title: SmiclMO injected embryos at St10.5 vs ControlMO (C)

status: Public on May 30 2009

type: RNA

city: Cambridge

first: Clara

last: Collart

address: Tennis court road

department: Gurdon Institute

country: United Kingdom

institute: Cambridge University

description: Embryos were injected at the one cell stage  with 80 ng of either Smicl antisense morpholino oligonucleotides (XlMO) or Control morpholino (coMO) dissolved in water. Ref: Collart, C., K. Verschueren, et al. (2005).

data_processing: log ratios (Cy5/Cy3) were lowess normalised

molecule: total RNA

organism: Xenopus laevis

source_name: SmiclMO injected embryos St10.5 (C)

tag: See description

source_name: ControlMO injected embryos St10.5 (C)


title: ControlMO injected embryos at St10.5 vs SmiclMO (C_swap)


title: HMVEC-L stimulated without LPS for 8 hours c08R2

status: Public on May 29 2009

city: Bethesda

first: Anya

middle: Carmen

last: Harry

state: MD

address: 10 Center Dr. MSC 1662 Bldg 10

department: CCMD

country: USA

institute: NIH

description: HMVEC-L stimulated without LPS for 8 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

organism: Homo sapiens

source_name: HMVEC-L

tag: Microvascular endothelial cells, lung


title: HMVEC-L stimulated without LPS for 24 hours c24R3

description: HMVEC-L stimulated without LPS for 24 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures.


title: ControlMO injected embryos at St10.5 vs SmiclMO (A_swap)

source_name: ControlMO injected embryos St10.5 (A)

source_name: SmiclMO injected embryos at St10.5 vs ControlMO (A)


title: HMVEC-L stimulated without LPS for 24 hours c24R1


title: HMVEC-L stimulated with LPS for 4 hours L04R3

description: HMVEC-L stimulated with LPS for 4 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures.


title: HMVEC-L stimulated with LPS for 8 hours L08R4

description: HMVEC-L stimulated with LPS for 8 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures.


title: HMVEC-L stimulated without LPS for 4 hours c04R1

description: HMVEC-L stimulated without LPS for 4 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures.


title: HMVEC-L stimulated without LPS for 8 hours c08R4


title: HMVEC-L stimulated with LPS for 24 hours L24R4

description: HMVEC-L stimulated with LPS for 24 hours. The cells were collected and total RNA was extracted, labeled and hybridized to human U133 microarrays following standard Affymatrix procedures.


title: HMVEC-L stimulated without LPS for 8 hours c08R1


title: HMVEC-L stimulated without LPS for 24 hours c24R2


title: SmiclMO injected embryos at St10.5 vs ControlMO (A)

description:
Embryos were injected at the one cell stage  with 80 ng of either Smicl antisense morpholino oligonucleotides (XlMO) or Control morpholino (coMO) dissolved in water. Ref: Collart, C., K. Verschueren, et al. (2005). "The novel Smad-interacting protein Smicl regulates Chordin expression in the Xenopus embryo." Development 132(20): 4575-86.. Embryos were harvested at Stage 10.5 for RNA analysis.
RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) "Single Step Method of RNA Isolation by Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction." Analytical Biochemistry 162, 156.
50 micrograms of RNA were used for hybridisation.
Probe labelling and hybridization conditions were carried out as detailed in this paper

source_name: SmiclMO injected embryos St10.5 (A)


title: HMVEC-L stimulated with LPS for 8 hours L08R2


title: HMVEC-L stimulated without LPS for 8 hours c08R3


title: HMVEC-L stimulated without LPS for 24 hours c24R4


title: HMVEC-L stimulated without LPS for 4 hours c04R2


title: HMVEC-L stimulated with LPS for 8 hours L08R3


title: HMVEC-L stimulated with LPS for 4 hours L04R2


title: HMVEC-L stimulated with LPS for 24 hours L24R1


title: HMVEC-L stimulated with LPS for 8 hours L08R1


title: HMVEC-L stimulated without LPS for 4 hours c04R3


title: ControlMO injected embryos at St10.5 vs SmiclMO (B_swap)

source_name: ControlMO injected embryos St10.5 (B)

source_name: SmiclMO injected embryos St10.5 (B)


title: HMVEC-L stimulated with LPS for 24 hours L24R3


title: HMVEC-L stimulated without LPS for 4 hours c04R4


title: HMVEC-L stimulated with LPS for 24 hours L24R2


title: SmiclMO injected embryos at St10.5 vs ControlMO (B)


title: 13689281 - Met2_shoot_3 vs Col_shoot_3

status: Public on May 28 2009

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

country: France

institute: INRA

description: Role of the MET2 methyltransferase on methylation and gene expression in arabidopsis

hyb_protocol: Col_shoot_3 Cy5 / Met2_shoot_3 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.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 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: aerial - Media : MS/2	 Temperature : 22°C	 Light : 16h day

