title: R137_dksA_ctrl5_ch1_Cy5_670_dksA_NO5_ch2_Cy3_650

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

hyb_protocol: 42C overnight in standard hybridization buffer (Roche Nimblegen)

scan_protocol: GenePix4000B scanner (Molecular Devices, Sunnyvale, CA) using Acuity 4.0 software.

data_processing: Signal extraction and quantitation with Roche’s NimbleScan 2.4 package

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

label_protocol: Incorporation of dye using about 1200U Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA), 40ng/ul random hexamer primers, 4nmol Cy dUTP (GE Healthcare, Fairfield, CT), and 80U RNAse Inhibitor (Roche, Indianapolis, IN), in 60ul reactions. Reverse transcription was performed for 2h at 42˚C, and the pH adjusted with 50mM NaOH. After a 10min incubation at 70˚C reactions were neutralized using HCl. Labeled cDNA was purified using the QIAGEN PCR purification kit as suggested by the manufacturer (Qiagen, Valencia, CA).

growth_protocol: dksa minus salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, let grow for an additional 30 min, replicate 05: 110208

extract_protocol: High Pure RNA isolation kit (Roche)

value: DKSA mutant

tag: agent

value: CTRL

growth_protocol: dksa minus salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, and treated with 5 mm detanonoate for 30 min, replicate 05: 110208

value: NO


title: rna14-1, biological rep. 2

status: Public on Mar 31 2014

type: RNA

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .DAT image files for each array were converted into .CEL files using Affimetrix GCOS software. These .CEL files were normalized using Robust Microarray Average (RMA) method by Irrizarry et al. Statistical analysis was performed using the limma package  (affyImGUI interface) of R/Bioconductor project. Genes showing at least 2-fold expression change compared to wild type, false discovery rate-adjusted p-value<0.01, B-statistic value>2, and average log2 intensity A>7 were considered as significantly altered.

label: biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Mutant rna14-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

growth_protocol: Each strain was grown to mid-log phase in liquid YPAD medium at 30°C

extract_protocol: Total RNA were isolated with the RNeasy Midi kit (QIAGEN)

tag: strain

value: rna14-1 W

tag: genotype


title: Normal brain tissue 1 - Normal-HT-12

city: Toronto

first: Pawel

last: Buczkowicz

state: Ontario

address: 686 Bay Street

department: Paediatric Laboratory Medicine

country: Canada

institute: Hospital for Sick Children

description:
Dx: diagnosis, OS: overral survival
Hybridized to HT-12

hyb_protocol: RNA was hybridized to each array according to the manufacturer's standard hybridization protocol.

scan_protocol: The arrays were scanned using standard Illumina scanning protocol

data_processing: The data was normalized using per-probe median centered quantile normalzation in Partek Genomic Suite v6.6

label: Biotin

organism: Homo sapiens

source_name: Normal brain tissue 1 - Normal

label_protocol: As per manufacturer (Illumina)

extract_protocol: Total RNA was extracted from formalin fixed parrafin embedded (FFPE) biopsy and autopsy samples from DIPG patients using the TRIzol extraction method. RNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Bioanalyzer 2100.

tag: tissue

value: normal brain

tag: cell type

tag: gender

tag: age at dx (years)

tag: os (years)


title: R127s1_dksA_NO1_ch1_Cy5_795_dksA_ctrl1_ch2_Cy3_585

country: USA

growth_protocol: dksa minus salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, and treated with 5 mm detanonoate for 30 min, replicate 01: 110109

tag: genotype/variation

growth_protocol: dksa minus salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, let grow for an additional 30 min, replicate 01: 110109


title: Diffuse Intrinsic Pontine Glioma 64 - Tumour-HT-12

value: Diffuse Intrinsic Pontine Glioma

value: DIPG

value: F


title: D_lesional_day43

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

hyb_protocol: Procedure used standard Affymetrix protocol.

data_processing: Scans were imported into Rosetta Resolver and pre-processed using the 'Resolver Affymetrix Rosetta Intensity Profile Builder (saves reporters)' pipeline.

source_name: Lesional skin biopsy from psoriasis patient, 700mg brodalumab treated, day 43

label_protocol: Total RNA was reverse-transcribed and amplified using the NuGen Ovation™ RNA amplification system V2 with Ovation™WB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation™ cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

extract_protocol: The frozen biopsy was homogenized using a TissueRuptor, and RNA was extracted using the mirVana™ kit with on-column DNase treatment.

tag: disease state

value: psoriasis

value: lesional skin

tag: treatment

value: 700mg brodalumab

tag: time

value: day 43

tag: patient

value: D


title: Tissue_CR_rep8

city: Cluj-Napoca

first: Ovidiu

last: Balacescu

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute I. Chiricuta

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_08

hyb_protocol: After fragmentation to an average size of 60 – 100 nucleotides, each cRNA was hybridized to whole-human-genome 4x44K microarray slides (product G4112F; Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven, following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: After hybridization, microarray slides were washed as follow: 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute at 37°C with GE Wash Buffer 2 (Agilent), 10 seconds with Acetonitrile at rome temperature and 30 seconds with Stabilization and Drying solution at room temperature. The slides were scanned with an Agilent G2505B US45102867 microarray scanner, and gridding was performed with Feature Extraction Software v.10.5.1.1

data_processing: The scanned images were analyzed with Feature Extraction Software version 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid:014850_D_20070820) to obtain Median Signal intensities. Quantile method was used for normalization.  Features flagged in Feature Extraction as Saturated and Feature Non-uniform outliers were excluded.

source_name: Cervical tumor tissue, complete response, replicate 8

label_protocol: Microarray probes (cRNA-Cy3) were synthesized from 200 ng of total RNA in two reaction steps using a one-color Agilent Low Input Quick Amp Labeling Kit according to the manufacturer’s instructions. All labeled cRNAs (Cy3) were purified using an RNeasy Mini kit (Qiagen) and were evaluated for quality control using a Nanodrop ND-1000 spectrophotometer. All cRNAs had a minimum yields of 1.65 µg and specific activities of 6 pmol/µl Cy3 per μg cRNA and were selected for further analysis.

growth_protocol: Twenty-one patients with locally advanced squamous cell carcinoma (FIGO stage IIB-IIIB) were enrolled in the genomics study. A tissue fragment from a primary biopsy specimen was harvested from each patient prior to the therapy. Tissue samples were stored in liquid nitrogen until use for RNA extraction.

extract_protocol: Tumor sections with a minimum of 70% tumor cells were harvested by macrodissection from primary biopsies of cervical cancers. Total RNA was extracted with TriReagent (Sigma-Aldrich) and purified using an RNeasy Mini kit (Qiagen) according to the manufacturer’s protocols.Extracted RNA was assessed for quality with a Lab-on-a-chip Bioanalyzer 2100 (Agilent Technologies). The RNA Integrity Number (RIN) and rRNA 28S/18S ratio were used to define the quality of the total RNA. The RNAs with RINs >7.5 and rRNA 28S/18S ratios >1.8 were used for further analysis. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: The patients were treated with concomitant chemoradiotherapy (CRT). The radiotherapy protocol includes external beam radiotherapy (EBRT) to the pelvis delivered by a linear accelerator at 15MV for a dose of 46Gy/23 fractions and a cervical boost given by intracavitary high-dose-rate (HDR) brachytherapy (BT) in a dose of 10 Gy/2 fractions. Cisplatin was administered concomitant with the radiotherapy as a radiosensitizer. The tumor response was clinically evaluated at 6 months after the end of the CRT treatment and was defined as complete response (CR) or non-complete response (NCR) (partial response and stable disease).

value: cervical primary biopsy

tag: clinical response (6 months after chemoradiotherapy treatment)

value: complete response


title: Tissue_CR_rep6

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_06

source_name: Cervical tumor tissue, complete response, replicate 6


title: A_lesional_day43

scan_protocol: Procedure used standard Affymetrix protocol.

source_name: Lesional skin biopsy from psoriasis patient, 140mg brodalumab treated, day 43

value: 140mg brodalumab

value: A


title: R125s1_wt_ctrl3_ch1_Cy5_650_wt_NO3_ch2_Cy3_520

growth_protocol: wt salmonella grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, let grow for an additional 30 min, replicate 03: 110117

value: WT

growth_protocol: wt salmonella grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, and treated with 5 mm detanonoate for 30 min, replicate 03: 110117


title: Diffuse Intrinsic Pontine Glioma 67 - Tumour-HT-12

value: M


title: R136_wt_ctrl5_ch1_Cy5_680_wt_NO5_ch2_Cy3_550

growth_protocol: wt salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, let grow for an additional 30 min, replicate 05: 110208

value: CTRL

growth_protocol: wt salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, and treated with 5 mm detanonoate for 30 min, replicate 05: 110208

value: NO


title: Z_lesional_day43

value: Z


title: R126s1_wt_NO1_ch1_Cy5_680_wt_ctrl1_ch2_Cy3_530

growth_protocol: wt salmonella grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, and treated with 5 mm detanonoate for 30 min, replicate 01: 110109

growth_protocol: wt salmonella grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, let grow for an additional 30 min, replicate 01: 110109


title: Tissue_CR_rep5

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_05

source_name: Cervical tumor tissue, complete response, replicate 5


title: Diffuse Intrinsic Pontine Glioma 62 - Tumour-HT-12

value: Diffuse Intrinsic Pontine Glioma


title: Tissue_CR_rep4

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_04

source_name: Cervical tumor tissue, complete response, replicate 4


title: Tissue_CR_rep7

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_07

source_name: Cervical tumor tissue, complete response, replicate 7


title: W_lesional_day43

value: W


title: R128s1_dksA_ctrl3_ch1_Cy5_620_dksA_NO3_ch2_Cy3_510

growth_protocol: dksa minus salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, let grow for an additional 30 min, replicate 03: 110117

value: DKSA mutant

growth_protocol: dksa minus salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, and treated with 5 mm detanonoate for 30 min, replicate 03: 110117


title: Diffuse Intrinsic Pontine Glioma 61 - Tumour-HT-12

value: DIPG


title: Diffuse Intrinsic Pontine Glioma 63 - Tumour-HT-12

value: F


title: J_lesional_day43

value: psoriasis

value: lesional skin

value: 700mg brodalumab

value: J


title: O_lesional_day43

source_name: Lesional skin biopsy from psoriasis patient, placebo treated, day 43

value: placebo

value: day 43

value: O


title: Tissue_CR_rep2

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_02

source_name: Cervical tumor tissue, complete response, replicate 2

value: cervical primary biopsy

value: complete response


title: Tissue_CR_rep3

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_03

source_name: Cervical tumor tissue, complete response, replicate 3


title: Diffuse Intrinsic Pontine Glioma 58 - Tumour-HT-12


title: Tissue_CR_rep1

description:
Gene expression in cervical primary biopsy of patient with 6-month complete response.
TT_01

source_name: Cervical tumor tissue, complete response, replicate 1


title: Diffuse Intrinsic Pontine Glioma 60 - Tumour-HT-12

value: M


title: X_lesional_day43

value: X


title: I_lesional_day43

value: I


title: K_lesional_day43

value: K


title: Diffuse Intrinsic Pontine Glioma 28 - Tumour-HT-12

value: Diffuse Intrinsic Pontine Glioma


title: Diffuse Intrinsic Pontine Glioma 29 - Tumour-HT-12


title: Diffuse Intrinsic Pontine Glioma 30 - Tumour-HT-12


title: F_lesional_day43


title: C_lesional_day43

value: C


title: BMDM, IFNg+LPS, 1

city: South San Francisco

first: Jason

middle: A

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

description: Gene expression data from bone marrow derived macrophages treated with IFNg and LPS

hyb_protocol: 12.5 micrograms of cRNA was fragmented and hybridized to Mouse Genome 430 2.0 arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.

