title: HIV-1 infected (0% CD3+) 2

city: Brussels

first: Chunyan

last: GU

address: Bld de Waterloo 127

department: Medecine (Jules Bordet Institute)

country: Belgium

institute: Free University of Brussels

description: Gene expression data from HIV-1 infected WE17/10 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data (CEL files) were analyzed in R version 2.3.0 for RMA normalization.

source_name: WE17/10 cells (3% TCR/CD3 surface positive) HIV-1 infected, replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: WE17/10 (a human IL-2-dependent CD4+ T cell line) was cultured in RPMI 1640 supplemented with 10% FBS, 2mM L-glutamine and 100 units/ml of recombinant human IL-2.

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

treatment_protocol: WE17/10 cells were infected with the Lai strain of HIV-1 with sampling taken at various time points post-infection. In this experiment, the infected cells were approximately 1 year post-infection at a TCR/CD3 negative stage and the controls were uninfected cells grown in paralllel.

value: human CD4+ IL-2 dependent memory T cell


title: Lung_PBSsens_OVAchal_rep4

status: Public on Dec 31 2015

type: RNA

city: New Lambton Heights

first: Maximilian

last: Plank

state: Australia

address: Lot 1 Kookaburra Circuit

country: Australia

institute: University of Newcastle

hyb_protocol: MiRNA microarrays were performed according to manufacturer’s protocol using the miRNA Complete Labeling and Hyb Kit and Mouse miRNA Microarray Release 12.0 slides (Agilent Technologies, Technology number 21828, version 2010.11.04).

scan_protocol: Samples were scanned with a High-Resolution C Scanner (Agilent Technologies, USA).

data_processing: Data was processed using the Feature Extraction software version 10.7.3.1 and data analysis was performed using Genespring GX version 11.5.1 (Agilent Technologies, USA).

molecule: total RNA

organism: Mus musculus

source_name: Lung, PBS sensitsation, OVA challenge, replicate 4

extract_protocol: Total RNA was extracted from lung samples using phenol-chloroform separation and isopropanol precipitation.

treatment_protocol: Mice were systemically sensitised via i.p. injection of 50 μg chicken egg OVA complexed with 1 mg Alhydrogel in PBS (day 0). Non-sensitized control mice were injected with 1 mg Alhydrogel in PBS. On days 12, 13, 14 and 15, all mice were challenged (i.n.) with 10 μg of OVA in PBS or PBS for non-challenged control mice. Endpoints were performed 24 hours after the last OVA challenge. Dexamethasone (DEX) treatments (3 mg/kg body weight, i.p.) were performed on day 11 and every second day thereafter 1 hour before challenges.

tag: tissue

value: Lung

tag: sensitisation

value: PBS

tag: challenge

value: OVA

tag: treatment


title: HaCaT_Wildtype

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

hyb_protocol: Probes were then loaded on the array hybridization chambers then hybridized at 65°C for 17 h.

scan_protocol: The slides were washed and scanned (Agilent, Santa Clara, CA) with Agilent DNA microarray scanner.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software X.X using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Homo sapiens

source_name: Wildtype

label_protocol: Fluorescent-labeled (Cy3) probes were prepared with the single color labeling kit from Agilent (Santa Clara, CA).

extract_protocol: Total RNA was isolated with miRNeasy kit (Qiagen, Germantown, MD) according to manufacturer's instructions.

tag: cell line

value: HaCaT

tag: time

value: Wildtype


title: HGF1

city: Tokushima

first: Yosuke

last: Shikama

address: 2-50-1 Kuramoto-cho

department: Tokushima University Hospital

country: Japan

institute: Clinical Research Center for Diabetes

description: US82800151_253949426377_S01_GE1_107_Sep09_1_3

hyb_protocol: 0.6 mg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human 8x60k ver. 2.0 (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan resolution 3 mm).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: HGF were prepared from explants of normal gingival tissues, and the explants were cut into pieces and cultured in DMEM supplemented with 10% fetal bovine serum. After three to four subcultures by trypsinization, homogeneous, slim, spindle-shaped cells grown in characteristic swirls were obtained.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. RNA quality was determined using an agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: HGF were treated with either 1% bovine serum albumin (without stimulation) or 100 mM palmitate. The cultures were incubated for 36 hours at 37C in a humidified incubator with 5% CO2.

tag: subject gender

value: male

tag: age

value: normal gingival tissue

tag: cell type

value: human gingival fibroblasts (HGF)

tag: stimulated with

value: 1% BSA (unstimulated control)


title: PTC-radiation not exposed-gr_1030

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

description: Gene expression data from PTC,radiation not exposed

hyb_protocol: Following fragmentation, 16 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 2.0 PLUS (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: Data was acquired using GeneChip Command Console Software 1.1 (Affymetrix). The preprocessing was performed by Robust Multi-Array expression measure using sequence information (GCRMA, Bioconducor)

label: biotin

source_name: PTC,radiation not exposed

label_protocol: Total RNA (2 ug) was used for synthesis of double stranded cDNA and aRNA labeling according to manufacturer's instructions (GeneChip 3' IVT Express Kit, Affymetrix).

extract_protocol: The material was provided by CTB as aliquots of total RNA from carefully selected PTC samples and respective normal thyroid tissue, after thorough histopathological review of specimens.

tag: type of thyroid tussue (ptc denotes papillary thyroid cancer)

value: PTC

tag: exposure to chernobyl radiation

value: no

tag: region of residence

value: Sumy

tag: age at ptc operation

tag: braf v600e mutation

value: not present

tag: ret/ptc rearrangements

tag: subtype of ptc (classical denotes classical variant of ptc; ptc-f denotes ptc with dominant pattern of follicular structures; ptc-s denotes ptc with dominant pattern of solid areas; ptc-fs denotes ptc with dominant pattern of folicular and solid areas)

value: PTC-S

tag: batch


title: HIV-1 infected (0% CD3+) 1

source_name: WE17/10 cells (3% TCR/CD3 surface positive) HIV-1 infected, replicate 1


title: WE 17/10 2

description: Gene expression data from uninfected WE17/10 cells

source_name: WE17/10 cells (99% TCR/CD3 surface positive) uninfected, replicate 2


title: HGF2

description: US82800151_253949426377_S01_GE1_107_Sep09_1_4

tag: tissue


title: LCL_truncating10

city: Madrid

first: Tereza

last: Vaclova

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

country: Spain

institute: CNIO - Spanish National Cancer Research Centre

description: Gene expression at basal conditions

hyb_protocol: 600 ng of Cy3-labelled extract of total volume 50 µl was hybridized in a rotating SureHyb hybridization chamber (Agilent) at 65°C for 17 hours.

scan_protocol: Slides were scanned on the G2505C DNA Microarray Scanner (Agilent).

data_processing: The raw data were extracted from scanned slides with Feature Extraction software (Agilent; version 10.7), which performed feature quantitation and additive detrend correction. Background correction (performed via the normexp method) and between arrays normalization (utilizing the quantiles method) of raw data was performed using Babelomics 4.3 web tool (Medina, Carbonell et al.), which is available at http://babelomics.bioinfo.cipf.es

source_name: LCL, truncating BRCA1

label_protocol: 100 ng of total RNA from LCLs was labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following manufacturer´s instructions and the One-Color Microarray-Based Gene Expression Analysis approach. Labeled samples were then purified with silica-based RNeasy spin columns (Qiagen).

extract_protocol: RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer´s instructions. Ten million cells from each LCL was used for RNA isolation. RNA quality and quantity was determined using LabChip technology on an Agilent 2100 BioAnalyser (Agilent Technologies).

treatment_protocol: No treatment applied.

value: lymphoblastoid cell line

tag: gender

value: female


title: WE 17/10 1

source_name: WE17/10 cells (99% TCR/CD3 surface positive) uninfected, replicate 1

value: human CD4+ IL-2 dependent memory T cell


title: Lung_PBSsens_OVAchal_rep1

source_name: Lung, PBS sensitsation, OVA challenge, replicate 1

label_protocol: MiRNA microarrays were performed according to manufacturer’s protocol using the miRNA Complete Labeling and Hyb Kit and Mouse miRNA Microarray Release 12.0 slides (Agilent Technologies, Technology number 21828, version 2010.11.04).

value: Lung

tag: sensitisation

tag: challenge

tag: treatment


title: LCL_truncating9

description: Gene expression at basal conditions


title: LCL_truncating8

description: Gene expression at basal conditions


title: LCL_truncating7

description: Gene expression at basal conditions


title: tat-2ex-wt (3% CD3+) 2

description: Gene expression data from WE17/10 cells transduced with sense Tat

data_processing: The data (CEL files) were analyzed in R version 2.5.1 for RMA normalization.

source_name: WE17/10 cells (3% TCR/CD3 surface positive) transduced with the HIV-1 Tat gene inserted in sense, replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit Manual, 2009, Affymetrix).

treatment_protocol: WE17/10 cells were transduced with the M420 lentiviral vector containing the coding sequences for two-exon HIV-1 LAI tat gene excised from the pREP9/tat2exon vector and subcloned into the BamHI site downstream from the spleen focus forming virus promoter in the M420 vector, creating the wild-type two exon (tat-2ex-wt) tat expression vector. A constructs carrying the two-exon tat gene inserted in the antisense direction (tat-2ex-wt-AS) was used as a negative control.