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes 1.02

tag: Arabidopsis thaliana (columbia)  mutant (Met2_16A1) - dev.stage (Boyes et al. Plant Cell 2001):boyes 1.02


title: 13689151 - Col_root_4 vs Met2_root_4

hyb_protocol: Met2_root_4 Cy5 / Col_root_4 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.

growth_protocol: root - Media : MS/2	 Temperature : 22°C	 Light : 16h day


title: 13689282 - Col_shoot_3 vs Met2_shoot_3

hyb_protocol: Met2_shoot_3 Cy5 / Col_shoot_3 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.


title: HMVEC-L stimulated with LPS for 4 hours L04R4


title: 13689278 - Met2_shoot_4 vs Col_shoot_4

hyb_protocol: Col_shoot_4 Cy5 / Met2_shoot_4 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.


title: 13689276 - Met2_root_3 vs Col_root_3

hyb_protocol: Col_root_3 Cy5 / Met2_root_3 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.


title: 13689277 - Col_root_3 vs Met2_root_3

hyb_protocol: Met2_root_3 Cy5 / Col_root_3 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.


title: 13689279 - Col_shoot_4 vs Met2_shoot_4

hyb_protocol: Met2_shoot_4 Cy5 / Col_shoot_4 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.


title: vCD01

status: Public on May 19 2009

city: Budapest

first: Norbert

last: Solymosi

state: Budapest

address: István u. 2.

country: Hungary

institute: ATE

description: Gene expression data from peripheral blood sample

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix HGU133 Plus 2.0 chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner

data_processing: The data were preprocessed by the function mas5 from the Bioconductor affy package

source_name: human peripheral blood sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Affymetrix Globin Reduction Protocol)

extract_protocol: PaxGene extraction of total RNA was performed according to the manufacturer instructions

tag: Blood

value: CD


title: HMVEC-L stimulated with LPS for 4 hours L04R1


title: vUC06

value: UC


title: 13689155 - Met2_root_4 vs Col_root_4

hyb_protocol: Col_root_4 Cy5 / Met2_root_4 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.


title: vUC02


title: vUC04


title: vUC05


title: vCD05


title: vCD03


title: vUC03


title: vUC01


title: vCD04


title: vCD02


title: HS 277 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 0 hrs treated replicate 2

status: Public on May 14 2009

type: mixed

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

description: Poorly diff. liposarcoma, LiSa-2 cells.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software.

data_processing: raw data as output from GenePix Pro 3.0 analysis software

source_name: Poorly diff. liposarcoma, LiSa-2 cells

label_protocol: RNA labeling was performed using the Genisphere 3DNA-350 indirect labeling kit. The total RNA (2 micrograms) was reversed transcribed using reverse transcript RT dT primers.  The synthesized tagged cDNA was hybridized with PCR products printed on the slides.  The fluorescent cDNA reagents (capture sequence for Cy3 or Cy54) were hybridized to the cDNA based on the complementarity to a sequence of the 5' end of the RT primer.

growth_protocol: Cells were grown in penicillin streptomycin containing media IMDM + 10% FBS (100 U/ml) for 48 hrs at 37 degrees C. This represents time zero hr.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit protocol for isolation of total RNA from tissues with addition of DNase treatment and an additional digestion with proteinase K, Trizol extraction, ethanol precipitation. For details see http://madb.eng.uiowa.edu/MICROARRAY/HTML/protocols/UI_human_37K/RNA_purification_protocol.htm

tag: Poorly diff. liposarcoma, LiSa-2 cells

molecule: other

source_name: human reference RNA

label_protocol: RNA labeling was performed using the Genisphere 3DNA-350 indirect labeling kit.  Reference RNA (440 ng) was reverse transcribed using reverse transcript RT dT primers.  The synthesized tagged cDNA was hybridized with PCR products printed on the slides.  The fluorescent cDNA reagent (capture sequence for Cy3 or Cty5) were hybridized to the cDNA based on the complementarity to a sequence of the 5' end of the RT primer.

