title: 255001210004_b4 - 236_LEVOVIL_STRESS vs 550_LEVOVIL_NO_STRESS

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: What are the genes implied in drought resistance in tomato ?

hyb_protocol: 550_LEVOVIL_NO_STRESS Cy5 / 236_LEVOVIL_STRESS Cy3 : 20pmol. (Hybridization_Protocol.txt) 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,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Solanum lycopersicum

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) 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: caulin leaf - Growth conditions (1-2-3-4):               1  2  Media   earth  earth  hygrometry   60%  100%  Temperature   J:23°C/N:18°C  J:23°C/N:18°C  Light   natural  natural

treatment_protocol: Name:NO_STRESS - environmental treatment - hydrometry,water:quantity 100percent time 2.5month . The seeds were sown on 9 February 2013 and then transplanted into pots (1 L 1 soil per pot) at 2-leaf stage (04/03/2013). Two weeks afte,r the plants (1 month after sowing-18/03/2013) are transplanted in 4l pots in a greenhouse at 100% irrigation. A week after, water stressed plants received 60% of irrigation. The culture was carried out under heated greenhouse at day temperatures of 23 ° C and night temperatures of 18 ° C

value: leaves

tag: strain

value: Levovil

tag: sample type

value: Solanum lycopersicum (levovil)  - harvest date 27-05-13

treatment_protocol: Name:DROUGHT_STRESS - environmental treatment - hydrometry,water:quantity 60percent time 2.5month . The seeds were sown on 9 February 2013 and then transplanted into pots (1 L 1 soil per pot) at 2-leaf stage (04/03/2013). Two weeks afte,r the plants (1 month after sowing-18/03/2013) are transplanted in 4l pots in a greenhouse at 100% irrigation. A week after, water stressed plants received 60% of irrigation. The culture was carried out under heated greenhouse at day temperatures of 23 ° C and night temperatures of 18 ° C

value: drought

value: Solanum lycopersicum (cervil)  - harvest date 27-05-13


title: 255001210003_b2 - 313_CERVIL_STRESS vs 7_CERVIL_NO_STRESS

status: Public on Jul 01 2015

type: RNA

country: France

hyb_protocol: 7_CERVIL_NO_STRESS Cy5 / 313_CERVIL_STRESS Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

molecule: total RNA

tag: treatment

tag: tissue

value: Cervil


title: 255001210004_b3 - 550_LEVOVIL_NO_STRESS vs 236_LEVOVIL_STRESS

hyb_protocol: 236_LEVOVIL_STRESS Cy5 / 550_LEVOVIL_NO_STRESS Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.


title: 255001210003_b3 - 8_CERVIL_NO_STRESS vs 314_CERVIL_STRESS

hyb_protocol: 314_CERVIL_STRESS Cy5 / 8_CERVIL_NO_STRESS Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.


title: HG01927 Replicate 1

type: genomic

city: Farmington

first: Charles

last: Lee

state: CT

address: 10 Discovery Dr.

country: USA

institute: Jackson Laboratory for Genomic Medicine

hyb_protocol: Labeled samples were purified using Agilent SureTag Purification columns. Test and reference samples were combined with Agilent Oligo aCGH/ChIP-on-Chip Blocking Agent, Agilent Hi-RPM Hybridization Buffer and Cot-1 DNA and applied to microarrays enclosed in Agilent Hybridization Chamber. After 40 hour incubation at 67 °C, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 and 2.

scan_protocol: Slides were scanned on an Agilent G2505C scanner (version A.8.5.1).

data_processing: Images were processed using Agilent Feature Extraction Software (version 10.5.1.1)

molecule: genomic DNA

organism: Homo sapiens

label_protocol: 1 to 1.5 ug of genomic DNA was digested using AluI and RsaI for 2 hours at 37 °C followed by a 20 minute enzyme-inactivation step at 65 °C. DNA was then labeled with Cyanine-3-dUTP (Reference samples) or Cyanine-5-dUTP (Test samples) at 37 °C for 2 hours followed by a 10 minute enzyme-inactivation step at 65 °C.

growth_protocol: We did not perform the growth in house. We received DNA samples from Coriell. This is the information available on their website for the cell culture of NA10851: Split ratio 1:2, Temperature: 37C, Percent CO2: 5%, Percent O2: Ambient, Medium: Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent, Serum: 15% fetal bovine serum Not Inactivated

extract_protocol: We did not perform the extraction in house. We received DNA samples from Coriell. This is the information available on their website for DNA extraction: gDNA is purified from fresh blood, immortalized lymphocyctes or fibroblasts using the Qiagen Autopure LS instrument according to the manufacturer’s instructions or manually by modified Miller’s Salting out procedures.

treatment_protocol: We, nor Coriell, did not perform any treatment on the samples. We received DNA samples from Coriell.

tag: coriell cell line


title: HG01918 Replicate 1


title: HG01932 Replicate 1


title: HG01920 Replicate 1


title: cross-fraction normalized NanoString counts for the 4-to-7 ribosomes pooled polysome fraction_GM05757_24 hrs anoxia

city: Toronto

first: Kenneth

middle: Chung-kan

last: Chu

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Hybridization was carried out according to the NanoString protocol.

scan_protocol: according to the NanoString protocol

data_processing: Assay bias was removed in a within cell-line fashion by globally scaling counts from each assay so that the geometric means of post-scaling positive control code counts are constant. Background noise was removed in a with-assay fashion by subtracting the sum of the mean and two times the standard deviation of the negative control code counts. Precipitation bias removal was performed only on the pooled polysome assays in a within-cell-line within-treatment fashion by globally scaling counts from each assay so that the geometric means of the post-scaling spike-in code counts are constant.