tag: cell line


title: Lung_PBSsens_PBSchal_rep2

source_name: Lung, PBS sensitsation, PBS challenge, replicate 2

value: PBS


title: LCL_truncating3

description: Gene expression at basal conditions

tag: age


title: Lung_PBSsens_PBSchal_rep1

source_name: Lung, PBS sensitsation, PBS challenge, replicate 1


title: tat-2ex-wt (99% CD3+) 2

source_name: WE17/10 cells (99% TCR/CD3 surface positive) transduced with the HIV-1 Tat gene inserted in sense, replicate 2

tag: cell type


title: LCL_missense2

description: Gene expression at basal conditions

source_name: LCL, missense BRCA1


title: LCL_truncating1

description: Gene expression at basal conditions


title: LCL_truncating6

description: Gene expression at basal conditions


title: LCL_missense4

description: Gene expression at basal conditions


title: tat-2ex-AS (99% CD3+) 1

description: Gene expression data from WE17/10 cells transduced with antisense Tat (control)

source_name: WE17/10 cells (99% TCR/CD3 surface positive) transduced with the HIV-1 Tat gene inserted in antisense, replicate 1


title: LCL_truncating5

description: Gene expression at basal conditions


title: LCL_truncating4

description: Gene expression at basal conditions


title: LCL_missense1

description: Gene expression at basal conditions


title: LCL_WT6

description: Gene expression at basal conditions

source_name: LCL, WT BRCA1


title: LCL_WT3

description: Gene expression at basal conditions


title: LCL_WT2

description: Gene expression at basal conditions


title: LCL_missense3

description: Gene expression at basal conditions


title: tat-2ex-wt (99% CD3+) 1

source_name: WE17/10 cells (99% TCR/CD3 surface positive) transduced with the HIV-1 Tat gene inserted in sense, replicate 1


title: LCL_truncating2

description: Gene expression at basal conditions


title: LCL_WT5

description: Gene expression at basal conditions


title: LCL_missense5

description: Gene expression at basal conditions


title: LCL_WT4

description: Gene expression at basal conditions


title: tat-2ex-AS (99% CD3+) 2

source_name: WE17/10 cells (99% TCR/CD3 surface positive) transduced with the HIV-1 Tat gene inserted in antisense, replicate 2


title: HK-2 cells, CdCl and Di, t48h, control sample, biological rep 3, All

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

hyb_protocol: 15 ug fragmented labelled cRNA was hybridized for 16 hours at 45oC to Affymetrix HGU133_Plus 2.0 GeneChips, which were then stained and washed on an Affymetrix Fluidics Station 400.

scan_protocol: Fluorescence was read with an Affymetrix 3000 Scanner.

data_processing: Data was normalized using the gcrma library (version 2.8.1) of Bioconductor.

source_name: Human renal proximal tubular epithelial cells, control for CdCl, t48h

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

growth_protocol: HK-2 cells were maintained in a 1-1 mixture of DMEM and Ham'sF12 containing 5 mM glucose supplemented with 10 ng/ml human recombinant EGF, 36 ng/ml hydrocortisone, 5 µg/ml bovine insulin, 5 µg/ml human transferrin, 5 ng/ml sodium selenite, 2 mM Glutamax (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy mini kit.

treatment_protocol: Cells were seeded 24 hours before treatment on Greiner 6-well plates at a density of 7x10^5 cells per well with 2mls of medium per well. Cells were treated at ~90% confluency with the required doses for the required timepoints. Control cells were exposed to an appropriate concentration of the control vehicle.

value: immortalized human renal proximal tubular epithelial cells

value: control

tag: treatment duration

value: 48 hrs


title: HK-2 cells, CdCl and Di, t48h, control sample, biological rep 1, All


title: LCL_WT1

description: Gene expression at basal conditions


title: HK-2 cells, CdCl and Di, t12h, control sample, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, control for CdCl, t12h

value: 12 hrs


title: tat-2ex-wt (3% CD3+) 1

source_name: WE17/10 cells (3% TCR/CD3 surface positive) transduced with the HIV-1 Tat gene inserted in sense, replicate 1


title: CPCG0382+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H10

type: genomic

city: Toronto

first: Paul

middle: C

last: Boutros

state: ON

address: 661 University Avenue

department: Informatics and Bio-Computing

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Hybridization was done manually using Multi+AC0-channel pilett. X+AC0-Stain was done using the robot Tacan evolution with the HD protocol.

scan_protocol: Done using HiScan from Illumina.

data_processing:
R Bioconductor ChAMP 1.0.7
Original beta values and beta values normalized with BMIQ method.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Prostate frozen sample

label_protocol: Standard Illumina Protocol - HumanMethylation450 BeadChip

extract_protocol:
4.1.  Genomic DNA Extraction:
4.1.1. Pellet Phase Lock Gel (PLG) down by centrifuge at 14,000g, 1min at RT.
4.1.2. Quickly spin down digested sample to avoid any volume lose.
4.1.3. Transfer 250ul digested tissue into pre-spun PLG tube.
4.1.4. Then Add equal volume (250ul) phenol: chloroform: isoamyl alcohol 25:24:1 to the same tube.
6.2.4. Thoroughly mix by invert several times. Do not vortex. Cap the tube tightly.
6.2.5. Centrifuge at 14,000g for 4min at room temperature. PLG will form a barrier between aqueous and organic phases.
6.2.6. Note: If second extraction is necessary, and maximum tube volume is not exceeded, more organic solvent can be added to the same tube, mix and recentrifuge.
6.2.7. Carefully remove upper aqueous phase into a new eppendorf tube.
6.2.8. Precipitate DNA by adding 1/10 volume 3M NaOAc pH5.2, mix and then add 625ul (=250ul x 2.5 vol) 100% EtOH or 250 ul Isopropanol (=1 vol). Mix well.
6.2.9. Place DNA tube at -20C degrees overnight.
6.2.10. Centrifuge in cold microcentrifuge 4C to max speed for 15min to get DNA pellet.
6.2.11. Discard EtOH and wash pellet with 500ul cold 80% EtOH.
6.2.12. Centrifuge in cold microcentrifuge at 4C to max speed for 5min.
6.2.13. Discard EtOH.
6.2.14. Air dry DNA pellet.
6.2.15. Depends on pellet size, resuspend pellet in a small volume of Sigma H2O.
6.2.16. Leave sample at room temperature for at least 1 hour (prefer 4C overnight) to allow DNA completely dissolve.
6.2.17. Store at -20C.

value: Male


title: HK-2 cells, CdCl and Di, t12h, control sample, biological rep 2, All


title: HK-2 cells, Di, t48h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with Di, t48h

value: Di


title: MSOD_rep4

city: Roma

first: Camilla

last: Bernardini

address: L.go F.Vito 1

country: Italy

institute: Università Cattolica del Sacro Cuore

hyb_protocol: Following fragmentation, 3.5 μg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene expression 2.0 st Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Mouse Gene Expression Arrays were scanned on GeneChip® Scanner 3000 7G.

data_processing: CEL files were analyzed with Affymetrix® Expression Console™ software (v.1.4). Background adjustment, qualtile normalization and summarization were perfomed using RMA-Sketch Algorithm. Diffferent Gene-Level expression was analyzed using Affymetrix® Trascriptome Analysis Console (TAC) and a unpaired one way ANOVA as statistical test.

label: Biotin

source_name: Lumbar Spinal Cord Ventral

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions. Tot RNA was purified using the RNAeasy mini purification kit (QIAGEN) according to the RNA cleanup protocol

tag: strain

value: FVB

tag: genotype/variation

value: MLC/SOD1G93A transgenic

value: 120 days

value: lumbar spinal cord


title: HK-2 cells, Di, t48h, biological rep 1, All


title: HK-2 cells, CdCl and Di, t12h, control sample, biological rep 1, All


title: HK-2 cells, Di, t12h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with Di, t12h


title: MSOD_rep3


title: MSOD_rep2


title: HK-2 cells, Di, t48h, biological rep 2, All


title: HEK293T_R142C

tag: time

value: mutation R142C


title: CPCG0389+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H11


title: FVB_rep4


title: HK-2 cells, Di, t12h, biological rep 1, All


title: HK-2 cells, Di, t12h, biological rep 2, All


title: CPCG0364+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H06


title: CPCG0357+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H04


title: FVB_rep3


title: HK-2 cells, CdCl, t48h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with CdCl, t48h

value: CdCl


title: CPCG0334+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-G11


title: MSOD_rep1


title: CPCG0365+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H07


title: CPCG0341+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H02


title: CPCG0346+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H03


title: CPCG0361+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H05


title: HK-2 cells, CdCl, t48h, biological rep 1, All


title: CPCG0366+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H08


title: CPCG0336+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-G12


title: CPCG0340+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H01


title: CPCG0282+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-G08


title: CPCG0267+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-G07


title: CPCG0324+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-G09


title: HK-2 cells, CdCl, t48h, biological rep 2, All


title: FVB_rep1


title: CPCG0379+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-H09


title: HK-2 cells, CdCl, t12h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with CdCl, t12h


title: CPCG0333+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-G10


title: HK-2 cells, CdCl, t12h, biological rep 2, All


title: CPCG0266+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-G06


title: CPCG0411+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-F01


title: CPCG0415+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-F05


title: FVB_rep2


title: HK-2 cells, CdCl and Di, t48h, control sample, biological rep 2, All


title: PbCre;T-3Mb-Erg/+;PtenL/L HGPIN lesions from mouse V130

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Gene expression data for microdissected HGPIN tissue from PbCre;T-3Mb-Erg/+;PtenL/L male mouse V130

