1.5 hour at 37°C and then washed with PBS.

value: THF

tag: supernatant from t cell line

source_name: TEC + T cell non-infected supernatant (CEM)-replicate 3

value: CEM


title: E3 X H3

description: Biological replicate 3 of 3, technical replicate 1 of 2. TEC + T cell non-infected supernatant (CEM)/TEC without supernatant


title: genomic DNA from lung tissue69


title: genomic DNA from lung tissue72


title: genomic DNA from lung tissue95


title: genomic DNA from lung tissue74


title: genomic DNA from lung tissue64


title: H2 X E2- DYE-SWAP ARRAY 3

description: Biological replicate 2 of 3, technical replicate 2 of 2. TEC without supernatant/TEC + T cell non-infected supernatant (CEM)

source_name: TEC without supernatant-replicate 2

source_name: TEC + T cell non-infected supernatant (CEM)-replicate 2


title: genomic DNA from lung tissue68


title: genomic DNA from lung tissue70


title: genomic DNA from lung tissue80


title: genomic DNA from lung tissue57


title: genomic DNA from lung tissue71


title: genomic DNA from lung tissue62


title: genomic DNA from lung tissue61


title: genomic DNA from lung tissue96


title: H1 X E1- DYE-SWAP ARRAY 1

description: Biological replicate 1 of 3, technical replicate 2 of 2. TEC without supernatant/TEC + T cell non-infected supernatant (CEM)

source_name: TEC without supernatant-replicate 1

source_name: TEC + T cell non-infected supernatant (CEM)-replicate 1


title: E1 X H1

description: Biological replicate 1 of 3, technical replicate 1 of 2. TEC + T cell non-infected supernatant (CEM)/TEC without supernatant


title: genomic DNA from lung tissue73


title: genomic DNA from lung tissue59


title: genomic DNA from lung tissue60


title: genomic DNA from lung tissue67


title: G3 X F3- DYE-SWAP ARRAY 18

description: Biological replicate 3 of 3, technical replicate 2 of 2. TEC + T cell-infected supernatant (C91PL)/TEC + T cell-infected supernatant (CIB)

source_name: TEC + T cell-infected supernatant (C91PL)-replicate 3

source_name: TEC + T cell-infected supernatant (CIB)-replicate 3

value: CIB


title: genomic DNA from lung tissue56


title: F3 X E3- DYE-SWAP ARRAY 17

description: Biological replicate 3 of 3, technical replicate 2 of 2. TEC + T cell-infected supernatant (CIB)/TEC + T cell non-infected supernatant (CEM)


title: genomic DNA from lung tissue55


title: genomic DNA from lung tissue66


title: genomic DNA from lung tissue53


title: genomic DNA from lung tissue63


title: genomic DNA from lung tissue54


title: genomic DNA from lung tissue97

source_name: heatlhy matched tissue for sample_128


title: F3 X G3

description: Biological replicate 3 of 3, technical replicate 1 of 2. TEC + T cell-infected supernatant (CIB)/TEC + T cell-infected supernatant (C91PL)


title: F2 X E2- DYE-SWAP ARRAY 9

description: Biological replicate 2 of 3, technical replicate 2 of 2. TEC + T cell-infected supernatant (CIB)/TEC + T cell non-infected supernatant (CEM)

source_name: TEC + T cell-infected supernatant (CIB)-replicate 2


title: E2 X G2- DYE-SWAP ARRAY 11

description: Biological replicate 2 of 3, technical replicate 2 of 2. TEC + T cell non-infected supernatant (CEM)/TEC + T cell-infected supernatant (C91PL)

source_name: TEC + T cell-infected supernatant (C91PL)-replicate 2


title: E2 X H2

description: Biological replicate 2 of 3, technical replicate 1 of 2. TEC + T cell non-infected supernatant (CEM)/TEC without supernatant


title: genomic DNA from lung tissue52


title: G2 X F2- DYE-SWAP ARRAY 10

description: Biological replicate 2 of 3, technical replicate 2 of 2. TEC + T cell-infected supernatant (C91PL)/TEC + T cell-infected supernatant (CIB)


title: E3 X G3- DYE-SWAP ARRAY 19

description: Biological replicate 3 of 3, technical replicate 2 of 2. TEC + T cell non-infected supernatant (CEM)/TEC + T cell-infected supernatant (C91PL)


title: G2 X E2

description: Biological replicate 2 of 3, technical replicate 1 of 2. TEC + T cell-infected supernatant (C91PL)/TEC + T cell non-infected supernatant (CEM)


title: E2 X F2

description: Biological replicate 2 of 3, technical replicate 1 of 2. TEC + T cell non-infected supernatant (CEM)/TEC + T cell-infected supernatant (CIB)


title: F2 X G2

description: Biological replicate 2 of 3, technical replicate 1 of 2. TEC + T cell-infected supernatant (CIB)/TEC + T cell-infected supernatant (C91PL)


title: genomic DNA from lung tissue58


title: E3 X F3

description: Biological replicate 3 of 3, technical replicate 1 of 2. TEC + T cell non-infected supernatant (CEM)/TEC + T cell-infected supernatant (CIB)


title: E1 X G1- DYE-SWAP ARRAY 3

description: Biological replicate 1 of 3, technical replicate 2 of 2.TEC + T cell non-infected supernatant (CEM)/TEC + T cell-infected supernatant (C91PL)

source_name: TEC + T cell-infected supernatant (C91PL)-replicate 1


title: G1 X F1- DYE-SWAP ARRAY 2

description: Biological replicate 1 of 3, technical replicate 2 of 2. TEC + T cell-infected supernatant (C91PL)/TEC + T cell-infected supernatant (CIB)

source_name: TEC + T cell-infected supernatant (CIB)-replicate 1


title: F1 X E1- DYE-SWAP ARRAY 1

description: Biological replicate 1 of 3, technical replicate 2 of 2. TEC + T cell-infected supernatant (CIB)/TEC + T cell non-infected supernatant (CEM)


title: genomic DNA from lung tissue49


title: genomic DNA from lung tissue47


title: genomic DNA from lung tissue50


title: genomic DNA from lung tissue48


title: G1 X E1

description: Biological replicate 1 of 3, technical replicate 1 of 2.TEC + T cell-infected supernatant (C91PL)/TEC + T cell non-infected supernatant (CEM)


title: F1 X G1

description: Biological replicate 1 of 3, technical replicate 1 of 2. TEC + T cell-infected supernatant (CIB)/TEC + T cell-infected supernatant (C91PL)


title: G3 X E3

description: Biological replicate 3 of 3, technical replicate 1 of 2. TEC + T cell-infected supernatant (C91PL)/TEC + T cell non-infected supernatant (CEM)


title: Burkitt Lymphoma EBVpositive 6

city: Santander

first: Lorena

last: Di Lisio

address: Avda Cardenal Herrera Oria s/n

institute: IFIMAV

hyb_protocol: Hybridization settings: 20 hours, at 55ºC, at 20rpm. Blocking agent, hybridization and washing buffers was performed according to agilent recomandation.

scan_protocol: Scanning was carried out immediately after washings using the Microarray Scanner System (Agilent Technologies G2565AA). Scan resolution 5um

data_processing:
A script was used for quantile normalization using R programme. Groups of sample were compared using a t-test corrected for multiple testing
Normalized quantile signal intensity is provided for each microRNA

source_name: Tumour-Fresh frozen sample

label_protocol: 100ng of total RNA were dephosphorilated, denaturalizated, treated with ligase T4 and labelled with Cy3 for 2 hours at 16ºC

extract_protocol: Total RNA was extraxted by trizol reagent (Invitrogen, Carlsbad, CA, USA)

value: Burkitt Lymphoma EBV positive


title: E1 X F1

description: Biological replicate 1 of 3, technical replicate 1 of 2. TEC + T cell non-infected supernatant (CEM)/TEC + T cell-infected supernatant (CIB)


title: Burkitt Lymphoma EBVpositive 5


title: Burkitt Lymphoma_EBVnegative 12

value: Burkitt Lymphoma_EBV negative


title: Burkitt Lymphoma EBVpositive 4


title: genomic DNA from lung tissue42

source_name: diseased lung tissue

value: Fibrosis

value: NSIP


title: genomic DNA from lung tissue38

value: tissue biopsy


title: Burkitt Lymphoma_EBVnegative 10


title: Burkitt Lymphoma EBVpositive 3


title: genomic DNA from lung tissue43


title: genomic DNA from lung tissue44

value: UIP


title: genomic DNA from lung tissue36

source_name: nomal lung tissue


title: genomic DNA from lung tissue34

value: HP


title: genomic DNA from lung tissue37


title: Burkitt Lymphoma_EBVnegative 8


title: Burkitt Lymphoma_EBVnegative 7


title: genomic DNA from lung tissue46


title: genomic DNA from lung tissue39


title: Burkitt Lymphoma_EBVnegative 6


title: genomic DNA from lung tissue51


title: genomic DNA from lung tissue33


title: Burkitt Lymphoma_EBVnegative 5


title: Burkitt Lymphoma_EBVnegative 4


title: genomic DNA from lung tissue29


title: genomic DNA from lung tissue31


title: genomic DNA from lung tissue45


title: genomic DNA from lung tissue35


title: Burkitt Lymphoma_EBVnegative 3


title: genomic DNA from lung tissue28


title: genomic DNA from lung tissue27


title: genomic DNA from lung tissue41


title: genomic DNA from lung tissue30


title: Burkitt Lymphoma_EBVnegative 1


title: Burkitt Lymphoma EBVpositive 1


title: Burkitt Lymphoma EBVpositive 2


title: Burkitt Lymphoma_EBVnegative 2


title: Burkitt Lymphoma_EBVnegative 11


title: genomic DNA from lung tissue32


title: WT control

city: Indianapolis

first: Debbie

middle: Carolyn

last: Thurmond

state: IN

address: 635 Barnhill Drive, MS 2031

department: Pediatrics

institute: Indiana University

hyb_protocol: each sample was hybridized to a mouse Gene 1.0 array using the standard Affymetrix protocol

scan_protocol: Scanned using the affymetrix GS30007G using Affymetrix Command Console (AGCC)

data_processing: Cel files were generated by AGCC and imported into Partek Genomics Suite  RMA (robust multi-array average) signals were generated using the RMA background correction, Quantile normalization and summarization by Median Polish. RMA data was log base 2 transformed.

