title: 13832718 - NadC 4.11 light 2 vs Ctrl light 2

hyb_protocol: Ctrl light 2 Cy5 / NadC 4.11 light 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ctrl, light

value: light

source_name: NadC 4.11, light

value: quinolinate


title: 13832710 - Ctrl dark 2 vs NadC 4.11 dark 2

status: Public on Nov 01 2009

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Establish which transcripts are affected by changes in NAD concentration, and whether this depends on light/dark.

hyb_protocol: NadC 4.11 dark 2 Cy5 / Ctrl dark 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: NadC 4.11, dark

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - light intensity: 100 µmol/m2/s temperature: 20/18°C day/night media : soil with nutritive solution twice a week humidité : 65%

treatment_protocol: Name:quinolinate, dark - compound based treatment - light,quinolinate:quantity 0.1mM time 48hour . 48h in the dark

tag: condition

value: dark

tag: treatment

tag: ecotype

value: Columbia

tag: age

value: 5 weeks

source_name: Ctrl, dark

extract_protocol: Ctrl dark 2:10.4ug.

treatment_protocol: Name:MOPS, dark - compound based treatment - compound addition,mops:quantity 50mM time 48hour . 48h in the dark


title: Infected rat day 13 T00189898

status: Public on Oct 01 2009

city: Lille

first: Jamal

last: Khalife

address: 1 rue du Prof. Calmette

institute: Inserm U547

description: integrity and purity of RNA were assessed by use of the Agilent Bioanalyser (Agilent Technologies). Ten micrograms of purified total RNA was then utilized for linear amplification following the CodeLink Gene Expression System Protocol (GE Healthcare). Ten micrograms of the resulting cRNA was hybridized to each CodeLink Rat UniSet I Bioarray following the CodeLink Gene Expression System Protocol without any modification. Each bioarray contains 9911 rat sequences and 300 negative bacterial control probes. The bioarrays were scanned using an Axon GenePix 4000B scanner at 635nm, 10µm resolution and a PMT value of 600.

hyb_protocol: CodeLink standard protocol

scan_protocol: CodeLink standard protocol

data_processing: Intensity is defined as the sum ofthe pixel signals in the area of interest minus the scaled 2-pixel median background. The intensities are then median-normalized by calculating the median of all spots except for the control probes and blanks and dividing each spot intensity by the median value

organism: Rattus norvegicus

source_name: Infected rat spleen day 13 T00189898

label_protocol: CodeLink standard protocol

extract_protocol: spleen was minced in 2ml/100mg tissue of RNA+ solution (Qbiogen) and crude RNA was isolated following the manufacturer's protocol

treatment_protocol: Rat was infected with Plasmodium berghei ANKA at age of 4 weeks. Spleen was recovered at day 13 post infection

tag: strain

tag: gender

value: male

value: 6 weeks

tag: tissue

value: spleen


title: Infected rat day 6 T00230001

source_name: Infected rat spleen day 6 T00230001

treatment_protocol: Rat was infected with Plasmodium berghei ANKA at age of 4 weeks. Spleen was recovered at day 6 post infection


title: Infected rat day 6 T00229998

source_name: Infected rat spleen day 6 T00229998


title: Infected rat day 13 T00189895

source_name: Infected rat spleen day 13 T00189895


title: Infected rat day 6 T00230000

source_name: Infected rat spleen day 6 T00230000


title: Infected rat day 6 T00229999

source_name: Infected rat spleen day 6 T00229999


title: Infected rat day 6 T00189870

source_name: Infected rat spleen day 6 T00189870


title: Infected rat day 6 T00189868

source_name: Infected rat spleen day 6 T00189868


title: Infected rat day 6 T00185457

source_name: Infected rat spleen day 6 T00185457


title: Infected rat day 6 T00185458

source_name: Infected rat spleen day 6 T00185458


title: Infected rat day 13 T00185459

source_name: Infected rat spleen day 13 T00185459


title: Infected rat day 13 T00185460

source_name: Infected rat spleen day 13 T00185460


title: Infected rat day 13 T00189872

source_name: Infected rat spleen day 13 T00189872


title: Control rat T00189874

source_name: Control rat spleen T00189874

treatment_protocol: healthy control rat


title: Control rat T00229996

source_name: Control rat spleen T00229996


title: Control rat T00189890

source_name: Control rat spleen T00189890


title: NSCLC_SCC_95T

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

description: gene-specific primer and probes (TaqMan Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50 C for 2 min and 95 C for 15 min, followed by 40 cycles of 15 sec at 95 C (denaturation) and 60 sec at 60 C (annealing and elongation).

data_processing: The accuracy of measurements for all samples was optimized by using technical triplicates. Statistical analysis was performed calculating the median Ct value (number of PCR cycles up to a constant fluorescent signal threshold) across the triplicates of every sample within the logarithmic PCR cycle phase and the related median absolute deviation (MAD) respectively. Samples with missing values (Ct value > 40 cycles) were not included in the advanced statistical analysis. To evaluate differences in gene expression, a relative quantification method based on the delta delta Ct-method was used [Pfaffl MW, Nucleic Acids Res, 2001]. Therefore, the gene expression value Ct of a sample for every experimental gene (Gx) were normalized (delta Ct = CtGx-CtGh) using the mean (Gh) of two housekeeping genes (Esterase D and Dnull directed RNA polymerase II polypeptide A), and compared to a reference value (median of all delta Ct values from normal bronchial samples or the matched normal sample) obtaining the normalized, relative value (delta delta Ct) or expression level (2^-delta delta Ct). Additionally, for each expression level an error is calculated based on the MAD divided by the square root of the triplicate Ct values of a sample.

