title: HMTclone_H6_biological repl 2

status: Public on Apr 30 2015

type: RNA

city: Odense

first: Rikke

last: Leth-Larsen

address: JB Winsloewsvej 25

department: Institute of Molecular Medicine

country: Denmark

institute: University of Southern Denmark

description:
H6_2
RLLa-12-H6-3-HuGene_1-a1.CEL

hyb_protocol: Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174 Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000175

scan_protocol: Affymetrix Gene ChIP Scanner 3000 Dx. Standard Affymetrix Cel file scan protocol.

data_processing:
Microarray data were normalized and processed by Partek® Genomics Suite (FDR 0.01) using RMA normalization methods
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174 Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174

extract_protocol: mRNA was purified by TRIzol followed by EtOH precipitation

tag: cell type source

value: human breast cancer cells

tag: cell type

value: cloned CD44hi populations

tag: cell subtype

value: CD44+/CD24- Basal B (H6) cells


title: HMTclone_AB_biological repl 1

description:
AB_1
RLLa-03-AB-1-HuGene_1-a1.CEL

value: CD44+/CD24low epithelioid Basal A (AB) cells


title: HMTclone_H6_biological repl 3

description:
H6_3
RLLa-13-H6-4-HuGene_1-a1.CEL


title: HMTclone_H6_biological repl 1

description:
H6_1
RLLa-11-H6-1-HuGene_1-a1.CEL


title: HMTclone_AB_biological repl 3

description:
AB_3
RLLa-05-AB-4-HuGene_1-a1.CEL


title: Poorly Chondrogenic Clone 4

city: Bristol

first: Anthony

last: Hollander

address: University Walk

department: School of Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

hyb_protocol: Fragmented and labelled DNA target was hybridized to a GeneChip Human Gene 1.0 ST array in a GeneChip Hybridization Oven 640 for 17 hours at 45ºC at 60rpm. Arrays were washed and stained using an Affymetrix Fluidics Station 450 following the standard protocol in GeneChip Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3) with Fluidics protocol FS450_0007

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 (GCS3000) and Affymetrix GeneChip Command Console (AGCC) software was utilised for initial image acquisition

data_processing: Affymetrix Expression Console software (v3.1) was used to generate probe set summarization (CHP) files from feature intensity (CEL) files using the gene level default RMA-sketch workflow. For normalisation between arrays, the log2 data for all was centred by subtracting the mean and dividing by the standard deviation for the whole array

label: Biotin

source_name: Mesenchymal stem cell clone, poorly chondrogenic

label_protocol: Amplified and biotinylated sense-strand DNA targets were generated from the entire expressed genome (from 200ng total RNA) using the 100ng Total RNA Labeling Protocol in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev. 5)

growth_protocol: Undifferentiated MSC clones were maintained in plastic-adherent culture in low-glucose DMEM containing 10% fetal bovine serum and fibroblast growth factor-2

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Micro Kit, according to the manufactures instructions

treatment_protocol: Not applicable

tag: tissue

value: Bone marrow

tag: developmental stage

value: Adult


title: HMTclone_AB_biological repl 2

description:
AB_2
RLLa-04-AB-2-HuGene_1-a1.CEL


title: Highly Chondrogenic Clone 4

source_name: Mesenchymal stem cell clone, highly chondrogenic


title: HMTclone_A4_biological repl 1

description:
A4_1
RLLa-01-A4-1-HuGene_1-a1.CEL

value: CD44+/CD24low epithelioid Basal A (A4) cells


title: Poorly Chondrogenic Clone 3


title: Highly Chondrogenic Clone 3


title: Highly Chondrogenic Clone 2


title: Poorly Chondrogenic Clone 2


title: Highly Chondrogenic Clone 1


title: HMTclone_G4_biological repl 1

description:
G4_1
RLLa-09-G4-2-HuGene_1-a1.CEL

value: CD44+/CD24- Basal B (G4) cells


title: HMTclone_A4_biological repl 2

description:
A4_2
RLLa-02-A4-2-HuGene_1-a1.CEL


title: HMTclone_G4_biological repl 2

description:
G4_2
RLLa-10-G4-3-HuGene_1-a1.CEL


title: Poorly Chondrogenic Clone 1


title: AD13_mir adult animal, biological rep3

city: Mannheim

first: Harsh

last: Dweep

state: baden wurttemberg

address: Theodor-Kutzer-Ufer 1-3

department: Medical Research Center, Medical Faculty of Mannheim of the University of Heidelberg

country: Germany

institute: University of Heidelberg

description: miRNA gene expression data from adult animals

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: Raw data files were imported into Expression Console 1.3 from Affymetrix The data were analyzed with JMP Genomics V. 6 from SAS. Gene expression profiling was performed using arrays of miRNA 3.0 from Affymetrix. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

organism: Rattus norvegicus

label_protocol: Fifteen μl (corresponding to 5-10 μg total RNA) of each biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was isolated using a kit from Qiagen and tested for quality.   sample were delivered for microarray analysis.

tag: strain

value: Wistar

tag: gender

value: male

tag: age


title: AD11_mir adult animal, biological rep1


title: NB4_mir young animal, biological rep4

description: miRNA gene expression data from young animals

value: Young


title: AD14_mir adult animal, biological rep4


title: NB3_mir young animal, biological rep3


title: NB1_mir young animal, biological rep1


title: NB2_mir young animal, biological rep2


title: CishKO CD8 T cell-0 hr-02

city: Bethesda

first: Shashank

last: Patel

state: MD

address: 10 Center Drive; Bldg10-CRC, Room 3-5816W

country: USA

institute: NCI, NIH

description: Primed T cells cultured for one week, stimulated with aCD3

hyb_protocol: Labeled cDNA was hybridized on the arrays following the manufacturer's directoins

scan_protocol: Arrays were stained and washed in the Affymetrix Fluidics Station 400 and scanned on an Affymetrix GeneChip Scanner 3000 7G system

data_processing: Raw CEL files were imported in Partek Genomics Suite and signal intensities adjusted for GC content. RMA algorithm was used for background correction, followed by quantile normalization. Normalized signal intensities were transformed to the log base 2 scale.

organism: Mus musculus

source_name: Cish KO CD8 T cells No stimulation

label_protocol: cDNA was fragmented and labeled using Affymetrix GeneChip WT Terminal Labeling Kit

growth_protocol: Mouse CD8 T cells were isolated and maintained in RPMI with 10% FCS

extract_protocol: Total RNA was extracted using RNAEasy Plus Kit (Qiagen) according to manufacturer instructions

treatment_protocol: Cells were stimulated for 2 hours with anti-CD3 and anti-CD28 in presence of 2 ng/ml IL2

tag: treatment

value: CD8 T cell

tag: genotype

value: Cish-/-

tag: genetic background


title: AD12_mir adult animal, biological rep2


title: CishKO CD8 T cell-0 hr-03


title: WT CD8 T cell-0 hr-03

source_name: WT CD8 T cells No stimulation

value: WT


title: CishKO CD8 T cell-stim 2 hr-03

source_name: Cish KO CD8 T cells stimulated in-vitro 2 hours

value: anti-CD3 and anti-CD28 in presence of 2 ng/ml IL2


title: Batf2_KD_rep2

city: Yokohama

first: Harukazu

last: Suzuki

address: 1-7-22 Suehiro-Cho, Tsurumi-Ku,

department: Division of genomic technology

country: Japan

institute: Riken yokohama, Riken center for life science technology

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the neqc function form the limma R package. ‘neqc’ performs background correction followed by quantile normalization, using negative control probes for background correction and use both negative and positive controls for normalization. After normalization, the intensities are log2 transformed and the control probes are removed.

label: BIOTIN

source_name: Bmdm cells, Batf2_KD

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

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

value: Babl/c

tag: age (weeks)

value: Bmdm


title: WT CD8 T cell-0 hr-01


title: WT CD8 T cell-stim 2 hr-03

source_name: WT CD8 T cells stimulated in-vitro 2 hours


title: WT CD8 T cell-0 hr-02


title: CishKO CD8 T cell-stim 2 hr-01


title: WT CD8 T cell-stim 2 hr-04


title: IFNg_rep2

description: Replicate 2

source_name: Bmdm cells, IFNg


title: CishKO CD8 T cell-0 hr-01


title: WT CD8 T cell-stim 2 hr-01


title: CishKO CD8 T cell-stim 2 hr-02


title: Batf2_KD_rep3

description: Replicate 3


title: WT CD8 T cell-stim 2 hr-02


title: IFNg_rep3

description: Replicate 3


title: Batf2_KD_IFNg_rep2

description: Replicate 2

source_name: Bmdm cells, Batf2_KD_IFNg


title: Batf2_KD_IFNg_rep1

description: Replicate 1


title: unstimulated_rep2

description: Replicate 2

source_name: Bmdm cells, unstimulated


title: unstimulated_rep3

description: Replicate 3


title: Batf2_KD_IFNg_rep3

description: Replicate 3


title: iNSCs derived using the BKSM polycistronic cassette

city: Boston

first: Ori

last: Bar-Nur

state: MA

address: 185 Cambridge st.

department: Center of Regenerative medicine

institute: Harvard University

description: BKSM-iNSCs

hyb_protocol: Hybridization was done by the Partners Center for Personalized Genetic Medicine.

scan_protocol: Scanning was done by the Partners Center for Personalized Genetic Medicine.

data_processing: Data was processed using Expression Console software, the processing algorithm was RMA

source_name: BKSM-iNSCs

label_protocol: Labeling was done by the Partners Center for Personalized Genetic Medicine.

growth_protocol: Cells were grown in ESC media or NSCs as described in the Online methods section

extract_protocol: RNA (Dnase treated) was islolated and extracted using the Rneasy Mini Kit (Qiagen).

tag: strain background

value: 2-3 month

value: both female and male

value: induced neural stem cells (iNSCs)


title: Batf2_KD_rep1

description: Replicate 1


title: iNSCs derived using the OKSM polycistronic cassette

description: OKSM-iNSCs

source_name: OKSM-iNSCs


title: primary tumor sample [41284E]

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

institute: IZBI

description: Gene expression data from cerebral tumor

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0 Arrays. 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: Raw probe intensities were calibrated and summarized into one expression value per probe set using the hook method, and then quantile-normalised. The expression value of each gene was transformed into log10-scale and centered with respect to its mean value averaged over all samples investigated

source_name: Human Brain, cerebral tumor sample

label_protocol: Sample preparation was done with 2.5 μg total-RNA using the One Cycle Target Labelling and Controls kit (Affymetrix).

extract_protocol: DNA and RNA were extracted by ultracentrifugation.

treatment_protocol: Tumor samples were shock-frozen after resection and stored at -80 °C. Only specimens with a histologically estimated tumor cell content of 80% or more were used for molecular analyses.