label: biotin

organism: Mus musculus

source_name: Hindlimb skeletal muscle

label_protocol: 100ng of RNA from each sample was labeled using the Ambion WT Expression kit and the Affymetrix WT Terminal Labeling kit

extract_protocol: Hindlimb skeletal muscle was dissected from Wt and Syn4 Tg mice and immediately frozen in liquid nitrogen to preserve RNA quality. Total RNA from Wt or Syn4 Tg was extracted using Qiagen RNAeasy kit.

treatment_protocol: Male mice were fed standard chow diet.

tag: genotype

value: Wild-type

value: male

value: hindlimb skeletal muscle

tag: strain


title: pancreatic ductal adenocarcinoma BxPC3 (resistant) cell line_rep3

city: Atlanta

first: Roman

middle: F. N.

last: Mezencev

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

description: subconfluent culture of cisplatin-resistant cell line BxPC3-R

hyb_protocol: as per manufacturer's protocol

scan_protocol: as per manufacturer's protocol

data_processing: Affymetrix Expression Console Software Build 1.2.1.20 using the default RMA-sketch

source_name: Pancreatic ductal adenocarcinoma

label_protocol: Amplified cDNA was prepared using the Applause WT-Amp ST (NuGEN, San Carlos, CA), fragmented and biotin-labelled using the  Encore Biotin Module (NuGEN) according to the manufacturers' instructions

growth_protocol:
AsPC1 and BxPC3 cells were grown in RPMI 1640 medium supplemented with 10% FBS (Atlanta Biologicals, Lawrenceville, GA) and 1% antibiotic-antimycotic solution (Mediatech-Cellgro, Manassas, VA)
AsPC1-R and BxPC3-R cells were maintained in full RPMI 1640 medium with 1.67 uM and 0.60 uM of cisplatin, respectively. The last sub-culture before harvesting was performed in cisplatin-free growth medium.

extract_protocol: Total cell RNA was extracted using the Rneasy Micro Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions


title: Syn4 transgenic

value: Syn4 transgene (overexpression)


title: genomic DNA from lung tissue24


title: pancreatic ductal adenocarcinoma BxPC3 (resistant) cell line_rep2


title: genomic DNA from lung tissue40


title: Burkitt Lymphoma_EBVnegative 9


title: pancreatic ductal adenocarcinoma BxPC3 (parental) cell line_rep3

description: subconfluent culture of parental cell line BxPC3


title: pancreatic ductal adenocarcinoma BxPC3 (resistant) cell line_rep1


title: genomic DNA from lung tissue22


title: genomic DNA from lung tissue20

value: healthy


title: genomic DNA from lung tissue15


title: genomic DNA from lung tissue25


title: pancreatic ductal adenocarcinoma BxPC3 (parental) cell line_rep1


title: pancreatic ductal adenocarcinoma BxPC3 (parental) cell line_rep2


title: pancreatic ductal adenocarcinoma AsPC1-R (resistant) cell line_rep3

description: subconfluent culture of cisplatin-resistant cell line AsPC1-R


title: genomic DNA from lung tissue21


title: genomic DNA from lung tissue26


title: genomic DNA from lung tissue19


title: pancreatic ductal adenocarcinoma AsPC1-R (resistant) cell line_rep2


title: pancreatic ductal adenocarcinoma AsPC1-R (resistant) cell line_rep1


title: pancreatic ductal adenocarcinoma AsPC1 (parental) cell line_rep3

description: subconfluent culture of parental cell line AsPC1


title: genomic DNA from lung tissue23


title: genomic DNA from lung tissue14

value: UIPimited


title: pancreatic ductal adenocarcinoma AsPC1 (parental) cell line_rep2


title: genomic DNA from lung tissue16


title: genomic DNA from lung tissue17


title: pancreatic ductal adenocarcinoma AsPC1 (parental) cell line_rep1


title: MC18-Tolerant

city: Liverpool

first: Suparna

last: Mitra

address: Block A: Waterhouse Buildings

department: Department of Molecular and Clinical Pharmacology

institute: University of Liverpool

description: Gene expression data from tolerant patient blood sample

hyb_protocol: Following fragmentation and labelling using the Affymetrix WT Terminal Labelling kit, 5ug of fragmented and labelled DNA was hybridised for 17 hours at 450C on GeneChip Human Gene 1.0ST arrays in the GeneChip hybridisation oven 640.  The arrays were washed and stained using the GeneChipHybridisation wash and stain kit on the Affymetrix Fluidics station 450 using fluidics protocol FS450_0007

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing: Signals were background corrected and the normalization method was ‘RMA16’ (baseline to median).

source_name: Tolerant Female; on neviraoine and tolerating treatment

label_protocol: Sense-strand cDNA was prepared from 100ng total RNA using the Ambion WT Expression kit.

growth_protocol: 18 HIV patients treatet with Nevirapine at a dose of 200 mg twice-daily (200 mg once daily within the first two weeks of therapy) lead-in dose.

extract_protocol: Total RNA was extracted from peripheral blood using PAXgene blood RNA removal kit (Qiagen) according to the manufacturer’s instructions. Samples were then globin-cleared.

treatment_protocol: 10ml blood was taken directly from patients into paxgene tubes which were then frozen within 15 minutes to -80°C until RNA extraction.

value: blood

tag: Sex

value: Female


title: genomic DNA from lung tissue11


title: genomic DNA from lung tissue13


title: MC15-Tolerant

source_name: Tolerant Male; on neviraoine and tolerating treatment

value: Male


title: MC17-Tolerant


title: MC14-Tolerant


title: MC13-Tolerant


title: genomic DNA from lung tissue18


title: genomic DNA from lung tissue7


title: B_TAS180_43

city: Bochum

last: Kumsta

address: Universitätsstraße 150

department: Department of Genetic Psychology

country: Germany

institute: Ruhr-University Bochum

description: Gene expression 180 minutes after psychosocial stress exposure in isolated monocytes

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Isolated monocytes, 180min post-stress, early adversity

label_protocol: In order to produce Cy3- labeled cRNA 100 ng of 176 out of the 180 RNA samples and 50 ng of the RNA samples 100, 166, 168 and 167  was used as template. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. The samples were processed in a high throughput approach using 96-well microtiter plates and the RNeasy® 96 kit (Qiagen) for the purification of the labeled / amplified cRNA.

extract_protocol: RNA was extracted using the NucleoSpin® RNA kit (Macherey-Nagel) following manufacturer's instructions

treatment_protocol: CD14+ monocyted were isolated (MACS, Miltenyi) from freshly drawn peripheral blood from healthy volunteers. Isolated monocytes were snap-frozen and stored at -80 degrees Celsius until RNA isolation

value: CD14+ monocytes

tag: age


title: MC12-Recovered

description: Gene expression data from recovered patient blood sample

source_name: Recovered Female; no longer taking nevirapine


title: B_TAS180_77

value: female


title: MC16-Tolerant


title: MC11-Recovered

source_name: Recovered Male; no longer taking nevirapine


title: genomic DNA from lung tissue9

tag: disease state


title: MC9-Recovered

tag: tissue


title: B_TAS180_37

tag: gender


title: genomic DNA from lung tissue12


title: genomic DNA from lung tissue6


title: B_TAS180_40


title: B_TAS180_36


title: MC10-Recovered


title: B_TAS180_38


title: genomic DNA from lung tissue5


title: genomic DNA from lung tissue8


title: MC8-Recovered


title: genomic DNA from lung tissue3


title: MC7-Recovered


title: genomic DNA from lung tissue10


title: B_TAS180_34


title: B_TAS180_30


title: genomic DNA from lung tissue4


title: MC6-Acute

description: Gene expression data from acute patient blood sample

source_name: ADR Acute Female; taking nevirapine


title: genomic DNA from lung tissue1


title: MC5-Acute

source_name: ADR Acute Male; taking nevirapine


title: B_TAS180_27


title: Group A Streptococcus strain 5448 (M1T1 clone) WT grown in THY + 1 mM zinc, rep3

city: St Lucia

first: Cheryl-lynn

middle: Yanwen

last: Ong

state: QLD

address: Cooper Road, Building 76, Rm 125

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

hyb_protocol: Single colored hybridization was performed according to the supplier's instructions (http://pfgrc.jcvi.org/index.php/microarray/protocols.html).

