title: 4689(5) vs. USU101 rep2

type: genomic

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: biological replicate of output strain 4689(5) from monkey 81G

hyb_protocol: The Cy3 and Cy5 reactions were combined and unincorporated dye removed by using a Qia-Quick PCR purification column according to the manufacturer’s instructions (Qiagen, Chatsworth, CA). The eluate from the columns was dried in a Speed Vac and resuspended in 11 microliters TE (10 mM Tris, pH 8.0/1 mM EDTA). To this was added 1 microliter of 25 mg/ml yeast tRNA, 2.55 microliters of 20X SSC (3 M NaCl/0.3 M trisodium citrate 2 H2O, pH 7), and 0.45 microliters of 10% SDS. The mixture was denatured 2 min at 99°C, cooled briefly, and centrifuged for 2 min at 13,800 X g in a microcentrifuge. The probes were applied to the microarrays for hybridization at 37 C overnight and washed.

scan_protocol: Scanned on a GenePix 4000B Feature extraction was performed using GenePixPro version 6.0.1.00

data_processing: Data for each channel of the microarray were normalized by using the default-computed normalization of the Stanford Microarray Database http://smd.princeton.edu

molecule: genomic DNA

organism: Helicobacter pylori

source_name: H. pylori strain USU101

label_protocol: 0.5 micrograms genomic DNA were suspended in a total volume 38 microliters water and denatured 5 min 99°C. Five microliters of 10X Buffer (400 mg/ml random octamers/0.5 M Tris-HCL/100 mM MgSO4/10 mM DTT)/5 microliter dNTP/dUTP mix (0.5 mM dGTP, dATP, dCTP, 0.2 mM aminoallyl dUTP/0.3 mM dTTP)/2 microliter Klenow was added and the reaction incubated 1 h at 37°C. Free amines were removed by adding the reaction (50 microliters) to a Microcon YM 30 (Millipore) containing 450 microliters of water. The samples were concentrated by centrifuging for 8 min at 11,750 X g in a microcentrifuge. The eluate was discarded and the wash step repeated two times. After the last wash, the samples were collected and dried in a Speed Vac (Savant). The probe was resuspended in 4.5 microliters water and labeled by the addition of 4.5 microliters of 0.1 M sodium bicarbonate, pH 9.0, containing 1/16 of one reaction vial FluoroLink Cy3 monofunctional dye (Amersham), and was incubated for 1 h at room temperature in the dark. The reaction was quenched by addition of 4.5 microliters of 4M hydroxylamine and incubated for 15 min at room temperature in the dark.

extract_protocol: Wizard genomic prep

source_name: H. pylori isolate 4689(5)

label_protocol: 0.5 micrograms genomic DNA were suspended in a total volume 38 microliters water and denatured 5 min 99°C. Five microliters of 10X Buffer (400 mg/ml random octamersy/0.5 M Tris-HCL/100 mM MgSO4/10 mM DTT)/5 microliter dNTP/dUTP mix (0.5 mM dGTP, dATP, dCTP, 0.2 mM aminoallyl dUTPy0.3 mM dTTP)/2 microliters Klenow was added and the reaction incubated 1 h at 37°C. Free amines were removed by adding the reaction (50 microliters) to a Microcon YM 30 (Millipore) containing 450 microliters of water. The samples were concentrated by centrifuging for 8 min at 11,750 X g in a microcentrifuge. The eluate was discarded and the wash step repeated two times. After the last wash, the samples were collected and dried in a Speed Vac (Savant). The probe was resuspended in 4.5 microliters water and labeled by the addition of 4.5 microliters of 0.1 M sodium bicarbonate, pH 9.0, containing 1/16 of one reaction vial FluoroLink Cy5 monofunctional dye (Amersham), and was incubated for 1 h at room temperature in the dark. The reaction was quenched by addition of 4.5 microliters of 4M hydroxylamine and incubated for 15 min at room temperature in the dark.

treatment_protocol: yes ENNG

tag: isolate


title: 4726(2) vs. USU101 Feb08_rep1

status: Public on Aug 18 2014

country: USA

description: biological replicate of output strain 4726(2) from monkey 08G

tag: strain

source_name: H. pylori isolate 4726(2)

treatment_protocol: no ENNG


title: 4721(1) vs. USU101 Feb08_rep1

description: biological replicate of output strain 4721(1) from monkey 57G

source_name: H. pylori isolate 4721(1)


title: 4726(1) vs. USU101 rep2

description: biological replicate of output strain 4726(1) from monkey 08G

source_name: H. pylori isolate 4726(1)


title: 4637(5) vs. USU101 Feb08_rep1

description: biological replicate of output strain 4637(5) from monkey 63G

source_name: H. pylori isolate 4637(5)


title: 4662(1) vs. USU101 Feb08_rep1

description: biological replicate of output strain 4662(1) from monkey 89G

source_name: H. pylori isolate 4662(1)


title: 4661(3) vs. USU101 Feb08_rep1

description: biological replicate of output strain 4661(3) from monkey 89G

source_name: H. pylori isolate 4661(3)


title: 4726(1) vs. USU101 rep1


title: 4689(5) vs. USU101 rep1


title: 4690(1) vs. USU101 Jan08_rep2

description: biological replicate of output strain 4690(1) from monkey 81G

source_name: H. pylori isolate 4690(1)


title: 4723(1) vs. USU101 Jan08_rep1

description: biological replicate of output strain 4723(1) from monkey 54H

source_name: H. pylori isolate 4723(1)


title: 4723(1) vs. USU101 Jan08_rep3


title: 4633(1) vs. USU101 Jan08_rep2

description: biological replicate of output strain 4633(1) from monkey 63G

source_name: H. pylori isolate 4633(1)


title: 4722(3) vs. USU101 Jan08_rep2

description: biological replicate of output strain 4722(3) from monkey 57G

source_name: H. pylori isolate 4722(3)


title: 4723(1) vs. USU101 Jan08_rep2


title: 4689(5) vs. USU101 Jan08_rep1


title: 4633(2) vs. USU101 Jan08_rep2

description: biological replicate of output strain 4633(2) from monkey 63G

source_name: H. pylori isolate 4633(2)


title: 4722(3) vs. USU101 Jan08_rep1


title: NT17_Subcutaneous adipose tissue_dexamethasone

type: RNA

city: Uppsala

first: Maria

middle: J

last: Pereira

address: Akademiska sjukhuset, Ing 70 3trp Lab 21

department: Department of Medical Sciences

country: Sweden

institute: Uppsala University

hyb_protocol: Following fragmentation, the resultant fragmented and labelled cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Following the hybridization for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridization Oven 640, the arrays were washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000

data_processing:
Expression data was processed with the General Linear Model implemented in Array Studio (Omicsoft Corporation) was used to compare the effects of dexamethasone treatment on subcutaneous and omental adipose tissue. The model included the factors Subject (random), Tissue (with levels subcutaneous and omental adipose tissue), and Treatment (with levels control and dexamethasone).
Background adjustment, quantile normalization and summarization were computed in the Array Studio software (v.3.6.2.268, Omicsoft Corporation) to generate RMA (Robust Multichip Average) expression values.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Subcutaneous adipose_Dex

label_protocol: The NuGEN WT-Ovation™ Exon Module was used to generate sense-strand cDNA targets ready for fragmentation and labelling with NuGEN’s FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Paired subcutaneous and omental adipose tissue obtained from subjects going throught elective surgery were placed in organ culture.

extract_protocol: Total RNA was extracted using the Lipid Tissue Kit (Qiagen) and was amplified using the NuGEN™ WT-Ovation™ Pico RNA Amplification System.

treatment_protocol: Adipose tissue fragments were cultured without or with dexamethasone (3 μM) for 24 h

tag: gender

value: male

tag: age

tag: bmi

tag: tissue

value: Subcutaneous adipose tissue

tag: incubated with

value: dexamethasone (Dex, 3 μM) for 24h


title: 4633(2) vs. USU101 Jan08_rep1


title: NT17_Subcutaneous adipose tissue_control

source_name: Subcutaneous adipose_control

value: none (control) for 24h


title: 4633(1) vs. USU101 Jan08_rep1


title: 4690(1) vs. USU101 Jan08_rep1


title: mild gastritis rep2

city: Yufu

first: Katsuhiro

last: Hanada

state: Oita

address: 1-1 Idaigaoka, Hasama-machi

department: Faculty of Medicine

country: Japan

institute: Oita University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Human Genome Microarray Kit v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: human stomach biopsy, mild gastritis

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: gastric mucosa


title: NT17_Omental adipose tissue_control

source_name: Omental adipose_control

value: Omental adipose tissue


title: NT13_Subcutaneous adipose tissue_dexamethasone


title: NT17_Omental adipose tissue_dexamethasone

source_name: Omental adipose_Dex


title: 4667(2) vs. USU101 Feb08_rep1

description: biological replicate of output strain 4667(2) from monkey 85G

source_name: H. pylori strain USU101

source_name: H. pylori isolate 4667(2)


title: Ramos control, rep 2

city: Porto

first: Rune

last: Matthiesen

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

description: Ramos control, replica 2

hyb_protocol: 3.5 µg of end-labeled, fragmented cDNA was used in a 150-µl  hybridization cocktail containing added hybridization controls  (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips,  Affymetrix), of which 120 ul were hybridized on array strips for 20 h at  48°C. Standard post hybridization wash and double-stain protocols  (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips,  Affymetrix) were used on an Affymetrix GeneAtlas system.

scan_protocol: Array strips were scanned on an Affymetrix GeneAtlas system using standard settings.

data_processing: AFFYLMGUI

source_name: Ramos control

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA)  human HuGENE-1_1-st-v1 Array Strips by using the Ambion WT Expression  Kit (Life Technologies, CA, USA) and Affymetrix GeneChip WT Terminal  Labeling Kit, according to the manufacturer’s protocols. Briefly, 100 ng  of total RNA containing spiked in Poly-A RNA controls (GeneChip  Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was  used in a reverse transcription reaction (Ambion WT Expression Kit) to  generate first-strand cDNA. After second-strand synthesis,  double-stranded cDNA was used in an in vitro transcription (IVT)  reaction to generate cRNA (Ambion WT Expression Kit). 15 ug of this cRNA  was used for a second cycle of first-strand cDNA synthesis (Ambion WT  Expression Kit). 5.5 ug of single stranded cDNA was fragmented and  end-labeled (GeneChip WT Terminal Labeling Kit; Affymetrix). Size  distribution of the fragmented and end-labeled cDNA, respectively, was  assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: All cell lines were cultured in Gibco RPMI medium 1640 GlutaMAX™ (Invitrogen) supplemented with 10% heat-inactivated FBS and penicillin/streptomycin in a humid environment of 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated from the various cell lines and cellular clones using the RNeasy Plus Mini Kit (QIAGEN, Stanford, CA) according to the manufacturer’s protocol.