tag: diagnosis


title: IFNg_rep1

description: Replicate 1


title: primary tumor sample [3436M]


title: IFNg_24h_rep3

description: Replicate 3

data_processing: The data were normalised using quantile normalisation with lumi R (bioconductor)

source_name: Bmdm cells, IFNg_24h


title: unstimulated_rep1

description: Replicate 1


title: primary tumor sample [1271M]


title: KO-Ter119+_914

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E. Chicago Ave

department: Pathology

institute: Northwestern University

description: replicate 2

data_processing: The data were normalised using quantile normalisation

source_name: mouse erythroblast

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrepTM RNA Amplification Kit from life technologiesTM.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

value: mDia2 KO

value: erythroblast

value: 4 months

value: Bone Marrow


title: KO-Ter119+_1122

description: replicate 3


title: KO-Ter119+_907

description: replicate 1


title: WT-Ter119+_1136

description: replicate 3

value: wildtype


title: NSCs derived from E13.5 mouse brain

description: Brain-derived NSCs

source_name: Brain-derived NSCs

value: neural stem cells (NSCs)


title: Unstimulated_24h_rep3

description: Replicate 3

source_name: Bmdm cells, Unstimulated_24h

value: male


title: WT-Ter119+_1125

description: replicate 2


title: iPSCs derived using the BKSM polycistronic cassette #7

source_name: BKSM-iPS

value: induced pluripotent stem cells (iPSCs)


title: IFNg_24h_rep2

description: Replicate 2


title: WT-Ter119+_917

description: replicate 1


title: Unstimulated_24h_rep1

description: Replicate 1


title: primary tumor sample [41387E]


title: primary tumor sample [21375E]


title: Unstimulated_24h_rep2

description: Replicate 2


title: iPSCs derived using the BKSM polycistronic cassette #2


title: IFNg_24h_rep1

description: Replicate 1


title: WT strain untreated versus WT strain treated with GB-AP-238 replicate 1

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: S. aureus HG001 exposed or not exposed to compound GB-AP-238

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

scan_protocol: 100% PMT using Agilent scanner

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

label: cyanine 3

organism: Staphylococcus aureus

source_name: S. aureus HG001 w/o GB-AP-238

label_protocol: Incorporation during reverse transcription

growth_protocol: mid-log phase at an optical density at 600 nm of 0.6 to 0.8 in Muller-Hinton

extract_protocol: RNAprotectTM Bacteria Reagent (Qiagen, Hilden, Germany) and immediately incubated on ice. After centrifugation for 10 min at 6.000 x g and 4°C, the supernatant was discarded and the pellet resuspended in 1 ml RLT-buffer (Qiagen) supplemented with 1 % (vol/vol) β-mercaptoethanol. Cells were disrupted in Lysing Matrix E (MP Biomedicals) using a FastPrep®-24 (MP Biomedicals, Solon, OH, USA), followed by cooling on ice for 2 min. After brief centrifugation, the supernatant was purified using RNeasy®Mini Kit. Final treatment with DNase for 1 h at 37°C and again purified with RNeasy®Mini Kit.

treatment_protocol: Exposition to GB-AP-238

value: untreated

label: cyanine 5

source_name: S. aureus HG001 with GB-AP-238


title: WT strain untreated versus WT strain treated with GB-AP-238 replicate 2


title: IFNg_6h_rep3

description: Replicate 3

source_name: Bmdm cells, IFNg_6h


title: primary tumor sample [2730F]


title: Unstimulated_6h_rep2

description: Replicate 2

source_name: Bmdm cells, Unstimulated_6h


title: IFNg_6h_rep1

description: Replicate 1


title: Unstimulated_6h_rep3

description: Replicate 3


title: IFNg_6h_rep2

description: Replicate 2


title: primary tumor sample [2694E]


title: primary tumor sample [3741H]


title: Unstimulated_6h_rep1

description: Replicate 1


title: IFNg_4h_rep3

description: Replicate 3

source_name: Bmdm cells, IFNg_4h


title: Group C MSCs-derived NPCs (Untreated) at day 5, biological rep 2

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group C_D5-2

hyb_protocol: Following biotinylation, 21.5 ul of cRNA were hybridized for 18 hr at 48C on miRNA GeneChip 2.0 Array in hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G system.

data_processing: Affymetrix Expression Console software v.1.2 was used for data summarization, normalization and quality control. Recommended processing algorithm RMA+DABG was applied.

source_name: Mesenchymal Stem Cells, (without growth factor), 120 hours

label_protocol: Biotinylated cRNA were prepared using FlashTag Biotin HSR RNA labeling kit according to the standard Affymetrix protocol from 100 ng total RNA (FlashTag Biotin HSR RNA Labeling Kit User Manual, 2013, Affymetrix).

growth_protocol: Both MSCs and MSCs-derived NPCs were cultured in humidified chamber at 37C with 5% CO2 supply.

extract_protocol: Total RNA extraction was performed using miRNeasy mini kit from Qiagen according to recommended protocol.

treatment_protocol: Group A was treated with neural basal media + EGF + bFGF; Group B was treated with neural basal media + EGF +bFGF + IGF-1;  Group C was cultured in neural basal media without any growth factor.

value: Sprague Dawley

value: Bone marrow

tag: agent

value: Untreated

tag: time

value: day 5

value: MSCs-derived NPCs


title: Group C MSCs-derived NPCs (Untreated) at day 5, biological rep 1

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group C_D5-1


title: Unstimulated_4h_rep3

description: Replicate 3

source_name: Bmdm cells, Unstimulated_4h

value: Babl/c

value: Bmdm


title: primary tumor sample [4214K]


title: Group C MSCs-derived NPCs (Untreated) at day 3, biological rep 3

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group C_D3-3

source_name: Mesenchymal Stem Cells, (without growth factor), 72 hours

value: day 3


title: IFNg_4h_rep1

description: Replicate 1


title: IFNg_2h_rep3

description: Replicate 3

source_name: Bmdm cells, IFNg_2h


title: Group C MSCs-derived NPCs (Untreated) at day 3, biological rep 2

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group C_D3-2


title: primary tumor sample [21100K]


title: primary tumor sample [2775F]


title: IFNg_4h_rep2

description: Replicate 2


title: Unstimulated_4h_rep1

description: Replicate 1


title: Unstimulated_4h_rep2

description: Replicate 2


title: primary tumor sample [3396P]


title: IFNg_2h_rep2

description: Replicate 2


title: Unstimulated_2h_rep3

description: Replicate 3

source_name: Bmdm cells, Unstimulated_2h


title: primary tumor sample [31206E]


title: Unstimulated_2h_rep1

description: Replicate 1


title: primary tumor sample [2526E]


title: primary tumor sample [3918N]


title: Sphere vs Adherent replicate 2

city: Naples

first: Angela

last: Nebbioso

state: Italy

address: Vico Luigi De Crecchio 7

department: Biophysics, Biochemestry and General Patology

country: Italy

institute: Seconda Università degli Studi di Napoli

description: Biological replicate 1 of 2. Sphere culture condition versus standard (aderent) condition

hyb_protocol: After the RNA fragmentation 55 µl of 2x Gex Hybridization Buffer HI-RPM were added to the 4*44K array, microarrayswere enclosed in Agilent SureHyb chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505 C micro array scanner.

data_processing: Agilent Feature Extraction Software (v10.5)

source_name: sphere culture

label_protocol: 3000ng of total RNA were converted in cDNA and then in cRNA following manufacturer's instruction (Agilent Technologies, Two-color). cRNA were labeled with Cy3-CTP and Cy5-CTP.

growth_protocol: Chondrosarcoma cells were cultured in DMEM medium supplemented with 2 mM glutamine, 100 IU/ml penicillin, 100 µg/ml streptomycin, and 10 or 20% heat-inactivated FBS (Invitrogen Life Technologies) at 37°C in a humidified atmosphere under 5% CO2. The medium was changed 2x/wk. Chondrospheres culture: the cells were plated in DMEM/F12 cell medium supplemented with progesterone (10nM), putrescine (50µM), sodium selenite (15nM), transferrin (13µg/ml), insulin (10µg/ml; Sigma, St. Louis, MO, USA), human EGF (10 ng/ml), and human bFGF (10 ng/ml; Sigma). Fresh aliquots of EGF and bFGF were added every day. After culture for 48–72 h, chondrospheres were visible with an inverted phase-contrast microscope (TS 100; Nikon, Milan, Italy). This medium was changed 2x/wk to renew the growth factors.

extract_protocol: Total RNA extracted using Pure Link RNA mini kit following manufacturer's instructions (Ambion, Life Technologies)

value: Primary chondrosarcoma

source_name: adherent culture


title: Group C MSCs-derived NPCs (Untreated) at day 3, biological rep 1

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group C_D3-1


title: Group C MSCs-derived NPCs (Untreated) at day 1, biological rep 2

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group C_D1-2

source_name: Mesenchymal Stem Cells, (without growth factor), 24 hours

value: day 1


title: Unstimulated_2h_rep2

description: Replicate 2


title: primary tumor sample [4769A]

source_name: Human Brain, cerebral tumor sample


title: Group C MSCs-derived NPCs (Untreated) at day 1, biological rep 1

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group C_D1-1


title: IFNg_2h_rep1

description: Replicate 1


title: primary tumor sample [21330E]


title: RS4;11_shCREB2

city: Groningen

first: Naomi

middle: Eline

last: van der Sligte

state: Nederland

address: Hanzeplein 1

department: Pediatrics

country: Netherlands

institute: University Medical Center Groningen

description: RS4;11 BCP-ALL cell line transduced with shCREB2

hyb_protocol: Standard Illumina protocol, Performed at ServiceXS B.V.

data_processing: Data was quantile normalized and log2-transformed

source_name: RS4;11 BCP-ALL cell line

label_protocol: lumina TotalPrep RNA Amplification Kit  van Ambion

growth_protocol: Cells were cultured in RPMI or amem medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin

extract_protocol: Total RNA was isolated from CREB or scrambled transduced cells using the RNA mini kit accoring to manufactures protocol.

treatment_protocol: Lentiviral vector (pLKO.1) containing shRNA sequences targeting CREB were genetically modified into a pLKO1-mCherry vector. Leukemic cells were incubated with lentiviral supernatants for one or two consecutive days after which stably transduced cells were expanded.

tag: cell line

value: RS4;11 BCP-ALL cell line


title: Group B MSCs-derived NPCs (EGF+bFGF+IGF1) at day 3, biological rep 3

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group B_D3-3

source_name: Mesenchymal Stem Cells, (EGF+bFGF+IGF-1), 72 hours


title: Sphere vs Adherent replicate 1


title: Nalm6_shCREB3

description: Nalm6 BCP-ALL cell line transduced with shCREB3

scan_protocol: Standard Illumina protocol, Performed at ServiceXS B.V.

