title: SAS3-HA_YPD_rep2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

description: exponential growth in YPD - Linear dye normalization

hyb_protocol: Labeled DNA was hybridized to the Yeast Whole Genome ChIP-on-chip Microarray (Agilent p/n G4491A, AMADID: 014741) according to manufacture instruction.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA)  following the Agilent protocol ChIP_1010_Sep10, grid template 014741_D_F_20091202  and the metric set ChIP_QCMT_Sep10.

data_processing: Agilent Feature Extraction Software (v10.10.1.1) was used for background subtraction and linear normalization.

source_name: IP anti-HA 3F10 High Affinity (Roche 1867423)

label_protocol: Labeling of DNA was obtained following the ‘Agilent Yeast ChIP-on-chip Analysis’ protocol Version 9.2 (Agilent Technologies, Palo Alto, California USA. p/n G4493-90010). 2000 ng of ChIP and reference samples were labeled respectively with Cyanine 5-dUTP and cyanine 3-dUTP using the ‘CGH Labeling Kit’ from Invitrogen (p/n 18095-011) according to the manufacturer’s instructions.

growth_protocol: Cells (40 mL of culture) were grow exponentially in  rich medium (YPD)  to OD600 0.5-0.8.

extract_protocol: Chromatin immunoprecipitation was performed as previously described [Ren B, et al., 2000]. Briefly crosslinked cell pellets were resuspended in 300 μL of lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1mM PMSF, 1mM benzamidine and protease inhibitor cocktail from Roche) and lysed by vortexing at 4ºC by 45 min with glass beads. Chromatin was sonicated to 200–1000 bp (average of 400bp). Immunoprecipitation was carried for 4h using 2 µg of rat anti-HA 3F10 (Roche) Ab coupled to 100 µL of a 50% (v/v) suspension of Protein G Sepharose 4FF (Amersham Biosciences) equilibrated in 5mg/mL BSA lysis buffer. We included control immunoprecipitations of lysates from wild type strains with anti-HA. Beads were washed twice with lysis buffer, twice with 500 mM NaCl lysis buffer, twice with wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% Nonidet P-40, 0.5% sodium deoxycholate, 1 mM EDTA pH 8.0, 1 mM PMSF, 1 mM benzamidine and protease inhibitor cocktail from Roche), once with TE containing 1mM PMSF, and finally collected. Two successive elutions were performed with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) by incubating 10 min at 65ºC. The eluted fraction was treated overnight at 65ºC to reverse the cross-linking. Proteins were degraded by proteinase K and DNA was purified by phenol/chloroform/isoamylic alcohol extraction. The sample as treated with RNAse A and purified. Ligation Mediated PCR was used for DNA amplification. Immunoprecipitated DNA was blunted by T4 phage DNA polymerase, phenol/chloroform/isoamylic alcohol extracted and ethanol precipitated. Sample was ligated to annealed linkers oJW102 and oJW103. The sample was PCR amplified and amplified size analyzed on a 1.2% agarose gel (average size of 150 bp).

treatment_protocol: Samples were  crosslinked with 1% formaldehyde for 30 min, quenched by adding glycine to a final concentration of 125 mM and washed three times with 30 mL of ice-cold PBS buffer.

tag: strain

value: BQS1217 strain (SAS3-HA tagged in wt strain BY4742)

value: BY4742 strain


title: Healthy, biological replicate 5

status: Public on Nov 07 2014

type: RNA

city: Alnarp

first: Itziar

last: Frades

address: Sundsvägen 14

department: Plant Protection Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: Gene expression data from human liver biopsia sample from healthy liver.

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix HG-U133_Plus_2.na22 platform. GeneChips were washed and stained in the Fluidics Station 450.

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

data_processing: The data were acquired with GCOS instrument and processed using RMA normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human liver, healthy

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

extract_protocol: 4 millimeter punch of liver biopsy. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: tissue

value: liver

tag: disease status

value: healthy


title: BxPC3-KO111 rep 6

city: Oslo

first: Petter

middle: Angell

last: Olsen

address: Gaustadalleen 34

department: Dep. of Microbiology

country: Norway

institute: Oslo University Hospital - Rikshospitalet

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalised using J-Express 2012

source_name: b-catenin deficient BxPC3 clone 111

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

growth_protocol: Exponentially growing cells

extract_protocol: Total RNA was extracted using the GenElute Mammalian Total RNA Purification Kit (Sigma-Aldrich)

tag: cell line

tag: genotype

value: CTNNB1 KO

tag: beta-catenin gene (ctnnb1)

value: gene disrupted


title: Healthy, biological replicate 7


title: Healthy, biological replicate 2


title: Healthy, biological replicate 6


title: SAS3-HA_YPD_rep1

type: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae


title: BxPC3-KO111 rep 5


title: parthenogenetic_haploid_ESC_1

city: Tokyo

first: Saori

last: Takahashi

address: 1-5-45 Yushima Bunkyo-ku, Tokyo

department: Epigenetics

country: Japan

institute: Tokyo Medical and Dental University

description: biological replicate 1

hyb_protocol: Cy3-labelled and Cy5-labelled genomic DNA was fragmented, and hybridized for 24 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner using two color scan setting for 4x180k array slides.

