title: Lymph node Ad 9h, replicate 2

description:
A9h 2
Replicate 2 of 4.

source_name: BALB/c mouse auricular draining lymph node, Ad, 9h


title: Lymph node Ad 9h, replicate 4

status: Public on Dec 01 2012

type: RNA

city: Oxford

first: Arturo

last: Reyes-Sandoval

state: Oxfordshire

address: ORCRB, Roosevelt Dr.

department: The Jenner Institute

country: United Kingdom

institute: University of Oxford

description:
A9h 4
Replicate 4 of 4.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: We used the quantile normalization method for all of the analyses reported here and implemented background correction within Illumina's proprietary BeadStudio software. The results of the experiment were analyzed using Bioconductor libraries limma and beadarray.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Standard Illumina label protocol.

extract_protocol: Total RNA was isolated using the miRNeasy kit (QIAGEN, UK) within 2 h of sample collection.

treatment_protocol: Mice were vaccinated with adenovirus, MVA or Ad+MVA mixed co-administration.

tag: strain

value: BALB/c

tag: age

value: 6 weeks

tag: tissue

value: lymph node

tag: treatment

value: Ad

tag: time


title: Lymph node Ad 9h, replicate 3

description:
A9h 3
Replicate 3 of 4.


title: Lymph node MVA 9h, replicate 3

description:
M9h 3
Replicate 3 of 4.

source_name: BALB/c mouse auricular draining lymph node, MVA, 9h

value: MVA


title: Lymph node Ad 9h, replicate 1

description:
A9h 1
Replicate 1 of 4.


title: SW780 cells with miR-137 precursor molecule

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: gene expression in SW780 cells transfected with miR-137 precursor molecule

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

organism: Homo sapiens

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: SW780 cells were cultured in Leibovitz's L-15 medium supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a TRIZOL reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: SW780 cells (3.0E+5 cells) were transfected with 100 pmol of a Pre-miR-137 miRNA Precursor Molecule (Ambion) or a Pre-miR miRNA Molecule Negative Control #1 (Ambion) using Lipofectamine 2000 according to the manufacturer’s instructions.  Forty-eight hours after transfection, total RNA extraction was carried out.

tag: cell line

tag: transfection


title: LERKO  biological rep 1

city: Huddinge

first: Marko

last: Matic

address: Halsovägen 7

country: Sweden

institute: Karolinska Institutet

hyb_protocol: The Gene Chip Mouse Gene 1.1 ST Array Plate was hybridized in the Affymetrix  Gene Titan  Instrument  standard procedure

scan_protocol: The Gene Chip Mouse Gene 1.1 ST Array Plate was scanned in Affymetrix  Gene Titan  Instrument standard procedure

data_processing: The data were analyzed with oilgo package (version 1.16.0) in Bioconductor. Transcripts level were summaried for core probesets using RMA.

source_name: Liver selective ERalpha knockout mouse

label_protocol: Fragmented single-stranded sense DNA was end labeled with biotin according to  the Affymetrx Gene chip WT Terminal Labeling and hybridization user manual

extract_protocol: Total RNA was isolated from frozen mouse tissues using the Trizol reagent (Invitrogen) as per manufacturer’s instructions. The isolated RNA was subsequently purified with the RNeasy Plus Mini Kits (Qiagen),

tag: Sex

value: female

tag: genotype

value: Liver selective ERalpha knockout mouse

value: liver

tag: genetic background


title: LERKO  biological rep 2


title: Control  biological rep 1

source_name: Control mouse

value: Control mouse


title: SW780 cells with control molecule

description: gene expression in SW780 cells transfected with control miRNA

value: control miRNA


title: LERKO  biological rep 3


title: Control  biological rep 3


title: Control  biological rep 2


title: NT2+cispl-rep2

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 South Lincoln Ave

department: Comparative Biosciences

country: USA

institute: University of Illinois

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol on Illumina BeadArray Reader

data_processing: The data were normalized using quantile normalization in Genome Studio

source_name: NT2/D1 +cispl (0.5 uM, 6 hour, then 24 hour off)

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

growth_protocol: Cells maintained with DMEM 10% FBS, 37oC, 5% CO2

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

treatment_protocol: cells were untreated or treated with 10 nm 5-aza deoxycytidine for 1 day or 3 days (added fresh each day) or cells were treated with 0.5 uM cisplatin for 6 hours, then taken off for 24 hours before RNA harvest.

tag: cell type

value: human ebryonal carcinoma


title: NT2+1dayaza-rep3

description: replicate 3

source_name: NT2/D1 +aza (10 nM, 1 day)


title: NT2+3dayaza-rep1

description: replicate 1

source_name: NT2/D1 +aza (10 nM, 3 day)


title: NT2+3dayaza-rep2

description: replicate 2


title: NT2+1dayaza-rep1

description: replicate 1


title: NT2+cispl-rep3

description: replicate 3


title: NT2+3dayaza-rep3

description: replicate 3


title: ARCaP-E Genistein 2R

city: Atlanta

first: Khanjan

last: Gandhi

state: Georgia

address: 1365-B Clifton Rd NE, Room 4107

institute: Winship Cancer Institute, Emory University.

scan_protocol: BeadChips were scanned using an Illumina BeadArray Scanner.

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.2.

label: Biotin

source_name: ARCaP-E prostate cancer cells, genistein

label_protocol: PCR product was prepared with standard Illumina protocol for arrays.

growth_protocol: ARCaP-E and ARCaP-M cells were purchased from Novicure Biotechnology and propagated in MCaP-Medium (Novicure Biotechnology, Inc, Birmingham, AL), supplemented with 5% FBS, 200mM L-glutamine, and pen-strep.

extract_protocol: Total RNA was isolated using RNeasy kits (QIAGEN, Valencia, CA) according to manufacturer instructions.

treatment_protocol: RNA was isolated from three independent experiments in which ARCaP-E and ARCaP-M cells were treated with DMSO control, 20 µM genistein, or 1 µM 5-aza-deoxycytidine for 6 days, 1µM vorinostat for 48 hrs, or a combination of 1µM vorinostat (48 hrs) plus 20 µM genistein (6 days).

value: ARCaP-E

value: prostate cancer

value: genistein


title: NT2+cispl-rep1

description: replicate 1


title: ARCaP-E DMSO 3R

source_name: ARCaP-E prostate cancer cells, DMSO

value: DMSO


title: ARCaP-M Genistein 3R

source_name: ARCaP-M prostate cancer cells, genistein

value: ARCaP-M


title: ARCaP-E Genistein 3R


title: NT2control-rep2

description: replicate 2

source_name: NT2/D1 control


title: ARCaP-M Genistein 2R


title: ARCaP-E DMSO 1R


title: NT2control-rep1

description: replicate 1


title: Dermis Ad 24h, replicate 3

description:
Ae 24h 3
Replicate 3 of 4.

source_name: BALB/c mouse ear biopsy, Ad, 24h

value: ear biopsy


title: ARCaP-E Genistein 1R


title: NT2+1dayaza-rep2

description: replicate 2


title: NT2control-rep3

description: replicate 3


title: ARCaP-E DMSO 2R


title: ARCaP-M DMSO 3R

source_name: ARCaP-M prostate cancer cells, DMSO


title: ARCaP-M DMSO 2R


title: ARCaP-M 5-aza 3

source_name: ARCaP-M prostate cancer cells, 5-aza-deoxycytidine


title: ARCaP-M DMSO 1R


title: ARCaP-M 5-aza 2


title: ARCaP-M DMSO 3


title: ARCaP-M Genistein 1R


title: ARCaP-M 5-aza 1


title: ARCaP-M DMSO 2


title: ARCaP-E 5-aza 3

source_name: ARCaP-E prostate cancer cells, 5-aza-deoxycytidine


title: ARCaP-E 5-aza 2


title: ARCaP-E DMSO 1


title: ARCaP-E 5-aza 1


title: ARCaP-M Vorinostat-Genistein 2

source_name: ARCaP-M prostate cancer cells, vorinostat-genistein

value: vorinostat-genistein


title: ARCaP-M Vorinostat-Genistein 1


title: ARCaP-E DMSO 2


title: ARCaP-M DMSO 1


title: ARCaP-E Vorinostat-Genistein 1

source_name: ARCaP-E prostate cancer cells, vorinostat-genistein


title: ARCaP-M Vorinostat 1

source_name: ARCaP-M prostate cancer cells, vorinostat

value: vorinostat


title: ARCaP-E DMSO 3


title: ARCaP-E Vorinostat 3

source_name: ARCaP-E prostate cancer cells, vorinostat


title: ARCaP-E Vorinostat 1


title: ARCaP-E Vorinostat-Genistein 3


title: ARCaP-M Vorinostat 2


title: ARCaP-E Vorinostat-Genistein 2


title: ARCaP-M Vorinostat-Genistein 3


title: ARM002B_Not_Responding

city: Cambridge

first: Naomi

middle: Laura

last: Sharma

address: Robinson Way

institute: Cambridge Research Institute

description:
ARM002B
17.11.2008

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised and log2 transformed using quantile normalisation with beadarray in R

source_name: Human Prostate

label_protocol: Standard Illumina label protocol

growth_protocol: From human samples

extract_protocol: RNA extraction using Trizol, as per manufacturer's protocol

treatment_protocol: No additional treatment to tissue

tag: group

tag: type

value: untreated


title: NS016D_Responding

description:
NS016D
15.10.2009

value: Responding

value: LHRH, androgen deprivation, monotherapy


title: NS015D_Not_Responding

description:
NS015D
30.9.2009


title: ARM003C_Not_Responding

description:
ARM003C
15.12.2008

value: HRPC, hormone-refractory prostate cancer


title: NS020D_Not_Responding

description:
NS020D
21.12.2009


title: ARM007B_Benign

description:
ARM007B
19.2.2009

value: Benign

value: benign


title: ARCaP-E Vorinostat 2


title: NS022J_Not_Responding

description:
NS022J
26.2.2010


title: NS021D_Not_Responding

description:
NS021D
14.1.2010

value: CPA, cyproterone acetate, monotherapy


title: NS013D_Responding

description:
NS013D
21.8.2009


title: NS018D_Not_Responding

description:
NS018D
28.10.2009


title: NS028F_Not_Responding

description:
NS028F
19.4.2010


title: NS017D_Not_Responding

description:
NS017D
23.10.2009


title: NS014D_Not_Responding

description:
NS014D
29.9.2009


title: NS027F_Responding

description:
NS027F
19.4.2010


title: NS023F_Benign

description:
NS023F
3.3.2010


title: Patient 18_RML_0 months

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Fragmented and labeled cDNA (2.5 micrograms) were hybridized onto Human Gene 1.0 ST arrays according to the manufacturer’s instructions (Affymetrix). Hybridization cocktails containing samples, control oligonucleotide and eukaryotic hybridization controls in addition to hybridization mixes, DMSO and nuclease-free water were heat denatured at 99oC for 5 minutes, cooled to 45oC for 5 minutes, and finally centrifuged at maximum speed for 1 minute.   After injecting 80 mL of the hybridization cocktails, arrays were incubated for 17 hours in a hybridization oven set to a temperature of 45oC with 60 rpm rotation.   Arrays were washed, stained and processed using Affymetrix GeneChip Fluidics Station 450 systems

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G for subsequent generation of raw data (*CEL files).

data_processing: Raw data were quantified using Robust Multichip Array (RMA) background correction, quantile normalization and RMA probe-level models (RmaPlm) summarization methods using the R language environment. After data preprocessing and normalization, a log base 2 transformation was applied.