label: FAM dye

organism: Homo sapiens

source_name: human non-small cell lung cancer tumor tissue

extract_protocol: total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. Reverse transcription was performed with 2 ug total RNA per reaction using RevertAid First Strand cDnull Synthesis Kit (Fermentas, Burlington, ON, Canada) according to the manufacturers instructions.

treatment_protocol: tumor tissue samples from surgically treated patients were collected intraoperatively, snap-frozen and stored at -80 C. All samples underwent a careful analysis of the histopathology, estimation of tumor and stromal content and subsequent macro-dissection of the tumor regions before enrollment into the microarray experiments.

tag: squamous cell carcinoma


title: NSCLC_SCC_95N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 95N.

extract_protocol: total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. Reverse transcription was performed with 2 ?g total RNA per reaction using RevertAid? First Strand cDnull Synthesis Kit (Fermentas, Burlington, ON, Canada) according to the manufacturers instructions.

treatment_protocol: matched normal tissue samples from surgically treated patients were collected intraoperatively, snap-frozen and stored at -80 C. All samples underwent a careful analysis of the histopathology.


title: Control rat T00189875

source_name: Control rat spleen T00189875


title: Infected rat day 13 T00189873

source_name: Infected rat spleen day 13 T00189873


title: NSCLC_AC_89T

tag: adenocarcinoma


title: NSCLC_AC_97N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 97N.


title: Control rat T00229997

source_name: Control rat spleen T00229997


title: NSCLC_AC_88T


title: NSCLC_AC_84T


title: Control rat T00185461

source_name: Control rat spleen T00185461


title: NHGRI_TRMT12-siRNA-3_hv35569

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

country: USA

institute: NIH

description: Human Breast cell line

hyb_protocol: 200 picomoles of Cy3 and 100 picomoles of Cy5 labeled cRNAs are put in a total volume of 24 ul (qsp with DEPC H20) and 6 microliter of 5x fragmentation buffer from Affymetrix. the mixture is incubated at 94 ¡C for 15 minutes. Then, 25 ul of 2X  hybridization buffer is added (250 _l Formamide, 250 _l 20xSSC and 20 _l 10%SDS). The mixture is then denatured for 2 minutes and applied on the Maui (BioMicro Systems, Inc) hybridization chamber/ array slide sandwich. The hybridization is performed at 45 degre for 20 hours.

scan_protocol: Agilent Scanner

data_processing: Lowess normalized log2 r/g ratio

source_name: SKbr3 TRMT12 siRNA-3

label_protocol: 1.0 microgram of total RNA was reverse transcribed with T7 Oligo-dT, followed by a second strand synthesis and overhight i9n vitro transcription in the presence of  Aminoallyl UTPs using the Amino Allyl MessageAmpª II aRNA Amplification kit from Ambion (Kit Cat#1753). The Aminoallyl UTP labeled cRNAs are then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The CyDyes labeled cRNAs are then purified with columns and reagents provided by the Kit (Cat#1753).

extract_protocol: RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns

tag: cell line

source_name: SKbr3 control siRNA-3

label_protocol: 1.0 microgram of total RNA was reverse transcribed with T7 Oligo-dT, followed by a second strand synthesis and overhight in vitro transcription in the presence of  Aminoallyl UTPs using the Amino Allyl MessageAmpª II aRNA Amplification kit from Ambion (Kit Cat#1753). The Aminoallyl UTP labeled cRNAs are then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The CyDyes labeled cRNAs are then purified with columns and reagents provided by the Kit (Cat#1753).


title: NHGRI_TRMT12-siRNA-2_hv35567

description: Human Breast cell line

source_name: SKbr3 TRMT12 siRNA-2

source_name: SKbr3 control siRNA-2


title: NHGRI_TRMT12-siRNA-3_hv35570

description: Human Breast cell line


title: NHGRI_TRMT12-siRNA-1_hv35564

description: Human Breast cell line

source_name: SKbr3 TRMT12 siRNA-1

source_name: SKbr3 control siRNA-1


title: NSCLC_AC_88N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 88N.


title: NSCLC_AC_84N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 84N.


title: NHGRI_TRMT12-siRNA-2_hv35566

description: Human Breast cell line


title: NHGRI_TRMT12-siRNA-1_hv35563

description: Human Breast cell line


title: NSCLC_SCC_77N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 77N.


title: NSCLC_AC_70T


title: NSCLC_AC_53T


title: NSCLC_SCC_55N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 55N.


title: NSCLC_AC_53N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 53N.


title: NSCLC_SCC_55T


title: NSCLC_SCC_65N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 65N.


title: NSCLC_AC_51T


title: NSCLC_AC_51N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 51N.


