title: broiler, white striping / wooden breast phenotype [R1157_20]

status: Public on Nov 30 2016

type: RNA

city: Bologna

first: Roberta

last: Davoli

state: Bologna

address: Viale G. Fanin, 46

department: DISTAL

country: Italy

institute: Bologna University

hyb_protocol: Hybridization was performed using the GeneAtlas™ Hybridization, Wash and Stain Kit (Affymetrix cat# 900299). Hybridizations were performed for 20 hours at 48°C in the GeneAtlas™ Hybridization Station. The Array Strips were washed and stained in the GeneAtlas™ Personal Fluidics Station. At the end of this procedure the array strips were placed into the imaging tray, which contains the Array Holding buffer.

scan_protocol: The array strips were imaged using the GeneAtlas™ Imaging Station. Affymetrix GeneAtlas™ Command Console software was used to acquire the Array Strip images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software.

data_processing: The data were analyzed with  Partek® Genomics Suite® software, version 6.6. Gene expression profiles from the six ABN biological replicates were compared to the six NORM biological ones in order to identify differentially expressed genes. Fold changes values between ABN an NORM broiler were obtained and statistical T-test with FDR was applied for multiple testing corrections.

label: biotin

molecule: total RNA

organism: Gallus gallus

source_name: Pectoralis major muscle collected after slaughter

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT Plus Kit (Affymetrix, Santa Clara, CA). With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled. All steps of the labeling protocol were performed as suggested by Affymetrix

growth_protocol: Male broiler were growt in a commercial farm on the same flock until the average live weight of 3.7 kg.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions. Each extracted RNA was checked for integrity and quality using an Agilent BioAnalyzer 2100.

treatment_protocol: The analysis was carried out comparing six broiler showing an abnormal myopaty of Pectoralis major muscle (ABN) and six broiler showing normal phenotype

tag: tissue

value: Pectoralis major muscle

tag: phenotype

value: white striping / wooden breast myopathy

tag: commercial hybrid

value: Ross 708

tag: gender

value: Male


title: broiler, white striping / wooden breast phenotype [R1157_13]


title: broiler, white striping / wooden breast phenotype [R1157_11]


title: NT shRNA#3-3 SHhES8,biological rep3

city: Shanghai

first: Zhexin

last: Zhu

address: 320 Yue Yang Road

country: China

institute: Chinese Academy of Sciences

description: Gene expression data from NT shRNA infected hESCs, biological rep3

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Homo sapiens

source_name: hESCs infected with NT shRNA

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: hESCs were culture in conditioned medium at 5% CO2, 37oC

extract_protocol: Four days after treatment, RNA from these cells was extracted respectively by TRIzol according to the manufacturer's instructions

treatment_protocol: hESCs were infected with concentrated NT and PHB shRNA lentiviruses respectively. One day after infection, cells were treated with 2ug/ml puromycine for the last 3 days.

tag: cell type

value: human embryonic stem cell line

tag: lentivirus

value: NT shRNA


title: PHB shRNA#3-2 SHhES8,biological rep2

description: Gene expression data from PHB shRNA infected hESCs, biological rep2

source_name: hESCs infected with PHB shRNA

value: PHB shRNA


title: broiler, white striping / wooden breast phenotype [R1157_17]


title: broiler, normal phenotype [R1157_07]

value: normal


title: PHB shRNA#3-3 SHhES8,biological rep3

description: Gene expression data from PHB shRNA infected hESCs, biological rep3


title: broiler, normal phenotype [R1157_10]


title: NT shRNA#3-2 SHhES8,biological rep2

description: Gene expression data from NT shRNA infected hESCs, biological rep2


title: NT shRNA#3-1 SHhES8,biological rep1

description: Gene expression data from NT shRNA infected hESCs, biological rep1


title: broiler, white striping / wooden breast phenotype [R1157_19]


title: broiler, normal phenotype [R1157_06]


title: broiler, white striping / wooden breast phenotype [R1157_18]


title: PHB shRNA#3-1 SHhES8,biological rep1

description: Gene expression data from PHB shRNA infected hESCs, biological rep1


title: broiler, normal phenotype [R1157_03]


title: broiler, normal phenotype [R1157_02]


title: A64-RT-2

type: genomic

city: Torrejón de Ardoz

first: Carlos

last: Briones

state: Madrid

address: Ctra de Torrejón a Ajalvir, km 4

department: Department of Molecular Evolution

country: Spain

institute: Centro de Astrobiología (CAB, CSIC-INTA)

hyb_protocol: Before hybridization, printed microarrays were washed in 2× saline-sodium citrate (SSC) buffer and 0.1% N-lauryl sarcosine, for 2 min at room temperature, followed by 2 additional min in 2× SSC. This step allowed removing unbound DNA from the microarray surface and washing the excess of spotting solution. Printed oligonucleotides were denatured by baking the slides for 2 min in boiling milli-Q water and cooling for 10 sec at room temperature. The oligonucleotides were immediately fixed by plunging the slides into ice-cold 100% ethanol for 2 min, followed by centrifugation at 500×g for 1 min (using an Arrayit minicentrifuge). Microarrays were prehybridized with 20 ul of hybridization buffer (6× SSC, 0.5% SDS, 1% BSA) for 45 min at 42°C, under a 24  24 mm cover slip in a hybridization chamber (Genetix). Finally, the microarrays were washed with distilled water, and dried by centrifugation. Hybridization with the labeled target (50 ng, equivalent to 0.3 pmol Alexa Fluor 647) was carried out in hybridization buffer at 50oC for 3 h, using microarray hybridization chambers (Genetix).

scan_protocol: Hybridized microarrays were washed at 45ºC in 2x SSC and 0.1% N-lauryl sarcosine for 5 min, then in 2x SSC for 5 min, rinsed in 0.2x SSC for 10 sec, and finally in distilled water for 5 min. Slides were dried by centrifugation at 500×g for 1 min and immediately scanned at 635 nm using either GenePix 4000B (Molecular Devices) or G2565AA  (Agilent) high resolution microarray scanners. Hybridization images were processed using GenePix Pro 6.0.0.68 (Molecular Devices) software in GenePix Scanner, and ScanArray Express 2.0 (Perkin Elmer) in Agilent one. No automatic normalization of images was performed.

data_processing: The selected raw fluorescence value for each spot was the median foreground signal after subtracting its local background. Technical replicates for each target-probe hybridization (4 spots per experiment) were clustered together. Since two different classes of signals (positive or negative) are expected, they were clustered into two groups using the K-means algorithm. Then, after removing the outliers from the positive group by applying the Grubb’s test with a significance level of 0.05, the mean of the positive signals was obtained. Two regions (containing the PR and RT probes, respectively) were separately normalized in each microarray by means of their own mean positive  signal. These two values were used as the normalization factor for each probe by applying the function (formula.pdf). where ǁPSǁ is the normalized probe signal, NRP is the total number of replicas per hybridized probe (typically, 4), IRP is the signal intensity of a replica probe i, NPS is the total number of positive probe signals per array region (either PR or RT), and IPS is the intensity of a positive probe signal i within such a region.

label: Alexa Fluor 647

molecule: genomic DNA

organism: Simian-Human immunodeficiency virus

source_name: Test sample from patient: A64

label_protocol: The phosphorylated strand of the HIV-1 DNA targets to be hybridized was specifically degraded using lambda exonuclease (New England Biolabs), and the resulting ssDNA was fluorescently labeled with Alexa Fluor 647, using the Ulysis Alexa Fluor 647 Nucleic Acid Labeling Kit (Life Technologies)

extract_protocol:
HIV-1 DNA target molecules corresponding to the training set were amplified from the cloned sequences using Expand High Fidelity DNA polymerase (EHF, Roche), as specified by the manufacturer. PCR amplification of the full PR-coding region was carried out using the forward primer 5’PROT2HindIII-P (5’-TCAGAGCAGACCAGAGCCAACAGCCCCACC-3’, corresponding to nucleotides [nts] 2138 to 2167 of HIV-1 CAM-1 strain, GenBank accession  number D10112) phosphorylated at its 5’-end, and the reverse primer 140RD (5’-CATTGTACTGATATCTAATCCCTGG-3’, complementary to positions 2969-2993). In turn, PCR amplifications of the queried codons of the RT-coding region involved the phosphorylated forward primers RT1-P (5’-CCAAAAGTTAAACAATGGCCATTG-3’, nts 2606-2629) or 55F-P (5’-CAAAAATTGGGCCTGAAAATCC-3’, nts 2694-2715), and the reverse primers 153RD (5’-TATTGCTGGTGATCCTTTCC-3’, nts 3009-3028), 13RD (5’-GTTCATAACCCATCCAAAGG-3’,nts 3232-3251) or 20RD (5’-ATTGACAGTCCAGCTGTCTTTTTCTGGC-3’, nts 3289-3316). Longer amplicons containing the PR-RT-coding regions were obtained by PCR amplification using as primers 5’PROT2HindIII-P and either 20RD or RT3333R (5’-CCACTAACTTCTGTATGTCATTG-3’, nts 3311-3333).
Viral RNA was extracted from plasma samples using the ‘HIV Sample Preparation Module’ of the ‘ViroSeq HIV-1 Genotyping System’ (Applied Biosystems), as specified by the manufacturer. The extracted RNA was retrotranscribed and PCR amplified by means of the ‘OneStep RT-PCR Kit’ (Qiagen), since this system showed higher sensitivity for samples with low viral load than other two-step protocols essayed (data not shown). Primers used were 5’PROT1 (5’-AGGCTAATTTTTTAGGGAAAATCTGGCCTTCC-3’, nts 2080-2111) and 153RD for the PR region, and RT-INI (5’-ACAGTATTAGTAGGACCTACACC-3’, nts 2474-2496) and RT3333R for the RT region. The RT-PCR amplification of a single amplicon containing the PR-RT-coding regions involved primers 5’PROT1 and RT3333R, though this approach showed less efficiency for samples with viral load lower than 104 copies/ml. Upon RT-PCR, nested PCR amplifications of the PR-coding region were performed with EHF, using the forward primer 5’PROT2HindIII-P and the reverse primer 140RD (positive amplification was successful in 53 out of the 57 samples), while those of the RT-coding region involved different combinations of the forward primers RT1-P or 55F-P, and the reverse primers 153RD, 13RD or 20RD (51 samples amplified).

tag: plasmid/patient id

tag: region

value: RT

tag: scanner

value: ScanArray

tag: sequence(s)


title: A65-PR-1

source_name: Test sample from patient: A65

value: PR


title: A64-RT-1


title: A63-RT-2

source_name: Test sample from patient: A63


title: A61-RT-1

source_name: Test sample from patient: A61


title: A60-RT-2

source_name: Test sample from patient: A60


title: A61-PR-2


title: A63-PR-1


title: A63-RT-1


title: A61-PR-1


title: A60-RT-1


title: broiler, normal phenotype [R1157_01]


title: A59-PR-2

source_name: Test sample from patient: A59


title: SK-N-AS

city: Bristol

first: Keith

middle: William

last: Brown

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

description: DNA methylation as assessed by methyl-CpG immunoprecipitation (MCIP), followed by hybridisation to microarrays covering human gene promoters and CpG islands.

hyb_protocol: The labeled MCIP and input DNAs were co-hybridized to the array for 16 - 20 hours (Nimblegen Inc).

scan_protocol: Nimblegen Inc.

data_processing: Raw pair data provide by Nimblegen was processed using ChipMonk software (www.bioinformatics.bbsrc.ac.uk/projects/chipmonk).  Data from each array was Lowess normalised, then probes were selected that were within 700bp of a transcriptional start site.

source_name: Input DNA from SK-N-AS (human neuroblastoma cells)

label_protocol: 4 micrograms of DNA was labelled using Klenow fragment-catalyzed primer extension using Cy dye coupled 9mer primers (Nimblegen Inc).

growth_protocol: DME/F12 medium + 10% fetal bovine serum

extract_protocol: Genomic DNA was extracted by HIRT solubilisation followed by standard phenol-chloroform extraction and alcohol precipitation.

value: Human neuroblastoma

value: I

tag: mycn amplification

value: No

source_name: MCIP DNA from SK-N-AS (human neuroblastoma cells)

tag: mcip

value: Methyl CpG immunoprecipitation (MCIP) with recombinant methyl-binding protein-Fc fusion was used to purify the methylated fraction from genomic DNA as described by Gedhard et al (2006) Cancer Res. 66 (12):6118-28.