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

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled genomic DNA and Cy-5 labeled reference genomic DNA was prepared from 0.5 ug DNA.  Dye incorporation and DNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: DNA was prepared using proteinase K reaction. DNA was quantified using a Qubit.

tag: cell type

value: embryonic stem cells


title: Healthy, biological replicate 4


title: Healthy, biological replicate 3


title: Healthy, biological replicate 1


title: parthenogenetic_diploid_ESC_1

description: gene expression parthenogenetic diploid ESCs

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. After fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol and RNaeasy Purification kit following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer.

tag: gender

value: female


title: parthenogenetic_diploid_ESC_2


title: Non-alcoholic steatohepatitis, biological replicate 9

description: Gene expression data from human liver biopsia sample, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.

source_name: Human liver, non-alcoholic steatohepatitis

value: non-alcoholic steatohepatitis


title: C57BL/6_liver_2

description: experimental control 2


title: BxPC3-KO111 rep 4


title: parthenogenetic_haploid_ESC_2

description: biological replicate 2


title: Sex-reversal 6

city: College Station

first: Sharmila

last: Ghosh

state: TX

address: VMS Building, Rm 107, 4458 TAMUS

department: VIBS

country: USA

institute: Texas A&M University

hyb_protocol: After probe denaturation and pre-annealing with Cot1-DNA (to mask repetitive sequences), the samples were hybridized at 65°C in hybridization oven with rotation for 40 hours. Array slides were washed according to Agilent’s washing protocol, two time wash with Wash Buffer 1, 2, and acetonitrile. In the experiment slide washing with Wash Buffer 1 was done 10 minutes instead of 5 minutes. The slides were dried with stabilizing and drying solution.

scan_protocol: Scanned with Agilent SureScan DNA Microarray Scanner and Agilent Scanner Control software v8.3 with the following settings: slide id - auto detect; channels - R+G; resolution – 2 µm; tiff – 16bit; R PMT and G PMT are 100%, and XDR set to “0.05”.

data_processing:
Data normalization was done with the Agilent Feature Extraction software (v11.0.1.1).
Data analysis was done using the CGH analytics software (v5.0). The CNVs were represented by gains and losses of normalized fluorescence intensities relative to the reference and identified using the ADM-2 aberration algorithm (Lipson et al. 2006). Parameters used in this analysis were as follows: Threshold of ADM-2: 6.0; Centralization: ON (Threshold: 6.0, Bin Size: 10); Fuzzy Zero: ON; Aberration Filters: ON (minProbes = 5 & minAvgAbsLogRatio = 0.5 & maxAberrations = 10000 AND percentPenetrance = 0); Feature Level Filters: ON, IntraArray: ON).
The CNVs were called with 5 neighboring probes with an average log2 ratio 0.5 aberration filters.

organism: Equus caballus

label_protocol: Samples were labeled with fluorescence dyes Cy3 and Cy5. The control DNA was labeled with Cy3 and cases with Cy5. The labeling reaction was done by random primer, 10XdNTP, 5X reaction buffer, exo-klenow enzyme and Cy3/Cy5-dUTP for 2 hours at 37C, 10 minutes at 65C. The labeled products were purified with Milipore 30k column and diluted with 1X buffer TE according to Agilent protocol.

extract_protocol: Genomic DNA was isolated from peripheral blood or hair follicles using QIAGEN Gentra PureGene Blood kit (Qiagen) according to manufacturer’s protocol.

value: Sex-reversal

value: Male


title: BxPC3-KO111 rep 3


title: C57BL/6_liver_1

description: experimental control 1


title: Sex-reversal 2


title: parthenogenetic_haploid_ESC_2

description: gene expression parthenogenetic haploid ESCs


title: Non-alcoholic steatohepatitis, biological replicate 8


title: Sex-reversal 3


title: Sex-reversal 4


title: BxPC3-KO111 rep 1


title: Sex-reversal 5


title: Non-alcoholic steatohepatitis, biological replicate 7


title: Sex-reversal 1


title: wt_totalRNA_0min_rep1

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

description: total cellular RNA of untreated wild-type yeast (CY3) vs. common reference pool (CY5)

hyb_protocol: Hybridisation to Yeast (V2) 8 x 15K Gene Expression Microarrays (Agilent) and washing were performed following the manufactures instructions.

scan_protocol: Slides were scanned with the two laser Agilent microarray scanner (G2565A). For raw data generation Agilent feature extraction software (version 7.5) was used.