source_name: Nalm6 BCP-ALL cell line

value: Nalm6 BCP-ALL cell line


title: Molt4_shCREB3

description: Molt4 T-ALL cell line transduced with shCREB3

source_name: Molt4 T-ALL cell line

value: Molt4 T-ALL cell line


title: RS4;11_Scrambled

description: RS4;11 BCP-ALL cell line transduced with Scrambled control

value: Scrambled


title: Group B MSCs-derived NPCs (EGF+bFGF+IGF1) at day 5, biological rep 3

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group B_D5-3

source_name: Mesenchymal Stem Cells, (EGF+bFGF+IGF-1), 120 hours


title: Group B MSCs-derived NPCs (EGF+bFGF+IGF1) at day 5, biological rep 2

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group B_D5-2


title: primary tumor sample [3021M]

description: Gene expression data from cerebral tumor


title: primary tumor sample [3774N]


title: Nalm6_Scrambled

description: Nalm6 BCP-ALL cell line transduced with Scrambled control


title: RS4;11_shCREB3

description: RS4;11 BCP-ALL cell line transduced with shCREB3


title: Nalm6_shCREB2

description: Nalm6 BCP-ALL cell line transduced with shCREB2


title: Group C MSCs-derived NPCs (Untreated) at day 5, biological rep 3

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group C_D5-3


title: Group B MSCs-derived NPCs (EGF+bFGF+IGF1) at day 5, biological rep 1

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group B_D5-1


title: Molt4_Scrambled

description: Molt4 T-ALL cell line transduced with Scrambled control


title: Molt4_shCREB2

description: Molt4 T-ALL cell line transduced with shCREB2


title: primary tumor sample [21076A]


title: Jurkat_shCREB3

description: Jurkat T-ALL cell line transduced with shCREB3

source_name: Jurkat T-ALL cell line

value: Jurkat T-ALL cell line


title: Group B MSCs-derived NPCs (EGF+bFGF+IGF1) at day 3, biological rep 1

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group B_D3-1


title: p75+HNK1+ E4

city: Seoul

first: Dong-Wook

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

country: South Korea

institute: Yonsei University College of Medicine

description:
Sample name: E4
replicate 3

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: p75+HNK1+ cells isolated from neural rosettes derived from human embryonic stem cells H9 (WA09)

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: H9 hESCs were grown in DMEM/F12 supplemented with 20% KnockOut Serum Replacement including basic FGF. Neural precursor cells were gorwn in DMEM/F12 N2 supplemented media with/without B27 supplement including basic FGF.

extract_protocol: Total RNA was isolated using the Easy-Spin® Total RNA Extraction Kit (iNtRON) according to the manufacturer's instructions

value: human embryonic stem cells H9

tag: passage

value: hESCs p35-45

value: p75+HNK1+ cells from neural rosettes


title: Group B MSCs-derived NPCs (EGF+bFGF+IGF1) at day 3, biological rep 2

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group B_D3-2

value: Sprague Dawley

value: Bone marrow

tag: cell type


title: primary tumor sample [4205H]


title: p75+HNK1+ E3

description:
Sample name: E3
replicate 2


title: Jurkat_Scrambled

description: Jurkat T-ALL cell line transduced with Scrambled control


title: Jurkat_shCREB2

description: Jurkat T-ALL cell line transduced with shCREB2


title: primary tumor sample [3026L]


title: primary tumor sample [2592H]


title: primary tumor sample [3582N]


title: PSA-NCAM- P1

description:
Sample name: P1
replicate 1

source_name: PSA-NCAM- cells isolated from neural rosettes derived from human embryonic stem cells H9 (WA09)

value: PSA-NCAM- cells from neural rosettes


title: PSA-NCAM- P2

description:
Sample name: P2
replicate 2


title: primary tumor sample [2501N]


title: p75+HNK1+ E1

description:
Sample name: E1
replicate 1


title: PSA-NCAM+ B10

description:
Sample name: B10
replicate 2

source_name: PSA-NCAM+ cells isolated from neural rosettes derived from human embryonic stem cells H9 (WA09)

value: PSA-NCAM+ cells from neural rosettes


title: Group B MSCs-derived NPCs (EGF+bFGF+IGF1) at day 1, biological rep 3

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group B_D1-3

source_name: Mesenchymal Stem Cells, (EGF+bFGF+IGF-1), 24 hours

value: MSCs-derived NPCs


title: Group B MSCs-derived NPCs (EGF+bFGF+IGF1) at day 1, biological rep 2

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group B_D1-2


title: PSA-NCAM- P3

description:
Sample name: P3
replicate 3


title: Group B MSCs-derived NPCs (EGF+bFGF+IGF1) at day 1, biological rep 1

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group B_D1-1


title: PSA-NCAM+ B12

description:
Sample name: B12
replicate 3


title: Neural Rosettes_d16 C8

description:
Sample name: C8
replicate 3

source_name: Neural rosettes derived from human embryonic stem cells H9 (WA09)

value: Neural rosettes


title: Group A MSCs-derived NPCs (EGF+bFGF) at day 5, biological rep 2

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group A_D5-2

source_name: Mesenchymal Stem Cells, (EGF+bFGF), 120 hours

value: EGF+bFGF

value: day 5


title: Group A MSCs-derived NPCs (EGF+bFGF) at day 5, biological rep 3

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group A_D5-3


title: Group A MSCs-derived NPCs (EGF+bFGF) at day 5, biological rep 1

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group A_D5-1


title: PSA-NCAM+ B8

description:
Sample name: B8
replicate 1


title: primary tumor sample [2580N]

description: Gene expression data from cerebral tumor


title: Neural Rosettes_d16 C7

description:
Sample name: C7
replicate 2


title: primary tumor sample [3016F]


title: Group A MSCs-derived NPCs (EGF+bFGF) at day 3, biological rep 2

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group A_D3-2

source_name: Mesenchymal Stem Cells, (EGF+bFGF), 72 hours

value: day 3


title: dAEC mechanical injury 24 hr SW_N79

first: Shwu-Fan

last: Ma

address: 5841 S. Maryland Ave.,

department: Medicine

institute: University of Chicago

data_processing: The data were normalized using quantile normalization with GenomeStudio software licensed by Illumina Inc.

source_name: lungs

growth_protocol: Primary human airway epithelial cells (AEC) in submersion and differentiated airway epithelial cells (dAEC) in air liquid interface culture system were grown and maintained as described (White SR et al., Am J Physiol Lung Cell Mol Physiol 2008;295(6):L1018-1027; 2009;297(1):L164-173; 2010; 299(5): L681–L693).

extract_protocol: Total RNA was collected at 4˚C using QIAzol lysis reagent per kit instructions followed by miRNeasy mini kits. RNA quality and quantity were assessed using Agilent 2100 Bioanalyzer and NanoDrop ND-1000 spectrophotometer.

treatment_protocol: Mechanical injury (MI) was produced by rake tines which were 0.3 mm in diameter and spaced 0.4 mm apart). Cells then were washed in culture medium to remove debris and incubated for 8 or 24 hr in standard medium. Control cells without MI were collected at the same time intervals.  Cyclic stretch (CS) injury was performed using FX-4000T Flexcell Tension Plus system 18% elongation, at 0.5 Hz continuously for either 8 or 24 hr. Control cells were incubated on BioFlex plates for the same time intervals but not subjected to CS. For dual injury, cells were seeded (1 x 106 cells/well) onto collagen-IV coated flexible bottom BioFlex plates. When confluent, plates were washed with culture medium and mechanical rake injury done as in preceding experiments prior to mount plates into the Flexcell system and exposed to CS of the desired magnitude and durations.

tag: culture condition

value: Air liquid interface

tag: cell line id

tag: injury type

value: Mechanical injury (MI)

tag: injury duration

value: 24 hr


title: primary tumor sample [3078F]


title: Group A MSCs-derived NPCs (EGF+bFGF) at day 3, biological rep 1

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group A_D3-1

tag: strain

tag: tissue


title: Group C MSCs-derived NPCs (Untreated) at day 1, biological rep 3

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group C_D1-3

value: Untreated

value: day 1


title: primary tumor sample [6428M]


title: primary tumor sample [1286P]


title: dAEC mechanical injury 24 hr SW_N78

value: differentiated airway epithelial cells (dAEC)


title: dAEC mechanical injury 8 hr SW_N76

value: 8 hr


title: primary tumor sample [4602M]


title: dAEC mechanical injury 8 hr SW_N73


title: Neural Rosettes_d16 C6

description:
Sample name: C6
replicate 1

value: human embryonic stem cells H9

value: hESCs p35-45


title: dAEC sham control 24 hr SW_N71


title: Group A MSCs-derived NPCs (EGF+bFGF) at day 3, biological rep 3

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group A_D3-3

value: Sprague Dawley

value: Bone marrow


title: dAEC mechanical injury 24 hr SW_N80


title: primary tumor sample [21961T]


title: dAEC mechanical injury 24 hr SW_N77


title: dAEC mechanical injury 8 hr SW_N75


title: Group A MSCs-derived NPCs (EGF+bFGF) at day 1, biological rep 3

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group A_D1-3

source_name: Mesenchymal Stem Cells, (EGF+bFGF), 24 hours


title: dAEC mechanical injury 8 hr SW_N74


title: dAEC sham control 24 hr SW_N72


title: Group A MSCs-derived NPCs (EGF+bFGF) at day 1, biological rep 2

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group A_D1-2


title: dAEC sham control 24 hr SW_N70


title: primary tumor sample [2922F]


title: dAEC sham control 8 hr SW_N68


title: primary tumor sample [41105N]


title: dAEC sham control 8 hr SW_N66


title: dAEC sham control 8 hr SW_N65


title: Group A MSCs-derived NPCs (EGF+bFGF) at day 1, biological rep 1

description:
Gene expression data from early differentiation of MSCs-derived NPCs at passage 1
Group A_D1-1


title: primary tumor sample [3662M]


title: primary tumor sample [7082P]


title: AQP3-/- OVA(-)

city: Kyoto

first: Kohei

last: Ikezoe

address: 54 Shogoin-kawaharacho, Sakyo-ku

department: Department of Respiratory Medicine

institute: Kyoto University Graduate School of Medicine

hyb_protocol: 2.0ug of Cy3-labelled cDNA was filled up to 50 ul containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) 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 SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Alveolar Macrophage, AQP3-/-, Before OVA challenge, replicate 1

label_protocol: cDNA were amplified by Ovation® Pico WTA System V2（NuGEN Technologies) from 4.694ng total RNA according to the manufacturer's instructions. Amplified cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared from 2.0ug cDNA using SureTag Complete DNA Labeling Kit (Agilent) according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Mice were sensitized with intraperitonial injection of 50 µg OVA (Sigma-Aldrich) and 1mg alum (LSL) on day 0 and day 11, and then were challenged with aerosolized 1% OVA on days 21-27. Mice were sacrificed before (on day 21) or after (on day 28) OVA challenge.

extract_protocol: RNA was prepared from alveolar macrophages using RNeasy Plus Micro Kit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: To obtain lung cell suspensions, we removed and minced lungs from mice. Minces were incubated in complete RPMI (RPMI 1640 supplemented with 10% heat-inactivated FBS, 50 µM 2-mercaptoethanol (Wako), 25 mM HEPES, 100 µM nonessential amino acids, and 10µM sodium pyruvate (Invitrogen), and 1% penicillin/streptomycin (Gibco)) and collagenase A (Roche) for 1 h at 37°C, and digests were filtered through a nylon mesh (70 µm). Dissociated cells were centrifuged at 1300 rpm for 10 min at 4°C, and the cell pellet was incubated during 5 min at room air with ACK lysing buffer (Life Technologies) to lyse RBCs. The single cell suspension was labeled with FITC-conjugated CD11c (eBioscience) and PE-conjugated F4/80 (Biolegend). Alveolar macrophages were sorted based on their expression of CD11c and F4/80 by FACS Aria.