source_name: Bronchial brushing from patient 18, Right Middle Lobe, 0 months

label_protocol: Fragmented and biotin-labeled cDNA was then generated using the EncoreTM Biotin Module (NuGEN Technologies) according to the manufacturer's instructions using 5 micrograms of amplified cDNA

extract_protocol: Total RNA was isolated using the Rneasy Mini kit from Qiagen according to the manufacturer's instructions

value: Bronchial brushing, normal airway epithelial cells

tag: patient id

tag: tumor location

value: RML

tag: airway site

value: Adjacent

tag: time point


title: NS025F_Responding

description:
NS025F
18.3.2010


title: NS026F_Not_Responding

description:
NS026F
19.3.2010


title: ARM010B_Responding

description:
ARM010B
6.7.2009


title: Patient 15_RML_0 months

source_name: Bronchial brushing from patient 15, Right Middle Lobe, 0 months

value: RLL

value: Non-adjacent


title: ARM011A_Responding

description:
ARM011A
20.7.2009


title: Patient 19_RML_0 months

source_name: Bronchial brushing from patient 19, Right Middle Lobe, 0 months

value: LUL

value: Contralateral


title: Patient 19_LB10_0 months

source_name: Bronchial brushing from patient 19, Left Lower Lobe, 0 months


title: NS012E_Not_Responding

description:
NS012E
19.8.2009


title: ARM005A_Benign

description:
ARM005A
19.2.2009


title: Patient 17_RML_0 months

source_name: Bronchial brushing from patient 17, Right Middle Lobe, 0 months

value: LLL


title: Patient 14_RML_0 months

source_name: Bronchial brushing from patient 14, Right Middle Lobe, 0 months


title: Patient 19_MC_0 months

source_name: Bronchial brushing from patient 19, Main Carina, 0 months

value: Main carina


title: Patient 18_RB10_0 months

source_name: Bronchial brushing from patient 18, Right Lower Lobe, 0 months


title: ARM009C_Responding

description:
ARM009C
19.2.2009


title: Patient 17_LUL_0 months

source_name: Bronchial brushing from patient 17, Left Upper Lobe, 0 months


title: ARM008B_Benign

description:
ARM008B
19.2.2009


title: NS019D_Not_Responding

description:
NS019D
13.11.2009


title: Patient 15_LUL_0 months

source_name: Bronchial brushing from patient 15, Left Upper Lobe, 0 months


title: Patient 10_RML_0 months

source_name: Bronchial brushing from patient 10, Right Middle Lobe, 0 months

value: RUL


title: Patient 13_LUL_0 months

source_name: Bronchial brushing from patient 13, Left Upper Lobe, 0 months


title: Patient 6_LB10_0 months

source_name: Bronchial brushing from patient 6, Left Lower Lobe, 0 months


title: Patient 8_LUL_0 months

source_name: Bronchial brushing from patient 8, Left Upper Lobe, 0 months


title: Patient 5_RUL_0 months

source_name: Bronchial brushing from patient 5, Right Upper Lobe, 0 months


title: Patient 7_RB10_0 months

source_name: Bronchial brushing from patient 7, Right Lower Lobe, 0 months


title: Patient 8_RML_0 months

source_name: Bronchial brushing from patient 8, Right Middle Lobe, 0 months


title: Patient 6_RML_0 months

source_name: Bronchial brushing from patient 6, Right Middle Lobe, 0 months


title: Patient 4_LB10_0 months

source_name: Bronchial brushing from patient 4, Left Lower Lobe, 0 months


title: Patient 11_LUL_0 months

source_name: Bronchial brushing from patient 11, Left Upper Lobe, 0 months


title: ARCaP-M Vorinostat 3

source_name: ARCaP-M prostate cancer cells, vorinostat

value: ARCaP-M

value: prostate cancer

value: vorinostat


title: Patient 14_LUL_0 months

source_name: Bronchial brushing from patient 14, Left Upper Lobe, 0 months


title: Patient 13_RUL_0 months

source_name: Bronchial brushing from patient 13, Right Upper Lobe, 0 months


title: Patient 9_RML_0 months

source_name: Bronchial brushing from patient 9, Right Middle Lobe, 0 months


title: Patient 10_LB10_0 months

source_name: Bronchial brushing from patient 10, Left Lower Lobe, 0 months


title: Patient 12_LUL_0 months

source_name: Bronchial brushing from patient 12, Left Upper Lobe, 0 months


title: Patient 5_LUL_0 months

source_name: Bronchial brushing from patient 5, Left Upper Lobe, 0 months


title: Patient 7_LB10_0 months

source_name: Bronchial brushing from patient 7, Left Lower Lobe, 0 months


title: Patient 11_RUL_0 months

source_name: Bronchial brushing from patient 11, Right Upper Lobe, 0 months


title: Patient 12_RML_0 months

source_name: Bronchial brushing from patient 12, Right Middle Lobe, 0 months


title: Patient 3_RUL_0 months

source_name: Bronchial brushing from patient 3, Right Upper Lobe, 0 months


title: Patient 9_RUL_0 months

source_name: Bronchial brushing from patient 9, Right Upper Lobe, 0 months


title: Patient 3_LUL_0 months

source_name: Bronchial brushing from patient 3, Left Upper Lobe, 0 months


title: Patient 2_RML_0 months

source_name: Bronchial brushing from patient 2, Right Middle Lobe, 0 months


title: Patient 2_RUL_0 months

source_name: Bronchial brushing from patient 2, Right Upper Lobe, 0 months


title: Patient 17_MC_0 months

source_name: Bronchial brushing from patient 17, Main Carina, 0 months


title: Patient 7_MC_24 months

source_name: Bronchial brushing from patient 7, Main Carina, 24 months


title: Patient 16_MC_0 months

source_name: Bronchial brushing from patient 16, Main Carina, 0 months


title: Patient 4_RB10_0 months

source_name: Bronchial brushing from patient 4, Right Lower Lobe, 0 months


title: Patient 3_MC_24 months

source_name: Bronchial brushing from patient 3, Main Carina, 24 months


title: Patient 12_MC_12 months X38

source_name: Bronchial brushing from patient 12, Main Carina, 12 months


title: Patient 5_MC_24 months X18

source_name: Bronchial brushing from patient 5, Main Carina, 24 months


title: Patient 12_MC_12 months X40


title: Patient 5_MC_24 months X16


title: Patient 1_LUL_0 months

source_name: Bronchial brushing from patient 1, Left Upper Lobe, 0 months


title: Patient 15_MC_0 months

source_name: Bronchial brushing from patient 15, Main Carina, 0 months


title: Patient 14_MC_0 months

source_name: Bronchial brushing from patient 14, Main Carina, 0 months


title: Patient 1_RB10_0 months

source_name: Bronchial brushing from patient 1, Right Lower Lobe, 0 months


title: Patient 9_MC_12 months

source_name: Bronchial brushing from patient 9, Main Carina, 12 months


title: Patient 12_MC_0 months

source_name: Bronchial brushing from patient 12, Main Carina, 0 months


title: Patient 6_MC_12 months

source_name: Bronchial brushing from patient 6, Main Carina, 12 months


title: Patient 4_MC_12 months

source_name: Bronchial brushing from patient 4, Main Carina, 12 months


title: Patient 4_MC_24 months

source_name: Bronchial brushing from patient 4, Main Carina, 24 months


title: Patient 11_MC_12 months

source_name: Bronchial brushing from patient 11, Main Carina, 12 months


title: Patient 2_MC_36 months

source_name: Bronchial brushing from patient 2, Main Carina, 36 months


title: Patient 10_MC_12 months

source_name: Bronchial brushing from patient 10, Main Carina, 12 months


title: Patient 13_MC_0 months

source_name: Bronchial brushing from patient 13, Main Carina, 0 months


title: Patient 1_MC_36 months

source_name: Bronchial brushing from patient 1, Main Carina, 36 months


title: Patient 2_LUL_0 months

source_name: Bronchial brushing from patient 2, Left Upper Lobe, 0 months


title: Patient 10_MC_0 months

source_name: Bronchial brushing from patient 10, Main Carina, 0 months


title: Patient 7_MC_0 months

source_name: Bronchial brushing from patient 7, Main Carina, 0 months


title: Patient 3_MC_12 months

source_name: Bronchial brushing from patient 3, Main Carina, 12 months


title: Patient 2_MC_12 months

source_name: Bronchial brushing from patient 2, Main Carina, 12 months


title: Patient 1_MC_24 months

source_name: Bronchial brushing from patient 1, Main Carina, 24 months


title: Patient 8_MC_0 months

source_name: Bronchial brushing from patient 8, Main Carina, 0 months


title: Patient 1_MC_12 months

source_name: Bronchial brushing from patient 1, Main Carina, 12 months


title: Patient 4_MC_0 months

source_name: Bronchial brushing from patient 4, Main Carina, 0 months


title: Patient 18_RUL_0 months

source_name: Bronchial brushing from patient 18, Right Upper Lobe, 0 months


title: Patient 5_MC_0 months

source_name: Bronchial brushing from patient 5, Main Carina, 0 months


title: Patient 2_MC_0 months

source_name: Bronchial brushing from patient 2, Main Carina, 0 months


title: Patient 6_MC_0 months

source_name: Bronchial brushing from patient 6, Main Carina, 0 months


title: Patient 19_RB10_0 months

source_name: Bronchial brushing from patient 19, Right Lower Lobe, 0 months


title: Patient 17_LB10_0 months

source_name: Bronchial brushing from patient 17, Left Lower Lobe, 0 months


title: Patient 19_RUL_0 months

source_name: Bronchial brushing from patient 19, Right Upper Lobe, 0 months


title: Patient 16_RB10_0 months

source_name: Bronchial brushing from patient 16, Right Lower Lobe, 0 months


title: Patient 18_LB10_0 months

source_name: Bronchial brushing from patient 18, Left Lower Lobe, 0 months


title: Patient 16_LUL_0 months

source_name: Bronchial brushing from patient 16, Left Upper Lobe, 0 months


title: Patient 18_LUL_0 months

source_name: Bronchial brushing from patient 18, Left Upper Lobe, 0 months


title: Patient 16_RML_0 months

source_name: Bronchial brushing from patient 16, Right Middle Lobe, 0 months


title: Patient 15_RB10_0 months

source_name: Bronchial brushing from patient 15, Right Lower Lobe, 0 months


title: Patient 1_MC_0 months

source_name: Bronchial brushing from patient 1, Main Carina, 0 months


title: Patient 14_LB10_0 months

source_name: Bronchial brushing from patient 14, Left Lower Lobe, 0 months


title: Patient 16_RUL_0 months

source_name: Bronchial brushing from patient 16, Right Upper Lobe, 0 months


title: Patient 17_RUL_0 months

source_name: Bronchial brushing from patient 17, Right Upper Lobe, 0 months


title: Patient 17_RB10_0 months

source_name: Bronchial brushing from patient 17, Right Lower Lobe, 0 months


title: Patient 15_LB10_0 months

source_name: Bronchial brushing from patient 15, Left Lower Lobe, 0 months


title: Patient 14_RB10_0 months

source_name: Bronchial brushing from patient 14, Right Lower Lobe, 0 months


title: Patient 19_LUL_0 months

source_name: Bronchial brushing from patient 19, Left Upper Lobe, 0 months


title: Patient 13_RB10_0 months

source_name: Bronchial brushing from patient 13, Right Lower Lobe, 0 months


title: Patient 13_RML_0 months

source_name: Bronchial brushing from patient 13, Right Middle Lobe, 0 months


title: Patient 10_RB10_0 months

source_name: Bronchial brushing from patient 10, Right Lower Lobe, 0 months


title: Patient 15_RUL_0 months

source_name: Bronchial brushing from patient 15, Right Upper Lobe, 0 months


title: Patient 14_RUL_0 months

source_name: Bronchial brushing from patient 14, Right Upper Lobe, 0 months


title: Patient 12_RB10_0 months

source_name: Bronchial brushing from patient 12, Right Lower Lobe, 0 months


title: Patient 11_LB10_0 months

source_name: Bronchial brushing from patient 11, Left Lower Lobe, 0 months


title: Patient 11_RB10_0 months

source_name: Bronchial brushing from patient 11, Right Lower Lobe, 0 months


title: Patient 12_LB10_0 months

source_name: Bronchial brushing from patient 12, Left Lower Lobe, 0 months


title: Col_RT-2

city: Wuhan

first: Zhulong

last: Chan

state: Hubei

address: Wuchang District, Moshan

country: China

institute: Wuhan Botanic Garden, Chinese Academy of Sciences

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: All the Affymetrix data files produced with Affymetrix GCOS software (*.CEL files) were analyzed using Bioconductor, a public source software for the analyses of genomic data rooted in the statistical computing environment R. The data were normalized by robust multioiarray normalization of probe-level data with RMA and analyzed using affylmGUI running on R software.