data_processing: Raw data were processed into R/Bioconductor. Intensities were log2 transformed, backgrounds were subtracted using normexp, and intensities were normalized within arrays by using the Loess method and between arrays by using Aquantile.

source_name: exponentially growing yeast cells (OD = 0.6)

label_protocol: Samples were labelled using the Low Input Quick Amp Labeling Kit Two Color (Agilent) following the manufactures instructions.

growth_protocol: Wild-type and rcm1 knockout yeast were grown overnight in 3 mL SC medium at 28°C with shaking. On the next day, 100 ml SD were inoculated with the overnight culture to an OD600 of 0.003 and grown at 28°C with shaking until the OD600 reached 0.5 - 0.6.

extract_protocol: 125 µg/ml cycloheximide (Sigma) were added and the cells were incubated at 28°C with shaking for further 15 min. Afterwards the flasks were placed on ice for 15 min with shaking from time to time. After pelleting the cells at 3,500 rpm and 4°C for 5 min, the pellets were washed two times with 2 mL cooled TMNSH buffer (10 mM Tris pH 7.4, 50 mM NH4Cl, 10 mM MgCl2, 12.5 mM 2-mercaptoethanol) and resuspended in 1 mL of lysis buffer (10 mM Tris pH 7.4, 50 mM NH4Cl, 10 mM MgCl2, 12.5 mM 2-mercaptoethanol, 50 mM KCl, 1 mM PMSF, 125 μg/ml cycloheximid). Lysis was performed by transferring the suspensions to glass tubes and vortexing with glass beads (0.4 - 0.6 mm diameter) 8 times for 30 sec, with at least 30 sec recovery on ice between each cycle. Afterwards the crude lysates were centrifuged at 4,000 rpm at 4°C for 10 min to remove insoluble debris. The supernatants were transferred to fresh tubes and were supplemented with 100 μl Triton X-100 (10% v/v). After centrifugation at full speed in a tabletop centrifuge at 4°C for 10 min, the supernatants were carefully transferred to fresh vials and the OD260 was recorded for quantification. A volume equalling 15 OD260 was loaded onto a 10 mL linear 7-52 % sucrose gradient in TMNSH buffer containing 50 mM KCl and centrifuged at 37,000 rpm at 4°C for 3 h. The profiles were recorded from the bottom of the tubes with a UV detector set to 254 nm. 300 µl polysomal fractions or total lysate were mixed with 900 µl Trizol LS and RNA was extracted following the manufacture's protocol.

treatment_protocol: After the culture reached an OF of 0.5 - 0.6, 0.4 mM H2O2 were added to the medium for 30 min or 90 min.

value: wild-type

tag: h2o2 stress [min]

tag: assayed molecule

value: total cellular RNA

value: pool of wild-type and rcm1Δ

value: pool of 0, 30 and 90 min

value: pool of polysomal RNA and total RNA


title: BxPC3-KO4 rep 6

source_name: b-catenin deficient BxPC3 clone 4


title: Przewalski's Horse female 2

source_name: Przewalski's Horse2

value: Female


title: Przewalski's Horse male 1

source_name: Przewalski's Horse1


title: Non-alcoholic steatohepatitis, biological replicate 6


title: Thoroughbred female 2, female reference


title: Non-alcoholic steatohepatitis, biological replicate 4


title: parthenogenetic_haploid_ESC_1


title: BxPC3-KO4 rep 4


title: Non-alcoholic steatohepatitis, biological replicate 5


title: BxPC3-KO4 rep 5


title: Non-alcoholic steatohepatitis, biological replicate 2


title: Non-alcoholic steatohepatitis, biological replicate 3


title: BxPC3-KO4 rep 1


title: BxPC3-WT rep 5

source_name: wild type BxPC3 cells

value: wild type


title: BxPC3-KO111 rep 2


title: Swiss Warmblood female 3

source_name: Swiss Warmblood3


title: Swiss Warmblood male 1

source_name: Swiss Warmblood1


title: BxPC3-KO4 rep 3


title: BxPC3-KO4 rep 2


title: Non-alcoholic steatohepatitis, biological replicate 1


title: BxPC3-WT rep 6


title: Thoroughbred male 1, male reference


title: BxPC3-WT rep 4


title: Steatosis, biological replicate 2

description: Gene expression data from human liver biopsia sample, when the tissue has been histopathologically determined to be steatosis.