scan_protocol: Slides were scanned using a GenePix 4000B (Axon instruments) scanner.

data_processing:
Analysis of scanned slides was done using GenePixPro 4.0 software (Axon Instruments).
Data from each point has undergone strict threshold normalization as described in Dalton T. et al., 2006, Journal of Bacteriology 188:77-85.

organism: Streptococcus pyogenes

source_name: Streptococcus pyogenes cell pellet from growth in THY + 1 mM zinc

label_protocol: Cy-3 labelled cDNA was generated using Fairplay microarray labelling kit (Stratagene).

growth_protocol: Bacterial cells were grown up to mid-exponential phase in either THY medium or THY medium supplemented with 1 mM zinc.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) with the additional DNase treatment (Qiagen).

treatment_protocol: The cells were washed in 1x PBS, and cell pellets were used for RNA extraction.

tag: strain/background

tag: genotype/variation

value: WT

tag: growth condition

value: THY + 1 mM zinc


title: B_TAS180_28


title: MC4-Acute


title: MC2-Acute


title: B_TAS180_25


title: genomic DNA from lung tissue2

value: Fibrosis


title: FACS-sorted CD166+ lung normal epithelial cells from patient

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description:
miRNAs expression in FACS-sorted CD166+ cells derived from human adjacent normal lung specimen
NorCellsLung_N+ve

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The data were normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 20.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: For tumorsphere formation, lung cancer patient-derived tumor cells were cultured in serum-free growth medium including 50 ng/ml EGF and 20 ng/ml bFGF (Invitrogen). Tumorspheres (LTS10b, LTS32a, LTS27 and LTS64) were cultured for 10-14 days and used for miRNA microarray assay. Normal lung epithelial cells NHBE and SAEC are purchased from Lonza and maintained in BEGM and SAGM complete growth medium, respectively. FACS sorted cells were not further cultured.

extract_protocol: Total RNA was extracted using mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Human lung cancer and adjacent normal samples were shipped to laboratory in cold phosphate buffer saline (PBS) with antibiotics (Sigma-Aldrich, St. Louis, MO) within one hr of removal from patients. Samples were washed with cold PBS with antibiotics three times, chopped with a sterile blade, and incubated in 0.001% DNAse (Sigma-Aldrich, St. Louis, MO), 1 mg/ml collagenase/dispase (Roche, Indianapolis, IN), 200 U/ml penicillin, 200 µg/ml streptomycin, 0.5 µg/ml amphotericin B (2% antibiotics, Sigma) in DMEM/F12 medium (GIBCO, GrandIsland, NY) at 37°C water bath for 3 hr with intermittent shaking. After incubation, the suspensions were repeatedly triturated, passed through 70 µm and 40 µm cell-strainers (BD Falcon, San Jose, CA), and centrifuged at 800 rpm for 5 min at 4°C. Cells were resuspended in red blood cell lysis buffer (eBioscience, San Diego, CA) for 4 min at room temperature with intermittent shaking, before resuspension in serum-free medium. After lysis, cell viability was evaluated by trypan blue dye exclusion. Live single cells account for 90% of the whole population and dead cells account for less than 10%. For luorescence-activated cell sorting (FACS), single cells were incubated with FcR Blocking Reagent (Miltenyi) in ice for 20 min, labelled with antibodies against CD166, and the lineage markers (human CD45/CD31 for patient tumors). 7-amino-actinomycin D (BD PharminGen) was added to exclude dead cells. Appropriate isotype antibodies were used as controls

tag: individual

value: patient

value: FACS-sorted CD166+ cells derived from adjacent normal lung specimen


title: FACS-sorted CD166- lung normal epithelial cells from patient

description:
miRNAs expression in FACS-sorted CD166- cells derived from human adjacent normal lung specimen
NorCellsLung_N-ve

tag: cell type

value: FACS-sorted CD166- cells derived from adjacent normal lung specimen


title: Group A Streptococcus strain 5448 (M1T1 clone) WT grown in THY, rep2

source_name: Streptococcus pyogenes cell pellet from growth in THY

value: THY


title: Group A Streptococcus strain 5448 (M1T1 clone) WT grown in THY, rep3


title: Group A Streptococcus strain 5448 (M1T1 clone) WT grown in THY + 1 mM zinc, rep1


title: Group A Streptococcus strain 5448 (M1T1 clone) WT grown in THY, rep1


title: B_TAS180_26


title: MC3-Acute


title: B_TAS180_19


title: B_TAS180_21


title: B_TAS180_15


title: Cultured normal human bronchial epithelial cell line from Lonza

description:
miRNAs expression in cultured normal lung epithelial cell line - NHBE
NorCellsLung_NHBE

tag: cell line


title: Cultured normal small airway epithelial cell line from Lonza

description:
miRNAs expression in cultured normal lung epithelial cell line - SAEC
NorCellsLung_SAEC


title: FACS-sorted CD166- lung cancer cells from patient #64

description:
miRNAs expression in FACS-sorted CD166- cells derived from human lung cancer specimen #64
TuCellsLung_ALC-64

source_name: FACS-sorted CD166- lung cancer cells

value: patient #64

value: FACS-sorted CD166- cells derived from lung cancer


title: FACS-sorted CD166+ lung cancer cells from patient #64

description:
miRNAs expression in FACS-sorted CD166+ cells derived from human lung cancer specimen #64
TuCellsLung_ALC+64

source_name: FACS-sorted CD166+ lung cancer cells

value: FACS-sorted CD166+ cells derived from lung cancer


title: FACS-sorted CD166- lung cancer cells from patient #27

description:
miRNAs expression in FACS-sorted CD166- cells derived from human lung cancer specimen #27
TuCellsLung_ALC-27

value: patient #27


title: Cultured lung tumorsphere cells from patient #64

description:
miRNAs expression in cultured tumorsphere cells derived from human lung cancer specimen #64
TuCellsLung_LTS64

source_name: Cultured lung tumorsphere cells

value: cultured tumorsphere cells derived from lung cancer


title: FACS-sorted CD166+ lung cancer cells from patient #27

description:
miRNAs expression in FACS-sorted CD166+ cells derived from human lung cancer specimen #27
TuCellsLung_ALC+27


title: Cultured lung tumorsphere cells from patient #27

description:
miRNAs expression in cultured tumorsphere cells derived from human lung cancer specimen #27
TuCellsLung_LTS27


title: FACS-sorted CD166- lung cancer cells from patient #32

description:
miRNAs expression in FACS-sorted CD166- cells derived from human lung cancer specimen #32
TuCellsLung_ALC-32b

value: patient #32


title: FACS-sorted CD166+ lung cancer cells from patient #32

description:
miRNAs expression in FACS-sorted CD166+ cells derived from human lung cancer specimen #32
TuCellsLung_ALC+32b


title: B_TAS180_14

value: male


title: B_TAS180_13


title: Cultured lung tumorsphere cells from patient #32

description:
miRNAs expression in cultured tumorsphere cells derived from human lung cancer specimen #32
TuCellsLung_LTS32a


title: B_TAS180_17


title: FACS-sorted CD166- lung cancer cells from patient #10

description:
miRNAs expression in FACS-sorted CD166- cells derived from human lung cancer specimen #10
TuCellsLung_ALC-10b

value: patient #10


title: B_TAS180_12

description: Gene expression 180 minutes after psychosocial stress exposure in isolated monocytes

value: CD14+ monocytes


title: MM68

city: Miami

first: Matthew

middle: G.

last: Field

state: FL

address: 1501 NW 10th Avenue

institute: University of Miami

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline normalization and background subtraction with GenomeStudio Gene Expression Module

source_name: primary uveal melanoma without metastasis

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

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

value: primary uveal melanoma

tag: gep subtype

value: Class 1

tag: metastasis

value: Fresh frozen sample from enucleated eye


title: Cultured lung tumorsphere cells from patient #10

description:
miRNAs expression in cultured tumorsphere cells derived from human lung cancer specimen #10
TuCellsLung_LTS10b


title: MM118

tag: sample type


title: B_TAS180_11

value: female


title: MM86


title: FACS-sorted CD166+ lung cancer cells from patient #10

description:
miRNAs expression in FACS-sorted CD166+ cells derived from human lung cancer specimen #10
TuCellsLung_ALC+10a


title: MM64


title: B_TAS180_9


title: MM101


title: MM82


title: B_TAS180_23


title: B_TAS180_10


title: MM65

source_name: primary uveal melanoma with metastasis

value: metastasis


title: B_TAS180_8


title: B_TAS180_6


title: MM16


title: B_TAS45_38

description: Gene expression 45 minutes after psychosocial stress exposure in isolated monocytes

source_name: Isolated monocytes, 45min post-stress, early adversity


title: B_TAS45_43


title: B_TAS45_36


title: B_TAS180_5


title: B_TAS45_37


title: overexpress mir-1290 on normal lung epithelial cell (Nuli-1), replicate 2

description:
Gene expression data from Nuli-1 cells with mir-1290 OE
pre1290_LBEt-2

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

source_name: Nuli-1 with mir-1290 overexpression

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

growth_protocol: The A549 cell was from ATCC and cultured by DMEM (high glucose) (GIBCO) with 10% FBS, 2 mM L-glutamine and 1% Penicillin-Streptomycin. Immortalized NuLi-1 cell line was from ATCC and cultured under BEGM serum-free complete growth medium (Lonza) supplemented with 50 µg/ml G418 (Sigma).