source_name: normal human fibroblast cell line

label_protocol: RNA was not labelled.

growth_protocol: Both cell lines, GM05757 and DU145, were cultured in alpha-modified Eagles Medium. DU145 was supplemented with 10% fetal calf serum and 1% L-Glutamine. GM05757 was supplemented with 15% of calf serum.

extract_protocol: Total RNA was extracted from GM05757 and DU145 with TRIZOL, according to the manufacturer's protocol. Polysome mRNAs from GM05757 and DU145 cytoplasmic lysates were isolated by sedimentation through a sucrose gradient and subsequent fractionation. Fractions containing the different numbers of polysomes were collected in 0.55 M final concentration of guanidinium–HCl, phenol-chloroform extracted and subjected to precipitation with ethanol. Spike-in control RNAs were added at this stage.  Glycogen was used as carrier.

treatment_protocol: GM05757 cells were exposed to anoxia (0% oxygen) and normoxia for 24 hours. DU145 cells were exposed to hypoxia (0.2% oxygen) and normoxia for 72 hours.

tag: cell line

tag: cell type

value: normal human fibroblast

value: 24 hours of anoxia

tag: pooled polysome fraction

value: 4 to 7 ribosomes

tag: molecule subtype

value: mRNA with 4 to 7 attached ribosomes


title: HG01924 Replicate 1


title: cross-fraction normalized NanoString counts for the 0-to-3 ribosomes pooled polysome fraction_GM05757_24 hrs anoxia

value: 0 to 3 ribosomes

value: mRNA with 0 to 3 attached ribosomes


title: 255001210004_b2 - 235_LEVOVIL_STRESS vs 549_LEVOVIL_NO_STRESS

hyb_protocol: 549_LEVOVIL_NO_STRESS Cy5 / 235_LEVOVIL_STRESS Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.


title: 255001210003_b4 - 314_CERVIL_STRESS vs 8_CERVIL_NO_STRESS

hyb_protocol: 8_CERVIL_NO_STRESS Cy5 / 314_CERVIL_STRESS Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.


title: HG01923 Replicate 1


title: 255001210004_b1 - 549_LEVOVIL_NO_STRESS vs 235_LEVOVIL_STRESS

hyb_protocol: 235_LEVOVIL_STRESS Cy5 / 549_LEVOVIL_NO_STRESS Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.


title: HG01921 Replicate 1


title: HG01915 Replicate 1


title: HG01917 Replicate 1


title: HG01914 Replicate 1


title: HG01896 Replicate 1


title: HG01912 Replicate 1


title: HG01886 Replicate 1


title: HG01889 Replicate 1


title: HG01883 Replicate 1


title: HG01892 Replicate 1


title: HG01890 Replicate 1


title: HG01872 Replicate 1


title: HG01879 Replicate 1


title: HG01878 Replicate 1


title: TCL1-AT monocytes 1

city: Heidelberg

first: Bola

last: Hanna

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

description:
Replicate 1
SAMPLE 1

hyb_protocol: Standard Illumina Hybridisation Protocol  Part # 11322355  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide). 1,5 ug of cRNA were hybridized for 17 hr at 58°C on Illumina Mouse (WG-6)-Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  Part # 11322355  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing:
A cluster analysis using Euclidean distances and average linkage was performed to search for unwanted grouping effects. Intensity values were normexp-by-control background corrected and quantile normalized with control probes (Shi et al. 2010).
Probes that failed to reach a detection P-value of 0.05 on at least two arrays were filtered as not expressed. Linear regression models approach of Smyth (2004) was used to derive moderated statistics to compare WT with TCL1 monocytes. To correct for multiple testing p values were adjusted using the method of Benjamini and Hochberg (1995) to control the false discovery rate (FDR).

label: biotin

organism: Mus musculus

source_name: Mouse spleen monocytes

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologie) is used to generate single-stranded cRNA from input amounts of 150ng total RNA, Label: Biotin, Cy3-Streptavidin

extract_protocol: RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: C57BL/6 mice transplanted with murine CLL cells and after 6 weeks total RNA from splenic monocytes (Lin- CD11b+ F4/80int CD11clow-int MHC-Iilow) from leukemic mice and WT controls was isolated.