source_name: Human liver, steatosis

value: steatosis


title: Steatosis, biological replicate 1

value: liver


title: Standardbred female 2


title: Standardbred male 1


title: BxPC3-WT rep 3


title: BxPC3-WT rep 2


title: Swiss Warmblood female 2

source_name: Swiss Warmblood2


title: Pgp1-4day-diff-3

city: La Jolla

first: Nathan

last: Lewis

state: CA

department: Pediatrics

institute: University of California, San Diego

description: Day 4 post NGN induction, biological replicate 3

hyb_protocol: standard manufacturer's protocol

scan_protocol: standard manufacturer's protocol

data_processing: standard manufacturer's protocol

source_name: iPS cells, PGP1

label_protocol: standard manufacturer's protocol

growth_protocol: The Personal Genome Project iPS cell line PGP1 (hu43860C) obtainable from Coriell (GM23338, the matching primary fibroblast line is GM23248). PGP1 cells were cultured in mTeSR media (05850, StemCell Technologies). This iPS line was genetically modified by lentiviral gene transfer and genomic integration of the doxycycline inducible Neurogenin vectors. Standard tissue culture plates were coated with Matrigel hESC-qualified Matrix (354277, BD Biosciences) for 1h at room temperature. For passaging, the cells were dissociated using TrypLE™ Express (12604013, Gibco), washed with Phosphate-Buffered Saline (pH 7.4) (10010031, Gibco) and replated using mTeSR supplemented with 3µg/ml InSolution™ Y-27632 Rho Kinase inhibitor (688001, EMD Millipore) and/or frozen using mFreSR media (05854, StemCell Technologies). The doxycycline (D9891-5G, Sigma) concentration for induction was 0.5ug/ml.

extract_protocol: The RNA extraction was performed using the mirVana™ miRNA Isolation Kit (AM1560, Ambion) following their protocol. The protocol was interrupted after the first column purification step to obtain the total RNA. The isolated RNA was stored at -80º C. 100 ng of total RNA (aliquots of the same samples used for RNA-Seq) were used for miRNA profiling by the nCounter technology (Nanostring). A 12-reaction size kit for human miRNAs (v1) was used. All samples were processed according to the manufacturer’s manual at the Broad Institute (Cambridge, MA).

treatment_protocol: After infection, the media was changed to plain mTeSR and the cells were cultured for another day until the doxycycline was added to mTeSR media. Two wells per plate were pooled for one biological replicate. In total, we generated triplicates for each time point. The day 0 samples were not treated with mTeSR plus 0.5ug/ml doxycycline (Sigma). The cells were enzymatically dissociated, washed with Phosphate-Buffered Saline (pH 7.4) (Gibco) and stored at 4º C overnight in RNAlater solution (Ambion). The next day, the samples were frozen at -20º C until RNA extraction. The day 1, day 3 and day 4 samples were harvested and treated accordingly.

value: Fibroblast derived iPS cells, differentiated neurons

tag: time

value: Day 4 post NGN induction


title: Pgp1-4day-diff-2

description: Day 4 post NGN induction, biological replicate 2


title: Pgp1-4day-diff-1

description: Day 4 post NGN induction, biological replicate 1


title: Percheron male 1


title: Sorraia female 2


title: Pgp1-3day-diff-2

description: Day 3 post NGN induction, biological replicate 2

value: Day 3 post NGN induction


title: Pgp1-3day-diff-3

description: Day 3 post NGN induction, biological replicate 3


title: Pgp1-3day-diff-1

description: Day 3 post NGN induction, biological replicate 1


title: Sorraia male 1


title: Percheron female 2


title: Fell Pony male 1

source_name: Fell Pony1


title: BxPC3-WT rep 1


title: Friesian female 2


title: Friesian male 4


title: Fell Pony female 2

source_name: Fell Pony2


title: Belgian Draft male 1

source_name: Belgian Draft1


title: Exmoor Pony female2

source_name: Exmoor Pony2


title: Friesian male 1


title: Exmoor Pony male1

source_name: Exmoor Pony1


title: Pgp1-1day-diff-2

description: Day 1 post NGN induction, biological replicate 2

value: Day 1 post NGN induction


title: Pgp1-1day-diff-3

description: Day 1 post NGN induction, biological replicate 3


title: Mongolian Native Horse female 2

source_name: Mongolian Native Horse2


title: Friesian male 3


title: Clydesdale male 1


title: Mongolian Native Horse male 1

source_name: Mongolian Native Horse1


title: PGP1-0day-diff-2

description: Day 0, biological replicate 2

value: Fibroblast derived iPS cells

value: Day 0


title: PGP1-0day-diff-1

description: Day 0, biological replicate 1


title: MEF Bptf Knockout 3

status: Public on Nov 06 2014

city: Richmond

first: Joseph

middle: William

last: Landry

state: Virginia

address: 401 College Street

department: Human and Molecular Genetics

institute: Virginia Commonwealth University

description: Comparison nucleosome DNA to sonicated total genomic DNA

hyb_protocol: Labeled DNA was hybridized to arrays using Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit using standard protocols.  Mouse Cot-1 DNA was used in the protocol.

scan_protocol: Arrays were scanned using Agilent Scanner using 70% sensitivity setting.