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

treatment_protocol: Lentivirus was produced in HEK293FT packaging cells and harvested 48–72 hr post-infection. For lentiviral overexpression or knockdown of miR-1246 or miR-1290, A549 and NuLi-1 cells were infected with the lentiviral supernatant for 48 hr in the presence of 8 μg/ml polybrene (Sigma). Two days after infection, puromycin was added to the media at 1 μg/ml, and cell populations were selected for 1-2 weeks.

value: overexpress mir-1290


title: B_TAS45_35


title: B_TAS180_22


title: B_TAS180_4


title: B_TAS180_7


title: overexpress mir-1246 on normal lung epithelial cell  (Nuli-1), replicate 2

description:
Gene expression data from Nuli-1 cells with mir-1246 OE
pre1246_LBEt-2

source_name: Nuli-1 with mir-1246 overexpression

value: overexpress mir-1246


title: MM77


title: MM10


title: MM89


title: MM47


title: B_TAS45_40


title: control normal lung epithelial cell (Nuli-1), replicate 2

description:
Gene expression data from Nuli-1 cells
ctrl_LBEt-2

value: control


title: overexpress mir-1246 on normal lung epithelial cell  (Nuli-1), replicate 1

description:
Gene expression data from Nuli-1 cells with mir-1246 OE
pre1246_LBEt-1


title: overexpress mir-1290 on normal lung epithelial cell (Nuli-1), replicate 1

description:
Gene expression data from Nuli-1 cells with mir-1290 OE
pre1290_LBEt-1


title: Gorilla Vs human Sample 31

city: Houston

first: Bo

last: Yuan

address: One Baylor Plaza

institute: Baylor College of Medicine

description: nonhuman primate-human array CGH

hyb_protocol: Labeled proband and control samples were combined in a mass ratio of 1:1 with addition of 2μg human Cot-1 DNA (Life Technologies), 10X Agilent Blocking Agent (Agilent Technologies) and 2X Hi-RPM Hybridisation Buffer (Agilent Technologies). The mixture was incubated at 95°C for 3 min and then at 37°C for 30 min for pre-hybridization. Afterwards, the mixture was hybridized onto the array placed in a hybridization chamber (Agilent Technologies) in a rotating over (Agilent Technologies) for at least 40 hours at 65°C.

scan_protocol: Washing step after hybridization were performed following the manufacturer’s protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis version 7.2, Agilent Technologies) with Agilent Oligo CGH Wash Buffer 1 and 2 (Agilent Technologies), Acetonitrile (Sigma-Aldrich), and Stabilization and Drying Solution (Agilent Technologies). The dried slides were scanned on Agilent Microarray Scanner (Agilent Technologies) for image acquisition.

data_processing:
The images after scanning were subsequently processed by Feature Extraction Software version 11.5 (Agilent Technologies) to generate FE files, which were subsequently imported into Agilent Genomic Workbench version 7.0 (Agilent Technologies) for copy number variation (CNV) analysis.
The copy number was defined by normalized log2 ratio of Cy5/Cy3 fluorescence signal of each probe. Human reference sequence GRCh37/hg19 assembly was used to define the genomic coordinated of detected CNVs.

organism: Gorilla gorilla

label_protocol: 0.9μg genomic DNA from proband (test sample) and control (NA10851) were digested with AluI and RsaI (Promega) for 2 hours at 37°C. Digestion product was run on 1% agarose gel for verification. Labeling of the digestion product was performed using BioPrime Array CGH Genomic Labelling Module (Life Technologies) following the manufacturer’s protocol. Cy5-dCTP and Cy3-dCTP from Cyanine Smart Pack dCTP (PerkinElmer) were used for proband and control digestion product, respectively. Labeling reaction was performed for 2 hours at 37°C. Labeling product underwent purification process using Amicon Ultra 0.5 Centrifugal Filter (30 kDa, Millipore). Labeling efficiency was quantitated using a NanoDrop ND-1000 UV-VIS spectrophotometer.

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: 45 kb lcr copy number

tag: sample characteristics

value: nonhuman primates


title: Gorilla Vs human Sample 32

description: nonhuman primate-human array CGH


title: Gorilla Vs human Sample 30

description: nonhuman primate-human array CGH


title: control normal lung epithelial cell (Nuli-1), replicate 1

description:
Gene expression data from Nuli-1 cells
ctrl_LBEt-1


title: B_TAS45_34


title: 5TGM1_Proliferating_biological-rep4

city: Darlinghurst

first: Peter

last: Croucher

state: New South Wales

address: 384 Victoria St

department: Bone

institute: Garvan Insititute of Medical Research

hyb_protocol: Following fragmentation, 3ug of cDNA DNA was hybridized to each array for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven and  arrays were washed according to manufacturers instructions on an Affymetrix FS450 fluidics station.

scan_protocol: Genechips were scanned using Affymetrix Scanner GC3000 7G

data_processing: Normalization and probe set summarization was performed using the robust multichip average implemented through the Affy library within R.

label: Biotin

source_name: Proliferating multiple myeloma population

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: did

value: Negative

tag: strain


title: knockdown mir-1246 on lung cancer cell (A549), replicate 2

description:
Gene expression data from A549 cells with mir-1246 KD
zip1246_A549-2

source_name: A549 with mir-1246 knockdown

value: knockdown mir-1246


title: B_TAS45_28

tag: age


title: 5TGM1_Transitioning_biological-rep4

source_name: Transitioning multiple myeloma population

value: Low


title: Chimpanzee Vs human Sample 29

description: nonhuman primate-human array CGH

organism: Pan troglodytes


title: B_TAS45_27


title: control lung cancer cell (A549), replicate 1

description:
Gene expression data from A549 cells
ctrl_A549-1


title: knockdown mir-1290 on lung cancer cell (A549), replicate 2

description:
Gene expression data from A549 cells with mir-1290 KD
zip1290_A549-2

source_name: A549 with mir-1290 knockdown

value: knockdown mir-1290


title: B_TAS45_25


title: B_TAS180_35

source_name: Isolated monocytes, 180min post-stress, early adversity


title: 5TGM1_Transitioning_biological-rep3

value: Transitioning multiple myeloma population


title: Chimpanzee Vs human Sample 28

description: nonhuman primate-human array CGH


title: knockdown mir-1290 on lung cancer cell (A549), replicate 1

description:
Gene expression data from A549 cells with mir-1290 KD
zip1290_A549-1


title: B_TAS45_30


title: Chimpanzee Vs human Sample 27

description: nonhuman primate-human array CGH


title: 5TGM1_Proliferating_biological-rep5

value: Proliferating multiple myeloma population


title: control lung cancer cell (A549), replicate 2

description:
Gene expression data from A549 cells
ctrl_A549-2


title: Chimpanzee Vs human Sample 25

description: nonhuman primate-human array CGH


title: knockdown mir-1246 on lung cancer cell (A549), replicate 1

description:
Gene expression data from A549 cells with mir-1246 KD
zip1246_A549-1


title: 5TGM1_Dormant_biological-rep3

source_name: Dormant multiple myeloma population

value: High

value: Dormant multiple myeloma population


title: MC1-Acute

description: Gene expression data from acute patient blood sample

source_name: ADR Acute Male; taking nevirapine

value: blood

tag: Sex

value: Male


title: B_TAS45_23

tag: tissue

value: CD14+ monocytes

value: male


title: B_TAS45_26

tag: gender

value: female


title: Chimpanzee Vs human Sample 23

description: nonhuman primate-human array CGH


title: Chimpanzee Vs human Sample 26

description: nonhuman primate-human array CGH


title: 5TGM1_Dormant_biological-rep2


title: Orangutan Vs human Sample 22

description: nonhuman primate-human array CGH

organism: Pongo abelii


title: 5TGM1_Transitioning_biological-rep2


title: B_TAS45_21


title: Rhesus Vs human Sample 21

description: nonhuman primate-human array CGH

organism: Macaca mulatta


title: B_TAS45_22


title: Stabilin-1 low monocytes, biological replicate2

city: Turku

first: Kati

last: Elima

address: Tykistökatu 6

department: MediCity

country: Finland

institute: University of Turku

hyb_protocol: 600 ng of Cy-3 labeled sample was hybridized onto Agilent’s 8x60K SurePrint G3 Human array (Design ID 028004) at 65 C overnight using Agilent’s GE Hybridization Kit (Product number 5188-5242).Washes were done with Agilent’s Gene Expression Wash Pack product number 5188-5327) with 0.005% Triton X-102.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2565CA.Numerical results were extracted with Feature Extraction version 10.7.1.Grid:   028004_D_F_20110819 Protocol:  GE1_107_Sep09.  Scan Profile:  AgilentG3_GX_1Color

data_processing: The signal intensities from the raw data lists were background corrected and normalized using quantile normalization. The normalized intensities were log2-transformed.  Protocol:  GE1_107_Sep09    Grid:   028004_D_F_20110819  Protocol:  GE1_107_Sep09

source_name: peripheral blood monocytes CD14+Stab1low

label_protocol: 100 ng total RNA was amplified / Cy3-labeled with Agilent’s Low Input Quick Amp Labeling kit, one-color (Product number 5190-2331). Samples were processed together with Agilent’s RNA Spike in kit, single-color (Product number 5188-5282). • Both before and after amplifications the RNA(starting material) and cRNA (labeled / amplified) concentrations (and also specific activity for cRNA) were checked with Nanodrop ND-2000 and RNA/cRNA quality was controlled by Agilent 2100 Bioanalyzer.

