title: E19.5_rep2 1 of 2

city: Boston

first: Maria

middle: Isabel

last: Ramirez

state: MA

address: 72 E. Concord St. E603

department: Medicine

institute: Boston University School of Medicine

scan_protocol: see protocol http://www.genomics.agilent.com/files/Manual/G4481-90010_MammalianProtocol_10.11.pdf. Arrays were scanned using an Agilent scanner model G2565BA.

data_processing: The image analysis was performed using Agilent’s Feature Extraction software v.9.5.3.1 set to the default ChIP protocol. To combine the replicates for each time point, the raw data was background subtracted and median normalized using limma library, part of the Bioconductor project, in the R statistical environment {Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80 and Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64}. The difference of binding between the IP and Input (Cy5/Cy3), for each probe/feature, was analyzed using empirical Bayes method implemented in the limma package. P-values obtained from the multiple comparison tests were corrected by false discovery rates. In addition, for the binding profiles, we calculated average binding ratio (Cy5/Cy3) for each probe by averaging the ratio between the candidate bound probe and the 2 closest neighboring probes.

source_name: Embryonic lung day19.5

label_protocol: For chip-on-chip experiments we followed previously described methods {Lee, 2006 #26}. Briefly, immunoprecipitated DNA (IP) and whole cell extract DNA (input) were purified by treatment with RNAse A, proteinase K and multiple phenol: chloroform: isoamyl alcohol extractions. Purified DNA was blunt-ended and ligated to linkers, and amplified using a two-stage PCR protocol. Amplified DNA was labeled and purified by using Bioprime random primer labeling kits (Invitrogen). Immunoprecipitated DNA (IP) was labeled with Cy5 fluorophore, and whole cell extract DNA (input) was labeled with Cy3 fluorophore. Cy5 and Cy3 labeled DNAs were mixed (~5 μg of each) and hybridized to arrays in Agilent hybridization chambers for 40 hours at 40°C, washed and immediately scanned.

extract_protocol: Five to ten embryonic lungs were used for each immunoprecipitation. E11.5 and E19.5 lungs were dissected, minced and immediately immersed in 2 volumes of 1xPBS. Lungs were chemically cross linked by the addition of one-tenth volume of fresh 11% formaldehyde solution, and incubated for 10 minutes at room temperature. Formaldehyde was then quenched with 2.5M glycine and tissues rinsed twice with 1xPBS. Crosslinked lung samples were flashed frozen in liquid nitrogen and stored at –80ºC. Lungs were lysed and sonicated to solubilize and shear crosslinked DNA. We sonicated samples on ice in a Branson Ultrasonic Sonicator coupled to a Fisher Scientific Sonic dismembrator 500 power supply at 90% amplitude for 12 cycles of 30 second pulses with 60 second pause between pulses, yielding fragments of about 500 bp. Part of the whole cell extract was saved as input material and the rest was incubated overnight at 4°C with 100 μl of Dynal Protein G magnetic beads (Invitrogen) that had been pre-incubated with 10 μg of the a-Nkx2.1 antibody  (07-601, Upstate-Millipore) or IgG (Santa Cruz Biotechnologies, Inc). Conditions were optimized for binding to chromatin from embryonic mouse lung.  Beads were washed 4-5 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by addition of elution buffer and by heating at 65°C for 15 min with 2 minutes interval of vortexing. Crosslinking in the IP and input samples was reversed by overnight incubation at 65°C.

tag: developmental stage

value: embryonic lung

tag: antibody

tag: antibody manufacturer

value: Upstate-Millipore

tag: antibody catalog #

tag: developmental time point

tag: sample type

value: input DNA


title: root, wildtype, replicate 2

status: Public on Nov 01 2011

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA (v2.15.3) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.

label: biotin

molecule: total RNA

organism: Medicago truncatula

source_name: root (meristem, elongation and differentiation zone)

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug total RNA. The protocol was conducted using the reagents provided by Affymetrix, as the manufacturer's instructions.

growth_protocol: Medicago plants used for gene expression analysis were grown vertically on Färhaeus medium plates without nitrate. RNA was isolated from the Nod factor susceptible zone of 7-day-old roots samples snap-frozen in liquid N2.

extract_protocol: Total RNA was extracted and purified from root Nod factor suspension zone using the Qiagen RNeasy plant mini kit (Qiagen, Venlo, The Netherlands). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 25S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 9.0.

tag: genotype/variation

value: Wildtype (Jemalong A17)

tag: age

value: 7 days old

tag: tissue

value: root meristem


title: OASM_End_2

city: Chicago

first: Carla

middle: R

last: Scanzello

state: IL

address: 1611 W. Harrison St., Ste. 510

department: Rheumatology

country: USA

institute: Rush University Medical Center

hyb_protocol: aRNA was hybridized on to chips by incubating at 45 C for 16hr (60 rpm rotation).  The chips were washed and stained with the program EukGE-WS2V5_450 on Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The chips were scanned with Affymetrix GeneChip scanner 3000.

data_processing: Robust Multi-Array Analysi (RMA; Irizarry et al. Biostatistics 4: 249.) in the Matlab software package (v2009a The MathWorks Inc., Natick, MA) was first used to do background corrections of raw expression data (.cel files) from individual sample sets.  Then quantile normalization over multiple arrays was done across the 26 samples sets being compared, and median polishing was conducted to reduce the contribution of outlier probes to the single expression value derived from multiple probes for a given gene in a sample set.

organism: Homo sapiens

source_name: Synovial Membrane, knee

label_protocol: Message Amp premier RNA amplification kit (Applied Biosystems, #AM1792) was used for labelling. The input total RNA was 150ng. Biotin was added during in Vitro transcription to synthesize biotin-modified aRNA.

extract_protocol: We extracted total RNA from homogenized samples of osteoarthritic synovial membranes by using the PerfectPure® RNA Fibrous Tissue kit (5Prime Inc.). All RNA was DNAse treated. RNA integrity was determined by electrophoresis on a microfluidics-based platform (Agilent Technologies).

value: Synovial Membrane, knee

tag: phenotype

value: end-stage osteoarthritis

tag: gender

value: F


title: OASM_End_1

value: M


title: root, wildtype, replicate 3


title: E19.5_rep3 1 of 2

type: genomic

molecule: genomic DNA

organism: Mus musculus


title: OASM_End_4


title: root, Mtnsp2-2 mutant, replicate 3

value: Mtnsp2-2 mutant (0-4)


title: E19.5_rep1 1 of 2


title: OASM_End_3


title: E11.5_rep1 1 of 2

source_name: Embryonic lung day11.5


title: root, Mtnsp1-1 mutant, replicate 3

value: Mtnsp1-1 mutant (B85)


title: Skin_age_26_individual_1

city: Perth

first: Daniel

middle: J

last: Haustead

state: WA

address: 35 stirling highway (M317)

department: Surgery

country: Australia

institute: University Of Western Australia

description:
n/a
Sample_probe_group_file  HuEx-1_0-st-v2.r2.pgf
Sample_meta-probeset_file  HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: RMA expression values were obtained for the core subsets of genes using Expression Console with default settings.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted from 3mm pounch biopsies of skin stored in RNALater (Qiagen), using manual dissection and hand-held rotor-stator homogenisation in Trizol reagent (Invitrogen), and purified using quick spin columns (Qiagen).  RNA quality was assessed using the Agilent BioAnalyzer (Agilent Technologies) and UV spectrophotometer for the presence of sharp peaks and 28S/18S RNA.

value: skin


title: Tonsil_57_control

city: Regensburg

first: Stefan

last: Bentink

state: Bayern

address: Josef Engertstr. 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

description: Gene expression data from germinal center B-cells transfected with an empty control vector

hyb_protocol: Fragmentation and hybridization of labelled anti sense RNA on Human Genome U133A Plus 2.0 Arrays (Affymetrix) was performed according to manufacturer recommendations.

scan_protocol: After hybridization of night (16 hours, 45 C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500).

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalized data (Irrizary et al. Nucleic Acids Research 2003, PMID: 12582260). Normalized and summarized probeset expression value on additive arcsin (log-like) scale VALUES are provided in the Sample table below.

label: Biotin

source_name: Germinal center B-cells transfected with control vector

label_protocol: RNA from the FACS sorted transfected GC B cells was amplified with ExpressArt mRNA Amplification kit protocol (Amptech). Amplified RNA was labelled for microarray hybridization using Affymetrix GeneChip® IVT Labelling Kit (Affymetrix)

growth_protocol: Tonsils were taken from pediatric patients with informed consent and with ethical approval. Mononuclear cells from tonsils were isolated as described in Vockerodt M, Morgan SL, Kuo M, et al. The Epstein-Barr virus oncoprotein, latent membrane protein-1, reprograms germinal centre B cells towards a Hodgkin's Reed-Sternberg-like phenotype. J Pathol. 2008;216:83-92.

extract_protocol: Isolation of total RNA from sorted cells was performed using the RNeasy® Micro Kit according manufacturers instructions (Qiagen)

treatment_protocol: Mononuclear cells from tonsils were transfected using a control or Myc expression vector and sorted as described in Vockerodt M, Morgan SL, Kuo M, et al. The Epstein-Barr virus oncoprotein, latent membrane protein-1, reprograms germinal centre B cells towards a Hodgkin's Reed-Sternberg-like phenotype. J Pathol. 2008;216:83-92.

value: Germinal center B-cells extracted from human tonsils

tag: sample

tag: treatment

value: ctrl


title: Tonsil_58_myc_high

description: Gene expression data from germinal center B-cells transfected with a myc expression vector showing high Myc expression levels

source_name: Germinal center B-cells transfected with Myc expression vector

value: myc


title: Tonsil_56_control


title: Tonsil_55_myc_high


title: root, Mtnsp2-2 mutant, replicate 1


title: Tonsil_56_myc-wt


title: root, Mtnsp1-1 mutant, replicate 1


title: Tonsil_57_myc-wt


title: root, Mtnsp1-1 mutant, replicate 2


title: Tonsil_55_control


title: Tonsil_58_control


title: Tonsil_51_control


title: Tonsil_51_myc_high


title: Tonsil_29_myc


title: E11.5_rep2 1 of 2


title: Tonsil_17_myc


title: Tonsil_28_myc


title: root, Mtnsp2-2 mutant, replicate 2


title: Tonsil_29_control


title: Tonsil_16_myc


title: Tonsil_16_control


title: Tonsil_21_control


title: Tonsil_28_control


title: Tonsil_21_myc


title: Tonsil_17_control


title: SCL005 DORF6 72H 1

city: Seattle

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

source_name: SCL005 DORF6 72H 1

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: 2B4 cells (a clonal derivative of Calu-3 cells) were infected with either icSARS CoV Urbani or the icSARS deltaORF6 mutant strain.  Each infected sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.)There are triplicate time-matched mock for each time point from the same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) was used for the mock infections. Calu-3 cells were seeded in 6-well plates (1.5 x 10^6 cells/well) two days prior to infection; immediately preceding infection, monolayers were washed twice with DF12 supplemented with 0.3% bovine serum albumin (DF12-BSA); and cells were inoculated with either the wild type SARS CoV virus or the mutant virus (multiplicity of infection [MOI] of 5 plaque forming unit [PFU] per cell) in DF12-BSA for 50 minutes at 37°C. Mock-infected controls were inoculated with DF12-BSA only. Cells were collected at 0, 3, 7, 12, 24, 30, 36, 48, 54, 60 or 72h post infection. The end of the inoculation period was considered the “0” hour time point.

extract_protocol: All TRIzol lysates were processed for RNA isolation: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: At each time point, triplicate wells of mock-infected and virus-infected Calu-3 monolayers were washed with 5 ml cold phosphate buffered saline (PBS) and lysed directly with 1 ml of TRIzol (Invitrogen), according to the manufacturer’s recommendation, and resulting lysates were stored at -80°C until further processing.

tag: time (post virus infection)

value: SARS delta ORF6 infected

tag: cell line


title: Tonsil_15_myc


title: SCL005 DORF6 72H 2

source_name: SCL005 DORF6 72H 2


title: SCL005 DORF6 72H 3

source_name: SCL005 DORF6 72H 3


title: Tonsil_15_control


title: SCL005 DORF6 60H 3

source_name: SCL005 DORF6 60H 3


title: SCL005 DORF6 60H 1

source_name: SCL005 DORF6 60H 1


title: KH209

city: Chuo-ku

first: Takashi

last: Kohno

address: 5-1-1 Tsukiji

country: Japan

institute: National Cancer Center Research Institute

description: Gene expression data from normal lung.