data_processing:
Values were normalized using default settings from the agilent scanner.  Probes which were saturated, nonuniform, flagged, or of low signal strength (<100) were removed.  Red and green chanel signal strength for duplicate probes were averaged, then watson and crick strand probes were averaged.  A linear interpolation was used to fill in gaps of 15 to 25 nucleotides.  A ratio of green to red was then taken and log 2 transformed.  A sliding window program was used to smooth the data (50 bp sliding window over 10 bp increments).  The resulting smoothed ratios were Z-score normalized.  Note that Control and KO 3 for the DP processed data sets are an average of 8858/8575 and 8859/8577 samples respectivly.
Each row in the processed data set represents an average of multiple probes (duplicates on the array, and Watson and Crick strand probes).

label: Alexa Fluor 555

source_name: Embryonic Fibroblasts

label_protocol: DNA was labeled using Invitrogen CGH labeling kit and aha-dUTP.  Labeled DNA was conjugated to reactive Alexa Fluor 555 or 647 accoring to standard protocols.

growth_protocol: MEF Growth Media

extract_protocol: Cells fixed with 1% PFA in PBS for 15 minutes.  Wash 3X5 minutes in PBS. Cells scraped from tissue culture plates and washed 3x 5minutes on ice at a concentration 60X10^6 cells/ml in nuclei prep buffer (10 mM Tris pH 7.4, 10 mM NaCl, 0.5% NP40, 3.5 mM MgCl2, 0.5 mM spermidine, 0.15 mM spermine).  Cells were frozen at 30X10^6 nuclei aliquots.  Nuclei were thawed at 30X10^6 nuclei/500ul in Mnase digestion buffer (50 mM Tris pH 8.0, 100 mM NaCl, 3 mM MgCl2, 2 mM CaCl2, 0.5 mM spermidine, 0.5 mM spermine).  Prewarmed to 37 C and 1,500 Units MNase/ml (Whorthington) was added.  Digested for 30 min at 37 C.  Reaction was stopped with 40 ul 0.5M EDTA, 100 ul 10% SDS, 100 ul NaCl.  Crosslinks were reversed ON at 65 C, and DNA was protenase K treated and extracted with phenol/ChCl3/isoamyl alcohol followed by ChCl3/Isoamyl alcohol.  DNA was ETOH precipitated prior to labeling.

value: Bptf Floxed/Floxed, rtTA, TetO-Cre

tag: strain number

value: C57/B6, 129 Mixed Background

value: Embryonic Fibroblasts

tag: dna

value: Mnase Digested Nucleosomal DNA

label: Alexa Fluor 647

value: Sonicated Genomic DNA


title: Arabian female 2


title: Belgian Draft female 2

source_name: Belgian Draft2


title: Arabian male 1

value: Male


title: MEF Control 2

value: Bptf Floxed/Floxed, rtTA


title: MEF Bptf Knockout 2


title: PGP1-0day-diff-3

description: Day 0, biological replicate 3


title: Clydesdale female 2

value: Female


title: MEF Bptf Knockout 1


title: Caspian Pony male 1

source_name: Caspian Pony1


title: ESC Bptf Knockout 3

source_name: Embryonic Stem Cells

growth_protocol: Standard ESC Media +LIF

value: Bptf -/-

value: Embryonic Stem Cells


title: MEF Control 1


title: ESC Control 3

value: Wild Type


title: Caspian Pony female 2

source_name: Caspian Pony2


title: ESC Bptf Knockout 2


title: American Quarter Horse female 2

source_name: American Quarter Horse2


title: American Quarter Horse male 1

source_name: American Quarter Horse1


title: ESC Bptf Knockout 1


title: ESC Control 1


title: DP Bptf Knockout 3 Replicate

description:
Comparison nucleosome DNA to sonicated total genomic DNA
DP Ave 8859_8577

source_name: CD8+, CD4+ Thymocytes

growth_protocol: Thymocyte Growth Media

value: Bptf Floxed/-, Lck-Cre

value: CD8+, CD4+ Thymocytes


title: ESC Control 2


title: DP Control 3

description:
Comparison nucleosome DNA to sonicated total genomic DNA
DP Ave 8858_8575

value: Bptf Floxed/-


title: DP Bptf Knockout 3


title: DP Control 2


title: DP Bptf Knockout 1


title: DP Bptf Knockout 2


title: Akhal-Teke male 1


title: American Quarter Horse male 2

source_name: American Quarter Horse3


title: DP Control 3 Replicate


title: DP Control 1


title: American Miniature Horse male 1

source_name: American Miniature Horse1


title: American Miniature Horse female 2

source_name: American Miniature Horse2


title: Akhal-Teke male 2


title: MEF Control 3


title: Apoe-KO-mice_Aortic-root_9w_non-administrated_replicate2

city: Higashi-ku

first: Shunsuke

last: Kanno

state: Fukuoka

address: 3-1-1 Maidashi

institute: Kyushu University

description: This sample contains 3 aortic roots from 3 mice. It is the second of 2 non-administrated biological replicates in 9-week-old mice.