growth_protocol: All clones of the human set were grown individually in 100 micro liters of appropriate cell culture media, OVN at 37 degrees C., in a 384-well plate.  The cell cultures were pooled together and a sample of this total pool was used to extract the plasmid DNA (Qiagen HiSpeed plasmid midi kit, Cat. no. 12643, following the manufacturer's recommendations).

extract_protocol: The plasmid DNA originated from all clones of the set.  It was linearized by a two-step PCR protocol and used to produce an 'in vitro' RNA.  This RNA was labeled and hybridized.  For details see http://madb.eng.uiowa.edu/MICROARRAY/HTML/protocols

tag: As a control RNA we used a set of human clones.  The clones were grown individually.  The cell clusters were pooled together and a sample of this total pool was used to extract the plasmid DNA (Qiagen HiSpeed plasmid midi kit, Cat. no. 12643, following the manufacturer's recommendations).


title: HS 270 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 6 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 269 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 6 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 278 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 11 days treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 261 human poorly diff. liposarcoma, LiSa-2 cells,  24 hrs no treatment

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 258 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 11 days treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 274 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 0 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 268 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 6 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 275 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 0 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 263 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 24 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 267 human poorly diff. liposarcoma, LiSa-2 cells,  6 hrs no treatment

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 262 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 24 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 259 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 11 days treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 256 human poorly diff. liposarcoma, LiSa-2 cells,  24 hrs no treatment

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 266 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 0 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 271 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 6 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 255 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 6 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 253 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 6 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 254 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 6 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 257 human poorly diff. liposarcoma, LiSa-2 cells,  11 days no treatment

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 265 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 24 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 276 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 0 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 260 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 11 days treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 246 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 24 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: anx/anx versus wild type hypothalamus replicate 3

status: Public on May 11 2009

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: Hypothalamus biological replicate 3 of 3. Has no technical replicates. anx/anx versus wild type littermate comparison.

hyb_protocol: Three biological replicate experiments were performed, each comparing anx/anx verus wild type tissue. For two of the three biological replicates each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects, whereas the third was only hybridized once. Thus, five microarray hybridizations were processed.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Target genes were considered as differentially expressed when above 0.001 false discovery rate (FDR), using significant analysis of microarrays (SAM) test implemented in the samr library in R (Tusher et al 2001). All quantitative and statistical analyses were performed using using Limma package in the R. environment (Smyth 2004).

organism: Mus musculus

source_name: hypothalamus

label_protocol: 500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).

growth_protocol: Homozygous anorexia mice were produced from heterozygous breeder pairs (B6C3Fe a/a-anx/J) obtained from the Jackson Laboratory. Postnatal day 16 weanling mice housed with their parents were separated into two groups: anx/anx and control mice. anx/anx mice were identified by their reduced body weight, body tremor, and mild hyperactivity. Because homozygous and heterozygous mice cannot be phenotypically distinguished from wild types, control groups probably contained both genotypes (wt/wt or wt/anx). anx/anx and control mice were allowed ad libitum access to the mother, food, and water. Three anx/anx and three control mice animals were anesthetized with isofluorane, decapitated and hypothalamus was dissected. Tissues were immediately frozen with liquid nitrogen and stored until the experiments were performed. Sex was determined by a simplex PCR assay as described (Clapcote and Roder 2005).

extract_protocol: RNA was extracted from the tissue using Trizol (Invitrogen), following manufracturer’s recommendations. RNA quantification was performed through a Nanodrop spectrophotometer, and their quality was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE). All RNAs used had RIN (RNA integrity number) ranging between 8.4 and 8.9, and 28S/18S ratios between 1.3 and 1.6.