treatment_protocol: 24 hours glucosamine treatment

tag: cell line

value: Ramos

tag: cell type

value: lymphocyte


title: NT02_Subcutaneous adipose tissue_control


title: F1_Subcutaneous adipose tissue_dexamethasone


title: NT02_Subcutaneous adipose tissue_dexamethasone


title: F1_Subcutaneous adipose tissue_control


title: NT13_Omental adipose tissue_dexamethasone


title: NT13_Subcutaneous adipose tissue_control


title: F1_Omental adipose tissue_control


title: NT13_Omental adipose tissue_control


title: NT02_Omental adipose tissue_control


title: F1_Omental adipose tissue_dexamethasone


title: 4723(2) vs. USU101 Jan08_rep1

description: biological replicate of output strain 4723(2) from monkey 54H

source_name: H. pylori isolate 4723(2)


title: 4668(1) vs. USU101 Feb08_rep1

description: biological replicate of output strain 4668(1) from monkey 85G

source_name: H. pylori isolate 4668(1)


title: 4723(2) vs. USU101 trpl


title: 4690(1) vs. USU101


title: 4633(2) vs. USU101 dupl

description: biological replicate of output strain 4633(2) from monkey 36G


title: 4641(3) vs. USU101 trpl

description: biological replicate of output strain 4641(3) from monkey 48H

source_name: H. pylori isolate 4641(3)


title: 4723(1) vs. USU101 dupl


title: 4637(5) vs. USU101 dupl

source_name: H. pylori isolate 4637(5)


title: 4722(2) vs. USU101 dupl

description: biological replicate of output strain 4722(2) from monkey 57G

source_name: H. pylori isolate 4722(2)


title: 4723(2) vs. USU101 dupl


title: 4723(1) vs. USU101 trpl

source_name: H. pylori isolate 4723(1)


title: 4633(2) vs. USU101


title: 4690(1) vs. USU101 dupl

source_name: H. pylori isolate 4690(1)


title: 4668(1) vs. USU101 dupl


title: 4721(1) vs. USU101 dupl

source_name: H. pylori isolate 4721(1)


title: 4661(3) vs. USU101 dupl

source_name: H. pylori isolate 4661(3)


title: 4667(2) vs. USU101 dupl


title: 4633(1) vs. USU101

description: biological replicate of output strain 4633(1) from monkey 36G

source_name: H. pylori isolate 4633(1)


title: 4722(3) vs. USU101

source_name: H. pylori isolate 4722(3)


title: 4668(1) vs. USU101


title: 4721(1) vs. USU101

description: biological replicate of output strain 4721(1) from monkey 57G


title: 4662(1) vs. USU101 dupl

source_name: H. pylori isolate 4662(1)


title: 4667(2) vs. USU101


title: 4694(2) vs. USU101 dupl

description: biological replicate of output strain 4694(2) from monkey 48H

source_name: H. pylori isolate 4694(2)


title: PBO_rep1

type: protein

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: Detection of proteins and protein modifications was performed using a direct two-step immunoassay using specific primary antibodies; details on the assay procedure are found in Pirnia et al., 2009 (PMID: 19609961).

scan_protocol: Images of the microarrays were taken using the ZeptoREADER microarray imager (Zeptosens), and image analysis was performed using the ZeptoVIEW Pro 3.1 software package (Zeptosens). Signal intensity for each spot was determined as background-corrected mean intensity with the local background subtracted from the spot intensity; the determined values were referenced against adjacent reference spots as implemented in the software package giving referenced fluorescence intensity.

data_processing: The blank-corrected normalized relative fluorescence intensities (RFI) were for each analyte centered to the median signal level observed for the corresponding control samples and then log2-transformed.  Measurements for which the background noise (i.e., signal of secondary antibody) was higher than the combined foreground and background signal (i.e., signal of primary and secondary antibody) were treated as missing values (<1%) and imputed using the k-Nearest-Neighbor (kNN) algorithm.

molecule: protein

organism: Rattus norvegicus

source_name: liver tissue

label_protocol: Fluorescence signal was generated using Alexa647-/Cy5-labeled anti-species secondary antibodies (Invitrogen, Darmstadt, Germany); details on the assay procedure are found in Pirnia et al., 2009 (PMID: 19609961).

growth_protocol: Male Wistar Hanover rats (Crl:WI[Gl/BRL/Han]IGS BR) from Charles River Laboratories, Inc. (Raleigh, NC) were maintained on certified rodent chow (Certified Rodent Diet 5200; Purina Mills, St. Louis, MO) ad libitum in individual suspended stainless steel wire-mesh cages. The animals were kept under controlled temperature (18–26°C), humidity (30–70%), and lighting (12 h light/dark cycle) and were acclimated for a minimum of 6 days.

extract_protocol: Frozen liver tissue was grinded using a ball mill (Mikro-Dismembrator U; Sartorius, Goettingen, Germany). Tissue lysates were generated under denaturing conditions by adding a 8-fold excess (vol/wt) of CeLyA Lysis Buffer CLB1 (Zeptosens).

treatment_protocol: Animals (8–10 weeks old) were assigned to dose groups (five rats/group) by weight using a weight stratification-based computer program. Substances were administered by gastric gavage for up to 14 days (in a volume of 5 ml/kg body weight/day) based on the group mean weekly body weight for each dose group.

tag: background strain

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)

value: liver

value: Piperonylbutoxide

value: Treatment

value: gastric gavage

value: 3 days

tag: treatment_dose [mg/kg/d]


title: TAA_rep3

value: Thioacetamid

value: 7 days


title: Wy_rep3


title: PBO_rep2


title: PBO_rep3


title: TAA_rep1


title: TAA_rep2


title: Wy_rep2


title: Nif_rep2

value: Nifedipine

value: 14 days


title: PB_rep1

value: male

value: Phenobarbital sodium


title: Nif_rep3


title: PB_rep3


title: PB_rep2


title: Wy_rep1


title: 4662(3) vs. USU101

description: biological replicate of output strain 4662(3) from monkey 89G

source_name: H. pylori strain USU101

source_name: H. pylori isolate 4662(3)


title: Nif_rep1


title: 4641(3) vs. USU101 dupl


title: MPy_rep3

value: Methapyrilene HCl


title: MPy_rep2


title: MPy_rep1


title: NT02_Omental adipose tissue_dexamethasone

source_name: Omental adipose_Dex

value: dexamethasone (Dex, 3 μM) for 24h


title: 4661(3) vs. USU101


title: 4637(3) vs. USU101 dupl

description: biological replicate of output strain 4637(3) from monkey 63G

source_name: H. pylori isolate 4637(3)


title: 4633(1) vs. USU101 dupl


title: MCpo_rep8

value: Methylcellulose

value: Control


title: MCpo_rep11


title: MCpo_rep9


title: MCpo_rep10


title: MCpo_rep5


title: MCpo_rep7


title: MCpo_rep2


title: MCpo_rep4


title: MCpo_rep3


title: Mcarb_rep2

value: Methylcarbamate


title: Mcarb_rep3

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: MCpo_rep1

value: liver


title: Mcarb_rep1


title: 4726(2) vs. USU101 Feb08_rep2

description: biological replicate of output strain 4726(2) from monkey 08G

source_name: H. pylori isolate 4726(2)


title: DMN_rep3

value: Dimethylnitrosamine


title: ETH_rep1

value: Ethionine

value: Treatment


title: ETH_rep2

value: gastric gavage


title: DMN_rep2


title: ETH_rep3


title: DHEA_rep2

value: Dehydroepiandrosterone


title: USU101 vs. 26695/J99 mix

description: Biological replicate of USU101 vs.26695/J99 mix to determine gene content.

source_name: H. pylori strain 26695/J99 mix


title: DHEA_rep3


title: DMN_rep1

value: 7 days


title: DHEA_rep1


title: USU101 vs. 26695/J99 mix rep1

source_name: H. pylori strains 26695 andJ99

label_protocol: 0.25 micrograms each 26695 and J99 genomic DNA were suspended in a total volume 38 microliters water and denatured 5 min 99°C. Five microliters of 10X Buffer (400 mg/ml random octamers/0.5 M Tris-HCL/100 mM MgSO4/10 mM DTT)/5 microliter dNTP/dUTP mix (0.5 mM dGTP, dATP, dCTP, 0.2 mM aminoallyl dUTP/0.3 mM dTTP)/2 microliter Klenow was added and the reaction incubated 1 h at 37°C. Free amines were removed by adding the reaction (50 microliters) to a Microcon YM 30 (Millipore) containing 450 microliters of water. The samples were concentrated by centrifuging for 8 min at 11,750 X g in a microcentrifuge. The eluate was discarded and the wash step repeated two times. After the last wash, the samples were collected and dried in a Speed Vac (Savant). The probe was resuspended in 4.5 microliters water and labeled by the addition of 4.5 microliters of 0.1 M sodium bicarbonate, pH 9.0, containing 1/16 of one reaction vial FluoroLink Cy3 monofunctional dye (Amersham), and was incubated for 1 h at room temperature in the dark. The reaction was quenched by addition of 4.5 microliters of 4M hydroxylamine and incubated for 15 min at room temperature in the dark.

extract_protocol: CsCl purified genomic DNA

label_protocol: 0.5 micrograms USU101 genomic DNA were suspended in a total volume 38 microliters water and denatured 5 min 99°C. Five microliters of 10X Buffer (400 mg/ml random octamersy/0.5 M Tris-HCL/100 mM MgSO4/10 mM DTT)/5 microliter dNTP/dUTP mix (0.5 mM dGTP, dATP, dCTP, 0.2 mM aminoallyl dUTPy0.3 mM dTTP)/2 microliters Klenow was added and the reaction incubated 1 h at 37°C. Free amines were removed by adding the reaction (50 microliters) to a Microcon YM 30 (Millipore) containing 450 microliters of water. The samples were concentrated by centrifuging for 8 min at 11,750 X g in a microcentrifuge. The eluate was discarded and the wash step repeated two times. After the last wash, the samples were collected and dried in a Speed Vac (Savant). The probe was resuspended in 4.5 microliters water and labeled by the addition of 4.5 microliters of 0.1 M sodium bicarbonate, pH 9.0, containing 1/16 of one reaction vial FluoroLink Cy5 monofunctional dye (Amersham), and was incubated for 1 h at room temperature in the dark. The reaction was quenched by addition of 4.5 microliters of 4M hydroxylamine and incubated for 15 min at room temperature in the dark.


title: DES_rep3

value: Diethylstilbestrol

value: 3 days


title: DES_rep2

value: male


title: COpo_rep4

value: Corn Oil


title: CPA_rep3

value: Cyproterone acetate

value: 14 days


title: DES_rep1


title: CPA_rep1


title: COpo_rep1


title: CPA_rep2


title: COpo_rep3


title: COpo_rep6


title: COpo_rep5


title: COpo_rep2


title: CIDB_rep2

value: C.I Direct Black


title: CIDB_rep3


title: CIDB_rep1


title: AA_rep2

value: Acetamide


title: AA_rep3


title: CFX_rep1

value: Cefuroxime


title: CFX_rep2

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: CFX_rep3

value: liver


title: AA_rep1


title: melanoma AJCCstageIII TumourID242

city: North Sydney

first: Graham

middle: J.

last: Mann

state: NSW

address: Poche Centre, 40 Rocklands Road

country: Australia

institute: Melanoma Institute Australia

hyb_protocol: Gene expression analysis was performed using the Sentrix Human-6 v3 Expression BeadChips (Illumina, Inc., San Diego, CA, USA), and BeadStation system from Illumina as per manufacturer’s instructions.

data_processing: Quality control was performed on all chips using R/Bioconductor and the lumi package (www.bioconductor.org). Data normalization was performed using a variance-stabilizing transform (VST) and quantile normalization as implemented in the lumi package for R/Bioconductor. To reduce false positives, unexpressed genes (detection p-value >0.01) were removed, reducing the number of probes analysed from 48,802 to 26,085.

source_name: melanoma lymph node, fresh frozen tissue (>80% tumor cell content, <30% necrosis)

label_protocol: cRNA amplification and labelling with biotin were performed using Illumina TotalPrep RNA amplification kit according to the manufacturer’s directions (Ambion, Inc., Austin, TX, USA) with 250ng total RNA as input material.