hyb_protocol: Hybridization was performed according to Roche NimbleGen's protocol.

scan_protocol: Scanning was performed on GenePix4000B (Molecular Devices) by Inter Medical co.,ltd., following Roche NimbleGen's protocol.

data_processing: Raw signal intensities were normalized in Robust Multiarray Average (RMA) method by NimbleScan v2.5 as described in the NimbleScan’s manual, and low intensity probe sets were filtered (Probe sets that Intensity at least 1 out of 8 samples have values >= lower cut-off: 30.0 were chosen for further analysis).

source_name: Apoe KO mice_aortic root_9w_no stimulation

label_protocol: Double-standard complementary DNA and Amino Allyl aRNA was synthesized, amplified, and purified by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion). The purified aRNA was then coupled with Cy3 dye according to Roche NimbleGen’s protocol.

growth_protocol: C57BL/6J Apoe knockout (KO) mice were housed in a specific pathogen-free environment and fed a normal chow diet.

extract_protocol: Total RNA was extracted using the RNeasy Fibrous Tissue Kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). The concentrations of RNA were determined using a  a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: At 5 weeks of age, mice were randomized to FK565-administrated mice and non-administrated mice. The administration protocol as follows: FK565 (50 μg) was orally administrated once a day for 2 consecutive days and then observed for the following 5 days per week. This course of the intermittent administration for a week was continued for 1 or 4 weeks, and mice were euthanized 6 days after last administration. To obtain sufficient amount of RNA for microarray analysis, the aortic roots removed from 3 animals were mixed, homogenized, and used as one sample.

value: male

tag: genotype/variation

value: Apoe KO

value: aortic root

tag: age


title: Apoe-KO-mice_Aortic-root_6w_non-administrated_replicate1

description: This sample contains 3 aortic roots from 3 mice. It is the first of 2 non-administrated biological replicates in 6-week-old mice.

source_name: Apoe KO mice_aortic root_6w_no stimulation


title: Apoe-KO-mice_Aortic-root_9w_FK565-administrated_replicate2

description: This sample contains 3 aortic roots from 3 mice. It is the second of 2 FK595-administrated biological replicates in 9-week-old mice.

source_name: Apoe KO mice_aortic root_9w_FK565 stimulation


title: Apoe-KO-mice_Aortic-root_9w_FK565-administrated_replicate1

description: This sample contains 3 aortic roots from 3 mice. It is the first of 2 FK595-administrated biological replicates in 9-week-old mice.


title: Apoe-KO-mice_Aortic-root_6w_FK565-administrated_replicate2

description: This sample contains 3 aortic roots from 3 mice. It is the second of 2 FK565-administrated biological replicates in 6-week-old mice.

source_name: Apoe KO mice_aortic root_6w_FK565 stimulation


title: Apoe-KO-mice_Aortic-root_9w_non-administrated_replicate1

description: This sample contains 3 aortic roots from 3 mice. It is the first of 2 non-administrated biological replicates in 9-week-old mice.


title: Hg-treated root 3

city: Beijing

first: Jing

last: Hou

address: No. 19, XinJieKouWai St., HaiDian District

country: China

institute: Beijing Normal University

description: Gene expression of root after 7d exposure to Hg-spiked soil.

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Agilent Technologies, Santa Clara, CA, USA) in a Hybridization Oven (Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. After 17 hours of hybridization, the slides were washed in staining dishes (Thermo Shandon, Waltham, MA, USA) using the Gene Expression Wash Buffer Kit (Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions.

scan_protocol: The slides were scanned with an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA) with the following default settings: Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing:
The data were extracted using the Feature Extraction software program version 10.7 (Agilent Technologies, Santa Clara, CA, USA).
The raw data were normalized using the Quantile algorithm, GeneSpring Software version 11.0.

organism: Solanum lycopersicum

source_name: Root of tomato, mercury, 7d

label_protocol: Total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. The labeled cRNA was then purified using the RNeasy Mini Kit (QIAGEN, GmBH, Germany).