tag: Hypothalamus tissue from individual postnatal day 16 weanling anx/anx mouse littermate (B6C3Fe a/a-anx/J strain)

tag: Hypothalamus tissue from individual postnatal day 16 weanling wild type mouse littermate (B6C3Fe a/a-anx/J strain)


title: HS 272 human poorly diff. liposarcoma, LiSa-2 cells,  6 hrs no treatment

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 252 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 6 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 264 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 24 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 250 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 0 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: flagellar regulon study(sigmaF overexpression1)

status: Public on May 01 2009

city: Madison

first: Kai

last: Zhao

state: WI

address: 2100 University Avenue

department: Oncology

institute: Mcardle Laboratory for Cancer Research

description:
This study examined the genes under the control of FlhDC and sigmaF in E. coli. Under defined steady-state growth condition, we used two different genetic approaches to alter the modulator concentration in cells; (1) moderately expressing FlhDC or sigmaF from anhydrotetracycline (aTc) inducible and Tet repressor-controlled PLtet promoter in a plasmid-borne flhDC or fliA gene; (2) disrupting the expression of FlhDC or sigmaF in flhDC or fliA deletion mutant strains. Samples were taken from culture with wild-type or deletion strains at mid log phase (OD=0.2) or from overexpression strains at mid log phase (OD=0.2) before or 5 minutes after moderate induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we characterized, when growth conditions decline, CRP activation allows E. coli to devote progressively more of its limited reserves to actively search for better conditions.
This sample is taken from culture subject to 5 minutes induction by anhydrotetracycline.

data_processing: Affymatrix Microarray Suite 5.0

organism: Escherichia coli

source_name: E. coli cell

tag: strain


title: HS 134 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 11 days treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 249 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 24 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 273 human poorly diff. liposarcoma, LiSa-2 cells,  0 hrs no treatment

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 248 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 24 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 133 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 0 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: flagellar regulon study(overexpression control1)

description:
This study examined the genes under the control of FlhDC and sigmaF in E. coli. Under defined steady-state growth condition, we used two different genetic approaches to alter the modulator concentration in cells; (1) moderately expressing FlhDC or sigmaF from anhydrotetracycline (aTc) inducible and Tet repressor-controlled PLtet promoter in a plasmid-borne flhDC or fliA gene; (2) disrupting the expression of FlhDC or sigmaF in flhDC or fliA deletion mutant strains. Samples were taken from culture with wild-type or deletion strains at mid log phase (OD=0.2) or from overexpression strains at mid log phase (OD=0.2) before or 5 minutes after moderate induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we characterized, when growth conditions decline, CRP activation allows E. coli to devote progressively more of its limited reserves to actively search for better conditions.
This sample is taken from pre-induction culture to serve as control (0 minutes induction).


title: HS 251 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 11 days treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: flagellar regulon study (sigmaF deletion2)

description:
This study examined the genes under the control of FlhDC and sigmaF in E. coli. Under defined steady-state growth condition, we used two different genetic approaches to alter the modulator concentration in cells; (1) moderately expressing FlhDC or sigmaF from anhydrotetracycline (aTc) inducible and Tet repressor-controlled PLtet promoter in a plasmid-borne flhDC or fliA gene; (2) disrupting the expression of FlhDC or sigmaF in flhDC or fliA deletion mutant strains. Samples were taken from culture with wild-type or deletion strains at mid log phase (OD=0.2) or from overexpression strains at mid log phase (OD=0.2) before or 5 minutes after moderate induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we characterized, when growth conditions decline, CRP activation allows E. coli to devote progressively more of its limited reserves to actively search for better conditions.
This sample is taken from fliA deletion strain at mid-log phase.


title: HS 131 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 0 hrs treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: flagellar regulon study (wild-type control3)

description:
This study examined the genes under the control of FlhDC and sigmaF in E. coli. Under defined steady-state growth condition, we used two different genetic approaches to alter the modulator concentration in cells; (1) moderately expressing FlhDC or sigmaF from anhydrotetracycline (aTc) inducible and Tet repressor-controlled PLtet promoter in a plasmid-borne flhDC or fliA gene; (2) disrupting the expression of FlhDC or sigmaF in flhDC or fliA deletion mutant strains. Samples were taken from culture with wild-type or deletion strains at mid log phase (OD=0.2) or from overexpression strains at mid log phase (OD=0.2) before or 5 minutes after moderate induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we characterized, when growth conditions decline, CRP activation allows E. coli to devote progressively more of its limited reserves to actively search for better conditions.
This sample is taken from wild-type strain at mid-log phase to serve as control.


title: anx/anx versus wild type hypothalamus replicate 1 dye swap

description: Hypothalamus biological replicate 1 of 3. Technical replicate 2 of 2, with dye reversal. anx/anx versus wild type littermate comparison.


title: anx/anx versus wild type hypothalamus replicate 2 dye swap

description: Hypothalamus biological replicate 2 of 3. Technical replicate 2 of 2, with dye reversal. anx/anx versus wild type littermate comparison.