tag: age

value: 3 months

tag: intervention

value: Transplantation with CLL


title: WT monocytes_pool 4

description:
Replicate 4
SAMPLE 9

value: No intervention


title: HG01885 Replicate 1


title: WT monocytes_pool 5

description:
Replicate 5
SAMPLE 10


title: HG01894 Replicate 1


title: HG01882 Replicate 1


title: TCL1-AT monocytes 4

description:
Replicate 4
SAMPLE 4


title: TCL1-AT monocytes 2

description:
Replicate 2
SAMPLE 2


title: WT monocytes_pool 3

description:
Replicate 3
SAMPLE 8


title: HG01873 Replicate 1


title: TCL1-AT monocytes 3

description:
Replicate 3
SAMPLE 3


title: TCL1-AT monocytes 5

description:
Replicate 5
SAMPLE 5


title: HG01874 Replicate 1


title: WT monocytes_pool 1

description:
Replicate 1
SAMPLE 6


title: WT monocytes_pool 2

description:
Replicate 2
SAMPLE 7


title: HG01871 Replicate 1


title: HG01870 Replicate 1


title: HG01869 Replicate 1


title: HG01893 Replicate 1


title: HG01880 Replicate 1


title: HG01867 Replicate 1


title: HG01866 Replicate 1


title: HG01863 Replicate 1


title: HG01859 Replicate 1


title: HG01862 Replicate 1


title: HG01855 Replicate 1


title: HG01857 Replicate 1


title: HG01858 Replicate 1


title: HG01861 Replicate 1


title: HG01860 Replicate 1


title: HG01850 Replicate 1


title: HG01853 Replicate 1


title: HG01849 Replicate 1


title: HG01851 Replicate 1


title: HG01843 Replicate 1


title: HG01848 Replicate 1


title: HG01845 Replicate 1


title: HG01847 Replicate 1


title: HG01846 Replicate 1


title: HG01864 Replicate 1


title: HG01840 Replicate 1


title: HG01842 Replicate 1


title: HG01868 Replicate 1


title: HG01865 Replicate 1


title: HG01815 Replicate 1


title: HG01817 Replicate 1


title: HG01813 Replicate 1


title: HG01841 Replicate 1


title: HG01852 Replicate 1


title: HG01812 Replicate 1


title: HG01809 Replicate 1


title: HG01808 Replicate 1


title: HG01807 Replicate 1


title: HG01811 Replicate 1


title: HG01805 Replicate 1


title: HG01806 Replicate 1


title: HG01804 Replicate 1


title: HG01810 Replicate 1


title: HG01801 Replicate 1


title: HG01802 Replicate 1


title: HG01800 Replicate 1


title: HG01799 Replicate 1


title: HG01798 Replicate 1


title: HG01844 Replicate 1


title: HG01816 Replicate 1


title: HG01794 Replicate 1


title: HG01790 Replicate 1


title: HG01795 Replicate 1


title: HG01784 Replicate 1


title: HG01786 Replicate 1


title: HG01785 Replicate 1


title: HG01789 Replicate 1


title: 255001210003_b1 - 7_CERVIL_NO_STRESS vs 313_CERVIL_STRESS

hyb_protocol: 313_CERVIL_STRESS Cy5 / 7_CERVIL_NO_STRESS Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.