organism: Arabidopsis thaliana

source_name: Col plant, room temperature

label_protocol: One µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Seeds were planted on 1/2 MS plate and incubated at 23/18 degree growth chamber

extract_protocol: Total RNA was extracted and purified using QIAGEN-RNeasy Mini Kit according to guidelines specified by the manufacturer.

value: leaf

value: Col

value: 20-day-old seedlings on plate


title: C24_3h-1

source_name: C24 plant, 4oC for 3h


title: Patient 8_RB10_0 months

source_name: Bronchial brushing from patient 8, Right Lower Lobe, 0 months


title: Patient 8_LB10_0 months

source_name: Bronchial brushing from patient 8, Left Lower Lobe, 0 months


title: Patient 10_RUL_0 months

source_name: Bronchial brushing from patient 10, Right Upper Lobe, 0 months


title: Patient 8_RUL_0 months

source_name: Bronchial brushing from patient 8, Right Upper Lobe, 0 months


title: Col_RT-1


title: C24_RT-1

source_name: C24 plant, room temperature


title: Patient 13_LB10_0 months

source_name: Bronchial brushing from patient 13, Left Lower Lobe, 0 months


title: C24_24h-2

source_name: C24 plant, 4oC for 24h


title: Patient 10_LUL_0 months

source_name: Bronchial brushing from patient 10, Left Upper Lobe, 0 months


title: C24_3h-2


title: Patient 9_RB10_0 months

source_name: Bronchial brushing from patient 9, Right Lower Lobe, 0 months


title: Patient 11_RML_0 months

source_name: Bronchial brushing from patient 11, Right Middle Lobe, 0 months


title: Patient 9_LB10_0 months

source_name: Bronchial brushing from patient 9, Left Lower Lobe, 0 months


title: C24_RT-2


title: Patient 9_LUL_0 months

source_name: Bronchial brushing from patient 9, Left Upper Lobe, 0 months


title: Patient 3_MC_0 months

source_name: Bronchial brushing from patient 3, Main Carina, 0 months


title: Col_24h-1

source_name: Col plant, 4oC for 24h


title: Col_24h-2


title: Patient 7_RUL_0 months

source_name: Bronchial brushing from patient 7, Right Upper Lobe, 0 months


title: Patient 6_RB10_0 months

source_name: Bronchial brushing from patient 6, Right Lower Lobe, 0 months


title: Patient 7_LUL_0 months

source_name: Bronchial brushing from patient 7, Left Upper Lobe, 0 months


title: Patient 7_RML_0 months

source_name: Bronchial brushing from patient 7, Right Middle Lobe, 0 months


title: Tumor #1, GFP+/mCherry+, Double Positive (DP) sorted cells

city: Charlestown

first: David

middle: M

last: Langenau

state: MA

department: Molecular Pathology

institute: Massachusetts General Hospital

description: Gene expression data from FACS sorted ERMS cell subpopulations

hyb_protocol: Washing and staining were performed on the GeneChip® Fluidics Station

scan_protocol: The GeneChip® Scanner 3000 was used for scanning the arrays

data_processing: Samples were imported into D-Chip, normalized against an invariant set, and log2 transformed

organism: Danio rerio

source_name: myf5-GFP+/mylz2-mCherry+ cell subfraction, Tumor #1

label_protocol: Ovation Pico WTA System

growth_protocol: ERMS tumors were transplanted into recipient animals, allowed to engraft, and then isolated at >20 days post-transplantation.

extract_protocol: NuGEN pico label

tag: strain

value: transgenic, CG1-strain (4 times outcrossed)

tag: sample type

value: FACS sorted ERMS cells

tag: disease state

value: embryonal rhabdomyosarcoma


title: Tumor #2, GFP+/mCherry+, Double Positive (DP) sorted cells

source_name: myf5-GFP+/mylz2-mCherry+ cell subfraction, Tumor #2


title: Patient 5_LB10_0 months

source_name: Bronchial brushing from patient 5, Left Lower Lobe, 0 months

tag: tissue

value: Bronchial brushing, normal airway epithelial cells


title: Tumor #2, GFP+/mCherry-negative sorted cells

source_name: myf5-GFP+/mylz2-mCherry negative cell subfraction, Tumor #2


title: Tumor #1, GFP-negative/mCherry+ sorted cells

source_name: myf5-GFP negative/mylz2-mCherry+ cell subfraction, Tumor #1


title: Patient 5_RB10_0 months

source_name: Bronchial brushing from patient 5, Right Lower Lobe, 0 months

value: RLL

value: Adjacent


title: Patient 6_RUL_0 months

source_name: Bronchial brushing from patient 6, Right Upper Lobe, 0 months


title: Tumor #2, GFP-negative/mCherry+ sorted cells

source_name: myf5-GFP negative/mylz2-mCherry+ cell subfraction, Tumor #2


title: Patient 6_LUL_0 months

source_name: Bronchial brushing from patient 6, Left Upper Lobe, 0 months

value: Non-adjacent


title: Patient 4_RUL_0 months

source_name: Bronchial brushing from patient 4, Right Upper Lobe, 0 months


title: Patient 5_RML_0 months

source_name: Bronchial brushing from patient 5, Right Middle Lobe, 0 months


title: Tumor #2, GFP-negative/mCherry-negative, Double Negative (DN) sorted cells

source_name: myf5-GFP negative/mylz2-mCherry negative cell subfraction, Tumor #2


title: Patient 3_RB10_0 months

source_name: Bronchial brushing from patient 3, Right Lower Lobe, 0 months


title: Tumor #1, GFP-negative/mCherry-negative, Double Negative (DN) sorted cells

source_name: myf5-GFP negative/mylz2-mCherry negative cell subfraction, Tumor #1


title: Valencia Symptomatic Juice Vesicle Rep4

city: Lake Alfred

first: Hui-Ling

last: Liao

state: Florida

address: 700 Experiment Station Road

department: Horticulture sciences

institute: University of Florida

description:
Burns_8026_SJV4
Gene expression data from fruit samples harvested from HLB disease trees

hyb_protocol: Samples were hybridized with rotation at 45°C for 16 hours to the Affymetrix GeneChip Citrus Genome Array.The arrays were washed and stained with the reagents supplied in GeneChip® Hybridization Wash and Stain kit (Affymetrix, Inc) on an Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned with a GeneChip® 7G Scanner (Affymetrix, Inc).

data_processing: Data were processed using RMA normalization Approach. The background correction for probe intensities was based upon the lowess normalizaion method. Limma package (Smyth GK et al. Bioinformatics, 2005, 2067-2075), R and BioConductor (http://www.bioconductor.org/) were used for statistic analysis.The linear models were firstly used to assess differential expression, then an empirical Bayes method was used to moderate the statndard errors.

organism: Citrus sinensis

source_name: Valencia Symptomatic Juice Vesicle

label_protocol: All microarray sample preparation used the GeneChip 3'IVT Express kit (Affymetrix, Inc). cDNA was synthesized from 250 ng of total RNA and template for in vitro transcription (IVT) during which a biotin-modified nucleotide was incorporated.The biotin-labeled aRNA was then purified and fragmented.

growth_protocol: sample collection : Fruit harvested from 18-year-old Citrus sinensis cv. 'Hamlin'and 'Valencia'citrus trees on 'Swingle'rootstock in groves located in Lake Placid, FL were used for microarray analysis. Healthy fruit (H) were collected from qRT-PCR-negative trees.  Symptomatic and asymptomatic fruit (S and AS, respectively) were selected from symptomatic trees (qRT-PCR-positive).

extract_protocol: Total RNA from plant tissues was extracted and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA), and DNA contamination was removed using DNase treatment (Qiagen).RNA concentration was determined on a NanoDrop Spectrophotometer (NanoDrop Technologies, Inc) and sample quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

tag: cultivar

value: Valencia

tag: rootstock

value: Swingle

value: wild-type

tag: age

tag: fruit stage

value: Mature

value: Juice Vesicle


title: Valencia Asymptomatic Juice Vesicle Rep4

description:
Burns_8027_ASJV4
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Asymptomatic Juice Vesicle

tag: genotype


title: Patient 4_RML_0 months

source_name: Bronchial brushing from patient 4, Right Middle Lobe, 0 months


title: Valencia Healthy Control Juice Vesicle Rep4

description:
Burns_8025_HJV4
Gene expression data from fruit samples harvested from healthy trees

source_name: Valencia Healthy Control Juice Vesicle


title: Patient 3_LB10_0 months

source_name: Bronchial brushing from patient 3, Left Lower Lobe, 0 months

value: RUL

value: Contralateral


title: Tumor #1, GFP+/mCherry-negative sorted cells

source_name: myf5-GFP+/mylz2-mCherry negative cell subfraction, Tumor #1


title: Valencia Asymptomatic Peel (Flavedo) Rep4

description:
Burns_8021_ASP4
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Asymptomatic Peel (Flavedo)

value: Peel (Flavedo)


title: Valencia Asymptomatic Vascular Core Rep4

description:
Burns_8024_ASC4
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Asymptomatic Vascular Core

value: Vascular core


title: Valencia Symptomatic Vascular Core Rep4

description:
Burns_8023_SC4
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Symptomatic Vascular Core


title: Valencia Healthy Control Vascular Core Rep4

description:
Burns_8022_HC4
Gene expression data from fruit samples harvested from healthy trees

source_name: Valencia Healthy Control Vascular Core


title: Patient 4_LUL_0 months

source_name: Bronchial brushing from patient 4, Left Upper Lobe, 0 months


title: Valencia Symptomatic Peel (Flavedo) Rep4

description:
Burns_8020_SP4
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Symptomatic Peel (Flavedo)


title: Patient 2_RLL_0 months

source_name: Bronchial brushing from patient 2, Right Lower Lobe, 0 months


title: Patient 3_RML_0 months

source_name: Bronchial brushing from patient 3, Right Middle Lobe, 0 months


title: Patient 1_LB10_0 months

source_name: Bronchial brushing from patient 1, Left Lower Lobe, 0 months

value: LUL


title: Valencia Asymptomatic Juice Vesicle Rep3

description:
Burns_8018_ASJV3
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 1_RML_0 months

source_name: Bronchial brushing from patient 1, Right Middle Lobe, 0 months


title: Patient 2_LLL_0 months

source_name: Bronchial brushing from patient 2, Left Lower Lobe, 0 months


title: Patient 14_RB10_24 months

source_name: Bronchial brushing from patient 14, Right Lower Lobe, 24 months


title: Patient 14_RML_12 months

source_name: Bronchial brushing from patient 14, Right Middle Lobe, 12 months


title: Valencia Symptomatic Vascular Core Rep3

description:
Burns_8014_SC3
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 14_LB10_12 months