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured

data_processing:
The raw CEL files were imported, normalized and analyzed with genepattern analysis tools (dCHIP, GSEA) from Broad institiute
After normalization, the model-based expression values were calculated by dCHIP and exported

label_protocol: Labeling, hybridization and scan performed by team led by Dr. Edward Fox at the Dana-Farber Cancer Institute Microarray Core Facility. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

growth_protocol: Prostate glands were isolated from aged mice with corresponding genotypes

extract_protocol: RNeasy kit (Qiagen, #73504) was used on laser microdissected tissue according to manufacturer's protocol

treatment_protocol: Prostates were fixed overnight in 10% formalin, washed with 70% ethanol, dehydrated, and paraffin embedded. Cut sections were stained with hematoxylin and used for laser capture microdissection (ArcturusXT)

tag: genotype and mouse id

value: male

value: prostate gland

tag: age (months)

value: mixed


title: PbCre;T-3Mb-Erg/+;PtenL/L HGPIN lesions from mouse W376

description: Gene expression data for microdissected HGPIN tissue from PbCre;T-3Mb-Erg/+;PtenL/L male mouse W376


title: HK-2 cells, CdCl, t12h, biological rep 1, All


title: CPCG0414+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-F04


title: CPCG0412+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-F02


title: CPCG0413+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-F03


title: CPCG0416+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-F06


title: HK-2 cells, Ra, t48h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with Ra, t48h

value: Ra


title: CPCG0410+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E12


title: PbCre;T-3Mb-Erg/+;PtenL/L solid tumors from mouse V130

description: Gene expression data for microdissected solid tumor tissue from PbCre;T-3Mb-Erg/+;PtenL/L male mouse V130


title: PbCre;T-3Mb-Erg/+;PtenL/L HGPIN lesions from mouse T390

description: Gene expression data for microdissected HGPIN tissue from PbCre;T-3Mb-Erg/+;PtenL/L male mouse T390


title: PbCre;T-3Mb-Erg/+;PtenL/L solid tumors from mouse W376

description: Gene expression data for microdissected solid tumor tissue from PbCre;T-3Mb-Erg/+;PtenL/L male mouse W376


title: HK-2 cells, Ra, t48h, biological rep 3, All


title: PbCre;PtenL/L HGPIN lesions mouse V87

description: Gene expression data for microdissected HGPIN tissue from PbCre;PtenL/L male mouse V87

source_name: PbCre;PtenL/L HGPIN lesions mouse V87

value: PbCre;PtenL/L HGPIN lesions mouse V87


title: PbCre;PtenL/L HGPIN lesions from mouse A132

description: Gene expression data for microdissected HGPIN tissue from PbCre;PtenL/L male mouse A132


title: HK-2 cells, Fk, t48h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with Fk, t48h

value: immortalized human renal proximal tubular epithelial cells

value: Fk


title: HK-2 cells, Fk, t48h, biological rep 2, All

value: 48 hrs


title: PbCre;T-3Mb-Erg/+;PtenL/L solid tumors from mouse T390

description: Gene expression data for microdissected solid tumor tissue from PbCre;T-3Mb-Erg/+;PtenL/L male mouse T390


title: HK-2 cells, Ra, t48h, biological rep 1, All


title: CPCG0409+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E11


title: CPCG0390+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E06


title: HK-2 cells, Fk, t48h, biological rep 1, All


title: PbCre;PtenL/L HGPIN lesions from mouse U476

description: Gene expression data for microdissected HGPIN tissue from PbCre;PtenL/L male mouse U476


title: CPCG0408+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E10


title: CPCG0389+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E05


title: CPCG0391+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E07


title: CPCG0407+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E09


title: HK-2 cells, Fk and Ra, t48h, control sample, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, control for Fk, t48h

value: control


title: HK-2 cells, Fk and Ra, t48h, control sample, biological rep 2, All


title: CPCG0387+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E04

value: Male


title: HK-2 cells, Fk and Ra, t48h, control sample, biological rep 1, All


title: CPCG0380+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E01


title: CPCG0381+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E02


title: HK-2 cells, Ra, t12h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with Ra, t12h

value: 12 hrs


title: HK-2 cells, Ra, t12h, biological rep 2, All


title: CPCG0375+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D08


title: CPCG0382+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E03


title: CPCG0401+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-E08


title: CPCG0369+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D03


title: CPCG0371+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D04


title: CPCG0374+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D07


title: CPCG0379+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D11


title: HK-2 cells, Ra, t12h, biological rep 3, All


title: CPCG0378+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D10


title: CPCG0373+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D06


title: HK-2 cells, Fk, t12h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with Fk, t12h


title: CPCG0363+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C10


title: HK-2 cells, Fk, t12h, biological rep 1, All


title: CPCG0377+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D09


title: CPCG0366+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D01


title: HK-2 cells, Fk and Ra, t12h, control sample, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, control for Fk, t12h


title: CPCG0364+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C11


title: CPCG0372+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D05


title: HK-2 cells, Fk and Ra, t12h, control sample, biological rep 2, All


title: CPCG0357+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C05


title: HK-2 cells, Fk and Ra, t12h, control sample, biological rep 1, All


title: CPCG0358+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C06


title: CPCG0360+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C07


title: CPCG0361+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C08


title: CPCG0365+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C12


title: HK-2 cells, Ota, ld, t72h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Ota, t72h

value: Ota

tag: treatment dosage

value: low

value: 72 hrs


title: CPCG0362+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C09


title: CPCG0368+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-D02


title: HK-2 cells, Fk, t12h, biological rep 2, All


title: HK-2 cells, Ota, ld, t72h, biological rep 3, All


title: HK-2 cells, Ota, hd, t72h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Ota, t72h

value: high


title: HK-2 cells, Ota, ld, t72h, biological rep 1, All


title: CPCG0353+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C01


title: CPCG0350+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B11


title: CPCG0352+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B12


title: CPCG0346+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B08


title: HK-2 cells, Ota, hd, t72h, biological rep 2, All


title: CPCG0349+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B10


title: CPCG0335+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B01


title: CPCG0342+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B06


title: HK-2 cells, Ota, hd, t72h, biological rep 1, All


title: CPCG0344+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B07


title: CPCG0341+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B05


title: CPCG0355+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C03


title: HK-2 cells, Ota, hd and ld, t72h, control sample, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, control for Ota, t72h


title: HK-2 cells, Ota, hd and ld, t72h, control sample, biological rep 3, All


title: CPCG0334+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A12


title: CPCG0356+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C04


title: CPCG0340+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B04


title: CPCG0348+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B09


title: CPCG0331+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A10


title: HCC70 RUX4_3

city: Nashville

first: Justin

middle: M

last: Balko

state: TN

address: 777 Preston Research Building

department: Medicine

institute: Vanderbilt University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. 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: R/Bioconductor RMA normalization

source_name: HCC70 cells

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

growth_protocol: ATCC-defined media + 10% fetal bovine serum

extract_protocol: Qiagen RNEasy

treatment_protocol: ruxolitinib 1uM in DMSO for 4 or 24 hrs, or DMSO at 0.1% for 24 hrs

value: ruxolitinib 1uM 4 hrs

tag: replicate


title: HK-2 cells, Ota, hd and ld, t72h, control sample, biological rep 1, All


title: CPCG0282+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A08

source_name: Prostate frozen sample


title: HK-2 cells, Ota, ld, t24h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Ota, t24h

value: 24 hrs


title: CPCG0339+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B03


title: HCC70 RUX4_2


title: HCC70 DMSO_3

value: DMSO 0.1% 24 hrs


title: CPCG0354+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-C02


title: CPCG0268+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A05


title: CPCG0324+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A09


title: CPCG0267+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A04


title: HK-2 cells, Ota, ld, t24h, biological rep 2, All


title: CPCG0266+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A03


title: HCC1143 DMSO_3

source_name: HCC1143 cells


title: HK-2 cells, Ota, ld, t24h, biological rep 1, All


title: CPCG0269+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A06


title: HK-2 cells, Ota, hd, t24h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Ota, t24h


title: CPCG0271+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A07


title: HK-2 cells, Ota, hd, t24h, biological rep 2, All


title: CPCG0182+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A01


title: CPCG0250+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D08


title: CPCG0255+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D10


title: HK-2 cells, Ota, hd, t24h, biological rep 1, All


title: HCC70 RUX24_2

value: ruxolitinib 1uM 24 hrs


title: CPCG0265+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D12


title: CPCG0336+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-B02


title: HCC70 RUX24_1


title: HK-2 cells, Ota, hd and ld, t24h, control sample, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, control for Ota, t24h


title: CPCG0251+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D09


title: CPCG0258+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D11


title: CPCG0263+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A02


title: HCC70 RUX4_1


title: CPCG0249+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D07


title: CPCG0246+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D05


title: HCC70 DMSO_2


title: HK-2 cells, Ota, hd and ld, t24h, control sample, biological rep 1, All


title: HK-2 cells, Nnm, ld, t48h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t48h

value: Nnm


title: SUM159PT DMSO_3

source_name: SUM159PT cells


title: CPCG0241+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D03


title: CPCG0242+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D04


title: CPCG0236+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D01


title: CPCG0248+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D06


title: HK-2 cells, Kbr, ld, t48h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t48h

value: Kbr


title: HCC70 DMSO_1


title: HCC38 RUX24_3

source_name: HCC38 cells


title: CPCG0238+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-D02


title: CPCG0232+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C10


title: CPCG0217+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C09


title: HK-2 cells, Aa, ld, t48h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t48h

value: Aa


title: HK-2 cells, Nnm, hd, t48h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t48h

value: immortalized human renal proximal tubular epithelial cells


title: HK-2 cells, Ota, hd and ld, t24h, control sample, biological rep 2, All


title: HCC38 RUX24_1


title: HCC38 RUX24_2


title: CPCG0233+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C11


title: CPCG0208+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C07


title: HK-2 cells, Aa, hd, t48h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Aa, t48h


title: HCC38 RUX4_3


title: CPCG0210+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C08


title: HK-2 cells, Kbr, hd, t48h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t48h


title: CPCG0189+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C03


title: HCC38 RUX4_2


title: CPCG0190+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C04


title: HCC70 RUX24_3


title: CPCG0191+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C05


title: CPCG0196+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C06


title: HK-2 cells, Nnm and Kbr, hd and ld, t48h, control sample, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t48h


title: HCC38 RUX4_1


title: CPCG0188+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C02


title: CPCG0235+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C12


title: HK-2 cells, Aa, hd and ld, t48h, control sample, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, control for Aa, t48h


title: CPCG0285+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B11


title: CPCG0333+AC0-F1+AF8-WG0001175+AC0-MSA4+AC0-A11


title: HK-2 cells, Nnm, ld, t24h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t24h


title: CPCG0286+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B12


title: HCC38 DMSO_2


title: CPCG0281+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B09


title: CPCG0279+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B08


title: CPCG0227+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B06


title: SUM159PT RUX24_3


title: HCC38 DMSO_1


title: HK-2 cells, Aa, ld, t24h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t24h