scan_protocol: Arrays were washed and stained using Affymrtrix HWS kit using their Fluidics station and then scanned on GeneChip scanner 3000.

organism: Mus musculus

source_name: Bone marrow derived macrophages, treated with IFNg and LPS

label_protocol: Preparation of cRNA was done using Affymetrix 3'IVT Express kit and protocol provided by Affymetrix. Briefly, 0.5 ug of total RNA was converted into double-stranded cDNA and used to generate biotin labeled cRNA which was then purified.

extract_protocol: The samples were harvested after 24h and RNA was isolated using Qiagen RNeasy mini kit.

treatment_protocol: Bone marrow derived macrophages from C56BL/6J mice were either untreated or treated with 10 ng/ml of IFNg , LPS or 10 ng/ml of IFNg+10 ng/ml of LPS.

value: bone marrow

value: macrophages

value: IFNg+LPS


title: BMDM, IFNg+LPS, 4


title: Diffuse Intrinsic Pontine Glioma 57 - Tumour-HT-12

value: DIPG

value: F


title: BMDM, IFNg+LPS, 3


title: BMDM, LPS, 3

description: Gene expression data from bone marrow derived macrophages treated with LPS

source_name: Bone marrow derived macrophages, treated with LPS

value: LPS


title: Diffuse Intrinsic Pontine Glioma 25 - Tumour-HT-12


title: V_lesional_day15

source_name: Lesional skin biopsy from psoriasis patient, placebo treated, day 15

value: psoriasis

value: lesional skin

value: placebo

value: day 15

value: V


title: P_lesional_day15

source_name: Lesional skin biopsy from psoriasis patient, 350mg brodalumab treated, day 15

value: 350mg brodalumab

value: P


title: BMDM, IFNg+LPS, 2


title: B_lesional_day15

value: B


title: Diffuse Intrinsic Pontine Glioma 27 - Tumour-HT-12

value: M


title: Diffuse Intrinsic Pontine Glioma 24 - Tumour-HT-12

value: Diffuse Intrinsic Pontine Glioma


title: BMDM, LPS, 4


title: Diffuse Intrinsic Pontine Glioma 26 - Tumour-HT-12


title: Y_lesional_day15

value: Y


title: Diffuse Intrinsic Pontine Glioma 22 - Tumour-HT-12


title: Q_lesional_day15

value: Q


title: Diffuse Intrinsic Pontine Glioma 21 - Tumour-HT-12


title: BMDM, LPS, 1

value: bone marrow

value: macrophages


title: L_lesional_day15

value: L


title: BMDM, LPS, 2


title: BMDM, IFNg, 4

description: Gene expression data from bone marrow derived macrophages treated with IFNg

source_name: Bone marrow derived macrophages, treated with IFNg

value: IFNg


title: BMDM, IFNg, 3


title: Diffuse Intrinsic Pontine Glioma 18 - Tumour-HT-12

value: DIPG


title: Diffuse Intrinsic Pontine Glioma 16 - Tumour-HT-12


title: G_lesional_day15

source_name: Lesional skin biopsy from psoriasis patient, 140mg brodalumab treated, day 15

value: psoriasis

value: 140mg brodalumab

value: G


title: S_lesional_day15

value: lesional skin

value: placebo

value: day 15

value: S


title: U_lesional_day15

value: U


title: H_lesional_day15

value: 350mg brodalumab

value: H


title: Diffuse Intrinsic Pontine Glioma 17 - Tumour-HT-12

value: Diffuse Intrinsic Pontine Glioma

value: F


title: BMDM, IFNg, 1

value: bone marrow


title: BMDM, untreated, 4

description: Gene expression data from untreated bone marrow derived macrophages

source_name: Bone marrow derived macrophages, untreated

value: macrophages

value: Untreated


title: BMDM, untreated, 1


title: Diffuse Intrinsic Pontine Glioma 14  - Tumour-HT-12


title: Diffuse Intrinsic Pontine Glioma 15 - Tumour-HT-12

value: M


title: E_lesional_day15

value: E


title: Diffuse Intrinsic Pontine Glioma 19 - Tumour-HT-12

value: DIPG


title: BMDM, IFNg, 2

value: IFNg


title: BMDM, untreated, 3


title: BMDM, untreated, 2


title: T_lesional_day15

value: psoriasis

value: T


title: M_lesional_day15

value: lesional skin


title: Diffuse Intrinsic Pontine Glioma 12 - Tumour-HT-12


title: Diffuse Intrinsic Pontine Glioma 13 - Tumour-HT-12


title: Smeg-infection-J774-4h

city: San Diego

first: Jay

last: Zhang

state: Southport

address: Gold Coast Campus

country: Australia

institute: Griffith Health Institute

description: Gene expression data from murine macrophage after infection

hyb_protocol: Standard Affymetrix 3' IVT Express Kit

scan_protocol: Affymetrix 7G scanner

data_processing: .chp files were generated by Expression Console (Version 1.1, Affymetrix, Santa Clara, CA, USA) using global normalization to a target intensity of 200 by the MAS5 algorithm

source_name: Non-pathogenic mycobacteria species

label_protocol: Standard Affymetrix 3' IVT Express Kit

growth_protocol: The murine macrophage cell line J774A.1 (American Type Culture Collection, ATCC) was used in this study. J774 cells were cultured in DMEM (HyClone from Thermo Scientific) medium containing 10% (v/v) fetal calf serum, 50 μg/ml of penicillin/streptomycin and 2 mM glutamine. Cells were used to conduct experiments when they reached ~70% confluence. All treatments were performed in serum-free medium.   All mycobacteria were grown on Middlebrook 7H11 agar at 37°C, 5% CO2-95% air atmosphere. For broth cultures, H37Ra (ATCC 25177, the lab strain of MTB) and BCG (ATCC 35734, the vaccine strain of M. Bovis) were grown in 7H9 medium supplemented with glycerol (0.5%, vol/vol) and OADC supplement. M. smegmatis (mc2-155, ATCC 700084) was grown in 7H9 medium supplemented with glycerol (0.5%, vol/vol) and ADS supplement. All liquid cultures were supplemented with 0.05% Tween 80.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol, followed by on-column digestion of DNA using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA). RNA quantity and quality were assessed with a Qubit RNA Assay Kit using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cells were infected 4 hrs

tag: cell line

tag: infection

value: Smeg


title: Diffuse Intrinsic Pontine Glioma 10 - Tumour-HT-12


title: Diffuse Intrinsic Pontine Glioma 11- Tumour-HT-12


title: A_lesional_day15

value: 140mg brodalumab

value: day 15

value: A


title: H37ra-infection-J774-4h

source_name: pathogenic derived mycobacteria species


title: D_lesional_day15

source_name: Lesional skin biopsy from psoriasis patient, 700mg brodalumab treated, day 15

value: 700mg brodalumab

value: D


title: R_lesional_day15

value: R


title: J_lesional_day15

value: J


title: W_lesional_day15

value: W


title: WT

city: Tampa

first: Ed

last: Seto

state: FL

address: 12902 Magnolia Dr.

department: Molecular Oncology

institute: H. Lee Moffitt Cancer Center

description: Gene expression data from freshly isolated macrophages from WT mice

hyb_protocol: 2.5 ug of fragmented and labeled cDNA was hybridized for 16 hr at 45C to the Affymetrix Mouse Gene 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the FS450_007 wash protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scaner.

data_processing: The data were analyzed with the Affymetrix Expression Console software v 1.2.1 using the RMA algorithm with default analysis settings.

source_name: macrophages

label_protocol: Biotinylated cDNA was prepared from 100 ng of total RNA using the Ambion WT Expression Kit according to the protocol. 5.5 ug of the the resulting single-stranded 2nd cycle cDNA was labeled using the Affymetrix GeneChip WT Terminal Labeling and Hybridization Kit.

growth_protocol: Thioglycollate induced peritoneal macrophages were isolated from HDAC11 knockout and WT mice. The cells were cultured overnight in RPMI+10%FBS medium. Total RNA was extracted form adherent cell population.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

treatment_protocol: No treatment was performed.

value: wild type

value: macrophages


title: Diffuse Intrinsic Pontine Glioma 9 - Tumour-HT-12

value: Diffuse Intrinsic Pontine Glioma

value: M


title: Z_lesional_day15

value: Z


title: C_lesional_day15

value: psoriasis

value: C


title: Diffuse Intrinsic Pontine Glioma 7 - Tumour-HT-12

value: DIPG


title: Diffuse Intrinsic Pontine Glioma 6 - Tumour-HT-12


title: Diffuse Intrinsic Pontine Glioma 1 - Tumour-HT-12

value: F


title: X_lesional_day15

value: lesional skin

value: X


title: K_lesional_day15

value: day 15

value: K


title: Control-J774-4h

source_name: Control


title: O_lesional_day15

value: placebo

value: O


title: HDAC11 KO

description: Gene expression data from freshly isolated macrophages from HDAC11 knockout  mice.

value: HDAC11 knockout


title: Diffuse Intrinsic Pontine Glioma 4 - Tumour-HT-12


title: Diffuse Intrinsic Pontine Glioma 8 - Tumour-HT-12


title: wholebody_1000ug/L_168pf_1

city: Muttenz

first: Susanne

last: Faltermann

address: Gründenstrasse 40

department: IEC

country: Switzerland

institute: Fachhochschule Nordwestschweiz

description: SAMPLE 9

hyb_protocol: Cy-3-labeled cRNA samples (1.65 µg) were mixed with Agilent blocking solution, subsequently fragmented randomly to 100-200 bp at 65 °C with fragmentation buffer and resuspended in hybridization buffer as provided by the gene expression hybridization Kit (Agilent Technologies). Target cRNA samples (100 µL) were hybridized to the Agilent Zebrafish 4x44K Gene Expression Microarray for 17 h at 65 °C. The hybridized arrays were then washed using Agilent GE wash buffers 1 and 2 according to the manufacturer's instructions.

scan_protocol: Slides were scanned by an Agilent Microarray Scanner (Agilent p/n G2565BA) at 5 μm resolution with the green photomultiplier tube set to 100% and a scan area of 61 x 21.6 mm.

data_processing: Image generation and feature extraction was performed using the Agilent Feature Extraction (FE) software version 9.5.3. Quality control was additionally considered before performing the statistical analysis. These included array hybridization pattern inspection: absence of scratches, bubbles, areas of non-hybridization, proper grid alignment, spike performance in controls with a linear dynamic range of 5 orders of magnitude and the number of green-feature non-uniformity outliers which should be below 100 for all samples.