growth_protocol: Total RNA was extracted from 20-30mg of fresh frozen tissue.

extract_protocol: The RNA was isolated and purified with an RNeasy purification kit (Qiagen RNeasy purification kit- Qiagen Pty Ltd., Clifton Hill, Victoria, Australia) with DNAse I digestion on the column. The quality of the RNA preparations was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA). RNA integrity scores were >8 for all samples analyzed.

treatment_protocol: Tissue samples were homogenized using a high-speed agitation polytron blender (Kinematica, Luzern, Switzerland) in the presence of Trizol.

tag: patient age at primary diagnosis (years)

tag: patient sex

value: Female

tag: patient age at stage iii sample banked (years)

tag: survival from stage iii tumour banked (months)

tag: survival from primary melanoma (months)

tag: patient last status

value: Dead Melanoma

tag: number of primary melanomas

tag: stage at primary diagnosis 5th edition

value: Stage II


title: melanoma AJCCstageIII TumourID194

scan_protocol: Gene expression analysis was performed using the Sentrix Human-6 v3 Expression BeadChips (Illumina, Inc., San Diego, CA, USA), and BeadStation system from Illumina as per manufacturer’s instructions.

value: Male

value: Stage I


title: melanoma AJCCstageIII TumourID366

value: Alive with Melanoma


title: melanoma AJCCstageIII TumourID66

value: Alive NSR

value: Stage III


title: PB_rep3

hyb_protocol: Starting with 5 μg of totalRNA with a 28S/18S rRNA peak ratio >1.7, biotin-labeled cRNA  samples for hybridization on Affymetrix GeneChip RAE230A arrays were prepared accord- ing to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis 701194 Rev.1). This protocol includes the use of the SuperScript Choice System (Invitro- gen Life Technologies) for cDNA synthesis and the ENZO RNA Transcript Labeling Kit (Affymetrix Inc.) for in vitro transcription. The cRNA (15 μg) was then fragmented in buffer supplied with the Cleanup Module and hybridized for 16 h at 45°C. The microarrays were washed and stained with streptavidin-phycoerythrin (SAPE, Molecular Probes) on the Affymetrix Fluidics Station 400 including an amplification step according to the manufacturer’s instructions.

scan_protocol: The fluorescent images of the GeneChips were captured with the Affymetrix GeneChip Scanner 3000.

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

label_protocol: Biotin-labeled cRNA samples for hybridization on Affymetrix GeneChip RAE230A arrays were prepared according to the protocol supplied with the GeneChip Sample Cleanup module (Affymetrix Inc., Santa Clara, CA).

extract_protocol: Frozen liver sections were grinded in a Mixer Mill MM 200 (Retsch GmbH and Co. KG, Haan, Germany) using precooled stainless steel balls. After adjusting the volume to 1ml with RLT lysis buffer, total RNA was isolated using Qiagen RNAeasy spin column kits, including a DNase digestion step according to the manufacturer’s instructions. A volume of lysate corresponding to 7mg of tissue was loaded RNeasy spin column. The final product was quality controlled by gel analysis using RNA 6000 Nano chips on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). Only samples with a peak area ratio >2.0 of 28S to 18S rRNA were used. RNA concentrations were determined with Ribogreen (Molecular Probes, Eugene, OR).

tag: gender

value: male

value: Phenobarbital sodium

value: Treatment

value: gastric gavage


title: Wy_rep3

value: 3 days


title: melanoma AJCCstageIII TumourID43

value: Alive Status Unknown


title: melanoma AJCCstageIII TumourID232


title: PBO_rep1

value: Piperonylbutoxide


title: Wy_rep2

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: TAA_rep3

value: liver

value: Thioacetamid

value: 7 days


title: TAA_rep1


title: melanoma AJCCstageIII TumourID172

value: Female


title: TAA_rep2


title: Wy_rep1


title: melanoma AJCCstageIII TumourID6

value: Dead Melanoma

value: Stage II


title: melanoma AJCCstageIII TumourID234

value: Male


title: PBO_rep2


title: melanoma AJCCstageIII TumourID231

value: Alive NSR


title: melanoma AJCCstageIII TumourID396


title: melanoma AJCCstageIII TumourID1


title: PBO_rep3


title: 4723(2) vs. USU101

tag: strain

source_name: H. pylori isolate 4723(2)

tag: isolate


title: melanoma AJCCstageIII TumourID5

value: Dead Not Melanoma


title: 4723(1) vs. USU101

description: biological replicate of output strain 4723(1) from monkey 54H

source_name: H. pylori isolate 4723(1)


title: melanoma AJCCstageIII TumourID16

value: Stage I


title: melanoma AJCCstageIII TumourID103


title: melanoma AJCCstageIII TumourID30


title: PB_rep2

value: male

tag: tissue

value: Phenobarbital sodium

value: 14 days


title: Nif_rep1

value: Nifedipine

value: Treatment

value: gastric gavage


title: Nif_rep2

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: MPy_rep3

value: liver

value: Methapyrilene HCl


title: PB_rep1


title: MPy_rep2

value: 7 days


title: melanoma AJCCstageIII TumourID61

value: Female

value: Stage III


title: MCpo_rep9

value: Methylcellulose

value: Control


title: Nif_rep3


title: melanoma AJCCstageIII TumourID32

value: Male

value: Alive NSR


title: MCpo_rep11


title: MPy_rep1


title: melanoma AJCCstageIII TumourID149

value: Dead Melanoma

value: Stage I


title: melanoma AJCCstageIII TumourID45


title: MCpo_rep12

value: male


title: MCpo_rep10

value: 14 days


title: melanoma AJCCstageIII TumourID25

value: Dead Cause Unknown


title: melanoma AJCCstageIII TumourID37


title: melanoma AJCCstageIII TumourID259

value: Stage II


title: melanoma AJCCstageIII TumourID351


title: MCpo_rep8

value: gastric gavage


title: melanoma AJCCstageIII TumourID88


title: MCpo_rep7

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: melanoma AJCCstageIII TumourID173


title: melanoma AJCCstageIII TumourID219

value: Alive with Melanoma


title: melanoma AJCCstageIII TumourID100

value: Dead Not Melanoma


title: melanoma AJCCstageIII TumourID54


title: melanoma AJCCstageIII TumourID74


title: MCpo_rep5

value: liver


title: MCpo_rep6


title: melanoma AJCCstageIII TumourID278


title: melanoma AJCCstageIII TumourID62

value: Female


title: MCpo_rep4


title: MCpo_rep1


title: melanoma AJCCstageIII TumourID64

value: Stage III


title: MCpo_rep12

value: Methylcellulose


title: ETH_rep3

value: Ethionine

value: Treatment


title: MCpo_rep6

value: Control


title: melanoma AJCCstageIII TumourID249

value: Alive NSR


title: melanoma AJCCstageIII TumourID126

value: Male

value: Dead Melanoma

value: Stage I


title: MCpo_rep3

value: male

value: 14 days


title: melanoma AJCCstageIII TumourID36


title: Mcarb_rep1

value: Methylcarbamate

value: gastric gavage


title: ETH_rep2

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: Mcarb_rep3


title: melanoma AJCCstageIII TumourID387

value: Stage II


title: melanoma AJCCstageIII TumourID142


title: Mcarb_rep2

value: liver


title: melanoma AJCCstageIII TumourID53


title: ETH_rep1


title: MCpo_rep2


title: melanoma AJCCstageIII TumourID152

value: Dead Not Melanoma


title: melanoma AJCCstageIII TumourID69

value: Stage III


title: DMN_rep2

value: Dimethylnitrosamine

value: 7 days


title: melanoma AJCCstageIII TumourID233


title: melanoma AJCCstageIII TumourID13


title: DMN_rep3

value: Treatment


title: melanoma AJCCstageIII TumourID47


title: melanoma AJCCstageIII TumourID350


title: melanoma AJCCstageIII TumourID333


title: DHEA_rep3

value: Dehydroepiandrosterone


title: DHEA_rep1


title: DMN_rep1


title: DHEA_rep2


title: DES_rep2

value: Diethylstilbestrol

value: 3 days


title: CPA_rep2

value: Cyproterone acetate


title: DES_rep3


title: CPA_rep3


title: melanoma AJCCstageIII TumourID394

value: Male

value: Dead Melanoma


title: melanoma AJCCstageIII TumourID196

value: Stage I


title: melanoma AJCCstageIII TumourID322


title: COpo_rep5

value: male

value: Corn Oil

value: Control


title: DES_rep1

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)

value: gastric gavage


title: melanoma AJCCstageIII TumourID237

value: Female

value: Stage II


title: melanoma AJCCstageIII TumourID273


title: COpo_rep4

value: liver


title: melanoma AJCCstageIII TumourID201

value: Alive with Melanoma

value: Stage III


title: melanoma AJCCstageIII TumourID94

value: Dead Cause Unknown


title: melanoma AJCCstageIII TumourID93


title: melanoma AJCCstageIII TumourID28

value: Alive NSR


title: COpo_rep3

value: 14 days


title: melanoma AJCCstageIII TumourID102


title: COpo_rep6

value: 7 days


title: COpo_rep2


title: melanoma AJCCstageIII TumourID139

value: Male


title: melanoma AJCCstageIII TumourID385


title: CIDB_rep3

value: C.I Direct Black

value: Treatment


title: melanoma AJCCstageIII TumourID356

value: Dead Not Melanoma


title: melanoma AJCCstageIII TumourID288

value: Stage I


title: CPA_rep1

value: male

value: Cyproterone acetate


title: COpo_rep1

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)

value: Corn Oil

value: Control

value: gastric gavage


title: melanoma AJCCstageIII TumourID52

value: Female

value: Dead Melanoma


title: melanoma AJCCstageIII TumourID334

value: Stage II


title: melanoma AJCCstageIII TumourID83

value: Stage III


title: melanoma AJCCstageIII TumourID349

value: Alive NSR

value: Stage Unknown


title: CIDB_rep2

value: liver

value: 7 days


title: CFX_rep3

value: Cefuroxime

value: Treatment

value: 14 days


title: AA_rep3

value: male

value: Acetamide


title: CFX_rep1

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: AA_rep2


title: CFX_rep2


title: melanoma AJCCstageIII TumourID343

value: Male


title: AA_rep1


title: melanoma AJCCstageIII TumourID179


title: CIDB_rep1

value: C.I Direct Black


title: melanoma AJCCstageIII TumourID51


title: melanoma AJCCstageIII TumourID49


title: Foxd3 conditional knockout cells treated with Tamoxifen, biological rep1

city: Shanghai

first: Shiyue

last: Zhang

address: 225 South Chongqing Road

department: Institute of Health Sciences

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

hyb_protocol: Following fragmentation, 10 ug of mRNA were hybridized for 16 hr at 45C on  Mouse 430 2.0 gene expression array chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Mus musculus

source_name: CGR8 embryonic stem cells

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

growth_protocol: CGR8 ESCs are cultured in GMEM medium plus 10% serum with LIF

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

treatment_protocol: ESCs were transfected with plasmids by LipofectAMIN 2000 (Invitrogen) and extracted RNA by Trizol

value: embryonic stem cells

tag: treatment


title: melanoma AJCCstageIII TumourID120

value: Female

value: Stage I


title: melanoma AJCCstageIII TumourID119

value: Dead Melanoma

value: Stage II


title: melanoma AJCCstageIII TumourID340


title: melanoma AJCCstageIII TumourID277

value: Alive NSR


title: melanoma AJCCstageIII TumourID17


title: Foxd3 conditional knockout cells treated with Tamoxifen, biological rep3

tag: cell line


title: melanoma AJCCstageIII TumourID205


title: Foxd3 conditional knockout cells treated with DMSO, biological rep2

tag: cell type


title: ESCs overexpressed Foxd3 and CA-NFATc3, biological rep3

value: overexpressed Foxd3 and CA-NFATc3


title: Foxd3 conditional knockout cells treated with DMSO, biological rep1


title: melanoma AJCCstageIII TumourID23


title: Wy_rep3

hyb_protocol: Arrays were hybridized according to the Agilent miRNA microarray method ‘miRNA Microarray System with miRNA Complete Labeling and Hyb Kit’ (G4170-90011).