title: NSCLC_AC_49T


title: NSCLC_AC_49N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 49N.


title: NSCLC_SCC_75N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 75N.


title: NSCLC_AC_489T


title: NSCLC_AC_492N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 492N.


title: NSCLC_AC_445T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 445T.


title: NSCLC_AC_434T


title: NSCLC_AC_445N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 445N.


title: NSCLC_AC_42N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 42N.


title: NSCLC_AC_434N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 434N.


title: NSCLC_AC_42T

description: gene-specific primer and probes (TaqMan Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50 C for 2 min and 95 C for 15 min, followed by 40 cycles of 15 sec at 95 C (denaturation) and 60 sec at 60 C (annealing and elongation).


title: NSCLC_AC_492T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 492T.


title: Whole_Blood_D

city: montpellier

first: tondeur

last: sylvie

address: 80 avenue augustin fliche

department: hopital saint eloi

institute: IRB

description: exon level expression; analysis conducted with Affymetrix probe group file HuEx-1_0-st-v2.r2.pgf

hyb_protocol: Hybridization was processed according manufacturer's intructions (http://www.affymetrix.com/products/arrays/specific/exon.affx)

scan_protocol: Probe arrays were scanned using the Affymetrix GCOS 3000 7G and the Gene-Chip Operating Software v.1.4 to obtain the .CEL files

data_processing: Expression signal values and p-values were obtained from .cel files for each probeset using the Robust Microarray Analysis (RMA) algorithm in ArrayAssit software (Stratagene). Normalisation of the 4 whole blood samples data of the serie was done together with 11 triplicates of human normal tissues: breast, cerebellum, heart, kidney, liver, muscle, pancreas, prostate, spleen, testes, thyroid (33 samples) (data from Affymetrix, http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx). Background was discarded with Detection Above Background (DABG) filter in Array Assist on the following criteria: 3 arrays with a p-value less or equal than 0.05.

label: biotin

source_name: whole blood cells (leucocytes, platelets and reticulocytes)

label_protocol: Ribosomal RNA reduction, first and double strand cDNA synthesis, cRNA synthesis, second round single-strand (ss) cDNA synthesis, ss-cDNA fragmentation and labelling were processed following the manufacturer’s instructions (http://www.affymetrix.com/products/arrays/specific/exon.affx).

extract_protocol: Total RNA was extracted with PAXgene Blood RNA kit (Qiagen, Courtaboeuf, France), including DNase I treatment. Globin RNA was removed using the GLOBINclear kit (Ambion, Austin, TX, USA). Two micrograms of total RNA, cleared from globin RNA, were used.

treatment_protocol: Whole blood was collected using PAXgene collection tubes (PreAnalytix/Qiagen, Courtaboeuf, France)

tag: whole blood from venipuncture from an healthy subject after informed consent


title: NSCLC_AC_426T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 426T.


title: NSCLC_AC_421T


title: NSCLC_AC_426N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 426N.


title: NSCLC_SCC_77T


title: NSCLC_AC_421N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 421N.


title: NSCLC_SCC_412T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 412T.


title: NSCLC_AC_402T


title: NSCLC_AC_40T


title: NSCLC_AC_400T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 400T.


title: NSCLC_AC_397T


title: NSCLC_AC_40N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 40N.


title: NSCLC_SCC_390T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 390T.


title: NSCLC_SCC_390N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 390N.


title: NSCLC_SCC_37T


title: NSCLC_SCC_37N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 37N.


title: NSCLC_AC_378T


title: NSCLC_AC_378N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 378N.


title: NSCLC_AC_368T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 368T.


title: NSCLC_AC_342T


title: Whole_Blood_B

treatment_protocol: Whole blood was collected using a PAXgene collection tube (PreAnalytix/Qiagen, Courtaboeuf, France)


title: NSCLC_SCC_347T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 347T.


title: NSCLC_SCC_364T


title: NSCLC_AC_368N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 368N.


title: NSCLC_AC_348N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 348N.

source_name: human non-small cell lung cancer matched normal tissue


title: NSCLC_AC_342N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 342N.


title: Whole_Blood_A


title: NSCLC_AC_334N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 334N.


title: NSCLC_SCC_30T

description: gene-specific primer and probes (TaqMan Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50 C for 2 min and 95 C for 15 min, followed by 40 cycles of 15 sec at 95 C (denaturation) and 60 sec at 60 C (annealing and elongation).


title: NSCLC_AC_334T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 334T.


title: NSCLC_AC_331T


title: NSCLC_SCC_30N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 30N.


title: NSCLC_AC_331N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 331N.


title: NSCLC_SCC_301T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
Gene expression data from human non-small cell lung cancer tumor tissue 301T.


title: NSCLC_AC_271T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 271T.


title: NSCLC_AC_276N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 276N.


title: NSCLC_AC_271N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 271N.


title: NSCLC_AC_276T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 276T.


title: NSCLC_AC_282T


title: NSCLC_AC_273T


title: NSCLC_AC_282N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 282N.


title: NSCLC_SCC_25T


title: NSCLC_AC_24T


title: NSCLC_AC_24N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 24N.


title: NSCLC_AC_273N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 273N.