title: A60-RT-3


title: SHSY-5Y

source_name: Input DNA from SHSY5Y (human neuroblastoma cells)

value: N

source_name: MCIP DNA from SHSY5Y (human neuroblastoma cells)


title: A58-RT-2

source_name: Test sample from patient: A58


title: BE(2)-C

source_name: Input DNA from BE(2)-C (human neuroblastoma cells)

value: Yes

source_name: MCIP DNA from BE(2)-C (human neuroblastoma cells)


title: IMR32

source_name: Input DNA from IMR32 (human neuroblastoma cells)

source_name: MCIP DNA from IMR32 (human neuroblastoma cells)


title: A58-PR-1


title: hNCC

source_name: Input DNA from hNCC (human neural crest cells)

value: Human neural crest

value: Not applicable

source_name: MCIP DNA from hNCC (human neural crest cells)


title: A56-RT-2

source_name: Test sample from patient: A56


title: A58-RT-1


title: A56-RT-1


title: A55-RT-1

source_name: Test sample from patient: A55


title: A55-RT-2


title: A54-RT-2

source_name: Test sample from patient: A54


title: A54-RT-1


title: A54-PR-1


title: A51-PR-1

source_name: Test sample from patient: A51


title: A46-RT-2

source_name: Test sample from patient: A46


title: A48-RT-1

source_name: Test sample from patient: A48


title: A47-RT-1

source_name: Test sample from patient: A47


title: A49-PR-1

source_name: Test sample from patient: A49


title: A46-RT-1


title: A47-PR-1


title: A53-RT-1

source_name: Test sample from patient: A53


title: A41-PR-2

source_name: Test sample from patient: A41


title: A45-PR-2

source_name: Test sample from patient: A45


title: A45-PR-1


title: A41-PR-1


title: A40-PR-2

source_name: Test sample from patient: A40


title: A44-RT-1

source_name: Test sample from patient: A44


title: A44-PR-1


title: A40-RT-1


title: A40-PR-1


title: A39-PR-1

source_name: Test sample from patient: A39


title: A45-RT-1


title: A39-RT-2


title: A39-RT-4


title: A39-RT-3


title: A41-RT-1


title: A39-RT-1


title: A34-PR-2

source_name: Test sample from patient: A34


title: A38-PR-1

source_name: Test sample from patient: A38


title: A34-PR-1


title: A45-RT-2


title: A32-RT-1

source_name: Test sample from patient: A32


title: A33-PR-2

source_name: Test sample from patient: A33


title: A33-PR-1


title: A32-PR-2


title: A31-PR-2

source_name: Test sample from patient: A31


title: A32-PR-1


title: A31-PR-1


title: A28-RT-1

source_name: Test sample from patient: A28


title: Sal (2)

city: San Francisco

first: Nikoleta

last: Tsvetanova

state: CA

address: 600 16th street

country: USA

institute: University of California, San Francisco

description: Sample 5

hyb_protocol: Cy5- and Cy3-labeled aRNA were combined in 3× SSC, 50 mM Hepes (pH 70), 20 µg of poly(A) RNA, 20 µg Cot-1 DNA, 20 µg tRNA, and 03% SDS to a total volume of 50uL Samples were then heated to 70°C for 5 min, spun at 14,000rpm at room temperature in a microfuge for 5 min, then hybridized at 65°C using the MAUI hybridization system (BioMicro) for 12–16 hrs

scan_protocol: Microarrays were scanned using AxonScanner 4000B (Molecular Devices), and PMTs were manually adjusted for every slide scanned to maximize signal without saturation

data_processing: GenePix was used to extract data from scanned microarray images Log2(Treated/Untreated) from duplicate sports were averaged and all log2 ratios were median-centered on an array-by-array basis

source_name: HEK293_agonist treated

label_protocol: Amersham Cy dye kit

growth_protocol: HEK293 cells were grown in a CO2 incubator at 37C in DMEM+FBS medium; drug was added directly to medium for 2 hrs

extract_protocol: RNeasy Mini Kit

treatment_protocol: Agonist added at indicated concentration for 2 hrs directly to medium

tag: cell line

tag: treated with

value: 50nM salmeterol for 2 hrs

source_name: Untreated cells

value: none (untreated)

tag: sample type

value: Reference


title: A31-RT-2


title: A27-RT-1

source_name: Test sample from patient: A27


title: A31-RT-1


title: SIC_1_1

city: NEW DELHI

first: DEVENDRA

middle: KUMAR

last: CHOUDHARY

state: DELHI

address: PUSA CAMPUS

department: PLANT PATHOLOGY

country: India

institute: INDIAN AGRICULTURAL RESEARCH INSTITUTE

description:
Gene expression data from twenty one day old mock inoculated plant
Technical rep1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1-121501. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the agilent microarray scanner laser.

data_processing: The data were analyzed with genespring 12.6 using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 plants mock inoculated

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

growth_protocol: Sterilized seeds were placed on Murashige and Skoog medium (Murashige and Skoog, 1962) and dilution of bacterial suspension (5µl per seed) were spot inoculated on seed. The seeds were arranged in line at two third of petri plate and transferred to growth chamber, after 48 hours of cold treatment at 4°C. The Growth conditions were 22/20˚C (day/night) temperature, 24 hours light period and 40 % relative humidity.

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

treatment_protocol: Seeds were sterilized 500 µl (0.1% SDS) + 500 µl (0.1% HgCl2) and five seed was placed on MS plate in a line and allowed for air drying, then the bacterial suspension (5µl) were spot inoculated and 5µl of sterile water was mock inoculated and again allowed for air drying.

value: Whole plants

tag: ecotype

tag: age

value: twenty one day


title: A27-PR-1


title: Sal (3)

description: Sample 6

growth_protocol: HEK293 cells were grown in a CO2 incubator at 37C in DMEM+FBS medium


title: Iso (3)

description: Sample 3

value: 10nM isoproterenol for 2 hrs


title: Seedlings of the wild type

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: NAIST

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. All signals were divided by median value of all probe sets.

source_name: Whole seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Seedlings were were grown at 22°C under the LD condition (16 h light/8 h dark) on the 1/2 strength MS medium.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen) following instruction.

tag: genotype

value: wild type

tag: developmental stage

value: Two-week-old seedlings


title: Seedlings of the transgenic plant overexpressing DRB3

value: transgenic plant overexpressing DRB3


title: Sal (1)

description: Sample 4


title: RS1_2

description:
Gene expression data from twenty one day old plant inoculated with Rs
Technical rep2

source_name: Arabidopsis Col-0 plants inouculated with Ralstonia solanacearum race 4

tag: tissue


title: Iso (2)

description: Sample 2


title: SIC_1_2

description:
Gene expression data from twenty one day old mock inoculated plant
Technical rep2


title: Iso (1)

description: Sample 1


title: Seedlings of the transgenic plant overexpressing DRB2

value: transgenic plant overexpressing DRB2


title: RS1_1

description:
Gene expression data from twenty one day old plant inoculated with Rs
Technical rep1


title: A26-RT-2

source_name: Test sample from patient: A26

value: RT

value: ScanArray


title: A25-RT-2

source_name: Test sample from patient: A25


title: A25-RT-1


title: A26-RT-1


title: A25-PR-1

value: PR


title: A23-PR-2

source_name: Test sample from patient: A23


title: A24-RT-1

source_name: Test sample from patient: A24


title: LP_54_1d_120ppm_liver

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

hyb_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit, page40-42 and GeneTitan® Instrument User Guide for Expression Array Plates

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6

organism: Mus musculus

source_name: Mouse Liver, Dose 120ppm, 1day, biological replicate 4

growth_protocol: Adult male C57Bl/6 mice were acquired from Taconic (Germantown, NY).  Animals were kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room.  The room was maintained on a 12-hr light-dark cycle (7 AM – 7 PM) at approximately 68-79°F with a relative humidity of approximately 30-70%. All animals were allowed access to Certified PicoLab Rodent 20 diet and reverse osmosis water ad libitum.

extract_protocol: Trizol® (ThermalFisher) organic extraction with Phase Lock Gel™ -Heavy- tubes (5Prime).  Aqueous phase placed in RB(QiaCube sample) tubes and loaded into QiaCube, the RNeasy Mini Protocol used.

treatment_protocol: Animals were placed individually in stainless-steel wire-mesh cages and exposed to styrene or air for a single 6 hour exposure.  On the morning following the last inhalation exposure, mice were euthanized by sodium pentobarbital and exsanguination.  Doses were 0 ppm (air only), 1 ppm, 5 ppm, 10 ppm, 20 ppm, 40 ppm and 120 ppm styrene.

tag: background strain

tag: gender

value: male

value: adult

value: Liver

tag: genotype/variation

value: Wild Type, (WT)

tag: time of exposure

value: 1 day

tag: dose (ppm)


title: LP_52_1d_120ppm_liver

source_name: Mouse Liver, Dose 120ppm, 1day, biological replicate 2

label_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit


title: LP_56_1d_120ppm_liver

source_name: Mouse Liver, Dose 120ppm, 1day, biological replicate 5


title: LP_53_1d_120ppm_liver

source_name: Mouse Liver, Dose 120ppm, 1day, biological replicate 3


title: A23-PR-1

tag: plasmid/patient id

tag: region

tag: scanner


title: LP_47_1d_40ppm_liver

source_name: Mouse Liver, Dose 40ppm, 1day, biological replicate 5


title: LP_49_1d_120ppm_liver

source_name: Mouse Liver, Dose 120ppm, 1day, biological replicate 1


title: A23-RT-2

tag: sequence(s)