scan_protocol: Following hybridization and washing, the arrays were scanned on an Agilent Microarray Scanner (#G2505B) according to the manufacturer’s protocol. Images from the scanner were processed using Agilent Feature Extraction Software v9.5.1.

data_processing: The raw microarray data was normalized using the Robust Multi-chip Average (RMA) method without background correction implemented in the package AgiMicroRna for R/Bioconductor. The probesets which were not expressed in any of the analyzed experimental conditions were removed.

label_protocol: 25ng total RNA was end-labeled using the miRNA complete labeling and hybridization kit (Agilent# 5190-0456).

extract_protocol: Total RNA including miRNA was isolated using the miRNeasy Mini Kit (QIAGEN, Hilden, Germany). RNA integrity was checked with an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, USA).

tag: background strain

value: liver

value: gastric gavage

value: 3 days


title: Foxd3 conditional knockout cells treated with Tamoxifen, biological rep2


title: melanoma AJCCstageIII TumourID15


title: TAA_rep1

value: Thioacetamid

value: Treatment

value: 7 days

tag: treatment_dose [mg/kg/d]


title: Foxd3 conditional knockout cells treated with DMSO, biological rep3


title: Wy_rep1

value: male


title: TAA_rep2

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: PBO_rep3

value: Piperonylbutoxide


title: melanoma AJCCstageIII TumourID360

tag: patient age at primary diagnosis (years)


title: ESCs overexpressed Foxd3 and CA-NFATc3, biological rep2


title: ESCs overexpressed CA-NFATc3, biological rep1

value: overexpressed CA-NFATc3


title: ESCs overexpressed CA-NFATc3, biological rep3

value: embryonic stem cells


title: melanoma AJCCstageIII TumourID217

tag: patient sex

value: Female


title: ESCs overexpressed CA-NFATc3, biological rep2


title: ESCs overexpressed Foxd3 and CA-NFATc3, biological rep1


title: WT-VC40 replicate 1

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

description: S. aureus VC40

hyb_protocol: A mixture of RNA from WT or mutant strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

organism: Staphylococcus aureus subsp. aureus VC40

source_name: S. aureus VC40

label_protocol: Incorporation of cyanine dye during reverse transcription

growth_protocol: S. aureus strains were grown in BHI until DO (600nm)= 1 UA

extract_protocol: Briefly, bacteria were stabilized in RNA protect for 5 minutes, then harvested. Cells were lysed in the presence of 200 - 400 µg/ml lysostaphin (Genmedics) and total RNA was extracted using the PrestoSpin R bug Kit including DNase I treatment (Molzym). Quality and quantity of total RNA were determined by agarose gel electrophoresis and measured by using the Nanodrop spectrophotometer (Nanodrop Technologies).

treatment_protocol: RNAProtect (Qiagen)

tag: sample type

value: S. aureus strains grown in BHI

tag: genotype

value: wild type

source_name: gDNA pool

value: Staphylococcus aureus gDNA mixture


title: melanoma AJCCstageIII TumourID125

value: Male

tag: patient age at stage iii sample banked (years)

tag: survival from stage iii tumour banked (months)

tag: survival from primary melanoma (months)

value: Dead Melanoma

value: Stage II


title: ESCs overexpressed Foxd3, biological rep2

value: overexpressed Foxd3


title: WT-VC40 replicate 3

description: S. aureus VC42


title: ESCs overexpressed vector control, biological rep3

value: overexpressed vector control


title: ESCs overexpressed Foxd3, biological rep3


title: ESCs overexpressed vector control, biological rep1


title: TAA_rep3

value: liver

value: Thioacetamid

value: gastric gavage


title: PBO_rep2

value: male

value: Treatment

value: 3 days


title: PBO_rep1

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)

value: Piperonylbutoxide


title: Nif_rep1

value: Nifedipine

value: 14 days


title: PB_rep1

value: Phenobarbital sodium


title: PB_rep2


title: MPy_rep2

value: Methapyrilene HCl

value: 7 days


title: ESCs overexpressed Foxd3, biological rep1

value: embryonic stem cells


title: Nif_rep2


title: MPy_rep3


title: MPy_rep1


title: MCpo_rep12

value: Methylcellulose

value: Control


title: MCpo_rep10


title: MCpo_rep6


title: MCpo_rep7


title: MCpo_rep5


title: MCpo_rep9


title: PB_rep3


title: MCpo_rep3


title: MCpo_rep1


title: RN4220∆mutS mutant replicate 3

value: S. aureus strains grown in BHI

value: Staphylococcus aureus gDNA mixture


title: Mcarb_rep2

value: liver

value: Methylcarbamate


title: MCpo_rep2

value: male

value: gastric gavage


title: Mcarb_rep3

value: Treatment


title: RN4220∆mutS mutant replicate 2


title: ESCs overexpressed vector control, biological rep2

value: overexpressed vector control


title: MCpo_rep11

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: RN4220∆mutS mutant replicate 1


title: ETH_rep1

value: Ethionine


title: ETH_rep2

value: 14 days


title: Nif_rep3

value: Nifedipine


title: DMN_rep3

value: Dimethylnitrosamine


title: ETH_rep3


title: MCpo_rep8


title: DMN_rep1

value: 7 days


title: MCpo_rep4


title: DMN_rep2


title: DES_rep2

value: Diethylstilbestrol

value: 3 days


title: DHEA_rep2

value: Dehydroepiandrosterone


title: CPA_rep3

value: Cyproterone acetate


title: CPA_rep2


title: DES_rep1


title: CPA_rep1


title: Mcarb_rep1


title: COpo_rep6

value: Corn Oil

value: Control


title: COpo_rep3

value: liver


title: COpo_rep5

value: male


title: COpo_rep2

value: gastric gavage


title: CIDB_rep3

value: C.I Direct Black

value: Treatment


title: DHEA_rep3

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)


title: CIDB_rep1


title: CIDB_rep2


title: DHEA_rep1


title: CFX_rep2

value: Cefuroxime


title: DES_rep3


title: CFX_rep1

value: 14 days


title: COpo_rep4


title: AA_rep3

value: Acetamide


title: AA_rep2


title: whole blood_subject_205

status: Public on Aug 17 2014

city: London

first: Leonard

middle: C

last: Schalkwyk

address: De Crespigny Park

department: IOP-SGDP

country: United Kingdom

institute: King's College London

hyb_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina HiScan System (Illumina).

data_processing:
Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization). Data was then  pre-processed in the R package wateRmelon using the dasen function. Array data for each of the tissues was normalized separately.
processed data: dasen normalized beta (betas.csv)
raw data: Unmethylated and methylated signal intensities (signal_intensities.csv)

label: Cy5 and Cy3

source_name: whole blood

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was isolated from ~100 mg of each dissected brain region or whole blood stored in EDTA collection tubes using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

tag: subjectid

tag: barcode

value: C

value: Exclude

tag: Sex

value: MALE

tag: source tissue

value: whole blood


title: AA_rep1

tag: gender

tag: tissue


title: cells treated with sip53, rep 1

city: Austin

first: Wei-Ta

last: Chen

state: TX

address: 2506 Speedway Stop A5000

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
Gene expression data from cells with sip53
18_sip53-1

hyb_protocol: Thes fragmented cDNA were hibridized to GeneChip Human Gene 2.0 ST array.

scan_protocol: The cDNA bound to complementary oligonucleotide probes is then fluorescently labeled using phycoeythrin-conjugated streptavidin (SAPE). Each cDNA is then excited using confocal laser scanner. Please check Microarray core at DANA-Farber Cancer Institute as we sent our RNA samples to there, and they performed the arrays for us.

data_processing: Normalization and gene expression analysis were performed in Affymetrix Transcriptome Analysis Concole (TAC).

label: Biotin

source_name: Human MDA-MB-231 cells treated with sip53

label_protocol: The fragmented cDNA were end-labeled with a biotinylated nucleotide analog.

growth_protocol: Cells Were maintained in DMEM medium supplemented with 10% FBS, 100U/ml penicillin, 100mg/ml streptomycin and 2 Mm L-glutamine.

extract_protocol: Cells were washed two times with iced PBS followed by extracting total RNA using RNeasy Mini kit (Qiagen).

treatment_protocol: Cells were treated with siATM, sip53 or control (siNC) siRNA by using Lipofectamine RNAiMAX (Invitrogen) following manufacturer's instructions.

tag: cell line

value: breast cancer MDA-MB-231 cells

tag: treatment protocol


title: cells treated with siATM, rep 1

description:
Gene expression data from cells with siATM
17_siATM-1

source_name: Human MDA-MB-231 cells treated with siATM

value: siATM


title: whole blood_subject_201

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina HiScan System (Illumina).


title: LM2_ubc13_1

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Array data were extracted at the probe level with no background correction using Illumina's BeadStudio software. These raw data were quantile normalized. Statistical analysis and differential gene expression were carried out using the limma package in R 2.12.2/Bioconductor. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate.

source_name: MDA-MB-231 LM2 cells

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

extract_protocol: RNA was extracted from cells using an RNAasy Mini Kit (Qiagen) as per manufacturers specifications. Extracted RNA was quantified on a Bioanalyser (Agilent) for quality control and used subsequently in microarray assay.