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Human U133 Plus 2.0 array according to the Affymetrix standard protcol.

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

data_processing: The data were normalized by the MAS5 algorhythm.

source_name: Frozen normal lung tissue

label_protocol: 100ng of total RNA was labeled using a Two-Cycle Target Labeling and Control Reagents.

extract_protocol: Trizol extraction according to the manufacturer's instructions.

value: normal lung

value: male

tag: smoking status

value: Ever-smoker

tag: bi


title: SCL005 DORF6 54H 3

source_name: SCL005 DORF6 54H 3


title: SCL005 DORF6 60H 2

source_name: SCL005 DORF6 60H 2


title: KH208

description: Gene expression data from normal lung.


title: KH207

description: Gene expression data from normal lung.


title: KH206

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH232

tag: age (years)

value: Never-smoker


title: SCL005 DORF6 48H 2

source_name: SCL005 DORF6 48H 2


title: SCL005 DORF6 54H 2

source_name: SCL005 DORF6 54H 2


title: KH210

description: Gene expression data from normal lung.

value: female


title: KH201

description: Gene expression data from normal lung.


title: SCL005 DORF6 48H 3

source_name: SCL005 DORF6 48H 3


title: KH203

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH055


title: SCL005 DORF6 36H 3

source_name: SCL005 DORF6 36H 3


title: SCL005 DORF6 30H 3

source_name: SCL005 DORF6 30H 3


title: KH200

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH141


title: SCL005 DORF6 48H 1

source_name: SCL005 DORF6 48H 1


title: SCL005 DORF6 36H 1

source_name: SCL005 DORF6 36H 1


title: SCL005 DORF6 54H 1

source_name: SCL005 DORF6 54H 1


title: KH202

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH161


title: KH205

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH086


title: SCL005 DORF6 24H 2

source_name: SCL005 DORF6 24H 2


title: SCL005 DORF6 24H 3

source_name: SCL005 DORF6 24H 3


title: SCL005 DORF6 30H 2

source_name: SCL005 DORF6 30H 2


title: KH198

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH120


title: KH204

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH073


title: KH195

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH081


title: SCL005 DORF6 36H 2

source_name: SCL005 DORF6 36H 2


title: SCL005 DORF6 12H 3

source_name: SCL005 DORF6 12H 3


title: KH197

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH026


title: KH194

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH039


title: KH193

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH017


title: KH196

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH025


title: SCL005 DORF6 30H 1

source_name: SCL005 DORF6 30H 1


title: KH269

description: Gene expression data from primary lung ADC

source_name: frozen tissue of primary lung tumors

value: primary lung tumor

tag: pathological stage

value: IA

tag: pstage iorii

value: I

tag: gene alteration status

value: EGFR mutation +

tag: myc

value: Low

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: alive

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH192

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH009

tag: tissue

tag: gender


title: SCL005 DORF6 7H 3

source_name: SCL005 DORF6 7H 3

tag: time (post virus infection)

tag: treatment


title: SCL005 DORF6 12H 1

source_name: SCL005 DORF6 12H 1

tag: cell line


title: SCL005 DORF6 12H 2

source_name: SCL005 DORF6 12H 2


title: KH262

tag: smoking status

tag: bi

value: High


title: SCL005 DORF6 3H 2

source_name: SCL005 DORF6 3H 2


title: SCL005 DORF6 24H 1

source_name: SCL005 DORF6 24H 1


title: KH191

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH007

tag: age (years)


title: KH199

description: Gene expression data from normal lung.

source_name: Frozen normal lung tissue for KH130


title: KH267

tag: pathological stage

tag: pstage iorii


title: SCL005 DORF6 3H 3

source_name: SCL005 DORF6 3H 3


title: KH263

tag: gene alteration status

tag: myc


title: SCL005 DORF6 7H 1

source_name: SCL005 DORF6 7H 1


title: SCL005 DORF6 7H 2

source_name: SCL005 DORF6 7H 2


title: SCL005 DORF6 0H 3

source_name: SCL005 DORF6 0H 3


title: KH260

tag: relapse

tag: days before relapse/censor


title: SCL005 DORF6 3H 1

source_name: SCL005 DORF6 3H 1


title: SCL005 DORF6 0H 1

source_name: SCL005 DORF6 0H 1


title: SCL005 DORF6 0H 2

source_name: SCL005 DORF6 0H 2


title: KH258

tag: months before relapse/censor

tag: death


title: KH253

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: SCL005 WT 72H 3

source_name: SCL005 WT 72H 3

value: SARS CoV Urbani infected


title: SCL005 WT 72H 2

source_name: SCL005 WT 72H 2


title: KH255

source_name: frozen tissue of primary lung tumors

tag: tissue

tag: gender


title: SCL005 WT 72H 1

source_name: SCL005 WT 72H 1

tag: time (post virus infection)

tag: treatment


title: KH254

tag: smoking status


title: KH251

tag: bi


title: KH249

tag: age (years)


title: KH248

tag: pathological stage


title: KH252

tag: pstage iorii


title: SCL005 WT 60H 2

source_name: SCL005 WT 60H 2

tag: cell line


title: KH245

tag: gene alteration status

tag: myc


title: SCL005 WT 60H 1

source_name: SCL005 WT 60H 1


title: SCL005 WT 60H 3

source_name: SCL005 WT 60H 3


title: KH240

tag: relapse

tag: days before relapse/censor


title: SCL005 WT 54H 1

source_name: SCL005 WT 54H 1


title: SCL005 WT 48H 3

source_name: SCL005 WT 48H 3


title: KH250

tag: months before relapse/censor

tag: death


title: SCL005 WT 54H 3

source_name: SCL005 WT 54H 3


title: KH241

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: SCL005 WT 54H 2

source_name: SCL005 WT 54H 2


title: SCL005 WT 48H 2

source_name: SCL005 WT 48H 2


title: KH239

tag: tissue

tag: gender


title: KH246


title: KH238


title: SCL005 WT 48H 1

source_name: SCL005 WT 48H 1

tag: time (post virus infection)

tag: treatment


title: SCL005 WT 36H 2

source_name: SCL005 WT 36H 2


title: KH235

tag: smoking status

tag: bi


title: KH236

tag: age (years)

tag: pathological stage


title: KH229

tag: pstage iorii


title: KH224

tag: gene alteration status


title: SCL005 WT 30H 3

source_name: SCL005 WT 30H 3

tag: cell line


title: KH226

tag: myc

tag: relapse

value: exclude


title: SCL005 WT 30H 1

source_name: SCL005 WT 30H 1


title: SCL005 WT 36H 3

source_name: SCL005 WT 36H 3


title: KH225

tag: days before relapse/censor

tag: months before relapse/censor


title: SCL005 WT 30H 2

source_name: SCL005 WT 30H 2


title: SCL005 WT 36H 1

source_name: SCL005 WT 36H 1


title: KH223

source_name: frozen tissue of primary lung tumors

tag: death

tag: days before death/censor


title: KH214

tag: tissue

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: SCL005 WT 24H 1

source_name: SCL005 WT 24H 1

tag: time (post virus infection)


title: SCL005 WT 24H 2

source_name: SCL005 WT 24H 2

tag: treatment


title: KH076

tag: gender

tag: smoking status


title: KH169

tag: age (years)

tag: bi


title: KH184

tag: pathological stage

tag: pstage iorii


title: KH187

tag: gene alteration status


title: SCL005 WT 12H 3

source_name: SCL005 WT 12H 3

tag: cell line


title: SCL005 WT 24H 3

source_name: SCL005 WT 24H 3


title: SCL005 WT 7H 3

source_name: SCL005 WT 7H 3


title: KH220

tag: myc

tag: relapse


title: SCL005 WT 12H 1

source_name: SCL005 WT 12H 1


title: SCL005 WT 3H 2

source_name: SCL005 WT 3H 2


title: SCL005 WT 7H 2

source_name: SCL005 WT 7H 2


title: SCL005 WT 12H 2

source_name: SCL005 WT 12H 2


title: KH146

tag: days before relapse/censor

tag: months before relapse/censor


title: SCL005 WT 7H 1

source_name: SCL005 WT 7H 1


title: SCL005 WT 3H 3

source_name: SCL005 WT 3H 3


title: KH176

tag: death

tag: days before death/censor


title: SCL005 WT 0H 2

source_name: SCL005 WT 0H 2


title: SCL005 WT 3H 1

source_name: SCL005 WT 3H 1


title: KH178

tag: tissue

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH188


title: SCL005 WT 0H 1

source_name: SCL005 WT 0H 1

tag: time (post virus infection)

tag: treatment


title: SCL005 WT 0H 3

source_name: SCL005 WT 0H 3


title: KH164

tag: gender

tag: smoking status


title: KH175

tag: age (years)

tag: bi


title: SCL005 mock 72H 3

source_name: SCL005 mock 72H 3

value: mock infected


title: KH186

source_name: frozen tissue of primary lung tumors

tag: pathological stage

tag: pstage iorii


title: SCL005 mock 72H 2

source_name: SCL005 mock 72H 2

tag: cell line


title: SCL005 mock 72H 1

source_name: SCL005 mock 72H 1


title: KH157

tag: gene alteration status

tag: myc


title: KH149

tag: relapse

tag: days before relapse/censor


title: KH128

tag: months before relapse/censor

tag: death


title: SCL005 mock 60H 1

source_name: SCL005 mock 60H 1


title: KH270

tag: tissue

tag: days before death/censor


title: KH124

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH134


title: KH158


title: SCL005 mock 60H 2

source_name: SCL005 mock 60H 2

tag: time (post virus infection)