value: alveolar macrophage

tag: gender

value: female

tag: age

value: 12 week


title: AQP3-/- OVA(+)

source_name: Alveolar Macrophage, AQP3-/-, After OVA challenge, replicate 1

tag: genotype


title: dAEC sham control 8 hr SW_N67


title: dAEC sham control 0 hr SW_N64

value: 0 hr


title: dAEC sham control 0 hr SW_N63


title: dAEC sham control 24 hr SW_N69


title: primary tumor sample [21272E]

source_name: Human Brain, cerebral tumor sample


title: primary tumor sample [31056M]


title: WT OVA(-)

source_name: Alveolar Macrophage, WT, Before OVA challenge, replicate 1

value: wild type


title: dAEC sham control 0 hr SW_N61


title: AEC mechanical injury 24 hr SW_N59

value: primary airway epithelial cells (AEC)

value: Submersion


title: WT OVA(+)

source_name: Alveolar Macrophage, WT, After OVA challenge, replicate 1


title: AEC mechanical injury 8 hr SW_N55

value: Mechanical injury (MI)


title: AEC mechanical injury 24 hr SW_N60

value: 24 hr


title: primary tumor sample [2025N]


title: primary tumor sample [2598K]


title: AEC mechanical injury 8 hr SW_N53


title: AEC mechanical injury 24 hr SW_N58


title: primary tumor sample [21094E]


title: primary tumor sample [41687L]


title: AEC sham control 24 hr SW_N50


title: AEC sham control 24 hr SW_N51


title: AEC mechanical injury 8 hr SW_N56


title: AEC sham control 8 hr SW_N46


title: AEC mechanical injury 8 hr SW_N54


title: AEC sham control 8 hr SW_N48


title: primary tumor sample [21156T]


title: AEC sham control 24 hr SW_N52


title: primary tumor sample [41899C]


title: AEC sham control 24 hr SW_N49


title: AEC sham control 0 hr SW_N44


title: AEC sham control 0 hr SW_N42


title: primary tumor sample [3601P]


title: AEC mechanical injury 24 hr SW_N57


title: AEC sham control 8 hr SW_N45


title: AEC sham control 8 hr SW_N47


title: primary tumor sample [2283T]


title: AEC sham control 0 hr SW_N43


title: primary tumor sample [8071L]


title: AEC dual injury 24 hr SW_N39

value: MI and CS


title: primary tumor sample [3853K]


title: AEC dual injury 24 hr SW_N40


title: primary tumor sample [2227A]


title: primary tumor sample [22505P]


title: AEC dual injury 24 hr SW_N37


title: primary tumor sample [8213E]


title: AEC cyclic stretch 24 hr SW_N32

value: Cyclic stretch (CS)


title: primary tumor sample [4627C]


title: AEC dual injury 8 hr SW_N33


title: AEC dual injury 8 hr SW_N35


title: dAEC sham control 0 hr SW_N62

value: differentiated airway epithelial cells (dAEC)

value: Air liquid interface


title: AEC dual injury 24 hr SW_N38


title: AEC dual injury 8 hr SW_N36

value: 8 hr


title: TM129

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: ovarian cancer

label_protocol: Biotinylated cDNA was prepared from 750ng of total RNA following miRNA DASL assay protocol provided by Illumina.

extract_protocol: RNA was extracted with Trizol reagent and miRNeasy Mini kit (Qiagen) according to manufacture's instructions.

tag: histotype

value: serous

tag: debulking

value: GRD

tag: Stage

value: IV

tag: grading

tag: therapy code

value: PT

tag: ttr (months)

tag: code ttr

value: 0=no relapse; 1=relapse:1

tag: overall survival (months)

tag: code os

value: 0=alive; 1=dead:1


title: TM126

value: mRD

value: III

value: 0=alive; 1=dead:0


title: TM128

value: endometrioid


title: TM127

value: 0=no relapse; 1=relapse:0


title: AEC dual injury 8 hr SW_N34

tag: cell type

value: primary airway epithelial cells (AEC)

tag: culture condition

value: Submersion

tag: cell line id


title: TM130

value: P


title: primary tumor sample [41121L]

tag: diagnosis


title: TM125

value: NED


title: TM124


title: TM122


title: TM123


title: AEC cyclic stretch 24 hr SW_N30

tag: injury type

value: Cyclic stretch (CS)

tag: injury duration

value: 24 hr


title: AEC cyclic stretch 24 hr SW_N29


title: AEC cyclic stretch 8 hr SW_N28

value: 8 hr


title: AEC cyclic stretch 24 hr SW_N31


title: AEC cyclic stretch 8 hr SW_N26


title: primary tumor sample [2371N]


title: AEC cyclic stretch 8 hr SW_N27


title: AEC cyclic stretch 8 hr SW_N25


title: TM121

tag: age

value: clear cells

value: GRD


title: AEC mechanical injury 24 hr SW_N21

value: Mechanical injury (MI)


title: AEC mechanical injury 24 hr SW_N22


title: primary tumor sample [3316M]


title: AEC mechanical injury 24 hr SW_N24


title: primary tumor sample [9029P]


title: AEC mechanical injury 8 hr SW_N20


title: AEC mechanical injury 8 hr SW_N19


title: AEC mechanical injury 24 hr SW_N23


title: TM120

value: serous

value: 0=no relapse; 1=relapse:1


title: TM119

value: IV

value: PT


title: TM118

value: III

value: 0=alive; 1=dead:0


title: primary tumor sample [41159P]


title: TM117

value: mixed

value: mRD


title: primary tumor sample [6327A]


title: primary tumor sample [3060L]


title: primary tumor sample [3114H]


title: AEC mechanical injury 0 hr SW_N15

value: primary airway epithelial cells (AEC)

value: Submersion

value: 0 hr


title: AEC mechanical injury 0 hr SW_N13


title: TM116


title: primary tumor sample [3960M]


title: TM115

value: 0=alive; 1=dead:1


title: AEC mechanical injury 0 hr SW_N14


title: AEC sham control 24 hr SW_N10

value: Sham

value: 24 hr


title: AEC sham control 24 hr SW_N12


title: AEC sham control 24 hr SW_N11


title: AEC mechanical injury 8 hr SW_N18

value: 8 hr


title: primary tumor sample [21621K]


title: primary tumor sample [61194H]


title: primary tumor sample [9076M]


title: AEC sham control 8 hr SW_N06


title: TM114


title: AEC sham control 8 hr SW_N05


title: primary tumor sample [9062M]


title: AEC sham control 8 hr SW_N07


title: AEC sham control 24 hr SW_N09


title: AEC sham control 8 hr SW_N08


title: primary tumor sample [4154C]


title: AEC mechanical injury 0 hr SW_N16


title: TM112


title: TM113

value: clear cells

value: NED


title: TM109

value: undifferentiated

value: GRD

value: P


title: TM111

value: PT

value: 0=no relapse; 1=relapse:1


title: TM110

value: III


title: TM108

value: serous


title: AEC sham control 0 hr SW_N41

value: Mechanical injury (MI)


title: AEC sham control 0 hr SW_N03

value: primary airway epithelial cells (AEC)


title: primary tumor sample [41137T]


title: primary tumor sample [3004M]


title: primary tumor sample [2595T]


title: primary tumor sample [3370E]


title: AEC sham control 0 hr SW_N01

value: Submersion


title: AEC sham control 0 hr SW_N04

value: 0 hr


title: primary tumor sample [4782F]


title: TM106

value: 0=alive; 1=dead:0


title: TM107

value: IV

value: 0=alive; 1=dead:1


title: TM103

value: mucinous


title: TM104


title: TM105

value: mRD


title: TM102


title: primary tumor sample [4826P]


title: primary tumor sample [61118T]


title: primary tumor sample [2601E]


title: primary tumor sample [6567A]


title: TM100

value: 0=no relapse; 1=relapse:0


title: TM95

value: mixed

value: NED


title: TM101


title: primary tumor sample [9096E]


title: TM99


title: TM92

value: GRD


title: primary tumor sample [41038M]


title: primary tumor sample [9104P]


title: primary tumor sample [4462H]


title: AEC sham control 0 hr SW_N02

value: Sham


title: primary tumor sample [22341F]


title: primary tumor sample [3957M]


title: primary tumor sample [2577N]


title: primary tumor sample [9070L]


title: primary tumor sample [1762P]


title: TM97

value: PT

value: 0=no relapse; 1=relapse:1


title: primary tumor sample [4644C]


title: TM91

value: serous

value: III


title: TM90


title: TM93

value: P


title: TM96

value: undifferentiated


title: primary tumor sample [2213A]


title: TM88


title: TM94

value: endometrioid


title: primary tumor sample [8081P]


title: TM89

value: 0=alive; 1=dead:0


title: primary tumor sample [22394E]


title: primary tumor sample [2604N]


title: AEC mechanical injury 8 hr SW_N17

value: primary airway epithelial cells (AEC)

value: Submersion

value: Mechanical injury (MI)

value: 8 hr


title: primary tumor sample [3200P]


title: primary tumor sample [8276H]


title: primary tumor sample [21703N]


title: primary tumor sample [21129M]


title: primary tumor sample [3403F]


title: TM86


title: primary tumor sample [42580K]


title: primary tumor sample [11079H]


title: TM87


title: BNACJ24: 252827911715_S002_GE1_1105_Oct12_2_3.txt

city: Montreal

first: Johanna

middle: Samantha

last: Selvaratnam

state: Quebec

address: 3655 Prom. Sir-William-Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for Agilent SurePrint G3 Rat GE 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: germ cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using TRIzol® (Invitrogen, Burlington, ON) following the manufacturer's recommendations.  This was followed by clean-up of RNA using RNeasy kit columns (Qiagen, Mississauga, ON) and quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Isolated germ cells (from either young or aged Brown Norway Rats) cultured in phenol-red-free media supplemented with 5% heat-inactivated fetal bovine serum.  The cultures were incubated for 13-hrs at 32°C in a humidified incubator with 5% CO2.  Following which they were either pre-treated with EUK-134 or media-only (controls), and 30-min later treated with either saline (controls) or SIN-1 (depending on treatment group)

tag: background strain

value: Brown Norway

tag: Sex

value: male

value: Aged

value: Round Spermatid

tag: treatment


title: BNACJ23: 252827911714_S002_GE1_1105_Oct12_2_3.txt

value: 13hr, Saline


title: BNACJ20: 252827911715_S002_GE1_1105_Oct12_1_2.txt

value: 17hr, SIN-1


title: BNYCJ23: 252827911715_S002_GE1_1105_Oct12_2_1.txt

value: Young


title: BNYCJ20: 252827911714_S002_GE1_1105_Oct12_2_1.txt


title: primary tumor sample [8439N]


title: BNACJ24: 252827911714_S002_GE1_1105_Oct12_1_2.txt


title: BNACJ20: 252827911714_S002_GE1_1105_Oct12_1_4.txt


title: BNACJ21: 252827911715_S002_GE1_1105_Oct12_1_4.txt


title: BNYCJ21: 252827911715_S002_GE1_1105_Oct12_1_3.txt


title: primary tumor sample [42639E]


title: BNACJ23: 252827911715_S002_GE1_1105_Oct12_2_2.txt


title: primary tumor sample [8273P]


title: BNYCJ20: 252827911715_S002_GE1_1105_Oct12_1_1.txt


title: primary tumor sample [3935N]


title: primary tumor sample [22232N]


title: BNACJ20: 252827911714_S002_GE1_1105_Oct12_2_2.txt


title: BNACJ23: 252827911716_S001_GE1_1105_Oct12_2_3.txt


title: BNYCJ21: 252827911714_S002_GE1_1105_Oct12_1_3.txt


title: BNACJ24: 252827911716_S001_GE1_1105_Oct12_1_4.txt

value: 17hr, Saline


title: GMP_AE3_3

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

institute: School of Life Sciences, University of Dundee

description: Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with leukemic splenocytes (LeuB)_Biological replicate 3

hyb_protocol: standard Agilent procedure

scan_protocol: standard Agilent procedure

data_processing: Agilent microarrays were normalized using the RMA function from the Bioconductor affy package (Gautier et al., 2004). The normalized arrays were then background corrected using the normal+exponential convolution model with saddle-point approximation to maximum likelihood (Ritchie et al., 2007) and normalized between arrays by Cyclic Loess using the limma package implementation (Smyth and Speed, 2003). In the processed data file, spike-in and control probes were removed and the remaining probe list was collapsed based on unique identifiers to only retain the best probe (lowest p-value) for a given transcript. This yielded a final processed data file containing a total of 37877 rows.