title: NSCLC_SCC_25N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 25N.


title: NSCLC_SCC_215T


title: NSCLC_AC_233N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 233N.


title: NSCLC_SCC_22T


title: NSCLC_AC_233T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 233T.


title: NSCLC_SCC_22N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 22N.


title: NSCLC_SCC_215N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 215N.


title: Whole_Blood_C

description: exon level expression; analysis conducted with Affymetrix probe group file HuEx-1_0-st-v2.r2.pgf


title: NSCLC_AC_210N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 210N.


title: NSCLC_SCC_248T

description: gene-specific primer and probes (TaqMan Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50 C for 2 min and 95 C for 15 min, followed by 40 cycles of 15 sec at 95 C (denaturation) and 60 sec at 60 C (annealing and elongation).


title: NSCLC_AC_202T


title: NSCLC_AC_210T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 210T.


title: NSCLC_AC_16N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 16N.


title: NSCLC_SCC_188N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 188N.


title: NSCLC_AC_202N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 202N.


title: NSCLC_AC_161N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 161N.


title: NSCLC_SCC_188T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 188T.


title: NSCLC_AC_161T


title: NSCLC_AC_169N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 169N.


title: NSCLC_AC_148T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 148T.


title: NSCLC_AC_169T


title: NSCLC_AC_148N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 148N.


title: NSCLC_SCC_165T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 165T.


title: NSCLC_AC_16T


title: NSCLC_AC_136T


title: NSCLC_AC_137T

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer tumor tissue 137T.


title: NSCLC_AC_113N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 113N.


title: NSCLC_AC_147N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 147N.


title: NSCLC_AC_136N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 136N.


title: NSCLC_AC_147T


title: NSCLC_AC_113T


title: NSCLC_AC_137N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 137N.


title: NSCLC_SCC_165N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 165N.


title: NSCLC_AC_10N

description:
gene-specific primer and probes (TaqMan? Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50?C for 2 min and 95?C for 15 min, followed by 40 cycles of 15 sec at 95?C (denaturation) and 60 sec at 60?C (annealing and elongation).
qRT-PCR gene expression data from human non-small cell lung cancer matched normal tissue 10N.


title: NSCLC_AC_10T

description: gene-specific primer and probes (TaqMan Assays, Applied Biosystems, Weiterstadt, Germany) were used in combination with QPCR Master Mix Reagent (Abgene, Epsom, UK) in 384-well format for the ABI Prism 7900HT Sequence Detection System (AB) . The input amount of cDnull in one single PCR reaction corresponded to 10 ng total RNA. PCR-amplification started with the activation of the Taq polymerase at 50 C for 2 min and 95 C for 15 min, followed by 40 cycles of 15 sec at 95 C (denaturation) and 60 sec at 60 C (annealing and elongation).


title: 896-07 in lung tissues vs 896-07 BHI broth 3 (expression)

status: Public on Sep 15 2009

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

country: Canada

institute: Université de Montréal - Faculté de Médecine Vétérinaire

description: Technical replicate 3

hyb_protocol: The hybridization profile for each strain was obtained by co-hybridizing labeled cDNA from the tested condition (in vivo growth) with labeled cDNA from the  control condition (BHI growth) to the microarray. cDNA from tested condition was labeled with Cy5 and cDNA from the control condition with Cy3. Labeled samples were normalized by selecting tested/control sample pairs with similar dye incorporation efficiencies. Equivalent amounts (2 μg) of labeled tested and control samples were pooled, lyophilized, and then re-suspended in 42 μl of hybridization buffer [1 × DIGEasy hybridization solution (Roche Applied Science); 0.5 μg/μl of Torulla yeast tRNA (Invitrogen); 0.5 μg/μl of salmon sperm genomic DNA (Invitrogen)].  Hybridizations were performed overnight at 37°C under 22 × 40-mm glass cover slips in a high-humidity chamber.

scan_protocol: Scanned with a Perkin-Elmer ScanArray Express scanner according to the manufacturer's recommendations. Image and data analysis were performed using TM4 suite of softwares. Raw data were generated using Spotfinder v.3.1.1.

data_processing: The integrated intensities of each spot, equivalent to the sum of unsaturated pixels in a spot were quantified and the integrated intensity of the local background was subtracted for each spot. The same operation was performed with the median spot intensities. Data were normalized with the MIDAS software tool using cross-channel Loess normalization. Spots with median intensities lower than 1000 were removed from the normalized data set. Intensities for duplicate spot were merged to generate the final normalized data set.

organism: Actinobacillus pleuropneumoniae

source_name: InVitro BHI

label_protocol: RNA was reverse-transcribed to cDNA, using Invitrogen's SuperScript II and amino-allyl dUTP. Samples were then indirectly labelled with Cy3 or Cy5 esters. Complete protocol is described in :  Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.

growth_protocol: In vivo growth : pigs were naturally infected with an infectious field strain of A. pleuropneumoniae serotype 5b (strain 896-07). Acute infection followed, that lead to the death of animals within 24-48h of infection. Pigs were sample within an hour of death. In vitro : the A. pleuropneumoniae infectious serotype 5b field strain was grown in BHI broth (Difco) supplemented with 5 ug per ml of NAD until an optical density at 600nm of 0.300 was reached.