title: CPCG0282+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B10

source_name: Prostate frozen sample


title: HK-2 cells, Nnm, hd, t24h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t24h


title: CPCG0213+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B05


title: HK-2 cells, Kbr, hd, t24h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t24h


title: CPCG0203+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B04


title: CPCG0240+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B07


title: SUM159PT RUX24_2


title: CPCG0185+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-C01


title: CPCG0158+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B01


title: HK-2 cells, Aa, hd, t24h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Aa, t24h


title: HK-2 cells, Kbr, ld, t24h, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t24h


title: CPCG0187+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B02


title: SUM159PT RUX24_1


title: CPCG0114+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A10


title: CPCG0200+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-B03


title: CPCG0154+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A12


title: HCC38 DMSO_3


title: HK-2 cells, Nnm and Kbr, hd and ld, t24h, control sample, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t24h


title: CPCG0132+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A11


title: HK-2 cells, Aa, hd and ld, t24h, control sample, biological rep 3, All

source_name: Human renal proximal tubular epithelial cells, control for Aa, t24h


title: SUM159PT RUX4_2

source_name: SUM159PT cells


title: SUM159PT RUX4_1


title: SUM159PT RUX4_3


title: CPCG0072+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A06


title: CPCG0094+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A08


title: HK-2 cells, Nnm, ld, t48h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t48h


title: SUM159PT DMSO_1


title: CPCG0048+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A03


title: MEF p27ko 23 Mphase

city: Columbus

first: Francesca

last: Lovat

address: 460 W 12th ave

institute: The Ohio State University

description: microRNA expression data from cells treated with double thymidine block procedure and nocodazole

hyb_protocol: Samples were hybridized in 6X SSPE/30% Formamide at 25 C for 18 hours

scan_protocol: Arrays were stained with Streptavidin-Alexa 647 conjugate (Invitrogen/Molecular Probes) and scanned at 10um resolution at 635nm with qred laser at 100% Power and 800 PMT. Data extracted with GenePix 6.0.

data_processing: BRB-ArrayTools. Normalize (center) each array using median over entire array. All 15 samples were normalized together in one batch, used median array as reference array.

source_name: MEF p27ko: M-phase

label_protocol: Biotinylated random octamers were used to reverse transcribe 2ug of total RNA into biotinylated cDNA

growth_protocol: MEF was cultured as recommended by ATCC.

treatment_protocol: MEFs were collected after different conditions: exponential growth (normal cell cycle), serum starvation (G0/G1-phase block) and double thymidine block (early S-phase block) and nocodazole (Mphase)

value: Mouse Embryonic Fibroblast

tag: growth

value: M-phase


title: CPCG0083+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A07


title: MEF p27ko 18 G1-phase block

description: microRNA expression data from cells treated with serum starvation

source_name: MEF p27ko: G1-phase


title: HCC1143 RUX24_3

source_name: HCC1143 cells


title: HK-2 cells, Kbr, ld, t48h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t48h

value: 48 hrs


title: CPCG0047+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A02

value: Male


title: HK-2 cells, Nnm, hd, t48h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t48h


title: HCC1143 RUX24_2


title: MEF p27ko 17 G1-phase block


title: CPCG0232+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E12


title: CPCG0057+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A04


title: HK-2 cells, Aa, ld, t48h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t48h


title: CPCG0262+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A09


title: CPCG0260+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A05


title: CPCG0196+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E11


title: HK-2 cells, Kbr, hd, t48h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t48h


title: CPCG0191+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E08


title: HCC1143 RUX24_1


title: MEF p27ko 16 G1-phase block


title: MEF p27ko 15 EXP GROWTH

description: microRNA expression data from exponential growth cells

source_name: MEF p27ko: Exponential phase

value: Exponential phase


title: CPCG0210+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E10

source_name: Prostate frozen sample


title: HK-2 cells, Nnm and Kbr, hd and ld, t48h, control sample, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t48h

value: control


title: MEF p27ko 14 EXP GROWTH


title: HK-2 cells, Aa, hd, t48h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Aa, t48h


title: HCC1143 RUX4_3


title: HK-2 cells, Aa, hd and ld, t48h, control sample, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, control for Aa, t48h


title: MEF p27wt 7 S-phade

description: microRNA expression data from cells treated with double thymidine block procedure

source_name: MEF wild-type: S-phase

value: wild-type

value: S-phase


title: MEF p27wt 8 S-phase


title: HCC1143 RUX4_2


title: CPCG0184+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E05


title: MEF p27wt 9 S-phase


title: SUM159PT DMSO_2


title: CPCG0208+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E09


title: CPCG0259+AC0-F1+AF8-WG0000672+AC0-MSA4+AC0-A01


title: CPCG0102+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E02


title: MEF p27wt 5 G1-phase block

source_name: MEF wild-type: G1-phase


title: HCC1143 RUX4_1


title: CPCG0100+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E07


title: CPCG0099+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E01


title: CPCG0183+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E04


title: CPCG0184+AC0-P2+AF8-WG0001171+AC0-MSA4+AC0-E06


title: MEF p27wt 4 G1-phase block


title: blood_2h_EDTA_H6

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

country: Germany

institute: Saarland University

description:
miRNA
EDTA blood healthy person H6; transferred after 2h into fresh PAXgene tube

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Array-chips were scanned in a high resolution microarray scanner from Agilent Technologies using Scan Control 8.5.1 software, 3 microns resolution in double path mode.

data_processing: Signal intensity values were extracted from the raw data file using feature extraction software (Agilent Technologies). The gTotalProbeSignals were summed up to calculate the total expression value for each miRNA per sample. Quantile normalization was applied to normalize expression values across the arrays using the preprocessCore package of the programming language R. After that we log2-transformed the expression values.  The quantile normalized signal intensity data are available on the series record.

source_name: whole blood

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit

extract_protocol: Total RNA including small RNAs was isolated using miRNeasy Micro Kit (Qiagen)  according to manufacturer’s instructions.

tag: tissue

value: whole blood

value: female


title: CPCG0233+AC0-F1+AF8-WG0001171+AC0-MSA4+AC0-E03

tag: gender


title: MEF p27wt 3 EXP GROWTH

source_name: MEF wild-type: Exponential phase


title: MEF p27wt 2 EXP GROWTH


title: MEF p27wt 1 EXP GROWTH


title: blood_0min_EDTA_H6

description:
miRNA
EDTA blood healthy person H6; transferred after 0min into fresh PAXgene tube


title: blood_10min_EDTA_H5

description:
miRNA
EDTA blood healthy person H5; transferred after 10min into fresh PAXgene tube


title: blood_2h_EDTA_H5

description:
miRNA
EDTA blood healthy person H5; transferred after 2h into fresh PAXgene tube


title: blood_0min_EDTA_H5

description:
miRNA
EDTA blood healthy person H5; transferred after 0min into fresh PAXgene tube


title: blood_0min_PAX_H5

description:
miRNA
PAXGene blood healthy person H5 0min


title: blood_10min_EDTA_H6

description:
miRNA
EDTA blood healthy person H6; transferred after 10min into fresh PAXgene tube


title: WDR5-2 (HuGene-2_0-st)

city: Randwick

first: Tao

last: Liu

state: NSW

address: Lowy Cancer Research Centre

institute: Children's Cancer Institute Australia

description: Gene expression data from neuroblastoma cells transfected with WDR5 siRNA-2

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human HuGene-2_0-st Array. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing:
Images were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
Results were further analysed in R (http://www.r-project.org/) with bioconductor package (http://www.bioconductor.org/).

source_name: BE(2)-C_WDR5 siRNA-2

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

growth_protocol: BE(2)-C neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum.

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

treatment_protocol: BE(2)-C cells were treated with control siRNA, WDR5 siRNA-1, andWDR5 siRNA-2 for 40 hours

value: peripheral nervous system tumour cell

value: MYCN-amplified neuroblastoma cells

tag: transfected with

value: WDR5 siRNA-2


title: blood_2h_EDTA_H4

description:
miRNA
EDTA blood healthy person H4; transferred after 2h into fresh PAXgene tube


title: HK-2 cells, Kbr, ld, t24h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t24h

value: low

value: 24 hrs


title: HK-2 cells, Aa, ld, t24h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t24h

value: Aa


title: HK-2 cells, Aa, hd, t24h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Aa, t24h

value: immortalized human renal proximal tubular epithelial cells

value: high


title: HCC1143 DMSO_1

source_name: HCC1143 cells

value: DMSO 0.1% 24 hrs


title: blood_10min_EDTA_H4

description:
miRNA
EDTA blood healthy person H4; transferred after 10min into fresh PAXgene tube


title: blood_0min_PAX_H6

description:
miRNA
PAXGene blood healthy person H6 0min


title: HK-2 cells, Kbr, hd, t24h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t24h

value: Kbr


title: WDR5-1 (HuGene-2_0-st)

description: Gene expression data from neuroblastoma cells transfected with WDR5 siRNA-1

source_name: BE(2)-C_WDR5 siRNA-1

value: WDR5 siRNA-1


title: 10 nM panobinostat - replicate 3

description:
panobinostat_3(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with panobinostat - replicate 3

data_processing:
Images were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
Results were further analyzed in R (http://www.r-project.org/) with bioconductor 'affy' package (http://www.bioconductor.org/).

source_name: neuroblastoma SK-N-BE(2) cells treated with panobinostat -3

growth_protocol: SK-N-BE(2) neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum.

treatment_protocol: SK-N-BE(2) cells were treated with vehicle control, 1 microM JQ1, 10nM panobinostat, or combination of JQ1 and panobinostat for 6 hours.