source_name: FACS-sorted GMP cells (LeuB/AE3)

label_protocol: Biological triplicates were labeled and hybridized to Agilent SurePrint G3 Mouse GE 8x60K arrays according to manufacturers instructions

growth_protocol: FACS-sorted in vivo GMP cells (Lin-cKit+Sca1-CD16/32+CD150-) were isolated from bone marrow of recipient mice one month after transplantation of WT bone marrow or splenic cells from two independent moribond Tet2-/-:AE leukemic mice (LeuA/AE1 or LeuB/AE3)

extract_protocol: Total RNA was isolated using the Allprep Micro Kit (Qiagen)

tag: strain background

tag: transplanted with

value: splenic cells from moribond Tet2-/-:AE leukemic mice (LeuA/AE3)

tag: tissue

value: bone marrow of recipient mice

tag: arrayslide

tag: subarray id


title: BNYCJ24: 252827911716_S001_GE1_1105_Oct12_1_3.txt


title: BNYCJ24: 252827911714_S002_GE1_1105_Oct12_1_1.txt


title: primary tumor sample [22721L]


title: GMP_AE3_2

description: Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with leukemic splenocytes (LeuB)_Biological replicate 2

value: FACS-sorted in vivo GMP cells (Lin-cKit+Sca1-CD16/32+CD150-)


title: GMP_AE3_1

description: Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with leukemic splenocytes (LeuB)_Biological replicate 1


title: primary tumor sample [21714E]


title: BNACJ22: 252827911716_S001_GE1_1105_Oct12_2_2.txt


title: BNACJ24: 252827911716_S001_GE1_1105_Oct12_1_2.txt


title: BNYCJ22: 252827911716_S001_GE1_1105_Oct12_2_1.txt


title: BNYCJ24: 252827911716_S001_GE1_1105_Oct12_1_1.txt


title: GMP_AE1_2

description: Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with leukemic splenocytes (LeuA)_Biological replicate 2

source_name: FACS-sorted GMP cells (LeuA/AE1)

value: splenic cells from moribond Tet2-/-:AE leukemic mice (LeuA/AE1)


title: GMP_AE1_3

description: Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with leukemic splenocytes (LeuA)_Biological replicate 3


title: primary tumor sample [9069T]


title: BNACJ24: 252827910932_S001_GE1_1105_Oct12_2_2.txt


title: GMP_AE1_1

description: Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with leukemic splenocytes (LeuA)_Biological replicate 1


title: BNACJ22: 252827910932_S001_GE1_1105_Oct12_1_4.txt


title: BNYCJ24: 252827910932_S001_GE1_1105_Oct12_2_1.txt


title: GMP_WT_3

description: Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with WT cells_Biological replicate 3

source_name: FACS-sorted GMP cells (WT)

value: WT bone marrow cells


title: primary tumor sample [61836F]


title: GMP_WT_2

description: Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with WT cells_Biological replicate 2


title: primary tumor sample [22461F]


title: primary tumor sample [62351F]


title: primary tumor sample [8274A]


title: BNYCJ22: 252827910932_S001_GE1_1105_Oct12_2_3.txt


title: primary tumor sample [31091P]


title: BNACJ22: 252827910932_S001_GE1_1105_Oct12_1_2.txt


title: GMP_WT_1

description: Gene expression data from in vivo FACS-sorted GMP cells isolated from secondary recipients transplanted with WT cells_Biological replicate 1


title: BNYCJ22: 252827910932_S001_GE1_1105_Oct12_1_3.txt


title: Allyl alcohol treated_3h_rep2

city: Bhopal

first: Raghuvir

middle: singh

last: Tomar

state: MP

address: ITI (Gas Rahat) Building Govindpura - Bhopal

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education & Research

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 30007G.

data_processing: The data were analyzed with RMA using Affymetrix Expression Console default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Saccharomyces cerevisiae

source_name: Allyl alcohol treated_3h

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: Saccharomyces cerevisiae strain (W1588-4c) was grown in standard Synthetic Complete liquid media (contain 2% glucose) at 30oC with orbital shaking.

extract_protocol: Total RNA was extracted from yeast cells by using heat/freeze RNA isolation method as previously described in [Schmitt ME, Brown TA, Trumpower BL. A Rapid and Simple Method for Preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Research, 1990; 18 (10): 3091–92.]. The quality of RNA was high as assessed by absorbance (260 and 280 nm), by Formaldehyde Agarose-Gel electrophoresis, and by Agilent 2100 Bioanalyzer.

treatment_protocol: The yeast cells (W1588-4c) were grown to exponential phase (OD600: ~1) and left untreated (Control) or treated with a dose of 0.4mM Allyl alcohol (freshly prepared 0.1M stock in water) for 3h at 30oC with shaking.

tag: strain

tag: genotype/variation

tag: growth phase

value: exponential phase

tag: treated with

value: 0.4mM of Allyl alcohol for 3h


title: BNACJ23: 252827910931_S001_GE1_1105_Oct12_2_3.txt

tag: cell type


title: BNYCJ23: 252827910932_S001_GE1_1105_Oct12_1_1.txt


title: Allyl alcohol treated_3h_rep1


title: primary tumor sample [41904E]

description: Gene expression data from cerebral tumor

tag: diagnosis


title: Untreated_Control_rep2

value: none (untreated control)


title: primary tumor sample [21052N]


title: BNYCJ21: 252827910931_S001_GE1_1105_Oct12_2_1.txt


title: Untreated_Control_rep1


title: TM98

tag: histotype

value: serous

tag: debulking

value: GRD

tag: Stage

value: III

tag: grading

tag: therapy code

value: PT

tag: ttr (months)

tag: code ttr

value: 0=no relapse; 1=relapse:1

tag: overall survival (months)

tag: code os

value: 0=alive; 1=dead:0


title: BNACJ21: 252827910931_S001_GE1_1105_Oct12_2_2.txt

tag: background strain

value: Brown Norway

tag: Sex

value: male

tag: age

value: Aged

value: Round Spermatid

tag: treatment

value: 17hr, SIN-1


title: primary tumor sample [42472C]


title: primary tumor sample [8444C]


title: BNACJ21: 252827910931_S001_GE1_1105_Oct12_1_4.txt

value: 17hr, Saline


title: BNYCJ21: 252827910931_S001_GE1_1105_Oct12_1_3.txt

value: Young


title: primary tumor sample [8267F]


title: primary tumor sample [8269M]


title: primary tumor sample [21639E]


title: HUVEC_GoxHbHp_6h_c

city: Zurich

first: Christian

middle: Andreas

last: Schaer

address: Raemistrasse 100

institute: University Hospital Zurich

description: Human umbilical vein endothelial cells (HUVEC), incubated with glucose oxidase and hemoglobin-haptoglobin complex

hyb_protocol: After purification of amplified cRNA according to the QIAgen RNeasy purification protocol (QIAGEN) 825 ng of Cy3 and Cy5 labeled cRNA were competitively hybridized for 17 hours at 65° C in a hybridization oven (Agilent G2545A) set to 10 rpm in GEx Hybridization buffer HI-RPM according to the manufacturer's protocol (Agilent’s Two-Color Microarray-Based Gene Expression Analysis). Washing was performed according to the recommended protocol including the Stabilization and Drying Solution step.

scan_protocol: Array slides were XDR scanned at 5 mcm resolution on a Agilent Microarray High-Resolution C Scanner (G2505C) with 100% PMT and 10% for lower intensity.

data_processing:
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.5.1.1. Spot values were normalized using the default linear-lowess normalization. To identify differentially expressed features, calculated log10 ratio values (Cy5/Cy3) were imported into JMP Genomics 5.1 without further normalization and the built-in Basic Expression Workflow (ANOVA, LSMeans Differences) was performed.
We don't provide a Matrix Table as we imported the calculated and lowess-normalized log10 ratios of the Feature Extraction result text files directly into JMP Genomis 5.1 and performed the statistical analysis without further normalization.

source_name: HUVEC

label_protocol: Fluorescently labeled cRNA was generated from 500 ng total RNA with the Quick Amp Labeling Kit (Agilent) according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7, March 2008 (Agilent publication number G4140-90050). In short, total RNA was reverse transcripted to cDNA using T7 Promotor Primer and MMLV-RT. Then cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

extract_protocol: After washing and lysing the cells with Buffer RLT, total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) according to the manufacturer’s instructions, including an on-column DNA digestion step (RNase-Free DNase Set; QIAGEN). To ensure that only high quality RNA (RIN >7.0) was used for gene expression analysis, each RNA sample was checked on a RNA Nanochip with a Bioanalyzer 2100 (Agilent Technologies, Basel, Switzerland). RNA was quantified spectrophotometrically with a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

value: HUVEC

value: no treatment

tag: time

value: Gox 20mU/mL + Hb 2mg/mL + Hp 2mg/mL


title: BNACJ21: 252827910931_S001_GE1_1105_Oct12_1_2.txt

value: 13hr, Saline


title: HUVEC_GoxHbHp_6h_d


title: primary tumor sample [3564L]


title: BNYCJ22: 252827910931_S001_GE1_1105_Oct12_1_1.txt


title: HUVEC_GoxHbHp_6h_a


title: primary tumor sample [3712N]


title: primary tumor sample [8454H]


title: HUVEC_GoxHbHp_6h_b


title: BNACJ23: 252827910933_S001_GE1_1105_Oct12_2_2.txt


title: HUVEC_GoxHb_6h_d

description: Human umbilical vein endothelial cells (HUVEC), incubated with glucose oxidase and hemoglobin

value: Gox 20mU/mL + Hb 2mg/mL


title: primary tumor sample [31120E]


title: BNYCJ24: 252827910933_S001_GE1_1105_Oct12_2_3.txt


title: BNYCJ22: 252827910933_S001_GE1_1105_Oct12_2_1.txt


title: BNACJ20: 252827910933_S001_GE1_1105_Oct12_1_2.txt


title: HUVEC_GoxHb_6h_a


title: BNACJ20: 252827910933_S001_GE1_1105_Oct12_1_4.txt


title: primary tumor sample [8268K]


title: Blood donor 9

first: Thomas

last: Matthes

address: Rue Gabrielle Perret-Gentil

department: Hematology

institute: Geneva University Hospital

data_processing:
To select adequate normalization genes from the series of nine candidates included in the CodeSet (ACTB, TBP, RPL19, RPLP0, G6PD, ABCF1, B2M, TPT1, RPS23), their relative stability was evaluated using geNorm-method (Vandesomple J. et al.;2002). For the final normalization of the sample values the geometric mean of the counts obtained for the three selected normalization genes (RPL19, RPLP0 and TPT1) was calculated and used as normalization factor.
Count data after normalisation refer to the realtive number of the specific mRNA molecules present in the various samples. Fold-changes in expression levels between two samples can be easily calculated using the ratio of the values from the two samples.