extract_protocol: In order to extract bacterial RNA from infected porcine lung tissues, we added a beadbeating step before a classic hot acid-phenol-chloroform RNA extraction protocol.  In order to release bacteria from pig tissues, we used 1.0 mm zirconia/silica beads.  While these beads can disrupt tissues to a certain degree, they do not cause bacterial lysis, which normally requires the use of 0.1 mm glass beads (Biospec, personal communication).  Centrifugation of homogenized samples enabled the removal of most cellular debris and the recovery of bacteria.  RNA was extracted from BHI grown bacteria using hot acid-phenol-chloroform.

tag: source

value: in vitro BHI

tag: serotype

tag: isolate

value: Fresh field isolate 896-07

source_name: InVivo growth

value: Bacteria recovered from infected lung tissues


title: 896-07 in lung tissues vs 896-07 BHI broth 2 (expression)

description: Technical replicate 2


title: 896-07 in lung tissues vs 896-07 BHI broth 1 (expression)

description: Technical replicate 1


title: 896-07 vs L20 2 (CGH)

type: genomic

description: Biological replicate 2

hyb_protocol: The hybridization profile for each strain was obtained by co-hybridizing labeled DNA from the tester strain with labeled DNA from the A. pleuropneumoniae serovar 5b (L20) control strain to the microarray. DNA from tester strains was labeled with Cy3 and DNA from the control strain with Cy5. Dye swaps were performed on selected strains to test for any dye-incorporation bias. Labeled samples were normalized by selecting tester/control sample pairs with similar dye incorporation efficiencies. Equivalent amounts (2 μg) of labeled tester and control samples were pooled, lyophilized, and then re-suspended in 42 μl of hybridization buffer [1 × DIGEasy hybridization solution (Roche Applied Science); 0.5 μg/μl of Torulla yeast tRNA (Invitrogen); 0.5 μg/μl of salmon sperm genomic DNA (Invitrogen)]. Labeled gDNA was denatured at 65°C for 5 min and applied to the microarray. Hybridizations were performed overnight at 37°C under 22 × 40-mm glass cover slips in a high-humidity chamber.

molecule: genomic DNA

label_protocol: Isolated genomic DNA was fragmented by nebulization. One hundred μg of DNA in H2O and 35% glycerol (v/v) was placed in an AeroMist Nebulizer chamber (IPI Medical Products, Chicago, IL), and sheared by passing nitrogen gas through the chamber at 15 psi for 1 min. The DNA was precipitated with ethanol and suspended in 100 μl of ddH2O. Typically, the DNA was fragmented to a range of 0.4 to 12 kb in size. Five μg of fragmented DNA were fluorescently labeled using direct chemical coupling with the Label-IT (Mirus Corp., Madison, WI) cyanine dyes Cy3 and Cy5 as recommended by the manufacturer. Probes were purified from unincorporated dyes by passing samples through Qiaquick columns (Qiagen, Mississauga, ON).

growth_protocol: Growth on BHI agar supplemented with 15 mg/ml NAD at 37C for 16-18h.

extract_protocol: A. pleuropneumoniae strains were harvested after growth on agar plates for 16-18 h, resuspended in H2O, and treated with lysozyme (Roche, Laval, QC) and RNase A (Qiagen, Mississauga, ON) for 10 min at room temperature. The cell suspensions were then digested with proteinase K (MBI Fermentas, Burlington, ON) for 1 h at 37°C, and complete lysis was obtained by addition of sodium dodecyl sulfate to a final concentration of 0.1% (wt/vol). Genomic DNA, extracted from the cell lysates by two extractions with phenol-chloroform-isoamyl alcohol (25:24:1) and two extractions with chloroform, was precipitated in ethanol.


title: 896-07 vs L20 1 (CGH)

description: Biological replicate 1


title: Fed-Batch - Ethanol response - conc EtOH = 125 g/l - 3

status: Public on Sep 01 2009

city: Toulouse

first: Laurent

last: Benbadis

address: 135 Av de Rangueil

institute: LISBP INSA CNRS UMR5504

description: Response to ethanol in aerated fed-batch : all conditions detailed in Cot et al, (2007) FEMS Yeast Res. 7 : 22-32.

hyb_protocol: Prehybridisation was performed with solution of 1% BSA, 2 ×SSC, 0.2% (v/v) SDS over 30 min at 42°C. After automatic washing according to manufacturer’s instructions, the slides were hybridised for 10 h in 200 µl of ChipHybeTM buffer (Ventana Medical System, Inc). After hybridisation, the slides were washed for 2 min in 2 ×SSC/0.2% (v/v) SDS, for 2 min in 0.2 ×SSC/0.2% (v/v) SDS and for 2 min in 0.2 ×SSC, immersed briefly in isopropanol and then dried under a stream of air.

scan_protocol: The hybridization signal was detected by scanning with GenePix 4000 laser Scanner (Axon Instruments)

data_processing: The signal quantification was transformed to numerical values using the integrated GenePix software version 3.0 The raw intensities were corrected from the local background measured around each spot. First step in averaging was to calculate the mean value over spot duplicates for a given gene on the same array then all spot mean normalization was applied. Log-ratios of all spot mean normalized intensities were obtained.