tag: sh transfrection


title: whole blood_subject_202

value: FEMALE


title: LM2_ubc13_3

scan_protocol: According to beadchip array manufacturer's protocol


title: LM2_ubc13_2


title: cells treated with control siNC, rep 2

description:
Gene expression data from cells with siNC
19_siNC-2

source_name: Human MDA-MB-231 cells treated with siNC

value: control siNC


title: cells treated with sip53, rep 2

description:
Gene expression data from cells with sip53
21_sip53-2


title: cerebellum_subject_126

source_name: cerebellum

value: cerebellum


title: frontal cortex_subject_126

source_name: frontal cortex

value: frontal cortex


title: superior temporal gyrus_subject_125

source_name: superior temporal gyrus

value: superior temporal gyrus


title: cells treated with control siNC, rep 1

description:
Gene expression data from cells with siNC
16_siNC-1


title: entorhinal cortex_subject_125

source_name: entorhinal cortex

value: entorhinal cortex


title: CFX_rep3

source_name: liver tissue

tag: background strain

value: male

value: liver

value: Treatment

value: gastric gavage

tag: treatment_dose [mg/kg/d]


title: superior temporal gyrus_subject_126


title: cells treated with siATM, rep 2

description:
Gene expression data from cells with siATM
20_siATM-2


title: LM2_control_3

value: GFP


title: whole blood_subject_204

value: C


title: whole blood_subject_203

value: Exclude


title: LM2_control_1


title: frontal cortex_subject_125


title: frontal cortex_subject_124

value: MALE


title: cerebellum_subject_124


title: entorhinal cortex_subject_126


title: cerebellum_subject_123

value: AD


title: superior temporal gyrus_subject_124


title: superior temporal gyrus_subject_123


title: entorhinal cortex_subject_124


title: entorhinal cortex_subject_123


title: superior temporal gyrus_subject_122


title: frontal cortex_subject_123


title: frontal cortex_subject_122


title: entorhinal cortex_subject_122


title: entorhinal cortex_subject_121


title: cerebellum_subject_122


title: cerebellum_subject_121


title: frontal cortex_subject_121


title: Wy_rep2

value: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)