growth_protocol: Thirty sterilized seeds were germinated in an 18 cm glass Petri dish filled with 500 g spiked soil. Water content of the soil is 70% of the maximum water-retaining capacity. The seeds were then incubated in a growth chamber at 25±1 °C with 70% humidity in complete darkness for 7 days.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Life Technologies, Carlsbad, CA, US) according to the manufacturer’s instructions, and the RIN number was determined to evaluate RNA integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The qualified total RNA was then further purified using the RNeasy Mini Kit (Cat 74106, QIAGEN, GmBH, Germany) and the RNase-Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: Tomato (Lycopersicon esculentum Mill. cv. Zhongza No.109) seeds were obtained from the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences. Prior to use, the seeds were surface sterilized in a 10% sodium hypochlorite solution for 10 minutes to prevent fungal or other microbial contamination, then rinsed and soaked in distilled water for 1 hour. Soil spiking was performed by adding stock solutions of Cd, Cr, Hg and Pb directly to the background soil. Briefly, the stock solutions of the different heavy metals were prepared in deionized water, and then the appropriate amount of each stock solution was poured into 500 g soil to reach the target concentration. Additional, deionized water was combined with the treatments that required less or no metal stock solutions to equalize the total added volumes for all treatments. The soil was thoroughly mixed and then aged for two weeks under natural conditions to allow for adsorption and equilibration of the heavy metals. A preliminary test was carried out to calculate the median lethal concentrations (LC50, test chemicals concentrations that caused 50% mortality), which are shown in Supporting Information and Figure S1 of the associated manuscript. The 1/10 LC50 test concentrations selected for this study were 3.3 mg Cd/kg soil, 1.2 mg Cr/kg soil, 2.3 mg Hg/kg soil and 194.4 mg Pb/kg soil, as these levels were below those that cause acute toxicity, which could lead to nonspecific gene expression responses.

tag: cultivar

value: Zhongza No.109

value: root

tag: treatment

value: mercury


title: Pgp1-1day-diff-1

description: Day 1 post NGN induction, biological replicate 1

source_name: iPS cells, PGP1

value: Fibroblast derived iPS cells, differentiated neurons

value: Day 1 post NGN induction


title: Cr-treated root 3

description: Gene expression of root after 7d exposure to Cr-spiked soil.

source_name: Root of tomato, chromium, 7d

value: chromium


title: Apoe-KO-mice_Aortic-root_6w_FK565-administrated_replicate1

description: This sample contains 3 aortic roots from 3 mice. It is the first of 2 FK565-administrated biological replicates in 6-week-old mice.

tag: strain


title: Pb-treated root 1

description: Gene expression of root after 7d exposure to Pb-spiked soil.

source_name: Root of tomato, lead, 7d

tag: tissue

value: lead


title: Pb-treated root 3


title: Hg-treated root 1


title: Cr-treated root 1


title: Pb-treated root 2


title: Hg-treated root 2


title: Cr-treated root 2


title: Control 2

description: Gene expression of root after 7d exposure to control soil.

source_name: Root of tomato, control, 7d

value: untreated


city: Pittsburgh

first: Victoria

last: Plamadeala

state: Pennsylvania

address: 2516 Jane St

institute: Precision Therapeutics

description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.1 (M33F002N)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

hyb_protocol: Fragmented and labelled cDNA was hybridized to HG-U133 Plus 2.0 microarray (Affymetrix) at 45C for 18 hours at a rotation speed of 60rpm. Arrays were washed and stained using the Affymetrix GeneChip Hybridization, Wash & Stain kit in the Affymetrix FS450Dx2 Fluidics Station.

scan_protocol: Arrays were scanned on the GeneChip System 3000Dx v.2 (Affymetrix) using the HG-U133+2.0 protocol.

data_processing: RefRMA

source_name: Lung

label_protocol: Extracted total RNA was amplified using the Ovation Pico WTA System V2 (NuGEN Technologies, Inc.) and then fragmented and labelled with the Encore Biotin Module (NuGEN Technologies, Inc.).

growth_protocol: Immediately upon surgical extraction, specimens were either flash frozen and stored at -80C or placed in RNAL. Specimens were not subjected to any type of growth environment between surgical extraction and total RNA extraction.

extract_protocol: Total RNA was extracted from each specimen via a phenol-chloroform protocol.

treatment_protocol: Specimens were treated in 2 different ways to ensure stabilization of genomic material, notably total RNA.  Specimens were either flash frozen and then stored at -80C or placed immediately in RNAL.

tag: study

value: PRECISION STUDY

value: non-small-cell lung carcinoma

tag: patient

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.1)

tag: risk

value: low


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-B;Rep.2 (M33F002R)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-B;Rep.2)


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.3 (M33F002M)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.3)


title: Apoe-KO-mice_Aortic-root_6w_non-administrated_replicate2

description: This sample contains 3 aortic roots from 3 mice. It is the second of 2 non-administrated biological replicates in 6-week-old mice.

value: male


title: Control 1


title: Control 3


title: Cd-treated root 3

description: Gene expression of root after 7d exposure to Cd-spiked soil.

source_name: Root of tomato, cadmium, 7d

value: cadmium


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.2 (M33F002O)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.2)


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.1 (M33F002K)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.1)


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-B;Rep.1 (M33F002P)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-B;Rep.1)


title: Cd-treated root 2

value: Zhongza No.109

value: root


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.3 (M33F002L)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.3)


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.1 (M33F002B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.1)


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M33F002H)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


title: Cd-treated root 1


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-B;Rep.2 (M33F001Q)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: high


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.2 (M33F002F)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: PRECISION STUDY

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.2)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-B;Rep.1 (M33F001R)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: non-small-cell lung carcinoma