title: HG01781 Replicate 1


title: HG01777 Replicate 1


title: HG01779 Replicate 1


title: HG01773 Replicate 1


title: HG01771 Replicate 1


title: HG01776 Replicate 1


title: HG01775 Replicate 1


title: HG01768 Replicate 1


title: HG01770 Replicate 1


title: HG01766 Replicate 1


title: HG01797 Replicate 1


title: HG01796 Replicate 1


title: HG01765 Replicate 1


title: HG01767 Replicate 1


title: HG01756 Replicate 1


title: HG01757 Replicate 1


title: HG01747 Replicate 1


title: HG01762 Replicate 1


title: HG01709 Replicate 1


title: HG01783 Replicate 1


title: HG01746 Replicate 1


title: HG01710 Replicate 1


title: HG01707 Replicate 1


title: HG01704 Replicate 1


title: HG01705 Replicate 1


title: HG01702 Replicate 1


title: HG01700 Replicate 1


title: HG01699 Replicate 1


title: HG01685 Replicate 1


title: HG01694 Replicate 1


title: HG01682 Replicate 1


title: HG01684 Replicate 1


title: HG01686 Replicate 1


title: HG01697 Replicate 1


title: HG01676 Replicate 1


title: HG01679 Replicate 1


title: HG01695 Replicate 1


title: HG01675 Replicate 1


title: HG01678 Replicate 1


title: HG01761 Replicate 1


title: HG01672 Replicate 1


title: HG01680 Replicate 1


title: HG01670 Replicate 1


title: HG01673 Replicate 1


title: HG01708 Replicate 1


title: HG01668 Replicate 1


title: HG01631 Replicate 1


title: HG01624 Replicate 1


title: HG01626 Replicate 1


title: HG01630 Replicate 1


title: HG01632 Replicate 1


title: HG01628 Replicate 1


title: HG01623 Replicate 1


title: HG01625 Replicate 1


title: HG01620 Replicate 1


title: HG01617 Replicate 1


title: HG01612 Replicate 1


title: HG01669 Replicate 1


title: HG01613 Replicate 1


title: HG01608 Replicate 1


title: HG01926 Replicate 1


title: HG01605 Replicate 1


title: HG01615 Replicate 1


title: HG01603 Replicate 1


title: HG01600 Replicate 1


title: HG01598 Replicate 1


title: HG01596 Replicate 1


title: HG01599 Replicate 1


title: HG01597 Replicate 1


title: HG01595 Replicate 1


title: HG01593 Replicate 1


title: HG01589 Replicate 1


title: HG01602 Replicate 1


title: HG01583 Replicate 1


title: HG01586 Replicate 1


title: HG01577 Replicate 1


title: HG01619 Replicate 1


title: HG01572 Replicate 1


title: HG01618 Replicate 1


title: HG01571 Replicate 1


title: HG01607 Replicate 1


title: HG01610 Replicate 1


title: HG01606 Replicate 1


title: HG01566 Replicate 1


title: HG01565 Replicate 1


title: HG01551 Replicate 1


title: HG01550 Replicate 1


title: HG01537 Replicate 1


title: HG01536 Replicate 1


title: HG01530 Replicate 1


title: HG01556 Replicate 1


title: HG01525 Replicate 1


title: HG01524 Replicate 1


title: HG01521 Replicate 1


title: HG01522 Replicate 1


title: HG01519 Replicate 1


title: HG01527 Replicate 1


title: HG01578 Replicate 1


title: HG01518 Replicate 1


title: HG01516 Replicate 1


title: HG01513 Replicate 1


title: HG01515 Replicate 1


title: HG01512 Replicate 1


title: HG01509 Replicate 1


title: HG01510 Replicate 1


title: HG01507 Replicate 1


title: HG01500 Replicate 1


title: HG01506 Replicate 1


title: HG01503 Replicate 1


title: HG01531 Replicate 1


title: HG01501 Replicate 1


title: HG01504 Replicate 1


title: HG01497 Replicate 1


title: HG01498 Replicate 1


title: HG01494 Replicate 1


title: HG01491 Replicate 1


title: HG01489 Replicate 1


title: HG01492 Replicate 1


title: HG01528 Replicate 1


title: HG01495 Replicate 1


title: HG01488 Replicate 1


title: HG01486 Replicate 1


title: HG01479 Replicate 1


title: HG01485 Replicate 1


title: HG01791 Replicate 1


title: HG01474 Replicate 1


title: HG01468 Replicate 1


title: HG01464 Replicate 1


title: HG01459 Replicate 1


title: HG01465 Replicate 1


title: HG01461 Replicate 1


title: HG01456 Replicate 1


title: HG01455 Replicate 1


title: HG01447 Replicate 1


title: HG01462 Replicate 1


title: HG01444 Replicate 1


title: HG01441 Replicate 1


title: HG01443 Replicate 1


title: HG01435 Replicate 1


title: HG01437 Replicate 1


title: HG01432 Replicate 1


title: HG01440 Replicate 1


title: HG01438 Replicate 1


title: HG01405 Replicate 1


title: HG01413 Replicate 1


title: HG01412 Replicate 1


title: HG01403 Replicate 1


title: HG01402 Replicate 1


title: HG01414 Replicate 1


title: HG01398 Replicate 1


title: HG01393 Replicate 1


title: HG01389 Replicate 1


title: HG01390 Replicate 1


title: HG01396 Replicate 1


title: HG01392 Replicate 1


title: HG01395 Replicate 1


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title: 550536A06 - nced2nced5nced6nced9_BR2 vs. nced2nced5nced9_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Identification of ABA signaling factors and targets in Arabidopsis developing seeds by comparing ABA deficient and wild type genotypes.

hyb_protocol: nced2nced5nced9_BR2 Cy5 / nced2nced5nced6nced9_BR2 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:532nm, pmt voltage 480V, laser power 35%; Cy5:635nm, pmt voltage 480V, laser power 30%.

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green). For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias. Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

growth_protocol: seed - Media=compost (Tref substrates) with Plan-Prod nutritive solution (Fertil)  hygrometry=65% Temperature=21°C light / 19°C dark Light=16h light (170 micromol photon) / 8h dark

treatment_protocol: No treatment

tag: ecotype/background

tag: genotype/variation

value: ABA-deficient mutant (nced2nced5nced9)

tag: developmental stage (boyes et al. plant cell 2001)

value: boyes:8 silique

value: 14 DAP

value: seed


title: 550536A01 - col_BR3 vs. nced2nced5nced6nced9_BR3

hyb_protocol: nced2nced5nced6nced9_BR3 Cy5 / col_BR3 Cy3 : 30pmol.

extract_protocol: col_BR3:4ug. (Qiagen_RNeasy.pdf)

value: wild type


title: 550536A02 - nced2nced5nced6nced9_BR3 vs. col_BR3

hyb_protocol: col_BR3 Cy5 / nced2nced5nced6nced9_BR3 Cy3 : 30pmol.


title: HG04023 Replicate 1


title: HG03998 Replicate 1


title: 557220A09 - nced2nced5nced6nced9_BR1 vs. col_BR1

hyb_protocol: col_BR1 Cy5 / nced2nced5nced6nced9_BR1 Cy3 : 30pmol.

extract_protocol: col_BR1:4ug. (Qiagen_RNeasy.pdf)


title: 557220A11 - col_BR2 vs. nced2nced5nced6nced9_BR2

hyb_protocol: nced2nced5nced6nced9_BR2 Cy5 / col_BR2 Cy3 : 30pmol.

extract_protocol: col_BR2:4ug. (Qiagen_RNeasy.pdf)


title: HG03990 Replicate 1


title: HG03991 Replicate 1


title: 550536A04 - nced2nced5nced6nced9_BR1 vs. nced2nced5nced9_BR1

hyb_protocol: nced2nced5nced9_BR1 Cy5 / nced2nced5nced6nced9_BR1 Cy3 : 30pmol.


title: HG03989 Replicate 1


title: HG03985 Replicate 1


title: HG03978 Replicate 1


title: HG03995 Replicate 1


title: HG03986 Replicate 1


title: HG03977 Replicate 1


title: 557220A10 - col_BR1 vs. nced2nced5nced6nced9_BR1

hyb_protocol: nced2nced5nced6nced9_BR1 Cy5 / col_BR1 Cy3 : 30pmol.


title: 550536A05 - nced2nced5nced9_BR2 vs. nced2nced5nced6nced9_BR2

hyb_protocol: nced2nced5nced6nced9_BR2 Cy5 / nced2nced5nced9_BR2 Cy3 : 30pmol.


title: HG04003 Replicate 1


title: 550536A07 - nced2nced5nced9_BR3 vs. nced2nced5nced6nced9_BR3

hyb_protocol: nced2nced5nced6nced9_BR3 Cy5 / nced2nced5nced9_BR3 Cy3 : 30pmol.


title: 550536A08 - nced2nced5nced6nced9_BR3 vs. nced2nced5nced9_BR3

hyb_protocol: nced2nced5nced9_BR3 Cy5 / nced2nced5nced6nced9_BR3 Cy3 : 30pmol.


title: 550536A03 - nced2nced5nced9_BR1 vs. nced2nced5nced6nced9_BR1

hyb_protocol: nced2nced5nced6nced9_BR1 Cy5 / nced2nced5nced9_BR1 Cy3 : 30pmol.