title: A23-RT-1


title: A21-RT-2

source_name: Test sample from patient: A21


title: A20-RT-2

source_name: Test sample from patient: A20


title: A21-RT-1


title: A59-PR-1

source_name: Test sample from patient: A59


title: A19-PR-1

source_name: Test sample from patient: A19


title: A20-PR-1


title: A20-RT-1


title: A19-RT-2


title: LP_44_1d_40ppm_liver

source_name: Mouse Liver, Dose 40ppm, 1day, biological replicate 2


title: A18-RT-2

source_name: Test sample from patient: A18


title: A19-RT-1


title: A18-RT-1


title: LP_40_1d_20ppm_liver

source_name: Mouse Liver, Dose 20ppm, 1day, biological replicate 5


title: A17-RT-2

source_name: Test sample from patient: A17


title: LP_39_1d_20ppm_liver

source_name: Mouse Liver, Dose 20ppm, 1day, biological replicate 4


title: LP_34_1d_20ppm_liver

source_name: Mouse Liver, Dose 20ppm, 1day, biological replicate 2


title: LP_45_1d_40ppm_liver

source_name: Mouse Liver, Dose 40ppm, 1day, biological replicate 3


title: LP_46_1d_40ppm_liver

source_name: Mouse Liver, Dose 40ppm, 1day, biological replicate 4


title: LP_43_1d_40ppm_liver

source_name: Mouse Liver, Dose 40ppm, 1day, biological replicate 1


title: A16-PR-2

source_name: Test sample from patient: A16


title: LP_38_1d_20ppm_liver

source_name: Mouse Liver, Dose 20ppm, 1day, biological replicate 3


title: A17-RT-1


title: A16-PR-1


title: LP_30_1d_10ppm_liver

source_name: Mouse Liver, Dose 10ppm, 1day, biological replicate 5


title: A15-RT-2

source_name: Test sample from patient: A15


title: LP_27_1d_10ppm_liver

source_name: Mouse Liver, Dose 10ppm, 1day, biological replicate 2


title: LP_28_1d_10ppm_liver

source_name: Mouse Liver, Dose 10ppm, 1day, biological replicate 3


title: LP_26_1d_10ppm_liver

source_name: Mouse Liver, Dose 10ppm, 1day, biological replicate 1


title: LP_20_1d_5ppm_liver

source_name: Mouse Liver, Dose 5ppm, 1day, biological replicate 3


title: LP_22_1d_5ppm_liver

source_name: Mouse Liver, Dose 5ppm, 1day, biological replicate 4


title: LP_17_1d_5ppm_liver

source_name: Mouse Liver, Dose 5ppm, 1day, biological replicate 1


title: LP_15_1d_1ppm_liver

source_name: Mouse Liver, Dose 1ppm, 1day, biological replicate 5


title: A15-RT-1


title: LP_23_1d_5ppm_liver

source_name: Mouse Liver, Dose 5ppm, 1day, biological replicate 5


title: LP_19_1d_5ppm_liver

source_name: Mouse Liver, Dose 5ppm, 1day, biological replicate 2


title: LP_13_1d_1ppm_liver

source_name: Mouse Liver, Dose 1ppm, 1day, biological replicate 4


title: LP_10_1d_1ppm_liver

source_name: Mouse Liver, Dose 1ppm, 1day, biological replicate 2


title: A15-PR-1


title: A15-PR-2


title: A13-PR-1

source_name: Test sample from patient: A13


title: A14-PR-1

source_name: Test sample from patient: A14


title: A14-PR-2


title: A14-RT-1


title: A13-RT-1


title: LP_33_1d_20ppm_liver

source_name: Mouse Liver, Dose 20ppm, 1day, biological replicate 1


title: A12-PR-1

source_name: Test sample from patient: A12


title: LP_11_1d_1ppm_liver

source_name: Mouse Liver, Dose 1ppm, 1day, biological replicate 3


title: A13-RT-2


title: LP_8_1d_0ppm_liver

source_name: Mouse Liver, Dose 0, 1day, biological replicate 5


title: LP_9_1d_1ppm_liver

source_name: Mouse Liver, Dose 1ppm, 1day, biological replicate 1


title: LP_3_1d_0ppm_liver

source_name: Mouse Liver, Dose 0, 1day, biological replicate 3


title: A12-RT-1


title: A12-RT-2


title: LP_6_1d_0ppm_liver

source_name: Mouse Liver, Dose 0, 1day, biological replicate 4


title: A11-RT-2

source_name: Test sample from patient: A11


title: A09-RT-2

source_name: Test sample from patient: A09


title: A11-RT-1


title: A09-RT-1


title: A08-RT-1

source_name: Test sample from patient: A08


title: A04-RT-2

source_name: Test sample from patient: A04


title: A05-RT-1

source_name: Test sample from patient: A05


title: A05-RT-2


title: A08-PR-1


title: A06-PR-1

source_name: Test sample from patient: A06


title: A09-PR-1


title: A06-RT-1


title: A08-RT-2


title: LP_1_1d_0ppm_liver

source_name: Mouse Liver, Dose 0, 1day, biological replicate 1


title: LP_29_1d_10ppm_liver

source_name: Mouse Liver, Dose 10ppm, 1day, biological replicate 4


title: LP_56_1d_120ppm_lung

source_name: Mouse Lung, Dose 120ppm, 1day, biological replicate 5

value: Whole Lung


title: LP_55_1d_120ppm_lung

source_name: Mouse Lung, Dose 120ppm, 1day, biological replicate 4


title: LP_45_1d_40ppm_lung

source_name: Mouse Lung, Dose 40ppm, 1day, biological replicate 4


title: LP_44_1d_40ppm_lung

source_name: Mouse Lung, Dose 40ppm, 1day, biological replicate 3


title: LP_51_1d_120ppm_lung

source_name: Mouse Lung, Dose 120ppm, 1day, biological replicate 1


title: A04-RT-1


title: LP_54_1d_120ppm_lung

source_name: Mouse Lung, Dose 120ppm, 1day, biological replicate 3


title: LP_43_1d_40ppm_lung

source_name: Mouse Lung, Dose 40ppm, 1day, biological replicate 2


title: A03-PR-2

source_name: Test sample from patient: A03


title: LP_42_1d_40ppm_lung

source_name: Mouse Lung, Dose 40ppm, 1day, biological replicate 1


title: LP_2_1d_0ppm_liver

source_name: Mouse Liver, Dose 0, 1day, biological replicate 2


title: LP_40_1d_20ppm_lung

source_name: Mouse Lung, Dose 20ppm, 1day, biological replicate 5


title: 1.95c9_2.94c64-PRRT-100-4

source_name: Training sample from mixed plasmids: 1.95c9 100% - 2.94c64 0%

value: PRRT

value: GenePix


title: A02-PR-1

source_name: Test sample from patient: A02


title: A03-PR-1


title: A02-RT-1


title: LP_53_1d_120ppm_lung

source_name: Mouse Lung, Dose 120ppm, 1day, biological replicate 2


title: 1.95c9_2.94c64-PRRT-99-1

source_name: Training sample from mixed plasmids: 1.95c9 99% - 2.94c64 1%


title: 1.95c9_2.94c64-PRRT-100-3


title: 1.95c9_2.94c64-PRRT-100-1


title: 1.95c9_2.94c64-PRRT-95-3

source_name: Training sample from mixed plasmids: 1.95c9 95% - 2.94c64 5%


title: 1.95c9_2.94c64-PRRT-90-1

source_name: Training sample from mixed plasmids: 1.95c9 90% - 2.94c64 10%


title: 1.95c9_2.94c64-PRRT-90-2


title: 1.95c9_2.94c64-PRRT-95-2


title: 1.95c9_2.94c64-PRRT-95-1


title: 1.95c9_2.94c64-PRRT-95-4


title: LP_47_1d_40ppm_lung

source_name: Mouse Lung, Dose 40ppm, 1day, biological replicate 5


title: 1.95c9_2.94c64-PRRT-99-2


title: 1.95c9_2.94c64-PRRT-100-2


title: 1.95c9_2.94c64-PRRT-50-3

source_name: Training sample from mixed plasmids: 1.95c9 50% - 2.94c64 50%


title: LP_39_1d_20ppm_lung

source_name: Mouse Lung, Dose 20ppm, 1day, biological replicate 4


title: LP_31_1d_10ppm_lung

source_name: Mouse Lung, Dose 10ppm, 1day, biological replicate 5


title: LP_38_1d_20ppm_lung

source_name: Mouse Lung, Dose 20ppm, 1day, biological replicate 3


title: LP_29_1d_10ppm_lung

source_name: Mouse Lung, Dose 10ppm, 1day, biological replicate 3


title: LP_35_1d_20ppm_lung

source_name: Mouse Lung, Dose 20ppm, 1day, biological replicate 1


title: LP_30_1d_10ppm_lung

source_name: Mouse Lung, Dose 10ppm, 1day, biological replicate 4


title: LP_36_1d_20ppm_lung

source_name: Mouse Lung, Dose 20ppm, 1day, biological replicate 2


title: LP_28_1d_10ppm_lung

source_name: Mouse Lung, Dose 10ppm, 1day, biological replicate 2


title: Tumor biopsy from patient 7

city: Copenhagen

first: Olga

last: Østrup

address: Blegdamsvej 9

department: Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital (Rigshospitalet)

description: Hybridized to CytoScanHD

hyb_protocol: affymetrix manufactures procedure

scan_protocol: affymetrix manufactures procedure

data_processing:
BioDiscovery software NEXUS 7.5
data represents the SNP data of cfDNA analysed by OncoScan and tumor DNA analysed by CytoScanHD

label: Biotin

source_name: patient sample

label_protocol: affymetrix manufactures procedure

extract_protocol: Qiagen manufactures procedure; specifically QIAsymphony Circulating DNA Kit and Rneasy MIniPrep. DNA quality and quantity was controled by BioAnalyzer and Nanodrop.

value: tumor biopsy


title: Tumor biopsy from patient 8

description: Hybridized to CytoScanHD


title: 1.95c9_2.94c64-PRRT-10-4

source_name: Training sample from mixed plasmids: 1.95c9 10% - 2.94c64 90%


title: 1.95c9_2.94c64-PRRT-50-2


title: Tumor biopsy from patient 10

description: Hybridized to CytoScanHD


title: Tumor biopsy from patient 6

description: Hybridized to CytoScanHD


title: 1.95c9_2.94c64-PRRT-50-4


title: 1.95c9_2.94c64-PRRT-5-2

source_name: Training sample from mixed plasmids: 1.95c9 5% - 2.94c64 95%


title: 1.95c9_2.94c64-PRRT-10-1


title: Tumor biopsy from patient 9

description: Hybridized to CytoScanHD


title: 1.95c9_2.94c64-PRRT-50-1


title: 1.95c9_2.94c64-PRRT-10-2


title: 1.95c9_2.94c64-PRRT-5-1


title: 1.95c9_2.94c64-PRRT-0-2

source_name: Training sample from mixed plasmids: 1.95c9 0% - 2.94c64 100%


title: 1.95c9_2.94c64-PRRT-1-2

source_name: Training sample from mixed plasmids: 1.95c9 1% - 2.94c64 99%


title: 1.95c9_2.94c64-PRRT-10-3


title: 1.95c9_2.94c64-RT-100-3

source_name: Training sample from mixed plasmids: 1.95c9 100% - 2.94c64 0%


title: In-treatment tumor biopsy from patient 5

description: Hybridized to CytoScanHD


title: Tumor biopsy from patient 4

description: Hybridized to CytoScanHD


title: 1.95c9_2.94c64-PRRT-0-1


title: 1.95c9_2.94c64-PRRT-1-1


title: LP_26_1d_10ppm_lung

source_name: Mouse Lung, Dose 10ppm, 1day, biological replicate 1


title: LP_21_1d_5ppm_lung

source_name: Mouse Lung, Dose 5ppm, 1day, biological replicate 2


title: Pre-treatment tumor biopsy from patient 5

description: Hybridized to CytoScanHD


title: 1.95c9_2.94c64-RT-99-2

source_name: Training sample from mixed plasmids: 1.95c9 99% - 2.94c64 1%


title: 1.95c9_2.94c64-RT-99-4


title: Tumor biopsy from patient 1

description: Hybridized to CytoScanHD


title: Tumor biopsy from patient 3

description: Hybridized to CytoScanHD


title: 1.95c9_2.94c64-RT-95-3

source_name: Training sample from mixed plasmids: 1.95c9 95% - 2.94c64 5%


title: 1.95c9_2.94c64-RT-100-4


title: Tumor biopsy from patient 2

description: Hybridized to CytoScanHD


title: LP_15_1d_5ppm_lung

source_name: Mouse Lung, Dose 5ppm, 1day, biological replicate 1


title: LP_23_1d_5ppm_lung

source_name: Mouse Lung, Dose 5ppm, 1day, biological replicate 4


title: LP_22_1d_5ppm_lung

source_name: Mouse Lung, Dose 5ppm, 1day, biological replicate 3


title: 1.95c9_2.94c64-RT-99-1


title: 1.95c9_2.94c64-RT-95-1


title: 1.95c9_2.94c64-RT-99-3


title: Transgenic_AhDGR_OE

city: Irapuato

first: John P

last: Délano-Frier

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Biotechnology and Biochemistry

country: Mexico

institute: CINVESTAV Irapuato

hyb_protocol: For pre-hybridization, the slide was re-hydrated with water vapor at 60ºC and fixed with two cycles of UV ligth. Then, the slide was submerged in boiling water for two minutes (92ºC) and washed with 95% ethanol for one minute. After that, the oligo array was prepared for hybridization in a buffer solution 5X SSC, 0.1% SDS and 1% BSA for one hour at 41ºC. Finally, the array was washed and dried for hybridization. Equal quantities of labeled cDNA were hybridized to the Arabidopsis array using hybridization solution UniHyb (TeleChem International INC) for 14 hr at 42ºC.

scan_protocol: Scanned on an ScanArray 4000 scanner with ScanArray 4000 software from Packard BioChips.

data_processing: The analysis of the microarray data: background correction, Lowess normalization, intensity filter and selection of differentially expressed genes, was performed with the software genArise (http://www.ifc.unam.mx/genarise/). The identification of differentially expressed genes was done by the calculation of a Z score using a sliding-window approach, where the algorithm calculates the mean and standard deviation (SD) within a window surrounding each data point to define a Z score, where Z is the number of SD a data point is from the window mean. To obtain the Z score, the next formula was applied, zi = (Ri - mean(R))/sd(R), where zi is the Z score for a given data point, Ri is the log ratio of signal intensity for each element, mean(R) and sd(R) are the mean and SD of the log ration of signal intensity of the surrounding window. Only the elements with an absolute Z score greater than 2 were considered differentially expressed (|Zscore| > 2) (Cheteleadle et al., 2003).

source_name: Rossete leaves, 5-week old Wt plants

label_protocol: Total RNA were used for cDNA synthesis incorporating Alexa555 or Alexa647 making use of First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was tested by measuring the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: Arabidospis plants were grown in controlled conditions of light (photosynthetic photon flux density (PPFD) of ≈ 200 µmol m-2 s-1), photoperiod (16 h light/ 8 h dark) and temperature (22 ± 1°C).

extract_protocol: Total RNA was extracted from 100–200 mg of frozen rosette tissue with the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions, with modifications. These consisted of the addition of a salt solution (sodium citrate 0.8 M + 1.2 M NaCl) during precipitation in a 1:1 v/v ratio with isopropanol and further purification with LiCl (8 M) for one hour at 4°C. All RNA samples were analyzed by formaldehyde agarose gel electrophoresis and visual inspection of the ribosomal RNA bands upon ethidium bromide staining.