organism: Saccharomyces cerevisiae

source_name: Yeast - Ethanol response - conc EtOH = 17 g/l

label_protocol: Incorporation of Cyanine 3- or Cyanine 5-dCTP (Amersham Bioscience) was performed during reverse transcription of 20 µg of denaturated RNA using CyScript Reverse Transcriptase (Amersham). Labeled cDNA was purified with CyScribe GFX spin columns (Amersham).

extract_protocol: Extraction protocol Frozen cells (10 mg dry biomass = 13 units of OD600) were mechanically disrupted (MicroDismembrator Braun, Melsungen) and total RNA was isolated using RNeasy Midi kit (Qiagen) following the protocol of the manufacturer.

treatment_protocol: Frozen in liquid nitrogen

value: Fed-Batch Ethanol 17 g/l

molecule: cytoplasmic RNA

source_name: Yeast - Ethanol response - conc EtOH = 125 g/l

value: Fed-Batch Ethanol 125 g/l


title: Fed-Batch - Ethanol response - conc EtOH = 125 g/l - 2


title: Fed-Batch - Ethanol response - conc EtOH = 100 g/l - 3

source_name: Yeast - Ethanol response - conc EtOH = 100 g/l

value: Fed-Batch Ethanol 100 g/l


title: Fed-Batch - Ethanol response - conc EtOH = 125 g/l - 1


title: Ago2 knockout mouse mature oocyte#1

city: Cambridge

first: Fuchou

last: Tang

state: Cambridgeshire

address: Tennis Court Road

department: Wellcome Trust/Cancer Research UK Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
The Ago2 floxed mice were mated with Zp3-Cre transgenic mice to obtain [Ago2F/F, Zp3-Cre] conditional knockout females
Gene expression data from single cell (AGo2 knockout mouse oocyte) using Applied Biosystems AB1700 Whole Genome Microarray

hyb_protocol: Hybridization was performed according to Applied Biosystems Chemiluminescence Detection Kit Protocol (PN 4339627) using 10 ug fragmented cRNA

scan_protocol: Image was captured using CCD camera came with AB1700 Microarray Analyzer

data_processing: Quantile normalization was performed separately for knockout and wild-type samples. The normalization was performed using ABarray bioconductor package

label: digoxigenin

organism: Mus musculus

source_name: Ago2 knockout mouse mature oocyte

label_protocol: Digoxigenin labeled cRNA was prepared according to Applied Biosystems nanoamp RT-IVT protocol

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

tag: genotype

value: Ago2 knockout

tag: cell type

value: mature oocyte

tag: replicate


title: Fed-Batch - Ethanol response - conc EtOH = 90 g/l - 2

source_name: Yeast - Ethanol response - conc EtOH = 90 g/l

value: Fed-Batch Ethanol 90 g/l


title: Fed-Batch - Ethanol response - conc EtOH = 95 g/l - 3

source_name: Yeast - Ethanol response - conc EtOH = 95 g/l

value: Fed-Batch Ethanol 95 g/l


title: Ago2 knockout mouse mature oocyte#3


title: wild-type mouse GV oocyte#2

description:
GV oocytes were collected from the oviducts from adult females and treated with hyaluronidase to remove the cumulus cells
Gene expression data from single cell (wild-type mouse GV oocyte) using Applied Biosystems AB1700 Whole Genome Microarray

source_name: wild-type mouse GV oocyte

value: wild-type

value: GV oocyte


title: wild-type mouse GV oocyte#3


title: wild-type mouse GV oocyte#1


title: Fed-Batch - Ethanol response - conc EtOH = 95 g/l - 2


title: Fed-Batch - Ethanol response - conc EtOH = 95 g/l - 1


title: Fed-Batch - Ethanol response - conc EtOH = 90 g/l - 3


title: Fed-Batch - Ethanol response - conc EtOH = 90g/l - 1

source_name: Yeast - Ethanol response - conc EtOH = 90g/l


title: Fed-Batch - Ethanol response - conc EtOH = 100 g/l - 2


title: Fed-Batch - Ethanol response - conc EtOH = 60 g/l - 3

source_name: Yeast - Ethanol response - conc EtOH = 60 g/l

value: Fed-Batch Ethanol 60g/l


title: Yersinia pestis_hfq mutant_37 C 3hr-rep8

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

country: China

institute: Institute of Microbiology and Epidemiology

description: Y. pestis strain 201 (F1+,VW+, Pgm+, and Pst+) is avirulent to humans, belonging to a newly established biovar, Microtus. Y. pestis strain 201 (WT) and the ∆hfq mutant were separately grown at 26 °C in LB medium to the middle exponential growth phase (A620nm approximately 0.7). Cell cultures were diluted 1:20 in fresh LB medium, and the cells were grown at 26 °C until reaching A620nm of approximately 0.7. The cultures were then transformed to 37 °C for 3 hr.