title: HG03973 Replicate 1

hyb_protocol: Labeled samples were purified using Agilent SureTag Purification columns. Test and reference samples were combined with Agilent Oligo aCGH/ChIP-on-Chip Blocking Agent, Agilent Hi-RPM Hybridization Buffer and Cot-1 DNA and applied to microarrays enclosed in Agilent Hybridization Chamber. After 40 hour incubation at 67 °C, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 and 2.


title: HG03971 Replicate 1


title: HG03968 Replicate 1


title: HG04018 Replicate 1


title: HG03967 Replicate 1


title: HG03960 Replicate 1


title: HG03965 Replicate 1


title: HG03963 Replicate 1


title: HG03974 Replicate 1


title: HG03969 Replicate 1


title: HG03955 Replicate 1


title: HG03976 Replicate 1


title: HG03953 Replicate 1


title: HG03951 Replicate 1


title: HG03948 Replicate 1


title: HG03949 Replicate 1


title: HG03947 Replicate 1


title: HG03944 Replicate 1


title: HG03945 Replicate 1


title: HG03943 Replicate 1


title: 557220A12 - nced2nced5nced6nced9_BR2 vs. col_BR2

hyb_protocol: col_BR2 Cy5 / nced2nced5nced6nced9_BR2 Cy3 : 30pmol.


title: HG03940 Replicate 1


title: HG03937 Replicate 1


title: HG03934 Replicate 1


title: HG03931 Replicate 1


title: HG03928 Replicate 1


title: HG03926 Replicate 1


title: HG03925 Replicate 1


title: HG03922 Replicate 1


title: HG03920 Replicate 1


title: HG03950 Replicate 1


title: HG03917 Replicate 1


title: HG03916 Replicate 1


title: HG03919 Replicate 1


title: HG03914 Replicate 1


title: HG03941 Replicate 1


title: HG03913 Replicate 1


title: HG03911 Replicate 1


title: HG03910 Replicate 1


title: JS_I4exp

city: Adelaide

first: John

middle: E

last: Schjenken

state: South Australia

address: The Robinson Research Institute and School of Paediatrics and Reproductive Health. Level 6. Medical School North. Frome Road

country: Australia

institute: The University of Adelaide

description: Intact replicate 4

hyb_protocol: Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

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

data_processing: RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. Cel files for each chip were generated using Affymetrix GeneChip Command Console (Affymetrix).  Quality control was assessed using the Affymetrix Expression Console software.  The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to Partek Genomic Suite. Differentially expressed probes were identified using the parameters (≥1.5-fold change, t-test p <0.05).  Bioinformatics was performed using Ingenuity Pathway Analysis (IPA) version 18488943 Build 308606M.

label: Biotin

source_name: Coitus with Intact male (coitus with seminal fluid exposure)

label_protocol: Total RNA was converted to biotinylated sense DNA as per the GeneChip® WT PLUS Reagent Kit Manual.

growth_protocol: All animal experiments were performed in accordance with the Guiding Principles for the Care and Use of Research Animals endorsed by the Society for the Study of Reproduction, with approval from the University of Adelaide Ethics Committee (approval numbers M-2010-095 and M-023-14). Mice were housed in a specific pathogen-free facility at the University of Adelaide with controlled temperature and lighting (12L:12D). Food and water were supplied ad libitum. CBA x C57Bl/6 F1 (CBAF1) females and Balb/c mice were purchased from the University of Adelaide Central Animal Facility. Females were stored at a maximum of 7 females per cage while males were stored separately. All mice were kept in individually ventilated cages (Techniplast).

extract_protocol: Total RNA was extracted using the miRNeasy extraction kit (Qiagen) and treated with TURBO DNA-free™ (Life Technologies) following the manufacturer’s instructions. RNA was quantified using a Nano-Drop Spectrophotometer ND-1000 (Thermo Scientific, Waltham, MA) and RNA integrity was analysed using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) to ensure all RNA preparations had an RNA Integrity Number (RIN) of >7.

treatment_protocol: The estrus cycle stage of CBAF1 females was determined using vaginal cytology. At 2300-0100 h on the evening after proestrus was detected, females were placed with either Intact (coitus with seminal fluid exposure) or SVX/VAS (coitus without seminal fluid exposure) Balb/c males. The occurrence and timing of mating events within the subsequent 2 h period were monitored by video recording (for both intact and SVX/VAS males) and confirmed by presence of a copulatory plug (for intact males). At 8 h post-mating (0700–0900 h) females were killed and the uterus was excised and processed for RNA analysis. The uterus was placed in cold PBS, and trimmed of fat, mesentery, and blood vessels under a dissection microscope (Olympus, New York, NY), then transferred into fresh PBS and slit lengthwise. Exposed endometrial tissue was scraped off using a razor blade into Qiazol RNA lysis solution (Qiagen, Venlo, Netherlands) and the myometrium was discarded. RNA was homogenized at a setting of one cycle at 3500 rpm for 10 seconds using the PowerLyzer® 24 Bench Top Bead-Based Homogenizer (MoBio Laboratories). Homogenized RNA was stored at -80 degrees celcius prior to extraction

tag: gender

value: female

value: Endometrium

tag: time point

value: 8 h post coitus


title: JS_S4exp

description: SVX/VAS replicate 4

source_name: Coitus with SVX/VAS male (coitus without seminal fluid exposure)


title: JS_S2exp

description: SVX/VAS replicate 2


title: 4.5g/l glucose_cultured vascular smooth muscle cells_6

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

description:
Sample name: 12_4.5G6
Aortic smooth muscle cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console software. Probe intensities, gene level expression were RMA summarized and then quantile normalized.
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: Primary Cells