organism: Danio rerio

source_name: Eleuthero-embryo whole body_168 hpf_1000ug/L CP1020

label_protocol: Total RNA samples (600 ng) were reverse-transcribed into double-strand cDNA in the presence of RNA poly-A controls with the Agilent One-Color RNA Spike-In Kit. Cy3 labeling and hybridization were performed according to the manufacturer's manual. After reverse-transcription of RNA into double-stranded cDNA, double-strand cDNA was in vitro transcribed into cRNA in the presence of Cy3 labeled nucleotides using a Low RNA Input Linear Amp Kit +Cy dye (Agilent Technologies, Basel, Switzerland). The Cy3-labeled cRNA was purified using an RNeasy mini kit (Qiagen, Basel, Switzerland), and quality and quantity was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. Only cRNA samples with a total cRNA yield higher than 2 µg and a dye incorporation rate between 9 pmol/µg and 20 pmol/µg were used for hybridization.

extract_protocol: Total RNA was extracted from zebrafish eleuthero-embryos using the RNeasy Mini Kit (Qiagen, Basel, Switzerland). Total RNA concentrations were measured spectrophotometrically using a NanoDrop ND-1000 UV-VIS Spectrophotometer at 260 nm and the Experion (Biorad). The integrity of each RNA sample was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Basel, Switzerland). Only samples containing a 260/280 nm ratio between 1.8-2.1, a 28S/18S ratio between 1.5-2 and an RNA integrity number (RIN) > 8 were processed further.

treatment_protocol: All zebrafish embryos used in the experiments were hatched. They were placed in 100mL covered glass beakers of reconstituted water (total hardness of 125 mg/L as CaCO3 and a conductivity of 270 μS/cm) and the appropriate concentration of CP1020 or DMSO (0.01 %, solvent control). The water temperature was held constant at 27±1 °C with the photoperiod set at 16:8 h light/dark. The static exposure setup consisted of 4 replicates of water control, solvent control (0.01 % DMSO) and two CP1020 doses. A total of 60 hatched embryos per replicate (n = 4) were exposed for 96 h to nominal concentrations of 100 μg/L and 1000 μg/L CP1020, respectively. Daily examinations under the stereo microscope were performed to check mortality and Eleuthero – embryos behaviour. The quality of the exposure water was continuously monitored by oxygen concentration determination (>70%), the pH value (6.7-7.2) and the temperature (27±1 °C). At the end of exposure,  2 x 30 eleuthero-embryos of each replicate were pooled in RNAlater for microarray and qRT-PCR.

value: Eleuthero-embryo whole body

tag: developmental stage

value: 168 hpf

tag: exposed to


title: wholebody_1000ug/L_168pf_3

description: SAMPLE 11


title: Diffuse Intrinsic Pontine Glioma 3 - Tumour-HT-12


title: wholebody_1000ug/L_168pf_2

description: SAMPLE 10


title: I_lesional_day15

value: 700mg brodalumab

value: I


title: Cmer_062907_b

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

hyb_protocol: Samples were hybridized per Nimblegen Hybridization System protocol v1.5 to a 12x135K array, and incubated with mixing for 19 hours at 42C.

scan_protocol: Slides were scanned on a GenePix 4000B scanner.

data_processing: The raw data was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

organism: Cyanidioschyzon merolae

source_name: Cyanidiales algal mat material, no UV treatment

label_protocol: 1 ug cDNA was labeled with Cy3 using NimbleGen's One-Color DNA Labeling kit (06370438001) per manufacturer protocol.

growth_protocol: Samples were taken at varying time points at Dragon Spring and/or Lemonade Creek from July 2007 to July 2010, and were collected axenically by transferring algal-covered rocks into sterile FalconTM tubes along with site water, vigorously shaking the tube by hand to dislodge the algal cells from the rock, transferring the algae to a sterile 15 mL Falcon tube, and flash freezing the material in a dry-ice/ethanol bath. The frozen samples were then transported back to the lab and stored at -80C until used for RNA extraction.

extract_protocol: Total RNA was extracted using the FastRNA Pro Soil-Direct Kit (MP Biomedicals, Solon, OH) and DNA was removed using the TURBO DNA-free kit (Ambion, Austin, TX). RNA quality and concentration were determined by analysis with an Agilent 2100 Bioanalyzer at the Functional Genomics Core Facility (Montana State University, Bozeman, MT USA).

treatment_protocol: Two types of irradiance screening materials were used in the field experiments, both transparent to photosynthetically active radiation (PAR) and installed in triplicate. The OP-4 filter material (Cyro Industries, Woodcliff Lake, NJ) transmitted about 90.0% of VIS, UVA, and UVB radiation, whereas the UF-5 filter material (Autohaas N. Am, Philadelphia, PA) transmitted about 90.0% VIS but blocked 99.9% of all UV below 390 nm (Norris et al. FEMS Microbiol. Rev. 39:193-209).

value: Cyanidiales algal mat material

value: no UV treatment

tag: sampling time point

tag: biological replicate

tag: location

value: Dragon Spring, Norris Geyser Basin, Yellowstone National Park


title: Diffuse Intrinsic Pontine Glioma 2 - Tumour-HT-12

tag: tissue

value: Diffuse Intrinsic Pontine Glioma

tag: cell type


title: Cmer_062907_c


title: wholebody_1000ug/L_168pf_4

description: SAMPLE 12


title: F_lesional_day15

value: psoriasis


title: Cmer_012508_a

value: January 25, 2008


title: Cmer_012508_b


title: Cmer_012508_c


title: Cmer_082008_UF5_c

source_name: Cyanidiales algal mat material, UF-5 filter

value: UF-5 filter material

tag: treatment description

value: transmits 90.0% of VIS, blocks 99.9% of all UV below 390 nm

value: August 8, 2008

value: Lemonade Creek, Amphitheater Springs, Yellowstone National Park


title: wholebody_100ug/L_168pf_3

description: SAMPLE 7

source_name: Eleuthero-embryo whole body_168 hpf_100ug/L CP1020


title: wholebody_100ug/L_168pf_4

description: SAMPLE 8


title: Cmer_082008_UF5_b


title: Cmer_062907_a


title: Cmer_082008_UF5_a


title: Cmer_082008_OP4_c

source_name: Cyanidiales algal mat material, OP-4 filter

value: OP-4 filter material

value: transmits 90.0% of VIS, UVA, and UVB radiation


title: Cmer_082008_OP4_b


title: wholebody_DMSO_168hpf_2

description: SAMPLE 2

source_name: Eleuthero-embryo whole body_168 hpf_solvent control_0.01% DMSO

value: 0.01% DMSO (control) for 96h


title: wholebody_100ug/L_168pf_2

description: SAMPLE 6

value: Eleuthero-embryo whole body


title: wholebody_100ug/L_168pf_1

description: SAMPLE 5

value: 168 hpf


title: 2013 control grapes, EL35,biological replicate 2

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

description: Gene expression data from skin and pulp of control grapes at veraison stage (EL 35)

hyb_protocol: If the quality control was correct, then 4 µg of labelled cDNA were hybridized. Hybridization solution (NimbleGen Hybridization kit) was added to each labelled cDNA and hybridization was performed for 16 h at 42ºC in a HS 4 Hybridization station (NimbleGen-Roche).

scan_protocol: Hybridized microarrays were washed with Wash buffer kit (NimbleGen-Roche) and scanned at 532 nm and 2 µm resolution in a DNA Microarray Scanner with Surescan High-Resolution Technology (Agilent technologies).

data_processing: After evaluation of hybridization quality by Experimental metrics report implemented in NimbleScan Software version 2.6 (NimbleGen-Roche), probeset signal values from all the microarray hybridizations were background corrected and normalized together using Robust Microarray Average (RMA) (Irizarry et al., 2003) in NimbleScan Software, which produces a calls file for each sample with normalized expression data for each gene.

organism: Vitis vinifera

source_name: veraison berries

label_protocol: cDNA was synthesized from 10 µg of total RNA using cDNA Synthesis System Kit (NimbleGen-Roche). The cDNA preparation (1 µg) was amplified and labelled with Cy3-random nonamers using One color labeling kit (NimbleGen-Roche).

growth_protocol: Field experiments were conducted in an experimental vineyard with 15 year old grapevines Vitis vinifera L. of cv. Trincadeira, at the Instituto Superior de Agronomia, University of Lisbon, Portugal.

extract_protocol: RNA extraction was carried out according to Fortes et al. (2011 BMC Plant Biology). A DNAse treatment was performed according to suppliers’ instructions (Invitrogen, San Diego, CA, USA). Samples were then extracted in phenol/chloroform/isoamylalcohol (75:24:1,v/v/v), precipitated with sodium acetate and ethanol, washed in 70% ethanol and dissolved in DEPC-treated water. RNA was further purified using RNeasy Plant Mini kit according to the manufacturer’s instructions (Quiagen, Valencia, CA, USA).

treatment_protocol: The Botrytis cinerea isolate used in this experiment was obtained from diseased grapevine plants and maintained in potato dextrose agar (PDA, Difco, Detroit, E.U.A.), at 5°C. Conidia production was achieved by exposing inoculated Petri dishes with PDA to continuous fluorescent light, at 24°C. Conidia were harvested from 14- to 20-day-old cultures and collected by rubbing with phosphate buffer (0.03M KH2PO4), filtered through cheesecloth to remove mycelia, and the concentration determined and adjusted to 105 conidia ml-1.  Infections were made on berries by spraying the conidia suspension at developmental stage of pepper-corn size (EL 29). Control clusters were sprayed with phosphate buffer. Following inoculation, the clusters were incubated by enclosing them in individual plastic bags for a period of one week. Collection of samples was performed in two stages of development at pre-véraison (EL33) and véraison (EL35) (Coombe, 1995). For each time point and each treatment (infected and mock) three-four biological replicates were collected. Trincadeira berries were harvested around 10 a.m. and were immediately frozen in liquid nitrogen and transported to the lab in dry ice and kept at -80ºC.

value: Trincadeira

value: pulp and skin

value: control

tag: Stage

value: veraison stage (EL 35)


title: 2013 control grapes, EL35,biological replicate 1

tag: genotype/variation


title: Cmer_082008_OP4_a

value: Cyanidiales algal mat material


title: 2013 infected grapes, EL35,biological replicate 3

description: Gene expression data from skin and pulp of infected grapes at veraison stage (EL 35)

value: infected with B. cinerea


title: 2013 control grapes, EL35,biological replicate 3


title: 2013 infected grapes, EL35,biological replicate 2


title: 2013 infected grapes, EL35,biological replicate 1


title: wholebody_DMSO_168hpf_4

description: SAMPLE 4


title: Cmer_111609_UF5_c

value: November 6, 2009


title: 2013 infected grapes with B. cinerea, EL33,biological replicate 2

description: Gene expression data from skin and pulp of infected grapes at green stage (EL 33)

source_name: green berries

value: green stage (EL 33)


title: MEF-BP40

city: Taichung

first: Shih-Ping

last: Liu

address: No.6, Hsueh-Shih Road

country: Taiwan

institute: China medical university

description: Gene expression of MEF treated with BP 40ug/ml

hyb_protocol: 0.6 g of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Mouse GE 8×60K microarray (Agilent Technologies, USA) at 65°C for 17 h.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: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3. Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA),