extract_protocol: Red blood cells were lysed from blood samples of healthy volunteers and leukocytes were stained for Stabilin-1 and CD14 FITC followed by sorting in FACS. Monocytes were identified using scatter profiles, and CD14 and Stabilin-1 double positive monocytes were gated using FACS Diva software, and the brightest and dimmest 10% of Stabilin-1+ monocytes were collected.


title: Stabilin-1 high monocytes, biological replicate 4

source_name: peripheral blood monocytes CD14+Stab1high


title: 5TGM1_Dormant_biological-rep1


title: B_TAS45_17


title: Stabilin-1 low monocytes, biological replicate 1

value: peripheral blood monocytes CD14+Stab1low


title: B_TAS45_19


title: Rhesus Vs human Sample 20

description: nonhuman primate-human array CGH


title: Stabilin-1 low monocytes, biological replicate3


title: human Vs human Sample 18

description: human-human array CGH

value: subjects affected with NPHP1


title: Stabilin-1 high monocytes, biological replicate 3

value: peripheral blood monocytes CD14+Stab1high


title: 5TGM1_Proliferating_biological-rep3


title: Baboon Vs human Sample 19

description: nonhuman primate-human array CGH

organism: Papio anubis

value: nonhuman primates


title: Chimpanzee Vs human Sample 24

description: nonhuman primate-human array CGH


title: 5TGM1_Proliferating_biological-rep2

value: Negative


title: 5TGM1_Proliferating_biological-rep1


title: 5TGM1_Transitioning_biological-rep1


title: B_TAS45_77


title: Stabilin-1 high monocytes, biological replicate 2


title: human Vs human Sample 17

description: human-human array CGH


title: B_TAS45_14


title: Stabilin-1 high monocytes, biological replicate 1


title: B_TAS45_12


title: B_TAS45_15


title: human Vs human Sample 15

description: human-human array CGH


title: B_TAS45_11


title: B_TAS45_13


title: B_TAS45_9


title: Patient 45 [Agilent]

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

institute: University of Brasília - UnB

description: Patient sample Cy3-labeled mixed with reference sample Cy5-labeled.

hyb_protocol: Standard Agilent Protocol. Labeled test and control samples were mixed and hybridized into a 4x 180K slide (Agilent Product Number - G4449A).

scan_protocol: The slides were scanned on an Agilent G2565B scanner (Agilent).

data_processing: Data were extracted using the Agilent Feature Extraction software (v 8.5.1.1) and analyzed using the Agilent CytoGenomics software (v 3.0.1.1) with the following parameters: ADM-2 algorithm, threshold of 6.0, at least four altered probes, log2 ratio > 0.35 for gains and < -0.35 for losses. The fuzzy zero correction was applied, with a detailed visual analysis being performed for all alterations, excluding regions with poor data quality.

source_name: blood from patient 45

label_protocol: Standard Agilent protocol. Test samples have been labeled with Cy3 and controls with Cy5.

growth_protocol: Not applicable.

extract_protocol: Genomic DNA was extracted using the Gentra Puregene Blood Kit (Qiagen, Valencia, CA, USA).

tag: disease status

value: Lynch Syndrome (LS)

tag: patient id

source_name: pooled normal reference DNA (Promega)

value: reference


title: Patient 42 [Agilent]

source_name: blood from patient 42


title: B_TAS45_8


title: B_TAS45_10


title: human Vs human Sample 14

description: human-human array CGH


title: human Vs human Sample 16

description: human-human array CGH


title: MM38

source_name: primary uveal melanoma without metastasis

value: primary uveal melanoma

value: Class 1

value: Fresh frozen sample from enucleated eye


title: B_TAS45_7


title: human Vs human Sample 11

description: human-human array CGH


title: Patient 40 [Agilent]

source_name: blood from patient 40


title: human Vs human Sample 9

description: human-human array CGH

value: human embryonic stem cell line, passage 22


title: Patient 44 [Agilent]

source_name: blood from patient 44


title: Patient 41 [Agilent]

source_name: blood from patient 41


title: human Vs human Sample 8

description: human-human array CGH

value: MCF7 cell line


title: B_TAS45_5

source_name: Isolated monocytes, 45min post-stress, early adversity


title: B_TAS45_6


title: human Vs human Sample 10

description: human-human array CGH

value: human embryonic stem cell line, passage 208


title: human Vs human Sample 7

description: human-human array CGH

value: subjects without NPHP1


title: Patient 43 [Agilent]

source_name: blood from patient 43

value: blood


title: Patient 37 [Agilent]

source_name: blood from patient 37

value: male


title: human Vs human Sample 12

description: human-human array CGH


title: B_TAS45_4

value: CD14+ monocytes

value: female


title: Patient 38 [Agilent]

source_name: blood from patient 38


title: Patient 36 [Agilent]

source_name: blood from patient 36


title: human Vs human Sample 6

description: human-human array CGH


title: B_TBS45_43

description: Gene expression 45 minutes before psychosocial stress exposure in isolated monocytes

source_name: Isolated monocytes, 45min pre-stress, early adversity


title: Patient 35 [Agilent]

source_name: blood from patient 35


title: B_TBS45_40


title: human Vs human Sample 5

description: human-human array CGH


title: human Vs human Sample 3

description: human-human array CGH


title: Patient 34 [Agilent]

source_name: blood from patient 34


title: Patient 33 [Agilent]

source_name: blood from patient 33


title: human Vs human Sample 1

description: human-human array CGH


title: B_TBS45_38


title: B_TBS45_36


title: human Vs human Sample 13

description: human-human array CGH

value: subjects affected with NPHP1


title: human Vs human Sample 4

description: human-human array CGH


title: human Vs human Sample 2

description: human-human array CGH


title: B_TBS45_35


title: B_TBS45_34


title: Patient 32 [Agilent]

source_name: blood from patient 32


title: Patient 28 [Agilent]

source_name: blood from patient 28


title: Patient 30 [Agilent]

source_name: blood from patient 30

source_name: pooled normal reference DNA (Promega)


title: Patient 29 [Agilent]

source_name: blood from patient 29


title: B_TBS45_27


title: B_TBS45_28


title: B_TBS45_30


title: B_TBS45_26


title: B_TBS45_25


title: Patient 27 [Agilent]

source_name: blood from patient 27


title: Patient 26 [Agilent]

source_name: blood from patient 26


title: Patient 25 [Agilent]

source_name: blood from patient 25


title: B_TBS45_22


title: B_TBS45_23


title: B_TBS45_21


title: Patient 22 [Agilent]

source_name: blood from patient 22


title: Patient 23 [Agilent]

source_name: blood from patient 23


title: Patient 24 [Agilent]

source_name: blood from patient 24


title: B_TBS45_17


title: Patient 21 [Agilent]

source_name: blood from patient 21


title: Patient 20 [Agilent]

source_name: blood from patient 20


title: B_TBS45_14

source_name: Isolated monocytes, 45min pre-stress, early adversity


title: B_TBS45_19


title: B_TBS45_13


title: Patient 14 [Agilent]

source_name: blood from patient 14


title: Patient 19 [Agilent]

source_name: blood from patient 19


title: Patient 17 [Agilent]

source_name: blood from patient 17


title: B_TBS45_12


title: B_TBS45_11


title: Patient 16 [Agilent]

source_name: blood from patient 16


title: Patient 15 [Agilent]

source_name: blood from patient 15


title: B_TBS45_15


title: Patient 18 [Agilent]

source_name: blood from patient 18


title: B_TBS45_10


title: Blood CD8 single positive T cell replicate2

city: Kyoto

first: Ryo

last: Inoue

address: 1-5, Hangi-cho, shimogamo

country: Japan

institute: Kyoto Prefectural University

description: Biological replicate 2 of 2. Blood CD8 single positive T cell

hyb_protocol: Slide was hybridized with 0.825 μg Cy3-labeled cDNA and 0.825 μg Cy5-labeled cDNA using a Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, USA) in a hybridization oven.

scan_protocol: After 17 h of hybridization at 65 °C, the slide was washed with a Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. The slide was then scanned by using GenePix 4100A (Axon, Foster City, CA).

data_processing: The data was extracted with Axon GenePix Pro 7.2 image analysis software. The spot sizes and intensities quantified by the software and automatically flagged spot qualities were followed manual examination. Abnormal shape spots or spots with high local background or spots that were quantified due to false intensity caused by dust were flagged bad and discarded. The background subtracted median intensity signals was imported to CLC Main workbench 6.0 and normalized by the quartile normalization method and log2 transformed.

label: Alexa Fluor 5

organism: Sus scrofa

source_name: Blood CD8 single positive T cell from sow#2

label_protocol: Complementary DNA amplification was carried out from 10 ng of total RNA using an Ovation PicoSL WTA System V2. After amplification, cDNA samples from colostrum were labeled with Alexa Fluor 3 and those from blood with Alexa Fluor 5 using a BioPrime Total Genomic Labeling System.

growth_protocol: colostrum and blood were collected from two Large White x Landrace sows. Mononuclear cells were isolated and fluorecently labeled by anti porcine CD3, CD4 and CD8 antibodies. CD3+/CD4-/CD8+ cells and CD3+/CD4+/CD8+ cells were separeted sorted by a cell sorter.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and purified by RNeasy MinElute Cleanup kit.