value: SK-N-BE(2) MYCN-amplified neuroblastoma cell line

value: 10 nM panobinostat


title: HK-2 cells, Nnm and Kbr, hd and ld, t24h, control sample, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t24h

value: control


title: blood_0min_EDTA_H4

description:
miRNA
EDTA blood healthy person H4; transferred after 0min into fresh PAXgene tube


title: Control (HuGene-2_0-st)

description: Gene expression data from neuroblastoma cells transfected with control siRNA

source_name: BE(2)-C_control siRNA

value: control siRNA


title: JQ1 + panobinostat - replicate 3

description:
JQ1 + panobinostat-3_(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with JQ1 + panobinostat - replicate 3

source_name: neuroblastoma SK-N-BE(2) cells treated with JQ1 + panobinostat -3

value: 1 microM JQ1 + 10 nM panobinostat


title: blood_2h_EDTA_H3

description:
miRNA
EDTA blood healthy person H3; transferred after 2h into fresh PAXgene tube

value: whole blood

value: female


title: blood_10min_EDTA_H3

description:
miRNA
EDTA blood healthy person H3; transferred after 10min into fresh PAXgene tube


title: vehicle control - replicate 3

description:
Control-3_(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with vehicle control -replicate 3

source_name: neuroblastoma SK-N-BE(2) cells treated with vehicle control - 3

value: vehicle control


title: blood_0min_EDTA_H3

description:
miRNA
EDTA blood healthy person H3; transferred after 0min into fresh PAXgene tube


title: blood_0min_PAX_H3

description:
miRNA
PAXGene blood healthy person H3 0min


title: blood_0min_PAX_H4

description:
miRNA
PAXGene blood healthy person H4 0min


title: HK-2 cells, Nnm, hd, t24h, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t24h

value: Nnm


title: blood_10min_EDTA_H2

description:
miRNA
EDTA blood healthy person H2; transferred after 10min into fresh PAXgene tube

value: male


title: HK-2 cells, Aa, hd and ld, t24h, control sample, biological rep 2, All

source_name: Human renal proximal tubular epithelial cells, control for Aa, t24h

value: 24 hrs


title: 1 microM JQ1 -replicate 3

description:
JQ1-3_(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with JQ1 - replicate 3

source_name: neuroblastoma SK-N-BE(2) cells treated with JQ1 -3

value: 1 microM JQ1


title: blood_2h_EDTA_H2

description:
miRNA
EDTA blood healthy person H2; transferred after 2h into fresh PAXgene tube

source_name: whole blood


title: blood_10min_EDTA_H1

description:
miRNA
EDTA blood healthy person H1; transferred after 10min into fresh PAXgene tube


title: blood_2h_EDTA_H1

description:
miRNA
EDTA blood healthy person H1; transferred after 2h into fresh PAXgene tube


title: HK-2 cells, Nnm, ld, t48h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t48h

value: immortalized human renal proximal tubular epithelial cells

value: low

value: 48 hrs


title: JQ1 + panobinostat - replicate 2

description:
JQ1 + panobinostat-2_(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with JQ1 + panobinostat - replicate 2

source_name: neuroblastoma SK-N-BE(2) cells treated with JQ1 + panobinostat -2


title: HK-2 cells, Aa, ld, t48h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t48h

value: Aa


title: MEF p27ko 13 EXP GROWTH

description: microRNA expression data from exponential growth cells

source_name: MEF p27ko: Exponential phase

value: Mouse Embryonic Fibroblast

value: Exponential phase


title: blood_0min_EDTA_H1

description:
miRNA
EDTA blood healthy person H1; transferred after 0min into fresh PAXgene tube


title: 10 nM panobinostat - replicate 2

description:
panobinostat-2_(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with panobinostat - replicate 2

source_name: neuroblastoma SK-N-BE(2) cells treated with panobinostat -2

value: SK-N-BE(2) MYCN-amplified neuroblastoma cell line

value: 10 nM panobinostat


title: HK-2 cells, Kbr, ld, t48h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t48h

value: Kbr


title: blood_0min_PAX_H1

description:
miRNA
PAXGene blood healthy person H1 0min


title: blood_0min_EDTA_H2

description:
miRNA
EDTA blood healthy person H2; transferred after 0min into fresh PAXgene tube


title: blood_0min_PAX_H2

description:
miRNA
PAXGene blood healthy person H2 0min


title: 1 microM JQ1 -replicate 2

description:
JQ1-2_(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with JQ1 - replicate 2

source_name: neuroblastoma SK-N-BE(2) cells treated with JQ1 -2


title: HK-2 cells, Nnm, hd, t48h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t48h

value: high


title: MEF p27wt 6 G1-phase block

description: microRNA expression data from cells treated with serum starvation

source_name: MEF wild-type: G1-phase

value: wild-type


title: JQ1 + panobinostat - replicate 1

description:
JQ1 + panobinostat-1_(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with JQ1 + panobinostat - replicate 1

source_name: neuroblastoma SK-N-BE(2) cells treated with JQ1 + panobinostat -1

value: 1 microM JQ1 + 10 nM panobinostat


title: HK-2 cells, Kbr, hd, t48h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t48h


title: 10 nM panobinostat - replicate 1

description:
panobinostat_1(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with panobinostat - replicate 1

source_name: neuroblastoma SK-N-BE(2) cells treated with panobinostat -1


title: vehicle control - replicate 2

description:
Control-2_(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with vehicle control -replicate 2

source_name: neuroblastoma SK-N-BE(2) cells treated with vehicle control -2

value: vehicle control


title: HK-2 cells, Aa, hd, t48h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Aa, t48h


title: 1 microM JQ1 -replicate 1

description:
JQ1_1(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with JQ1 - replicate 1

source_name: neuroblastoma SK-N-BE(2) cells treated with JQ1 -1


title: HK-2 cells, Aa, hd and ld, t48h, control sample, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, control for Aa, t48h

value: control


title: HK-2 cells, Nnm and Kbr, hd and ld, t48h, control sample, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t48h


title: HK-2 cells, Nnm, ld, t24h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t24h

value: Nnm


title: HK-2 cells, Nnm, ld, t24h, biological rep 2, All

value: 24 hrs


title: vehicle control - replicate 1

description:
Control_1(HuGene-2_0-st)
peripheral nervous system tumor cell
Gene expression data from neuroblastoma cells treated with vehicle control -replicate 1

source_name: neuroblastoma SK-N-BE(2) cells treated with vehicle control -1


title: NFSV replicate9

city: Seoul

first: Dong-Mi

last: Shin

address: 1 gwanak-ro

country: South Korea

institute: seoul national university

description: Biological replicate 9 for normal control

hyb_protocol: Chips were prehybridized in a sealed chamber immersed in a 42°C waterbath using established procedures.Chips were then washed twice for 2 min with agitation, first in ultra-pure water, then in isopropyl alcohol. After the last isopropyl alcohol wash, samples were quickly placed in a room-temperature centrifuge and spun dry (3000 rmp, 5 min). The chips were hybridized overnight in a sealed humidified slide chamber immersed in a light-protected 42°C waterbath, then washed, dried, and stored in the dark until scanned.

scan_protocol: Chips were scanned using an Axon 4000B scanner and GenePix 4.0 software. Photomultiplier tube voltage settings were adjusted to allow 1% saturation of signal in both channels.

data_processing: Image data were extracted, and extracted data were normalized with lowess smoothing function.

source_name: Normal spleen

label_protocol: Labeling RNA,(one for Cy3 and one for Cy5) using dUTP-Cy3 OR dUTP Cy5 by incubating reverse transcription reaction mixture at 42°C for 90 min, followed by degrading RNA and cleaning up labeled cDNA.

growth_protocol: SJL/J mice were obtained from the Jackson Laboratory (Bar Harbor, ME). NFS.V+ mice, inbred sublines of NFS/N mice of Swiss origin were maintained at the NIH (Hartley et al., Laboratory investigation; a journal of technical methods and pathology 80:159-169, 2000)

extract_protocol: Isolate RNA using Trizol Reagent and clean up RNAs with Qiagen Rnase kit

treatment_protocol: All animal studies were carried out under protocols approved by the Animal Care and Use Committees of the NIH (LIG 16E)

tag: tissues

value: Normal spleen

value: NFS.V+, inbred sublines of NFS/N mice of Swiss origin

source_name: Reference RNA

tag: reference

value: Universal reference RNA


title: NFSV replicate7

description: Biological replicate 7 for normal control


title: NFSV replicate6

description: Biological replicate 6 for normal control


title: HK-2 cells, Kbr, ld, t24h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t24h

tag: cell line

value: immortalized human renal proximal tubular epithelial cells

tag: treatment

value: low


title: Cells overexpressing HRASV12, biological rep2

first: Manish

last: Neupane

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Gene expression data from HRASV12 overexpressing cells

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA were hybridized for 16 hr at 45C on Human Gene 2.0St . GeneChips 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 Affymetrix Expression Console using RMA sketch quantile normalization with Affymetrix default analysis settings.

source_name: Human mammary epithelial cells overexpressing activated allele of Harvey rat sarcoma viral oncogene homolog (HRASV12)

label_protocol: The Ambion WT Expression Kit (cat # 4425209) was used followed by labeling with Affymetrix GeneChip WT Terminal Labeling and Hybridization kit (cat # 702880).

growth_protocol: Cells were grown in Mammary Epthelial Growth Medium (MEGM) (Lonza), a commercially available growth medium for these cells

extract_protocol: Total RNA was extracted using RNeasy minkit , as per manufacturer's instructions.