label: not applicable

source_name: purified B lymphocytes

extract_protocol: No extraction protocol was used. Cells were lysed in RNA lysis buffer (Qiagen) and directly used for the hybridisation with the Nanostring CodeSet according to the manufacturer's instructions.

treatment_protocol: Fresh blood was collected and Lysis of Red blood cells was performed.Total white blood cells were stored in RNA lysis buffer (Qiagen).

value: not known

tag: gender

tag: binet stage

value: not applicable


title: HUVEC_GoxHb_6h_b

tag: cell type


title: primary tumor sample [31149H]

tag: diagnosis


title: HUVEC_Gox_6h_a

description: Human umbilical vein endothelial cells (HUVEC), incubated with glucose oxidase

value: Gox 20mU/mL


title: primary tumor sample [8272M]


title: HUVEC_GoxHb_6h_c


title: BNACJ24: 252827911713_S001_GE1_1105_Oct12_2_2_3.txt

value: Pachytene Spermatocyte


title: Blood donor 8


title: primary tumor sample [21707K]


title: BNYCJ20: 252827910933_S001_GE1_1105_Oct12_1_3.txt


title: BNYCJ21: 252827910933_S001_GE1_1105_Oct12_1_1.txt


title: Blood donor 7


title: BNACJ21: 252827911713_S001_GE1_1105_Oct12_2_2_2.txt


title: HUVEC_Gox_6h_b


title: primary tumor sample [22701A]


title: primary tumor sample [6209H]


title: primary tumor sample [21710K]


title: Blood donor 6


title: HPAEC_Gox_huHb_8h_f

description: Human pulmonary artery endothelial cells (HPAEC), incubated with glucose oxidase and human hemoglobin

data_processing:
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.7.3.1. Spot values were normalized using the default linear-lowess normalization. To identify differentially expressed features, calculated log10 ratio values (Cy5/Cy3) were imported into JMP Genomics 5.1 without further normalization and the built-in Basic Expression Workflow (ANOVA, LSMeans Differences) was performed.
We don't provide a Matrix Table as we imported the calculated and lowess-normalized log10 ratios of the Feature Extraction result text files directly into JMP Genomis 5.1 and performed the statistical analysis without further normalization.

source_name: HPAEC

value: HPAEC

value: Gox 2.5mg/mL + huHb 2mg/mL


title: HPAEC_Gox_huHb_8h_h


title: BNYCJ23: 252827911713_S001_GE1_1105_Oct12_2_2_1.txt

value: Brown Norway

value: male


title: Blood donor 5

source_name: Peripheral blood; fresh


title: HUVEC_Gox_6h_c


title: HPAEC_Gox_huHb_8h_g


title: BNACJ21: 252827911713_S001_GE1_1105_Oct12_2_1_4.txt

value: Aged


title: Blood donor 4


title: primary tumor sample [3595L]

data_processing: Raw probe intensities were calibrated and summarized into one expression value per probe set using the hook method, and then quantile-normalised. The expression value of each gene was transformed into log10-scale and centered with respect to its mean value averaged over all samples investigated


title: primary tumor sample [22884E]


title: HPAEC_Gox_huHb_8h_c


title: HPAEC_Gox_huHb_8h_e


title: Blood donor 3


title: BNYCJ21: 252827911713_S001_GE1_1105_Oct12_2_1_3.txt


title: HPAEC_Gox_huHb_8h_d


title: BNACJ20: 252827911713_S001_GE1_1105_Oct12_2_1_2.txt

value: 17hr, SIN-1


title: primary tumor sample [8270F]


title: Blood donor 1


title: BNACJ20: 252827911712_S001_GE1_1105_Oct12_2_2.txt


title: primary tumor sample [8058F]


title: Blood donor 2


title: primary tumor sample [22919M]


title: BNYCJ20: 252827911713_S001_GE1_1105_Oct12_2_1_1.txt


title: CLL30

value: m

value: A


title: CLL29

value: C


title: HPAEC_Gox_bvHb_LDL_8h_h

description: Human pulmonary artery endothelial cells (HPAEC), incubated with glucose oxidase , bovine hemoglobin and low density lipoprotein

value: no treatment

value: Gox 2.5mU/mL + bvHb 2mg/mL + LDL 2mg/mL


title: HPAEC_Gox_huHb_8h_a


title: primary tumor sample [21117A]


title: BNYCJ20: 252827911712_S001_GE1_1105_Oct12_2_1.txt

value: Young


title: HPAEC_Gox_bvHb_LDL_8h_i


title: BNACJ20: 252827911712_S001_GE1_1105_Oct12_1_4.txt


title: CLL26

value: B


title: primary tumor sample [8195F]


title: CLL28


title: BNYCJ21: 252827911712_S001_GE1_1105_Oct12_1_3.txt


title: CLL27


title: HPAEC_Gox_bvHb_LDL_8h_g


title: BNYCJ24: 252827911712_S001_GE1_1105_Oct12_1_1.txt


title: HPAEC_Gox_bvHb_LDL_8h_e


title: CLL25

value: f


title: primary tumor sample [11288H]


title: BNACJ24: 252827911712_S001_GE1_1105_Oct12_1_2.txt


title: BNACJ23: 252827911712_S001_GE1_1105_Oct12_2_3.txt

value: 13hr, Saline


title: primary tumor sample [22190L]


title: CLL23


title: CLL24


title: HPAEC_Gox_bvHb_LDL_8h_f


title: HPAEC_Gox_bvHb_LDL_8h_d


title: primary tumor sample [8453E]


title: BNYCJ22: 252827911711_S001_GE1_1105_Oct12_2_1.txt


title: BNACJ23: 252827911711_S001_GE1_1105_Oct12_2_3.txt


title: HPAEC_Gox_bvHb_LDL_8h_b


title: HPAEC_Gox_bvHb_LDL_8h_c


title: HPAEC_Gox_bvHb_LDL_8h_a


title: HPAEC_Gox_bvHb_8h_g

description: Human pulmonary artery endothelial cells (HPAEC), incubated with glucose oxidase and bovine hemoglobin

value: Gox 2.5mU/mL + bvHb 2mg/mL


title: BNACJ23: 252827911711_S001_GE1_1105_Oct12_1_4.txt

value: Pachytene Spermatocyte

value: 17hr, Saline


title: BNACJ22: 252827911711_S001_GE1_1105_Oct12_2_2.txt


title: CLL22


title: CLL21


title: BNYCJ24: 252827911711_S001_GE1_1105_Oct12_1_3.txt


title: CLL20


title: CLL19

value: ND


title: HPAEC_Gox_bvHb_8h_f

value: HPAEC


title: BNACJ24: 252827911711_S001_GE1_1105_Oct12_1_2.txt

value: Brown Norway

value: male


title: CLL18


title: CLL17


title: HPAEC_Gox_bvHb_8h_e


title: BNYCJ22: 252827910939_S001_GE1_1105_Oct12_2_3.txt

value: 17hr, SIN-1


title: BNYCJ24: 252827910939_S001_GE1_1105_Oct12_2_1.txt


title: HPAEC_Gox_bvHb_8h_c


title: CLL16

value: m


title: CLL15

value: A


title: CLL14


title: BNACJ24: 252827910939_S001_GE1_1105_Oct12_2_2.txt

value: Aged


title: HPAEC_Gox_bvHb_8h_d

value: no treatment


title: BNYCJ24: 252827911711_S001_GE1_1105_Oct12_1_1.txt


title: BNACJ22: 252827910939_S001_GE1_1105_Oct12_1_4.txt


title: HPAEC_Gox_bvHb_8h_b


title: BNACJ22: 252827910939_S001_GE1_1105_Oct12_1_2.txt


title: BNYCJ22: 252827910939_S001_GE1_1105_Oct12_1_3.txt


title: CLL13


title: HPAEC_Gox_8h_d

description: Human pulmonary artery endothelial cells (HPAEC), incubated with glucose oxidase

value: GOX 2.5mU/mL


title: HPAEC_Gox_8h_c


title: BNYCJ23: 252827910939_S001_GE1_1105_Oct12_1_1.txt

value: Young


title: CLL12


title: HPAEC_Gox_8h_b


title: HPAEC_Gox_8h_a


title: CLL11


title: HPAEC_bvhuHb_8h_f

description: Human pulmonary artery endothelial cells (HPAEC), incubated with bovine and human hemoglobin

value: bvHb + huHb, total 2mg/mL


title: CLL10

value: f


title: BNACJ24: 252827910938_S001_GE1_1105_Oct12_2_3.txt


title: CLL8


title: BNACJ21: 252827910938_S001_GE1_1105_Oct12_2_2.txt


title: CLL6


title: CLL9

value: B


title: BNYCJ21: 252827910938_S001_GE1_1105_Oct12_2_1.txt


title: HPAEC_bvhuHb_8h_e


title: CLL7


title: CLL5


title: CLL4


title: HPAEC_bvhuHb_8h_d


title: BNYCJ21: 252827910938_S001_GE1_1105_Oct12_1_3.txt


title: CLL3


title: HPAEC_bvhuHb_8h_b


title: HPAEC_bvhuHb_8h_c


title: HPAEC_bvhuHb_8h_a


title: BNACJ21: 252827910938_S001_GE1_1105_Oct12_1_2.txt

value: 13hr, Saline


title: BNACJ21: 252827910938_S001_GE1_1105_Oct12_1_4.txt

value: Pachytene Spermatocyte


title: CLL1


title: BNYCJ24: 252827910937_S001_GE1_1105_Oct12_2_3.txt


title: HPAEC_Gox_bvHb_8h_a

value: Gox 2.5mU/mL + bvHb 2mg/mL


title: MSX, biological rep7

city: Kanagawa

first: Asuka

last: Kamei

address: LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Project for development of food functionality assessment methods

institute: Kanagawa Academy of Science and technology

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing:
The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using the Factor Analysis for Robust Microarray Summarization (qFARMS).
Two independent normalizations were performed: high fat diet group data with low fat diet group and high fat diet group with MSX group. Each normalization data set is available on the series record and includes the log2 qFARMS signal.

source_name: mice fed high fat diet with 0.06% maple syrup extract for 8 weeks

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip® 3' IVT Express kit, Affymetrix).

growth_protocol: Male C57BL/6J mice aged 3 weeks were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 23 ± 1°C and 49 ± 16% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00).  For 1 week acclimation period after purchase, all the mice were fed a low-fat diet (10 kcal% fat).  Then, they were randomly divided into three different dietary groups: the first group with the food containing fat at 10 kcal% as low-fat diet, the second group with 45 kcal% as high-fat diet, and the third with HFD plus 0.06% MSX.  The mice were fed ad libitum for 8 weeks.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Livers were excised and stored at -80˚C

tag: strain

tag: tissue

value: liver

value: twelve-week-old


title: CLL2


title: HPAEC_Gox_huHb_8h_b

value: HPAEC

value: Gox 2.5mg/mL + huHb 2mg/mL


title: BNYCJ22: 252827910938_S001_GE1_1105_Oct12_1_1.txt

value: Brown Norway

value: male


title: BNACJ23: 252827910937_S001_GE1_1105_Oct12_2_2.txt


title: BNYCJ22: 252827910937_S001_GE1_1105_Oct12_2_1.txt


title: BNACJ20: 252827910937_S001_GE1_1105_Oct12_1_4.txt

value: 17hr, Saline


title: Hox6 null biological rep2

city: Ann Arbor

first: Deneen

last: Wellik

state: MI

address: 109 Zina Pitcher

department: Internal Medicine

institute: University of Michigan

description: Gene expression data from E12.5 Hox6 null Bl6 mouse pancreas

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the limma, oligo and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: E12.5 mouse pancreas

label_protocol: Biotinylated cDNA were prepared according to the Nugen WT-Pico Ovation kit protocol from 10 ng total RNA (WT-Pico Ovation RNA Amplification System Manual, 2007, NuGEN). Subsequently cDNA is made double stranded fragmented and end-labeled following manufacturers standard protocol (NuGEN encore end-labeling module).