treatment_protocol: Plants were subjected to normal growing conditions

source_name: Rossete leaves, 5-week old transgenic plants

value: transgenic


title: 1.95c9_2.94c64-RT-95-2


title: 1.95c9_2.94c64-RT-90-4

source_name: Training sample from mixed plasmids: 1.95c9 90% - 2.94c64 10%


title: LP_24_1d_5ppm_lung

source_name: Mouse Lung, Dose 5ppm, 1day, biological replicate 5


title: LP_10_1d_1ppm_lung

source_name: Mouse Lung, Dose 1ppm, 1day, biological replicate 2


title: LP_15_1d_1ppm_lung

source_name: Mouse Lung, Dose 1ppm, 1day, biological replicate 5


title: 1.95c9_2.94c64-RT-95-4


title: LP_14_1d_1ppm_lung

source_name: Mouse Lung, Dose 1ppm, 1day, biological replicate 4


title: LP_9_1d_1ppm_lung

source_name: Mouse Lung, Dose 1ppm, 1day, biological replicate 1


title: LP_12_1d_1ppm_lung

source_name: Mouse Lung, Dose 1ppm, 1day, biological replicate 3


title: 1.95c9_2.94c64-RT-90-1


title: 1.95c9_2.94c64-RT-90-2


title: LP_7_1d_0ppm_lung

source_name: Mouse Lung, Dose 0, 1day, biological replicate 4


title: 1.95c9_2.94c64-RT-50-4

source_name: Training sample from mixed plasmids: 1.95c9 50% - 2.94c64 50%


title: 1.95c9_2.94c64-RT-50-3


title: 1.95c9_2.94c64-RT-10-3

source_name: Training sample from mixed plasmids: 1.95c9 10% - 2.94c64 90%


title: 1.95c9_2.94c64-RT-10-4


title: 1.95c9_2.94c64-RT-50-2


title: 1.95c9_2.94c64-RT-90-3


title: 1.95c9_2.94c64-RT-10-1


title: 1.95c9_2.94c64-RT-50-1


title: 1.95c9_2.94c64-RT-10-2


title: 1.95c9_2.94c64-RT-5-2

source_name: Training sample from mixed plasmids: 1.95c9 5% - 2.94c64 95%


title: 1.95c9_2.94c64-RT-5-3


title: 1.95c9_2.94c64-RT-5-4


title: 1.95c9_2.94c64-RT-5-1


title: LP_1_1d_0ppm_lung

source_name: Mouse Lung, Dose 0, 1day, biological replicate 1


title: LP_6_1d_0ppm_lung

source_name: Mouse Lung, Dose 0, 1day, biological replicate 3


title: TG_244_4w_120ppm_lung

source_name: Dose 120ppm, 4week, TG, biological replicate 3

growth_protocol: Adult male C57Bl/6 WT, KO and TG mice were acquired from Taconic (Germantown, NY).  Animals were kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room.  The room was maintained on a 12-hr light-dark cycle (7 AM – 7 PM) at approximately 20-25°C with a relative humidity of approximately 35-65%. All animals were allowed access to Certified LabDiet 5002 diet and reverse osmosis water ad libitum.

treatment_protocol: During exposure periods, animals were placed individually in stainless-steel wire-mesh cages and exposed to styrene or air 5 days per week for 6 hours per day for either 1 or 4 weeks.  On the morning following the last inhalation exposure, mice were euthanized by sodium pentobarbital and exsanguination.  Doses were 0 ppm (air only),  40 ppm and 120 ppm styrene.

value: Transgenic, (TG)


title: LP_8_1d_0ppm_lung

source_name: Mouse Lung, Dose 0, 1day, biological replicate 5


title: 1.95c9_2.94c64-RT-1-4

source_name: Training sample from mixed plasmids: 1.95c9 1% - 2.94c64 99%


title: 1.95c9_2.94c64-RT-1-3


title: 1.95c9_2.94c64-RT-0-1

source_name: Training sample from mixed plasmids: 1.95c9 0% - 2.94c64 100%


title: TG_247_4w_120ppm_lung

source_name: Dose 120ppm, 4week, TG, biological replicate 4


title: 1.95c9_2.94c64-RT-1-2


title: 1.95c9_2.94c64-RT-0-2


title: KO_147_4w_120ppm_lung

source_name: Dose 120ppm, 4week, KO, biological replicate 5

value: Knockout, (KO)


title: LP_4_1d_0ppm_lung

source_name: Mouse Lung, Dose 0, 1day, biological replicate 2


title: TG_248_4w_120ppm_lung

source_name: Dose 120ppm, 4week, TG, biological replicate 5


title: 1.95c9_2.94c64-RT-1-1


title: TG_241_4w_120ppm_lung

source_name: Dose 120ppm, 4week, TG, biological replicate 1


title: pWT_pINS-RT-100-10

source_name: Training sample from mixed plasmids: pWT 100% - pINS 0%


title: pWT_pINS-RT-100-9


title: pWT_pINS-RT-100-8


title: TG_242_4w_120ppm_lung

source_name: Dose 120ppm, 4week, TG, biological replicate 2


title: KO_146_4w_120ppm_lung

source_name: Dose 120ppm, 4week, KO, biological replicate 4


title: pWT_pINS-RT-100-5


title: pWT_pINS-RT-100-4


title: pWT_pINS-RT-100-3


title: pWT_pINS-RT-100-6


title: pWT_pINS-RT-100-1


title: pWT_pINS-RT-99-7

source_name: Training sample from mixed plasmids: pWT 99% - pINS 1%


title: pWT_pINS-RT-99-8


title: pWT_pINS-RT-99-6


title: pWT_pINS-RT-100-2


title: pWT_pINS-RT-99-3


title: pWT_pINS-RT-99-4


title: pWT_pINS-RT-100-7


title: pWT_pINS-RT-99-2


title: pWT_pINS-RT-95-6

source_name: Training sample from mixed plasmids: pWT 95% - pINS 5%


title: pWT_pINS-RT-99-1


title: pWT_pINS-RT-95-5


title: pWT_pINS-RT-95-4


title: pWT_pINS-RT-95-2


title: pWT_pINS-RT-99-5


title: KO_145_4w_120ppm_lung

source_name: Dose 120ppm, 4week, KO, biological replicate 3


title: KO_143_4w_120ppm_lung

source_name: Dose 120ppm, 4week, KO, biological replicate 1


title: WT_47_4w_120ppm_lung

source_name: Dose 120ppm, 4week, WT, biological replicate 4


title: pWT_pINS-RT-95-1


title: KO_144_4w_120ppm_lung

source_name: Dose 120ppm, 4week, KO, biological replicate 2


title: pWT_pINS-RT-90-6

source_name: Training sample from mixed plasmids: pWT 90% - pINS 10%


title: WT_48_4w_120ppm_lung

source_name: Dose 120ppm, 4week, WT, biological replicate 5


title: pWT_pINS-RT-90-5


title: pWT_pINS-RT-90-4


title: uterus control C, biological rep1

city: lucknow

first: anila

last: dwivedi

state: Uttar Pradesh

address: jankipuram ext. sitapur road

department: Endocrinology division

institute: CSIR CDRI

description: Sprague Dawley rat uterus (pre-implantation period) treated with vehicle

hyb_protocol: Following fragmentation of single stranded DNA were hybridized in Affymetrix Genchip hybridization oven 645 for 16 h at 40 C on GeneChip® Rat Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0002.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner  scanner 3000.Affymetrix Genechip command console used for scanning.

data_processing: Expression console was used to generate CHP file .The intensity values of different probe sets (genes) in the GeneChip operating software (Affymetrix) were imported into GeneSpring GX version 12.6 software (Agilent Technologies, Santa Clara, CA) and processed using the robust multi array analysis algorithm for background adjustment, normalization.

organism: Rattus norvegicus

label_protocol: Biotinylated single stranded DNA were prepared according to the standard Affymetrix protocol from 100ng of total RNA  (GeneChip WT terminal labeling kit, Affymetrix).

treatment_protocol: In one group rats were fed with 1.25 mg kg-1dose of Orm prepared in gum -acacia on day 1 of pregnancy and rats of second group were given vehicle alone,i.e. treated (T) and control (C)

value: pre-implantation uterus

tag: strain

value: Sprague Dawley

value: 10-12 week old adult


title: uterus treated T, biological rep2

description: Sprague Dawley rat uterus (pre-implantation period) treated with Orm


title: pWT_pINS-RT-90-2

value: RT


title: pWT_pINS-RT-90-3


title: uterus control C, biological rep2

description: Sprague Dawley rat (pre-implantation period) uterus treated with vehicle

source_name: Sprague Dawley rat uterus (pre-implantation period) treated with vehicle


title: WT_43_4w_120ppm_lung

source_name: Dose 120ppm, 4week, WT, biological replicate 2


title: WT_46_4w_120ppm_lung

source_name: Dose 120ppm, 4week, WT, biological replicate 3


title: TG_237_4w_40ppm_lung

source_name: Dose 40ppm, 4week, TG, biological replicate 4


title: TG_240_4w_40ppm_lung

source_name: Dose 40ppm, 4week, TG, biological replicate 5


title: TG_234_4w_40ppm_lung

source_name: Dose 40ppm, 4week, TG, biological replicate 2


title: pWT_pINS-RT-90-1


title: TG_233_4w_40ppm_lung

source_name: Dose 40ppm, 4week, TG, biological replicate 1


title: TG_236_4w_40ppm_lung

source_name: Dose 40ppm, 4week, TG, biological replicate 3


title: uterus treated T, biological rep1

source_name: Sprague Dawley rat uterus (pre-implantation period) treated with Orm


title: WT_42_4w_120ppm_lung

source_name: Dose 120ppm, 4week, WT, biological replicate 1


title: MK2206+GSKJ4

city: Singapore

first: Keng Gat

last: Lim

address: 60 Biopolis St, #02-01,

country: Singapore

institute: Genome Institute of Singapore

description:
9479187073_J
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analysed with GeneSpring 12.5

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

growth_protocol: MCF-7 cells were grown in DMEM supplemented with 10% Fetal Bovinse Serum and penicillin/streptomycin

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

treatment_protocol: MCF-7 cells were treated with the indicated inhibitors for 3 days

tag: cell line

tag: treatment duration

value: 3 days


title: GDC0941+GSKJ4

description:
9479187073_L
Replicate 1


title: pWT_pINS-RT-50-6

source_name: Training sample from mixed plasmids: pWT 50% - pINS 50%


title: KO_140_4w_40ppm_lung

source_name: Dose 40ppm, 4week, KO, biological replicate 5

value: male


title: pWT_pINS-RT-50-5


title: pWT_pINS-RT-50-2


title: pWT_pINS-RT-50-3


title: pWT_pINS-RT-50-4


title: pWT_pINS-RT-5-4

source_name: Training sample from mixed plasmids: pWT 5% - pINS 95%


title: pWT_pINS-RT-5-1


title: KO_139_4w_40ppm_lung

source_name: Dose 40ppm, 4week, KO, biological replicate 4

value: adult


title: MK2206

description:
9479187073_I
Replicate 1


title: pWT_pINS-RT-5-3


title: GSKJ4

description:
9479187073_H
Replicate 1


title: KO_136_4w_40ppm_lung

source_name: Dose 40ppm, 4week, KO, biological replicate 2


title: pWT_pINS-RT-5-2


title: pWT_pINS-RT-1-4

source_name: Training sample from mixed plasmids: pWT 1% - pINS 99%


title: KO_135_4w_40ppm_lung

source_name: Dose 40ppm, 4week, KO, biological replicate 1


title: pWT_pINS-RT-1-1


title: pWT_pINS-RT-1-3


title: WT_40_4w_40ppm_lung

source_name: Dose 40ppm, 4week, WT, biological replicate 5


title: WT_39_4w_40ppm_lung

source_name: Dose 40ppm, 4week, WT, biological replicate 4


title: pWT_pINS-RT-1-2


title: pWT_pINS-RT-0-3

source_name: Training sample from mixed plasmids: pWT 0% - pINS 100%


title: DMSO

description:
9479187073_G
Replicate 1


title: pWT_pINS-RT-0-4


title: pWT_pINS-RT-95-3

source_name: Training sample from mixed plasmids: pWT 95% - pINS 5%


title: pWT_pINS-RT-0-2


title: V75T-RT-2.3

source_name: Training sample from plasmid V75T

value: ScanArray


title: pWT_pINS-RT-0-1


title: V75T-RT-2.4


title: V75T-RT-2.2


title: V75T-RT-2.1


title: V75T-RT-1.2


title: V75I-RT-2.2

source_name: Training sample from plasmid V75I


title: V75I-RT-2.3


title: V75T-RT-1.1


title: V75I-RT-1


title: V75I-RT-2.1


title: WT_34_4w_40ppm_lung

source_name: Dose 40ppm, 4week, WT, biological replicate 1

value: Wild Type, (WT)