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature. Normalized signal by 75th percentile.

source_name: MEF

label_protocol: 0.2 g of total RNA was amplified by a Low Input Quick-Amp Labeling kit(Agilent Technologies, USA) and labeled with Cy3 (CyDye, PerkinElmer, USA) during the in vitro transcription process.

growth_protocol:
MEF cells were cultured in DMEM with 10% heat-inactivated FBS (both GIBCO BRL), penicillin (100 U per ml), streptomycin (100 µg/ml), non-essential amino acids (0.1 mM), and L-glutamine (2 mM) in a humidified incubator with 5% CO2 (37°C)
MEF-BP 10 and 40ug/ml cells were cultured in DMEM with 10% heat-inactivated FBS (both GIBCO BRL), penicillin (100 U per ml), streptomycin (100 µg/ml), non-essential amino acids (0.1 mM), L-glutamine (2 mM) and BP (10 or 40ug/ml)  in a humidified incubator with 5% CO2 (37°C)

extract_protocol: Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), and followed by RNeasy Mini Kit (Qiagen, Germany). RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).

value: BP 40ug/ml

tag: stain


title: wholebody_DMSO_168hpf_3

description: SAMPLE 3


title: wholebody_DMSO_168hpf_1

description: SAMPLE 1


title: 2013 infected grapes with B. cinerea, EL33,biological replicate 3

tag: treatment


title: Cmer_111609_UF5_a

value: UF-5 filter material

value: transmits 90.0% of VIS, blocks 99.9% of all UV below 390 nm


title: Cmer_111609_UF5_b

value: Lemonade Creek, Amphitheater Springs, Yellowstone National Park


title: Cmer_111609_OP4_a

value: OP-4 filter material


title: MEF-BP10

description: Gene expression of MEF treated with BP 10ug/ml

value: BP 10 ug/ml


title: 2013 control grapes, EL33,biological replicate 3

description: Gene expression data from skin and pulp of control grapes at green stage (EL 33)


title: 2013 infected grapes with B. cinerea, EL33,biological replicate 1


title: MEF, control

description: Gene expression of MEF


title: Cmer_111609_OP4_c

value: transmits 90.0% of VIS, UVA, and UVB radiation


title: 2013 control grapes, EL33,biological replicate 1


title: Cmer_111609_OP4_b


title: Skel. Muscle-1

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Tissue was extracted from three different pig (12 month old) and total RNA was pooled.

hyb_protocol: Fragmented aRNA was hybridized to pre-hybridized 90K Combimatrix microarrays. Pre-hybridization was performed for 2 hours at 42° C with the following solution: 1X Hyb solution stock prepared as suggested by Combimatrix; 5X Denhardt’s solution; Salmon sperm DNA 100 ng/μl; SDS 0.05%. Hybridizations were performed with 4.8 μg of fragmented aRNA at 42° C for 18 hours mixing the hybridization solution (1X Hyb solution stock prepared as suggested by Combimatrix; 25% of DI Formammide; Salmon sperm DNA 100 ng/μl; SDS 0.04% and 4.8 ug of fragmented aRNA). After hybridization microarrays were washed with:  6X SSPET (SSPE added with 0.05% of Tween-20) preheated at 42° C for 5 min.;  3X SSPET for 1 min. at room temperature;  0.5X SSPET for 1 min. at room temperature;  PBST for 1 min. at room temperature;  The array chamber was than filled with Biotin Blocking solution and incubated at room temperature for 1 hour. Labeling was performed incubating the microarray with the Dye labeling solution (Cy3 streptavidin in biotin blocking solution) for 1 hour at room temperature.  After we performed these wash steps:   PBST for 1 min. at room temperature two times;  PBS for 1 min. at room temperature.

scan_protocol: Microarrays were scanned at 3 μm resolution with the VersArray ChiprRaderTM (BioRad)

data_processing:
Before performing all analysis replicated probes (same probe sequence) were averaged (FG Median values were used). Raw data were normalized with the quantile method. After data normalization intensity fluorescence of genes presenting the expression lower than the average of median of all negative controls plus 1 standard deviation (see Filter Table)  was set as NA. We used the negative controls present on the array to calculate background value used in the filter table. Genes presenting NA in more than 6 experiments were excluded from the analysis (see Analysis Table).
R based quantile normalization.

organism: Sus scrofa

source_name: Skeletal muscle. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

label_protocol: 1 μg of total RNA was amplified with biotin dUTP and after hybridization the Cy3-streptavidin was added. Amplification was performed with the Ambion MessageAmp™ II aRNA Amplification kit (Ambion). The procedure includes reverse transcription with an oligo-dT primer bearing a T7 promotor using reverse transcriptase to produce the first-strand cDNA. After second-strand synthesis and cleanup, the cDNA becomes a template for the in vitro transcription technology to generate antisense RNA (aRNA) copies of each mRNA molecule. Biotinilated UTPs were incorporated into the aRNA during the in vitro transcription reaction. Following purification 18 μg of aRNA was fragmented using the Ambion Fragmentetion Kit (Ambion). aRNAs and fragmented aRNAs were tested on Agilent Bioanalizer 2100 using RNA 6000 Nano LabChip. All aRNAs presented length from 300 and 4,000 nucleotides while fragmented aRNAs from 50 and 250 nucleotides.

growth_protocol: Pigs were maintained at normal food regime

extract_protocol: Total RNA and miRNAs were extracted independently from each tissue sample by TRIzol reagent (Invitrogen) in association with PureLink miRNA isolation kit (Invitrogen). Briefly, approximately 200 mg of tissue was homogenized in 3.5 ml of TRIzol reagent (Invitrogen) using a tissue homogenizer (IKA Werke). After chloroform addition and centrifugation colorless upper aqueous phase containing RNAs was added with 96-100% ethanol to obtain a final concentration of 35% of ethanol and charged to PureLink membrane (Invitrogen) to separate total RNA and small RNAs from the same sample following the manufacturer manual. Total RNA and small RNAs were quantized using Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific). Samples derived from the same tissues were pooled adding the same quantity from the three pigs used. “Pool tissues” were performed using 1 ug of total RNA from each sample while for small RNAs it was used 1.5 ug from each sample. Quality of total RNA of pooled samples was tested on Agilent Bioanalizer 2100 using RNA 6000 Nano LabChip.

treatment_protocol: After the sedation, pigs were sacrificed and portions of the described organs were took and maintained in the RNALater solution (Ambion), excluding blood that was collected in the BD Vacutainer CPT cell preparation tubes, and processed according to manufacturer's directions to recover white blood cells..

value: Skeletal muscle

tag: age

value: 12 month old

tag: breed

value: vietnamite


title: Cmer_072209_UF5_c


title: Skel. Muscle-2


title: Cmer_072209_UF5_a


title: Tongue-2

source_name: Tongue. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Tongue


title: Cmer_072209_UF5_b


title: Cmer_072209_OP4_c


title: Tongue-1


title: 2013 control grapes, EL33,biological replicate 2

value: Trincadeira

value: pulp and skin

value: control


title: Cmer_072209_OP4_b

value: Cyanidiales algal mat material


title: BCG-infection-J774-4h

value: BCG


title: Ventricle sin.-2

source_name: Ventricle sinistrum. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Ventricle sinistrum


title: Atrium sin.-2

source_name: Atrium sinistrum. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Atrium sinistrum


title: Atrium sin.-1


title: Tissue Pool

description: All tissues were extracted from three different pig (12 month old) and same tissues were pooled.

hyb_protocol: Fragmented aRNA was hybridized to pre-hybridized 90K Combimatrix microarrays. Pre-hybridization was performed for 2 hours at 42° C with the following solution: 1X Hyb solution stock prepared as suggested by Combimatrix; 5X Denhardt’s solution; Salmon sperm DNA 100 ng/μl; SDS 0.05%. Hybridizations were performed with 4.8 μg of fragmented aRNA at 42° C for 18 hours mixing the hybridization solution (1X Hyb solution stock prepared as suggested by Combimatrix; 25% of DI Formammide; Salmon sperm DNA 100 ng/μl; SDS 0.04% and 4.8 ug of fragmented aRNA). After hybridization microarrays were washed with:  6X SSPET (SSPE added with 0.05% of Tween-20) preheated at 42° C for 5 min.;  3X SSPET for 1 min. at room temperature;  0.5X SSPET for 1 min. at room temperature;  PBST for 1 min. at room temperature;  The array chamber was than filled with Biotin Blocking solution and incubated at room temperature for 1 hour. Labeling was performed incubating the microarray with the Dye labeling solution (Cy3 streptavidin) for 1 hour at room temperature.  After we performed these wash steps:   PBST for 1 min. at room temperature two times;  PBS for 1 min. at room temperature.

data_processing: Microarray images were quantized using imaging Combimatrix software and probes with the same sequence were analyzed to detect those more responsive.  Please see "analysis.txt" file on the Series record for full details about bioinformatics analysis.

source_name: Pool of tissues listed in 'characteristics' below

label_protocol:
Amplification was performed with the Ambion MessageAmp™ II aRNA Amplification kit (Ambion). The procedure includes reverse transcription with an oligo-dT primer bearing a T7 promotor using reverse transcriptase to produce the first-strand cDNA. After second-strand synthesis and cleanup, the cDNA becomes a template for the in vitro transcription technology to generate antisense RNA (aRNA) copies of each mRNA molecule. Biotinilated UTPs were incorporated into the aRNA during the in vitro transcription reaction. Following purification 18 μg of aRNA was fragmented using the Ambion Fragmentetion Kit (Ambion). aRNAs and fragmented aRNAs were tested on Agilent Bioanalizer 2100 using RNA 6000 Nano LabChip. All aRNAs had length from 300 and 4,000 nucleotides while fragmented aRNAs from 50 and 250 nucleotides.
1 μg of total RNA was amplified with biotin dUTP and after hybridization the Cy3-streptavidin was added.

extract_protocol: Total RNA and miRNAs were extracted independently from each tissue sample by TRIzol reagent (Invitrogen) in association with PureLink miRNA isolation kit (Invitrogen). Briefly, approximately 200 mg of tissue was homogenized in 3.5 ml of TRIzol reagent (Invitrogen) using a tissue homogenizer (IKA Werke). After chloroform addition and centrifugation colorless upper aqueous phase containing RNAs was added with 96-100% ethanol to obtain a final concentration of 35% of ethanol and charged to PureLink membrane (Invitrogen) to separate total RNA and small RNAs from the same sample following the manufacturer manual. Total RNA and small RNAs were quantized using Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific). Samples derived from the same tissues were pooled adding the same quantity from the three pigs used. “Pool tissues” were performed using 1 ug of total RNA from each sample. Quality of total RNA of pooled samples was tested on Agilent Bioanalizer 2100 using RNA 6000 Nano LabChip.

treatment_protocol: After the sedation, pigs were sacrificed and portions of the described organs were took and maintained in the RNALater solution (Ambion), excluding blood that was collected in the BD Vacutainer CPT cell preparation tubes, and processed according to manufacturer's directions to recover white blood cells.

value: 12 months old

value: Superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node.


title: Diffuse Intrinsic Pontine Glioma 67 - Tumour-450K

type: genomic

description:
Hybridized to Infinium 450K
Dx: diagnosis, OS: overall survival

hyb_protocol: DNA was hybridized to each array according to the manufacturer's standard hybridization protocol.