title: anx/anx versus wild type hypothalamus replicate 1

description: Hypothalamus biological replicate 1 of 3. Technical replicate 1 of 2. anx/anx versus wild type littermate comparison.


title: flagellar regulon study(flhDC deletion3)

description:
This study examined the genes under the control of FlhDC and sigmaF in E. coli. Under defined steady-state growth condition, we used two different genetic approaches to alter the modulator concentration in cells; (1) moderately expressing FlhDC or sigmaF from anhydrotetracycline (aTc) inducible and Tet repressor-controlled PLtet promoter in a plasmid-borne flhDC or fliA gene; (2) disrupting the expression of FlhDC or sigmaF in flhDC or fliA deletion mutant strains. Samples were taken from culture with wild-type or deletion strains at mid log phase (OD=0.2) or from overexpression strains at mid log phase (OD=0.2) before or 5 minutes after moderate induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we characterized, when growth conditions decline, CRP activation allows E. coli to devote progressively more of its limited reserves to actively search for better conditions.
This sample is taken from flhDC deletion strain at mid-log phase.


title: flagellar regulon study(sigmaF overexpression3)


title: flagellar regulon study (sigmaF deletion1)


title: HS 132 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 0 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: flagellar regulon study(flhDC deletion2)


title: flagellar regulon study(overexpression control2)


title: flagellar regulon study (overexpression control3)


title: HS 125 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 11 days treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 130 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 0 hrs treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: flagellar regulon study (sigmaF overexpression2)


title: flagellar regulon study (wild-type control2)


title: HS 124 human poorly diff. liposarcoma, LiSa-2 cells,  11 days no treatment

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: flagellar regulon study (sigmaF deletion3)


title: HS 129 human poorly diff. liposarcoma, LiSa-2 cells,  0 hrs no treatment

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: HS 127 human poorly diff. liposarcoma, LiSa-2 cells, DMSO+CDDO 11 days treated replicate 1

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: flagellar regulon study (wild-type control1)

description:
This study examined the genes under the control of FlhDC and sigmaF in E. coli. Under defined steady-state growth condition, we used two different genetic approaches to alter the modulator concentration in cells; (1) moderately expressing FlhDC or sigmaF from anhydrotetracycline (aTc) inducible and Tet repressor-controlled PLtet promoter in a plasmid-borne flhDC or fliA gene; (2) disrupting the expression of FlhDC or sigmaF in flhDC or fliA deletion mutant strains. Samples were taken from culture with wild-type or deletion strains at mid log phase (OD=0.2) or from overexpression strains at mid log phase (OD=0.2) before or 5 minutes after moderate induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we characterized, when growth conditions decline, CRP activation allows E. coli to devote progressively more of its limited reserves to actively search for better conditions.
This sample is taken from wild-type strain at mid-log phase to serve as control


title: HS 128 human poorly diff. liposarcoma, LiSa-2 cells,  6 hrs no treatment

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: anx/anx versus wild type hypothalamus replicate 2

description: Hypothalamus biological replicate 2 of 3. Technical replicate 1 of 2. anx/anx versus wild type littermate comparison.

tag: Hypothalamus tissue from individual postnatal day 16 weanling mice anx/anx mouse (B6C3Fe a/a-anx/J strain)

tag: Hypothalamus tissue from individual postnatal day 16 weanling mice wild type mouse (B6C3Fe a/a-anx/J strain)


title: MG63 IN2

type: genomic

city: Toronto

first: Bekim

last: Sadikovic

state: Ontario

address: 555 University Avenue

country: Canada

institute: The SickKids Hospital and Princess Margaret Hospital

description: Input DNA - Replicate 2

hyb_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx) at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada)