source_name: Bronchial brushing from patient 14, Left Lower Lobe, 12 months


title: Valencia Asymptomatic Vascular Core Rep3

description:
Burns_8015_ASC3
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 14_LB10_24 months

source_name: Bronchial brushing from patient 14, Left Lower Lobe, 24 months


title: Valencia Symptomatic Juice Vesicle Rep3

description:
Burns_8017_SJV3
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Symptomatic Juice Vesicle


title: Patient 14_RML_24 months

source_name: Bronchial brushing from patient 14, Right Middle Lobe, 24 months


title: Valencia Asymptomatic Peel (Flavedo) Rep3

description:
Burns_8012_ASP3
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Asymptomatic Peel (Flavedo)


title: Valencia Symptomatic Juice Vesicle Rep2

description:
Burns_8008_SJV2
Gene expression data from fruit samples harvested from HLB disease trees


title: Valencia Symptomatic Peel (Flavedo) Rep3

description:
Burns_8011_SP3
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 14_RB10_12 months

source_name: Bronchial brushing from patient 14, Right Lower Lobe, 12 months


title: Valencia Healthy Control Peel (Flavedo) Rep4

description:
Burns_8019_HP4
Gene expression data from fruit samples harvested from healthy trees

source_name: Valencia Healthy Control Peel (Flavedo)


title: Valencia Healthy Control Peel (Flavedo) Rep3

description:
Burns_8010_HP3
Gene expression data from fruit samples harvested from healthy trees


title: Patient 1_RUL_0 months

source_name: Bronchial brushing from patient 1, Right Upper Lobe, 0 months


title: Valencia Healthy Control Vascular Core Rep3

description:
Burns_8013_HC3
Gene expression data from fruit samples harvested from healthy trees

source_name: Valencia Healthy Control Vascular Core


title: Valencia Asymptomatic Juice Vesicle Rep2

description:
Burns_8009_ASJV2
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Asymptomatic Juice Vesicle


title: Valencia Healthy Control Juice Vesicle Rep3

description:
Burns_8016_HJV3
Gene expression data from fruit samples harvested from healthy trees

source_name: Valencia Healthy Control Juice Vesicle


title: Patient 14_LUL_24 months

source_name: Bronchial brushing from patient 14, Left Upper Lobe, 24 months


title: Patient 14_RUL_12 months

source_name: Bronchial brushing from patient 14, Right Upper Lobe, 12 months


title: Patient 14_MC_24 months

source_name: Bronchial brushing from patient 14, Main Carina, 24 months

value: Main carina


title: Valencia Asymptomatic Vascular Core Rep2

description:
Burns_8006_ASC2
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Asymptomatic Vascular Core


title: Valencia Healthy Control Juice Vesicle Rep2

description:
Burns_8007_HJV2
Gene expression data from fruit samples harvested from healthy trees


title: Patient 14_RUL_24 months

source_name: Bronchial brushing from patient 14, Right Upper Lobe, 24 months


title: Patient 14_MC_12 months

source_name: Bronchial brushing from patient 14, Main Carina, 12 months


title: Valencia Asymptomatic Peel (Flavedo) Rep2

description:
Burns_8003_ASP2
Gene expression data from fruit samples harvested from HLB disease trees


title: Valencia Healthy Control Vascular Core Rep2

description:
Burns_8004_HC2
Gene expression data from fruit samples harvested from healthy trees


title: Patient 11_LB10_24 months

source_name: Bronchial brushing from patient 11, Left Lower Lobe, 24 months


title: C24_24h-1

source_name: C24 plant, 4oC for 24h

value: leaf

value: 20-day-old seedlings on plate


title: Valencia Symptomatic Vascular Core Rep2

description:
Burns_8005_SC2
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Symptomatic Vascular Core


title: Patient 11_RB10_24 months

source_name: Bronchial brushing from patient 11, Right Lower Lobe, 24 months

value: Bronchial brushing, normal airway epithelial cells


title: Valencia Asymptomatic Juice Vesicle Rep1

description:
Burns_8000_ASJV1
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 11_RML_24 months

source_name: Bronchial brushing from patient 11, Right Middle Lobe, 24 months


title: Valencia Asymptomatic Vascular Core Rep1

description:
Burns_7997_ASC1
Gene expression data from fruit samples harvested from HLB disease trees


title: Valencia Healthy Control Peel (Flavedo) Rep2

description:
Burns_8001_HP2
Gene expression data from fruit samples harvested from healthy trees


title: Patient 11_RB10_12 months

source_name: Bronchial brushing from patient 11, Right Lower Lobe, 12 months


title: Patient 11_RML_12 months

source_name: Bronchial brushing from patient 11, Right Middle Lobe, 12 months


title: Valencia Symptomatic Vascular Core Rep1

description:
Burns_7996_SC1
Gene expression data from fruit samples harvested from HLB disease trees


title: Valencia Healthy Control Juice Vesicle Rep1

description:
Burns_7998_HJV1
Gene expression data from fruit samples harvested from healthy trees


title: Valencia Symptomatic Peel (Flavedo) Rep2

description:
Burns_8002_SP2
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Symptomatic Peel (Flavedo)


title: Valencia Healthy Control Vascular Core Rep1

description:
Burns_7995_HC1
Gene expression data from fruit samples harvested from healthy trees

source_name: Valencia Healthy Control Vascular Core


title: Patient 11_LUL_24 months

source_name: Bronchial brushing from patient 11, Left Upper Lobe, 24 months


title: Patient 11_LUL_12 months

source_name: Bronchial brushing from patient 11, Left Upper Lobe, 12 months


title: Patient 11_RUL_24 months

source_name: Bronchial brushing from patient 11, Right Upper Lobe, 24 months


title: Valencia Asymptomatic Peel (Flavedo) Rep1

description:
Burns_7994_ASP1
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Asymptomatic Peel (Flavedo)


title: Patient 11_LB10_12 months

source_name: Bronchial brushing from patient 11, Left Lower Lobe, 12 months


title: Valencia Symptomatic Juice Vesicle Rep1

description:
Burns_7999_SJV1
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Valencia Symptomatic Juice Vesicle


title: Patient 11_MC_24 months

source_name: Bronchial brushing from patient 11, Main Carina, 24 months


title: Patient 19_LB10_12 months

source_name: Bronchial brushing from patient 19, Left Lower Lobe, 12 months


title: Patient 19_RB10_24 months

source_name: Bronchial brushing from patient 19, Right Lower Lobe, 24 months


title: Valencia Healthy Control Peel (Flavedo) Rep1

description:
Burns_7992_HP1
Gene expression data from fruit samples harvested from healthy trees

source_name: Valencia Healthy Control Peel (Flavedo)


title: Patient 19_RB10_12 months

source_name: Bronchial brushing from patient 19, Right Lower Lobe, 12 months


title: Valencia Symptomatic Peel (Flavedo) Rep1

description:
Burns_7993_SP1
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 11_RUL_12 months

source_name: Bronchial brushing from patient 11, Right Upper Lobe, 12 months


title: Patient 19_RML_24 months

source_name: Bronchial brushing from patient 19, Right Middle Lobe, 24 months


title: Hamlin Symptomatic Seed Rep3

description:
7682_SS3_Burns
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Hamlin Symptomatic Seed

value: Hamlin

value: Seed


title: Hamlin Symptomatic Seed Rep4

description:
7683_SS4_Burns
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 19_LB10_24 months

source_name: Bronchial brushing from patient 19, Left Lower Lobe, 24 months

value: Non-adjacent


title: Hamlin Symptomatic Seed Rep1

description:
7680_SS1_Burns
Gene expression data from fruit samples harvested from HLB disease trees


title: Hamlin Healthy Control Peel (Flavedo) Rep4

description:
7679_CP4_Burns
Gene expression data from fruit samples harvested from healthy trees

source_name: Hamlin Healthy Control Peel (Flavedo)


title: Patient 19_LUL_24 months

source_name: Bronchial brushing from patient 19, Left Upper Lobe, 24 months

value: Adjacent


title: Patient 19_RML_12 months

source_name: Bronchial brushing from patient 19, Right Middle Lobe, 12 months


title: Hamlin Healthy Control Peel (Flavedo) Rep3

description:
7678_CP3_Burns
Gene expression data from fruit samples harvested from healthy trees

value: Swingle


title: Hamlin Symptomatic Seed Rep2

description:
7681_SS2_Burns
Gene expression data from fruit samples harvested from HLB disease trees

value: wild-type


title: Hamlin Healthy Control Peel (Flavedo) Rep2

description:
7677_CP2_Burns
Gene expression data from fruit samples harvested from healthy trees

value: Mature


title: Hamlin Healthy Control Peel (Flavedo) Rep1

description:
7676_CP1_Burns
Gene expression data from fruit samples harvested from healthy trees


title: Hamlin Symptomatic Peel (Flavedo) Rep4

description:
7675_SP4_Burns
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Hamlin Symptomatic Peel (Flavedo)


title: Patient 14_LUL_12 months

source_name: Bronchial brushing from patient 14, Left Upper Lobe, 12 months


title: Patient 19_LUL_12 months

source_name: Bronchial brushing from patient 19, Left Upper Lobe, 12 months


title: Hamlin Symptomatic Peel (Flavedo) Rep2

description:
7673_SP2_Burns
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 19_RUL_24 months

source_name: Bronchial brushing from patient 19, Right Upper Lobe, 24 months


title: Hamlin Healthy Control Seed Rep4

description:
7671_CS4_Burns
Gene expression data from fruit samples harvested from healthy trees

source_name: Hamlin Healthy Control Seed


title: Patient 19_RUL_12 months

source_name: Bronchial brushing from patient 19, Right Upper Lobe, 12 months


title: Hamlin Symptomatic Peel (Flavedo) Rep1

description:
7672_SP1_Burns
Gene expression data from fruit samples harvested from HLB disease trees


title: Hamlin Symptomatic Peel (Flavedo) Rep3

description:
7674_SP3_Burns
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 18_LB10_14 months

source_name: Bronchial brushing from patient 18, Left Lower Lobe, 14 months

value: RML


title: Patient 18_RB10_24 months

source_name: Bronchial brushing from patient 18, Right Lower Lobe, 24 months


title: Patient 18_LB10_24 months

source_name: Bronchial brushing from patient 18, Left Lower Lobe, 24 months


title: Hamlin Healthy Control Seed Rep3

description:
7670_CS3_Burns
Gene expression data from fruit samples harvested from healthy trees


title: Hamlin Healthy Control Seed Rep2

description:
7669_CS2_Burns
Gene expression data from fruit samples harvested from healthy trees


title: Patient 18_RB10_12 months

source_name: Bronchial brushing from patient 18, Right Lower Lobe, 12 months


title: Hamlin Healthy Control Juice Vesicle Rep4

description:
7654_CJV4_BURNS
Gene expression data from fruit samples harvested from healthy trees

source_name: Hamlin Healthy Control Juice Vesicle

value: Juice Vesicle


title: Patient 19_MC_24 months

source_name: Bronchial brushing from patient 19, Main Carina, 24 months


title: Patient 19_MC_12 months

source_name: Bronchial brushing from patient 19, Main Carina, 12 months


title: Hamlin Healthy Control Juice Vesicle Rep1

description:
7651_CJV1_BURNS
Gene expression data from fruit samples harvested from healthy trees


title: Hamlin Symptomatic Juice Vesicle Rep4

description:
7650_SJV4_BURNS
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Hamlin Symptomatic Juice Vesicle