value: Large white x Landrace


title: Blood double positive single positive T cell replicate2

description: Biological replicate 2 of 2. Bloodl double positive single positive T cell

source_name: Blood double positive single positive T cell from sow#2


title: B_TBS45_8


title: Patient 13 [Agilent]

source_name: blood from patient 13

source_name: pooled normal reference DNA (Promega)


title: Colostral double positive single positive T cell replicate1

description: Biological replicate 1 of 2. Colostral double positive single positive T cell

label: Alexa Fluor 3

source_name: Colostral double positive single positive T cell from sow#1


title: Blood double positive single positive T cell replicate1

description: Biological replicate 1 of 2. Blood double positive single positive T cell

source_name: Blood double positive single positive T cell from sow#1


title: Blood CD8 single positive T cell replicate1

description: Biological replicate 1 of 2. Blood CD8 single positive T cell

source_name: Blood CD8 single positive T cell from sow#1


title: Patient 10 [Agilent]

source_name: blood from patient 10


title: B_TBS45_77


title: B_TBS45_37


title: Colostral double positive single positive T cell replicate2

description: Biological replicate 2 of 2. Colostral double positive single positive T cell

source_name: Colostral double positive single positive T cell from sow#2


title: B_TBS45_9


title: B_TBS45_7


title: Colostral CD8 single positive T cell replicate2

description: Biological replicate 2 of 2. Colostral CD8 single positive T cell

source_name: Colostral CD8 single positive T cell from sow#2


title: Patient 12 [Agilent]

source_name: blood from patient 12


title: B_TBS45_6

source_name: Isolated monocytes, 45min pre-stress, early adversity


title: Patient 39 [Agilent]

source_name: blood from patient 39


title: Patient 31 [Agilent]

source_name: blood from patient 31


title: Patient 9 [Agilent]

source_name: blood from patient 9


title: Patient 11 [Agilent]

source_name: blood from patient 11


title: Patient 8 [Agilent]

source_name: blood from patient 8


title: Patient 7 [Agilent]

source_name: blood from patient 7


title: A_TAS180_69

description: Gene expression 180 minutes after psychosocial stress exposure in isolated monocytes

source_name: Isolated monocytes, 180min post-stress, control group


title: B_TBS45_4


title: A_TAS180_55


title: A_TAS180_68


title: Colostral CD8 single positive T cell replicate 1

description: Biological replicate 1 of 2. Colostral CD8 single positive T cell

source_name: Colostral CD8 single positive T cell from sow#1


title: A_TAS180_57


title: A_TAS180_54


title: A_TAS180_56


title: A_TAS180_58


title: B_TBS45_5


title: Patient 6 [Agilent]

source_name: blood from patient 6

source_name: pooled normal reference DNA (Promega)


title: Patient 3 [Agilent]

source_name: blood from patient 3


title: A_TAS180_53


title: Patient 4 [Agilent]

source_name: blood from patient 4


title: Patient 5 [Agilent]

source_name: blood from patient 5


title: Patient 2 [Agilent]

source_name: blood from patient 2


title: ptREX-NIK1

city: México

first: Vilma

middle: Araceli

last: Maldonado

state: Distrito Federal

address: Periferico  4809

department: Investigacion

country: Mexico

institute: INMEGEN

description: Gene expression data of MCF7ptREX-NIK1

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw CEL data were normalized using the Robust Multi-array Average (RMA) method, as implemented in the oligo package . The Limma R package was used for differential expression analysis . We identified genes with a >2-fold change and a crude p<0.05.

label: non

source_name: MCF7 cell line

label_protocol: standard Affymetrix protocol

growth_protocol: MCF7 cells were transiently transfected with a shRNA-NIK using lipofectamine 2000 (invitrogen) . A shRNA directed against luciferase (siRNA-Luc) was employed as a control. In addition, to overexpress NIK, MCF7 cells were transiently transfected with an expression vector (pt-REX-NIK), which contains the complete ORF of NIK. . The cells were analyzed for NIK expression 48 hours after transfection

extract_protocol: RNA Extraction  with Trizol

treatment_protocol: Only the transfection

value: NIK overexpressed


title: A_TAS180_52


title: Patient 1 [Agilent]

source_name: blood from patient 1


title: ptREX-NIK2

description: Gene expression data of MCF7ptREX-NIK2


title: ptREX-NIK3

description: Gene expression data of MCF7ptREX-NIK3


title: shRNANIK3

description: Gene expression data of MCF7shRNANIK3

value: NIK inhibited


title: A_TAS180_50


title: A_TAS180_47


title: A_TAS180_51


title: A_TAS180_45


title: A_TAS180_42


title: shRNANIK2

description: Gene expression data of MCF7shRNANIK2


title: A_TAS180_44


title: A_TAS180_41


title: A_TAS180_46


title: shRNALuc2

description: Gene expression data of MCF7shRNALUC2

value: Vector control


title: shRNANIK1

description: Gene expression data of MCF7shRNANIK1


title: shRNALuc3

description: Gene expression data of MCF7shRNALUC3


title: A_TAS180_39


title: A_TAS180_33


title: A_TAS180_32


title: 24531-50-30311

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

institute: University of Manchester

description: Gene expression data from GHD patient

hyb_protocol: A final quality check performed before hybridization to Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays.

scan_protocol: Arrays were then scanned on an Affymetrix GeneChip 7G scanner and assessed for quality against internal and hybridization controls.

data_processing: Processing and normalization of gene expression data were performed using a Robust Multi-array Average background correction modified for probe sequence with quantile normalization and median polish (Partek Genomics Suite, version 6.3, St Louis, MO, USA). Confounding effects due to variations in cell populations and outliers were examined by cross validation using principal component analysis and iso-map multidimensional scaling (Qlucore Omics Explorer 2.2, Qlucore, Lund, Sweden).

source_name: Human whole blood

label_protocol: Complementary RNA was generated using the Two-Cycle Eukaryotic Target Labelling Kit (Affymetrix, Santa Clara, CA, USA)

extract_protocol: PAXgene 96 blood RNA kit (Qiagen, Crawley, UK). Reduction of globin messenger RNA was undertaken using the Ambion GLOBIN Clear Human Kit (Life Technologies, Paisley, UK).

tag: age (years)

tag: height velocity at one year of treatment

tag: summer daylight exposure

tag: batch

value: Male


title: LaminB1 DamID in AML12 cell (rep4)

city: Shanghai

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

country: China

institute: Fudan University

description: Biological replicate 4 of 4. LaminB1 DamID in AML12 cell

hyb_protocol: Hybridized to Agilent-027414 arrays.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization. we also smoothed the probe signals using a moving average approach with a window size of 100k bps. The smoothing procedure takes into consideration of the spatial correlation of signals.

label_protocol: Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.

growth_protocol: AML12 cell were kept in complete growth medium：a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, 90%; fetal bovine serum, 10%.

extract_protocol: 2X10e6 AML12 cells were planted in 6-well plates, and infected with lenti-virus expressing Dam or Dam-Lamin B1 after 48 hours. gDNA was isolated with the Dneasy Tissue kit (Qiagen) per the manufacturers protocol after 72 hours. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR),see Vogel et al., 2008, Nature Protocols for details.

value: liver

value: The AML12 (alpha mouse liver 12) cell line was established from hepatocytes from a mouse (CD1 strain, line MT45) transgenic for human TGF alpha.


title: A_TAS180_31

first: Robert


title: 24531-50-30230

description: Gene expression data from GHD patient

value: Female


title: A_TAS180_29


title: LaminB1 DamID in AML12 cell (rep2)

description: Biological replicate 2 of 4. LaminB1 DamID in AML12 cell

value: The AML12 (alpha mouse liver 12) cell line was established from hepatocytes from a mouse (CD1 strain, line MT43) transgenic for human TGF alpha.


title: A_TAS180_24


title: Group A Streptococcus strain 5448 (M1T1 clone) WT grown in THY + 1 mM zinc, rep2

source_name: Streptococcus pyogenes cell pellet from growth in THY + 1 mM zinc

tag: strain/background

tag: genotype/variation

value: WT

tag: growth condition

value: THY + 1 mM zinc


title: 24531-50-30328

description: Gene expression data from GHD patient


title: shRNALuc1

description: Gene expression data of MCF7shRNALUC1

tag: cell line

tag: sample type


title: LaminB1 DamID in AML12 cell (rep3)

description: Biological replicate 3 of 4. LaminB1 DamID in AML12 cell

value: The AML12 (alpha mouse liver 12) cell line was established from hepatocytes from a mouse (CD1 strain, line MT44) transgenic for human TGF alpha.


title: LaminB1 DamID in AML12 cell (rep1)

description: Biological replicate 1 of 4. LaminB1 DamID in AML12 cell

value: The AML12 (alpha mouse liver 12) cell line was established from hepatocytes from a mouse (CD1 strain, line MT42) transgenic for human TGF alpha.