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

growth_protocol: DMEM 10%FCS

extract_protocol: mRNeasy mini kit

treatment_protocol: 0.3g/l glucose or 4.5g/l glucose for 1 week

value: Aortic smooth muscle cells

tag: culture condition

value: 4.5g/l glucose


title: 4.5g/l glucose_cultured vascular smooth muscle cells_5

description:
Sample name: 11_4.5G5
Aortic smooth muscle cells

tag: strain


title: HG03907 Replicate 1


title: HG03905 Replicate 1


title: 4.5g/l glucose_cultured vascular smooth muscle cells_3

description:
Sample name: 9_4.5G3
Aortic smooth muscle cells


title: JS_S1exp

description: SVX/VAS replicate 1


title: JS_I1exp

description: Intact replicate 1


title: JS_S3exp

description: SVX/VAS replicate 3


title: JS_I3exp

description: Intact replicate 3


title: HG03902 Replicate 1


title: HG03900 Replicate 1


title: HG03899 Replicate 1


title: 4.5g/l glucose_cultured vascular smooth muscle cells_2

description:
Sample name: 8_4.5G2
Aortic smooth muscle cells


title: JS_I2exp

description: Intact replicate 2


title: 4.5g/l glucose_cultured vascular smooth muscle cells_1

description:
Sample name: 7_4.5G1
Aortic smooth muscle cells


title: HG03898 Replicate 1


title: HG03908 Replicate 1


title: HG03897 Replicate 1


title: 0.3g/l glucose_cultured vascular smooth muscle cells_6

description:
Sample name: 6_0.3G6
Aortic smooth muscle cells

value: 0.3g/l glucose


title: HG03894 Replicate 1


title: HG03896 Replicate 1


title: HG03890 Replicate 1


title: HG03888 Replicate 1


title: HG03895 Replicate 1


title: 4.5g/l glucose_cultured vascular smooth muscle cells_4

description:
Sample name: 10_4.5G4
Aortic smooth muscle cells


title: HG03887 Replicate 1


title: 0.3g/l glucose_cultured vascular smooth muscle cells_2

description:
Sample name: 2_0.3G2
Aortic smooth muscle cells


title: 0.3g/l glucose_cultured vascular smooth muscle cells_1

description:
Sample name: 1_0.3G1
Aortic smooth muscle cells


title: 0.3g/l glucose_cultured vascular smooth muscle cells_5

description:
Sample name: 5_0.3G5
Aortic smooth muscle cells


title: FOXA3_rep3

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: murine adult bone marrow

hyb_protocol: Labeled targets were hybridized on the mogene2st arry and processed using the Affymetrix system.

scan_protocol: Scanning uses the Affymetrix scanner

data_processing: The data were analyzed with Partek Genomics Suite 6.6 by the RMA method.

source_name: murine adult bone marrow_FOXA3_knockout

label_protocol: RNA was amplified using the NuGEN Ovation Pico WTA V2 system and then labeled with the NuGEN Encore Biotin Module.

growth_protocol: Isolated whole bone marrow Lineage- Sca-1 + c-Kit+ (LSK) CD150+ CD48-  cells were cultured in SFEM media (StemCell Technologies, Vancouver, British Columbia, Canada) supplemented with 2 mM glutamine, 30 U/mL penicillin/streptomycin, 10 ng/mL rmScf, 20 ng/mL rmTpo, 20 ng/mL rmIgf-2 (all from Peprotech, Rocky Hill, NJ), 10 ng/mL rhFGF-1 (R&D Systems, Minneapolis, MN) and 10 mg/ml heparin (Sigma, St Louis, MO) at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated from 10,000 sorted LSK CD150+ CD48- cells from Foxa3+/+ and Foxa3-/- C57BL/6J mice using the Qiagen RNeasy Micro Kit (Qiagen, Santa Clarita, CA). RNA was amplified using the NuGEN Ovation Pico WTA V2 system and then labeled with the NuGEN Encore Biotin Module (NuGen, San Carlos, CA).

tag: genotype

value: bone marrow

tag: developmental stage

value: adult

tag: cell markers

value: Sca-1 + c-Kit+ (LSK) CD150+ CD48-


title: HG03886 Replicate 1

tag: coriell cell line


title: FOXA3_rep2

description: murine adult bone marrow

tag: tissue


title: HG03884 Replicate 1


title: wt_rep3

description: murine adult bone marrow

source_name: murine adult bone marrow_wildtype


title: HG03882 Replicate 1


title: 0.3g/l glucose_cultured vascular smooth muscle cells_4

description:
Sample name: 4_0.3G4
Aortic smooth muscle cells

tag: cell type


title: wt_rep1

description: murine adult bone marrow


title: FOXA3_rep1

description: murine adult bone marrow


title: wt_rep2

description: murine adult bone marrow


title: HG03874 Replicate 1


title: HG03873 Replicate 1


title: 0.3g/l glucose_cultured vascular smooth muscle cells_3

description:
Sample name: 3_0.3G3
Aortic smooth muscle cells


title: HG03875 Replicate 1


title: HG03870 Replicate 1


title: HG03885 Replicate 1


title: HG03869 Replicate 1


title: HG03871 Replicate 1


title: HG03868 Replicate 1


title: HG03866 Replicate 1


title: HG03867 Replicate 1


title: HG03864 Replicate 1


title: AhR KO keratinocyte_1

city: University Park

first: Adam

middle: B.