data_processing: The Me-DIP-chip .cel files for HOB, U2OS and MG63 (2 IP and 2 IN) were log2 transformed, normalized and imported into Partek Genomic Suite Software as previously described [ Sadikovic B, Andrews J, Carter D, Robinson J, Rodenhiser DI (2008) Genome-wide H3K9 histone acetylation profiles are altered in benzopyrene-treated MCF7 breast cancer cells. J Biol Chem 283: 4051-4060]. We baseline normalized the signal using the matched-pair normalization tool in PGS, by subtracting log2 IN signal intensity at each of 4.2 million from cell type-matched IP signals resulting in 6  corrected datasets (IP1 cor. and IP2 cor. for each cell line). In order to determine the relative enrichment of IP cor. signals in U2OS or MG63 relative to  HOB, we used the PGS 1-way ANOVA tool and calculated the fold change using the geometric mean (for log-transformed data).  Thus generated signals represented baseline-normalized, HOB-relative, and cancer cell-specific enrichment levels for each of 4.2 million probes. Significant region detection (both enrichment/hypermethylation and depletion/hypomethylation) was performed using Hidden Markov Model (HMM) tool in PGA by applying it to the fold change data for both U2OS and MG63. In order to capture significant differences in enrichment in each cancer cell line vs. HOB across shorter genomic regions (min. ~350 nucleotides) with robust enrichment differences as well as intermediate (min. ~500 nucleotides) and large regions (min. 1400 nucleotides), three HMM algorithms were applied (s-HMM, m-HMM, and l-HMM). Following cutoffs were used: s-HMM (min. probes: 10, detection states: -5,5, ignore state: 0, max. probability: 0.99, genomic decay: 10,000, sigma: 2), m-HMM (min. probes: 15, detection states: -3,3, ignore state: 0, max. probability: 0.99, genomic decay: 10,000, sigma: 1), and l-HMM  (min. probes: 40, detection states: -1.5,1.5, ignore state: 0, max. probability: 0.99, genomic decay: 10,000, sigma: 1). Significantly enriched/hypermethylated and depleted/hypomethylated HMM regions were annotated to the corresponding genes present on the Affymetrix Gene 1.0 Array using the  HuGene-1_0-st-v1.na24.hg18.transcript.csv file. Normalized data provided as Series supplementary file.

label: streptavidin/phycoerythrin

molecule: genomic DNA

source_name: OS cell line 2

growth_protocol: The human OS cell lines U2OS (ATCC # HTB-96) and MG63 (ATCC # CRL-1427) were purchased from American Type Culture Collection ATCC (Rockville, MD) and maintained in alpha-Minimum Essential Medium (alpha-MEM) supplemented with 10% heat inactivated Fetal Bovine Serum and 2 mM L-Glutamine. Normal human osteoblasts (HOB) are primary osteoblasts from the hip bone of a normal male donor that were purchased from PromoCell (Heidelberg, Germany, Catalogue # C-12760) and maintained in medium provided by the manufacturer and used at culture passage 3. Three days after plating (~80% confluent), cells where harvested for DNA or RNA extractions.

extract_protocol: DNA was extracted by phenol-chloroform extraction and subsequent precipitation in 100% ethanol. DNA precipitate was washed with 70% ethanol then eluted in DNAse free water

treatment_protocol: Cells were harvested with Trypsin (Invitrogen) as per manifacturer's instructions

tag: MG63 cell line (ATCC # CRL-1427)


title: MG63 IN1

description: Input DNA - Replicate 1

scan_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx) at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada)


title: MG63 IP2

description: Methyl-Cytosine Immunoprecipitated fraction - Replicate 2

label_protocol: The uracil glycosilase treatment, streptavidin/phycoerythrin labeling, hybridization and microarray scanning were performed as per Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/products/arrays/specific/human_promoter.affx) at The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, ON, Canada)


title: MG63 IP1

description: Methyl-Cytosine Immunoprecipitated fraction - Replicate 1


title: U2OS IN2

description: Input DNA - Replicate 2

source_name: OS cell line 1

tag: U2OS cell line (ATCC # HTB-96)


title: U2OS IP2


title: U2OS IN1

description: Input DNA - Replicate 1


title: U2OS IP1


title: HS 126 human poorly diff. liposarcoma, LiSa-2 cells, DMSO 11 days treated replicate 2

description: Poorly diff. liposarcoma, LiSa-2 cells.


title: flagellar regulon study (FlhDC deletion1)


title: WT-Cy5 vs WT-CoCl2-Cy3 - repeat 3 - mAdbID:72628

first: Yun

last: Chang

address: 10 Center Dr.