tag: treatment


title: KH131

tag: gender

tag: smoking status


title: SCL005 mock 54H 3

source_name: SCL005 mock 54H 3


title: SCL005 mock 48H 3

source_name: SCL005 mock 48H 3


title: SCL005 mock 54H 2

source_name: SCL005 mock 54H 2


title: KH151

tag: age (years)

tag: bi


title: KH127

tag: pathological stage

tag: pstage iorii


title: KH138

tag: gene alteration status


title: KH042

tag: myc


title: SCL005 mock 60H 3

source_name: SCL005 mock 60H 3

tag: cell line


title: SCL005 mock 48H 2

source_name: SCL005 mock 48H 2


title: KH166

tag: relapse

tag: days before relapse/censor


title: SCL005 mock 36H 2

source_name: SCL005 mock 36H 2


title: KH165

tag: months before relapse/censor

tag: death


title: KH150

tag: tissue

tag: days before death/censor


title: SCL005 mock 36H 1

source_name: SCL005 mock 36H 1

tag: time (post virus infection)


title: SCL005 mock 48H 1

source_name: SCL005 mock 48H 1

tag: treatment


title: SCL005 mock 54H 1

source_name: SCL005 mock 54H 1


title: KH174

tag: gender

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: SCL005 mock 30H 2

source_name: SCL005 mock 30H 2


title: SCL005 mock 30H 1

source_name: SCL005 mock 30H 1


title: KH271

tag: age (years)

tag: smoking status


title: KH170

tag: bi

tag: pathological stage


title: SCL005 mock 36H 3

source_name: SCL005 mock 36H 3


title: SCL005 mock 24H 3

source_name: SCL005 mock 24H 3


title: KH227

source_name: frozen tissue of primary lung tumors

tag: pstage iorii

tag: gene alteration status


title: KH167

tag: myc


title: KH126

tag: relapse


title: SCL005 mock 12H 2

source_name: SCL005 mock 12H 2

tag: cell line


title: SCL005 mock 30H 3

source_name: SCL005 mock 30H 3


title: KH137

tag: days before relapse/censor

tag: months before relapse/censor


title: SCL005 mock 24H 1

source_name: SCL005 mock 24H 1


title: KH095

tag: tissue

tag: death


title: SCL005 mock 12H 3

source_name: SCL005 mock 12H 3

tag: time (post virus infection)


title: SCL005 mock 24H 2

source_name: SCL005 mock 24H 2

tag: treatment


title: SCL005 mock 12H 1

source_name: SCL005 mock 12H 1


title: SCL005 mock 7H 3

source_name: SCL005 mock 7H 3


title: KH190

tag: gender

tag: days before death/censor


title: SCL005 mock 3H 3

source_name: SCL005 mock 3H 3


title: KH142

tag: age (years)

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: SCL005 mock 7H 1

source_name: SCL005 mock 7H 1


title: KH144

tag: smoking status

tag: bi


title: KH141

tag: pathological stage

tag: pstage iorii


title: SCL005 mock 7H 2

source_name: SCL005 mock 7H 2


title: KH231

value: IB

tag: gene alteration status

tag: myc


title: KH234

tag: relapse


title: SCL005 mock 0H 3

source_name: SCL005 mock 0H 3

tag: cell line


title: KH140

tag: days before relapse/censor

tag: months before relapse/censor


title: KH130

tag: tissue

tag: death


title: SCL005 mock 3H 1

source_name: SCL005 mock 3H 1

tag: time (post virus infection)

tag: treatment


title: SCL005 mock 0H 2

source_name: SCL005 mock 0H 2


title: KH218

tag: gender

tag: days before death/censor


title: KH217

tag: age (years)

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: SCL005 mock 0H 1

source_name: SCL005 mock 0H 1


title: SCL005 mock 3H 2

source_name: SCL005 mock 3H 2


title: KH122

tag: smoking status

tag: bi


title: KH216

tag: pathological stage

tag: pstage iorii


title: KH215

tag: gene alteration status

tag: myc


title: TCL001 mock g 21h 2 B

source_name: Calu-3 mock g 21h 2

growth_protocol: Calu-3 cells were treated with 1000 Units/ml of INFa (Sigma I4276) or 500 Units/ml of IFN γ (Sigma I3265).  Each treated sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.)There are triplicate time-matched mock for each time point from the same cell stock as rest of samples. Calu-3 cells were seeded in 6-well plates (0.5 x 10^5 cells/well) two days prior to treatment. Cells were collected for RNA isolation at 0, 3, 6, and 18 or 22 h post treatment.

tag: time (post-treatment)

value: mock treated (associated with gamma treatment)

tag: cell line


title: KH136

source_name: frozen tissue of primary lung tumors

value: male

tag: relapse

tag: days before relapse/censor

tag: months before relapse/censor


title: TCL001 mock g 6h 3

source_name: Calu-3 mock g 6h 3


title: KH162

tag: tissue

tag: death


title: TCL001 mock g 3h 3

source_name: Calu-3 mock g 3h 3

tag: treatment


title: TCL001 mock g 6h 2

source_name: Calu-3 mock g 6h 2


title: TCL001 mock g 6h 1

source_name: Calu-3 mock g 6h 1


title: KH135

tag: gender

value: Ever-smoker

tag: days before death/censor


title: KH181

tag: age (years)

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: TCL001 mock g 3h 1

source_name: Calu-3 mock g 3h 1


title: TCL001 mock g 3h 2

source_name: Calu-3 mock g 3h 2


title: KH185

tag: smoking status

value: Never-smoker

tag: bi


title: TCL001 mock g 0h 1

source_name: Calu-3 mock g 0h 1


title: TCL001 mock g 21h 2


title: TCL001 mock g 21h 3

source_name: Calu-3 mock g 21h 3


title: TCL001 mock g 0h 3

source_name: Calu-3 mock g 0h 3


title: TCL001 mock a 6h 2

source_name: Calu-3 mock a 6h 2

value: mock treated (associated with alpha treatment)


title: KH120

value: primary lung tumor

tag: pathological stage

tag: pstage iorii


title: KH133

value: female

tag: gene alteration status

tag: myc


title: KH143

value: I


title: KH116

value: II

value: EGFR mutation +


title: TCL001 mock g 21h 1

source_name: Calu-3 mock g 21h 1

tag: time (post-treatment)

tag: cell line


title: KH173

value: Low

tag: relapse

value: not relapsed

tag: days before relapse/censor


title: KH079

tag: tissue

tag: months before relapse/censor

value: alive


title: KH044

tag: death


title: TCL001 mock a 6h 3

source_name: Calu-3 mock a 6h 3

tag: treatment


title: KH039

tag: gender

tag: days before death/censor


title: TCL001 mock g 0h 2

source_name: Calu-3 mock g 0h 2


title: TCL001 mock a 3h 1

source_name: Calu-3 mock a 3h 1


title: KH072

tag: age (years)

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: TCL001 mock a 3h 3

source_name: Calu-3 mock a 3h 3


title: KH034

tag: smoking status

tag: bi


title: TCL001 mock a 3h 2

source_name: Calu-3 mock a 3h 2


title: KH064

source_name: frozen tissue of primary lung tumors

tag: pathological stage

tag: pstage iorii


title: KH071

tag: gene alteration status

tag: myc


title: TCL001 mock a 18h 2

source_name: Calu-3 mock a 18h 2

tag: time (post-treatment)

tag: cell line


title: TCL001 mock a 6h 1

source_name: Calu-3 mock a 6h 1


title: TCL001 mock a 18h 3

source_name: Calu-3 mock a 18h 3


title: TCL001 mock a 0h 3

source_name: Calu-3 mock a 0h 3


title: TCL001 mock a 0h 2

source_name: Calu-3 mock a 0h 2


title: TCL001 mock a 18h 1

source_name: Calu-3 mock a 18h 1


title: KH084

value: IA

value: High

tag: relapse

value: relapsed

tag: days before relapse/censor

value: dead


title: KH075

tag: tissue

tag: months before relapse/censor

value: exclude


title: TCL001 IFNg 6h 1

source_name: Calu-3 IFNg 6h 1

tag: treatment

value: IFNgamma treated, 500 units/ml


title: TCL001 IFNg 6h 2

source_name: Calu-3 IFNg 6h 2


title: KH055

tag: gender

tag: death


title: TCL001 IFNg 6h 3

source_name: Calu-3 IFNg 6h 3


title: KH028

tag: age (years)

tag: days before death/censor


title: KH037

tag: smoking status

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: TCL001 mock a 0h 1

source_name: Calu-3 mock a 0h 1


title: KH053

value: male

value: Ever-smoker

tag: bi

tag: pathological stage


title: TCL001 IFNg 3h 2

source_name: Calu-3 IFNg 3h 2


title: KH086

tag: pstage iorii

tag: gene alteration status


title: KH257

value: IB

tag: myc


title: KH051

value: primary lung tumor


title: KH005


title: KH065

value: female

value: Never-smoker

value: nd


title: TCL001 IFNg 3h 3

source_name: Calu-3 IFNg 3h 3

tag: time (post-treatment)

tag: cell line


title: TCL001 IFNg 21h 3

source_name: Calu-3 IFNg 21h 3


title: KH093

value: I

value: EGFR mutation +

tag: relapse

tag: days before relapse/censor


title: KH030

tag: tissue

value: Low

tag: months before relapse/censor


title: KH023

tag: gender


title: KH010

tag: death


title: TCL001 IFNg 21h 2

source_name: Calu-3 IFNg 21h 2

tag: treatment


title: KH089

tag: age (years)

tag: days before death/censor


title: TCL001 IFNg 3h 1

source_name: Calu-3 IFNg 3h 1


title: KH062

tag: smoking status

value: alive

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: TCL001 IFNa 6h 1

source_name: Calu-3 IFNa 6h 1

value: IFNa treated, 1000 units/ml


title: TCL001 IFNg 21h 1

source_name: Calu-3 IFNg 21h 1


title: TCL001 IFNg 0h 1

source_name: Calu-3 IFNg 0h 1


title: TCL001 IFNg 0h 3

source_name: Calu-3 IFNg 0h 3


title: KH213

source_name: frozen tissue of primary lung tumors

tag: bi

tag: pathological stage


title: TCL001 IFNa 6h 3

source_name: Calu-3 IFNa 6h 3


title: TCL001 IFNg 0h 2

source_name: Calu-3 IFNg 0h 2


title: KH052

tag: pstage iorii

tag: gene alteration status


title: TCL001 IFNa 6h 2

source_name: Calu-3 IFNa 6h 2

tag: time (post-treatment)