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.1 (M33F002D)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.1)

value: low


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.3 (M33F001M)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.3)


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2 (M33F002G)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-B;Rep.3 (M33F001P)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-B;Rep.3)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.2 (M33F001O)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.2)


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.3 (M33F002E)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.3)


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3 (M33F002I)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3)


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.2 (M33F002C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.2)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.3 (M33F001L)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.2 (M33F002J)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.2)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.1 (M33F001N)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1211102-A;Rep.1)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.2 (M33F001J)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
PRECISION STUDY::Patient in 2nd sub-study;Low Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.3 (M33F002A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.3)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M33F001H)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.1 (M33F001K)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-D;Encore lot1209110-D;Rep.1)

value: high


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.3 (M33F001E)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: PRECISION STUDY


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2 (M33F001G)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: non-small-cell lung carcinoma


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3 (M33F001I)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.2 (M33F001D)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.2)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.3 (M33F001C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.1 (M33F001F)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1211102-A;Rep.1)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.1 (M33F001A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.1)


description:
PRECISION STUDY::Patient 3 in 1st sub-study;Low Risk;Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F006-3.1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 3 in 1st sub-study (Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)

value: low


description:
PRECISION STUDY::Patient 3 in 1st sub-study;Low Risk;Operator 1;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F006-1.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 3 in 1st sub-study (Operator 1;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3 (M32F004-3.3A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3)


description:
PRECISION STUDY::Patient 3 in 1st sub-study;Low Risk;Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F006-2.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 3 in 1st sub-study (Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 2 in 1st sub-study;Low Risk;Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F005-3.1)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 2 in 1st sub-study (Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient in 2nd sub-study;High Risk;Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.2 (M33F001B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient in 2nd sub-study (Operator 2;Day 4;NuGen lot 1211216-A;Encore lot1209110-D;Rep.2)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3 (M32F004-3.2B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3)


description:
PRECISION STUDY::Patient 2 in 1st sub-study;Low Risk;Operator 1;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F005-1.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 2 in 1st sub-study (Operator 1;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 3 in 1st sub-study;Low Risk;Operator 2;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F006-2.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 3 in 1st sub-study (Operator 2;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 2;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2 (M32F004-2.3C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 2;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2 (M32F004-3.1B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2)


description:
PRECISION STUDY::Patient 3 in 1st sub-study;Low Risk;Operator 1;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F006-1.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: PRECISION STUDY

value: Patient 3 in 1st sub-study (Operator 1;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 3 in 1st sub-study;Low Risk;Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F006-3.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: non-small-cell lung carcinoma

value: Patient 3 in 1st sub-study (Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 2 in 1st sub-study;Low Risk;Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F005-3.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 2 in 1st sub-study (Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 2 in 1st sub-study;Low Risk;Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F005-2.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 2 in 1st sub-study (Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F004-3.2A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)

value: low


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F004-3.1C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2 (M32F004-3.2C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2 (M32F004-3.3B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2)


description:
PRECISION STUDY::Patient 2 in 1st sub-study;Low Risk;Operator 1;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F005-1.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 2 in 1st sub-study (Operator 1;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3 (M32F004-3.1A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 3;Day 1;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F004-3.3C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 2;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F004-2.3B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 2;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2 (M32F004-2.2C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.2)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3 (M32F004-2.2B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F004-2.2A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: PRECISION STUDY

value: Patient 1 in 1st sub-study (Operator 2;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 2;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3 (M32F004-2.3A)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: non-small-cell lung carcinoma

value: Patient 1 in 1st sub-study (Operator 2;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3)


description:
PRECISION STUDY::Patient 3 in 1st sub-study;Low Risk;Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F006-3.2)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 3 in 1st sub-study (Operator 3;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 1;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3 (M32F004-1.3B)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 1;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.3)


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 1;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F004-1.3C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 1;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)


description:
PRECISION STUDY::Patient 3 in 1st sub-study;High Risk;Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F003-3.3)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 3 in 1st sub-study (Operator 3;Day 3;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)

value: high


description:
PRECISION STUDY::Patient 1 in 1st sub-study;Low Risk;Operator 1;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1 (M32F004-1.2C)
Tissues included in these studies were required to be histologically confirmed as adenocarcinoma, squamous or large cell carcinoma; to not have been previously treated with chemotherapy, targeted therapy or radiation therapy; to contain a minimum of 20% tumor; to be collected and treated with RNAL medium within one hour of surgical resection; to remain in the solution for at least 24 hours at 4°C for adequate stabilization; and upon receipt, to be removed from the reagent and frozen at -80°C until RNA extraction.   Also, to ensure sufficient penetration of RNAlater into tissues, it was required that the minimal ratio of RNAlater to tissue volume be 10:1 and at least one dimension of the tissue be no more than 5mm.

value: Patient 1 in 1st sub-study (Operator 1;Day 2;NuGen lot 1211216-A;Encore lot1211102-B;Rep.1)

value: low