hyb_protocol: For hybridization, the slides were incubated in 50 µl of prehybridization buffer (5XSSC, 0.1% SDS and 0.1% BSA) at 42 °C for at least 1 hr. The slides were washed twice in water for 1 min and once in 95% ethanol for 1 min, and then blown to dry with hot air. Dual-fluorescence labeled dried probes were resuspended in 35 µl of hybridization solution (50% deionized formamide, 5×SSC, 0.1% SDS, 5XDenhardt’s solution, and 0.5 µg/µl of sheared salmon sperm DNA). The mixture was denatured at 98 °C for 5 min, and then was applied to the microarray slide followed by covering a 24×50 mm glass coverslip. The slides were hybridized in a moisture chamber at 42 °C for 18 to 20 hr in a hybridization incubator (Robbins Scintific). After hybridization, the slides were washed in 1XSSC with 0.06% SDS for 2 min, then in 0.06XSSC for 2 min and finally in ethanol for 1 min. The slides were blown dry for scanning.

scan_protocol: The slides were scanned at a resolution of 10 µm by using a GenePix Personal 4100A Microarray Scanner (Axon Instruments).

data_processing: The scanning images were processed and the data were further analyzed by using GenePix Pro 4.1 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels less than two folds of background intensity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods. The normalized log2 ratio of test/reference (∆hfq/WT) signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded as well. The averaged log2 ratio for each remaining gene on the eight replicate slides was ultimately calculated. Significant changes of gene transcription level were identified with SAM software using one class mode.

label: Cy5 or Cy3

organism: Yersinia pestis

source_name: Yersinia pestis hfq mutant, 37 C 3hr

label_protocol: Each RNA preparation was used to prepare fluorescence-labeled probes for three separate slides. For the total of eight replicate slides, the incorporated dye was reversed to make up three flip dye pairs. 20 µg of total RNA was mixed with 5 µg of GDPs and 5 µg random hexamer primers, heated to 70 °C for 10 min, and cooled quickly on ice. 1 µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript II reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 42 °C for 1 hr, after which an additional 200 U of Superscript II reverse transcriptase was added. The mixture was then incubated at 42 °C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65 °C for 20 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50 °C, and then was labeled by the addition of 1/10 of one reaction vial of Cy5 or Cy3 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark. The Cy3 and Cy5 reaction mixtures were combined, and the unincorporated dye was removed by using MinElute reaction cleanup columns (Qiagen). The purified probe was air dried at 50 °C, and was stored at -20 °C until use.

extract_protocol: Total RNA was extracted from two independent batches of cultures. To minimize bacterial RNA degradation and preserve gene transcription profile, double-volume of RNAprotect Bacteria Reagent (Qiagen) was added immediately to each aliquot, mixed thoroughly and placed at room temperature for 5 min. Total RNA extraction was performed by using MasterPureTM RNA Purification kits (Epicenter), exactly following the kit’s manual. Briefly, cell pellets were collected from the bacteria cultures by centrifugation. The lysis of cell samples was performed by Protease K digest at 65 °C for 15min, and protein was then removed from the lysed sample with the protein precipitation reagent provided by the kit. Isopropanol was added to precipitate nucleic acid and the residue DNA was removed with RNase-free DNase I. The RNA was then recovered with isopropanol. The RNAs from each four aliquots were pooled together. RNA quality was monitored by agarose gel electrophoresis and RNA quantity was measured by spectrophotometer.

value: Yersinis pestis hfq mutant

label: Cy3 or Cy5

source_name: Yersinia pestis strain 201, 37 C 3hr

growth_protocol: growth condition: grown at 26 °C until reaching A620nm of approximately 0.7, then transformed to 37 °C for 3 hr.

value: Yersinis pestis WT strain 201


title: Fed-Batch - Ethanol response - conc EtOH = 100 g/l - 1


title: Fed-Batch - Ethanol response - conc EtOH = 60 g/l - 2


title: Fed-Batch - Ethanol response - conc EtOH = 60 g/l - 1


title: Balb/c 2

status: Public on Aug 30 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 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. The trimmed mean target intensity of each array was arbitrarily set to 150.

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

extract_protocol: Rneasy

treatment_protocol: RRV Infection d3

tag: genetic modification:

value: Liver


title: C57/Bl6 2


title: Balb/c 3


title: Balb/c 1


title: Schizosaccharomyces pombe clr3 mutant compared to wt KCl treatment,replicate 2 (slide 3)

status: Public on Aug 01 2009

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description: Schizosaccharomyces pombe clr3 mutant strain compared to wild type strain, both treated with 1M KCl in rich medium at 25C.

hyb_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

scan_protocol: Slides were scanned using Bio-rad Vers-Array ChipReader.

data_processing: canned slides were quantified with Imagene 4.2 software. Quantified data were loaded to GeneSpring software and normalized by lowess normalization.