title: KH009

value: II

tag: myc


title: KH033

tag: relapse

value: relapsed


title: TCL001 IFNa 3h 3

source_name: Calu-3 IFNa 3h 3

tag: cell line


title: KH032

tag: tissue

value: High

tag: days before relapse/censor


title: KH078

tag: gender

tag: months before relapse/censor

value: exclude


title: KH025

tag: death


title: TCL001 IFNa 3h 2

source_name: Calu-3 IFNa 3h 2

tag: treatment


title: TCL001 IFNa 18h 1

source_name: Calu-3 IFNa 18h 1


title: TCL001 IFNa 18h 2

source_name: Calu-3 IFNa 18h 2


title: KH038

tag: age (years)

value: dead

tag: days before death/censor


title: KH047

tag: smoking status

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: TCL001 IFNa 18h 3

source_name: Calu-3 IFNa 18h 3


title: KH021

value: male

tag: bi

tag: pathological stage


title: TCL001 IFNa 3h 1

source_name: Calu-3 IFNa 3h 1


title: KH008

value: Ever-smoker

tag: pstage iorii

tag: gene alteration status


title: KH056

tag: myc


title: TCL001 IFNa 0h 2

source_name: Calu-3 IFNa 0h 2

tag: time (post-treatment)


title: KH031

tag: relapse


title: KH057

tag: tissue


title: Mock 0hr

source_name: calu3,mock,0H,rep 1

growth_protocol: Calu-3 cells were infected with VN1203 and havested at 0, 1.5, 3, 7, 12, and 24 hours post-infection (hpi); Calu-3 cells were seeded in 6-well plates (1 x 106 cells/well) two days prior to infection; immediately preceding infection, monolayers were washed twice with DF12 supplemented with 0.3% bovine serum albumin (DF12-BSA); and cells were inoculated with VN1203 (multiplicity of infection [MOI] of 1 plaque forming unit [PFU] per cell) in DF12-BSA for 50 minutes at 37°C. Mock-infected controls were inoculated with DF12-BSA only. Following inoculation, monolayers were washed once with DF12-BSA and incubated in DF12-BSA containing 0.5 μg/ml of TPCK-treated trypsin (Worthington Biochemical Corporation, Lakewood, NJ) until cells were collected at 0, 1.5, 3, 7, 12, and 24 hours post-infection (hpi). The end of the inoculation period was considered the “0” hour time point.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

tag: time

tag: infection

value: mock infected

tag: cell line


title: 1203-1 3hr

source_name: calu3,vn1203 infected,3H,rep1

value: Influenza A/VN/1203/04 infected


title: KH002

value: primary lung tumor

tag: gender

value: female

tag: days before relapse/censor

tag: months before relapse/censor

tag: death


title: TCL001 IFNa 0h 1

source_name: Calu-3 IFNa 0h 1

tag: treatment


title: 1203-2 24hr

source_name: calu3,vn1203 infected,24H,rep 2


title: TCL001 IFNa 0h 3

source_name: Calu-3 IFNa 0h 3


title: 1203-2 12hr

source_name: calu3,vn1203 infected,12H,rep 2


title: Mock 24hr

source_name: calu3,mock,24H,rep 1


title: KH264

source_name: frozen tissue of primary lung tumors

tag: age (years)

tag: smoking status

value: Never-smoker

value: IA

value: EGFR/KRAS/ALK -

tag: cluster

tag: group

value: GroupB

value: not relapsed

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH061

tag: bi

tag: pathological stage

tag: pstage iorii

tag: gene alteration status

value: EGFR mutation +

tag: myc

value: Low

value: alive


title: 1203-2 0hr

source_name: calu3,vn1203 infected,0H,rep 2

tag: time

tag: infection

tag: cell line


title: 1203-1 1.5hr

source_name: calu3,vn1203 infected,1.5H,rep 1


title: KH261

tag: tissue

tag: gender

value: I

value: GroupA

tag: relapse

tag: days before relapse/censor

tag: months before relapse/censor


title: KH233

tag: age (years)

tag: smoking status

tag: cluster

tag: death


title: Mock 3hr


title: KH265

tag: bi

tag: group

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH247

tag: pathological stage

tag: pstage iorii

tag: gene alteration status

tag: myc


title: 1203-2 1.5hr

source_name: calu3,vn1203 infected,1.5H,rep 2

tag: time

tag: infection

tag: cell line


title: KH243

tag: tissue

tag: gender

value: High

tag: relapse

tag: days before relapse/censor


title: Mock 1.5hr

source_name: calu3,mock,1.5H,rep 1


title: KH256

tag: age (years)

tag: smoking status

tag: cluster

tag: months before relapse/censor


title: KH069

value: male

tag: bi

tag: group

tag: death

tag: days before death/censor


title: Mock 7hr

source_name: calu3,mock,7H,rep 1


title: KH172

value: Ever-smoker

tag: pathological stage

tag: pstage iorii

tag: gene alteration status

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH228

tag: myc


title: KH179

tag: tissue


title: 1203-1 0hr

source_name: calu3,vn1203 infected,0H,rep 1

tag: time

tag: infection

tag: cell line


title: Mock 12h

source_name: calu3,mock,12H,rep 1

value: mock infected


title: 1203-1 7hr

source_name: calu3,vn1203 infected,7H,rep 1

value: Influenza A/VN/1203/04 infected


title: 1203-2 3hr

source_name: calu3,vn1203 infected,3H,rep2


title: 1203-1 12hr

source_name: calu3,vn1203 infected,12H,rep 1


title: KH121

value: primary lung tumor

tag: age (years)

tag: gender

tag: relapse

tag: days before relapse/censor


title: KH177

tag: smoking status

tag: bi

tag: cluster

tag: months before relapse/censor


title: KH147

tag: pathological stage

tag: group

tag: death

tag: days before death/censor


title: KH155

value: female

tag: pstage iorii

tag: gene alteration status

tag: myc

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Donor 2 SMC Na rep 1

city: Nesher

first: Diana

last: Gershtein

address: Bar Yehuda Rd

country: Israel

institute: MGVS

description: Gene expression after gene transfer in human vascular cells

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. Briefly, 1.65ug Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent recommended hybridization chamber and oven).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System.

data_processing: The Agilent Feature Extraction Software was used to read out and process the microarray image files. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system.

source_name: untreated smooth muscle cells

label_protocol: For the linear T7-based amplification step, 1ug of totatl RNA was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Quick Amp Labeling kit (Agilent Technilogies) following the manufacturer's protocol.

growth_protocol: Human cells derived from a freshly stripped saphenous vein were cultured, subsequently transduced with either therapeuitic gene or reporter gene and after reaching the desired volume, harvested and snap frozen in LN2 for subsequent total RNA isolation.

extract_protocol: Frozen RNA samples were sent to Miltenyi Biotec for RNA isolation and array hybridization service. RNA was isolated using standard RNA extraction protocol (NucleoSpin RNA II, Macherey-Nagel).

tag: source tissue

value: vein

tag: cell type

value: smooth muscle cells

tag: donor

value: Donor 2

tag: treatment

value: untreated


title: Donor 2 SMC Lac Z rep 3

source_name: smooth muscle cells transduced with reporter gene

tag: gender

value: transduced with LacZ


title: KH161

tag: tissue

tag: age (years)

tag: smoking status

value: Never-smoker

value: IA

value: EGFR/KRAS/ALK -

value: GroupB

tag: relapse

value: not relapsed

tag: days before relapse/censor


title: 1203-1 24hr

source_name: calu3,vn1203 infected,24H,rep 1

tag: time

tag: infection

tag: cell line


title: KH156

tag: bi

tag: pathological stage

tag: pstage iorii

value: I

value: Low

tag: cluster

tag: group

tag: months before relapse/censor

tag: death

value: alive

tag: days before death/censor


title: Donor 2 SMC Na rep 2

tag: source tissue

tag: cell type

tag: gender

value: male

tag: donor

tag: treatment


title: Donor 2 SMC Lac Z rep 1


title: KH219

tag: tissue

tag: age (years)

tag: smoking status

value: Ever-smoker

value: IB

tag: gene alteration status

tag: myc

tag: relapse

tag: days before relapse/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Donor 2 SMC Lac Z rep 2


title: Donor 2 SMC VEGF rep 2

source_name: smooth muscle cells transduced with therapeutic gene

value: transduced with VEGF


title: KH163

value: primary lung tumor

tag: bi

tag: pathological stage

tag: pstage iorii

tag: cluster

tag: group


title: KH145

value: female

tag: months before relapse/censor

tag: death

tag: days before death/censor


title: KH268

tag: gender

value: High

value: GroupA


title: 1203-2 7hr

source_name: calu3,vn1203 infected,7H,rep 2

tag: time

tag: infection

value: Influenza A/VN/1203/04 infected

tag: cell line


title: KH123

tag: tissue

tag: age (years)

tag: smoking status

value: Never-smoker

tag: gene alteration status


title: KH152

value: IA

tag: myc

tag: relapse

tag: days before relapse/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Donor 2 SMC Na rep 3

tag: source tissue

value: vein

tag: cell type

value: smooth muscle cells

tag: donor

value: Donor 2

tag: treatment

value: untreated


title: Donor 2 SMC VEGF rep 1


title: Donor 2 endothelial cells Na rep 3

source_name: untreated endothelial cells

value: endothelial cells


title: Donor 2 SMC VEGF rep 3


title: Donor 2 endothelial cells Na rep 2


title: QA vs RMP

city: Philadelphia

first: James

middle: M.

last: Burns

state: PA

address: 2900 Queen Lane

department: Microbiology and Immunology

institute: Drexel University College of Medicine

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P11-s29.gpr
Channel 1 raw data file: P11-s30.gpr
Channel 1 raw data file: P11-s99.gpr
Channel 2 raw data file: P11-s84.gpr
Channel 2 raw data file: P11-s85.gpr
Channel 2 raw data file: P11-s102.gpr

hyb_protocol: Pairs of Cy3 and Cy5 labeled aRNA probes (1 µg/probe) were pooled, fragmented (Ambion RNA Fragmentation Reagent) and hybridized to the P. yoelii microarrays for 14-16 hours at 65oC.  Hybridization buffer included 20mM HEPES (pH 7), 3X SSC, 0.2% SDS, 10 µg poly d(A).  Hybridized slides were sequentially washed in 1X SSC, 0.03%SDS; 0.2X SSC, 0.05XSSC (2X) and rinsed in 0.01X SSC

scan_protocol: Slides were scanned using a GenePix 4000A microarray laser scanner (Axon Instruments, Inc., Union City, CA) and the fluorescence intensity of each DNA feature was determined at 532 nm (Cy3) and 635 nm (Cy5).    Data for each gene was obtained from replicate features on each array.    Fluorescence data were acquired and initially analyzed using GenePixPro 5.1 Software (Axon Instruments, Inc.).   Irregular and missing features flagged during image acquisition, features with a diameter of ≤ 60 µm and features with a signal to noise ratio (SNR) of <2 on the 532 nm channel and SNR <2 on the 635 nm channel were removed from the analysis.