title: 24531-50-30176

description: Gene expression data from GHD patient


title: 24531-50-30260

description: Gene expression data from GHD patient


title: A_TAS180_20

value: male


title: 24531-50-30349

description: Gene expression data from GHD patient


title: A_TAS180_49

value: CD14+ monocytes


title: 24531-50-30366

description: Gene expression data from GHD patient


title: A_TAS180_2

value: female


title: A_TAS180_18


title: A_TAS180_16


title: A_TAS180_1


title: A_TAS45_69

description: Gene expression 45 minutes after psychosocial stress exposure in isolated monocytes

source_name: Isolated monocytes, 45min post-stress, control group


title: A_TAS45_68


title: 24531-50-30282

description: Gene expression data from GHD patient


title: 24531-50-30301

description: Gene expression data from GHD patient


title: A_TAS45_58


title: 24531-50-30316

description: Gene expression data from GHD patient


title: 24531-50-30300

description: Gene expression data from GHD patient


title: 24531-50-30193

description: Gene expression data from GHD patient


title: 24531-50-30238

description: Gene expression data from GHD patient


title: A_TAS45_56


title: A_TAS45_54


title: A_TAS45_57


title: A_TAS45_55


title: 24531-50-30358

description: Gene expression data from GHD patient


title: 24531-50-30220

description: Gene expression data from GHD patient


title: A_TAS45_53


title: 24531-50-30229

description: Gene expression data from GHD patient


title: 24531-50-30219

description: Gene expression data from GHD patient


title: A_TAS45_52


title: 24531-50-30232

description: Gene expression data from GHD patient


title: A_TAS45_50


title: A_TAS45_51


title: A_TAS45_49


title: 24531-50-30387

description: Gene expression data from GHD patient


title: 24531-50-30376

description: Gene expression data from GHD patient


title: 24531-50-30338

description: Gene expression data from GHD patient


title: A_TAS180_48


title: A_TAS45_48


title: Patient 42 [Affymetrix]

description: Hybridized to Affymetrix CytoScan HD chip.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
Data normalization and copy number calls were generated using the Affymetrix Chromosome Analysis Suite software (ChAS v 3.0), considering at least 25 markers for losses, 50 markers for gains and copy neutral loss of heterozygosity with a minimum of 5 Mb. The CNV calls were generated after comparison with data of 360 normal samples included in the ChAS software. A detailed visual analysis has been performed for all alterations, excluding regions with poor data quality.
The CYCHP files were generated using the standard analysis of ChAS 3.0 software.

source_name: blood from patient 42

label_protocol: Standard Affymetrix protocol. Test samples have been labeled with biotin.

treatment_protocol: Not applicable.

value: Lynch Syndrome (LS)

value: blood


title: 24531-50-30335

description: Gene expression data from GHD patient


title: 24531-50-30348

description: Gene expression data from GHD patient


title: 24531-50-30323

description: Gene expression data from GHD patient


title: A_TAS45_47


title: A_TAS45_45


title: A_TAS45_46


title: Patient 44 [Affymetrix]

source_name: blood from patient 44


title: Patient 45 [Affymetrix]

source_name: blood from patient 45


title: A_TAS45_44


title: A_TAS45_42


title: 24531-50-30362

description: Gene expression data from GHD patient


title: 24531-50-30086

description: Gene expression data from GHD patient


title: 24531-50-30365

description: Gene expression data from GHD patient


title: 24531-50-30095

description: Gene expression data from GHD patient


title: A_TAS45_33


title: Patient 35 [Affymetrix]

source_name: blood from patient 35


title: Patient 32 [Affymetrix]

source_name: blood from patient 32


title: Patient 28 [Affymetrix]

source_name: blood from patient 28


title: Patient 20 [Affymetrix]

source_name: blood from patient 20


title: Patient 23 [Affymetrix]

source_name: blood from patient 23


title: Patient 37 [Affymetrix]

source_name: blood from patient 37


title: A_TAS45_32


title: 24531-50-30279

description: Gene expression data from GHD patient


title: 24531-50-30280

description: Gene expression data from GHD patient


title: 24531-50-30269

description: Gene expression data from GHD patient


title: A_TAS45_29


title: 24531-50-30295

description: Gene expression data from GHD patient


title: A_TAS45_31


title: 24531-50-30357

description: Gene expression data from GHD patient


title: Patient 31 [Affymetrix]

source_name: blood from patient 31


title: A_TAS45_41


title: 24531-50-30326

description: Gene expression data from GHD patient


title: Patient 19 [Affymetrix]

source_name: blood from patient 19


title: A_TAS45_24


title: Patient 30 [Affymetrix]

source_name: blood from patient 30


title: 20133327 Mesenteric Fat Low gain-high intake

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

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

scan_protocol: GeneChips were scanned with the Affymetrix GeneAtlas Imager.

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

organism: Bos taurus

source_name: Mesenteric fat, low gain-high intake

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

growth_protocol: Steers were fed a high-concentrate diet with WDGS for 78 days.

extract_protocol: TriPure Reagent was used to extract total RNA according to manufacturer's instructions, except that a 20 minute centrifugation (rather than 15 min) was used following the addition of chloroform. RNA pellets were centrifuged through RNeasy Plus Mini Kit co

treatment_protocol: Animals most divergent from the bivariate mean from each of the four phenotypic Cartesian quadrants for gain x intake were selected and mesenteric fat tissue samples were collected. The transcriptomes of the samples from the 16 animals selected were evalu

tag: sex type

value: steer

value: mesenteric fat

tag: gain and feed intake phenotype

value: low gain-high intake


title: A_TAS45_20

tag: age


title: 20133452 Mesenteric Fat Low gain-high intake


title: 24531-50-30299

description: Gene expression data from GHD patient

value: Male


title: A_TAS45_18


title: Patient 29 [Affymetrix]

source_name: blood from patient 29


title: Patient 8 [Affymetrix]

source_name: blood from patient 8


title: 20133062 Mesenteric Fat Low gain-high intake


title: 20133403 Mesenteric Fat Low gain-low intake

source_name: Mesenteric fat, low gain-low intake

value: low gain-low intake


title: Patient 9 [Affymetrix]

source_name: blood from patient 9


title: Patient 6 [Affymetrix]

source_name: blood from patient 6


title: Patient 4 [Affymetrix]

source_name: blood from patient 4


title: Patient 12 [Affymetrix]

source_name: blood from patient 12


title: 24531-50-30089

description: Gene expression data from GHD patient

source_name: Human whole blood


title: 20133181 Mesenteric Fat Low gain-low intake


title: A_TAS45_1

source_name: Isolated monocytes, 45min post-stress, control group


title: 24531-50-30247

description: Gene expression data from GHD patient


title: A_TBS45_68

source_name: Isolated monocytes, 45min pre-stress, control group


title: 24531-50-30342

description: Gene expression data from GHD patient


title: A_TAS45_39


title: A_TAS45_2


title: 24531-50-30164

description: Gene expression data from GHD patient


title: A_TBS45_58


title: Patient 7 [Affymetrix]

source_name: blood from patient 7


title: 20133179 Mesenteric Fat Low gain-low intake


title: 24531-50-30320

description: Gene expression data from GHD patient


title: 20133045 Mesenteric Fat High gain-low intake

source_name: Mesenteric fat, high gain-low intake

value: high gain-low intake


title: 24531-50-30292

description: Gene expression data from GHD patient


title: 24531-50-30157

description: Gene expression data from GHD patient


title: 20133697 Mesenteric Fat High gain-low intake


title: A_TBS45_69


title: A_TAS45_16


title: Patient 14 [Affymetrix]

source_name: blood from patient 14


title: 20133101 Mesenteric Fat Low gain-low intake


title: WT-48hr-replicate 2

city: Lexington

first: Phillip

middle: J

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

description: Gene expression data from mouse oviducts

hyb_protocol: Following fragmentation, 10 µg of labeled cRNA was hybridized to Affymetrix Bovine Genome Array for 16 hr at 45°C using the gene chips in the GeneChip Hybridization Oven 640, using 1 chip per RNA sample. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were stained with R-Phycoerythrin Streotavidin, followed by an antibody solution and a second R-Physcoerythrin Streptavidin solution, with all lquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip Scanner (GCS) with AGCC software (Command Console).

data_processing: Microarray data were analyzed by importing raw expression intensity values (*.cel files) into Partek Genomics Suite 6.6 (Partek Inc., St. Louis, MO), where the GC-Robust Multiarray Analysis algorithm (GC-RMA), quantile normalization, and Median Polish was applied for GeneChip background correction, log base 2 transformation, conversion of expression values and probeset summarization.  Annotation was performed using NetAffx annotation database (Release 34) on December 3rd, 2014.  Quality of data was assessed using light intensity expression values on a per chip and per gene basis and visualized as box plots

source_name: WT oviduct 48hr

label_protocol: Biotinylated cRNA were prepared from 3 µg of total RNA according to Affymetrix protocol. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA, USA) and oligo(dT)24 primers. Bio-labeled cRNA was prepared by cDNA in vitro transcription biotinylated UTP.

extract_protocol: Oviducts were pooled from 3-4 mice per treatment group and genotype and total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA) and purified through RNeasy columns (Qiagen, Valencia, CA).