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces Pombe clr3 mutant Hu0369 treated with KCl

growth_protocol: Strain was grown on YEA medium at 25C to log phase then treated with 1M KCl for 60min.

treatment_protocol: Schizosaccharomyces pombe clr3 mutant Hu0369 treated with 1M KCl for 60min at 25C.

tag: genotype/variation

value: gcn5 mutant Hu0369

tag: agent

value: 1M KCl

tag: time

tag: temperature

source_name: Schizosaccharomyces pombe wild type strain Fy368 treated with KCl for 60min.

treatment_protocol: Schizosaccharomyces pombe wild type strain fy368 treated with 1M KCl for 60min.

value: wild type strain Fy368

value: KCl


title: Interplay between HDAC clr3 and HAT gcn5 replicate 2

description: Expression profile of Schizosaccharomyces pombe gcn5-clr3- double mutant strain was compared to gcn5-strain, both treated with 1M KCl in rich medium at 25C.

data_processing: Scanned slides were quantified with Imagene 4.2 software. Quantified data were loaded to GeneSpring software and normalized by lowess normalization.

source_name: Schizosaccharomyces pombe gcn5-clr3- double mutant strain Hu1036 treated with KCl

label_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

treatment_protocol: Schizosaccharomyces pombe gcn5-clr3- double mutant strain Hu1036 treated with 1M KCl for 60min at 25C.

value: gcn5-clr3- double mutant strain Hu1036

source_name: Schizosaccharomyces pombe gcn5 mutant Hu0799 treated with KCl

treatment_protocol: Schizosaccharomyces pombe gcn5 mutant Hu0799 treated with 1M KCl for 60min at 25C.

value: gcn5 mutant Hu0799


title: Interplay between HDAC clr3 and HAT gcn5 replicate 1

extract_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).


title: C57/Bl6 1


title: Schizosaccharomyces pombe clr3 mutant compared to wt KCl treatment,replicate 1 (slide 2)

value: clr3 mutant Hu0369


title: MDS.U187

city: Tokyo

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U187

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CNAG/AsCNAR 3.0

source_name: MDS primary specimens

label_protocol: Affymetrix standard protocol

extract_protocol: As per PUREGENE DNA extracting kit

tag: disease

value: Myelodysplastic syndromes (MDS)

tag: who classification


title: MDS.U200

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U200

value: RCMD


title: MDS.U196

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U196

value: t-MDS


title: MDS.U197

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U197

value: RA


title: MDS.U190

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U190


title: MDS.U185

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U185


title: MDS.U195

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U195


title: MDS.U199

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U199


title: MDS.U201

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U201


title: MDS.U191

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U191


title: MDS.U186

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U186


title: MDS.U188

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U188


title: MDS.U202

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U202


title: MDS.U182

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U182


title: MDS.U178

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U178


title: MDS.U183

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U183


title: MDS.U189

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U189

value: AML


title: MDS.U198

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U198


title: MDS.U192

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U192


title: MDS.U177

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U177


title: MDS.U175

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U175


title: MDS.U174

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U174


title: MDS.U172

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U172


title: MDS.U165

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U165


title: MDS.U173

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U173


title: MDS.U170

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U170


title: MDS.U166

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U166


title: MDS.U176

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U176


title: MDS.U171

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U171


title: MDS.U167

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U167


title: MDS.U164

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U164


title: MDS.U157

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U157


title: MDS.U159

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U159


title: MDS.U156

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U156


title: MDS.U163

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U163


title: MDS.U158

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U158


title: MDS.U161

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U161


title: MDS.U162

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U162


title: MDS.U118

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U118


title: MDS.U180

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U180


title: MDS.U168

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U168


title: MDS.U117

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U117

value: MDS–unclassified


title: MDS.U179

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U179


title: MDS.U116

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U116


title: MDS.U113

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U113


title: MDS.U115

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U115


title: MDS.U160

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U160


title: MDS.U114

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U114


title: MDS.U155

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U155

value: 5q– syndrome


title: MDS.U152

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U152


title: MDS.U112

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U112


title: MDS.U154

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U154


title: MDS.U111

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U111


title: MDS.U151

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U151


title: MDS.U153

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U153


title: MDS.U120

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U120


title: MDS.U119

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U119


title: MDS.U140

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U140


title: MDS.U121

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U121


title: MDS.U132

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U132


title: MDS.U129

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U129


title: MDS.U128

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U128


title: MDS.U104

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U104


title: MDS.U106

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U106


title: MDS.U127

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U127


title: MDS.U102

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U102


title: MDS.U131

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U131


title: MDS.U101

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U101


title: MDS.U109

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U109


title: MDS.U108

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U108


title: MDS.U105

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U105


title: MDS.U130

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U130


title: MDS.U194

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U194


title: MDS.U123

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U123


title: MDS.U203

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U203


title: MDS.U184

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U184


title: MDS.U122

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U122


title: MDS.U110

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U110


title: MDS.U193

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U193


title: MDS.U9

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U9


title: MDS.U8

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U8


title: MDS.U7

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U7


title: MDS.U126

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U126


title: MDS.U181

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U181


title: MDS.U169

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U169


title: MDS.U75

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U75


title: MDS.U72

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U72


title: MDS.U71

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U71


title: MDS.U103

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U103


title: MDS.U6

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U6


title: MDS.U74

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U74


title: MDS.U76

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U76


title: MDS.U70

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U70


title: MDS.U69

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U69


title: MDS.U68

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U68


title: MDS.U66

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U66


title: MDS.U64

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U64


title: MDS.U73

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U73


title: MDS.U65

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U65


title: MDS.U67

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U67


title: MDS.U63

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U63


title: MDS.U62

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U62