title: pWT-RT-9.2

source_name: Training sample from plasmid pWT

value: pWT


title: WT_38_4w_40ppm_lung

source_name: Dose 40ppm, 4week, WT, biological replicate 3

value: Whole Lung


title: pWT-RT-8.1


title: pWT-RT-8.2


title: TG_232_4w_0ppm_lung

source_name: Dose 0, 4week, TG, biological replicate 5


title: pWT-RT-7.2


title: pWT-RT-7.1


title: TG_231_4w_0ppm_lung

source_name: Dose 0, 4week, TG, biological replicate 4


title: KO_131_4w_0ppm_lung

source_name: Dose 0, 4week, KO, biological replicate 4


title: KO_130_4w_0ppm_lung

source_name: Dose 0, 4week, KO, biological replicate 3


title: TG_226_4w_0ppm_lung

source_name: Dose 0, 4week, TG, biological replicate 1


title: pWT-RT-9.1


title: TG_230_4w_0ppm_lung

source_name: Dose 0, 4week, TG, biological replicate 3


title: pWT-RT-6.4


title: WT_35_4w_40ppm_lung

source_name: Dose 40ppm, 4week, WT, biological replicate 2


title: pWT-RT-6.3


title: KO_127_4w_0ppm_lung

source_name: Dose 0, 4week, KO, biological replicate 2


title: pWT-RT-6.2


title: pWT-RT-6.1


title: pWT-RT-5.3


title: KO_138_4w_40ppm_lung

source_name: Dose 40ppm, 4week, KO, biological replicate 3


title: TG_229_4w_0ppm_lung

source_name: Dose 0, 4week, TG, biological replicate 2


title: pWT-RT-5.4


title: pWT-RT-5.2


title: pWT-RT-5.1


title: KO_126_4w_0ppm_lung

source_name: Dose 0, 4week, KO, biological replicate 1


title: pWT-RT-4.4


title: WT_32_4w_0ppm_lung

source_name: Dose 0, 4week, WT, biological replicate 5


title: KO_132_4w_0ppm_lung

source_name: Dose 0, 4week, KO, biological replicate 5


title: WT_31_4w_0ppm_lung

source_name: Dose 0, 4week, WT, biological replicate 4


title: pWT-RT-3.2


title: pWT-RT-4.1


title: pWT-RT-13.2


title: pWT-RT-3.1


title: pWT-RT-2.2


title: pWT-RT-2.1


title: WT_27_4w_0ppm_lung

source_name: Dose 0, 4week, WT, biological replicate 3


title: WT_26_4w_0ppm_lung

source_name: Dose 0, 4week, WT, biological replicate 2


title: pWT-RT-13.1

source_name: Training sample from plasmid pWT


title: pWT-RT-1.2


title: WT_25_4w_0ppm_lung

source_name: Dose 0, 4week, WT, biological replicate 1


title: TG_221_1w_120ppm_lung

source_name: Dose 120ppm, 1week, TG, biological replicate 4


title: pWT-RT-12.2


title: pWT-RT-12.1


title: pWT-RT-1.1


title: TG_220_1w_120ppm_lung

source_name: Dose 120ppm, 1week, TG, biological replicate 3


title: pWT-RT-11.2


title: pWT-RT-11.1


title: pWT-RT-10.2


title: pWT-RT-10.1


title: TG_217_1w_120ppm_lung

source_name: Dose 120ppm, 1week, TG, biological replicate 1


title: TG_224_1w_120ppm_lung

source_name: Dose 120ppm, 1week, TG, biological replicate 5


title: KO_121_1w_120ppm_lung

source_name: Dose 120ppm, 1week, KO, biological replicate 5


title: KO_120_1w_120ppm_lung

source_name: Dose 120ppm, 1week, KO, biological replicate 4


title: pINS-RT-6.1

source_name: Training sample from plasmid pINS

value: pINS


title: pINS-RT-5.2

value: GenePix


title: pINS-RT-8.1


title: pINS-RT-5.1


title: KO_119_1w_120ppm_lung

source_name: Dose 120ppm, 1week, KO, biological replicate 3


title: pINS-RT-4.1


title: pINS-RT-6.2


title: pINS-RT-7.1


title: TG_218_1w_120ppm_lung

source_name: Dose 120ppm, 1week, TG, biological replicate 2


title: WT_22_1w_120ppm_lung

source_name: Dose 120ppm, 1week, WT, biological replicate 5


title: pIns-RT-3.4

source_name: Training sample from plasmid pIns

value: pIns


title: pINS-RT-4.2


title: pIns-RT-3.3


title: pINS-RT-3.2


title: KO_118_1w_120ppm_lung

source_name: Dose 120ppm, 1week, KO, biological replicate 2


title: pIns-RT-3.2


title: pINS-RT-3.1


title: WT_21_1w_120ppm_lung

source_name: Dose 120ppm, 1week, WT, biological replicate 4


title: GDC0941

description:
9479187073_K
Replicate 1


title: WT_20_1w_120ppm_lung

source_name: Dose 120ppm, 1week, WT, biological replicate 3


title: pIns-RT-3.1


title: pINS-RT-2.2


title: WT_19_1w_120ppm_lung

source_name: Dose 120ppm, 1week, WT, biological replicate 2


title: pIns-RT-2.2


title: pINS-RT-2.1


title: pIns-RT-2.1


title: pIns-RT-1


title: pINS-RT-1.2


title: WT_18_1w_120ppm_lung

source_name: Dose 120ppm, 1week, WT, biological replicate 1


title: TG_213_1w_40ppm_lung

source_name: Dose 40ppm, 1week, TG, biological replicate 5


title: L2.22-RT.2

source_name: Training sample from plasmid L2.22


title: L2.22-RT.1


title: D67N-RT.3

source_name: Training sample from plasmid D67N


title: L2.22-RT.3


title: pINS-RT-1.1


title: D67N-RT.1


title: 2.94c64-RT-8.2

source_name: Training sample from plasmid 2.94c64


title: 2.94c64-RT-7.2


title: 2.94c64-RT-8.1


title: TG_211_1w_40ppm_lung

source_name: Dose 40ppm, 1week, TG, biological replicate 3


title: 2.94c64-RT-6.2


title: 2.94c64-RT-7.1


title: TG_212_1w_40ppm_lung

source_name: Dose 40ppm, 1week, TG, biological replicate 4


title: pWT-RT-4.2

source_name: Training sample from plasmid pWT


title: KO_116_1w_40ppm_lung

source_name: Dose 40ppm, 1week, KO, biological replicate 5


title: TG_210_1w_40ppm_lung

source_name: Dose 40ppm, 1week, TG, biological replicate 2


title: pWT_pINS-RT-50-1

source_name: Training sample from mixed plasmids: pWT 50% - pINS 50%


title: D67N-RT.2


title: 2.94c64-RT-5.2


title: KO_113_1w_40ppm_lung

source_name: Dose 40ppm, 1week, KO, biological replicate 4


title: KO_112_1w_40ppm_lung

source_name: Dose 40ppm, 1week, KO, biological replicate 3


title: 2.94c64-RT-6.1


title: 2.94c64-RT-4.2


title: TG_209_1w_40ppm_lung

source_name: Dose 40ppm, 1week, TG, biological replicate 1


title: KO_111_1w_40ppm_lung

source_name: Dose 40ppm, 1week, KO, biological replicate 2


title: 2.94c64-RT-5.1


title: 2.94c64-RT-3.2


title: 2.94c64-RT-4.1


title: WT_14_1w_40ppm_lung

source_name: Dose 40ppm, 1week, WT, biological replicate 5


title: KO_110_1w_40ppm_lung

source_name: Dose 40ppm, 1week, KO, biological replicate 1


title: WT_12_1w_40ppm_lung

source_name: Dose 40ppm, 1week, WT, biological replicate 4


title: 2.94c64-RT-3.1


title: 2.94c64-RT-2.2


title: 2.94c64-RT-2.1


title: 2.94c64-RT-1.2


title: 2.94c64-RT-1.1


title: 2.94c63-RT-8.2

source_name: Training sample from plasmid 2.94c63


title: 2.94c63-RT-8.1


title: WT_11_1w_40ppm_lung

source_name: Dose 40ppm, 1week, WT, biological replicate 3


title: 2.94c63-RT-7.2


title: 2.94c63-RT-7.1


title: 2.94c63-RT-6.1


title: 2.94c63-RT-6.2


title: WT_9_1w_40ppm_lung

source_name: Dose 40ppm, 1week, WT, biological replicate 1


title: pINS-RT-8.2

source_name: Training sample from plasmid pINS


title: 2.94c63-RT-5.1


title: TG_208_1w_0ppm_lung

source_name: Dose 0, 1week, TG, biological replicate 5


title: AT13ox rep2

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

institute: Kyushu Institute Technology

hyb_protocol: Hybridization was performed using the in situ Hybridization Kit Plus (Agilent Technologies, Tokyo, Japan)

scan_protocol: Hybridized and washed material on each glass slide was scanned by an Agilent G2505 B DNA microarray scanner (Agilent Technologies)

data_processing: Data analysis was performed by Feature Extraction and Image Analysis software (Agilent Technologies, Tokyo, Japan).

molecule: polyA RNA

label_protocol: cRNA amplification and fluorescence labeling were performed using the Agilent Low RNA Input Linear Amplification Kit (Agilent Technology, Tokyo, Japan) according to the manufacturer's protocol. A primer containing poly dT and a T7 polymerase promoter was annealed to the poly A+ RNA. First and second strands of cDNA were reverse transcribed from 500 ng total RNA using MMLV-RT enzyme. Cyanine 3- labeled cRNA was synthesized using T7 RNA polymerase. Labeled cRNA was purified by RNeasy Mini Kit (Qiagen, Tokyo, Japan).

extract_protocol: Approximately 500 ng of total RNA was three times extracted from each sample using TRIzol (Invitrogen).

tag: Stage

value: Seedling


title: TG_204_1w_0ppm_lung

source_name: Dose 0, 1week, TG, biological replicate 2

value: Transgenic, (TG)


title: 2.94c63-RT-4.2


title: TG_207_1w_0ppm_lung

source_name: Dose 0, 1week, TG, biological replicate 4


title: WT rep2

source_name: WT

value: wild type


title: KO_105_1w_0ppm_lung

source_name: Dose 0, 1week, KO, biological replicate 5

value: Knockout, (KO)


title: WT_10_1w_40ppm_lung

source_name: Dose 40ppm, 1week, WT, biological replicate 2


title: 2.94c63-RT-4.1


title: WT rep1


title: 2.94c63-RT-3.2


title: 2.94c63-RT-5.2


title: 2.94c63-RT-2.2


title: 2.94c63-RT-3.1


title: AT13ox rep1


title: 2.94c63-RT-2.1


title: 2.94c63-RT-1.2


title: 2.94c63-RT-1.1


title: TG_205_1w_0ppm_lung

source_name: Dose 0, 1week, TG, biological replicate 3


title: AT13 peptide treatment rep2

source_name: AT13 peptide treatment

tag: treatment

value: AT13 peptide


title: KO_102_1w_0ppm_lung

source_name: Dose 0, 1week, KO, biological replicate 2


title: 1.95c9-RT-9.1

source_name: Training sample from plasmid 1.95c9


title: 1.95c9-RT-9.2


title: 1.95c9-RT-8.1


title: TG_202_1w_0ppm_lung

source_name: Dose 0, 1week, TG, biological replicate 1


title: pWT-RT-4.3

source_name: Training sample from plasmid pWT


title: KO_103_1w_0ppm_lung

source_name: Dose 0, 1week, KO, biological replicate 3


title: non treatment rep1

value: non treatment


title: KO_104_1w_0ppm_lung

source_name: Dose 0, 1week, KO, biological replicate 4


title: non treatment rep2


title: WT_5_1w_0ppm_lung

source_name: Dose 0, 1week, WT, biological replicate 5


title: 1.95c9-RT-7.1

value: RT


title: 1.95c9-RT-8.2


title: WT_3_1w_0ppm_lung

source_name: Dose 0, 1week, WT, biological replicate 3


title: 1.95c9-RT-6.2


title: WT_2_1w_0ppm_lung

source_name: Dose 0, 1week, WT, biological replicate 2


title: 1.95c9-RT-6.1


title: 1.95c9-RT-5.1


title: 1.95c9-RT-5.2


title: KO_101_1w_0ppm_lung

source_name: Dose 0, 1week, KO, biological replicate 1


title: 1.95c9-RT-4.2


title: WT_4_1w_0ppm_lung

source_name: Dose 0, 1week, WT, biological replicate 4


title: 1.95c9-RT-7.2


title: pINS-RT-7.2

source_name: Training sample from plasmid pINS


title: WT_1_1w_0ppm_lung

source_name: Dose 0, 1week, WT, biological replicate 1


title: 1.95c9-RT-3.2


title: 1.95c9-RT-3.1


title: 1.95c9-RT-4.1


title: KO_117_1w_120ppm_lung

source_name: Dose 120ppm, 1week, KO, biological replicate 1


title: 1.95c9-RT-1.1


title: 1.95c9-RT-1.2


title: 1.95c5-RT-7.2

source_name: Training sample from plasmid 1.95c5


title: 1.95c9-RT-2.2


title: 1.95c5-RT-7.1


title: 1.95c9-RT-2.1


title: AT13 peptide treatment rep1


title: 1.95c5-RT-6.1


title: 1.95c5-RT-6.2


title: 1.95c5-RT-5.1


title: 1.95c5-RT-5.2


title: 1.95c5-RT-4.2


title: P98_T3

city: Los Angeles

first: Kamilla

last: Mundbjerg

address: 1441 Eastlake Ave

department: Norris Comprehensive Cancer Center

institute: USC Keck School of Medicine

hyb_protocol: DNA was bisulfite converted, restored, amplified, fragmented, and hybridized to Illumina Infinium Human Methylation 450 Beadchip using standard Illumina protocol