title: Hamlin Healthy Control Juice Vesicle Rep3

description:
7653_CJV3_BURNS
Gene expression data from fruit samples harvested from healthy trees


title: Patient 18_LUL_12 months

source_name: Bronchial brushing from patient 18, Left Upper Lobe, 12 months

value: Contralateral


title: Patient 18_LUL_24 months

source_name: Bronchial brushing from patient 18, Left Upper Lobe, 24 months


title: Hamlin Symptomatic Juice Vesicle Rep2

description:
7648_SJV2_BURNS
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 18_RUL_24 months

source_name: Bronchial brushing from patient 18, Right Upper Lobe, 24 months


title: Hamlin Healthy Control Seed Rep1

description:
7668_CS1_Burns
Gene expression data from fruit samples harvested from healthy trees


title: Hamlin Symptomatic Juice Vesicle Rep3

description:
7649_SJV3_BURNS
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 18_RML_24 months

source_name: Bronchial brushing from patient 18, Right Middle Lobe, 24 months


title: Patient 18_RML_12 months

source_name: Bronchial brushing from patient 18, Right Middle Lobe, 12 months


title: Patient 18_RUL_12 months

source_name: Bronchial brushing from patient 18, Right Upper Lobe, 12 months


title: Patient 18_MC_24 months

source_name: Bronchial brushing from patient 18, Main Carina, 24 months


title: Patient 18_MC_12 months

source_name: Bronchial brushing from patient 18, Main Carina, 12 months


title: Hamlin Symptomatic Juice Vesicle Rep1

description:
7647_SJV1_BURNS
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 17_LB10_12 months

source_name: Bronchial brushing from patient 17, Left Lower Lobe, 12 months

value: LLL


title: Patient 17_LB10_24 months

source_name: Bronchial brushing from patient 17, Left Lower Lobe, 24 months


title: Hamlin Symptomatic Vascular Core Rep3

description:
7641_SC3_BURNS
Gene expression data from fruit samples harvested from HLB disease trees

source_name: Hamlin Symptomatic Vascular Core

value: Vascular core


title: Patient 17_RB10_12 months

source_name: Bronchial brushing from patient 17, Right Lower Lobe, 12 months


title: Patient 17_RB10_24 months

source_name: Bronchial brushing from patient 17, Right Lower Lobe, 24 months


title: Hamlin Healthy control Vascular Core Rep1

description:
7643_CC1_BURNS
Gene expression data from fruit samples harvested from healthy trees

source_name: Hamlin Healthy control Vascular Core


title: Hamlin Healthy control Vascular Core Rep3

description:
7645_CC3_BURNS
Gene expression data from fruit samples harvested from healthy trees


title: Hamlin Symptomatic Vascular Core Rep2

description:
7640_SC2_BURNS
Gene expression data from fruit samples harvested from HLB disease trees


title: Hamlin Healthy control Vascular Core Rep4

description:
7646_CC4_BURNS
Gene expression data from fruit samples harvested from healthy trees


title: Patient 17_RML_12 months

source_name: Bronchial brushing from patient 17, Right Middle Lobe, 12 months


title: Hamlin Symptomatic Vascular Core Rep1

description:
7639_SC1_BURNS
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 17_LUL_24 months

source_name: Bronchial brushing from patient 17, Left Upper Lobe, 24 months


title: Hamlin Symptomatic Vascular Core Rep4

description:
7642_SC4_BURNS
Gene expression data from fruit samples harvested from HLB disease trees


title: Patient 17_RUL_24 months

source_name: Bronchial brushing from patient 17, Right Upper Lobe, 24 months


title: Hamlin Healthy control Vascular Core Rep2

description:
7644_CC2_BURNS
Gene expression data from fruit samples harvested from healthy trees


title: Patient 17_RML_24 months

source_name: Bronchial brushing from patient 17, Right Middle Lobe, 24 months


title: Microglia at 24 months biological replicate 1

city: Rockville

first: Radu

last: Cojocaru

state: MD

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

hyb_protocol: Following fragmentation and labelling, 5 ug of cDNA were hybridized at 45C for 21 hours.  Arrays were washed using Affymetrix fluidics stations and then scanned in an Affymetrix GeneChip Scanner 3000 7G.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using GeneSpring 11.5. RMA was used for normalization (median polish was used for summarization).

source_name: Microglia at 24 months

label_protocol: Biotinylated cDNA were prepared for the Affymetrix GeneChip Mouse Exon 1.0 ST Arrays using Nugen WT-Ovation One-Direct RNA Amplification System and Encore Biotin Module starting with less than 5 ng of total RNA.

extract_protocol: extraction protocol

tag: genotype/variation

value: wild type

value: 24 months

value: Flow sorted Microglia


title: Microglia at 24 months biological replicate 4

tag: cell type


title: Patient 16_LB10_24 months

source_name: Bronchial brushing from patient 16, Left Lower Lobe, 24 months


title: Microglia at 24 months biological replicate 2


title: Patient 17_LUL_12 months

source_name: Bronchial brushing from patient 17, Left Upper Lobe, 12 months


title: Microglia at 24 months biological replicate 3


title: Microglia at 18 months biological replicate 3

source_name: Microglia at 18 months

value: 18 months


title: Microglia at 18 months biological replicate 4


title: Patient 17_RUL_12 months

source_name: Bronchial brushing from patient 17, Right Upper Lobe, 12 months

value: Bronchial brushing, normal airway epithelial cells


title: Microglia at 18 months biological replicate 2


title: Patient 17_MC_24 months

source_name: Bronchial brushing from patient 17, Main Carina, 24 months

value: Main carina


title: Patient 17_MC_12 months

source_name: Bronchial brushing from patient 17, Main Carina, 12 months


title: Microglia at 18 months biological replicate 1


title: Patient 16_LB10_12 months

source_name: Bronchial brushing from patient 16, Left Lower Lobe, 12 months


title: Microglia at 12 months biological replicate 4

source_name: Microglia at 12 months

value: 12 months


title: Microglia at 3 months biological replicate 4

source_name: Microglia at 3 months

value: 3 months


title: Microglia at 12 months biological replicate 1


title: Microglia at 12 months biological replicate 3


title: Microglia at 12 months biological replicate 2


title: Microglia at 3 months biological replicate 3


title: Patient 16_LUL_12 months

source_name: Bronchial brushing from patient 16, Left Upper Lobe, 12 months

value: Non-adjacent


title: Patient 16_RML_12 months

source_name: Bronchial brushing from patient 16, Right Middle Lobe, 12 months


title: Microglia at 3 months biological replicate 2


title: Patient 16_RB10_24 months

source_name: Bronchial brushing from patient 16, Right Lower Lobe, 24 months


title: Patient 16_RML_24 months

source_name: Bronchial brushing from patient 16, Right Middle Lobe, 24 months


title: Patient 16_RUL_12 months

source_name: Bronchial brushing from patient 16, Right Upper Lobe, 12 months


title: ompR mutant in LB, replicate 1

type: mixed

city: norwich

first: Gary

last: Rowley

address: Norwich Research Park

department: School of Biological Sciences

institute: University of East Anglia

hyb_protocol: Slides were blocked with DCE according to the protocol in PMID 11266573. For hybridisation and washing protocols, see www.ifr.ac.uk/safety/Microarrays/default.html#protocols.

scan_protocol: Scanned on a GenePix 4000A scanner (Axon Instruments, Inc.). Images were quantified using Axon GenePix Pro7.

data_processing: Spots showing a reference signal lower than background plus two standard deviations or obvious blemishes were excluded from subsequent analyses. Local background was subtracted from spot signals, and fluorescence ratios were calculated. To compensate for unequal dye incorporation or any effect of the amount of template, data centering was performed by bringing the median natural logarithm of the ratios for each group of spots printed by the same pin to zero.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: ompR mutant in LB

label_protocol: Total RNA (10 μg) was converted to cDNA and fluorescently labelled by random priming to incorporate Cy5-dCTP (Amersham) using reverse transcriptase (StrataScript, Stratagene).

growth_protocol: The media was inoculated with 1/1000 of an overnight culture and grown to OD600=0.3 at 37 C upon 200rpm agitation.

extract_protocol: Total RNA was extracted using the Promega SV total RNA extraction kit following the manufacturer's instructions.

treatment_protocol: The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior to centrifugation.

value: ompR mutant

molecule: genomic DNA

source_name: Wild type in LB

label_protocol: Genomic DNA was labeled with Cy3.

extract_protocol: Genomic DNA was extracted.


title: Microglia at 3 months biological replicate 1


title: Wild type in LB, replicate 4


title: ompR mutant in LB, replicate 2


title: ompR mutant in LB, replicate 4


title: ompR mutant in LB, replicate 3


title: Patient 16_RB10_12 months

source_name: Bronchial brushing from patient 16, Right Lower Lobe, 12 months


title: Patient 16_RUL_24 months

source_name: Bronchial brushing from patient 16, Right Upper Lobe, 24 months


title: Patient 16_MC_24 months

source_name: Bronchial brushing from patient 16, Main Carina, 24 months


title: Patient 16_MC_12 months

source_name: Bronchial brushing from patient 16, Main Carina, 12 months


title: Patient 16_LUL_24 months

source_name: Bronchial brushing from patient 16, Left Upper Lobe, 24 months


title: Patient 15_LB10_24 months

source_name: Bronchial brushing from patient 15, Left Lower Lobe, 24 months

value: RLL


title: Patient 15_LB10_36 months

source_name: Bronchial brushing from patient 15, Left Lower Lobe, 36 months


title: Patient 15_LB10_12 months

source_name: Bronchial brushing from patient 15, Left Lower Lobe, 12 months


title: Patient 15_RB10_24 months

source_name: Bronchial brushing from patient 15, Right Lower Lobe, 24 months

value: Adjacent


title: Wild type in LB, replicate 3


title: Patient 15_RB10_36 months

source_name: Bronchial brushing from patient 15, Right Lower Lobe, 36 months


title: Wild type in LB, replicate 1


title: Patient 15_RB10_12 months

source_name: Bronchial brushing from patient 15, Right Lower Lobe, 12 months


title: Wild type in LB, replicate 2


title: Patient 15_RUL_36 months

source_name: Bronchial brushing from patient 15, Right Upper Lobe, 36 months


title: Patient 15_RUL_24 months

source_name: Bronchial brushing from patient 15, Right Upper Lobe, 24 months


title: Patient 15_RML_24 months

source_name: Bronchial brushing from patient 15, Right Middle Lobe, 24 months


title: Patient 15_RML_12 months

source_name: Bronchial brushing from patient 15, Right Middle Lobe, 12 months


title: Patient 15_MC_12 months

source_name: Bronchial brushing from patient 15, Main Carina, 12 months


title: Patient 15_LUL_12 months

source_name: Bronchial brushing from patient 15, Left Upper Lobe, 12 months


title: Patient 15_MC_36 months

source_name: Bronchial brushing from patient 15, Main Carina, 36 months


title: Patient 15_LUL_24 months

source_name: Bronchial brushing from patient 15, Left Upper Lobe, 24 months


title: Patient 15_MC_24 months

source_name: Bronchial brushing from patient 15, Main Carina, 24 months


title: Patient 15_RUL_12 months

source_name: Bronchial brushing from patient 15, Right Upper Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266051_H]

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description: F2 hybrid

hyb_protocol: A total of 750 ng biotinylated cRNA was hybridized in accordance with standard Illumina protocols.

scan_protocol: Standard Illumina scan protocol

data_processing: Illumina’s default pre-processing steps were performed using beadarray. A variance-stabilization transformation was applied to the summarized data and the resulting data was quantile normalized.

source_name: left ventricle_free-wall

label_protocol: Synthesis, amplification and purification of anti-sense RNA was performed using the Illumina TotalPrep RNA Amplification Kit (Ambion) following the Illumina Sentrix Array Matrix expression protocol.

growth_protocol: All mice were supplied with the same SDS diet (SDS CRM(E) PL; Special Diets Services, UK) and water ad libitum and maintained on a 12-hour light/dark cycle in a temperature and humidity controlled environment.