treatment_protocol: Cells were first engineered to carry hTERT gene and SV40 large T and small T antigen, and then transduced with one of the following four genes: EGFP, MECP2, OTX2, HRASV12

tag: cell type

value: epithelial cells

value: breast


title: Cells overexpressing OTX2, biological rep2

description: Gene expression data from OTX2 overexpressing cells

source_name: Human mammary epithelial cells overexpressing Orthodenticle homeobox 2 (OTX2) gene


title: HK-2 cells, Nnm, hd, t24h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t24h

tag: treatment duration


title: NFSV replicate4

description: Biological replicate 4 for normal control

tag: strain


title: NFSV replicate10

description: Biological replicate 10 for normal control


title: NFSV replicate2

description: Biological replicate 2 for normal control


title: HK-2 cells, Kbr, hd, t24h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t24h


title: NFSV replicate5

description: Biological replicate 5 for normal control


title: HK-2 cells, Aa, hd, t24h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with high dose Aa, t24h

value: Aa


title: NFSV replicate1

description: Biological replicate 1 for normal control


title: Cells overexpressing HRASV12, biological rep1


title: HK-2 cells, Aa, ld, t24h, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t24h


title: NFSV replicate8

description: Biological replicate 8 for normal control


title: SJL 12months replicate4

description: Biological replicate 4 for 12 month old SJL mouse

source_name: Spleen from SJL mice

value: Spleen

tag: age

value: 12 month old

value: SJL/J


title: Cells overexpressing MECP2, biological rep2

description: Gene expression data from MECP2 overexpressing cells

source_name: Human mammary epithelial cells overexpressing Methyl CpG Binding Protein 2 (MECP2) gene


title: NFSV replicate3

description: Biological replicate 3 for normal control


title: HCC1143 DMSO_2

source_name: HCC1143 cells

value: DMSO 0.1% 24 hrs


title: Cells overexpressing OTX2, biological rep1


title: SJL 12months replicate2

description: Biological replicate 2 for 12 month old SJL mouse


title: Cells overexpressing EGFP, biological rep2

description: Gene expression data from EGFP overexpressing cells

source_name: Human mammary epithelial cells overexpressing enhanced green fluorescent protein (EGFP) gene


title: SJL 6months replicate3

description: Biological replicate 3 for 6 month old SJL mouse

value: 6 month old


title: Cells overexpressing MECP2, biological rep1


title: SJL 6months replicate4

description: Biological replicate 4 for 6 month old SJL mouse


title: HK-2 cells, CsA, t48h, control sample, biological rep 3, lab 3, All

source_name: Human renal proximal tubular epithelial cells, control for CsA, t48h

value: 48 hrs


title: SJL 12months replicate1

description: Biological replicate 1 for 12 month old SJL mouse


title: SJL 6months replicate2

description: Biological replicate 2 for 6 month old SJL mouse


title: HK-2 cells, Aa, hd and ld, t24h, control sample, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, control for Aa, t24h

value: control


title: HK-2 cells, CsA, t48h, control sample, biological rep 2, lab 3, All


title: SJL 12months replicate3

description: Biological replicate 3 for 12 month old SJL mouse


title: SJL 6weeks replicate1

description: Biological replicate 1 for 6 week old SJL mouse

value: 6 week old


title: SJL 6weeks replicate2

description: Biological replicate 2 for 6 week old SJL mouse


title: HK-2 cells, Nnm and Kbr, hd and ld, t24h, control sample, biological rep 1, All

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t24h

value: 24 hrs


title: HK-2 cells, CsA, t48h, control sample, biological rep 1, lab 3, All


title: Chicken Liver Ya, biological rep 3

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

institute: Korea University

description: Gene expression data from liver tissue of Hoengseong Yakdak chicken

hyb_protocol: Following fragmentation, ss-cRNA were hybridized for 16 hr at 45℃ on GeneChip Chicken Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with gene level RMA (quantile normalization) using Affymetrix Genechip Expression Console 1.3.1.

organism: Gallus gallus

source_name: Chicken Liver from Hoengseong Yakdak breed

label_protocol: Biotinylated single-stranded cDNA (ss-cDNA) were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® WT PLUS Reagent Kit Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays, 2013, Affymetrix).

growth_protocol: We collected the fertilized eggs from local farms and transferred them to Suwon Animal Farm, Seoul National University. Then WL, Og, Bl, Hw and Ya chicks hatched from the eggs were grown by ad libitum fed until 13 weeks old.

treatment_protocol: WL, Og, Bl, Hw and Ya chickens were maintained according to a standard management program at Suwon Animal Farm, Seoul National University (SNU). The procedures for animal  management followed the standard operating protocols of animal-care-laboratory in SNU.

value: Liver

value: 13 weeks old

tag: breed

value: Hoengseong Yakdak


title: WF+EMF2

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

hyb_protocol: Fluidics station FS450

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: rma normalization by apt-probeset-summarize.exe from Affymetrix

source_name: Adult hMSCs_EMF treated

label_protocol: Nugen Applause WTA ST and Encore Biotin labelling kit

growth_protocol: High-glucose Dulbecco`s modified Eagle`s medium (DMEM; Biochrom) supplemented with 10 mg/l insulin, 5.5 mg/l transferrin, 5 µg/l selenium, 0.5 mg/ml bovine serum albumin, 4.7 µg/ml linoleic acid, 0.1 µM dexamethasone, 0.2 mM L-ascorbic acid-2-phosphate, 0.35 mM L-proline (all Sigma-Aldrich, Steinheim, Germany), 30 U/ml penicillin/streptomycin (Biochrom) and 10 ng/ml recombinant human transforming growth factor-β3 (TGF-β3; R&D Systems, Wiesbaden, Germany)].  All cells were maintained at 37 °C and 5 % CO2 in a 95 % air-humidified incubator.

extract_protocol: Trizol

treatment_protocol: A flux density of 5 mT using a current of 1.2 A was applied three times a day (every 435 minutes) for 45 minutes throughout the differentiation period of 21 days.

value: human bone marrow–derived mesenchymal stem cells (hBMSCs)

tag: passage

value: passage 5

tag: treated with

value: electromagnetic fields (EMF)


title: HK-2 cells, CsA, t48h, biological rep 3, lab 3, All

source_name: Human renal proximal tubular epithelial cells, treated with CsA, t48h

value: immortalized human renal proximal tubular epithelial cells

value: CsA


title: SJL 6weeks replicate4

description: Biological replicate 4 for 6 week old SJL mouse

value: Spleen

source_name: Reference RNA

value: Universal reference RNA


title: WF+EMF3


title: SJL 6weeks replicate3

description: Biological replicate 3 for 6 week old SJL mouse

value: SJL/J


title: Chicken Liver Ya, biological rep 1


title: SJL 6months replicate1

description: Biological replicate 1 for 6 month old SJL mouse


title: Chicken Liver Ya, biological rep 2


title: Cells overexpressing EGFP, biological rep1

value: epithelial cells

value: breast


title: WF+EMF1


title: WF3

source_name: Adult hMSCs_untreated control

value: none (untreated control)


title: HK-2 cells, CsA, t48h, biological rep 2, lab 3, All

value: 48 hrs


title: Chicken Liver Hw, biological rep 1

description: Gene expression data from liver tissue of Hwangbong chicken

source_name: Chicken Liver from Hwangbong breed

value: Hwangbong


title: Chicken Liver Bl, biological rep 2

description: Gene expression data from liver tissue of Hyunin Black chicken

source_name: Chicken Liver from Hyunin Black breed

value: Hyunin Black


title: Chicken Liver Hw, biological rep 2

value: Liver


title: HK-2 cells, CsA, t12h, control sample, biological rep 3, lab 3, All

source_name: Human renal proximal tubular epithelial cells, control for CsA, t12h

value: control

value: 12 hrs


title: Chicken Liver Og, biological rep 3

description: Gene expression data from liver tissue of Yeonsan Ogye chicken

source_name: Chicken Liver from Yeonsan Ogye breed

value: 13 weeks old

value: Yeonsan Ogye


title: Chicken Liver Og, biological rep 2


title: WF2

value: human bone marrow–derived mesenchymal stem cells (hBMSCs)

value: passage 5


title: HK-2 cells, CsA, t48h, biological rep 1, lab 3, All

value: immortalized human renal proximal tubular epithelial cells

value: CsA


title: HK-2 cells, CsA, t12h, control sample, biological rep 2, lab 3, All


title: Chicken Liver WL, biological rep 3

description: Gene expression data from liver tissue of White Leghorn chicken

source_name: Chicken Liver from White Leghorn breed

value: White Leghorn


title: HK-2 cells, CsA, t12h, control sample, biological rep 1, lab 3, All


title: HK-2 cells, CsA, t12h, biological rep 3, lab 3, All

source_name: Human renal proximal tubular epithelial cells, treated with CsA, t12h


title: Chicken Liver Bl, biological rep 1


title: Chicken Liver Bl, biological rep 3


title: WF1


title: Chicken Liver Hw, biological rep 3


title: Chicken Liver Og, biological rep 1


title: Chicken Liver WL, biological rep 1


title: g72_2

city: Taichung Ciy

first: Hao-Teng

last: Chang

address: No.91, Hsueh-shih Rd. N. Dist.

country: Taiwan

institute: China Medical University

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm power 100 ) and quantify the fluoresence intensity.