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

data_processing: Methylumi R package

label: Cy5 and Cy3

source_name: tumor_prostate_FFPE_patient 98

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted using Qiagen miRNeasy FFPE kit and Rneasy plus mini kit

tag: patient id

value: patient 98

tag: tissue type

value: Prostate

tag: disease state

value: Tumor

tag: sample info

value: Primary tumor focus 3 from patient 98

tag: sample type

value: FFPE


title: P98_T4

tag: gender

value: male

value: Primary tumor focus 4 from patient 98


title: 1.95c5-RT-4.1


title: 1.95c5-RT-3.2


title: P98_PL

source_name: met_lymphnode_FFPE_patient 98

value: Lymph node

value: Metastasis

value: Lymph node metastasis sample from patient 98


title: P98_AN

source_name: norm_prostate_FFPE_patient 98

value: Normal

value: Adjacent normal prostate sample from patient 98


title: P88_PL

source_name: met_lymphnode_FFPE_patient 88

value: patient 88

value: Lymph node metastasis sample from patient 88


title: 1.95c5-RT-2.1

value: GenePix


title: 1.95c5-RT-2.2


title: P88_T1

source_name: tumor_prostate_FFPE_patient 88

value: Primary tumor focus 1 from patient 88


title: 1.95c5-RT-1.2

value: RT


title: P88_T3

value: Primary tumor focus 3 from patient 88


title: P98_T1

value: patient 98

value: Prostate

value: Primary tumor focus 1 from patient 98


title: P88_AN

source_name: norm_prostate_FFPE_patient 88

value: Adjacent normal prostate sample from patient 88

value: FFPE


title: 1.95c5-RT-3.1


title: 1.95c5-RT-1.1


title: P98_T2

value: male

value: Tumor

value: Primary tumor focus 2 from patient 98


title: P88_T2

value: Primary tumor focus 2 from patient 88


title: P84_T4

source_name: tumor_prostate_FFPE_patient 84

value: patient 84

value: Primary tumor focus 4 from patient 84


title: P84_T3

value: Primary tumor focus 3 from patient 84


title: P85_T1

source_name: tumor_prostate_FFPE_patient 85

value: patient 85

value: Primary tumor focus 1 from patient 85


title: P85_NL

source_name: norm_lymphnode_FFPE_patient 85

value: Lymph node

value: Normal

value: Normal lymph node sample from patient 85


title: P84_T5

value: Primary tumor focus 5 from patient 84


title: P84_PL

source_name: met_lymphnode_FFPE_patient 84

value: Metastasis

value: Lymph node metastasis sample from patient 84


title: P85_PL

source_name: met_lymphnode_FFPE_patient 85

value: Lymph node metastasis sample from patient 85


title: P85_T2

value: Prostate

value: Primary tumor focus 2 from patient 85

value: FFPE


title: P84_AN

source_name: norm_prostate_FFPE_patient 84

value: male

value: Adjacent normal prostate sample from patient 84


title: 9.95c10-PRRT

source_name: Training sample from plasmid 9.95c10

value: PRRT

value: ScanArray


title: P85_T3

value: Tumor

value: Primary tumor focus 3 from patient 85


title: 6.95c8-PRRT-4.2

source_name: Training sample from plasmid 6.95c8


title: P84_T1

value: patient 84

value: Primary tumor focus 1 from patient 84


title: 6.95c8-PRRT-4.4


title: 6.95c8-PRRT-4.1


title: 6.95c8-PRRT-4.3


title: Leucocytes_healthy control [09-344CM]

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

institute: Biodonostia Institute

hyb_protocol: GeneChip Hybridization, Wash and Stain kit was used for hybridization in a GeneChip Hybridization oven 640 and in a GeneChip Fluidics Station 450 using the protocol FS450-0003, as explained in the protocol provided by Affymetrix.

scan_protocol: Arrays were scanned in a GeneChip 7G scanner and analysed in Affymetrix GeneChip Command Console Scan Control v4.0.0.1567.

data_processing: Quality control, summarization and normalization of the data were performed with miRNA QC Tool v.1.0.33.0 following the following workflow: Background detection, RMA Global Background correction, Quantile normalization and summarization with median polish.

source_name: Healthy control

label_protocol: Total RNA was labeled using FlashTag Biotin HSR RNA labeling kit (Genisphere)

extract_protocol: LeucoLOCK Total RNA isolation system with the alternative protocol to recover small RNA fraction (ThermoFisher)

tag: subject status

value: Healthy control_leucocytes

tag: age

value: Male

tag: cell type

value: Leucocytes


title: Leucocytes_healthy control [10-060CM]


title: P56_T5

source_name: tumor_prostate_FFPE_patient 56

value: patient 56

value: Primary tumor focus 5 from patient 56


title: P84_T2

value: Primary tumor focus 2 from patient 84


title: 6.95c8-PRRT-3.4

tag: plasmid/patient id

tag: region


title: P56_T4

value: Prostate

value: Primary tumor focus 4 from patient 56


title: Leucocytes_healthy control [09-241CM]


title: 6.95c8-PRRT-3.3

tag: scanner

tag: sequence(s)


title: P4 Axin2+ AEC2s_5

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4A25

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets, 18,494 probesets were considered expressed.  Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package ( http://www.tm4.org/mev/).

source_name: Cell sort P4 lung Axin2+/EpCAM+ cells

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

growth_protocol: Primary cell isolation

extract_protocol: RNA was extracted using Rneasy mini kit (Qiagene)

treatment_protocol: No treatment

tag: tissue

value: lung

value: postnatal day 4

tag: genotype

tag: background strain

value: Mixed C57BL/6 x 129S6 x CD-1


title: 6.95c8-PRRT-3.2

value: PRRT


title: Leucocytes_healthy control [09-376CM]


title: P56_T3

value: male

value: Primary tumor focus 3 from patient 56

value: FFPE


title: P56_T1

value: Tumor

value: Primary tumor focus 1 from patient 56


title: P4 Axin2+ AEC2s_3

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4A23


title: Leucocytes_healthy control [09-275CM]

value: Healthy control_leucocytes


title: P4 Axin2+ AEC2s_4

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4A24


title: 6.95c8-PRRT-2.2

value: ScanArray


title: P56_T2

value: Primary tumor focus 2 from patient 56


title: P56_PL2

source_name: met_lymphnode_FFPE_patient 56

value: patient 56

value: Lymph node

value: Metastasis

value: Lymph node metastasis sample 2 from patient 56


title: P54_T2

source_name: tumor_prostate_FFPE_patient 54

value: patient 54

value: Prostate

value: Primary tumor focus 2 from patient 54


title: P56_PL1

value: Lymph node metastasis sample 1 from patient 56


title: Leucocytes_healthy control [09-337CF]

value: Female

value: Leucocytes


title: Leucocytes_healthy control [09-239CF]


title: Leucocytes_healthy control [09-383CF]


title: 6.95c8-PRRT-2.1

value: PRRT


title: P52_T3

source_name: tumor_prostate_FFPE_patient 52

value: patient 52

value: male

value: Primary tumor focus 3 from patient 52

value: FFPE


title: 6.95c8-PRRT-1.1

value: ScanArray


title: Leucocytes_healthy control [09-274CF]

value: Healthy control_leucocytes


title: 6.95c8-PRRT-3.1


title: 6.95c8-PRRT-1.2


title: Leucocytes_healthy control [09-345CF]


title: P4 SP-C+ AEC2s_3

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4SPC3

source_name: Cell sort P4 lung SP-C + cells

value: lung

value: postnatal day 4

value: Mixed C57BL/6 x 129S6 x CD-1


title: P54_PL

source_name: met_lymphnode_FFPE_patient 54

value: Lymph node

value: Metastasis

value: Lymph node metastasis sample from patient 54


title: P4 SP-C+ AEC2s_4

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4SPC4


title: P4 Axin2+ AEC2s_2

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4A22


title: P4 Axin2+ AEC2s_1

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4A21


title: P4 SP-C+ AEC2s_5

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4SPC5


title: P4 SP-C+ AEC2s_2

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4SPC2


title: P54_T1

value: patient 54

value: Prostate

value: Tumor

value: Primary tumor focus 1 from patient 54


title: 5.96c9-PRRT-3.3

source_name: Training sample from plasmid 5.96c9

value: PRRT


title: Leucocytes_healthy control [09-208CF]

value: Female

value: Leucocytes


title: 5.96c9-PRRT-3.2


title: P54_AN

source_name: norm_prostate_FFPE_patient 54

value: male

value: Normal

value: Adjacent normal prostate sample from patient 54


title: 5.96c9-PRRT-3.1

value: ScanArray


title: 5.96c9-PRRT-2.2


title: Leucocytes_healthy control [09-335CM]

value: Healthy control_leucocytes


title: Leucocytes_healthy control [09-381CF]


title: P52_T1

value: patient 52

value: Primary tumor focus 1 from patient 52

value: FFPE


title: P52_PL

source_name: met_lymphnode_FFPE_patient 52

value: Lymph node

value: Metastasis

value: Lymph node metastasis sample from patient 52


title: P52_T2

value: Prostate

value: Primary tumor focus 2 from patient 52


title: Leucocytes_healthy control [08-584CV]

value: Male


title: P4 SP-C+ AEC2s_1

description:
Gene expression data from P3 and adult type 2 alveolar epithelial cells isolated by cell sorting using YFP from SftpcCreERT2-R26REYFP mice and TdTomato+, EpCAM+, CD31-, CD45- from Axin2CreERT2-TdTomato mice
P4SPC1

value: lung

value: postnatal day 4

value: Mixed C57BL/6 x 129S6 x CD-1


title: Leucocytes_healthy control [09-898CM]

value: Female

value: Leucocytes


title: 5.96c9-PRRT-2.1

value: PRRT


title: Leucocytes_healthy control [09-170CF]


title: P43_PL

source_name: met_lymphnode_FFPE_patient 43

value: patient 43

value: male

value: Lymph node metastasis sample from patient 43


title: 5.96c9-PRRT-1.3

value: ScanArray


title: ischemia_cortex_P1.5_ischemia1

city: Shinjuku-ku

first: Kazunori

last: Nakajima

state: Tokyo

address: 35 Shinanomachi

department: Department of Anatomy

institute: Keio University School of Medicine

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >13.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GE Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE Microarrays 8 x 60k(G4858A#28005) 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).

scan_protocol: Slides were scadnned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: cortex, P1.5, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from cortex of control or ischemic mouse at P1.5 using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) following the manufacturer's recommendations.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Uterine arteries of pregnant mice at E16.5 were occluded with clips for 14 min under anesthesia to induce ischemia in the embryonic mouse brains.