value: 3 days


title: WT-VC40 replicate 2

description: S. aureus VC41

value: S. aureus strains grown in BHI

value: wild type

value: Staphylococcus aureus gDNA mixture


title: superior temporal gyrus_subject_117


title: frontal cortex_subject_116

value: frontal cortex


title: entorhinal cortex_subject_120

value: FEMALE


title: frontal cortex_subject_118


title: frontal cortex_subject_120


title: cerebellum_subject_119

value: cerebellum


title: superior temporal gyrus_subject_120

value: superior temporal gyrus


title: cerebellum_subject_116


title: frontal cortex_subject_115


title: frontal cortex_subject_119


title: cerebellum_subject_117


title: superior temporal gyrus_subject_116


title: superior temporal gyrus_subject_119


title: entorhinal cortex_subject_119

value: entorhinal cortex


title: superior temporal gyrus_subject_118


title: superior temporal gyrus_subject_121


title: cerebellum_subject_120


title: entorhinal cortex_subject_118


title: cerebellum_subject_118


title: frontal cortex_subject_117


title: entorhinal cortex_subject_117


title: entorhinal cortex_subject_116


title: entorhinal cortex_subject_115


title: superior temporal gyrus_subject_114


title: cerebellum_subject_115


title: superior temporal gyrus_subject_115


title: frontal cortex_subject_112


title: cerebellum_subject_113


title: superior temporal gyrus_subject_113


title: frontal cortex_subject_113


title: cerebellum_subject_112


title: entorhinal cortex_subject_110


title: superior temporal gyrus_subject_110


title: frontal cortex_subject_109


title: entorhinal cortex_subject_111


title: superior temporal gyrus_subject_111


title: superior temporal gyrus_subject_109


title: cerebellum_subject_114


title: frontal cortex_subject_114


title: entorhinal cortex_subject_112


title: whole blood_subject_113

value: whole blood


title: frontal cortex_subject_111


title: superior temporal gyrus_subject_112


title: entorhinal cortex_subject_109


title: cerebellum_subject_111


title: whole blood_subject_109


title: cerebellum_subject_110


title: cerebellum_subject_109


title: whole blood_subject_108


title: entorhinal cortex_subject_114


title: frontal cortex_subject_108


title: frontal cortex_subject_110


title: superior temporal gyrus_subject_108


title: cerebellum_subject_107


title: entorhinal cortex_subject_107


title: cerebellum_subject_108


title: superior temporal gyrus_subject_107


title: entorhinal cortex_subject_108


title: whole blood_subject_107


title: frontal cortex_subject_107


title: cerebellum_subject_105


title: whole blood_subject_106


title: superior temporal gyrus_subject_106


title: whole blood_subject_105


title: entorhinal cortex_subject_104


title: cerebellum_subject_103


title: entorhinal cortex_subject_105


title: frontal cortex_subject_104


title: superior temporal gyrus_subject_105


title: frontal cortex_subject_105


title: cerebellum_subject_106


title: cerebellum_subject_104


title: whole blood_subject_112


title: frontal cortex_subject_103


title: whole blood_subject_103


title: entorhinal cortex_subject_103


title: superior temporal gyrus_subject_103


title: whole blood_subject_104


title: frontal cortex_subject_102


title: cerebellum_subject_102


title: entorhinal cortex_subject_102


title: superior temporal gyrus_subject_102


title: superior temporal gyrus_subject_104


title: entorhinal cortex_subject_101


title: whole blood_subject_100


title: frontal cortex_subject_100


title: whole blood_subject_102


title: frontal cortex_subject_101


title: superior temporal gyrus_subject_101


title: cerebellum_subject_101


title: cerebellum_subject_100


title: superior temporal gyrus_subject_97


title: whole blood_subject_99


title: cerebellum_subject_97


title: cerebellum_subject_99


title: superior temporal gyrus_subject_100


title: frontal cortex_subject_99


title: entorhinal cortex_subject_100


title: entorhinal cortex_subject_97


title: frontal cortex_subject_96


title: whole blood_subject_97


title: frontal cortex_subject_97


title: whole blood_subject_96


title: cerebellum_subject_96


title: frontal cortex_subject_95


title: whole blood_subject_95


title: superior temporal gyrus_subject_99


title: cerebellum_subject_95


title: entorhinal cortex_subject_95


title: whole blood_subject_94


title: cerebellum_subject_94


title: entorhinal cortex_subject_96


title: entorhinal cortex_subject_99


title: superior temporal gyrus_subject_95


title: entorhinal cortex_subject_94


title: frontal cortex_subject_94


title: entorhinal cortex_subject_93


title: superior temporal gyrus_subject_94


title: superior temporal gyrus_subject_93


title: cerebellum_subject_93


title: whole blood_subject_93


title: frontal cortex_subject_93


title: whole blood_subject_92


title: COpo_rep1

value: male

value: liver

value: Corn Oil

value: Control

value: gastric gavage

value: 14 days


title: entorhinal cortex_subject_92

value: Exclude


title: cerebellum_subject_92


title: cerebellum_subject_125

value: C


title: superior temporal gyrus_subject_92


title: whole blood_subject_91


title: superior temporal gyrus_subject_96


title: frontal cortex_subject_90

value: MALE


title: entorhinal cortex_subject_91


title: superior temporal gyrus_subject_91


title: cerebellum_subject_90


title: superior temporal gyrus_subject_90


title: frontal cortex_subject_89

value: AD


title: whole blood_subject_89


title: whole blood_subject_88


title: cerebellum_subject_89


title: frontal cortex_subject_91


title: superior temporal gyrus_subject_89


title: entorhinal cortex_subject_88


title: cerebellum_subject_88


title: cerebellum_subject_87


title: superior temporal gyrus_subject_88


title: entorhinal cortex_subject_89


title: frontal cortex_subject_87


title: frontal cortex_subject_86


title: frontal cortex_subject_92


title: entorhinal cortex_subject_87


title: frontal cortex_subject_88


title: entorhinal cortex_subject_90


title: cerebellum_subject_86


title: superior temporal gyrus_subject_87


title: whole blood_subject_86


title: entorhinal cortex_subject_86


title: cerebellum_subject_85


title: whole blood_subject_90


title: whole blood_subject_85


title: entorhinal cortex_subject_85


title: frontal cortex_subject_84


title: superior temporal gyrus_subject_84


title: whole blood_subject_83


title: whole blood_subject_84


title: superior temporal gyrus_subject_86


title: superior temporal gyrus_subject_83


title: whole blood_subject_82


title: frontal cortex_subject_83


title: entorhinal cortex_subject_81


title: frontal cortex_subject_82


title: entorhinal cortex_subject_82


title: LM2_control_2

value: GFP


title: cerebellum_subject_82


title: frontal cortex_subject_81

value: frontal cortex


title: superior temporal gyrus_subject_81

value: FEMALE


title: cerebellum_subject_81

value: cerebellum


title: cerebellum_subject_80


title: superior temporal gyrus_subject_82

value: superior temporal gyrus


title: frontal cortex_subject_85


title: superior temporal gyrus_subject_80


title: whole blood_subject_80


title: entorhinal cortex_subject_80

value: entorhinal cortex


title: frontal cortex_subject_80


title: cerebellum_subject_84


title: whole blood_subject_79

value: whole blood


title: superior temporal gyrus_subject_79


title: frontal cortex_subject_79


title: entorhinal cortex_subject_83


title: cerebellum_subject_79


title: whole blood_subject_81


title: entorhinal cortex_subject_77


title: whole blood_subject_77


title: frontal cortex_subject_77


title: whole blood_subject_76


title: cerebellum_subject_76


title: superior temporal gyrus_subject_76


title: cerebellum_subject_77


title: frontal cortex_subject_76


title: entorhinal cortex_subject_76


title: entorhinal cortex_subject_75


title: frontal cortex_subject_75


title: frontal cortex_subject_72


title: whole blood_subject_72


title: cerebellum_subject_75


title: superior temporal gyrus_subject_72


title: whole blood_subject_75


title: entorhinal cortex_subject_79


title: cerebellum_subject_72


title: whole blood_subject_71


title: cerebellum_subject_71


title: superior temporal gyrus_subject_77


title: whole blood_subject_69


title: superior temporal gyrus_subject_69


title: frontal cortex_subject_71


title: entorhinal cortex_subject_71


title: superior temporal gyrus_subject_75


title: whole blood_subject_67


title: frontal cortex_subject_69


title: frontal cortex_subject_67


title: entorhinal cortex_subject_69


title: superior temporal gyrus_subject_67


title: cerebellum_subject_67


title: cerebellum_subject_69


title: entorhinal cortex_subject_67


title: cerebellum_subject_65


title: whole blood_subject_65


title: superior temporal gyrus_subject_71


title: entorhinal cortex_subject_65


title: cerebellum_subject_64


title: entorhinal cortex_subject_64


title: superior temporal gyrus_subject_63


title: cerebellum_subject_63


title: superior temporal gyrus_subject_64


title: frontal cortex_subject_64


title: entorhinal cortex_subject_63


title: entorhinal cortex_subject_62


title: frontal cortex_subject_63


title: superior temporal gyrus_subject_62


title: cerebellum_subject_62


title: frontal cortex_subject_62


title: entorhinal cortex_subject_61


title: frontal cortex_subject_65


title: superior temporal gyrus_subject_65


title: frontal cortex_subject_60


title: cerebellum_subject_60


title: whole blood_subject_60


title: superior temporal gyrus_subject_60


title: entorhinal cortex_subject_60


title: superior temporal gyrus_subject_59


title: cerebellum_subject_58


title: whole blood_subject_59


title: frontal cortex_subject_58


title: superior temporal gyrus_subject_58


title: entorhinal cortex_subject_58


title: entorhinal cortex_subject_59


title: cerebellum_subject_57


title: entorhinal cortex_subject_57


title: superior temporal gyrus_subject_57


title: frontal cortex_subject_57


title: superior temporal gyrus_subject_56


title: whole blood_subject_57


title: cerebellum_subject_56


title: frontal cortex_subject_56


title: frontal cortex_subject_61


title: entorhinal cortex_subject_56


title: cerebellum_subject_61


title: superior temporal gyrus_subject_54


title: frontal cortex_subject_54


title: cerebellum_subject_53


title: superior temporal gyrus_subject_52


title: superior temporal gyrus_subject_53


title: frontal cortex_subject_59


title: entorhinal cortex_subject_51


title: cerebellum_subject_51


title: superior temporal gyrus_subject_51


title: superior temporal gyrus_subject_50


title: frontal cortex_subject_50


title: cerebellum_subject_50


title: entorhinal cortex_subject_50


title: superior temporal gyrus_subject_49


title: superior temporal gyrus_subject_48


title: cerebellum_subject_49


title: frontal cortex_subject_51


title: cerebellum_subject_48


title: frontal cortex_subject_47


title: entorhinal cortex_subject_47


title: frontal cortex_subject_48


title: whole blood_subject_45


title: superior temporal gyrus_subject_47


title: cerebellum_subject_52


title: entorhinal cortex_subject_45


title: frontal cortex_subject_53


title: cerebellum_subject_47


title: frontal cortex_subject_45


title: entorhinal cortex_subject_44


title: superior temporal gyrus_subject_45


title: cerebellum_subject_45


title: superior temporal gyrus_subject_44


title: cerebellum_subject_44


title: cerebellum_subject_43


title: frontal cortex_subject_44


title: frontal cortex_subject_43


title: superior temporal gyrus_subject_43


title: entorhinal cortex_subject_43


title: superior temporal gyrus_subject_42


title: frontal cortex_subject_42


title: entorhinal cortex_subject_42


title: cerebellum_subject_42


title: superior temporal gyrus_subject_41


title: entorhinal cortex_subject_41


title: frontal cortex_subject_41


title: cerebellum_subject_41


title: cerebellum_subject_40


title: whole blood_subject_41


title: cerebellum_subject_39


title: entorhinal cortex_subject_40


title: whole blood_subject_40


title: superior temporal gyrus_subject_40


title: whole blood_subject_39


title: frontal cortex_subject_40


title: entorhinal cortex_subject_39


title: frontal cortex_subject_39


title: superior temporal gyrus_subject_39


title: cerebellum_subject_38


title: cerebellum_subject_83


title: superior temporal gyrus_subject_38


title: entorhinal cortex_subject_84


title: superior temporal gyrus_subject_37


title: entorhinal cortex_subject_37


title: cerebellum_subject_37


title: entorhinal cortex_subject_38


title: whole blood_subject_36


title: entorhinal cortex_subject_36


title: frontal cortex_subject_36


title: entorhinal cortex_subject_35


title: cerebellum_subject_35


title: superior temporal gyrus_subject_36


title: whole blood_subject_34


title: frontal cortex_subject_34


title: frontal cortex_subject_37


title: superior temporal gyrus_subject_35


title: superior temporal gyrus_subject_34


title: frontal cortex_subject_35


title: whole blood_subject_33


title: frontal cortex_subject_38


title: whole blood_subject_38


title: entorhinal cortex_subject_33


title: superior temporal gyrus_subject_61


title: frontal cortex_subject_33


title: entorhinal cortex_subject_32


title: cerebellum_subject_33


title: frontal cortex_subject_32


title: cerebellum_subject_36


title: entorhinal cortex_subject_34


title: superior temporal gyrus_subject_33


title: superior temporal gyrus_subject_32


title: whole blood_subject_31


title: whole blood_subject_32


title: superior temporal gyrus_subject_31


title: cerebellum_subject_31


title: frontal cortex_subject_31


title: whole blood_subject_30


title: entorhinal cortex_subject_31


title: superior temporal gyrus_subject_30


title: entorhinal cortex_subject_30


title: frontal cortex_subject_30


title: superior temporal gyrus_subject_29


title: cerebellum_subject_30


title: whole blood_subject_29


title: entorhinal cortex_subject_28


title: cerebellum_subject_29


title: cerebellum_subject_32


title: cerebellum_subject_28


title: entorhinal cortex_subject_29


title: frontal cortex_subject_28


title: frontal cortex_subject_29


title: cerebellum_subject_26


title: frontal cortex_subject_27


title: superior temporal gyrus_subject_28


title: frontal cortex_subject_26


title: entorhinal cortex_subject_27


title: superior temporal gyrus_subject_26


title: whole blood_subject_26


title: cerebellum_subject_27


title: cerebellum_subject_34


title: entorhinal cortex_subject_26


title: superior temporal gyrus_subject_25


title: frontal cortex_subject_25


title: whole blood_subject_25


title: entorhinal cortex_subject_25


title: entorhinal cortex_subject_24


title: cerebellum_subject_24


title: frontal cortex_subject_24


title: whole blood_subject_23


title: entorhinal cortex_subject_23


title: cerebellum_subject_23


title: frontal cortex_subject_23


title: whole blood_subject_27


title: cerebellum_subject_22


title: entorhinal cortex_subject_22


title: superior temporal gyrus_subject_27


title: superior temporal gyrus_subject_22


title: superior temporal gyrus_subject_23


title: cerebellum_subject_25


title: whole blood_subject_22


title: entorhinal cortex_subject_21


title: frontal cortex_subject_21


title: cerebellum_subject_21


title: whole blood_subject_21


title: superior temporal gyrus_subject_21


title: superior temporal gyrus_subject_24


title: entorhinal cortex_subject_20


title: frontal cortex_subject_20


title: superior temporal gyrus_subject_20


title: frontal cortex_subject_22


title: frontal cortex_subject_19


title: whole blood_subject_19


title: entorhinal cortex_subject_19


title: B16-F1 tumor established in Mouse, WT, Rep 2

city: Philadelphia

first: Ana

middle: Maria

last: Gamero

state: PA

address: 3440 N. Broad St.

department: Biochemistry

institute: Temple University

hyb_protocol: RNA samples were labeled and hybridized to the Affymetrix mouse Gene 2.0 ST Array according to the manufacturer's instructions

data_processing: The data were analyzed using the Affymetrix Gene Expression Console Software, version 1.3.1 with RMA normalization algorithm.

source_name: WT_B16 melanoma tumor

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

growth_protocol: Tumor cells growing in the log-phase at 37C were collected by trypsinization, washed with PBS twice and resuspended at 5x106/mL prior to the inoculation of mice.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) and further purified by RNeasy kit (Qiagen, Valencia, CA).  The quality of total RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Individual tumors established in WT or S2KO mice were harvested at day 20 of the study and snapped frozen in liquid nitrogen prior to RNA extraction with TRIzol.

tag: strain background

tag: genotype/variation

value: WT

tag: inoculated with

value: B16-F1 melanoma tumor cells

value: B16 melanoma tumor establised in mice


title: superior temporal gyrus_subject_19


title: B16-F1 tumor established in Mouse, WT, Rep 1


title: cerebellum_subject_20


title: frontal cortex_subject_18


title: whole blood_subject_18


title: B16-F1 tumor established in Mouse, WT, Rep 3


title: cerebellum_subject_18


title: B16-F1 tumor established in Stat2 KO, Rep 3

source_name: Stat2 KO_B16 melanoma tumor

value: Stat2 KO


title: superior temporal gyrus_subject_18


title: B16-F1 tumor established in Stat2 KO, Rep 1


title: B16-F1 tumor established in Stat2 KO, Rep 2


title: week13-pbsoral-3

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 200 Hawkins Dr, 40025 PFP

institute: University of Iowa

hyb_protocol: Following fragmentation, 10 ug of cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G3000.

data_processing: The data were analyzed with Bioconductor/R and were RMA normalized.

source_name: skin- week 12/13 tx

label_protocol: 3' IVT Express Kit, Affymetrix

extract_protocol: Qiagen miRNeasy with on-column DNase digestion

tag: treatment

value: PBS- gavage

tag: weeks of treatment

tag: strain

value: skin


title: week13-pbsoral-2


title: week13-pbspump-3

value: PBS- pump


title: frontal cortex_subject_17

tag: subjectid


title: entorhinal cortex_subject_17

tag: barcode


title: week13-pbsip-1

value: PBS- ip


title: week13-pbspump-2


title: cerebellum_subject_17

tag: Sex


title: week13-jak12i-3


title: week13-pbsoral-1


title: whole blood_subject_17

tag: source tissue


title: week13-pbspump-1


title: superior temporal gyrus_subject_17


title: whole blood_subject_16


title: week13-jak12i-2


title: entorhinal cortex_subject_18


title: week13-pbsip-2


title: frontal cortex_subject_16


title: week13-jak3i-3


title: superior temporal gyrus_subject_16


title: superior temporal gyrus_subject_85


title: week13-il15rb-3


title: week13-jak12i-1


title: week13-jak3i-2


title: week13-il15rb-1


title: cerebellum_subject_16


title: week13-jak3i-1


title: superior temporal gyrus_subject_15

value: MALE


title: week6-pbsoral-4

source_name: skin- week 5/6 tx


title: whole blood_subject_15

value: AD


title: cerebellum_subject_15


title: frontal cortex_subject_15


title: cerebellum_subject_14

value: Exclude


title: whole blood_subject_14


title: frontal cortex_subject_14

value: frontal cortex


title: week6-pbsoral-3


title: week13-il15rb-2


title: superior temporal gyrus_subject_14


title: week6-pbsoral-5


title: entorhinal cortex_subject_13

value: FEMALE


title: entorhinal cortex_subject_14


title: superior temporal gyrus_subject_13


title: cerebellum_subject_13

value: cerebellum


title: whole blood_subject_13


title: week6-jak12i-5


title: week6-pbsoral-1


title: week6-pbsoral-2


title: frontal cortex_subject_13


title: week6-pbspump-2


title: week6-jak12i-3


title: week6-pbspump-3


title: week6-jak12i-4


title: week6-jak12i-2


title: week6-pbspump-1


title: whole blood_subject_12


title: week6-jak12i-1


title: superior temporal gyrus_subject_12

value: superior temporal gyrus


title: entorhinal cortex_subject_12

value: entorhinal cortex


title: frontal cortex_subject_12


title: week6-jak3i-1


title: frontal cortex_subject_11


title: superior temporal gyrus_subject_11


title: cerebellum_subject_12


title: entorhinal cortex_subject_11


title: whole blood_subject_11

value: whole blood


title: cerebellum_subject_11


title: week6-jak3i-4


title: week6-jak3i-3


title: week5-sham-3

value: sham


title: week5-sham-4


title: week6-jak3i-2


title: week5-pbsip-4


title: week5-sham-1


title: week6-jak3i-5


title: week5-pbsip-2


title: cerebellum_subject_10


title: week5-sham-2


title: whole blood_subject_10


title: frontal cortex_subject_10


title: week5-pbsip-5


title: week5-il15rb-3


title: superior temporal gyrus_subject_10


title: superior temporal gyrus_subject_9


title: cerebellum_subject_9


title: entorhinal cortex_subject_10


title: week5-il15rb-1


title: entorhinal cortex_subject_9


title: week5-il15rb-2


title: week5-pbsip-3


title: frontal cortex_subject_9


title: week5-pbsip-1


title: whole blood_subject_8


title: frontal cortex_subject_8


title: superior temporal gyrus_subject_8


title: entorhinal cortex_subject_8


title: skin-PBS-12W-1

value: PBS

tag: treatment time


title: skin-PBS-12W-3

tag: tissue


title: cerebellum_subject_19


title: cerebellum_subject_8


title: week13-pbsip-3


title: skin-PBS-6W-2


title: whole blood_subject_7


title: superior temporal gyrus_subject_7


title: frontal cortex_subject_7


title: skin-PBS-0W-3


title: cerebellum_subject_7


title: skin-PBS-6W-3


title: skin-PBS-12W-2


title: skin-PBS-0W-1


title: skin-PBS-6W-1


title: entorhinal cortex_subject_7


title: skin-J3-24W-1


title: skin-J3-24W-2


title: skin-J3-12W-2


title: skin-J3-6W-2


title: whole blood_subject_6

value: C


title: skin-J3-12W-1


title: entorhinal cortex_subject_16


title: superior temporal gyrus_subject_6


title: cerebellum_subject_6


title: skin-J3-0W-3


title: skin-J3-0W-2


title: skin-J1-12W-3


title: (-)litR dark 2

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

description: (-)litR strain grown on a TM medium, dark condition

hyb_protocol: 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50°C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 20 micro g of herring sperm DNA (Promega), 0.1 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The expression levels were summarized by one-step Tukey’s biweight algorithm and normalized by global scaling method using GeneChip Operating Software, version 1.4 (Affymetrix, Santa Clara, CA). The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Thermus thermophilus HB8

source_name: T. thermophilus HB8, (-)litR, dark, 8 h

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.2 units of DNase I (GE Healthcare Bio-Science Corp.) at 37°C for 10 min, and after inactivation at 98°C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer's instructions (Affymetrix).