data_processing: Cy3 and Cy5 fluorescence intensity data were processed and analyzed using limma version 2.18.2 (Linear Models for Microarray Data) through limmaGUI version 1.20.0 in the R programming environment (http://www.r-project.org).  The normexp method with an offset value of 16 was utilized for background correction.    Data were normalized using the print-tip loess method.    After fit of a linear model to the expression data, differential expression of genes in two samples was determined via the common reference (P. yoelii 17XL comparator) and a 'treatment-contrasts' parameterization.   Genes differentially expressed by at least 2 fold were identified (log2-fold change >1 or <-1) and considered significant based on a p-value ≤ 0.01 obtained from the moderated t-statistic and adjusted for multiple testing using the method of Benjamini and Hochberg.

organism: Plasmodium yoelii

source_name: Infected Quil A immunized

label_protocol: P. yoelii RNA (5 µg/sample) was amplified in the presence of aminoallyl-dUTP using the Amino Allyl MessageAmp II aRNA amplification kit (Ambion, Inc., Austin, TX).    aRNA was then fluorescently labeled by reaction with monofunctional, NHS-activated Cy3 or Cy5 dyes (Amersham Biosciences Inc., Piscataway, NJ).    Cy dye labeled aRNA was purified with yield and specific activity of each probe determined by absorption spectroscopy.

growth_protocol: Mice were infected by intraperitoneal injection of 100,000 P. yoelii 17X iRBCs obtained from a donor mice

extract_protocol: P. yoelii parasites were resuspended directly in the TRIzol Reagent (Invitrogen).    Total RNA was extracted, precipitated and purified using an RNeasy RNA isolation kit (Qiagen, Inc., Valencia, CA).

treatment_protocol: Blood from P. yoelii 17X infected mice was recovered at the indicated time points post-infection.  Infected RBCs were separated from uninfected RBCs by density gradient centrifugation on a 70% Percoll gradient (GE Healthcare, Uppsala, Sweden).    Recovered iRBCs were treated with PBS-0.05% saponin and intact parasites recovered by centrifugation.

tag: strain

tag: developmental stage

value: blood-stage parasites

source_name: Infected RMP immunized


title: KH212

source_name: frozen tissue of primary lung tumors

tag: gender

tag: bi

tag: pathological stage

tag: pstage iorii

value: I

value: EGFR/KRAS/ALK -

value: Low

tag: cluster

tag: group

value: not relapsed

tag: months before relapse/censor

tag: death

value: alive

tag: days before death/censor


title: WT vs JHD

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P14-s43.gpr
Channel 1 raw data file: P14-s44.gpr
Channel 1 raw data file: P14-s67.gpr
Channel 2 raw data file: P14-s41.gpr
Channel 2 raw data file: P14-s42.gpr
Channel 2 raw data file: P14-s66.gpr

source_name: Infected Balb/c-WT

source_name: Infected Balb/c-JHD


title: KH211

tag: tissue

value: primary lung tumor

tag: age (years)

value: male

tag: smoking status

value: IB

tag: gene alteration status

tag: myc

value: GroupB

tag: relapse

tag: days before relapse/censor


title: Donor 2 endothelial cells Lac Z rep 2

source_name: endothelial cells transduced with reporter gene

tag: source tissue

tag: cell type

tag: donor

tag: treatment

value: transduced with LacZ


title: Donor 2 endothelial cells Lac Z rep 3

tag: gender


title: KH221

value: Ever-smoker

tag: bi

tag: pathological stage

tag: pstage iorii

tag: cluster

value: GroupA

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Donor 2 endothelial cells Na rep 1

value: vein


title: D10 vs D14

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P12-s109.gpr
Channel 1 raw data file: P12-s110.gpr
Channel 1 raw data file: P12-s113.gpr
Channel 2 raw data file: P12-s111.gpr
Channel 2 raw data file: P12-s112.gpr
Channel 2 raw data file: P12-s114.gpr

source_name: Day 10 Post-Infection

tag: strain

tag: developmental stage

source_name: Day 14 Post-Infection


title: I1 vs I4

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P11-s29.gpr
Channel 1 raw data file: P11-s30.gpr
Channel 1 raw data file: P11-s99.gpr
Channel 2 raw data file: P14-s43.gpr
Channel 2 raw data file: P14-s44.gpr
Channel 2 raw data file: P14-s67.gpr

source_name: Infection #1

source_name: Infection #4


title: I2 vs I4

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P12-s109.gpr
Channel 1 raw data file: P12-s110.gpr
Channel 1 raw data file: P12-s113.gpr
Channel 2 raw data file: P14-s43.gpr
Channel 2 raw data file: P14-s44.gpr
Channel 2 raw data file: P14-s67.gpr

source_name: Infection #2


title: I2 vs I3

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P12-s109.gpr
Channel 1 raw data file: P12-s110.gpr
Channel 1 raw data file: P12-s113.gpr
Channel 2 raw data file: P13-s38.gpr
Channel 2 raw data file: P13-s40.gpr

source_name: Infection #3


title: KH182

tag: tissue

tag: age (years)

tag: smoking status

tag: group

tag: months before relapse/censor

tag: death

tag: days before death/censor


title: Donor 2 endothelial cells Lac Z rep 1

tag: source tissue

tag: cell type

tag: donor

value: Donor 2


title: I1 vs I3

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P11-s29.gpr
Channel 1 raw data file: P11-s30.gpr
Channel 1 raw data file: P11-s99.gpr
Channel 2 raw data file: P13-s38.gpr
Channel 2 raw data file: P13-s40.gpr


title: KH180

tag: gender

tag: bi

tag: gene alteration status

tag: myc

tag: relapse

tag: days before relapse/censor


title: I1 vs I2

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P11-s29.gpr
Channel 1 raw data file: P11-s30.gpr
Channel 1 raw data file: P11-s99.gpr
Channel 2 raw data file: P12-s109.gpr
Channel 2 raw data file: P12-s110.gpr
Channel 2 raw data file: P12-s113.gpr

tag: strain

tag: developmental stage


title: I3 vs I4

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P13-s38.gpr
Channel 1 raw data file: P13-s40.gpr
Channel 2 raw data file: P14-s43.gpr
Channel 2 raw data file: P14-s44.gpr
Channel 2 raw data file: P14-s67.gpr


title: Donor 2 endothelial cells Ang rep 3

source_name: endothelial cells transduced with therapeutic gene

tag: treatment

value: transduced with Ang


title: D vs M3

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P15-s68.gpr
Channel 1 raw data file: P15-s72.gpr
Channel 1 raw data file: P15-s76.gpr
Channel 2 raw data file: P18-s71.gpr
Channel 2 raw data file: P18-s75.gpr
Channel 2 raw data file: P18-s79.gpr

source_name: Infected Donor Mouse

source_name: Infected Mouse #3


title: KH171

tag: tissue

tag: age (years)

value: female

tag: smoking status

value: Never-smoker

tag: pathological stage

tag: pstage iorii

tag: cluster

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH160

value: I

tag: group

tag: months before relapse/censor

tag: death

tag: days before death/censor


title: Donor 2 endothelial cells Ang rep 1

tag: source tissue

tag: cell type

value: endothelial cells

tag: gender

tag: donor


title: D vs M2

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P15-s68.gpr
Channel 1 raw data file: P15-s72.gpr
Channel 1 raw data file: P15-s76.gpr
Channel 2 raw data file: P17-s70.gpr
Channel 2 raw data file: P17-s74.gpr
Channel 2 raw data file: P17-s78.gpr

tag: strain

tag: developmental stage

value: blood-stage parasites

source_name: Infected Mouse #2


title: Donor 2 endothelial cells Ang rep 2

tag: treatment


title: KH074

tag: tissue

tag: age (years)

tag: bi

tag: gene alteration status

value: EGFR mutation +

tag: myc

value: Low

tag: relapse

value: relapsed

tag: days before relapse/censor


title: KH125

value: primary lung tumor

tag: smoking status

tag: pathological stage

tag: pstage iorii

value: EGFR/KRAS/ALK -

tag: cluster

tag: group

value: not relapsed

tag: months before relapse/censor

value: alive

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: M1 vs M3

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P16-s69.gpr
Channel 1 raw data file: P16-s73.gpr
Channel 1 raw data file: P16-s77.gpr
Channel 2 raw data file: P18-s71.gpr
Channel 2 raw data file: P18-s75.gpr
Channel 2 raw data file: P18-s79.gpr

source_name: Infected Mouse #1

tag: strain


title: KH016

tag: gender

value: II

value: GroupB

tag: death

tag: days before death/censor


title: M1 vs M2

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P16-s69.gpr
Channel 1 raw data file: P16-s73.gpr
Channel 1 raw data file: P16-s77.gpr
Channel 2 raw data file: P17-s70.gpr
Channel 2 raw data file: P17-s74.gpr
Channel 2 raw data file: P17-s78.gpr

tag: developmental stage


title: ExactMatch_4

city: Koto

first: Jun

last: Sese

state: Tokyo

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole 8x15k Oligo Microarrays (027003) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 030829_D_F_20101021) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

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

extract_protocol: All RNAs are provided by Takara Co. Ltd. We extracted them accroding to their manuals.

tag: sample type

value: reference total RNA


title: M2 vs M3

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P17-s70.gpr
Channel 1 raw data file: P17-s74.gpr
Channel 1 raw data file: P17-s78.gpr
Channel 2 raw data file: P18-s71.gpr
Channel 2 raw data file: P18-s75.gpr
Channel 2 raw data file: P18-s79.gpr


title: D vs M1

description:
Test RNA on each array compared to P. yoelii 17XL total RNA reference.