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

source_name: U87 cells/G72

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

growth_protocol: U87 cells growth in MEM + 10% FBS, at 37 degree C with 5% CO2

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

treatment_protocol: transfection reagent:PolyJet. Following the manufacturer provided by PolyJet.

tag: genotype/variation

value: G72 overexpression


title: Chicken Liver WL, biological rep 2

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


title: g72_1


title: HK-2 cells, CsA, t12h, biological rep 1, lab 3, All


title: gE2_2

source_name: U87 cells/empty vector


title: g71_2


title: g71_1


title: HK-2 cells, ethanol control, t48h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, ethanol control, t48h

value: ethanol


title: Liver slices 2h ex vivo incubation versus control

city: Hannover

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 800ng of each cRNA population to be cohybridized were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
Data extraction and processing of raw fluorescence intensity values was performed with the 'Feature Extraction Software V10.7.3.1' by using the recommended default extraction protocol file: 'GE2_107_Sep09.xml'. For normalization, processed intensity values as generated in the Feature Extraction procedure, 'gProcessedSignal' (gPS) and 'rProcessedSignal' (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray ('Array i' in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a 'reference 75th Percentile value' (fixed as 1500) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) and for all channels were calculated by the following formula:
normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)

label_protocol: Synthesis of AlexaFluor555- or AlexaFluor647 (Invitrogen) labeled cRNA was performed with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#5190-0444, Life Technologies) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1).

growth_protocol: Rosa26-CreERT2:THOC5 (flox/flox) mices were scarified and liver was isolated.

extract_protocol: Total RNA was extracted by use of the Pure RNA isolation Kit (Roche).

treatment_protocol: Liver was cut 5 mm from liver surface and incubated for 2h in oxygen saturated PFA and Williams´ Medium E  at 37° C in an atmosphere with 5% CO2 and 95% humidity.

tag: strain (genetic background)

value: Primary Hepatocytes

source_name: Primary Hepatocytes (Rosa26ERT2 Cre: THOC5 (flox/flox)) 2h ex vivo incubation


title: HK-2 cells, CsA, t12h, biological rep 2, lab 3, All


title: HK-2 cells, ethanol control, t48h, biological rep 2


title: HK-2 cells, ethanol control, t24h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, ethanol control, t24h

value: 24 hrs


title: Deletion_MRE11

city: Bangalore

first: Malathi

last: Srinivasan

state: Karnataka

address: Allalasandra, GKVK Post, Bellary Road

department: Lipidomic Center

country: India

institute: Central Food Technological Research Institute

description:
Stationary Phase cells
4(58)

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent Platform Custom Saccharomyces cerevisiae 8x15k designed by Genotypic Technology Private Limited (AMADID: 016333) 600ng of cy3 labeled samples were  fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Agilent Microarray Scanner G2505C at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software (Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version 11.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Gene based Analysis was performed)

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: synthetic minimal medium (SM) (6.7g/L of Yeast Nitrogen Base (Difco), 1.92 g/L of Yeast Synthetic Drop-out (Sigma) and 2% Dextrose

extract_protocol: RNA was extracted using the TRIzol (Invitrogen) method with glass beads (Sigma, 425-600um, Cat #G8772) for homogenization following the manufacturer's recommendations.

tag: genotype


title: gE1_1


title: HK-2 cells, ethanol control, t48h, biological rep 1

value: 48 hrs


title: Wild Type BY4741(2)

description:
Stationary Phase cells
2(47(2)

value: Wild Type BY4741(2)


title: SK-N-SH

city: Duarte

first: Linda

last: Malkas

state: CA

address: 1500 E. Duarte Rd

institute: City of Hope

description: Gene expression data

hyb_protocol: Labeled cDNA was hybridized to Affymetrix HuGene Array1.0 by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.6.

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay

growth_protocol: DMEM and 10% FBS

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen)

treatment_protocol: Untreated

value: neuroblastoma


title: SH-SY5Y

description: Gene expression data


title: SK-N-BE(2)c

description: Gene expression data


title: HK-2 cells, medium control, t48h, biological rep 3

data_processing: Data was normalized using the gcrma library (version 2.8.1) of Bioconductor.

source_name: Human renal proximal tubular epithelial cells, medium control, t48h

value: medium


title: CHP-212

description: Gene expression data


title: hBM-MSCs

description: Gene expression data

value: bone marrow mesenchymal stem cells


title: HK-2 cells, ethanol control, t24h, biological rep 1


title: HCN1-A

description: Gene expression data

value: cortical neuronal


title: HK-2 cells, ethanol control, t24h, biological rep 2


title: gE1_2

value: control


title: Wild Type BY4741(1)

description:
Stationary Phase cells
1 (47(1))

value: Wild Type BY4741(1)


title: SK-N-AS

description: Gene expression data


title: Deletion_RAD50

description:
Stationary Phase cells
3(50)


title: SK-N-DZ

description: Gene expression data


title: HK-2 cells, medium control, t48h, biological rep 2


title: SW480/DBC1 knockout, biological rep3

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

institute: Sungkyunkwan University

description: Gene expression data from DBC1 knockout SW480 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Image analysis was performed by Affymetrix GCOS Software, and data was normalized by RMA.

source_name: SW480 colorectal cancer cells

label_protocol: Total RNA was reverse-transcribed, and the double stranded cDNAs were used to generate biotin-labeled cRNA.

growth_protocol: SW480 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen)

treatment_protocol: The DBC1/CCAR2 gene was knocked out using transcription activator-like effector nucleases (TALENs).

value: DBC1 knockout


title: HK-2 cells, medium control, t48h, biological rep 1

first: Peadar

last: O'Gaora

address: Belfield

institute: UCD

hyb_protocol: 15 ug fragmented labelled cRNA was hybridized for 16 hours at 45oC to Affymetrix HGU133_Plus 2.0 GeneChips, which were then stained and washed on an Affymetrix Fluidics Station 400.

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


title: HK-2 cells, medium control, t24h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, medium control, t24h


title: SW480/WT, biological rep3

description: Gene expression data from wild-type SW480 cells

value: Wild-type


title: SW480/DBC1 knockout, biological rep1


title: SW480/DBC1 knockout, biological rep2


title: HK-2 cells, medium control, t24h, biological rep 2

value: immortalized human renal proximal tubular epithelial cells


title: SW480/WT, biological rep2


title: SW480/WT, biological rep1


title: HK-2 cells, medium control, t24h, biological rep 1


title: BE(2)c

description: Gene expression data


title: gE2_1


title: G9a knockdown MCF7 at hypoxic condition

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

hyb_protocol: Following labeling, cDNAs were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing:
Intensities of arrays have been normalized and summarized using RMA in Affymetrix Expression Console (v.1.2.0.20)
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: G9a knockdown, MCF7 cell line

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

growth_protocol: Breast epithelial cells grown in DMEM supplemented with 10% fetal calf serum.

treatment_protocol: Cells were exposed to either normoxia or hypoxia for 9 hours.

tag: knockdown

value: 1% oxygen for 9 hours


title: wild type MCF7 at hypoxic condition

source_name: wild-type, MCF7 cell line


title: HK-2 cells, DMSO control, t48h, biological rep 3

scan_protocol: Fluorescence was read with an Affymetrix 3000 Scanner.

source_name: Human renal proximal tubular epithelial cells, DMSO control, t48h

value: DMSO


title: HK-2 cells, DMSO control, t24h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, DMSO control, t24h


title: wild type MCF7 at normoxic condition

value: 21% oxygen for 9 hours


title: HK-2 cells, DMSO control, t48h, biological rep 2


title: NOA POST 10 (gene)

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: Biomarkers project

hyb_protocol: Array hybridization, washing, and scanning were performed according to manufacturer’s recommendations by using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix, Santa Clara, CA).

scan_protocol: Microarrays scanned using Affymetrix 3000 Scanner according to the instructions of the manufacturer

data_processing: Raw data were normalized with RMA method using Affymetrix software delivered to the scanner.

source_name: testicular biopsy with nonobstructive azoospermia

label_protocol: The sense-strand cDNA was fragmentized and labeled using the Affymetrix GeneChip® WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Not applicable, total RNA extracted from testicular biopsy cells

extract_protocol:
Tri-Reagent (Sigma-Aldrich, St. Louis, USA)  and post-purification using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany)
Testicular biopsy

treatment_protocol: Not applicable, samples extracted from untreated patients with various stages of azoospermia

tag: Sex

value: male

tag: tissue

value: testis

tag: testis

value: left

tag: histopatological desription

value: postmeiotic arrest

tag: response to the hormonal therapy

value: positive response (sperm cells appered in ejaculate


title: G9a knockdown MCF7 at normoxic condition

tag: cell line

tag: treatment


title: HK-2 cells, Ota, ld, t72h, biological rep 3, Tox3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Ota, t72h

growth_protocol: HK-2 cells were maintained in a 1-1 mixture of DMEM and Ham'sF12 containing 5 mM glucose supplemented with 10 ng/ml human recombinant EGF, 36 ng/ml hydrocortisone, 5 µg/ml bovine insulin, 5 µg/ml human transferrin, 5 ng/ml sodium selenite, 2 mM Glutamax (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy mini kit.

tag: cell type

value: Ota

tag: treatment dosage

value: low

tag: treatment duration

value: 72 hrs


title: NOA POST 2 (gene)

description: Biomarkers project

tag: age

value: no response


title: HK-2 cells, DMSO control, t48h, biological rep 1

value: 48 hrs


title: NOA POST 4 (gene)

description: Biomarkers project

value: right


title: HK-2 cells, DMSO control, t24h, biological rep 1

value: 24 hrs


title: NOA POST 3 (gene)

description: Biomarkers project


title: IMR-32

description: Gene expression data

value: neuroblastoma


title: HK-2 cells, Ota, ld, t72h, biological rep 1, Tox3

value: immortalized human renal proximal tubular epithelial cells


title: HK-2 cells, DMSO control, t24h, biological rep 2


title: Leishmania major infected  MDM at T12h, donor 1

city: Tunis-Belvedere

first: Dhafer

last: Laouini

address: 13, place Pasteur. BP74

country: Tunisia

institute: Institut Pasteur de Tunis

description: Gene expression data from MDM at 12h post-infection with metacyclic Leishmania major parasites

hyb_protocol: The fragmented and labeled ssDNA was hybridized to Affymetrix/HuGene-1_0-st-v1 for human analyses (Affymetrix, Santa Clara, CA), washed with the Fluidics station 450

scan_protocol: Samples were scanned using the Affymetrix Scanner 30007G.