growth_protocol: T. thermophilus HB8 litR (TTHB100) deficient strain was pre-cultured at 60 °C for 16 h in 100 mL of TM broth.  The cells (1 mL) were inoculated into 100 mL of the same medium and then cultivated at 60 °C for 8 h under dark condition.

extract_protocol: Cells were collected from 10 mL of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: genotype

value: (-)litR


title: (-)litR dark 1


title: skin-J1-12W-2


title: skin-J3-0W-1


title: entorhinal cortex_subject_6


title: skin-J3-6W-1


title: (-)litR dark 3


title: skin-J1-24W-2


title: frontal cortex_subject_5


title: wild type dark 1

description: wild-type strain grown on a TM medium, dark condition

source_name: T. thermophilus HB8, wild-type, dark, 8 h

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 60°C for 16 h in 100 mL of TM broth. The cells (1 mL) were inoculated into 100 mL of the same medium and then cultivated at 60°C for 8 h under dark condition.

value: wild-type


title: skin-J1-6W-2

value: skin


title: frontal cortex_subject_6


title: wild type dark 3


title: skin-J1-24W-1


title: skin-J1-12W-1


title: skin-J3-12W-3


title: entorhinal cortex_subject_5


title: wild type dark 2


title: skin-J1-0W-3


title: superior temporal gyrus_subject_5


title: skin-J1-6W-1


title: whole blood_subject_5


title: skin-J1-6W-3


title: skin-J1-0W-2


title: cerebellum_subject_4


title: skin-J1-0W-1


title: skin-J3-6W-3


title: normal_adrenal_medulla_3

city: Seoul

first: Yoon-La

last: Choi

address: 81 Irwon-Ro, Gangnam-gu

department: Department of pathology

country: South Korea

institute: Samsung medical center

hyb_protocol: After addition of 2 μl GEx hybridisation buffer Hi-RPM, the amplified fragmented RNA was hybridised in a DNA microarray hybridisation oven (Agilent Technologies) at 10 rpm and 65°C for 17 hours.

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: raw data was normalized by quantile normalization using qunatile normalizaion provided by limma package (http://bioconductor.org).

source_name: adrenal medulla

label_protocol: Cyanine 3-labelled linearly amplified cRNA was mixed with 10 μl blocking agent, nuclease-free water, and 25 μl fragmentation buffer provided in the Agilent Gene Expression Hybridization Kit (Agilent Technologies) and incubated for 30 minutes at 60°C to fragment the RNA.

extract_protocol: performed using the Agilent Oligo Microarray Kit 8_60K according to the Agilent One-Color Microarray-based Gene Expression Analysis Protocol (Agilent Technologies). Briefly, 0.1 mg of total RNA and diluted Spike-in mix was amplified and labelled using the Agilent Quick Amp Labeling Kit (Agilent Technologies).

tag: diagnosis

value: normal

value: adrenal medulla

tag: tissue type


title: normal_adrenal_medulla_1


title: mouse skin-unaffected-1

source_name: unaffected skin

label_protocol: 3' IVT Express Kit

tag: phenotype

value: unaffected


title: superior temporal gyrus_subject_4


title: mouse skin-aa-1

source_name: affected alopecic skin

value: Alopecia Areata


title: normal_adrenal_medulla_2


title: entorhinal cortex_subject_4


title: malignant_PCPG_3

source_name: pheochomocytoma/paraganglioma

tag: subject gender

value: M

tag: subject age (yrs)

value: paraganglioma (PGL)

value: pheochromocytoma/paraganglioma (PCPG)

tag: primary site

value: retroperitoneum

value: malignant


title: mouse skin-aa-2


title: malignant_PCPG_3 [aCGH]

hyb_protocol: After labelling, the individual samples and reference samples were combined and concentrated using Microcon YM-30 filters (Millipore, Billerica, MA). After probe denaturation and preannealing with Cot-1 DNA, hybridisation was performed at 65°C with rotation for 40 hours. Four washing steps were completed with Agilent Oligo CGH washes as follows: Wash Buffer 1 at room temperature for 5 min, Wash Buffer 2 at 37°C for 1 min, an acetonitrile rinse at room temperature for 1 min, and a 30-second wash at room temperature in Agilent’s Stabilization and Drying Solution.

scan_protocol: All slides were scanned on an Agilent DNA microarray scanner G2505C.

data_processing: Raw log2 ratio was normalized using qunatile normalizaion provided by limma package (http://bioconductor.org).

label_protocol: Test DNA and reference DNA samples were labelled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS.

extract_protocol: Array CGH was performed using the Agilent Human whole genome CGH 60 K microarray.1.5 g of test DNA and reference DNAs was digested with Alu I and Rsa I (Promega, Madison, WI) and purified using the QIAprep Spin Miniprep kit (Qiagen, Germantown, MD).

source_name: reference DNA

tag: sample type

value: reference DNA (Promega human genomic DNA male G1471)


title: malignant_PCPG_2 [aCGH]

value: bladder


title: mouse skin-unaffected-2


title: malignant_PCPG_2


title: cerebellum_subject_3

value: AD

value: Exclude

value: MALE

value: cerebellum


title: Control subject 2

hyb_protocol: Following fragmentation, 3.75 ug of cDNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: Control subject 2

label_protocol: NuGen Encore Biotin Protocol using 3.75 ug cDNA from NuGen Ovation RNA Amplification V2 system

extract_protocol: PreAnalytiX - PAXgene Tissue miRNA Kit

treatment_protocol: scalp biopsy specimens were fixed using PAXgene kits

tag: disease

tag: treatment


title: malignant_PCPG_1


title: benign_PCPG_8

value: benign


title: benign_PCPG_9 [aCGH]

value: F

value: retoperitoneum


title: superior temporal gyrus_subject_3

value: superior temporal gyrus


title: mouse skin-unaffected-3

value: skin

tag: strain

value: unaffected


title: entorhinal cortex_subject_3

tag: subjectid

value: entorhinal cortex


title: mouse skin-aa-3

value: Alopecia Areata


title: benign_PCPG_9

value: paraganglioma (PGL)

value: pheochromocytoma/paraganglioma (PCPG)


title: Control subject 3

source_name: Control subject 3

value: normal

tag: weeks of treatment


title: Patient 2, week 12

source_name: Patient 2, week 12

value: alopecia areata

value: ruxolinitib


title: benign_PCPG_7

value: pheochromocytoma (PCC)

value: adrenal gland


title: frontal cortex_subject_3

source_name: frontal cortex

tag: barcode

value: AD

value: Exclude

tag: Sex

value: MALE

value: frontal cortex


title: benign_PCPG_8 [aCGH]

value: M

value: retroperitoneum

value: benign

value: reference DNA (Promega human genomic DNA male G1471)


title: entorhinal cortex_subject_2

source_name: entorhinal cortex

value: FEMALE

tag: source tissue

value: entorhinal cortex


title: malignant_PCPG_1 [aCGH]

value: paraganglioma (PGL)

tag: tissue

value: malignant


title: benign_PCPG_6

value: F

value: pheochromocytoma/paraganglioma (PCPG)

value: retrocaval


title: frontal cortex_subject_2


title: Control subject 1

source_name: Control subject 1

value: normal

value: skin


title: Patient 1, week 12

source_name: Patient 1, week 12

value: alopecia areata

value: ruxolinitib


title: benign_PCPG_5

value: adbomen


title: Patient 2, week 0

source_name: Patient 2, week 0


title: benign_PCPG_6 [aCGH]


title: superior temporal gyrus_subject_2

source_name: superior temporal gyrus

value: Exclude

value: superior temporal gyrus


title: human scalp-unaffected-5

hyb_protocol: Following fragmentation, 5 ug of cDNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Bioconductor/R and were RMA normalized after Harshlight correction.

source_name: unaffected subject skin

label_protocol: NuGen Ovation Amplification System 2 and Encore Biotin Module

value: skin from scalp

value: unaffected


title: benign_PCPG_7 [aCGH]

value: pheochromocytoma (PCC)

value: adrenal gland

value: benign

value: reference DNA (Promega human genomic DNA male G1471)


title: cerebellum_subject_2

source_name: cerebellum

value: FEMALE

value: cerebellum


title: benign_PCPG_4

value: M

value: paraganglioma (PGL)

value: pheochromocytoma/paraganglioma (PCPG)

value: retoperitoneum


title: superior temporal gyrus_subject_1

value: C


title: skin-PBS-0W-2

value: skin

value: PBS

tag: treatment time


title: Patient 1, week 0

source_name: Patient 1, week 0

value: alopecia areata

value: ruxolinitib


title: benign_PCPG_5 [aCGH]

tag: diagnosis

value: adbomen


title: whole blood_subject_2

source_name: whole blood

value: Exclude

value: whole blood


title: benign_PCPG_3 [aCGH]

value: pheochromocytoma (PCC)

value: adrenal gland

tag: tissue type


title: benign_PCPG_2

value: F

value: intrabdominal

value: benign


title: benign_PCPG_4 [aCGH]

value: M

value: reference DNA (Promega human genomic DNA male G1471)


title: whole blood_subject_1

value: FEMALE


title: entorhinal cortex_subject_1

value: entorhinal cortex


title: frontal cortex_subject_1

value: C

value: frontal cortex


title: benign_PCPG_2 [aCGH]

value: paraganglioma (PGL)

value: pheochromocytoma/paraganglioma (PCPG)


title: human scalp-unaffected-2

value: skin from scalp

tag: phenotype

value: unaffected


title: benign_PCPG_1

tag: subject gender

value: retroperitoneum


title: human scalp-unaffected-1


title: human scalp-unaffected-3


title: benign_PCPG_1 [aCGH]

tag: subject age (yrs)


title: human scalp-unaffected-4


title: human scalp-aa-3

value: alopecia areata


title: human scalp-aa-5


title: human scalp-aa-4


title: human scalp-aa-1


title: benign_PCPG_3

value: pheochromocytoma (PCC)

tag: primary site


title: Newly-diagnosed type 1 diabetes patient 11 (microRNA)

status: Public on Aug 16 2014

city: shanghai

first: wei

middle: qiong

last: gu

address: 197#,second ruijin road

institute: ruijin hospital

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 48°C on Affymetrix miRNA-1_0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Gene expression levels were normalized using the robust multiarray average (RMA) procedure using Partek GS 6.5.

source_name: peripheral blood mononuclear cell (PBMC)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA.

extract_protocol: The RNA was purified with the  miRNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: PBMC was isolated within six hours by LymphoprepTm gradient purification according to the manufacturer’s instructions (Axis-Shield PoC AS, Oslo, Norway) and stored in liquid nitrogen until use.

tag: cell type

value: Human primary peripheral blood mononuclear cell

tag: disease state

value: type 1 diabetes


title: Newly-diagnosed type 1 diabetes patient 10 (microRNA)


title: Newly-diagnosed type 1 diabetes patient 12 (microRNA)


title: human scalp-aa-2

source_name: affected alopecic skin


title: NMBA wk29 2

city: columbus

first: Ni

last: Shi

address: 400w 12th ave

department: comprehensive cancer center

institute: ohio state university

hyb_protocol: Affymetrix protocol

scan_protocol: Affy GeneChip Scanner 3000

data_processing:
The data were analyzed with Expression Console.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Rat230_2
program-version = 1.2.0.20

source_name: rat esophageal epithelia tissue 29 weeks after NMBA treatment

label_protocol: Affymetrix protocol

growth_protocol: rats were housed 3 per cage under standard conditions: 20 ± 2ºC, 50±10% relative humidity, and 12 hours light/dark cycles

extract_protocol: Half of esophagus was stripped of submucosal and muscularis layers and frozen in liquid nitrogen. The total RNA was extracted from frozen rat esophageal tissues using RNeasy Mini Kit.