Raw files listed below are linked to the Series record:
Channel 1 raw data file: P15-s68.gpr
Channel 1 raw data file: P15-s72.gpr
Channel 1 raw data file: P15-s76.gpr
Channel 2 raw data file: P16-s69.gpr
Channel 2 raw data file: P16-s73.gpr
Channel 2 raw data file: P16-s77.gpr


title: ExactMatch_5


title: Donor 1 SMC Na rep 1

source_name: untreated smooth muscle cells

tag: source tissue

value: vein

tag: cell type

value: smooth muscle cells

value: male

tag: donor

value: Donor 1

tag: treatment

value: untreated


title: Donor 1 SMC Na rep 3


title: KH118

description: Gene expression data from primary lung ADC

tag: tissue

tag: age (years)

tag: smoking status

value: Ever-smoker

tag: bi

tag: gene alteration status

tag: myc

value: GroupA

tag: relapse

tag: days before relapse/censor


title: ExactMatch_6


title: ExactMatch_3


title: KH015

tag: gender

tag: pathological stage

tag: pstage iorii

tag: cluster

tag: group

tag: months before relapse/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: ExactMatch_2

tag: sample type


title: Donor 1 SMC Na rep 2

description: Gene expression after gene transfer in human vascular cells

tag: source tissue

tag: cell type

tag: donor

tag: treatment


title: ExactMatch_1


title: RM10002-Stationary phase-REP3

type: mixed

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

hyb_protocol: Labeled reference genomic DNA and test cDNAs were combined in 45 µl Pronto! cDNA hybridization solution (Corning, Corning, NY) and heated to 95°C for 5 min. Then, 15 µl of the hybridization mixture was put onto a microarray slide and sealed with a cover slip. The microarray slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18 h. Following hybridization, the slides were washed twice in 2× SSC, 0.1% sodium dodecyl sulfate at 42°C for 10 min, followed by twice in 1× SSC at room temperature for 10 min, and finally twice in 0.2× SSC at room temperature for 5 min. The microarray slides were dried by centrifugation at 300 × g for 10 min before scanning.

scan_protocol: Scanned on an Axon GenePix4000B scanner at 10nm resolution using GenePix software. Images were quantified using GenePix software (version 6.0).

data_processing: Fluorescence ratios were calculated after local background was subtracted from spot signals. To compensate for any effect of the amount of template and uneven Cy-dye incorporation, data normalization (centering) was performed by bringing the median natural logarithm of the ratios for each group of spots printed by the same pin to zero using the following equation: ln(Ti ) = ln(Ri /Gi ) - c, where T is the centered ratio, i is the gene index, R and G are the red and green intensities, respectively, and c is the 50th percentile of all red/green ratios.

organism: Escherichia coli O157:H7

source_name: Escherichia coli RM10002-Stationary phase

label_protocol: 2 µg of genomic DNA were Cy5-dUTP labeled during random primed synthesis with Klenow fragment (NEB) at 37°C for 16 h. 20 µg of total RNA were labeled during reverse transcription with random primed hexamers to cDNA with Cy3-dUTP using Stratascript (Stratagene, Palo Alto, CA) at 42°C for 16 h.

growth_protocol: Liquid cultures of E. coli were obtained by inoculation of colonies into LB broth and growth at 37°C with shaking (150 rpm) to stationary phase (16 h).

extract_protocol: Total E. coli RNA was extracted from stationary phase cultures with the Promega SV Total RNA Isolation Kit according to the manufacturer’s specifications.

tag: strain

value: Escherichia coli O157:H7 str. RM10002

source_name: Genomic DNA E. coli strain RM6067

extract_protocol: E. coli genomic DNA was prepared with the Qiagen Dneasy Blood and Tissue kit.

value: Escherichia coli O157:H7 str. RM6067


title: RM10002-Stationary phase-REP2


title: RM10002-Stationary phase-REP1


title: KH082

source_name: frozen tissue of primary lung tumors

tag: tissue

tag: age (years)

tag: smoking status

tag: bi

tag: gene alteration status

value: High

tag: death

tag: days before death/censor


title: KH003

value: primary lung tumor

tag: gender

tag: pathological stage

tag: pstage iorii

tag: myc

value: Low

tag: cluster

tag: relapse

tag: days before relapse/censor

value: exclude


title: Donor 1 SMC VEGF rep 3

source_name: smooth muscle cells transduced with therapeutic gene

tag: source tissue

tag: cell type

tag: donor

value: transduced with VEGF


title: KH046

tag: tissue

value: II

value: EGFR/KRAS/ALK -

tag: group

value: not relapsed

tag: months before relapse/censor

value: alive

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Donor 1 SMC Lac Z rep 3

source_name: smooth muscle cells transduced with reporter gene

value: vein

value: smooth muscle cells

tag: treatment

value: transduced with LacZ


title: Donor 1 SMC Lac Z rep 2

value: male

value: Donor 1


title: Donor 1 SMC Lac Z rep 1


title: RM9998-Stationary phase-REP2

source_name: Escherichia coli RM9998-Stationary phase

tag: strain

value: Escherichia coli O157:H7 str. RM9998


title: KH017

tag: age (years)

value: female

tag: smoking status

value: Ever-smoker

tag: bi

tag: gene alteration status

value: GroupA

tag: death

tag: days before death/censor


title: RM9998-Stationary phase-REP3

value: Escherichia coli O157:H7 str. RM6067


title: RM9998-Stationary phase-REP1


title: RM9997-Stationary phase-REP3

source_name: Escherichia coli RM9997-Stationary phase

value: Escherichia coli O157:H7 str. RM9997


title: KH050

value: primary lung tumor

tag: gender

tag: pathological stage

tag: pstage iorii

tag: myc

value: Low

tag: cluster

value: GroupB

tag: relapse


title: RM9997-Stationary phase-REP2


title: RM9992-Stationary phase-REP2

source_name: Escherichia coli RM9992-Stationary phase

value: Escherichia coli O157:H7 str. RM9992


title: RM9992-Stationary phase-REP1


title: RM9992-Stationary phase-REP3


title: RM9997-Stationary phase-REP1


title: Donor 1 SMC VEGF rep 2

tag: source tissue

tag: cell type

tag: donor

value: transduced with VEGF


title: RM6658-Stationary phase-REP3

source_name: Escherichia coli RM6658-Stationary phase

value: Escherichia coli O157:H7 str. RM6658


title: KH117

tag: tissue

value: Never-smoker

value: II

value: EGFR/KRAS/ALK -

tag: group

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

value: dead

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH013

tag: age (years)

value: male

tag: smoking status

tag: bi

tag: gene alteration status

value: alive


title: KH153

tag: gender

tag: pathological stage

value: IA

value: I

value: High

tag: death

tag: days before death/censor


title: KH132

value: female

tag: pstage iorii

tag: myc

tag: cluster

tag: relapse

value: relapsed


title: KH041

tag: tissue

value: primary lung tumor

value: Low


title: RM6655-Stationary phase-REP3

source_name: Escherichia coli RM6655-Stationary phase

tag: strain

value: Escherichia coli O157:H7 str. RM6655

value: Escherichia coli O157:H7 str. RM6067


title: RM6658-Stationary phase-REP2

value: Escherichia coli O157:H7 str. RM6658


title: RM6658-Stationary phase-REP1


title: Donor 1 SMC VEGF rep 1

tag: source tissue

value: vein

tag: cell type

value: smooth muscle cells

tag: donor

value: Donor 1

tag: treatment

value: transduced with VEGF


title: KH092

tag: age (years)

tag: smoking status

value: Never-smoker

value: EGFR/KRAS/ALK -

tag: group

value: GroupB

tag: days before relapse/censor

tag: months before relapse/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy

value: exclude


title: Donor 1 endothelial cells Na rep 2

source_name: untreated endothelial cells

value: endothelial cells

tag: gender

value: male

value: untreated


title: Donor 1 endothelial cells Na rep 3


title: RM6655-Stationary phase-REP2


title: RM6149-Stationary phase-REP3

source_name: Escherichia coli RM6149-Stationary phase

value: Escherichia coli O157:H7 str. RM6149


title: Donor 1 endothelial cells Lac Z rep 3

source_name: endothelial cells transduced with reporter gene

value: transduced with LacZ


title: RM6149-Stationary phase-REP2


title: RM6655-Stationary phase-REP1


title: RM6149-Stationary phase-REP1


title: RM6103-Stationary phase-REP3

source_name: Escherichia coli RM6103-Stationary phase

value: Escherichia coli O157:H7 str. RM6103


title: RM6103-Stationary phase-REP1


title: RM6103-Stationary phase-REP2


title: Donor 1 endothelial cells Ang rep 2

source_name: endothelial cells transduced with therapeutic gene

value: transduced with Ang


title: KH018

value: primary lung tumor

value: female

tag: bi

tag: pathological stage

value: IA

tag: pstage iorii

value: I

tag: gene alteration status

value: Low

value: GroupA

value: relapsed

tag: death

value: dead

tag: days before death/censor


title: RM6102-Stationary phase-REP3

source_name: Escherichia coli RM6102-Stationary phase

tag: strain

value: Escherichia coli O157:H7 str. RM6102

value: Escherichia coli O157:H7 str. RM6067


title: KH045

tag: tissue

value: Ever-smoker

value: EGFR/KRAS/ALK -

tag: myc

tag: cluster

tag: relapse


title: KH090

tag: age (years)

tag: smoking status

value: Never-smoker

value: IB

value: alive


title: RM6102-Stationary phase-REP2


title: Donor 1 endothelial cells Lac Z rep 1

tag: source tissue

value: vein

tag: cell type

value: endothelial cells

value: male

tag: donor

value: Donor 1

tag: treatment

value: transduced with LacZ


title: Donor 1 endothelial cells Ang rep 3

tag: gender

value: transduced with Ang


title: RM6101-Stationary phase-REP3

source_name: Escherichia coli RM6101-Stationary phase

value: Escherichia coli O157:H7 str. RM6101


title: RM6102-Stationary phase-REP1


title: Donor 1 endothelial cells Ang rep 1


title: RM6101-Stationary phase-REP2


title: KH094

value: primary lung tumor

value: female

tag: bi

tag: pathological stage

value: I

value: Low

tag: group

value: GroupB

tag: days before relapse/censor

tag: months before relapse/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: RM6069-Stationary phase-REP3

source_name: Escherichia coli RM6069-Stationary phase

tag: strain

value: Escherichia coli O157:H7 str. RM6069

value: Escherichia coli O157:H7 str. RM6067


title: Donor 1 endothelial cells Lac Z rep 2


title: KH049

tag: tissue

value: Ever-smoker

tag: pstage iorii

tag: gene alteration status

value: EGFR/KRAS/ALK -

tag: myc

value: GroupA

value: relapsed

tag: death

value: dead

tag: days before death/censor


title: RM6101-Stationary phase-REP1

source_name: Genomic DNA E. coli strain RM6067


title: KH087

source_name: frozen tissue of primary lung tumors

tag: age (years)

value: male

tag: smoking status

value: IB

tag: cluster

tag: relapse


title: KH159

tag: gender

value: Never-smoker

tag: bi

value: IA


title: KH011

tag: pathological stage

tag: group


title: RM6069-Stationary phase-REP2


title: RM6067-Stationary phase-REP3

source_name: Escherichia coli RM6067-Stationary phase


title: RM6069-Stationary phase-REP1


title: RM6067-Stationary phase-REP2


title: high grade GIST 12

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description: gene expression in clinical GIST

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 9.5) was used for background subtraction.

source_name: Human GIST tissue 12

label_protocol: Total RNA (700 ng) was labeled using a Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

extract_protocol: Total RNA was extracted using a mirVana miRNA isolation kit (Ambion).