growth_protocol: Mice were bred in our building's animal facility under normal conditions.

extract_protocol: RNA was extracted using a Qiagen RNEasy Micro Kit following the manufacturer's protocol.

treatment_protocol: E12.5 pancreata were dissected in ice cold PBS and flash frozen using liquid nitrogen. Samples were stored at -80 C until RNA extraction.

tag: genotype

value: Hox6 null

value: pancreas

tag: developmental stage


title: Hox6 null biological rep3


title: BNYCJ21: 252827910937_S001_GE1_1105_Oct12_1_1.txt


title: Hox6 null biological rep1


title: MSX, biological rep5


title: Control biological rep3

description: Gene expression data from E12.5 WT Bl6 mouse pancreas

value: wild type


title: MSX, biological rep6


title: MSX, biological rep4


title: MSX, biological rep3


title: Subject 3 - Tconv

city: Gainesville

first: Christopher

middle: A.

last: Fuhrman

state: FL

address: 1275 Center Drive, BMSB J513

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

hyb_protocol: 100 ng of total RNA was incubated overnight with the capture and reporter probes from Nanostring  GX Human Immunology V1 panel.

scan_protocol: Hybridized probes were purified on the nCounter Prep Station and counted on the Digital Analyzer (Nanostring) following the manufacturer’s instructions.  For each assay, a max-density scan was performed.

data_processing: In nSolver 1.0 (Nanostring) counts were normalized to the spiked-in positive controls then to the 10 internal housekeeping genes.

growth_protocol: Following FACS isolation, cells were activated with Dynabeads Human T-Expanded CD3/CD28 (Life Technologies) at a 1:1 bead:cell ratio. Treg and Tconv were regularly maintained with complete RPMI and supplemented with IL-2 (Aldesleukin), 300 IU/mL or 20 IU/mL, respectively. On day 9, T cells were restimulated with beads (1:1 ratio) and maintained until day 14. Dynabeads were removed and the cells were 5.0e5 cells were snap frozen for analysis.

extract_protocol: RNA was isolated with AllPrep DNA/RNA Mini Kit (Qiagen) and quantified on a Bioanalyzer with the RNA Nano Chip (Agilent Technologies).

treatment_protocol: No treatment.


title: Control biological rep2


title: Subject 3 - Treg - CD226-TIGIT+

source_name: CD4+CD25+CD327-/lo CD226-TIGIT+


title: BNACJ20: 252827910937_S001_GE1_1105_Oct12_1_2.txt

value: Aged


title: BNYCJ20: 252827910937_S001_GE1_1105_Oct12_1_3.txt

value: Young


title: Subject 3 - Treg - CD226+TIGIT-

source_name: CD4+CD25+CD327-/lo CD226+TIGIT-


title: Tg(fabp10a:pt-beta-catenin) vs non-transgenic control, replicate 2

city: San Francisco

first: Kimberley

middle: Jane

last: Evason

state: CA

address: 513 Parnassus Ave, Room M545

institute: University of California, San Francisco

hyb_protocol: cDNA preparation and microarray hybridization were performed at MoGene (St. Louis, MO), using standard procedures

scan_protocol: cDNA preparation and microarray hybridization were performed at MoGene (St. Louis, MO), using Agilent Technologies Scanner G2505C US83800207

data_processing: Background subtraction and normalization were performed at MoGene (St. Louis, MO), to obtain gProcessedSignal and rProcessedSignal

organism: Danio rerio

growth_protocol: Zebrafish were maintained under standard conditions as described (Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF. Stages of embryonic development of the zebrafish. Dev Dyn Off Publ Am Assoc Anat. 1995;203: 253–310. doi:10.1002/aja.1002030302)

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions

treatment_protocol: No chemical treatments.

source_name: non-transgenic, replicate 2

value: non-transgenic


title: Control biological rep1


title: Subject 2 - Treg - CD226-TIGIT+

source_name: CD4+CD25+CD227-/lo CD226-TIGIT+


title: Subject 3 - Treg - CD226+TIGIT+

source_name: CD4+CD25+CD327-/lo CD226+TIGIT+


title: ALDEFLUOR of RMG1 (Cy3/Cy5)

city: Sapporo

first: Tasuku

last: Mariya

state: Hokkaido

address: South 1 West 16, Chuo-ku

institute: Sapporo Medical University

description: Cancer stem like cells, sorted out from ovarian cancer cell line using ALDEFLUOR assay.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: ALDEFLUOR high cells

label_protocol: 3 µg of total RNA were primed with 2 µl of 100 µM T7 promoter DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label.

growth_protocol: Ovarian cancer cell line RMG1 was kept in medium DMEM/F12, containing 10% fetal bovine serum and 1% PC/SM.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit following manufacturer's instructions.

tag: cell line

value: ovarian cancer cell line

tag: aldefluor assay

value: positive

source_name: ALDEFLUOR low cells

value: negative


title: Tg(fabp10a:pt-beta-catenin) vs non-transgenic control, replicate 1

label_protocol: cDNA preparation and microarray hybridization were performed at MoGene (St. Louis, MO), using standard procedures

source_name: non-transgenic, replicate 1


title: high fat diet, biological rep4

description:
45F_11
HFD

source_name: mice fed high fat diet for 8 weeks


title: NB_7 young animal, biological rep2

city: Mannheim

first: Harsh

last: Dweep

address: Theodor-Kutzer-Ufer 1-3

department: Medical Research Center, Medical Faculty of Mannheim of the University of Heidelberg

institute: University of Heidelberg

description: Gene expression data from young animals

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with JMP Genomics V. 6 from SAS. Gene expression profiling was performed using arrays of GeneChip® Rat Gene 1.0 from Affymetrix. A Custom CDF Version 18 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

label_protocol: Fifteen μl (corresponding to 5-10 μg total RNA) of each biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was isolated using a kit from Qiagen and tested for quality.   sample were delivered for microarray analysis.

value: Wistar


title: NB_22 young animal, biological rep4

description: Gene expression data from young animals


title: NB_8 young animal, biological rep3

description: Gene expression data from young animals


title: AD_17 adult animal, biological rep1

description: Gene expression data from adult animals

value: Adult


title: AD_27 adult animal, biological rep4

description: Gene expression data from adult animals


title: ALDEFLUOR of RMG1 (Cy5/Cy3)


title: NB_6 young animal, biological rep1

description: Gene expression data from young animals


title: Subject 2 - Treg - CD226-TIGIT-

source_name: CD4+CD25+CD227-/lo CD226-TIGIT-


title: Subject 3 - Treg - CD226-TIGIT-

source_name: CD4+CD25+CD327-/lo CD226-TIGIT-


title: MSX, biological rep1

value: liver

value: twelve-week-old


title: Subject 1 - Tconv


title: Subject 2 - Tconv


title: high fat diet, biological rep6

description:
45F_25
HFD


title: MSX, biological rep2


title: high fat diet, biological rep5

description:
45F_14
HFD


title: high fat diet, biological rep1

description:
45F_3
HFD


title: high fat diet, biological rep7

description:
45F_28
HFD


title: Subject 1 - Treg - CD226-TIGIT+

source_name: CD4+CD25+CD127-/lo CD226-TIGIT+


title: high fat diet, biological rep3

description:
45F_8
HFD


title: AD_26 adult animal, biological rep3

description: Gene expression data from adult animals


title: AD_18 adult animal, biological rep2

description: Gene expression data from adult animals


title: Subject 2 - Treg - CD226+TIGIT-

source_name: CD4+CD25+CD227-/lo CD226+TIGIT-


title: low fat diet, biological rep6

source_name: mice fed low fat diet for 8 weeks


title: high fat diet, biological rep2

description:
45F_4
HFD


title: Subject 2 - Treg - CD226+TIGIT+

source_name: CD4+CD25+CD227-/lo CD226+TIGIT+


title: low fat diet, biological rep7


title: Subject 1 - Treg - CD226+TIGIT-

source_name: CD4+CD25+CD127-/lo CD226+TIGIT-


title: SDP8 + 8h DOX Exp_1

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description:
The strain SDP8 (CML476 background), contains a KanMX4-tetO7 cassette replacing about 0.5 kbp of the PKH2 promoter, and located immediately before the PKH2 coding region.
Spots with either a diameter smaller than 120 um, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 ºC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 ul of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 micro m. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing:
The Gene Expression Profile Analysis Suite, GEPAS v4.0 package (http://www.gepas.org/) was used to the processing of data: the Preprocessing tool was used to merge replicates and give the average value.
The normalization method we used to generate the data reported in the VALUE columns was the ratio of medians for the non-flagged genes. Spots with saturated values were excluded from the normalization process.

source_name: SDP8 conditional mutant strain treated with doxycycline for 8 h

label_protocol: Fluorescent labeled cDNA was prepared from 8 microg of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Saturated culture grown in YPD medium was diluted at OD660 0.05 in YPD supplemented with doxycycline for 8h. Cells from 50 ml of culture, at OD660 0.609, were collected by centrifugation and washed with cold water. The dried cell pellet was kept at -80 ºC until RNA purification.