treatment_protocol: After two weeks of acclimation to the animal facility, the rats were administered s.c. injections of 0.2 ml of either NMBA (0.3 mg/kg body weight) or a 1:4 mixture of dimethyl sulfoxide (DMSO):H2O (the solvent for NMBA) 3 times per week for 5 weeks.

tag: tumor development stage

value: Late stage of tumor development


title: NMBA wk15 3

source_name: rat esophageal epithelia tissue 15 weeks after NMBA treatment

value: Middle stage of tumor development


title: NMBA wk15 1


title: NMBA wk29 3


title: NMBA wk29 1


title: resting zone rep 3

city: Stockholm

last: Chau

address: Astrid Lindgren Children's Hospital, Q2:08

department: Department of Women's and Children's Health

institute: Karolinska Institutet

description: RZ #3

hyb_protocol: Following fragmentation and biotinylation (Affymetrix Gene Chip WT Labeling Kit), 5 ug of ss cDNA were hybridized for 16 hr at 45C on GeneChipRat 1.0 STArray. They were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using robust multi-array average (RMA) analysis, which adjusts for background noise on each array using only the PM probe intensitites and subsequently normalizes data across all arrays using quantile normalization followed by median polish summarization to generate a single measure of expression.  These expression measures were then log transformed (base 2) and lists of spatially regulated genes were generated.

source_name: growth plate cartilage resting zone of 10-day-old rat proximal tibia

label_protocol: ss cDNA was prepared with the Ambion WT Expression kit from 100ng of total RNA

growth_protocol: Animals were maintained under standardized conditions and handled in accordance with the Animal Ethics Committee of Northern Stockholm.

extract_protocol: Total RNA was extracted using phenol:chloroform:isozmyl alcohol (25:24:1), precipitated in 3M NaOAc and then 8M LiCl, and washed with 75% ethanol.  For the complete protocol please refer to Nilsson et al. J Endocrinol April 1, 2007 193 75-84 (doi: 10.1677/joe.1.07099).

treatment_protocol: Proximal tibial epiphyses of 10-day-old Sprague-Dawley rats (n=8) were rapidly excised, trimmed of any soft connective tissues, embedded in Tissue-Tek O.C.T. Compound, sectioned (60 μm thick), mounted on Superfrost Plus slides, and stored at -80°C for subsequent processing.  Slides were thawed for 15 s and then placed in 70% ethanol, fixed in 100% methanol, washed in 95% ethanol, stained in eosin (0.2% eosin, 0.5% acetic acid, 75% ethanol), washed in 70% ethanol, dehydrated in 100% ethanol, and placed in xylene (each step for 1 min, at room temperature).  Microdissection was performed using an inverted microscope, razor blades, and hypodermic needles.  Tissues were microdissected in a xylene droplet and collected in 10 μl of 4M guanidine thiocyanate, 25mM sodium citrate pH7, and 0.1M β-mercaptoethanol on ice.  Enzymatic digestion of microdissected tissues was performed using buffered proteinase K solution (1,500 μl DEPC-treated water, 30 μl 1M Tris-HCl pH7, and 57.5 μl proteinase K (20 mg/ml in glycerol)).

tag: strain

value: Sprague-Dawley

value: proximal tibial epiphysis

tag: number of tissues

value: 4 from animals 5 and 6

tag: age

value: 10 days postnatal

tag: zone

value: resting zone


title: Newly-diagnosed type 1 diabetes patient 9 (microRNA)


title: NMBA wk6 3

source_name: rat esophageal epithelia tissue 6 weeks after NMBA treatment

value: Early stage of tumor development


title: NMBA wk6 2


title: Control 1

source_name: rat esophageal epithelia tissue

value: NormaL control


title: Newly-diagnosed type 1 diabetes patient 8 (microRNA)


title: Newly-diagnosed type 1 diabetes patient 7 (microRNA)


title: Newly-diagnosed type 1 diabetes patient 6 (microRNA)


title: resting zone rep 2

description: RZ #2

value: 4 from animals 3 and 4


title: Newly-diagnosed type 1 diabetes patient 5 (microRNA)


title: NMBA wk15 2


title: Control 3


title: Newly-diagnosed type 1 diabetes patient 4 (microRNA)


title: Newly-diagnosed type 1 diabetes patient 3 (microRNA)


title: resting zone rep 4

description: RZ #4

value: 4 from animals 7 and 8


title: intermediate/deep zone rep3

description: IDZ #3

source_name: articular cartilage intermediate/deep zone of 10-day-old rat proximal tibia

value: intermediate/deep zone


title: Newly-diagnosed type 1 diabetes patient 2 (microRNA)


title: frontal cortex_subject_4

source_name: frontal cortex

tag: subjectid

tag: barcode

value: C

tag: Sex

value: FEMALE

value: frontal cortex


title: resting zone rep 1

description: RZ #1

tag: tissue

value: 4 from animals 1 and 2


title: intermediate/deep zone rep4

description: IDZ #4


title: Control 2


title: Newly-diagnosed type 1 diabetes patient 8 (mRNA)

hyb_protocol: Following fragmentation, 2ug of cRNA were hybridized for 16 hr at 4°C onAffymetrix Human Genome U133 Plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

value: Human primary peripheral blood mononuclear cell

value: type 1 diabetes


title: superficial zone rep 2

description: SZ #2

source_name: articular cartilage superficial zone of 10-day-old rat proximal tibia

value: 2 from animal 6

value: superficial zone


title: Newly-diagnosed type 1 diabetes patient 10 (mRNA)


title: superficial zone rep 3

description: SZ #3

value: Sprague-Dawley

value: proximal tibial epiphysis

value: 2 from animal 7


title: Newly-diagnosed type 1 diabetes patient 1 (microRNA)


title: Newly-diagnosed type 1 diabetes patient 11 (mRNA)


title: Newly-diagnosed type 1 diabetes patient 5 (mRNA)


title: superficial zone rep 1

description: SZ #1

value: 2 from animal 5

value: 10 days postnatal


title: intermediate/deep zone rep1

description: IDZ #1


title: Normal control  10 (microRNA)

value: control


title: Newly-diagnosed type 1 diabetes patient 4 (mRNA)


title: Newly-diagnosed type 1 diabetes patient 6 (mRNA)


title: Normal control  9 (microRNA)


title: Newly-diagnosed type 1 diabetes patient 3 (mRNA)


title: Newly-diagnosed type 1 diabetes patient 12 (mRNA)


title: Newly-diagnosed type 1 diabetes patient 9 (mRNA)


title: Newly-diagnosed type 1 diabetes patient 1 (mRNA)


title: Normal control  8 (microRNA)


title: Normal control  10 (mRNA)


title: Inactive FVMs_2

city: Fukuoka

first: Keijiro

last: Ishikawa

address: 3-1-1  Maidashi, Higashi-ku

department: Ophthalmology

institute: Kyushu University

description: SAMPLE 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw gene expression data were summarized using the Illumina Bead Studio software. Thresholding of the signal values to 1is done and then normalized the data to 75th percentile and performs baseline transformation to median of all samples.These are performed by Genespring v 11.

source_name: FVMs with no active NV

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

extract_protocol: To extract the RNAs, FVMs isolated from patients with PDR were homogenized with a Polytron homogenizer in extraction reagent, extracted with chloroform, and the aqueous phase was precipitated in isopropanol.

value: Proliferative diabetic retinopathy (PDR)

value: fibrovascular membranes (FVMs)

tag: specimen

value: no active NV


title: Normal control  6 (microRNA)


title: Normal control  7 (microRNA)


title: Normal control  8 (mRNA)


title: Normal control  5 (microRNA)


title: Inactive FVMs_3

description: SAMPLE 6


title: Active FVMs_3

description: SAMPLE 6

source_name: FVMs with active NV

value: active NV


title: Newly-diagnosed type 1 diabetes patient 2 (mRNA)


title: Normal control  9 (mRNA)


title: Normal control  4 (microRNA)


title: Normal control  7 (mRNA)


title: Inactive FVMs_1

description: SAMPLE 4


title: Normal control  3 (microRNA)


title: Normal control  5 (mRNA)


title: Normal control  4 (mRNA)


title: Normal control  2 (microRNA)


title: Leaf_small_RNA_seq

type: SRA

city: Greenville

first: Baohong

state: NC

address: 562 Science and Technology Building

department: Biology

institute: East Carolina University

description: small RNA mixture from 5 replicates used for sequencing

library_source: transcriptomic

data_processing:
Base-calling using ACGT101-miR-v3
A, C, G, and T composition filter
Adaptor removal
length filter (>=15)
junk filter and low copy filter (>=3)
Supplementary_files_format_and_content: Tab-delimited text files include original read count for each sample

organism: Gossypium hirsutum

source_name: Young leaf near the ovule

growth_protocol: cotton plants were grown in greenhouse

extract_protocol:
Cotton ovules -1 to +1 day post anthesis (DPA) and young leaves were harvested for five biological replicates and immediately frozen in liquid nitrogen. They were then stored at -80°C following RNA extraction.
Totals RNAs were extracted from each tissue sample using the mirVana miRNA isolation kit (Ambion, Austin, TX) according to the manufacturer’s protocol. The small RNA samples extracted from the five biological replicates were pooled together for leaf and ovule, respectively.

tag: developmental stage

value: Young leaf near the ovules -1 to +1 day post anthesis

tag: replicates

tag: cultivar


title: Newly-diagnosed type 1 diabetes patient 7 (mRNA)

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


title: Ovule_small_RNA_seq

source_name: Ovule

value: ovules -1 to +1 day post anthesis


title: Normal control  3 (mRNA)


title: Normal control  1 (microRNA)


title: Normal control  1 (mRNA)


title: Normal control  6 (mRNA)


title: Normal control  2 (mRNA)


title: Retina_2

description: SAMPLE 2

source_name: retina

value: retina


title: Retina_1

description: SAMPLE 1


title: Retina_3

description: SAMPLE 3


title: Active FVMs_1

description: SAMPLE 4


title: superficial zone rep 4

description: SZ #4

value: 2 from animal 8


title: Snail overexpression (FS)

city: Taipei

first: Dennis

middle: Shin-Shian

last: Hsu

state: Taiwan

address: No.155, Sec.2, Linong Street

department: Clinical medicine

country: Taiwan

institute: National Yang Ming University

description:
FaDU-Snail
18632_FS.txt:gProcessedSignal(raw)

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

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.

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. The complete data matrix including control probesets (2,028 data rows) is linked to Series records.

Please note that sample data table contains Cy3 signal intensity after dye normalization, and the normalized data (generated from gProcessedSignal after quantile normalization) are linked to Series records (18632-18636_samples_analysis*.xls)

source_name: Head and neck cell line

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: Cells were cultivated in RPMI + 10% fetal bovine serum

extract_protocol: Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry.

treatment_protocol: Cells were infected with lentivirus harboring ctrl vector,  wild Snail  and mutant Snail .

tag: cell line

value: FaDu

value: hypopharyngeal carcinoma cell line

tag: transfected with

value: pCDH-Snail