scan_protocol: The arrays were scanned using iScan with standard Illumina scanning protocol

data_processing: GenomeStudio v2011.1 using HumanMethulation450_15017482_v.1.2. annotation file

label: Cy5 and Cy3

molecule: genomic DNA

extract_protocol: Genomic DNA was extracted from snap frozen biopsy and autopsy samples from DIPG patients using Qiagen DNeasy Blood & Tissue kit. Bisulfite conversion was performed using EZ DNA methulation kit from Zymo Research using the Infinium Assay Methylation protocol guide.

value: DIPG

tag: gender

value: M

tag: age at dx (years)

tag: os (years)


title: Cmer_070910_UF5_c

value: UF-5 filter material

value: transmits 90.0% of VIS, blocks 99.9% of all UV below 390 nm

value: Lemonade Creek, Amphitheater Springs, Yellowstone National Park


title: Diffuse Intrinsic Pontine Glioma 78 - Tumour-450K

value: F


title: Diffuse Intrinsic Pontine Glioma 63 - Tumour-450K


title: Cmer_070910_UF5_b


title: Kidney-2

source_name: Kidney. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Kidney

value: 12 month old

value: vietnamite


title: Stomach-1

source_name: Stomach. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Stomach


title: Ventricle sin.-1


title: Stomach-2


title: Diffuse Intrinsic Pontine Glioma 64 - Tumour-450K


title: Diffuse Intrinsic Pontine Glioma 61 - Tumour-450K


title: Diffuse Intrinsic Pontine Glioma 62 - Tumour-450K


title: Diffuse Intrinsic Pontine Glioma 60 - Tumour-450K


title: Cmer_072209_OP4_a

value: OP-4 filter material

value: transmits 90.0% of VIS, UVA, and UVB radiation


title: Cmer_070910_OP4_b

value: Cyanidiales algal mat material


title: Cmer_070910_OP4_c


title: Cmer_070910_OP4_a


title: Cmer_070910_UF5_a


title: Kidney-1


title: Spleen-2

source_name: Spleen. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Spleen


title: Spleen-1


title: Cmer_042210_UF5_a


title: Lymph node-1

source_name: Lymph node. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Lymph node


title: Skel. Muscle-2

description:
Tissue was extracted from three different pig (12 month old) and small RNA was pooled.
RAKE using hybridized miRNA as primer. Incorporated biotin dATP was labelled with Cy3-streptavidin

hyb_protocol: Microarrays were probed with 800-900 ng of the small RNA from each tissue for 20 hours at 37° C in a static hybridization oven (SSPE 6X; BSA 8 mg/ml; 800 - 900 ng of small RNAs and spike-in). First, microarrays were pre-hybridized for 2 hours at 37° C with the following pre-hybridization water solution: SSPE 6X and BSA 8 mg/ml. After the retrotranscribed small RNAs hybridization, microarrays were washed with the following stringent washing solutions: 1 minute at room temperature with 6x SSPET (SSPE added with 0.05% of Tween-20); 1 minute at room temperature with 3x SSPET; 1 minute at room temperature with PBS 2X; 1 minute at room temperature with Buffer 2, 1X (the buffer for the klenow enzyme). After the washing step it was performed the RAKE reaction at 36.5° C incubating the microarray for 1 hour and 30 minutes with the following solution: Buffer 2 1X; Biotin-14-dATP (Invitrogen) 16 μM; Klenow Fragment (3´→5´ exo–) (NEB) 0.25 U/μl. Than microarray was washed two times with Buffer 2 1X and than incubated with the biotin blocking solution (PBS 2X; Tween-20 0.1% and BSA 10 mg/ml) for one hour at room temperature. Extended miRNAs (primers) were labeled incubating the microarray with the Dye labeling solution (PBS 2X; Tween-20 0.1% ; BSA 10 mg/ml and 1.6 ng of Cy3-streptavidin; Amersham) for one hour at room temperature. Microarray was rinsed with PBST (PBS 2X added with Tween-20 0.1%) for one minute at room temperature and with PBS 2X for one minute at room temperature.

scan_protocol: Microarrays were scanned with the VersArray scanner (Biorad) (6 μm resolution).

data_processing: The RAKE experimental setup associates fluorescence levels to specific and backrground probes. Before spike-in based miRNA quantization inter-arrays fluorescence was normalized using cyclic loess method . This is an algorithm that allows good grade of normalization in miRNA gene expression experiments as discussed by Wu (Comparison of normalization methods for CodeLink Bioarray data. BMC Bioinformatics) exhibiting the best improvement in the reduction of variability and yield the highest number of significant differentially expressed miRNAs. After inter-arrays normalization intensity fluorescence of specific probe for the miRNA was subtracted of the corresponding background fluorescence and than used to extrapolate concentration basing the spike-in derived curve.

label_protocol: The small RNA was not labelled when it was used to probe microarray. RNA-primed Array-based Klenow Extension (RAKE) is based on the ability of a RNA molecule to function as a primer for Klenow polymerase extension when fully base-paired with a microarray probe. As we known the exact 3’ end of the miRNA by previously performed tailed microarray experiments, we designed a microarray with a specific probe for each 3' end identified and a background probe. This microarray design was avoided for known miRNAs.

extract_protocol: Total RNA and miRNAs were extracted independently from each tissue sample by TRIzol reagent (Invitrogen) in association with PureLink miRNA isolation kit (Invitrogen). Briefly, approximately 200 mg of tissue was homogenized in 3.5 ml of TRIzol reagent (Invitrogen) using a tissue homogenizer (IKA Werke). After chloroform addition and centrifugation colorless upper aqueous phase containing RNAs was added with 96-100% ethanol to obtain a final concentration of 35% of ethanol and charged to PureLink membrane (Invitrogen) to separate total RNA and small RNAs from the same sample following the manufacturer manual. Total RNA and small RNAs were quantized using Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific). Samples derived from the same tissues were pooled adding the same quantity from the three pigs used. Quality of small RNA of pooled samples from the same tissue was tested on Agilent Bioanalizer 2100 using the RNA small LabChip.

value: Skeletal muscle


title: Lymph node-2


title: Lung-2

source_name: Lung. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Lung


title: Tongue-1

value: Tongue


title: Tongue-2


title: Lung-1


title: Cmer_042210_OP4_c


title: Cmer_042210_UF5_c

source_name: Cyanidiales algal mat material, UF-5 filter


title: Skel. Muscle-1


title: Cmer_042210_UF5_b


title: Diffuse Intrinsic Pontine Glioma 58 - Tumour-450K

value: DIPG


title: Adipose T.-2

source_name: Adipose tissue. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Adipose tissue


title: Diffuse Intrinsic Pontine Glioma 30 - Tumour-450K

value: M


title: Diffuse Intrinsic Pontine Glioma 29 - Tumour-450K


title: Adipose T.-1


title: Cmer_042210_OP4_b

source_name: Cyanidiales algal mat material, OP-4 filter

value: Lemonade Creek, Amphitheater Springs, Yellowstone National Park


title: Atrium sin.-2

value: Atrium sinistrum


title: Atrium sin-1


title: Ventricle sin.-2

value: Ventricle sinistrum


title: Cmer_042210_OP4_a


title: Skin-2

source_name: Skin. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Skin

value: 12 month old


title: Ventricle sin.-1

value: vietnamite


title: Diffuse Intrinsic Pontine Glioma 26 - Tumour-450K

value: F


title: Cmer_020809_UF5_c

value: UF-5 filter material

value: transmits 90.0% of VIS, blocks 99.9% of all UV below 390 nm

value: February 8, 2009


title: Cmer_020809_UF5_b

value: Cyanidiales algal mat material


title: Diffuse Intrinsic Pontine Glioma 56 - Tumour-450K


title: Diffuse Intrinsic Pontine Glioma 28 - Tumour-450K


title: Diffuse Intrinsic Pontine Glioma 52 - Tumour-450K


title: Diffuse Intrinsic Pontine Glioma 25 - Tumour-450K


title: Diffuse Intrinsic Pontine Glioma 27 - Tumour-450K


title: Skin-1


title: Stomach-2

value: Stomach


title: Diffuse Intrinsic Pontine Glioma 57 - Tumour-450K


title: Liver-1

source_name: Liver. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: Liver


title: Liver-2


title: Cmer_020809_UF5_a


title: Stomach-1


title: W_B_A-2

source_name: Arteriosum blood collected in the BD Vacutainer CPT cell preparation tubes, and processed according to manufacturer's directions to recover white blood cells. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: White blood cells


title: Cmer_020809_OP4_c

value: OP-4 filter material

value: transmits 90.0% of VIS, UVA, and UVB radiation


title: Kidney-1

value: Kidney


title: Kidney-2


title: W_B_A-1


title: Spleen-2

value: Spleen


title: Diffuse Intrinsic Pontine Glioma 19 - Tumour-450K

value: DIPG


title: Diffuse Intrinsic Pontine Glioma 24 - Tumour-450K


title: Cmer_010810_UF5_c

value: January 8, 2010

value: Lemonade Creek, Amphitheater Springs, Yellowstone National Park


title: Spleen-1

value: 12 month old


title: Lymph node-2

value: Lymph node

value: vietnamite


title: Diffuse Intrinsic Pontine Glioma 9 - Tumour-450K

value: M


title: Cmer_020809_OP4_b


title: Diffuse Intrinsic Pontine Glioma 8 - Tumour-450K

value: F


title: Lymph node-1


title: Diffuse Intrinsic Pontine Glioma 18 - Tumour-450K


title: Lung-2

value: Lung


title: Cmer_020809_OP4_a

value: Cyanidiales algal mat material

value: February 8, 2009


title: Cmer_010810_UF5_b

value: UF-5 filter material

value: transmits 90.0% of VIS, blocks 99.9% of all UV below 390 nm


title: Cmer_010810_OP4_c

value: OP-4 filter material


title: Cmer_010810_UF5_a


title: W_B_V-2

source_name: Venosum blood collected in the BD Vacutainer CPT cell preparation tubes, and processed according to manufacturer's directions to recover white blood cells. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: White blood cells


title: Lung-1


title: W_B_V-1


title: Diffuse Intrinsic Pontine Glioma 7 - Tumour-450K


title: Cmer_010810_OP4_b

value: transmits 90.0% of VIS, UVA, and UVB radiation


title: Adipose T.-2

value: Adipose tissue


title: Cmer_010810_OP4_a


title: Diffuse Intrinsic Pontine Glioma 6 - Tumour-450K

value: DIPG


title: Skin-2

value: Skin


title: Diffuse Intrinsic Pontine Glioma 5 - Tumour-450K


title: Adipose T.-1


title: Diffuse Intrinsic Pontine Glioma 1 - Tumour-450K


title: Mu3V6_large-colony1

city: Bunkyo-Ku

first: tomomi

last: hishinuma

state: Tokyo

country: Japan

institute: juntendo university

description: Sample 3

hyb_protocol: Labeled samples were hybridized onto the microarray at 50°C for 16-20 hr. After hybridization, the arrays were washed in the following buffers, and dry by spin slide. 2X SSC/0.05% SDS, for 15 min 0.2X SSC/0.05% SDS, for 15 min 0.5X SSC, for 3 min 0.2X SSC, for 3 min

scan_protocol: Nimblegen MS200

data_processing:
Software: NimbleScan
Algorithm: Robust Multi-Array Analysis (Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Biostatistics. 2003 Apr;4(2):249-64 (PMID 12925520)).
Normalize: global normalization

organism: Staphylococcus aureus

label_protocol: SuperScript Indirect cDNA Labeling System (Invitrogen Life Technologies, Carlsbad, California).