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy mini kit. Total RNA yield and purity (260nm:280nm) were determined spectrophotometrically. The integrity (RIN>9.0) of the re-suspended total RNA was determined using the RNA Nano Chip Kit on the Bioanalyzer 2100 and the 2100 Expert software (Agilent).

value: cardiac

tag: background strain


title: heart_Scn5a-1798insD/+ mutant [4700266053_F]

description: F2 hybrid


title: Patient 15_RML_36 months

source_name: Bronchial brushing from patient 15, Right Middle Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266053_H]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266053_A]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266051_F]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266051_G]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266053_E]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266053_C]

description: F2 hybrid


title: Patient 15_LUL_36 months

source_name: Bronchial brushing from patient 15, Left Upper Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266053_B]

description: F2 hybrid


title: Patient 13_LB10_24 months

source_name: Bronchial brushing from patient 13, Left Lower Lobe, 24 months

value: LUL


title: heart_Scn5a-1798insD/+ mutant [4700266051_E]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266051_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266051_B]

description: F2 hybrid


title: Patient 13_LB10_12 months

source_name: Bronchial brushing from patient 13, Left Lower Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266050_G]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266051_C]

description: F2 hybrid


title: Patient 13_LB10_36 months

source_name: Bronchial brushing from patient 13, Left Lower Lobe, 36 months


title: Patient 13_Mainstem_12 months

source_name: Bronchial brushing from patient 13, Mainstem, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266053_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266050_H]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266051_A]

description: F2 hybrid


title: Patient 13_RB10_24 months

source_name: Bronchial brushing from patient 13, Right Lower Lobe, 24 months

value: Contralateral


title: Patient 13_RML_36 months

source_name: Bronchial brushing from patient 13, Right Middle Lobe, 36 months


title: Patient 13_RML_12 months

source_name: Bronchial brushing from patient 13, Right Middle Lobe, 12 months


title: Patient 13_RB10_12 months

source_name: Bronchial brushing from patient 13, Right Lower Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266050_E]

description: F2 hybrid


title: Patient 13_RB10_36 months

source_name: Bronchial brushing from patient 13, Right Lower Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266050_F]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266050_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266050_C]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266050_B]

description: F2 hybrid


title: Patient 13_RUL_36 months

source_name: Bronchial brushing from patient 13, Right Upper Lobe, 36 months


title: Patient 13_LUL_24 months

source_name: Bronchial brushing from patient 13, Left Upper Lobe, 24 months


title: Patient 13_RML_24 months

source_name: Bronchial brushing from patient 13, Right Middle Lobe, 24 months


title: Patient 13_LUL_36 months

source_name: Bronchial brushing from patient 13, Left Upper Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266048_H]

description: F2 hybrid


title: Patient 13_RUL_12 months

source_name: Bronchial brushing from patient 13, Right Upper Lobe, 12 months


title: Patient 13_RUL_24 months

source_name: Bronchial brushing from patient 13, Right Upper Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266050_A]

description: F2 hybrid

source_name: left ventricle_free-wall


title: Patient 12_Mainstem_24 months

source_name: Bronchial brushing from patient 12, Mainstem, 24 months

value: RUL


title: Patient 12_LB10_12 months

source_name: Bronchial brushing from patient 12, Left Lower Lobe, 12 months


title: Patient 13_MC_36 months

source_name: Bronchial brushing from patient 13, Main Carina, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266048_F]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266048_B]

description: F2 hybrid


title: Patient 12_LB10_36 months

source_name: Bronchial brushing from patient 12, Left Lower Lobe, 36 months


title: Patient 12_Mid trachea_24 months

source_name: Bronchial brushing from patient 12, Mid trachea, 24 months


title: Patient 12_LB10_24 months

source_name: Bronchial brushing from patient 12, Left Lower Lobe, 24 months


title: Patient 13_MC_24 months

source_name: Bronchial brushing from patient 13, Main Carina, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266048_C]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266048_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266048_G]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266048_E]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266047_F]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266053_G]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266047_H]

description: F2 hybrid


title: Patient 12_RB10_36 months

source_name: Bronchial brushing from patient 12, Right Lower Lobe, 36 months


title: Patient 12_RB10_24 months

source_name: Bronchial brushing from patient 12, Right Lower Lobe, 24 months


title: Patient 12_RML_36 months

source_name: Bronchial brushing from patient 12, Right Middle Lobe, 36 months


title: Patient 12_RB10_12 months

source_name: Bronchial brushing from patient 12, Right Lower Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266047_E]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266047_G]

description: F2 hybrid


title: Patient 12_LUL_36 months

source_name: Bronchial brushing from patient 12, Left Upper Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266047_A]

description: F2 hybrid


title: Patient 12_RML_24 months

source_name: Bronchial brushing from patient 12, Right Middle Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266047_B]

description: F2 hybrid


title: Patient 12_LUL_24 months

source_name: Bronchial brushing from patient 12, Left Upper Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266047_C]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266047_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266042_H]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266042_G]

description: F2 hybrid


title: Patient 12_RML_12 months

source_name: Bronchial brushing from patient 12, Right Middle Lobe, 12 months


title: Patient 12_LUL_12 months

source_name: Bronchial brushing from patient 12, Left Upper Lobe, 12 months


title: Patient 12_MC_36 months

source_name: Bronchial brushing from patient 12, Main Carina, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266042_F]

description: F2 hybrid

source_name: left ventricle_free-wall


title: heart_Scn5a-1798insD/+ mutant [4700266042_E]

description: F2 hybrid


title: Patient 10_LB10_12 months

source_name: Bronchial brushing from patient 10, Left Lower Lobe, 12 months


title: Patient 12_MC_24 months

source_name: Bronchial brushing from patient 12, Main Carina, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266042_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266041_G]

description: F2 hybrid


title: Patient 10_LB10_36 months

source_name: Bronchial brushing from patient 10, Left Lower Lobe, 36 months


title: Patient 10_LB10_24 months

source_name: Bronchial brushing from patient 10, Left Lower Lobe, 24 months


title: Patient 12_RUL_36 months

source_name: Bronchial brushing from patient 12, Right Upper Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266042_A]

description: F2 hybrid


title: Patient 10_RML_24 months

source_name: Bronchial brushing from patient 10, Right Middle Lobe, 24 months


title: Patient 10_RB10_36 months

source_name: Bronchial brushing from patient 10, Right Lower Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266041_H]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266042_C]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266042_B]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266041_B]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266041_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266041_C]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266041_F]

description: F2 hybrid


title: Patient 10_RB10_12 months

source_name: Bronchial brushing from patient 10, Right Lower Lobe, 12 months


title: Patient 10_RML_12 months

source_name: Bronchial brushing from patient 10, Right Middle Lobe, 12 months


title: Patient 10_LUL_24 months

source_name: Bronchial brushing from patient 10, Left Upper Lobe, 24 months


title: Patient 10_RB10_24 months

source_name: Bronchial brushing from patient 10, Right Lower Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266041_E]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266041_A]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266036_F]

description: F2 hybrid


title: Patient 10_RUL_36 months

source_name: Bronchial brushing from patient 10, Right Upper Lobe, 36 months


title: Patient 10_MC_24 months

source_name: Bronchial brushing from patient 10, Main Carina, 24 months


title: Patient 10_LUL_12 months

source_name: Bronchial brushing from patient 10, Left Upper Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266036_G]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266036_D]

description: F2 hybrid


title: Patient 10_MC_36 months

source_name: Bronchial brushing from patient 10, Main Carina, 36 months


title: Patient 10_LUL_36 months

source_name: Bronchial brushing from patient 10, Left Upper Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266036_E]

description: F2 hybrid

source_name: left ventricle_free-wall


title: heart_Scn5a-1798insD/+ mutant [4700266035_G]

description: F2 hybrid


title: Patient 9_LB10_12 months

source_name: Bronchial brushing from patient 9, Left Lower Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266035_H]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266036_H]

description: F2 hybrid


title: Patient 10_RUL_12 months

source_name: Bronchial brushing from patient 10, Right Upper Lobe, 12 months


title: Patient 10_RUL_24 months

source_name: Bronchial brushing from patient 10, Right Upper Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266035_F]

description: F2 hybrid


title: Patient 9_LB10_24 months

source_name: Bronchial brushing from patient 9, Left Lower Lobe, 24 months


title: Patient 9_LB10_36 months

source_name: Bronchial brushing from patient 9, Left Lower Lobe, 36 months


title: Patient 9_RB10_24 months

source_name: Bronchial brushing from patient 9, Right Lower Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266036_B]

description: F2 hybrid


title: Patient 9_RB10_36 months

source_name: Bronchial brushing from patient 9, Right Lower Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266035_E]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266035_C]

description: F2 hybrid


title: Patient 9_RML_36 months

source_name: Bronchial brushing from patient 9, Right Middle Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266035_D]

description: F2 hybrid


title: Patient 9_RML_24 months

source_name: Bronchial brushing from patient 9, Right Middle Lobe, 24 months


title: Patient 9_RB10_12 months

source_name: Bronchial brushing from patient 9, Right Lower Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266048_A]

description: F2 hybrid


title: Patient 9_RML_12 months

source_name: Bronchial brushing from patient 9, Right Middle Lobe, 12 months


title: Patient 9_LUL_36 months

source_name: Bronchial brushing from patient 9, Left Upper Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266035_B]

description: F2 hybrid


title: Patient 9_LUL_24 months

source_name: Bronchial brushing from patient 9, Left Upper Lobe, 24 months


title: Patient 9_LUL_12 months

source_name: Bronchial brushing from patient 9, Left Upper Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266034_G]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266035_A]

description: F2 hybrid


title: Patient 9_RUL_36 months

source_name: Bronchial brushing from patient 9, Right Upper Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266034_H]

description: F2 hybrid


title: Patient 9_RUL_24 months

source_name: Bronchial brushing from patient 9, Right Upper Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266034_F]

description: F2 hybrid

source_name: left ventricle_free-wall


title: Patient 10_RML_36 months

source_name: Bronchial brushing from patient 10, Right Middle Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266034_D]

description: F2 hybrid


title: Patient 9_RUL_12 months

source_name: Bronchial brushing from patient 9, Right Upper Lobe, 12 months


title: Patient 8_Leftmainstem_12 months

source_name: Bronchial brushing from patient 8, Leftmainstem, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266034_A]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266034_E]

description: F2 hybrid


title: Patient 9_MC_36 months

source_name: Bronchial brushing from patient 9, Main Carina, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266031_H]

description: F2 hybrid


title: Patient 8_LB10_14 months

source_name: Bronchial brushing from patient 8, Left Lower Lobe, 14 months


title: heart_Scn5a-1798insD/+ mutant [4700266031_G]

description: F2 hybrid


title: Patient 8_LB10_24 months

source_name: Bronchial brushing from patient 8, Left Lower Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266034_C]

description: F2 hybrid


title: Patient 9_MC_24 months

source_name: Bronchial brushing from patient 9, Main Carina, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266031_F]

description: F2 hybrid


title: Patient 8_RML_12 months

source_name: Bronchial brushing from patient 8, Right Middle Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266031_E]

description: F2 hybrid


title: Patient 8_RML_24 months

source_name: Bronchial brushing from patient 8, Right Middle Lobe, 24 months


title: Patient 8_RB10_12 months

source_name: Bronchial brushing from patient 8, Right Lower Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266034_B]