tag: strain


title: 5.96c9-PRRT-1.2


title: P43_PIN

source_name: pin_prostate_FFPE_patient 43

tag: patient id

value: PIN

value: PIN sample from patient 43

value: FFPE


title: P43_T1

source_name: tumor_prostate_FFPE_patient 43

tag: tissue type

value: Tumor

value: Primary tumor focus 1 from patient 43


title: ischemia_cortex_P1.5_ischemia3


title: 5.96c9-PRRT-3.4


title: Leucocytes_healthy control [09-881CM]

value: Healthy control_leucocytes


title: ischemia_cortex_P1.5_control4


title: P43_AN

source_name: norm_prostate_FFPE_patient 43

value: Prostate

tag: disease state

value: Normal

value: Adjacent normal prostate sample from patient 43


title: P43_T2

tag: sample info

value: Primary tumor focus 2 from patient 43


title: ischemia_cortex_P1.5_control3


title: ischemia_cortex_P1.5_ischemia2


title: 5.96c9-PRRT-1.1


title: Leucocytes_healthy control [09-171CM]

value: Female


title: ischemia_cortex_P1.5_control1


title: P41_T4

source_name: tumor_prostate_FFPE_patient 41

value: patient 41

value: Primary tumor focus 4 from patient 41

tag: sample type


title: P52_AN

source_name: norm_prostate_FFPE_patient 52

value: patient 52

tag: gender

value: Adjacent normal prostate sample from patient 52


title: 2.94c64-PRRT-2.2

source_name: Training sample from plasmid 2.94c64

value: PRRT

value: GenePix


title: P41_T3

value: male

value: Primary tumor focus 3 from patient 41


title: 2.94c64-PRRT-1.2


title: 2.94c64-PRRT-2.1


title: P41_T2

value: Primary tumor focus 2 from patient 41

value: FFPE


title: 2.94c64-PRRT-1.1


title: Leucocytes_healthy control [11-502CM]

source_name: Healthy control

tag: subject status

value: Leucocytes


title: Leucocytes_healthy control [09-900CVhsrbis]

value: Healthy control_leucocytes

tag: age

value: Male


title: 2.94c63-PRRT-2.2

source_name: Training sample from plasmid 2.94c63


title: Leucocytes_healthy control [08-759]

tag: cell type


title: 2.94c63-PRRT-2.1

tag: plasmid/patient id


title: P41_PL

source_name: met_lymphnode_FFPE_patient 41

value: Lymph node

value: Metastasis

value: Lymph node metastasis sample from patient 41


title: Leucocytes_healthy control [D6CM]

value: Female


title: P41_T1

value: patient 41

value: Prostate

value: Tumor

value: Primary tumor focus 1 from patient 41


title: OT-1 Lck-/- 24h activated replicate #3

city: Edinburgh

first: Thomas

last: Tan

address: Charlotte Auerbach Road

department: Institute of Immunology and Infection Research

institute: The University of Edinburgh

description: Gene expression in CD8 T cells after withdrawal of doxycycline from diet for 7 days to remove the knocked-in Lck expression, and then activated with cognate antigen for 24h.

hyb_protocol: 600 ng Cy-3 labelled sample fragmented using fragmentation buffer from the Agilent Gene Expression Hybridisation Kit (Agilent) for 30 min at 60°C. Fragmented samples were mixed 1:1 with Hybridisation Buffer (v/v) and hybridised to a 60K high-density oligonucleotide microarray overnight. Microarrays were loaded as per the manufacturer’s instructions and hybridisation was performed at 65°C, in an Agilent Hybridisation Oven with rotation set to 10 RPM.

scan_protocol: Following hybridisation, the microarray slides were washed in Gene Expression wash buffers 1 and 2 (Agilent) and immediately scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies).

data_processing: GenePix Pro 6.0 was used to quantify fluorescence intensities for individual spots on the microarray. All statistical analysis was performed in the statistical environment R, version 3.2.2 and the Limma (Smyth and Speed, 2003) and RankProd (Breitling et al., 2004) packages.

source_name: Mouse CD8 T lymphocyte, OT-1het, Rag-/-, Lck-/-

label_protocol: 50 ng RNA was Cy-3 labelled using Agilent Low Input Quick Amp 1-colour Labelling Kit (Agilent). The level of dye incorporation was measured using a Nanodrop ND1000 spectrophotometer (LabTech, Sussex, UK).

extract_protocol: Total RNA was exracted using RNeasy column (Qiagen). RNA was first checked for quality using a 2100 Bioanalyser (Agilent). RNA with a RIN score of > 8 was used for microarray analysis.

treatment_protocol: Ex vivo lymphocytes were cultured in complete IMDM and activated with 100nM SIINFEKL peptide for 24h. Cell pellets were snap-frozen on dry ice.

tag: activation

value: 24h with SIINFEKL


title: P41_PIN

source_name: pin_prostate_FFPE_patient 41

value: PIN

value: PIN sample from patient 41


title: OT-1 Lck-/- 24h activated replicate #1


title: 2.94c63-PRRT-1.2

tag: region

value: PRRT

tag: scanner

value: GenePix


title: P41_NL

source_name: norm_lymphnode_FFPE_patient 41

value: male

value: Normal

value: Normal lymph node sample from patient 41

value: FFPE


title: OT-1 Lck-/- 24h activated replicate #2

tag: tissue

value: Lymph node


title: ischemia_cortex_P1.5_ischemia4


title: Leucocytes_healthy control [09-708CM]

value: Healthy control_leucocytes

value: Leucocytes


title: OT-1 WT 24h activated replicate #4

description: Gene expression in CD8 T cells activated with cognate antigen for 24h.

source_name: Mouse CD8 T lymphocyte, OT-1het, Rag-/-


title: OT-1 WT 24h activated replicate #3


title: 2.94c63-PRRT-1.1

tag: sequence(s)


title: Leucocytes_healthy control [09-883CVhsr]

value: Male


title: Leucocytes_healthy control [D1CV]


title: 2.94c5-PRRT.4

source_name: Training sample from plasmid 2.94c5

value: ScanArray


title: OT-1 WT 24h activated replicate #2


title: 2.94c5-PRRT.3


title: 2.94c5-PRRT.2


title: Leucocytes_healthy control [08-659CM]

value: Female


title: Leucocytes_healthy control [10-321CM]


title: Leucocytes_healthy control [D18CM]


title: OT-1 WT 24h activated replicate #1


title: 2.94c5-PRRT.1


title: P32_T4

source_name: tumor_prostate_FFPE_patient 32

value: patient 32

value: Prostate

value: Tumor

value: Primary tumor focus 4 from patient 32


title: OT-1 Lck-/- naïve replicate #2

description: Gene expression in naïve CD8 T cells after withdrawal of doxycycline from diet for 7 days to remove the knocked-in Lck expression.

treatment_protocol: Freshly isolated ex vivo lymphocytes were sorted for CD8b+ and CD44low, cell pellets were snap-frozen on dry ice.


title: OT-1 Lck-/- naïve replicate #1


title: OT-1 Lck-/- naïve replicate #3


title: OT-1 Lck-/- naïve replicate #4


title: Leucocytes_healthy control [08-588]


title: 1.95c9-PRRT-4.1

source_name: Training sample from plasmid 1.95c9


title: Leucocytes_healthy control [08-647CV]


title: Leucocytes_healthy control [D17CM]


title: P32_T2

value: Primary tumor focus 2 from patient 32


title: Leucocytes_healthy control [09-901]


title: P32_AN

source_name: norm_prostate_FFPE_patient 32

value: Adjacent normal prostate sample from patient 32


title: OT-1 WT naive replicate #3

description: Gene expression in naïve CD8 T cells


title: P26_T5

source_name: tumor_prostate_FFPE_patient 26

value: patient 26

value: Primary tumor focus 5 from patient 26


title: Leucocytes_healthy control [11-504CM]


title: P26_T3

value: male

value: Primary tumor focus 3 from patient 26


title: P32_PL

source_name: met_lymphnode_FFPE_patient 32

value: Metastasis

value: Lymph node metastasis sample from patient 32

value: FFPE


title: 1.95c9-PRRT-3.2

value: PRRT

value: GenePix


title: 1.95c9-PRRT-3.1


title: 1.95c9-PRRT-4.2


title: 1.95c9-PRRT-2.2


title: Leucocytes_healthy control [09-221CV]

value: Healthy control_leucocytes

value: Male

value: Leucocytes


title: Leucocytes_healthy control [09-902CV]


title: P26_PL

source_name: met_lymphnode_FFPE_patient 26

value: Lymph node

value: Lymph node metastasis sample from patient 26


title: 1.95c9-PRRT-2.1


title: P26_AN

source_name: norm_prostate_FFPE_patient 26

value: Prostate

value: Normal

value: Adjacent normal prostate sample from patient 26


title: P26_T2

value: patient 26

value: Tumor

value: Primary tumor focus 2 from patient 26


title: Leucocytes_healthy control [09-1203CM]

value: Female


title: OT-1 WT naive replicate #1

description: Gene expression in naïve CD8 T cells


title: 1.95c9-PRRT-1.2


title: Leucocytes_healthy control [09-880CV]


title: Leucocytes_healthy control [08-650CM]


title: ischemia_cortex_P1.5_control2

source_name: cortex, P1.5, replicate 1

value: male


title: OT-1 WT replicate #2 dye swap

hyb_protocol: 300 ng Cy-3 labelled sample and 300 ng Cy-5 labelled sample were pooled and fragmented using fragmentation buffer from the Agilent Gene Expression Hybridisation Kit (Agilent) for 30 min at 60°C. Fragmented samples were mixed 1:1 with Hybridisation Buffer (v/v) and hybridised to a 60K high-density oligonucleotide microarray overnight. Microarrays were loaded as per the manufacturer’s instructions and hybridisation was performed at 65°C, in an Agilent Hybridisation Oven with rotation set to 10 RPM.

data_processing: GenePix Pro 6.0 was used to quantify fluorescence intensities for individual spots on the microarray. All statistical analysis was performed in the statistical environment R, version 2.6.1 and the Limma (Smyth and Speed, 2003), RankProd (Breitling et al., 2004) and Siggenes (Schwender H., 2012) packages. Briefly, raw intensities for both channels (Cy5 Polysomal RNA and Cy3 Subpolysomal RNA) were background corrected and normalised by scaling. Dye-swapped samples were averaged to correct for bias. Differentially expressed genes between WT and OFF samples were identified using RankProd test.

source_name: Mouse T lymphocyte, OT-1het, Rag-/-

label_protocol: 1.5 μl subs RNA was Cy-3 labelled and 1.5 μl polys RNA was Cy-5 labelled using Agilent Low Input Quick Amp 2-colour Labelling Kit (Agilent). The level of dye incorporation was measured using a Nanodrop ND1000 spectrophotometer (LabTech, Sussex, UK).

growth_protocol: Ex vivo cells were cultured in IMDM supplemented with 10% FCS, L-glutamine, 100U/ml penicillin, 100U/ml streptomycin and 50μM 2β-ME

extract_protocol: Cells were harvested and lysed in Gradient Buffer (300 mM NaCl, 15 mM MgCl2, 15 mM Tris/HCl pH 7.5, 2 mM DTT, 100 μg/mL cycloheximide) supplemented with 1% Triton X-100, 0.5 U/μl RNAse inhibitor (Promega), and a cocktail of protease inhibitors (Sigma). Postnuclear supernatants were loaded onto 10%-50% sucrose step gradients in Gradient Buffer and separated by centrifugation at 38,000 rpm for 2 hours at 4°C in a SW-40 rotor (Beckman Coulter). RNA content was read across the gradients through a live 254 nm UV spectrometer (Isco) and each sample was collected in ten fractions. Fraction 1-5 were pooled and define as the sub-polysomal fraction, while Fraction 6-10 were pooled and defined as the polysomal fraction. Total RNA was extracted from the pooled fractions using Trizol reagent (Thermo Fisher Scientific) and further purified with acid phenol-chloroform and ethanol precipitation.

treatment_protocol: Cells were stimulated with 100nM SIINFEKL peptide antigen for 24h. Cells were treated with 100 μg/ml cycloheximide for 10 minutes before harvest. Cell pellets were flash-frozen in dry ice on stored at -80°C until extraction.

tag: fraction

value: Sub-polysomal

tag: genotype/variation

value: OT-1 Wild Type

value: Polysomal


title: OT-1 WT replicate #1 dye swap


title: P26_T1

tag: patient id

value: Primary tumor focus 1 from patient 26

value: FFPE


title: 1.95c9-PRRT-1.1

hyb_protocol: Before hybridization, printed microarrays were washed in 2× saline-sodium citrate (SSC) buffer and 0.1% N-lauryl sarcosine, for 2 min at room temperature, followed by 2 additional min in 2× SSC. This step allowed removing unbound DNA from the microarray surface and washing the excess of spotting solution. Printed oligonucleotides were denatured by baking the slides for 2 min in boiling milli-Q water and cooling for 10 sec at room temperature. The oligonucleotides were immediately fixed by plunging the slides into ice-cold 100% ethanol for 2 min, followed by centrifugation at 500×g for 1 min (using an Arrayit minicentrifuge). Microarrays were prehybridized with 20 ul of hybridization buffer (6× SSC, 0.5% SDS, 1% BSA) for 45 min at 42°C, under a 24  24 mm cover slip in a hybridization chamber (Genetix). Finally, the microarrays were washed with distilled water, and dried by centrifugation. Hybridization with the labeled target (50 ng, equivalent to 0.3 pmol Alexa Fluor 647) was carried out in hybridization buffer at 50oC for 3 h, using microarray hybridization chambers (Genetix).