extract_protocol:
See reference:
Neoh HM, et al.: Mutated response regulator graR is responsible for phenotypic conversion of Staphylococcus aureus from heterogeneous vancomycin-intermediate resistance to vancomycin-intermediate resistance. Antimicrob Agents Chemother. 2008 Jan;52(1):45-53.

tag: background strain

value: rpoB mutation (R512L)

value: wild-type


title: Mu3V6_large-colony2

description: Sample 4

value: rpoB mutation (R512S)


title: Liver-2

value: Liver

value: 12 month old

value: vietnamite


title: Liver-1


title: ΔIP vs Mu3

description: Sample 5

source_name: ΔIP

value: ΔIP


title: Skin-1


title: W_B_A-2


title: W_B_A-1


title: ΔIP_rpoBmutant

description: Sample 1

value: rpoB mutation (R512P)


title: Mu3V6_small colony

description: Sample 2


title: W_B_V-1


title: Pool_Biofilm_rep5

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

description: Sample 7

hyb_protocol: The Cy3- and Cy5-labeled DNAs were mixed in 50 µl of DIG Easy Hyb solution (Roche) and hybridized overnight at 24°C to a barcode microarray

scan_protocol: Images of Cy5 and Cy3 fluorescence intensities were generated by scanning the barcode arrays using an Axon Autoloader 4200AL scanner (Molecular Devices, Downington, PA). Images were subsequently analyzed with the GenePix Pro 6.1.0.2 software (Molecular Devices, Downington, PA).

data_processing:
GenePix Results (GPR) files were imported into Arraypipe 2.0 (http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl). Following background subtraction, spot filtering and bad-spot flagging, global signal intensities were normalized using Loess normalization. Replicate slides were combined and Z-scores and P-values (standard Student’s t-test) were calculated.
Z-score > 2 indicates increased fitness/strain occupancy; Z-score < -2 indicates decreased fitness/strain occupancy.

organism: Candida albicans

source_name: C. albicans pooled strains, untreated, grown during 40h on a thermanox slide

label_protocol: A modified base [5-(3-aminoallyl)-dUTP] was included during PCR at a ratio of two 5-(3-aminoallyl)-dUTP molecules to three dTTP molecules. The PCR products were purified, and the DNA was labeled with either Cy3 (control) or Cy5 (Dox-treated) monoreactive NHS esters.

growth_protocol: For fitness profiling of planktonic cells, the pool of overexpression strains was grown at 30ºC with agitation (200 rpm) during 16 generations in synthetic dextrose medium (0.67% Yeast Nitrogen Base, 2% D-glucose) supplemented with arginine, uridine, histidine, and methionine (at final concentrations of 1 mg.mL-1, 0.02 mg.mL-1, 1 mg.mL-1, and 2 mg.mL-1, respectively, also referred to as GHAUM medium), in the absence or presence of 50 µg/ml doxycycline. Genomic DNA was purified and used as template to PCR-amplify barcodes, which were then used as probes for microarray hybridization. This experiment was done twice independently. For  quantification of strain abundance during multi-strain biofilm formation, strain pools were grown in minimal GHAUM medium with or without doxycycline, each inoculum was then diluted to an OD600 of 1 in fresh minimal GHAUM medium with or without doxycycline and left at room temperature for 30 min, to allow further overexpression. Plastic slides (Thermanox™; Nunc) were immersed in the inoculum for 30 min at room temperature to allow adhesion of cells to the plastic substrate. The plastic slides were then transferred to the glass vessel of a 40-mL incubation chamber. This vessel has two glass tubes inserted to drive the entry of medium and air, while used medium is evacuated through a third tube. The flow of medium is controlled by a recirculation pump (Ismatec®) set at 0.6 mL.min-1 and pushed by pressured air supplied at 105 Pa, conditions minimizing planktonic phase growth and promoting biofilm formation. The chambers with the plastic substrate were incubated at 37ºC and biofilms were grown for 40h followed by genomic DNA extraction, barcode amplification and differential labeling (dox-treated samples with Cy5, untreated samples with Cy3) and hybridization to barcode microarrays.

extract_protocol: Genomic DNA was extracted as described for S. cerevisiae in Rose, M.D., Winston, F., and Hieter, P. (1990) Methods in Yeast Genetics: A Laboratory Course Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. Barcodes were amplified from genomic DNA by PCR using specific primers

treatment_protocol: Pools were treated or not with 50 µg/ml doxycycline

tag: sample group

value: untreated

source_name: C. albicans pooled strains, inducing conditions (+ doxycycine), grown during 40 h on a thermanox slide

value: dox-treated samples


title: Pool_Biofilm_rep6

description: Sample 8


title: 4thMammaryGlands_ContolateralVsCleared_d15_3BRs

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

description: 3 biological replicates available, dye swap for each

hyb_protocol: hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto epoxy coated slide spotted with PCR products (see supplementary file for details)

scan_protocol: Axon 4000B scanner was used with GenePix 5 software.

data_processing:
Spots showing low intensity, inhomogeneity, saturation and too small diameters were filtered out. In order to increase the dynamic range of the system all slides were scanned with two photo multiplier tube voltage settings. An algorithm was implemented in Perl which supplements the saturated spots in the high intensity scan with the corresponding values from the low intensity scan multiplied with a correction factor (Lyng et al., 2004). Normalization was done with the help of the software Carmaweb (Rainer J et al., 2006). Parameters:
1) Pintip Loess Normalization
2) Normalization of dyeswap pairs
3) Log2 transformation of resulting ratios

source_name: Cleared vs controlateral 4th mammary gland, d15 of pregnancy

label_protocol: labeling of eukaryotic total RNA with aminoallyl labeled nucleotides via first strand cDNA synthesis followed by a coupling of the aminoallyl groups to either Cyanine 3 or 5 (Cy 3/Cy5) fluorescent molecules (see supplementary file for details)

growth_protocol: Animal experimentation was performed using CD1 mice housed in the Animal Facility of the Polytechnic University of Marche. Animals were fed a standard chow diet and they were kept at 12hr light/12hr dark cycle.  Animal care and handling were performed in accordance with the Italian Institutional Guidelines, and the experimental protocol was approved by the local Ethical Committee for Animal Experimentation  For the study 60 female CD1 mice were used.

extract_protocol: RNA isolation using TriZol (see supplementary file for details)

treatment_protocol: For the study 60 female CD1 mice obtained by in-house breeding. At the weaning age (3 weeks old) they were subjected to the removing of the epithelial component of the 4th right mammary gland in order to obtain a cleared fat pad. The 4th left gland of the same animal underwent a simple skin excision for control evaluations. The success of the clearing procedure was assessed by whole-mount analysis (Rasmussen SB et al. 2000) revealing the presence of the entire ductal tree in the removed part of mammary fat pad.   At the adult stage (10-15 weeks of age), mice that underwent appropriate epithelial clearing of the mammary gland were mated and subsequently sacrificed on pregnancy day 0, 10, 15, 17 and 19 (6 mice/group) to collect tissue samples from cleared and control mammary glands. Collected specimens were appropriately sampled for RNA extraction and microarray analysis and eventual morphological examination.

value: female

tag: strain

value: 4th mammary glands

tag: developmental stage

value: d15 of pregnancy

source_name: Controlateral vs cleared 4th mammary gland, d15 of pregnancy


title: 4thMammaryGlands_ContolateralVsCleared_d19_2BRs

description: 2 biological replicates available, dye swap for 1

source_name: Cleared vs controlateral 4th mammary gland, d19 of pregnancy

value: d19 of pregnancy

source_name: Controlateral vs cleared 4th mammary gland, d19 of pregnancy


title: Med-4-9003179

description:
Tissue was extracted from three different pig (12 month old) and small RNA was pooled.
RAKE technology. Extended primer (hybridized miRNA) incorporate dATP biotinilated than labelled with Cy3-streptavidin
RNA-primed Array-based Klenow Extension (RAKE) is based on the ability of a RNA molecule to function as a primer for Klenow polymerase extension when fully base-paired with a microarray probe. As the exact 3’ end of the miRNA should be known for successful extension, and computational predictions are not optimal for predicting the correct start and end of the mature miRNA, we designed a tiling path of 22 probes complementary to the predicted pre-miRNAs to detect the exact 3’ end of the miRNA

hyb_protocol: Microarrays were probed with 1 ug of the small RNA pool for 20 hours at 37° C in a static hybridization oven (SSPE 6X; BSA 8 mg/ml; 1 ug of small RNAs and spike-in). First, microarrays were pre-hybridized for 2 hours at 37° C with the following pre-hybridization water solution: SSPE 6X and BSA 8 mg/ml. After the small RNAs hybridization microarrays were washed with the following stringent washing solutions: 1 minute at room temperature with 6x SSPET (SSPE added with 0.05% of Tween-20); 1 minute at room temperature with 3x SSPET; 1 minute at room temperature with PBS 2X; 1 minute at room temperature with Buffer 2, 1X (the buffer for the klenow enzyme). After the washing step it was performed the RAKE reaction at 36.5° C incubating the microarray for 1 hour and 30 minutes with the following solution: Buffer 2 1X; Biotin-14-dATP (Invitrogen) 16 μM; Klenow Fragment (3´→5´ exo–) (NEB) 0.25 U/μl. Than microarray was washed two times with Buffer 2 1X and than incubated with the biotin blocking solution (PBS 2X; Tween-20 0.1% and BSA 10 mg/ml) for one hour at room temperature. Extended miRNAs (primers) were labeled incubating the microarray with the Dye labeling solution (PBS 2X; Tween-20 0.1% ; BSA 10 mg/ml and 1.6 ng of Cy3-streptavidin; Amersham) for one hour at room temperature. Microarray was rinsed with PBST (PBS 2X added with Tween-20 0.1%) for one minute at room temperature and with PBS 2X for one minute at room temperature.

scan_protocol: Microarrays were scanned with the VersArray scanner (Biorad) (3 μm resolution).

data_processing:
The RAKE experimental setup associates fluorescence levels to 22 tailed probes corrponding to the 3' ends of each predicted pre-miRNA. Tailing probes were constructed in each pre-miRNA arm. To identify the most probable endpoints, we then need to analyze these values looking for spots with a fluorescence level significantly higher from the rest of the group. We implemented this search with a bootstrap approach. Given a group of 22 measures, we extract in turn one of them and we build ten thousand simulated groups by sampling the remaining 21 values with replacement. The number of samples with an average fluorescence level lower than the value of the observed group, divided by ten thousand, is taken as an estimate of the probability of having picked a true endpoint for the miRNA. For the rest of the analysis, we keep only the results with a probability higher than 0.75.
Data for the identification of the 3' end of the miRNAs did not need to be normalized because we did not compared different experiments, but we extracted from each experiments peaks corresponding to miRNA end.