description: F2 hybrid


title: Patient 8_RUL_12 months

source_name: Bronchial brushing from patient 8, Right Upper Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266031_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266031_B]

description: F2 hybrid


title: Patient 8_RB10_24 months

source_name: Bronchial brushing from patient 8, Right Lower Lobe, 24 months


title: Patient 8_LUL_12 months

source_name: Bronchial brushing from patient 8, Left Upper Lobe, 12 months


title: Patient 8_LUL_24 months

source_name: Bronchial brushing from patient 8, Left Upper Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266031_C]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266024_H]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266024_G]

description: F2 hybrid


title: Patient 7_LB10_36 months

source_name: Bronchial brushing from patient 7, Left Lower Lobe, 36 months


title: Patient 8_RUL_24 months

source_name: Bronchial brushing from patient 8, Right Upper Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266031_A]

description: F2 hybrid

source_name: left ventricle_free-wall


title: Patient 7_LB10_24 months

source_name: Bronchial brushing from patient 7, Left Lower Lobe, 24 months


title: Patient 7_LB10_12 months

source_name: Bronchial brushing from patient 7, Left Lower Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266036_A]

description: F2 hybrid


title: Patient 7_RB10_24 months

source_name: Bronchial brushing from patient 7, Right Lower Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266024_E]

description: F2 hybrid


title: Patient 7_RML_24 months

source_name: Bronchial brushing from patient 7, Right Middle Lobe, 24 months


title: Patient 7_RB10_36 months

source_name: Bronchial brushing from patient 7, Right Lower Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266024_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266023_H]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266024_F]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266024_C]

description: F2 hybrid


title: Patient 7_RML_36 months

source_name: Bronchial brushing from patient 7, Right Middle Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266024_A]

description: F2 hybrid


title: Patient 7_RML_12 months

source_name: Bronchial brushing from patient 7, Right Middle Lobe, 12 months


title: Patient 7_RB10_12 months

source_name: Bronchial brushing from patient 7, Right Lower Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266023_G]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266024_B]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266023_F]

description: F2 hybrid


title: Patient 7_LUL_36 months

source_name: Bronchial brushing from patient 7, Left Upper Lobe, 36 months


title: Patient 7_LUL_24 months

source_name: Bronchial brushing from patient 7, Left Upper Lobe, 24 months


title: Patient 7_RUL_12 months

source_name: Bronchial brushing from patient 7, Right Upper Lobe, 12 months


title: Patient 7_RUL_36 months

source_name: Bronchial brushing from patient 7, Right Upper Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266023_D]

description: F2 hybrid


title: Patient 7_LUL_12 months

source_name: Bronchial brushing from patient 7, Left Upper Lobe, 12 months


title: Patient 7_RUL_24 months

source_name: Bronchial brushing from patient 7, Right Upper Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266023_B]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266020_H]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266023_C]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266023_E]

description: F2 hybrid


title: Patient 7_MC_36 months

source_name: Bronchial brushing from patient 7, Main Carina, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266036_C]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266023_A]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266020_G]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266020_E]

description: F2 hybrid


title: Patient 6_RML_36 months

source_name: Bronchial brushing from patient 6, Right Middle Lobe, 36 months

value: LLL


title: Patient 6_RB10_36 months

source_name: Bronchial brushing from patient 6, Right Lower Lobe, 36 months


title: Patient 6_RB10_24 months

source_name: Bronchial brushing from patient 6, Right Lower Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266020_D]

description: F2 hybrid

source_name: left ventricle_free-wall


title: Patient 6_LB10_36 months

source_name: Bronchial brushing from patient 6, Left Lower Lobe, 36 months


title: Patient 6_LLL_24 months

source_name: Bronchial brushing from patient 6, Left Lower Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266019_H]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266020_F]

description: F2 hybrid


title: Patient 6_RML_24 months

source_name: Bronchial brushing from patient 6, Right Middle Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266020_A]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266019_E]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266019_B]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266019_F]

description: F2 hybrid


title: Patient 6_RUL_36 months

source_name: Bronchial brushing from patient 6, Right Upper Lobe, 36 months


title: Patient 6_RML_12 months

source_name: Bronchial brushing from patient 6, Right Middle Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266020_C]

description: F2 hybrid


title: Patient 6_RB10_12 months

source_name: Bronchial brushing from patient 6, Right Lower Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266019_D]

description: F2 hybrid


title: heart_Scn5a-1798insD/+ mutant [4700266020_B]

description: F2 hybrid


title: Patient 6_LUL_12 months

source_name: Bronchial brushing from patient 6, Left Upper Lobe, 12 months


title: Patient 6_LUL_24 months

source_name: Bronchial brushing from patient 6, Left Upper Lobe, 24 months


title: heart_Scn5a-1798insD/+ mutant [4700266019_G]

description: F2 hybrid


title: Patient 6_RUL_12 months

source_name: Bronchial brushing from patient 6, Right Upper Lobe, 12 months


title: heart_Scn5a-1798insD/+ mutant [4700266019_C]

description: F2 hybrid


title: Patient 6_RUL_24 months

source_name: Bronchial brushing from patient 6, Right Upper Lobe, 24 months


title: Patient 6_MC_36 months

source_name: Bronchial brushing from patient 6, Main Carina, 36 months


title: Patient 6_LUL_36 months

source_name: Bronchial brushing from patient 6, Left Upper Lobe, 36 months


title: heart_Scn5a-1798insD/+ mutant [4700266019_A]

description: F2 hybrid


title: 4616726060_C

city: Woolloongabba

first: Gethin

last: Thomas

state: QLD

address: Princess Alexandra Hospital

country: Australia

institute: University of Queensland Diamantina Institute

description: RNA extracted from FFPE biopsies

data_processing: Array data were processed using the Illumina BeadStudio software then the processed data were assessed for quality control and normalised in Lumi. Analysis of gene expression patterns was performed in BRB-ArrayTools. For quality control scanned images of the arrays were visually inspected for artefacts in Illumina BeadStudio followed by the graphical analysis of density plots in Lumi.  The microarray data were transformed by variance stabilization transformation (VST) then normalized by robust spline normalization (RSN). Post-normalization quality control was carried out using density plots to ensure all samples had similar distribution and variance. To reduce background noise in the data analysis all probes that were not expressed in any of the samples, i.e. whose intensity was below background in all samples, were excluded from the analysis. This did not exclude probes for genes whose expression was either “switched-on” or “switched-off”.

source_name: Synovial biopsy

label_protocol: 200ng of RNA was used in the Illumina Whole-Genome DASL® (cDNA-mediated Annealing, Selection, Extension, and Ligation) Gene Expression Assay according to the Illumina protocol. This technique has been specifically developed for whole-genome expression profiling of degraded RNA samples from archived tissue biopsies. This protocol has been specifically developed for whole-genome expression profiling of degraded RNA samples from archived tissue biopsies. RNA is first converted to cDNA through a reverse transcription reaction with biotinylated primers. The biotinylated cDNA is then annealed to assay oligonucleotide probes specific for each of the 24000 cDNAs targeted by the array. The hybridized oligonucleotides are then extended and ligated in a second-strand cDNA synthesis forming a synthetic template that is transferred to a PCR reaction containing a fluorescently labelled primer. The labelled PCR product strand is then isolated and the fluorescent products were hybridised to Illumina Ref-8 Expression BeadChips and scanned.

extract_protocol:
biopsy collection: Fifteen knee synovial biopsy tissue samples consisting of six seronegative spondyloarthropy (SpA), two ankylosing spondylitis (AS), three osteoarthritis (OA) and four normal control biopsies were obtained from the Synovial Tissue Bank at the Repatriation General Hospital in Adelaide, South Australia with the appropriate ethical approval (Supplementary Table 1). All patients provided informed written consent.
RNA was extracted from the formaldehyde-fixed paraffin-embedded (FFPE) tissue blocks using the Arcturus Paradise© Plus Reagent System (Molecular Devices, Sunnyvale, CA) as per the manufacturer’s protocol.

tag: biopsy

value: seronegative spondyloarthropy


title: Patient 5_LB10_24 months

source_name: Bronchial brushing from patient 5, Left Lower Lobe, 24 months

tag: patient id


title: 4616726060_B

description: RNA extracted from FFPE biopsies


title: Patient 5_LB10_12 months

source_name: Bronchial brushing from patient 5, Left Lower Lobe, 12 months

tag: tumor location


title: Patient 5_RML_24 months

source_name: Bronchial brushing from patient 5, Right Middle Lobe, 24 months

tag: airway site


title: 4616726057_H

description: RNA extracted from FFPE biopsies


title: Patient 5_RB10_24 months

source_name: Bronchial brushing from patient 5, Right Lower Lobe, 24 months

tag: time point


title: 4616726057_F

description: RNA extracted from FFPE biopsies

value: ankylosing spondylitis


title: Patient 5_LUL_12 months

source_name: Bronchial brushing from patient 5, Left Upper Lobe, 12 months


title: Patient 4_RB10_24 months

source_name: Bronchial brushing from patient 4, Right Lower Lobe, 24 months


title: Patient 4_LB10_12 months

source_name: Bronchial brushing from patient 4, Left Lower Lobe, 12 months


title: 4616726057_G

description: RNA extracted from FFPE biopsies


title: Patient 5_LUL_24 months

source_name: Bronchial brushing from patient 5, Left Upper Lobe, 24 months


title: 4616726057_E

description: RNA extracted from FFPE biopsies

value: osteoarthritis


title: 4616726055_F

description: RNA extracted from FFPE biopsies


title: 4616726055_E

description: RNA extracted from FFPE biopsies


title: Patient 4_LB10_24 months

source_name: Bronchial brushing from patient 4, Left Lower Lobe, 24 months


title: 4616726055_C

description: RNA extracted from FFPE biopsies


title: 4616726057_D

description: RNA extracted from FFPE biopsies

value: normal control


title: Patient 4_RML_24 months

source_name: Bronchial brushing from patient 4, Right Middle Lobe, 24 months

value: Bronchial brushing, normal airway epithelial cells


title: 4616726057_A

description: RNA extracted from FFPE biopsies


title: 4616726055_H

description: RNA extracted from FFPE biopsies


title: Patient 5_RUL_24 months

source_name: Bronchial brushing from patient 5, Right Upper Lobe, 24 months


title: 4616726055_A

description: RNA extracted from FFPE biopsies


title: 4616726055_G

description: RNA extracted from FFPE biopsies


title: Patient 5_RUL_12 months

source_name: Bronchial brushing from patient 5, Right Upper Lobe, 12 months


title: 4616726055_B

description: RNA extracted from FFPE biopsies


title: Patient 4_RML_12 months

source_name: Bronchial brushing from patient 4, Right Middle Lobe, 12 months


title: Patient 4_RB10_12 months

source_name: Bronchial brushing from patient 4, Right Lower Lobe, 12 months


title: Patient 4_LUL_12 months

source_name: Bronchial brushing from patient 4, Left Upper Lobe, 12 months


title: Patient 4_LUL_24 months

source_name: Bronchial brushing from patient 4, Left Upper Lobe, 24 months


title: Patient 4_RUL_24 months

source_name: Bronchial brushing from patient 4, Right Upper Lobe, 24 months


title: Breast-normal-rep6b

city: Grand Rapids

first: Min-Han

last: Tan

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

hyb_protocol: Illumina standard protocol

scan_protocol: Illumina standard protocol

data_processing: Quantile normalization

source_name: NORMAL

label_protocol: AmbionMessageAmp kit.