treatment_protocol: Mice with a global deletion of ESR1 (ESR1KO) on a C57BL/6 background were generated.  Briefly, two transgenic mouse lines were used; male ESR1flox/flox were bred with female Zp3cre to produce a line expressing Cre recombinase in the oocyte.  The F1 heterozygotes (ESR1flox/+Zp3cre) were bred with ESR1flox/flox resulting in ESR1flox/floxZp3cre mice, where females produce oocytes that are ESR1-.  ESR1flox/floxZp3cre females were then bred with ESR1flox/- males to produce ESR1KO progeny (ESR1-/- and ESR1-/- ZP3Cre) or sibling controls (ESR1flox/- and ESR1flox/- ZP3Cre).  Genomic DNA was extracted from ear punches using the Easy DNA kit (Invitrogen, Carlsbad CA) to confirm genotypes.  Whole oviducts were collected for extraction of RNA from immature female mice (ESR1KO and WT) killed at 23 days of age, or ESR1KO and WT mice treated with 5 IU PMSG at 23 days of age and killed 48 h later.

tag: strain background

value: whole oviduct

tag: strain

value: ESR1 wildtype

tag: treatment

value: PMSG


title: A_TBS45_57

description: Gene expression 45 minutes before psychosocial stress exposure in isolated monocytes

tag: tissue

tag: gender


title: A_TBS45_56


title: Patient 1 [Affymetrix]

source_name: blood from patient 1

tag: disease status

tag: patient id


title: Patient 17 [Affymetrix]

source_name: blood from patient 17


title: 20133337 Mesenteric Fat High gain-low intake


title: ERKO-48hr-replicate 3

source_name: ERKO oviduct 48hr

value: ESR1 knockout


title: 20133110 Mesenteric Fat High gain-low intake


title: 24531-50-30343

description: Gene expression data from GHD patient

tag: age (years)

tag: height velocity at one year of treatment

tag: summer daylight exposure

value: Female


title: A_TBS45_54


title: 20133356 Mesenteric Fat High gain-high intake

source_name: Mesenteric fat, high gain-high intake

value: high gain-high intake


title: WT-48hr-replicate 1


title: ERKO-48hr-replicate 2


title: A_TBS45_55


title: 24531-50-30231

description: Gene expression data from GHD patient

tag: batch


title: ERKO-48hr-replicate 1


title: A_TBS45_53

value: male


title: A_TBS45_52

value: CD14+ monocytes


title: 24531-50-30209

description: Gene expression data from GHD patient


title: 20133390 Mesenteric Fat High gain-high intake


title: 24531-50-30270

description: Gene expression data from GHD patient


title: 24531-50-30081

description: Gene expression data from GHD patient


title: 24531-50-30274

description: Gene expression data from GHD patient


title: 24531-50-30296

description: Gene expression data from GHD patient


title: A_TBS45_49

value: female


title: 24531-50-30384

description: Gene expression data from GHD patient


title: 20133015 Mesenteric Fat High gain-high intake


title: A_TBS45_50


title: A_TBS45_51


title: WT-0hr-replicate 2

source_name: WT oviduct 0hr

value: no treatment


title: 24531-50-30268

description: Gene expression data from GHD patient


title: A_TBS45_47


title: 20133412 Mesenteric Fat High gain-high intake


title: A_TBS45_48


title: 24531-50-30287

description: Gene expression data from GHD patient


title: WT-0hr-replicate 3


title: 24531-50-30248

description: Gene expression data from GHD patient

data_processing:
Processing and normalization of gene expression data were performed using a Robust Multi-array Average background correction modified for probe sequence with quantile normalization and median polish (Partek Genomics Suite, version 6.3, St Louis, MO, USA). Confounding effects due to variations in cell populations and outliers were examined by cross validation using principal component analysis and iso-map multidimensional scaling (Qlucore Omics Explorer 2.2, Qlucore, Lund, Sweden).

This sample excluded from downstream analysis.


title: WT-0hr-replicate 1


title: ERKO-0hr-replicate 2

source_name: ERKO oviduct 0hr


title: 24531-50-30374

description: Gene expression data from GHD patient


title: 24531-50-30341

description: Gene expression data from GHD patient


title: ERKO-0hr-replicate 3


title: ERKO-0hr-replicate 1


title: A_TBS45_46


title: 24531-50-30092

description: Gene expression data from GHD patient


title: A_TBS45_42


title: 24531-50-30327

description: Gene expression data from GHD patient


title: A_TBS45_31


title: A_TBS45_39


title: A_TBS45_44


title: A_TBS45_41


title: A_TBS45_33


title: A_TBS45_20


title: A_TBS45_24


title: 24531-50-30325

description: Gene expression data from GHD patient


title: A_TBS45_32


title: 24531-50-30364

description: Gene expression data from GHD patient


title: A_TBS45_16


title: Huvecs, EG treated, 72h, Biological Rep2

first: Rui

middle: Augusto

last: Martins Cordeiro

state: Merseyside

address: Crown Street

department: Integrative Biology

hyb_protocol: Following amplification 15ug of RNA was fragmented and 12.5ug of fragmented labelled RNA was hybridised onto Affymetrix GeneChip C. elegans Genome Arrays as per the manufacturer’s instructions. These were hybridised for 16 hours at 45°C and 60rpm in an Affymetrix hybridisation oven 640. Hybridised arrays were washed using Affymetrix Hybridisation wash and stain kit on a GeneChip Fluidics station 450

scan_protocol: scanned using an Affymetrix GeneChip scanner 3000 7G

data_processing: Affymetrix GeneChip Command Console Software and Affymetric Expression Console were used to generate .CEL files and QC metrics. Analysis of gene expression data was done with the Affymetrix® Transcriptome Analysis Console (TAC) Software. Affymetrix Transcriptome Analysis Console (TAC) Software was used to analyze gene expression data. Normalization was performed using the Robust Multi-chip Average (RMA) method. The data in the matrix table contains the log2 transformed RMA normalized signal from all 15 samples.

source_name: Huvecs exposed to 4°C for 2hours while perfused with LM5 and increasing concentrations of Ethylene Glycol and then left to incubate under normal growth conditions for 72h

label_protocol: labelled using the Affymetric GeneChip 3@ IVT Express labelling kit as per the manufacturer’s instructions using 200ng of total RNA was input into the labelling reaction

extract_protocol: qiagen's Rneasy according to manufacture's instructions

value: Human Umbilical Vein


title: A_TBS45_2

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

label_protocol: In order to produce Cy3- labeled cRNA 100 ng of 176 out of the 180 RNA samples and 50 ng of the RNA samples 100, 166, 168 and 167  was used as template. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. The samples were processed in a high throughput approach using 96-well microtiter plates and the RNeasy® 96 kit (Qiagen) for the purification of the labeled / amplified cRNA.


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 3 DNEV-1

type: other

first: Maria

middle: L

last: Muñoz

address: Av. Instituto Politécnico Nacional 2508

department: Genetics and Molecular Biology

institute: CIVESTAV-IPN

hyb_protocol: DNA microarray chip was prepare for hybridization by washing extensively with 0.1% SDS, rinsed twice with double deionizer water and heated in double deionizer water for 3 min at 95° C. After blocking with prehybridization buffer (4X SSC, 1 %SDS nd 10 mg/ml BSA) for 45 min at 42° C, DNA microarray chip was washed with double deionizer water for 20 s and dried under filtered air flow. A volume of 5 µl containing specific primer for serotype was used. The microarray substrates and coverslips were sealed in a chamber from BIO-RAD (Bio-Rad Laboratories, Inc., Ca., USA) and incubated at 42o C for 16-18 h at high humidity. Coverslip and supports were gently removed (4× SSC in a wash bottle) and arrays were washed by immersion into 1× SSC, 0.1% SDS for 10 min (10 slides in 250 ml), 0.1× SSC, 0.1% SDS twice for 10 min and 0.1× SSC twice for 10 min. Finally, blow the slide dry with air by pushing the liquid away from the spots and towards the outer edges.

scan_protocol: Slides were scanned using Scanner GeneTac LS IV (Genomic Solutions, Molecular Dynamics Generation III) to detect Texas Red fluorescence. For the detection of DENV serotypes we used the excitation lines at 583 nm wavelength of a laser scanner (Scanner Gene TAC LSIV from Genomic Solutions) by adding pixel intensities of each spot image

data_processing: Data was normalized by experiment mean after background correction.

label: Texas Red

molecule: other

organism: Dengue virus

source_name: Specific primer for DENV-1

label_protocol: Peformed during the synthesis of the oligonucleotide by The Midland Certified reagent Company Inc. (Midland, TX, USA).

extract_protocol: The primer was synthesized with 5´ C6 amino linker by The Midland Certified reagent Company Inc. (Midland, TX, USA). Synthesis was validated using each pair of oligonucleotides by RT-PCR and found to yield PCR products of the expected size.

tag: primer

value: 5´-(Texas Red) AGTTTCTTTTCCTAAACACCTCG-3´; DENV-1


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 1 DNEV-1


title: Huvecs, Cold Control, 72h, Biological Rep3

source_name: Huvecs exposed to 4°C for 2hours while perfused with LM5 and then left to incubate under normal growth conditions for 72h


title: CINVESTAV - Dengue 0.6k diagnostic: Experiment 2 DNEV-1


title: Huvecs, EG treated, 72h, Biological Rep1

value: exposed to 4°C for 2hours while perfused with LM5 and increasing concentrations of Ethylene Glycol and then left to incubate under normal growth conditions for 72h


title: 24531-50-30267

description: Gene expression data from GHD patient


title: Huvecs, EG treated, 72h, Biological Rep3


title: A_TBS45_18

extract_protocol: RNA was extracted using the NucleoSpin® RNA kit (Macherey-Nagel) following manufacturer's instructions