data_processing:
Data processing entailed: (i) an intrachip normalisation step which corrects for the GC content of the probes; (ii) the interchip normalisation step which reduces non- biological differences between chips; and (iii) the summarisation step which combines the probe intensities into single gene expression values.For the intrachip normalisation the 'Model-based Analysis of Tiling-arrays' (MAT) was implemented (Kapur et al. 2007) as this method provides the most advanced GC correction for whole-transcript prepared samples by combining content and position dependency of probe sequences in a unified linear model. The parameters of the model are estimated from the control probes and subsequently the probe affinities are calculated for the perfect matches. On linear intensity scale, the probe intensities are divided by an estimated probe affinity. Interchip normalisation was applied as a quantile normalisation to adjust the intensity distributions over the arrays to reduce unwanted effects between 3' expression arrays (Irizarry et al. 2003). Finally, probe intensities were summarised to a probe set expression by computing a median over the intensities in two replicate dimensions: a) The different probe intensities within the probe set; b) The arrays with the same biological condition. This provides very robust summarised expression values also for low-replicate settings.
Detection call p-values were computed for each probeset with a paired Wilcoxon signed rank test that compares probe intensity to control probes of similar GC content. More precisely, each probe is compared to the 75% quantile of the set of control probes with similar GC content. A gene probeset was called present when the corresponding FDR corrected p-value was below 5%. The sole threshold in this approach is the height of the quantile (75%) in the GC bin. The same probe-Entrez gene assignment and subsequent mapping was used as in the summarisation process.

label_protocol: 100ng of RNA from each biological condition were amplified and labelled with biotin according to the GeneChip whole transcript sense target labeling assay manual and using the GeneChip WT cDNA Synthesis and amplification Kit and WT terminal labeling Kit. The fragmented ssDNA was checked on Agilent RNA Pico LabChips.

growth_protocol:
Human donors were selected as negative for any recent infection and with no history of Leishmaniasis. Their peripheral blood mononuclear cells (PBMC) do not proliferate in vitro in response to soluble Leishmania antigens and they were not taking medication at the time of the study. For intial transcriptomics and proteomics, three human donors were used.
Human PBMC were isolated from cytapheresis leukopacks peripheral blood mononuclear cells using Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient centrifugation. Cells were washed and resuspended at 107 cells/ml in RPMI 1640 medium supplemented with 2 mM L-glutamine, 100 U/ml penicillin, 100 /ml  streptomycin and 5% heat inactivated fetal calf serum. Monocytes were purified by fibronectin-mediated adhesion using gelatin (Sigma) and autologous heat inactivated serum substratum. Monocyte cell purity was assessed by flow cytometry (FACSVantage; Becton Dickinson, Sunnyvale, CA) using directly conjugated anti-CD3, anti-CD19 and anti-CD14 antibodies (Becton-Dickinson, San Jose, CA) and was routinely greater than 85% of CD14+ cells. Macrophages (MDM) were derived from monocytes cultured for 8 days at 37°C, 5% CO2 in endotoxin-free RPMI 1640 medium supplemented with 5% heat-inactivated normal human AB serum and 10% heat-inactivated fetal calf serum (HyClone Laboratories, Logan, UT), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine at 2 x 106 cells/ml, in 6-well tissue-culture plates.

extract_protocol: Human macrophages were lysed directly in 3 ml Trizol reagent (Invitrogen). Total RNA from uninfected and infected macrophages were prepared using the RNeasy mini kit (Qiagen) and treated with DNase according to the manufacturer’s protocol. Extracted RNAs were stored at -80°C. RNAs were quantified using NanoDrop ND-1000 micro-spectrophotometer and RNA quality was monitored on Agilent RNA Pico LabChips (Agilent Technologies, Palo Alto, CA).

treatment_protocol: L. major GLC94 isolate (MHOM/TN/95/GLC94) was obtained from the field and cultured at 26°C in RPMI medium supplemented with 2mM L-glutamine 100 U/ml of penicillin, 10mg/ml of streptomycin, 10% heat-inactivated fetal calf serum (HyClone ) was used to prepare metacyclic promastigotes using Ficoll density gradients centrifugation (Sigma) as previously described (Spath and Beverley 2001). MDM were exposed to metacyclic parasites of L. major at a ratio of 5 parasites per cell; for 3, 6, 12 and 24hr at 37°C/5% CO2, washed to remove extracellular parasites, and then harvested. Non-infected MDM were used as controls for the same conditions.

value: Monocyte-derived Macrophages purified from Peripheral Blood Leucocytes

value: Adult

tag: infection

value: Leishmania major infected

tag: time

tag: individual

value: donor 1


title: Leishmania major infected  MDM at T6h, donor 3

description: Gene expression data from MDM at 6h post-infection with metacyclic Leishmania major parasites

value: donor 3


title: Leishmania major infected  MDM at T12h, donor 3

source_name: MDM at 12h post-infection with metacyclic Leishmania major parasites


title: Leishmania major infected  MDM at T3h, donor 1

description: Gene expression data from MDM at 3h post-infection with metacyclic Leishmania major parasites


title: HK-2 cells, Ota, hd, t72h, biological rep 3, Tox3

city: Dublin

source_name: Human renal proximal tubular epithelial cells, treated with high dose Ota, t72h

treatment_protocol: Cells were seeded 24 hours before treatment on Greiner 6-well plates at a density of 7x10^5 cells per well with 2mls of medium per well. Cells were treated at ~90% confluency with the required doses for the required timepoints. Control cells were exposed to an appropriate concentration of the control vehicle.

value: high


title: Leishmania major infected  MDM at T6h, donor 2

source_name: MDM at 6h post-infection with metacyclic Leishmania major parasites

value: donor 2


title: NOA POST 6 (gene)

description: Biomarkers project

value: male

value: testis

value: left

value: postmeiotic arrest

value: positive response (sperm cells appered in ejaculate


title: Leishmania major infected  MDM at T3h, donor 2

source_name: MDM at 3h post-infection with metacyclic Leishmania major parasites


title: Leishmania major infected  MDM at T6h, donor 1


title: HK-2 cells, Ota, ld, t72h, biological rep 2, Tox3

value: Ota

value: low

value: 72 hrs


title: NOA POST 7 (gene)

description: Biomarkers project

value: no response


title: Non infected MDM at T24h, donor 3

description: Gene expression data from MDM at 24h

source_name: MDM at 24h

value: non-infected


title: Leishmania major infected  MDM at T3h, donor 3

value: Monocyte-derived Macrophages purified from Peripheral Blood Leucocytes


title: Leishmania major infected  MDM at T24h, donor 1

description: Gene expression data from MDM at 24h post-infection with metacyclic Leishmania major parasites

value: Adult


title: Leishmania major infected  MDM at T12h, donor 2

value: Leishmania major infected


title: HK-2 cells, Ota, hd, t72h, biological rep 2, Tox3

value: immortalized human renal proximal tubular epithelial cells


title: Non infected MDM at T24h, donor 2

description: Gene expression data from MDM at 24h


title: Fibroblast, apoptotic bodies (24h), biological rep3

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

description: miRNA expression data from fibroblast apoptotic bodies.

hyb_protocol: Hybridization was performed for 16 hr at 48°C and 60 rpm on GeneChip miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics script FS450-0002.

scan_protocol: GeneChip miRNA 3.0 Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The image data were analyzed with the miRNA QC Tool software for quality control. The expression values were summarized and normalized with robust multi-array average (RMA) using RMA package in Bioconductor 2.5 under R2.10.  Only miRNAs that were detectable in all three arrays for each group and whose expression levels were found to have changed significantly (P<0.05), at least by twofold, were considered to be differentially expressed.

source_name: apoptotic bodies collected 24h after CHX treatment, fibroblasts

label_protocol: Labelling was prepared according to the standard FlashTag (Genisphere) protocol.

growth_protocol: Cells were cultured in endothelial growth medium (PromoCell) to confluency before starting apoptosis.

extract_protocol: Total RNA was isolated from apoptotic bodies with the ZR RNA MicroPrep kit (Zymo Research) according to the manufacturer's instructions.

treatment_protocol: To induce apoptosis, the cells were incubated with cycloheximide (5µg/ml) in hypoxia (2% O2) for 24 hours. Afterwards, the apoptotic bodies were collected.

tag: cell source

value: primary dermal fibroblasts

value: apoptotic bodies


title: HK-2 cells, Ota, hd, t72h, biological rep 1, Tox3

value: high


title: Non infected MDM at T24h, donor 1

description: Gene expression data from MDM at 24h

value: donor 1


title: Leishmania major infected  MDM at T24h, donor 2

source_name: MDM at 24h post-infection with metacyclic Leishmania major parasites

value: donor 2


title: Fibroblast, apoptotic bodies (24h), biological rep2


title: Fibroblast, apoptotic bodies (24h), biological rep1


title: HUVEC, apoptotic bodies (24h), biological rep2

description: miRNA expression data from HUVEC apoptotic bodies.

source_name: apoptotic bodies collected 24h after CHX treatment, HUVECs

value: primary human umbilical veno-endothelial cells (HUVECs)


title: HUVEC, apoptotic bodies (24h), biological rep3


title: Leishmania major infected  MDM at T24h, donor 3

value: donor 3


title: Non infected MDM at T12h, donor 3

description: Gene expression data from MDM at 12h

source_name: MDM at 12h


title: Non infected MDM at T12h, donor 2

description: Gene expression data from MDM at 12h


title: HK-2 cells, Ota, hd and ld, t72h, control sample, biological rep 3, Tox3

source_name: Human renal proximal tubular epithelial cells, control for Ota, t72h

value: control


title: Non infected MDM at T6h, donor 2

description: Gene expression data from MDM at 6h

source_name: MDM at 6h


title: Non infected MDM at T12h, donor 1

description: Gene expression data from MDM at 12h


title: Non infected MDM at T6h, donor 3

description: Gene expression data from MDM at 6h


title: HK-2 cells, Ota, ld, t24h, biological rep 2, Tox3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Ota, t24h

value: Ota

value: 24 hrs


title: Non infected MDM at T3h, donor 1

description: Gene expression data from MDM at 3h

source_name: MDM at 3h


title: Non infected MDM at T3h, donor 3

description: Gene expression data from MDM at 3h


title: Non infected MDM at T6h, donor 1

description: Gene expression data from MDM at 6h


title: HK-2 cells, Ota, hd and ld, t72h, control sample, biological rep 2, Tox3

value: 72 hrs


title: HK-2 cells, Ota, ld, t24h, biological rep 3, Tox3

value: low


title: HUVEC, apoptotic bodies (24h), biological rep1