extract_protocol: RNA was extracted using RNEasy (Qiagen) kit

value: NORMAL

value: normal breast tissue

tag: treatment

tag: status


title: Patient 3_LB10_36 months

source_name: Bronchial brushing from patient 3, Left Lower Lobe, 36 months


title: Breast-cancer-rep6b

source_name: CANCER

tag: disease state

value: CANCER

value: breast cancer tumor

value: paclitaxel

value: taxane resistant


title: Breast-normal-rep7b

tag: tissue


title: Patient 3_RB10_24 months

source_name: Bronchial brushing from patient 3, Right Lower Lobe, 24 months

value: Non-adjacent


title: Patient 3_LB10_12 months

source_name: Bronchial brushing from patient 3, Left Lower Lobe, 12 months


title: Breast-cancer-rep3b


title: Breast-cancer-rep8b


title: Patient 3_RML_24 months

source_name: Bronchial brushing from patient 3, Right Middle Lobe, 24 months


title: Breast-normal-rep6a


title: Breast-normal-rep4b


title: Breast-cancer-rep8a


title: Breast-normal-rep2


title: Patient 3_RB10_36 months

source_name: Bronchial brushing from patient 3, Right Lower Lobe, 36 months


title: Patient 3_LUL_36 months

source_name: Bronchial brushing from patient 3, Left Upper Lobe, 36 months


title: Breast-cancer-rep6a


title: Patient 3_RML_12 months

source_name: Bronchial brushing from patient 3, Right Middle Lobe, 12 months


title: Breast-cancer-rep7a


title: Patient 3_LB10_24 months

source_name: Bronchial brushing from patient 3, Left Lower Lobe, 24 months


title: Patient 3_RB10_12 months

source_name: Bronchial brushing from patient 3, Right Lower Lobe, 12 months


title: Breast-normal-rep7a


title: Breast-cancer-rep2b


title: Patient 4_RUL_12 months

source_name: Bronchial brushing from patient 4, Right Upper Lobe, 12 months

value: RLL


title: Patient 3_LUL_12 months

source_name: Bronchial brushing from patient 3, Left Upper Lobe, 12 months


title: Breast-cancer-rep5b


title: Patient 3_RML_36 months

source_name: Bronchial brushing from patient 3, Right Middle Lobe, 36 months


title: Breast-cancer-rep7b


title: Patient 3_LUL_24 months

source_name: Bronchial brushing from patient 3, Left Upper Lobe, 24 months


title: Breast-cancer-rep5a


title: Patient 3_RUL_24 months

source_name: Bronchial brushing from patient 3, Right Upper Lobe, 24 months

value: Adjacent


title: Breast-cancer-rep1b


title: Breast-cancer-rep4b


title: Patient 3_RUL_12 months

source_name: Bronchial brushing from patient 3, Right Upper Lobe, 12 months


title: Patient 2_LB10_36 months

source_name: Bronchial brushing from patient 2, Left Lower Lobe, 36 months

value: Contralateral


title: Breast-cancer-rep3a


title: Breast-cancer-rep2a


title: Patient 2_LB10_12 months

source_name: Bronchial brushing from patient 2, Left Lower Lobe, 12 months


title: Patient 2_RB10_36 months

source_name: Bronchial brushing from patient 2, Right Lower Lobe, 36 months


title: Patient 2_RB10_24 months

source_name: Bronchial brushing from patient 2, Right Lower Lobe, 24 months


title: Patient 2_RML_12 months

source_name: Bronchial brushing from patient 2, Right Middle Lobe, 12 months


title: Patient 2_RML_24 months

source_name: Bronchial brushing from patient 2, Right Middle Lobe, 24 months


title: Patient 2_RML_36 months

source_name: Bronchial brushing from patient 2, Right Middle Lobe, 36 months


title: Patient 3_MC_36 months

source_name: Bronchial brushing from patient 3, Main Carina, 36 months

value: RUL

value: Main carina


title: Patient 2_RB10_12 months

source_name: Bronchial brushing from patient 2, Right Lower Lobe, 12 months


title: Breast-normal-rep1

source_name: NORMAL


title: Patient 2_LB10_24 months

source_name: Bronchial brushing from patient 2, Left Lower Lobe, 24 months


title: Patient 2_LUL_36 months

source_name: Bronchial brushing from patient 2, Left Upper Lobe, 36 months


title: Breast-normal-rep4a


title: Breast-cancer-rep1a

source_name: CANCER


title: Patient 2_LUL_12 months

source_name: Bronchial brushing from patient 2, Left Upper Lobe, 12 months


title: Patient 2_LUL_24 months

source_name: Bronchial brushing from patient 2, Left Upper Lobe, 24 months


title: Patient 2_RUL_36 months

source_name: Bronchial brushing from patient 2, Right Upper Lobe, 36 months


title: Serum_T1DH_8265

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

hyb_protocol: Approximately 750ng of labeled cRNA was fragmented, and hybridized to the Illumina HumanRef-8 v3.0 beadchips in accordance to the Illumina technical manual. RNA from each culture was independently analyzed.

scan_protocol: After hybridization, arrays were washed, stained with Cy3-conjugated streptavidin, and scanned. Image data were analyzed with BeadStudio V2.0.

data_processing: The raw data were normalized using Robust Spline Normalization.

source_name: PBMC

label_protocol: Total RNA (200 ng) was coverted into biotin labeled cRNA using Target Amp cDNA synthesis kit (Epicenter catalog no. TAB1R6924).

extract_protocol: Total RNA was extracted using Qiagen RNeasy minikit

tag: IL-1Ra High


title: Serum_T1DL_7223

tag: IL-1Ra Low


title: Serum_AbNH_6920

tag: Antibody Negative


title: Serum_AbNL_7463


title: Serum_T1DH_4451


title: Serum_T1DH_7059


title: Serum_AbNH_7467


title: Patient 2_RUL_24 months

source_name: Bronchial brushing from patient 2, Right Upper Lobe, 24 months


title: Serum_AbNL_4810


title: Serum_T1DL_8228


title: Patient 2_RUL_12 months

source_name: Bronchial brushing from patient 2, Right Upper Lobe, 12 months


title: Patient 1_LUL_36 months

source_name: Bronchial brushing from patient 1, Left Upper Lobe, 36 months

value: LUL


title: Patient 1_LB10_36 months

source_name: Bronchial brushing from patient 1, Left Lower Lobe, 36 months


title: Patient 1_MC_36 months dup

source_name: Bronchial brushing from patient 1, Main Carina, 36 months


title: Serum_AbNL_6722


title: Patient 1_LB10_24 months

source_name: Bronchial brushing from patient 1, Left Lower Lobe, 24 months


title: Patient 1_RB10_36 months

source_name: Bronchial brushing from patient 1, Right Lower Lobe, 36 months


title: Breast-cancer-rep4a


title: Patient 1_LB10_12 months

source_name: Bronchial brushing from patient 1, Left Lower Lobe, 12 months


title: Patient 1_RB10_24 months

source_name: Bronchial brushing from patient 1, Right Lower Lobe, 24 months


title: Cell_conversion_Fibroblast_PPARG2_rep3

city: Yokohama

first: Ryota

last: Hasegawa

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Omics science center

institute: RIKEN Yokohama

hyb_protocol: Standard Illumina hybridyzation protocol

data_processing: The data were normalized using quantile normalization with lumi in R.

label_protocol: Biotinylated cRNA were prepared with TotalPrep™ RNA Amplification Kit for Illumina arrays

growth_protocol: Human dermal Fibroblast (FIB) was maintained in minimum essential medium (MEM-α) supplemented with 10% fetal bovine serum (FBS), 10ml of L-Glutamine and 0.5 ul of antibiotics (Takara Inc).

extract_protocol: RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were seeded onto a dish at 5.2*103/cm2 before one day of transduction. Lentivirus was added to cells in growth medium containing (1ug/ul) polybrene (Millipore) and cells were incubated overnight at 37°C, 5% CO2. The medium was changed to fresh growth medium next day. Cells were maintained for 1 week without medium change, then medium was changed to adipocyte maintenance medium for 1 week.

value: PPARG2 lentivirus vector transduced


title: Cell_conversion_Fibroblast_PPARG2_rep2


title: Cell_conversion_Fibroblast_PPARG2+ZNF395_rep1

value: PPARG2 and ZNF395 lentivirus vector co-transduced


title: Serum_AbNH_8058


title: Cell_conversion_Fibroblast_PPARG2_rep1


title: Serum_T1DL_7523


title: Cell_conversion_Fibroblast_PPARG2+ZNF395_rep3


title: Cell_conversion_Fibroblast_ctrl_rep2

value: Mock lentivirus vector transduced


title: Patient 1_RML_24 months

source_name: Bronchial brushing from patient 1, Right Middle Lobe, 24 months

value: Bronchial brushing, normal airway epithelial cells


title: Cell_conversion_Fibroblast_ctrl_rep3


title: Patient 1_RML_12 months

source_name: Bronchial brushing from patient 1, Right Middle Lobe, 12 months


title: Patient 1_RML_36 months

source_name: Bronchial brushing from patient 1, Right Middle Lobe, 36 months


title: Cell_conversion_Fibroblast_PPARG2+ZNF395_rep2


title: Patient 1_RB10_12 months

source_name: Bronchial brushing from patient 1, Right Lower Lobe, 12 months


title: Cell_conversion_Fibroblast_ctrl_rep1


title: MSC 15d_rep3

data_processing: The data were normalized using quantile normalization with lumi in R

source_name: MSC 15d

growth_protocol: Human bone marrow derived mesenchymal stem cells (MSC) were maintained in Mesenchymal stem cell basal medium (MSCBM) supplemented with 10% fetal bovine serum (FBS), 10ml of L-Glutamine and 0.5 ul of antibiotics (Takara Inc). They were cultured at 37oC, 5% CO2. Medium was changed every 2 or 3 days.

treatment_protocol: Adipocyte differentiation was induced by incubating 100% confluent MSCs in Adipogenic induction medium (Takara Inc) containing 2ml of human-insulin, 1ml of dexamethasone, and 0.4ml of indomethacin and 0.2ml of IBMX. Three days post induction cells were maintained with the maintenance medium (Takara Inc) containing 2ml of h-insulin for 1day. Both induction and maintenance medium were supplemented with 10% fetal bovine serum (FBS) 4ml of L-Glutamine and 0.2 ul of antibiotics (Takara Inc). Total four cycles of induction medium (3d) and maintenance medium (1d) was performed to differentiate into adipocyte.

value: mesenchymal stem cells (MSC)

tag: time after induction


title: Patient 1_RUL_36 months

source_name: Bronchial brushing from patient 1, Right Upper Lobe, 36 months


title: Patient 1_RUL_12 months

source_name: Bronchial brushing from patient 1, Right Upper Lobe, 12 months


title: MSC 12d_rep2

source_name: MSC 12d


title: MSC 12d_rep3


title: Patient 1_LUL_12 months

source_name: Bronchial brushing from patient 1, Left Upper Lobe, 12 months


title: 46,XY 6lt gene expression

city: Lund

first: Josef

last: Davidsson

address: BMC B13

department: Clinical Genetics

institute: Lund University

description: Expression array

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix gene expression console and Pearson signal correlation testing

source_name: Fibroblast

label_protocol: standard Affymetrix protocol

growth_protocol: cells were maintained and passaged in RPMI 1640 medium (Invitrogen) containing 10% FBS (Sigma-Aldrich) in 250 ml cell culture flasks (BD Falcon) for 8 weeks.

extract_protocol: mirVana

treatment_protocol: Single-cell cloned and reference fibroblasts

tag: genotype

value: fibroblast


title: Patient 1_RUL_24 months

source_name: Bronchial brushing from patient 1, Right Upper Lobe, 24 months