data_processing: The selected raw fluorescence value for each spot was the median foreground signal after subtracting its local background. Technical replicates for each target-probe hybridization (4 spots per experiment) were clustered together. Since two different classes of signals (positive or negative) are expected, they were clustered into two groups using the K-means algorithm. Then, after removing the outliers from the positive group by applying the Grubb’s test with a significance level of 0.05, the mean of the positive signals was obtained. Two regions (containing the PR and RT probes, respectively) were separately normalized in each microarray by means of their own mean positive  signal. These two values were used as the normalization factor for each probe by applying the function (formula.pdf). where ǁPSǁ is the normalized probe signal, NRP is the total number of replicas per hybridized probe (typically, 4), IRP is the signal intensity of a replica probe i, NPS is the total number of positive probe signals per array region (either PR or RT), and IPS is the intensity of a positive probe signal i within such a region.

label_protocol: The phosphorylated strand of the HIV-1 DNA targets to be hybridized was specifically degraded using lambda exonuclease (New England Biolabs), and the resulting ssDNA was fluorescently labeled with Alexa Fluor 647, using the Ulysis Alexa Fluor 647 Nucleic Acid Labeling Kit (Life Technologies)

value: PRRT

value: GenePix


title: OT-1 WT replicate #3 dye swap

value: Lymph node


title: 1.95c5-PRRT-5.2

source_name: Training sample from plasmid 1.95c5


title: OT-1 Lck-/- replicate #4 dye swap

source_name: Mouse T lymphocyte, OT-1het, Rag-/-, Lck-/-

value: OT-1 Lck-/-


title: 1.95c5-PRRT-5.1


title: P32_T3

value: patient 32

tag: tissue type

value: Prostate

value: Primary tumor focus 3 from patient 32


title: 1.95c5-PRRT-4.4

value: ScanArray


title: P24_T6

source_name: tumor_prostate_FFPE_patient 24

value: patient 24

tag: disease state

value: Tumor

value: Primary tumor focus 6 from patient 24


title: FAPs_5'ss_VMO_rep1

city: Palo Alto

middle: A

last: Rando

address: 3801 Miranda Ave

department: Neurology and Neurological Sciences

institute: Stanford University School of Medicine

description: Gene expression data from WT fibro/adipogenic progenitors isolated from WT C57Bl/6 mice injured with glycerol, injected with 5'ss-VMO 3 days post-injury, and subsequently isolated 2 days post-VMO injection.

hyb_protocol: Fragmented biotin-labeled single stranded DNA was hybridized to Affymetrix Mouse Gene 1.0 Array according to the standard Affymetrix protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymertix Expression Console software using Affymetrix default RMA analysis settings.

source_name: Fibro/adipogenic progenitors isolated from hindlimb skeletal muscles treated in vivo with 5'ss-VMO

label_protocol: Biotinylated single stranded cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: RNA was isolated from cells that were pelleted and snap-frozen immediately after isolation from the muscle.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit as per the manufacturer’s instructions (Qiagen).

treatment_protocol: Tibialis anterior muscles from C57Bl/6 mice were each injured with 30 µL of 50% v/v glycerol and injected with the indicated vivo morpholino (VMO) after 3 days. FAPs were then isolated from the muscles 2 days post-VMO injection.

value: male

value: skeletal muscle

value: 8-12 weeks

tag: strain

tag: treatment

value: 5' Splice Site VMO


title: P24_T5

tag: gender

tag: sample info

value: Primary tumor focus 5 from patient 24

tag: sample type


title: OT-1 Lck-/- replicate #3 dye swap

value: Sub-polysomal

value: Polysomal


title: OT-1 Lck-/- replicate #2 dye swap


title: P24_T4

value: Primary tumor focus 4 from patient 24

value: FFPE


title: FAPs_5'ss_VMO_rep2

tag: age


title: FAPs_pA_VMO_rep2

description: Gene expression data from WT fibro/adipogenic progenitors isolated from WT C57Bl/6 mice injured with glycerol, injected with pA-VMOs 3 days post-injury, and subsequently isolated 2 days post-VMO injection.

source_name: Fibro/adipogenic progenitors isolated from hindlimb skeletal muscles treated in vivo with pA-VMOs

value: Polyadenylation Site VMOs


title: FAPs_pA_VMO_rep1


title: FAPs_Cntrl_VMO_rep2

description: Gene expression data from WT fibro/adipogenic progenitors isolated from WT C57Bl/6 mice injured with glycerol, injected with Control VMO 3 days post-injury, and subsequently isolated 2 days post-VMO injection.

source_name: Fibro/adipogenic progenitors isolated from hindlimb skeletal muscles treated in vivo with Control VMO

value: Control VMO


title: 1.95c5-PRRT-4.2

city: Torrejón de Ardoz

last: Briones

address: Ctra de Torrejón a Ajalvir, km 4

institute: Centro de Astrobiología (CAB, CSIC-INTA)

scan_protocol: Hybridized microarrays were washed at 45ºC in 2x SSC and 0.1% N-lauryl sarcosine for 5 min, then in 2x SSC for 5 min, rinsed in 0.2x SSC for 10 sec, and finally in distilled water for 5 min. Slides were dried by centrifugation at 500×g for 1 min and immediately scanned at 635 nm using either GenePix 4000B (Molecular Devices) or G2565AA  (Agilent) high resolution microarray scanners. Hybridization images were processed using GenePix Pro 6.0.0.68 (Molecular Devices) software in GenePix Scanner, and ScanArray Express 2.0 (Perkin Elmer) in Agilent one. No automatic normalization of images was performed.

extract_protocol:
HIV-1 DNA target molecules corresponding to the training set were amplified from the cloned sequences using Expand High Fidelity DNA polymerase (EHF, Roche), as specified by the manufacturer. PCR amplification of the full PR-coding region was carried out using the forward primer 5’PROT2HindIII-P (5’-TCAGAGCAGACCAGAGCCAACAGCCCCACC-3’, corresponding to nucleotides [nts] 2138 to 2167 of HIV-1 CAM-1 strain, GenBank accession  number D10112) phosphorylated at its 5’-end, and the reverse primer 140RD (5’-CATTGTACTGATATCTAATCCCTGG-3’, complementary to positions 2969-2993). In turn, PCR amplifications of the queried codons of the RT-coding region involved the phosphorylated forward primers RT1-P (5’-CCAAAAGTTAAACAATGGCCATTG-3’, nts 2606-2629) or 55F-P (5’-CAAAAATTGGGCCTGAAAATCC-3’, nts 2694-2715), and the reverse primers 153RD (5’-TATTGCTGGTGATCCTTTCC-3’, nts 3009-3028), 13RD (5’-GTTCATAACCCATCCAAAGG-3’,nts 3232-3251) or 20RD (5’-ATTGACAGTCCAGCTGTCTTTTTCTGGC-3’, nts 3289-3316). Longer amplicons containing the PR-RT-coding regions were obtained by PCR amplification using as primers 5’PROT2HindIII-P and either 20RD or RT3333R (5’-CCACTAACTTCTGTATGTCATTG-3’, nts 3311-3333).
Viral RNA was extracted from plasma samples using the ‘HIV Sample Preparation Module’ of the ‘ViroSeq HIV-1 Genotyping System’ (Applied Biosystems), as specified by the manufacturer. The extracted RNA was retrotranscribed and PCR amplified by means of the ‘OneStep RT-PCR Kit’ (Qiagen), since this system showed higher sensitivity for samples with low viral load than other two-step protocols essayed (data not shown). Primers used were 5’PROT1 (5’-AGGCTAATTTTTTAGGGAAAATCTGGCCTTCC-3’, nts 2080-2111) and 153RD for the PR region, and RT-INI (5’-ACAGTATTAGTAGGACCTACACC-3’, nts 2474-2496) and RT3333R for the RT region. The RT-PCR amplification of a single amplicon containing the PR-RT-coding regions involved primers 5’PROT1 and RT3333R, though this approach showed less efficiency for samples with viral load lower than 104 copies/ml. Upon RT-PCR, nested PCR amplifications of the PR-coding region were performed with EHF, using the forward primer 5’PROT2HindIII-P and the reverse primer 140RD (positive amplification was successful in 53 out of the 57 samples), while those of the RT-coding region involved different combinations of the forward primers RT1-P or 55F-P, and the reverse primers 153RD, 13RD or 20RD (51 samples amplified).

tag: plasmid/patient id

value: PRRT


title: P32_T1

value: patient 32

value: Prostate

value: Primary tumor focus 1 from patient 32


title: OT-1 WT replicate #4 dye swap

value: Lymph node

value: OT-1 Wild Type


title: 1.95c5-PRRT-4.3

value: ScanArray


title: P24_T1

value: patient 24

value: male

value: Tumor

value: Primary tumor focus 1 from patient 24


title: P24_T3

value: Primary tumor focus 3 from patient 24


title: 1.95c5-PRRT-4.1


title: 1.95c5-PRRT-3.2

value: GenePix


title: P24_T2

value: Primary tumor focus 2 from patient 24


title: P24_PL

source_name: met_lymphnode_FFPE_patient 24

value: Metastasis

value: Lymph node metastasis sample from patient 24

value: FFPE


title: P23_T3

source_name: tumor_prostate_FFPE_patient 23

value: patient 23

value: Primary tumor focus 3 from patient 23


title: OT-1 WT replicate #2

value: Sub-polysomal

value: Polysomal


title: FAPs_Cntrl_VMO_rep1

value: skeletal muscle

value: 8-12 weeks

value: Control VMO


title: FAPs_5'ss_AMO_PDGF_50_rep2

description: Gene expression data from WT fibro/adipogenic progenitors isolated from a noninjured animal and treated in vitro with Intronic PDGFRα 5' splice site AMO and 50uM PDGF-AA.

source_name: Fibro/adipogenic progenitors isolated from hindlimb skeletal muscles, treated with 5'ss AMO and 50uM PDGF-AA

growth_protocol: Cells were grown for 2.5 days in DMEM supplemented with 10% FBS prior to treatment.

treatment_protocol: The media was switched to Ham’s F10 supplemented with 10% horse serum and transfected with 10 µM AMO as indicated for 48 hours. The media was then replaced with Opti-Mem and cells re-transfected with 10 µM AMO with 50uM PDGF-AA or control. After 48 hours, total RNA was extracted.

tag: cell type

value: fibro/adipogenic progenitors

value: 5' Splice Site AMO, 50uM PDGF-AA


title: 1.95c5-PRRT-3.1

tag: region

value: PRRT


title: OT-1 Lck-/- replicate #1 dye swap

value: Lymph node

value: OT-1 Lck-/-


title: OT-1 WT replicate #1

value: OT-1 Wild Type


title: FAPs_5'ss_AMO_PDGF_50_rep1

description: Gene expression data from WT fibro/adipogenic progenitors isolated from a noninjured animal and treated in vitro with intronic PDGFRα 5' splice site AMO and 50uM PDGF-AA.

value: male


title: P24_NL

source_name: norm_lymphnode_FFPE_patient 24

value: patient 24

value: Normal

value: Normal lymph node sample from patient 24


title: P23_PL1

source_name: met_lymphnode_FFPE_patient 23

value: patient 23

value: Metastasis

value: Lymph node metastasis sample 1 from patient 23

value: FFPE


title: OT-1 WT replicate #3

value: Sub-polysomal

value: Polysomal


title: FAPs_pA_AMO_PDGF_50_rep1

description: Gene expression data from WT fibro/adipogenic progenitors isolated from a noninjured animal and treated in vitro with Intronic PDGFRα polyA site AMO and 50uM PDGF-AA.

source_name: Fibro/adipogenic progenitors isolated from hindlimb skeletal muscles, treated with pA AMOs and 50uM PDGF-AA

value: skeletal muscle

value: 8-12 weeks

value: Polyadenylation Site AMOs, 50uM PDGF-AA


title: 1.95c5-PRRT-1.2

value: PRRT

tag: scanner

value: ScanArray


title: OT-1 Lck-/- replicate #3

tag: tissue

value: Lymph node

value: OT-1 Lck-/-


title: FAPs_pA_AMO_PDGF_50_rep2

value: male

value: fibro/adipogenic progenitors


title: 1.95c4-PRRT-2.3

source_name: Training sample from plasmid 1.95c4

tag: sequence(s)


title: P26_T4

source_name: tumor_prostate_FFPE_patient 26

value: patient 26

value: Prostate

value: Tumor

value: Primary tumor focus 4 from patient 26


title: P23_T1

value: patient 23

value: Primary tumor focus 1 from patient 23


title: P23_PL2

value: Metastasis

value: Lymph node metastasis sample 2 from patient 23

value: FFPE