source_name: Pool of same quantity of small RNA from tissues listed in 'characteristics'

label_protocol: The small RNA was not labelled when it was used to probe microarray. RNA-primed Array-based Klenow Extension (RAKE) is based on the ability of a RNA molecule to function as a primer for Klenow polymerase extension when fully base-paired with a microarray probe. As the exact 3’ end of the miRNA should be known for successful extension, and computational predictions are not optimal for predicting the correct start and end of the mature miRNA, we designed a tiling path of 22 probes complementary to the predicted pre-miRNAs to detect the exact 3’ end of the miRNA

extract_protocol: Total RNA and miRNAs were extracted independently from each tissue sample by TRIzol reagent (Invitrogen) in association with PureLink miRNA isolation kit (Invitrogen). Briefly, approximately 200 mg of tissue was homogenized in 3.5 ml of TRIzol reagent (Invitrogen) using a tissue homogenizer (IKA Werke). After chloroform addition and centrifugation colorless upper aqueous phase containing RNAs was added with 96-100% ethanol to obtain a final concentration of 35% of ethanol and charged to PureLink membrane (Invitrogen) to separate total RNA and small RNAs from the same sample following the manufacturer manual. Total RNA and small RNAs were quantized using Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific). Samples derived from the same tissues were pooled adding the same quantity from the three pigs used. “Pool tissues” were performed with 700 ng of small RNAs from each pool sample. Quality of small RNA of pooled samples was tested on Agilent Bioanalizer 2100 using the RNA small LabChip.

value: superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node


title: Pool_Biofilm_rep4

description: Sample 6


title: Pool_Biofilm_rep3

description: Sample 5


title: Pool_Fitness_planktonic_rep2

description: Sample 2

source_name: C. albicans pooled strains, untreated, 16 generations planktonic growth in SD medium

source_name: C. albicans pooled strains, inducing conditions (+ doxycycine), 16 generations planktonic growth in SD medium


title: Pool_Biofilm_rep2

description: Sample 4


title: Pool_Biofilm_rep1

description: Sample 3


title: 4thMammaryGlands_ContolateralVsCleared_d0_3BRs

source_name: Cleared vs controlateral 4th mammary gland, d0

source_name: Controlateral vs cleared 4th mammary gland, d0


title: 4thMammaryGlands_ContolateralVsCleared_d17_3BRs

description: 3 biological replicates available, dye swap for 2

source_name: Cleared vs controlateral 4th mammary gland, d17 of pregnancy

value: d17 of pregnancy

source_name: Controlateral vs cleared 4th mammary gland, d17 of pregnancy


title: 4thMammaryGlands_ContolateralVsCleared_d10_3BRs

source_name: Cleared vs controlateral 4th mammary gland, d10 of pregnancy

value: d10 of pregnancy

source_name: Controlateral vs cleared 4th mammary gland, d10 of pregnancy


title: Med-2-9003179


title: Med-3-9003179


title: Low-4-9003179


title: Pool_Fitness_planktonic_rep1

description: Sample 1


title: Low-2-9003179


title: Diffuse Intrinsic Pontine Glioma 3 - Tumour-450K

label_protocol: As per manufacturer (Illumina)

value: DIPG

value: M


title: Diffuse Intrinsic Pontine Glioma 4 - Tumour-450K


title: Low-1-9003179


title: High-4-9003179


title: High-3-9003179


title: Med-1-9003179


title: Low-3-9003179


title: High-2-9003179


city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

description: bone marrow-derived stromal cells from double transgenic rats (of Sprague-Dawley origin) harbouring the human angiotensinogen and human renin genes

hyb_protocol: Accoding to Agilent protocol

scan_protocol: Accoding to Agilent protocol

data_processing: The data was normalized to median per chip and log2 transformed

organism: Rattus norvegicus

label_protocol: Accoding to Agilent protocol

growth_protocol: bone marrow-derived stromal cells  (150,000cells/well) grown to subconfluency on a 6-well plate

extract_protocol: Cells lyzed with 1ml of Trizol  followed by chloroform-isopropanol RNA isolation procedure, and treated with DNAse  to remove remnant DNA.

tag: genotype

value: double transgenic harbouring the human angiotensinogen and human renin genes

tag: genetic background

value: Sprague-Dawley

value: bone marrow-derived stromal cells

value: bone marrow


title: High-1-9003179

tag: tissue

value: 12 month old

value: vietnamite


title: HERVH shRNA, rep3

status: Public on Mar 30 2014

city: Singapore

first: Xinyi

last: Lu

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singpaore

description:
Poly(A) RNA
Replicate 3.

hyb_protocol: 750 ng cRNA was used for hybridization to each lane of the HumanHT-12 v4 Expression BeadChip.

scan_protocol: After washing and drying of the chip, the microarray chip was scanned with a BeadArray Reader.

data_processing: Data was extracted with GenomeStudio and normalized with the rank-invariant method.

source_name: Embryonic stem cells, HERVH shRNA

label_protocol: 500 ng total RNA was used for cRNA synthesis and cRNA lableing with the TotalPrep RNA Amplification Kit (Illumina).

growth_protocol: The H1 hESC line (WA-01, passage p32) was cultured under feeder-free conditions on Matrigel (BD) in conditioned medium, which contains 1 mM L-glutamine (Gibco), 1% non-essential amino acids (Gibco) and 0.1 mM 2-mercaptoethanol (Gibco), 4 ng/ml human basic fibroblast growth factor (bFGF) (Invitrogen), 20% Knock-out serum replacement (Gibco), 78% DMEM/F12 media (Gibco), and medium was supplemented with additional bFGF (8 ng/ml) before use. For expansion, the H1 hESCs were passaged with 1 mg/ml collagenase IV (Gibco) every 5-7 days.

extract_protocol: For microarray, total RNA extracted from control samples and HERVH-depleted samples using TRIzol was treated with DNase for 1 hour. RNA was then purified by the PureLink RNA mini kit (Invitrogen).

treatment_protocol: For transfection, the hESCs were passaged with 0.25% trypsin (Invitrogen) for dissociation and transfected with 2 µg pSUPER-Luciferase shRNA (control) or pSUPER-HERVH shRNA and 6 µl Mirus LT1 transfection reagents the following day. Cells were harvested 5-days post transfection for RNA extraction.

tag: cell line

tag: cell type

value: embryonic stem cells

tag: shRNA

value: HERVH


title: Control shRNA, rep3

description:
Poly(A) RNA
Replicate 3.

source_name: Embryonic stem cells, control shRNA

value: control


title: HERVH shRNA, rep2

description:
Poly(A) RNA
Replicate 2.


title: HERVH shRNA, rep1

description:
Poly(A) RNA
Replicate 1.


title: Control shRNA, rep2

description:
Poly(A) RNA
Replicate 2.


title: normal Sprague-Dawley rats

description: bone marrow-derived stromal cells from normal Sprague-Dawley rats

value: wild type


title: Flag Leaf of R-Line, biological rep1

city: New Delhi

first: Sanjay

last: Kapoor

state: Delhi

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Gene expression data of flag leaf of 90-days-old plants of R-line

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix fluidic station model 450 using protocol FS_450_0001

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 7000 (Affymetrix)

data_processing: The data were analyzed with ArrayAssist Version 5.5 using default analysis settings and global scaling GCRMA as normalization method.

organism: Oryza sativa Indica Group

source_name: Flag Leaves of 90-days-old plants

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rice seeds of B, H and R line were surface sterilized with 0.1% HgCl2 and were soaked in RO (reverse osmosis purified) water overnight in dark. Next day, the seeds were spread on a gauze float and grown hydroponically in RGM medium at 28±2 oC in culture room conditions. Shoots and roots were separated and frozen in liquid nitrogen

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

value: Leaf

tag: cultivar

value: Indica

value: 90-days-old plants


title: Control shRNA, rep1

description:
Poly(A) RNA
Replicate 1.


title: Mature Root of R-Line, biological rep2

description: Gene expression data of root tissue of 40-60-days-old palnt of R-line

source_name: Roots of 40-60-days-old plants

value: Root

value: 40-60-days-old plants


title: Flag Leaf of R-Line, biological rep2


title: Mature Root of R-Line, biological rep3


title: Mature Leaf of R-Line, biological rep3

description: Gene expression data of leaf tissue of 40-60-days-old plants of R-line

source_name: Leaves of 40-60-days-old plants


title: Mature Leaf of R-Line, biological rep2


title: Mature Root of R-Line, biological rep1


title: Young Root of R-Line, biological rep3

description: Gene expression data of root tissue of 14 days old seedling of R-line

source_name: Roots of 14-days-old seedlings

value: 14-days-old seedlings


title: Flag Leaf of R-Line, biological rep3


title: Young Root of R-Line, biological rep2


title: Young Leaf of R-Line, biological rep3

description: Gene expression data of leaf tissue of 14-days-old seedling of R-line

source_name: Leaves of 14-days-old seedlings


title: Mature Leaf of R-Line, biological rep1


title: Young Root of R-Line, biological rep1


title: Young Leaf of R-Line, biological rep1


title: W_B_V-2

source_name: Venosum blood collected in the BD Vacutainer CPT cell preparation tubes, and processed according to manufacturer's directions to recover white blood cells. Samples from 3 different pig were extracted and than pooled because pigs were not inbred.

value: White blood cells


title: Young Leaf of R-Line, biological rep2


title: Flag Leaf of B-Line, biological rep2

description: Gene expression data of flag leaf of 90-days-old plants of B-line


title: Flag Leaf of B-Line, biological rep3


title: Flag Leaf of B-Line, biological rep1


title: Mature Leaf of B-Line, biological rep2

description: Gene expression data of leaf tissue of 40-60-days-old plants of B-line


title: Mature Leaf of B-Line, biological rep3


title: Mature Root of B-Line, biological rep2

description: Gene expression data of root tissue of 40-60-days-old palnt of B-line


title: Mature Root of B-Line, biological rep3


title: Mature Root of B-Line, biological rep1


title: Young Root of B-Line, biological rep2

description: Gene expression data of root tissue of 14 days old seedling of B-line


title: Young Root of B-Line, biological rep3


title: Mature Leaf of B-Line, biological rep1


title: Young Leaf of B-Line, biological rep3

description: Gene expression data of leaf tissue of 14-days-old seedling of B-line


title: Young Root of B-Line, biological rep1


title: Young Leaf of B-Line, biological rep2


title: Young Leaf of B-Line, biological rep1


title: Flag Leaf of hybrid, biological rep2

description: Gene expression data of flag leaf of 90-days-old plants of hybrid


title: Flag Leaf of hybrid, biological rep3


title: CGH: PI518.751_v_Wm82

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 9.1)

scan_protocol: Slides were scanned on the NimbleGen MS 200 Scanner (Roche/NimbleGen, Madison,WI) according to the array manufacturer instructions (NimbleGen CGH User Guild Ver 9.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

organism: Glycine max

source_name: DNA from soybean line PI518.751

label_protocol: 500 ng of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 9.1.