last: Glick

state: PA

address: 101 Life Sciences Bld

department: Veterinary and Biomedical Sciences

institute: The Pennsylvania State University

hyb_protocol: Samples were hybridized according to manufacturer's instructions using the GeneChip Hybridization Wash and Stain Kit  and Affymetrix GeneChip Hybridization Oven 640. Arrays were washed and stained using the  Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’s protocol.

data_processing:
Data were processed using ArrayStar 11 software. RMA background correction was applied to probe intensities. Gene level expression were summarized from the corrected intensities and quantile normalized.
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st-v1.na33.mm10.transcript.csv

source_name: primary mouse keratinocyte cell culture

label_protocol: cDNA was generated from 100 ng of total RNA from each sample using the Ambion WT Expression Kit according to the manufacturer’s protocol. The sense strand cDNA was fragmented and labelled using the Affymetrix GeneChip WT Terminal Labeling Kit according to the manufacturer’s instructions

growth_protocol: Primary mouse keratinocytes were isolated from newborn genotyped AhR Wt (C57BL/6) or AhR Ko mice according to standard protocols and cultured in EMEM media with 8% chelexed serum antibiotics and 0.05 mM calcium chloride for 5 days before isolation of RNA.

extract_protocol: Total RNA was isolated Ahr Wt and Ahr Ko primary mouse keratinocyte cultures using Ribozol. RNA quality assesed using Agilent Bioanalyzer.

value: primary keratinocyte cell culture

value: AhR KO (-/-)


title: HG03872 Replicate 1


title: HG03863 Replicate 1


title: HG03861 Replicate 1


title: HG03862 Replicate 1


title: HG03858 Replicate 1


title: AhR KO keratinocyte_3


title: HG03857 Replicate 1


title: HG03856 Replicate 1


title: AhR WT keratinocyte_4

value: AhR WT (+/+)


title: AhR WT keratinocyte_1


title: AhR WT keratinocyte_3


title: HG03854 Replicate 1


title: HG03844 Replicate 1


title: HG03846 Replicate 1


title: AhR KO keratinocyte_2


title: AhR WT keratinocyte_2


title: Saos [miRNA]

city: Yufu

first: Masanori

last: Kawano

address: 1-1 Idaigaoka, Hasama-machi

country: Japan

institute: Oita University

description: Gene expression data from human osteosarcoma cell line

hyb_protocol: The double-strand cDNA was used as a template for in vitro transcription to generate biotin-labeled cRNA. After fragmentation, 12.5 ug of cRNA was hybridized to the GeneChip array for 16 hr.

scan_protocol: The GeneChips were washed and stained using the GeneChip Fluidics Station 450 (Affymetrix) and then scanned with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The microarray numerical values were analyzed using the GeneSpring GX 11.0 software, according to the RMA16 Algorithm: quantile normalization, filter by flags (detected), filter by expression on the normalized data (20.0–100.0th percentile).

source_name: Human Osteosarcoma Cell Line

label_protocol: Biotinylated cRNA was synthesized from total RNA using the Affymetrix 3` IVT Express Kit according to manufacturer’s protocols.

growth_protocol: Osteosarcoma cells were cultured in a high-glucose medium, DMEM supplemented with 10% FBS and 1% penicillin and streptomycin.

extract_protocol: Total RNA was extracted with the TRizol reagent and cDNA was synthesized according to the manufacturer's protocol.

treatment_protocol: Cultured Cells are removed by treatment with Trypsin-EDTA　when they reach to 70–80% confluence.

tag: cell line

value: Saos

value: osteosarcoma cells


title: NY [miRNA]

value: NY


title: HG03849 Replicate 1


title: HOS [miRNA]

value: HOS


title: Hu09 [miRNA]


title: hMSC [miRNA]

source_name: Human Mesenchyamal Stem Cell Line

value: hMSC

value: mesenchymal stem cells


title: HG03837 Replicate 1


title: HG03838 Replicate 1


title: MG63 [miRNA]