value: gastrointestinal stromal tumor

tag: grade

value: high

tag: location

value: small intestine

tag: age

value: F


title: KH001

tag: tissue

value: primary lung tumor

value: I

value: High

tag: days before relapse/censor

tag: months before relapse/censor

value: alive

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: RM6067-Stationary phase-REP1

tag: strain

value: Escherichia coli O157:H7 str. RM6067


title: KH073

value: Ever-smoker

tag: pstage iorii

tag: gene alteration status

value: EGFR/KRAS/ALK -

tag: myc

value: Low

tag: death

tag: days before death/censor


title: high grade GIST 11

description: gene expression in clinical GIST

source_name: Human GIST tissue 11

value: stomach

tag: gender

value: M


title: low grade GIST 13

description: gene expression in clinical GIST

source_name: Human GIST tissue 13

value: low


title: intermediate grade GIST 8

description: gene expression in clinical GIST

source_name: Human GIST tissue 8

value: intermediate


title: KH148

tag: age (years)

value: male

tag: smoking status

tag: bi

value: IB

tag: cluster

value: GroupA

tag: relapse

value: relapsed

value: dead


title: low grade GIST 14

description: gene expression in clinical GIST

source_name: Human GIST tissue 14

value: gastrointestinal stromal tumor

tag: grade

tag: location

tag: age

value: F


title: KH070

tag: tissue

value: primary lung tumor

tag: pathological stage

value: I

tag: group

tag: days before relapse/censor

tag: months before relapse/censor


title: high grade GIST 9

description: gene expression in clinical GIST

source_name: Human GIST tissue 9

value: high


title: high grade GIST 7

description: gene expression in clinical GIST

source_name: Human GIST tissue 7


title: KH048

value: Ever-smoker

tag: pstage iorii

tag: gene alteration status

tag: myc

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy

value: exclude


title: intermediate grade GIST 10

description: gene expression in clinical GIST

source_name: Human GIST tissue 10

value: small intestine

tag: gender


title: KH036

tag: age (years)

tag: smoking status

value: II

value: EGFR/KRAS/ALK -

value: Low

tag: death

tag: days before death/censor


title: unknown grade GIST 6

description: gene expression in clinical GIST

source_name: Human GIST tissue 6

tag: grade

value: stomach


title: high grade GIST 4

description: gene expression in clinical GIST

source_name: Human GIST tissue 4

tag: location


title: KH059

value: male

tag: bi

tag: cluster

value: GroupB

tag: relapse

value: alive


title: low grade GIST 5

description: gene expression in clinical GIST

source_name: Human GIST tissue 5

tag: tissue

value: low

tag: age


title: high grade GIST 3

description: gene expression in clinical GIST

source_name: Human GIST tissue 3


title: KH063

value: female

value: Never-smoker

tag: pathological stage

tag: group

value: relapsed

tag: days before relapse/censor

tag: months before relapse/censor

value: dead


title: high grade GIST 2

description: gene expression in clinical GIST

source_name: Human GIST tissue 2

value: gastrointestinal stromal tumor

value: M


title: KH080

value: primary lung tumor

tag: pstage iorii

tag: gene alteration status

tag: myc

value: GroupA

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: high grade GIST 1

description: gene expression in clinical GIST

source_name: Human GIST tissue 1

value: high

tag: gender


title: KH026

tag: age (years)

tag: smoking status

value: II

tag: death

tag: days before death/censor


title: KH077

value: Ever-smoker

tag: bi

value: EGFR/KRAS/ALK -

tag: cluster


title: KH035

tag: tissue

value: Low

tag: relapse


title: KH060

value: male

tag: pathological stage


title: KH006

tag: group

value: GroupB


title: Infant at timeC, rep128

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

hyb_protocol: GeneChip Hybridization Oven, 16-18 hours, 45oC, 60 rotations/min; washing and staining on Fluidics Station 450, protocol FS450_0007

scan_protocol: GeneChip Scanner 3000 7G controlled by GeneChip Operating Software

data_processing: Robust multiarray average (R/Bioconductor, using the library aroma.affymetrix)

source_name: Infant at 24-33 days of life rep 128

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Samples were collected from children in the Neonatal Intensive Care Unit of the University Children's Hospital

extract_protocol: Ficoll isopaque gradient centrifugation and RiboPure Blood Kit (Ambion, Life Technologies, Carlsbad, USA) were used for total RNA extraction

treatment_protocol: Blood samples (0.3 ml) were drawn from all the study participants on the 5th, 14th and 28th day of life for the assessment of whole genome expression in peripheral blood leukocytes.

value: blood

tag: days of life

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 1 (oxygen therapy =>28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 1 (on oxygen at the age of 36 wpma)

tag: bronchopulmonary dysplasia (bpd) group

value: 3 (severe BPD)

tag: retinopathy of prematurity (rop) group

value: 2 (ROP which need laser therapy)

tag: rop lasertherapy

value: 1 (laser therapy  due to prethreshold or threshold ROP)

tag: periventricular leukomalacia (pvl)

value: 1 (PVL)


title: KH043

source_name: frozen tissue of primary lung tumors

value: primary lung tumor

tag: age (years)

tag: gender

tag: smoking status

tag: pstage iorii

tag: gene alteration status

tag: myc

value: relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: dead

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Infant at timeC, rep130

source_name: Infant at 24-33 days of life rep 130

tag: tissue

tag: days of life

value: 1 (female)

tag: gestational age (weeks)

tag: birth weight (grams)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (mild BPD)

value: 0 (no PVL)


title: SK Mel-28_TiO2_5ug/cm2

city: Salt Lake City

first: Philip

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description:
TiO2 at low dose v. control
raw file: 6536E11_251485041038_S01_GE2-v5.1_10_Apr08_2_1_3.txt

hyb_protocol: Agilent two-color GE hyb/wash protocol

scan_protocol: Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802

data_processing: Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted

source_name: SK Mel-28_TiO2_5ug/cm2

label_protocol: Agilent two-color LRILAK labeling protocol

growth_protocol: All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Advanced DMEM media (supplemented with 2% FBS, and glutamax) and allowed to begin growing overnight.

extract_protocol: Total RNA was collected using Qiagen RNeasy Mini kits.

treatment_protocol:
Cells were allowed to grow overnight, then media was removed and replaced with 2 ml of media with the nanoparticulate material for 4 hrs prior to RNA collection. Three biological replicates were combined for the gene expression analysis for each experimental group, six control samples were processed and three were combined for each of the control experiments - all six control samples were combined for the Cy3 channel control sample.
For cells grown in Transwell inserts, cells were plated into the Transwell and the particulate was added outside the Transwell insert.

tag: cell line

value: SK Mel-28

tag: agent

tag: dose

value: 5 μg/cm2

source_name: SK Mel-28 [reference]

value: media control


title: SK Mel-28_ZnCl2_100uM

description:
soluble ZnCl2 v. control
raw file: 7287E3_251485056075_S01_GE2-v5.1_10_Apr08_2_1_3.txt

source_name: SK Mel-28_ZnCl2_100uM


title: Infant at timeC, rep131

source_name: Infant at 24-33 days of life rep 131

value: blood

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

tag: bronchopulmonary dysplasia (bpd) group

value: 0 (no BPD)

tag: retinopathy of prematurity (rop) group

value: 0 (no ROP)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)


title: SK Mel-28_TiO2_10ug/cm2

description:
TiO2 at modest dose v. control
raw file: 6536E12_251485041038_S01_GE2-v5.1_10_Apr08_2_1_4.txt

source_name: SK Mel-28_TiO2_10ug/cm2

value: 10 μg/cm2


title: Infant at timeC, rep132

source_name: Infant at 24-33 days of life rep 132

tag: gender

value: 2 (male)


title: Infant at timeC, rep129

source_name: Infant at 24-33 days of life rep 129


title: SK Mel-28_ZnO_1ug/cm2

description:
ZnO at low dose v. control
raw file: 6536E9_251485041038_S01_GE2-v5.1_10_Apr08_2_1_1.txt

source_name: SK Mel-28_ZnO_1ug/cm2

value: ZnO

value: 1 μg/cm2


title: Infant at timeC, rep122

source_name: Infant at 24-33 days of life rep 122


title: SK Mel-28_control 2

description:
control v. control to highlight Cy-dye hyb preference
raw file: 6536E8_251485038477_S01_GE2-v5.1_10_Apr08_2_1_4.txt

source_name: SK Mel-28_control 2


title: Donor 1 endothelial cells Na rep 1

source_name: untreated endothelial cells

tag: source tissue

value: vein

tag: cell type

value: endothelial cells

value: male

tag: donor

value: Donor 1

tag: treatment

value: untreated


title: Infant at timeC, rep120

source_name: Infant at 24-33 days of life rep 120

tag: tissue

tag: days of life

value: 1 (oxygen therapy =>28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (mild BPD)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 0 (no PVL)


title: KH230

value: primary lung tumor

tag: age (years)

value: female

tag: smoking status

value: Never-smoker

tag: bi

tag: pathological stage

value: IA

tag: pstage iorii

value: I

tag: gene alteration status

value: KRAS mutation +

tag: myc

value: Low

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: alive

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Infant at timeC, rep121

source_name: Infant at 24-33 days of life rep 121

value: blood

tag: gender

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 1 (on oxygen at the age of 36 wpma)

tag: bronchopulmonary dysplasia (bpd) group

value: 2 (moderate BPD)

tag: retinopathy of prematurity (rop) group

tag: rop lasertherapy

tag: periventricular leukomalacia (pvl)


title: KH237

tag: tissue

tag: age (years)

tag: smoking status

tag: bi

tag: pathological stage

tag: pstage iorii

tag: gene alteration status


title: Infant at timeC, rep118

source_name: Infant at 24-33 days of life rep 118

tag: days of life

value: 1 (oxygen therapy =>28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 1 (mild BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Infant at timeC, rep116

source_name: Infant at 24-33 days of life rep 116

tag: gender

value: 1 (female)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 0 (no PVL)


title: Infant at timeC, rep119

source_name: Infant at 24-33 days of life rep 119

tag: gestational age (weeks)


title: KH168

source_name: frozen tissue of primary lung tumors

value: primary lung tumor

value: male

value: Ever-smoker

value: IA

value: I

value: KRAS mutation +

tag: myc

tag: relapse

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH183

tag: tissue

value: female

value: Never-smoker

value: Low

value: not relapsed

value: alive


title: SK Mel-28_control 1

description:
control v. control to highlight Cy-dye hyb preference
raw file: 6536E7_251485038477_S01_GE2-v5.1_10_Apr08_2_1_3.txt

source_name: SK Mel-28_control 1

tag: cell line

value: SK Mel-28

tag: agent

value: media control


title: Infant at timeC, rep115

source_name: Infant at 24-33 days of life rep 115

value: blood

value: 1 (female)

tag: birth weight (grams)

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 0 (no BPD)

tag: retinopathy of prematurity (rop) group

value: 0 (no ROP)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)


title: SK Mel-28_ZnO_5ug/cm2

description:
ZnO at modest dose v. control
raw file: 6536E10_251485041038_S01_GE2-v5.1_10_Apr08_2_1_2.txt

source_name: SK Mel-28_ZnO_5ug/cm2

value: ZnO

tag: dose

value: 5 μg/cm2

source_name: SK Mel-28 [reference]


title: HaCaT_ZnO_5ug/cm2_Transwell

description:
soluble Zn liberated from ZnO v. control
raw file: 7287E2_251485056075_S01_GE2-v5.1_10_Apr08_2_1_2.txt

value: HaCaT

source_name: HaCaT [reference]


title: HaCaT_ZnCl2_100uM

description:
soluble ZnCl2 v. control
raw file: 7287E1_251485056075_S01_GE2-v5.1_10_Apr08_2_1_1.txt


title: Infant at timeC, rep111

source_name: Infant at 24-33 days of life rep 111

tag: days of life

tag: gender

value: 2 (male)

tag: gestational age (weeks)