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

treatment_protocol: Treated with 100 microg/ml doxycycline, from a 5 g/l stock in an ethanol:water mix (1:1), for 8h.

value: teto7:PKH2 pkh1::HIS3 pkh3::NatMX4

value: with doxycycline for 8 h

source_name: Wild type strain treated with doxycycline for 8 h

growth_protocol: Saturated culture grown in YPD medium was diluted at OD660 0.05 in YPD supplemented with doxycycline for 8h. Cells from 50 ml of culture, at OD660 0.554, were collected by centrifugation and washed with cold water. The dried cell pellet was kept at -80 ºC until RNA purification.


title: SDP8 + 8h DOX Exp_2


title: SDP8 + 24h DOX Exp_2

source_name: SDP8 conditional mutant strain treated with doxycycline for 24 h

growth_protocol: Saturated culture grown in YPD medium was diluted at OD660 0.05 in YPD supplemented with doxycycline. Eight h later, when OD660: 0.609, a new culture was prepared at initial OD660: 0.01 that was also supplemented with doxycycline and was grown for 16 h.  Cells present in 50 ml of the culture were collected by centrifugation and washed with cold water. The dried cell pellet was kept at -80 ºC until RNA purification.

treatment_protocol: Treated with 100 microg/ml doxycycline, from a 5 g/l stock in an ethanol:water mix (1:1), for 24h.

value: with doxycycline for 24 h

source_name: Wild type strain treated with doxycycline for 24 h

growth_protocol: Saturated culture grown in YPD medium was diluted at OD660 0.05 in YPD supplemented with doxycycline. Eight h later, when OD660: 0.554, a new culture was prepared at initial OD660: 0.01 that was also supplemented with doxycycline and was grown for 16 h.  Cells present in 50 ml of the culture were collected by centrifugation and washed with cold water. The dried cell pellet was kept at -80 ºC until RNA purification.


title: SDP8 + 24h DOX Exp_1


title: Subject 1 - Treg - CD226+TIGIT+

source_name: CD4+CD25+CD127-/lo CD226+TIGIT+

value: male


title: low fat diet, biological rep5


title: low fat diet, biological rep4


title: Subject3-pTregs

scan_protocol: Hybridized probes were purified on the nCounter Prep Station and counted on the Digital Analyzer (NanoString) following the manufacturer’s instructions.  For each assay, a max-density scan was performed.

data_processing: In Partek Genomic Suite (Partek Inc.) counts were normalized to the 10 internal housekeeping genes and the average of the background counts (noise) was subtracted with values lower than background set to one.

source_name: pTreg (CD4+FOXP3+Helios–)

growth_protocol: Freshly isolated from peripheral blood.

extract_protocol: RosetteSep (Stemcell) enriched CD4 T cells were stained with CD4-Pacific Blue (RPA-T4), fixed and permeabilized with the FOXP3 Fix/Perm (Biolegend) and stained with Helios -AF647 (22F6), FOXP3- PE (206D).  Different cell populations, tTreg (CD4+FOXP3+Helios+), pTreg (CD4+FOXP3+Helios–) and Tconv (CD4+FOXP3–Helios–), were then sorted on a BD FACSAria III into into RNALater (Life Technologies). RNA was extracted with the RNeasy FFPE Kit (Qiagen) by proteinase K digestion followed by incubation at 80°C then verified on a Bioanalyzer (>300 bp length) with the RNA Nano Chip (Agilent Technologies).

tag: cell population

value: pTreg (CD4+FOXP3+Helios–)


title: Subject3-Tconv

source_name: Tconv (CD4+FOXP3–Helios–)

value: Tconv (CD4+FOXP3–Helios–)


title: lhp1-4, untreated_biological rep1

city: Tuebingen

first: Dierk

last: Wanke

address: Auf der Morgenstelle 32

department: Plant Physiology

institute: University of Tuebingen

description: Gene expression data from 18 days old shoots; untreated plants

hyb_protocol: After fragmentation of cRNA using the RNA Fragmentation Reagents (Ambion), 15 µg of cRNA was hybridized to Affymetrix Arabidopsis ATH1 Genome Array (ATH1-121501; GEO accession GPL198) according to manufacturers manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the protocol 'EukGE-WS2V4'.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® scanner GS3000 7G according to manufacturers manual.

data_processing: The data was analyzed with GeneSpring GX (vers. 7.3.1) from Agilent. Preprocessing was performed with included RMA Plugin.

organism: Arabidopsis thaliana

source_name: Arabidopsis plants untreated

label_protocol: 1µg of total RNA were used to synthesize amplified labeled cRNA (MessageAmp™ II aRNA Biotin Amplification Kit; Ambion).

growth_protocol: Arabidopsis thaliana (accession Columbia) were grown in the greenhouse under constant temperature of 20°C, 35% humidity and a 18-h light period.

extract_protocol: For RNA extraction RNeasy Plant Mini kit was used ( according instructions from Quiagen).  Extracted RNA was precipitated 100ul RNA;  8 µl 3 M Sodium acetate (pH 5.2); 2 µl Glycogen(5mg/ml); -80°C over night. then 30 min 13000 rpm 4°C. 2 times washing with 70% ethanol. resuspended in DEPC water. RNA quantity and integrity were assessed using RNA 6000 Nano LabChip Kit and the BioAnalyzer software (Agilent).

treatment_protocol: No treatment was applied

tag: ecotype

tag: genotype/variation

value: shoot

value: 18 days


title: Subject 1 - Treg - CD226-TIGIT-

source_name: CD4+CD25+CD127-/lo CD226-TIGIT-

tag: Sex


title: Subject3-tTregs

source_name: tTregs (CD4+FOXP3+Helios+)

tag: age

value: tTregs (CD4+FOXP3+Helios+)


title: wildtype, untreated_biological rep2

value: wildtype


title: lung, nontumor adjacent_18974

type: genomic

city: Bethesda

first: Ana

middle: I

last: Robles

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

description: nontumor adjacent

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2; Fluorescent signals were collated via Bead Studio software and converted into -values. Illumina Bead Studio software output data were normalized using SSN (simple scaling normalization), to correct for dye bias and transformed into M-values (M = log2 intensity of methylated probe/ intensity of unmethylated probe), using the R package lumi. Raw signals can be found on the series level in the file Unmethylated_and_methylated_signal_intensities.txt

label: Cy5 and Cy3

molecule: genomic DNA

source_name: lung, nontumor adjacent

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tissue samples using Qiagen DNeasy Kit according to standard instructions

value: lung

tag: analysis batch

value: Male

tag: race

value: European American

tag: disease state

value: non-small cell lung cancer (NSCLC)

tag: histology

value: normal

tag: smoking status

value: ever

tag: smoking packyears

tag: death due to cancer

value: yes

tag: survival after surgery (days)


title: bpc4 bpc6, untreated_biological rep1

value: bpc4 bpc6

tag: tissue


title: wildtype, untreated_biological rep1


title: lung, adenocarcinoma_18318

description: adenocarcinoma

source_name: lung, adenocarcinoma

value: adenocarcinoma

tag: 7th tnm stage

value: Ia

tag: tumor size (cm)

tag: kras status

value: WT

tag: tp53 mutation

value: unknown

value: no


title: low fat diet, biological rep1

tag: strain

tag: gender

value: male

value: liver

value: twelve-week-old


title: bpc4 bpc6, untreated_biological rep2

tag: ecotype

tag: genotype/variation

value: shoot

value: 18 days


title: Subject2-pTregs

tag: Sex

tag: age

tag: cell population

value: pTreg (CD4+FOXP3+Helios–)


title: low fat diet, biological rep3


title: lung, adenocarcinoma_18133

description: adenocarcinoma

value: lung

tag: analysis batch

value: Female

tag: race

value: European American

tag: disease state

tag: histology

value: never


title: lhp1-4, untreated_biological rep2


title: low fat diet, biological rep2


title: lhp1-4 bpc4 bpc6, untreated_biological rep2

value: lhp1-4 bpc4 bpc6


title: lung, adenocarcinoma_18193

description: adenocarcinoma

value: Male

value: non-small cell lung cancer (NSCLC)

value: Ib

tag: smoking status

value: ever

tag: smoking packyears

value: MT

tag: death due to cancer

tag: survival after surgery (days)


title: Subject2-Tconv

value: Tconv (CD4+FOXP3–Helios–)


title: lung, nontumor adjacent_18318

description: nontumor adjacent

tag: tissue

value: normal

value: no


title: lung, adenocarcinoma_21229

description: adenocarcinoma

hyb_protocol: Labeled cRNA was hybridised to Illumina HumanRefseq8 v3

data_processing: Genome Studio v2010.3

label_protocol: Standard Illumina Protocol Illumina TotalPrep-96 RNA Amplification Kit (Life Technologies)

extract_protocol: Total cellular RNA was extracted from tumor and matching adjacent non-tumor lung using miRNA Kit (QIAGEN). RNA quality was determined using Agilent Bioanalyzer. RNA was hybridized to Illumina HumanRef-8 v3 Expression Beadchip arrays.

value: African American

value: adenocarcinoma

tag: 7th tnm stage

value: Ia

tag: tumor size (cm)

tag: kras status

value: WT

tag: tp53 mutation


title: Subject1-Tconv

value: male


title: lung, nontumor adjacent_21229

description: nontumor adjacent


title: lhp1-4 bpc4 bpc6, untreated_biological rep1

tag: ecotype

tag: genotype/variation

value: shoot

value: 18 days


title: Subject1-pTregs

tag: Sex

tag: age

value: pTreg (CD4+FOXP3+Helios–)


title: Subject1-tTregs

tag: cell population

value: tTregs (CD4+FOXP3+Helios+)


title: lung, adenocarcinoma_18087

description: adenocarcinoma

value: lung

tag: analysis batch

value: Female

tag: race

value: European American

value: unknown


title: Subject2-tTregs


title: lung, nontumor adjacent_19840

description: nontumor adjacent

value: Male

tag: disease state

value: non-small cell lung cancer (NSCLC)

tag: histology

value: ever


title: lung, adenocarcinoma_21272

description: adenocarcinoma

hyb_protocol: Standard Nanostring Protocol

scan_protocol: Standard Nanostring Protocol

data_processing: Nanostring Nsolver

label_protocol: Standard Nanostring Protocol

extract_protocol: Total cellular RNA was extracted from tumor and matching adjacent non-tumor lung using miRNA Kit (QIAGEN), according to the manufacturer’s instructions. RNA quality was determined using Agilent Bioanalyzer.

value: lung, adenocarcinoma

tag: smoking status

tag: smoking packyears

value: no


title: AuditoryNerve_ouabain_7d_rep3

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Targets (12.5 ug) were hybridized to Affymetrix Mouse 430 2.0 GeneChips according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files imported into Affymetrix Expression Console software and data were normalized by: 1) RMA to obtain probe set expression values, and 2) MAS5 to obtain probe set detection calls.

source_name: Auditory nerve_7d post surgery_ouabain treatment

label_protocol: Total RNA (100 ng) was converted into biotin-labeled cRNA and then fragmented using the Affymetrix 3' IVT Express Kit in accordance with manufacturer protocols.

growth_protocol: CBA/CaJ mice were bred in-house in a low-noise environment at the Animal Research Facility of the Medical University of South Carolina (MUSC) with original breeding pairs purchased from The Jackson Laboratory (Bar Harbor, ME).   All mice received food and water ad libitum and were maintained on a 12-hour light/dark cycle.  Mice of both genders were used in the study.  All aspects of the animal research were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee of the MUSC.  Prior to treatment, mice were examined for signs of external ear canal and middle ear obstruction, and mice exhibiting these signs were excluded from the study.

extract_protocol: Microdissected cochlear tissues containing auditory nerves underwent total RNA preparation using the RNeasy Minikit (Qiagen). Total RNA preparations were run on an Agilent 2100 Bioanalyzer to ensure sample quality.

treatment_protocol: Adult Mice (CBA/CaJ, aged 8 to 12 weeks) were anesthetized and subjected to survival surgery to expose the bulla of the right ear. A ouabain solution (3 mM, approximately 10 ul) was administered in the round window niche. This solution was wicked away and replaced with fresh ouabain approximately every 10 min during a cummulative exposure period of 60 min. The left ears (i.e., contralateral) were not surgically manipulated and were used as controls. Mice were maintained for 3 days or 7 days following treatments, then euthanized, and the oubain-treated and contralateral cochleas were removed. Cochleas underwent microdissection to remove the outer bony cochlear shell and cochlear lateral wall, thus preserving the modiolus portion of cochlea which contains mainly the auditory nerve. All sample types were prepared in experimental triplicate (n=3).

tag: strain background

value: CBA/CaJ

value: adult; 8 to 12 weeks

tag: sample group

value: ouabain injury

tag: days after treatment

value: auditory nerve