growth_protocol: single plant leaf tissue

extract_protocol: Genomic DNA samples were isolated using the Qiagen Plant DNeasy protocol

value: single plant leaf tissue

source_name: DNA from soybean line Wm82-ISU-01


title: CGH: PI507.681B_v_Wm82

source_name: DNA from soybean line PI507.681B


title: CGH: PI574.486_v_Wm82

source_name: DNA from soybean line PI574.486


title: CGH: PI404.188A_v_Wm82

source_name: DNA from soybean line PI404.188A


title: CGH: PI398.881_v_Wm82

source_name: DNA from soybean line PI398.881


title: Flag Leaf of hybrid, biological rep1


title: CGH: IA3023_v_Wm82_Rep2

source_name: DNA from soybean line IA3023


title: CGH: PI437.169B_v_Wm82

source_name: DNA from soybean line PI437.169B


title: Mature Root of hybrid, biological rep3

description: Gene expression data of root tissue of 40-60-days-old palnt of hybrid


title: Mature Root of hybrid, biological rep2


title: CGH: LG00-3372_v_Wm82

source_name: DNA from soybean line LG00-3372


title: CGH: IA3023_v_Wm82_Rep1


title: Mature Root of hybrid, biological rep1


title: CGH: LG92-1255_v_Wm82

source_name: DNA from soybean line LG92-1255


title: Mature Leaf of hybrid, biological rep3

description: Gene expression data of leaf tissue of 40-60-days-old plants of hybrid


title: CGH: LG94-1128_v_Wm82

source_name: DNA from soybean line LG94-1128


title: CGH: LG98-1605_v_Wm82

source_name: DNA from soybean line LG98-1605


title: CGH: PI427.136_v_Wm82

source_name: DNA from soybean line PI427.136


title: Mature Leaf of hybrid, biological rep2

source_name: Leaves of 40-60-days-old plants


title: CGH: LG97-7012_v_Wm82

source_name: DNA from soybean line LG97-7012


title: CGH: LG94-1906_v_Wm82

source_name: DNA from soybean line LG94-1906


title: CGH: LG05-4464_v_Wm82

source_name: DNA from soybean line LG05-4464


title: CGH: PI561.370_v_Wm82

source_name: DNA from soybean line PI561.370


title: CGH: LG90-2550_v_Wm82

source_name: DNA from soybean line LG90-2550

source_name: DNA from soybean line Wm82-ISU-01


title: CGH: LG05-4832_v_Wm82

source_name: DNA from soybean line LG05-4832


title: CGH: LG04-6000_v_Wm82

source_name: DNA from soybean line LG04-6000


title: CGH: LG04-4717_v_Wm82

source_name: DNA from soybean line LG04-4717


title: Young Root of hybrid, biological rep3

description: Gene expression data of root tissue of 14 days old seedling of hybrid

source_name: Roots of 14-days-old seedlings


title: CGH: LG05-4292_v_Wm82

source_name: DNA from soybean line LG05-4292


title: Young Root of hybrid, biological rep2


title: Young Root of hybrid, biological rep1


title: CGH: LG05-4317_v_Wm82

source_name: DNA from soybean line LG05-4317


title: Mature Leaf of hybrid, biological rep1


title: IL6raKO macrophages biological replicate 4

city: Heidelberg

first: Jan

last: Mauer

state: BW

address: Im Neuenheimer Feld, 583

country: Germany

institute: BioMed X Innovation Center

description:
IL-6 treated bone marrow-derived macrophages from IL6radmyel animals biological replicate 4
IL6raKO_4

hyb_protocol: cDNAs were hybridized for 17 h at 45°C to GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) and scanned on a GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Affymetrix Powertools and robust multi-array average (RMA) were used for background correction, quantile normalization and summarization of the raw intensity values. RMA, statistical analyses (Student’s t-test), calculation of the fold change of intensity values and graphical illustrations were performed using R software (version 2.13.1) along with the Bioconductor software package. Genes were considered significantly deregulated if p-values ≤ 0.05.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: IL6ralpha flox/flox LysMCre tg/wt mouse

label_protocol: Biotin-labeled cDNA was synthesized using GeneChip Whole Transcript Sense Target Labeling Assay (Affymetrix)

growth_protocol: primary murine bone marrow cells were differentiated into macophages in the presence of 10ng/ml rec. murine M-CSF for 10 days

extract_protocol: total RNA was isolated from cells using the Qiagen RNeasy Kit (Qiagen); Quality of RNA was assessed using the ExperionTM RNA StdSens Analysis Kit (BIO-RAD)

treatment_protocol: Bone marrow-derived macrophages were serum-starved overnight and subsequently treated with 50ng/ml rec. murine IL-6 for 4 hours

value: macrophage

tag: genotype/variation

tag: agent


title: Young Leaf of hybrid, biological rep3

description: Gene expression data of leaf tissue of 14-days-old seedling of hybrid

source_name: Leaves of 14-days-old seedlings


title: Young Leaf of hybrid, biological rep2


title: Young Leaf of hybrid, biological rep1


title: IL6raKO macrophages biological replicate 3

description:
IL-6 treated bone marrow-derived macrophages from IL6radmyel animals biological replicate 3
IL6raKO_3


title: CGH: LG03-2979_v_Wm82

source_name: DNA from soybean line LG03-2979


title: CGH: LG03-3191_v_Wm82

source_name: DNA from soybean line LG03-3191


title: IL6raKO macrophages biological replicate 1

description:
IL-6 treated bone marrow-derived macrophages from IL6radmyel animals biological replicate 1
IL6raKO_1


title: Ctrl macrophages biological replicate 4

description:
IL-6 treated bone marrow-derived macrophages from Ctrl animals biological replicate 4
Ctrl_4

source_name: IL6ralpha flox/flox mouse

value: Ctrl


title: CGH: NE3001_v_Wm82

source_name: DNA from soybean line NE3001


title: IL6raKO macrophages biological replicate 2

description:
IL-6 treated bone marrow-derived macrophages from IL6radmyel animals biological replicate 2
IL6raKO_2

value: bone marrow


title: Ctrl macrophages biological replicate 3

description:
IL-6 treated bone marrow-derived macrophages from Ctrl animals biological replicate 3
Ctrl_3


title: CGH: Skylla_v_Wm82

source_name: DNA from soybean line Skylla

value: Skylla


title: Ctrl macrophages biological replicate 1

description:
IL-6 treated bone marrow-derived macrophages from Ctrl animals biological replicate 1
Ctrl_1


title: HaCaT_96Hr_ELF-EMF/24Hr_ELF-EMF

status: Public on Mar 29 2014

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

institute: nthu

description:
Sample 18
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

hyb_protocol: Two-step hybridizations were performed. During the first hybridization, cDNA products was pipetted onto the array. Then, the array was incubated in the hybridization chamber in a water bath at 65℃ for 16 to 20 hours for the probe/target hybridization. At the second hybridization, the 3DNA dendrimer was pipetted onto the array and the array was submerged in a 65℃ water bath for only 2 to 3 hours for capture primer – 3DNA dendrimer hybridization. After hybridization, array was washed with SSC and SDS mixed buffer suggested by manufacturer's instruction of 3DNA array 50 kit.

scan_protocol: Microarrays were scanned by using GenePix 4100A (Axon, Foster City, CA) and images were taken at a resolution of 5μm. GenePix Pro 5.1 software was used to analyze image data.

data_processing: Spots were first selected by (1) excluding spots defined as flag or absent (2) keeping only channels with signal - background / SD of background greater than 1 (3) keeping spot diameter greater 75μm (4) eliminating spots with intensity CV greater than 100 in ether channel. The log ratio of the last spots were calculated and normalized by pin-wised LOWESS fit normalization.

source_name: Sample harvested at 96 h continuous ELF-EMF exposure

label_protocol: 3DNA Array 50 kit was used for fluorescence labeling on cDNA. Each total RNA (20μg) sample was reversely transcribed by Superscript II to single strand cDNA with the capture primer. cDNA was then purified by microcon YM-30 column.

growth_protocol: HaCaT cells were cultured in Dulbecco's Modified Eagle's Medium (Gibco BRL, Grand Island, NY) supplemented with 10% heat-inactivated fetal bovine serum (HyClone, Laboratories Inc., Logan, UT) and antibiotics (100 U/ml of penicillin, 100 μg/ml of streptomycin, 2mM L-glutamine; Gibco BRL, Grand Island, NY) at 37℃ in an incubator containing 5% CO2 humidified atmosphere.

extract_protocol: HaCaT cells were harvested with TRIzol reagent (Invitrogen) to extract total RNA according to the manufacture's protocols at scheduled time points. Total RNA were further purified by RNeasy (Quiagen). The quality of total RNA was assessed using the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip kit (Agilent Technologies).

treatment_protocol: Cells were seeded in 10 cm cell culture dish and incubated for at least 12 hr before ELF-EMF exposure; following by continuous exposure at 1.5 mT, 60 Hz ELF-EMF for 4, 8, 12, 24, 48, 72 and 96 h without medium replacement.

value: HaCaT

value: male

tag: age

value: 62 years

value: in vitro spontaneously transformed keratinocytes

source_name: Sample harvested at 24 h continuous ELF-EMF exposure


title: HaCaT_Control1/48Hr_ELF-EMF

description:
Sample 20
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

source_name: Control samples1

tag: gender

source_name: Sample harvested at 48 h continuous ELF-EMF exposure


title: HaCaT_12Hr_ELF-EMF/UVB

description:
Sample 16
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

source_name: Sample harvested at 12 h continuous ELF-EMF exposure

source_name: Sample harvested at 8 h after 233 J/m2 UVB irradiation


title: HaCaT_72Hr_ELF-EMF/12Hr_ELF-EMF

description:
Sample 17
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

source_name: Sample harvested at 72 h continuous ELF-EMF exposure


title: HaCaT_48Hr_ELF-EMF/8Hr_ELF-EMF

description:
Sample 15
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

source_name: Sample harvested at 8 h continuous ELF-EMF exposure


title: HaCaT_Control2/4Hr_ELF-EMF

description:
Sample 13
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

source_name: Control samples2

source_name: Sample harvested at 4 h continuous ELF-EMF exposure


title: HaCaT_24Hr_ELF-EMF/Control1

description:
Sample 11
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)


title: Ctrl macrophages biological replicate 2

description:
IL-6 treated bone marrow-derived macrophages from Ctrl animals biological replicate 2
Ctrl_2


title: HaCaT_8Hr_ELF-EMF/96Hr_ELF-EMF

description:
Sample 14
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)


title: HaCaT_4Hr_ELF-EMF/72Hr_ELF-EMF

description:
Sample 12
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)


title: CGH: U03-100612_v_Wm82

source_name: DNA from soybean line U03-100612

source_name: DNA from soybean line Wm82-ISU-01


title: HaCaT_Control1/UVB

description:
Sample 10
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)


title: HaCaT_UVB/96Hr_ELF-EMF

description:
Sample 9
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)


title: HaCaT_72Hr_ELF-EMF/48Hr_ELF-EMF

description:
Sample 7
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)


title: HaCaT_4Hr_ELF-EMF/Control1

description:
Sample 1
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)


title: HaCaT_96Hr_ELF-EMF/72Hr_ELF-EMF

description:
Sample 8
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)


title: HaCaT_Control2/24Hr_ELF-EMF

description:
Sample 5
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)