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 1 (ROP not requiring treatment)

value: 0 (no PVL)


title: Infant at timeC, rep113

source_name: Infant at 24-33 days of life rep 113

value: 2 (moderate BPD)


title: KH222

value: primary lung tumor

tag: age (years)

value: female

tag: smoking status

value: Never-smoker

tag: bi

tag: pathological stage

value: IB

tag: pstage iorii

value: I

tag: gene alteration status

value: KRAS mutation +

tag: myc

value: Low

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: alive


title: HaCaT_TiO2_10ug/cm2

description:
TiO2 at modest dose v. control
raw file: 6536E6_251485038477_S01_GE2-v5.1_10_Apr08_2_1_2.txt

tag: cell line

value: HaCaT

tag: agent

value: 10 μg/cm2

value: media control


title: KH266

tag: tissue

value: male

value: Ever-smoker

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: KH232

tag: gender


title: Infant at timeC, rep106

source_name: Infant at 24-33 days of life rep 106

value: blood

tag: days of life

value: 1 (female)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 1 (oxygen therapy =>28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 1 (mild BPD)

tag: retinopathy of prematurity (rop) group

value: 0 (no ROP)

tag: rop lasertherapy

value: 0 (no lasertherapy)

tag: periventricular leukomalacia (pvl)


title: Infant at timeC, rep114

source_name: Infant at 24-33 days of life rep 114

value: 2 (male)

value: 2 (ROP which need laser therapy)

value: 1 (laser therapy  due to prethreshold or threshold ROP)

value: 0 (no PVL)


title: Infant at timeC, rep112

source_name: Infant at 24-33 days of life rep 112

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)


title: Infant at timeC, rep108

source_name: Infant at 24-33 days of life rep 108

value: 1 (ROP not requiring treatment)


title: Infant at timeC, rep110

source_name: Infant at 24-33 days of life rep 110


title: Infant at timeC, rep109

source_name: Infant at 24-33 days of life rep 109


title: Infant at timeC, rep105

source_name: Infant at 24-33 days of life rep 105

value: 1 (PVL)


title: Infant at timeC, rep104

source_name: Infant at 24-33 days of life rep 104

value: 2 (moderate BPD)


title: HaCaT_TiO2_5ug/cm2

description:
TiO2 at low dose v. control
raw file: 6536E5_251485038477_S01_GE2-v5.1_10_Apr08_2_1_1.txt

value: HaCaT

tag: dose

value: 5 μg/cm2

value: media control


title: Infant at timeC, rep100

source_name: Infant at 24-33 days of life rep 100

value: blood

value: 1 (female)

value: 1 (oxygen therapy =>28 days)


title: HaCaT_ZnO_1ug/cm2

description:
ZnO at low dose v. control
raw file: 6536E3_251485038476_S01_GE2-v5.1_10_Apr08_2_1_3.txt

value: ZnO

value: 1 μg/cm2


title: HaCaT_ZnO_5ug/cm2

description:
ZnO at modest dose v. control
raw file: 6536E4_251485038476_S01_GE2-v5.1_10_Apr08_2_1_4.txt


title: KH154

source_name: frozen tissue of primary lung tumors

value: primary lung tumor

tag: age (years)

value: female

tag: smoking status

value: Never-smoker

tag: bi

tag: pathological stage

value: IB

tag: pstage iorii

value: I

tag: gene alteration status

value: KRAS mutation +

tag: myc

value: Low

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

tag: death

value: alive


title: KH129

tag: tissue

tag: gender

value: male

value: Ever-smoker

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Infant at timeC, rep101

source_name: Infant at 24-33 days of life rep 101

tag: days of life

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 1 (on oxygen at the age of 36 wpma)

tag: bronchopulmonary dysplasia (bpd) group

value: 2 (moderate BPD)

tag: retinopathy of prematurity (rop) group

value: 2 (ROP which need laser therapy)

tag: rop lasertherapy

value: 1 (laser therapy  due to prethreshold or threshold ROP)

tag: periventricular leukomalacia (pvl)

value: 0 (no PVL)


title: Infant at timeC, rep99

source_name: Infant at 24-33 days of life rep 99

value: blood

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: HaCaT_control 1

description:
control v. control to highlight Cy-dye hyb preference
raw file: 6536E1_251485038476_S01_GE2-v5.1_10_Apr08_2_1_1.txt

source_name: HaCaT_control 1

tag: cell line

value: HaCaT

tag: agent

value: media control


title: Infant at timeC, rep98

source_name: Infant at 24-33 days of life rep 98

value: 1 (oxygen therapy =>28 days)

value: 1 (mild BPD)


title: HaCaT_control 2

description:
control v. control to highlight Cy-dye hyb preference
raw file: 6536E2_251485038476_S01_GE2-v5.1_10_Apr08_2_1_2.txt

source_name: HaCaT_control 2

source_name: HaCaT [reference]


title: KH068

description: Gene expression data from primary lung ADC

value: primary lung tumor

tag: age (years)

value: male

tag: smoking status

value: Ever-smoker

tag: bi

tag: pathological stage

value: II

tag: pstage iorii

tag: gene alteration status

value: KRAS mutation +

tag: myc

value: Low

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: months before relapse/censor

value: alive


title: Infant at timeC, rep96

source_name: Infant at 24-33 days of life rep 96

tag: tissue

value: blood

tag: days of life

tag: gender

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (no PVL)


title: KH022

tag: age (years)

tag: death

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Infant at timeC, rep95

source_name: Infant at 24-33 days of life rep 95

value: 1 (on oxygen at the age of 36 wpma)

tag: bronchopulmonary dysplasia (bpd) group

value: 3 (severe BPD)

tag: retinopathy of prematurity (rop) group

value: 2 (ROP which need laser therapy)

tag: rop lasertherapy

value: 1 (laser therapy  due to prethreshold or threshold ROP)

tag: periventricular leukomalacia (pvl)


title: Infant at timeC, rep93

source_name: Infant at 24-33 days of life rep 93

value: 1 (female)

value: 1 (oxygen therapy =>28 days)

value: 2 (moderate BPD)


title: Infant at timeC, rep92

source_name: Infant at 24-33 days of life rep 92

value: 0 (oxygen therapy <28 days)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

value: 0 (no BPD)

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: Infant at timeC, rep91

source_name: Infant at 24-33 days of life rep 91

value: 1 (mild BPD)


title: Infant at timeC, rep89

source_name: Infant at 24-33 days of life rep 89


title: Infant at timeC, rep86

source_name: Infant at 24-33 days of life rep 86


title: Infant at timeC, rep88

source_name: Infant at 24-33 days of life rep 88


title: KH085

value: primary lung tumor

value: male

tag: smoking status

value: Ever-smoker

tag: bi

tag: pathological stage

value: IA

tag: pstage iorii

value: I

tag: gene alteration status

value: KRAS mutation +

tag: myc

value: Low

tag: relapse

value: relapsed

tag: days before relapse/censor

value: alive


title: KH054

tag: tissue

tag: gender

value: II

value: not relapsed

tag: months before relapse/censor

value: exclude


title: Stressed-Fibroblasts-miR-200c 48h

city: PARIS

first: Fatima

last: Mechta-Grigoriou

address: 26 rue d'Ulm

department: INSERM U830

country: France

institute: Institut Curie

description: Immortalized fibroblast transfected with miR-200

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Rank invariant with GenomeStudio (Illumina)

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

extract_protocol: RNA was extracted wih miRNeasy Mini kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: transfection

tag: treatment

tag: time

value: 2 hours

tag: cell type

value: immortalized fibroblasts


title: KH067

tag: age (years)

value: female

value: Never-smoker

value: IB

tag: death

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: Infant at timeC, rep82

source_name: Infant at 24-33 days of life rep 82

value: blood

tag: days of life

value: 2 (male)

tag: gestational age (weeks)

tag: birth weight (grams)

tag: oxygen 28 days

value: 0 (oxygen therapy <28 days)

tag: oxygen 36 weeks postmenstrual age (wpma)

value: 0 (finished oxygen therapy earlier than the age of 36 wPMA)

tag: bronchopulmonary dysplasia (bpd) group

value: 0 (no BPD)

tag: retinopathy of prematurity (rop) group

value: 2 (ROP which need laser therapy)

tag: rop lasertherapy

value: 1 (laser therapy  due to prethreshold or threshold ROP)

tag: periventricular leukomalacia (pvl)

value: 1 (PVL)


title: Stressed-Fibroblasts-Control 48h

description: Immortalized fibroblast transfected with control miRNA

source_name: Control

tag: transfection

value: Control miRNA


title: Infant at timeC, rep83

source_name: Infant at 24-33 days of life rep 83

tag: tissue

tag: gender

value: 1 (female)

value: 1 (oxygen therapy =>28 days)

value: 1 (on oxygen at the age of 36 wpma)

value: 3 (severe BPD)

value: 0 (no PVL)


title: Infant at timeC, rep85

source_name: Infant at 24-33 days of life rep 85

value: 0 (no ROP)

value: 0 (no lasertherapy)


title: KH058

source_name: frozen tissue of primary lung tumors

value: primary lung tumor

value: male

tag: smoking status

value: Ever-smoker

tag: bi

tag: pathological stage

value: IA

tag: pstage iorii

value: I

tag: gene alteration status

value: KRAS mutation +

tag: myc

value: Low

tag: relapse

value: relapsed

tag: days before relapse/censor

tag: months before relapse/censor

value: alive


title: SM001 SARS 10^5pfu D7 5

source_name: SM001 SARS 10^5pfu D7 5

growth_protocol: Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^2,10^3, 10^4 or 10^5 PFU of SARS CoV MA15 in 50 µl of PBS or mock-infected with PBS alone.  At days 1, 2, 4 and 7 days post-infection, lungs were harvested.

treatment_protocol: Specific lobs of the lung from each animal were harvested and briefly rinse tissue in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and place immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC further processing. Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation.

tag: strain

value: Female

tag: time (post-infection)

value: 7 day

tag: age

value: 20 week old

tag: treatment

value: SARS CoV MA15 infected with 10^5 PFU

value: lung


title: Stressed-Fibroblasts-miR-141 48h

description: Immortalized fibroblast transfected with miR-141

tag: time

value: 2 hours

tag: cell type

value: immortalized fibroblasts


title: KH004

tag: tissue

tag: age (years)

value: II

value: not relapsed

tag: death

tag: days before death/censor

tag: exclude for prognosis analysis due to incomplete resection or adjuvant therapy


title: SM001 SARS 10^5pfu D7 4

source_name: SM001 SARS 10^5pfu D7 4

tag: gender


title: Stressed-Fibroblasts-Transfectant 48h

description: Immortalized fibroblast transfected with transfectant only

source_name: Transfectant

tag: transfection