title: HG03836 Replicate 1


title: HG03830 Replicate 1


title: HG03826 Replicate 1


title: HG03824 Replicate 1


title: HG03829 Replicate 1


title: HG03815 Replicate 1


title: HG03832 Replicate 1


title: HG03817 Replicate 1


title: HG03851 Replicate 1


title: HG03850 Replicate 1


title: HG03812 Replicate 1


title: HG03814 Replicate 1


title: HG03848 Replicate 1


title: HG03821 Replicate 1


title: HG03809 Replicate 1


title: HG03805 Replicate 1


title: HG03808 Replicate 1


title: HG03803 Replicate 1


title: HG03796 Replicate 1


title: HG03790 Replicate 1


title: HG03789 Replicate 1


title: HG03793 Replicate 1


title: HG03802 Replicate 1


title: HG03800 Replicate 1


title: HG03787 Replicate 1


title: HG03788 Replicate 1


title: HG03792 Replicate 1


title: HG03785 Replicate 1


title: HG03833 Replicate 1


title: HG03784 Replicate 1


title: HG03780 Replicate 1


title: HG03782 Replicate 1


title: HG03775 Replicate 1


title: HG03777 Replicate 1


title: HG03778 Replicate 1


title: HG03772 Replicate 1


title: HG03770 Replicate 1


title: HG03774 Replicate 1


title: HG03773 Replicate 1


title: HG03771 Replicate 1


title: HG03762 Replicate 1


title: HG03765 Replicate 1


title: HG03786 Replicate 1


title: HG03760 Replicate 1


title: HG03757 Replicate 1


title: HG03754 Replicate 1


title: HG03755 Replicate 1


title: HG03756 Replicate 1


title: HG03753 Replicate 1


title: HG03750 Replicate 1


title: HG03744 Replicate 1


title: HG03745 Replicate 1


title: HG03746 Replicate 1


title: HG03823 Replicate 1


title: HG03781 Replicate 1


title: HG03743 Replicate 1


title: HG03779 Replicate 1


title: HG03740 Replicate 1


title: HG03741 Replicate 1


title: HG03767 Replicate 1


title: HG03736 Replicate 1


title: HG03738 Replicate 1


title: HG03742 Replicate 1


title: HG03729 Replicate 1


title: HG03730 Replicate 1


title: HG03733 Replicate 1


title: HG03727 Replicate 1


title: HG03722 Replicate 1


title: HG03720 Replicate 1


title: HG03718 Replicate 1


title: HG03752 Replicate 1


title: HG03731 Replicate 1


title: HG03717 Replicate 1


title: HG03714 Replicate 1


title: HG03715 Replicate 1


title: HG03716 Replicate 1


title: HG03713 Replicate 1


title: HG03708 Replicate 1


title: HG03706 Replicate 1


title: HG03705 Replicate 1


title: HG03709 Replicate 1


title: HG03703 Replicate 1


title: HG03702 Replicate 1


title: HG03697 Replicate 1


title: HG03698 Replicate 1


title: HG03696 Replicate 1


title: HG03691 Replicate 1


title: HG03693 Replicate 1


title: HG03689 Replicate 1


title: HG03686 Replicate 1


title: HG03687 Replicate 1


title: HG03690 Replicate 1


title: HG03692 Replicate 1


title: HG03684 Replicate 1


title: HG03679 Replicate 1


title: HG03685 Replicate 1


title: HG03681 Replicate 1


title: HG03711 Replicate 1


title: HG03672 Replicate 1


title: HG03680 Replicate 1


title: HG03660 Replicate 1


title: HG03663 Replicate 1


title: HG03653 Replicate 1


title: HG03667 Replicate 1


title: HG03694 Replicate 1


title: HG03652 Replicate 1


title: HG03695 Replicate 1


title: HG03649 Replicate 1


title: HG03673 Replicate 1


title: NA21144 Replicate 1


title: NA21143 Replicate 1


title: HG03646 Replicate 1


title: HG03668 Replicate 1


title: VUMC-Rb-83

city: Amsterdam

first: Irsan

last: Kooi

state: Noord-Holland

address: van der Boechorstraat 7

department: Clininical Genetics

country: Netherlands

institute: VU university medical centre

description: fresh frozen Rb material from a randomly selected cohort

hyb_protocol: Per sample, 7.5 µg cRNA of the obtained biotinylated cRNA samples was fragmented and hybridized in a final concentration of 0.0375 µg/µl on the Affymetrix [HT HG U133 + PM96] (Affymetrix, Santa Clara, CA, U.S.A.). After an automated process of washing and staining by the GeneTitan machine (Affymetrix, Santa Clara, CA, U.S.A) using the Affymetrix HWS Kit for GeneTitan (part nr. 901530), absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v3.2 software.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system

data_processing: Data were background adjusted, normalized and summarized by the RMA method. The affy package from Bioconductor was used for this analysis.

source_name: primary Rb tissue

label_protocol: Biotinylated cRNA was prepared using the Affymetrix 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s specifications with an input of 100 ng of total RNA

extract_protocol: Frozen tumour samples were homogenized in Trizol Reagent (Invitrogen, Carlsbad, Canada) with a rotor-stator homogenizer, and RNA was extracted following the manufacturer's instructions. Trizol extracted RNA was treated with rDNase (Macherey-Nagel, Düren, Germany) to digest any contaminating DNA and subsequently purified with the NucleoSpin RNA Clean-up XS kit (Macherey-Nagel)

value: primary Rb tissue

tag: uhc-subgroup

value: group 1


title: NA21142 Replicate 1


title: NA21137 Replicate 1


title: NA21141 Replicate 1


title: VUMC-Rb-99

value: group 3


title: VUMC-Rb-98


title: NA21133 Replicate 1


title: NA21130 Replicate 1


title: VUMC-Rb-81

value: group 2


title: VUMC-Rb-82


title: VUMC-Rb-76


title: VUMC-Rb-69


title: VUMC-Rb-75


title: VUMC-Rb-74


title: VUMC-Rb-73


title: VUMC-Rb-79


title: VUMC-Rb-72


title: NA21125 Replicate 1


title: VUMC-Rb-70


title: NA21127 Replicate 1


title: NA21129 Replicate 1


title: NA21128 Replicate 1


title: NA21126 Replicate 1


title: NA21123 Replicate 1


title: NA21120 Replicate 1


title: NA21122 Replicate 1


title: NA21119 Replicate 1


title: NA21118 Replicate 1


title: VUMC-Rb-61


title: VUMC-Rb-62


title: NA21124 Replicate 1


title: VUMC-Rb-60


title: VUMC-Rb-67


title: NA21115 Replicate 1


title: NA21116 Replicate 1


title: VUMC-Rb-71


title: NA21117 Replicate 1


title: VUMC-Rb-63


title: VUMC-Rb-66


title: VUMC-Rb-68


title: NA21114 Replicate 1


title: VUMC-Rb-59


title: NA21113 Replicate 1


title: NA21112 Replicate 1


title: VUMC-Rb-55


title: VUMC-Rb-58


title: NA21111 Replicate 1


title: VUMC-Rb-54


title: VUMC-Rb-53


title: VUMC-Rb-48


title: NA21109 Replicate 1


title: NA21110 Replicate 1


title: VUMC-Rb-50


title: NA21107 Replicate 1