description: mAdb experiment ID: 72628

hyb_protocol: Sample Hybridization Protocol Other: Buffer (30 mM sodium citrate, 300 mM sodium chloride, 50% formamide, 0.4% SDS, pH 7.0) was held at 42ºC. Twenty five µl was added to each sample along with 3 µl of 1:1 salmon sperm/tRNA blocker, heated for 2 min at 98ºC, centrifuged for 3 min at 14,000 x g, and then 50 µl was transferred into a microarray hybridization chamber (MAUI Mixer, Biomicro Systems). After overnight hybridization at 45ºC, slides were inserted into a jig and submerged in Buffer A, comprised of 1X SSC and 0.05% SDS. The adhesive MAUI Mixer lid was removed and the slide was placed in a rack in a jar containing fresh Buffer A. Once all slides were in the rack, they were agitated for 1 min, transferred to fresh Buffer A, agitated 2 min, transferred to Buffer B (0.1X SSC) for 2 min and then into fresh Buffer B. Slides were centrifuged for 5 min starting at 220 rpm and increasing to 580 rpm in increments of approximately 100 rpm. Once dry, the slides were removed from the centrifuge and scanned on a GenePix4000B Scanner (Axon Instruments/Molecular Devices).

scan_protocol: Creator: GenePix Pro 6.0.0.74 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 3;; 3.69 Temperature: 31.09

data_processing:
Data Processing Protocol
Calculation Method: Default Ratio: ChanB/ChanA (Cy5/Cy3). Signal calculation: Mean Intensity minus Median Background. Any Features designated Control were excluded. Normalization method: 50th Percentile (Median) using all spot filtered Genes. Spot Filter Options: Include Spots not flagged BAD or Not Found AND Target diameter >= 50 um AND Target diameter <= 300 um AND Both Chan A and Chan B Percentage of Target Pixels Saturated <= 50% AND Both Chan A and Chan B Signal/Background Ratios >= 2.000 Override other Chan A & B criteria and Include if Chan A Signal >= 5000 OR Chan B Signal >= 5000. Data was extracted and aligned by the Inventory Well ID. Any multiple occurrences of Well ID were reduced to a single instance by selecting the one with the strongest signal (Chan A + Chan B). Note: For all GenePix results from Axon scanned arrays Chan A is CY3 and Chan B is CY5.

organism: Cryptococcus neoformans

source_name: WT Control - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: cDNA labelled with Cyanine 5 (Cy5) (Amersham, Piscataway, NJ) was synthesized with FairplayII Microarray Labelling Kit (Stratagene, La Jolla, CA) according to manufacturer’s manual.

extract_protocol:
Sample Extraction Protocol
Other: RNA was extracted from yeast cells using Trizol (Invitrogen, Carlsbad, CA), treated with RNAse-free DNase (Ambion, Austin, TX) for the removal of genomic DNA, and purified with RNeasy MinElute cleanup kit (Qiagen, Valencia, CA).

tag: Strain

source_name: CoCl2 Treated WT - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: cDNA labelled with Cyanine 3 (Cy3) (Amersham, Piscataway, NJ) was synthesized with FairplayII Microarray Labelling Kit (Stratagene, La Jolla, CA) according to manufacturer’s manual.

treatment_protocol:
Treatment type: compound
Agent: CoCl2
Treatment dose: 0.6 mM
Treatment time: 2 hrs
Treatment temperature: 30C
In-vivo treatment: Overnight cultures of wild-type (B-3501A) strain was refreshed and grown in YES for 5 h and incubated for an additional 2 h in the presence of 0.6 mM CoCl2.


title: C33KD2_with doxycycline_3

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

institute: CABIMER

description: No further information

hyb_protocol: Mycroarrays were hybridized using the Agilent 60-mer oligo microarray processing protocol. Version 4.1. April 2004.

scan_protocol: The microarrays were scanned on an Agilent G2565 scanner (Agilent Technologies) and images were extracted and quality assessed with the Agilent Feature Extraction software (Agilent Technologies), using "Lowess" processing.

data_processing: Data from individual hybridizations were normalized using the RMA algorithm, and the data were then further analyzed using the microarray software package Genespring GX 7.3software (Agilent Technologies).

source_name: Pool stratagene human

label_protocol: Standard Agilent protocol for use with 11K, 22K, and 44K Agilent oligo microarrays. Version 4.0.1 February 2006. Agilent Low RNA Input Fluorescent Linear Amplification Kit was used.

extract_protocol: Commercial

tag: Stratagene Human Universal Reference Pool

source_name: C33KD2 cells with doxycycline

extract_protocol: Total RNA isolation using RNAeasy from QIAGEN.

treatment_protocol: Control cells cultured during 48 hours without doxycycline.

tag: C33KD2 is a stable clone derived from C33 cervical carcinoma cell line. These cells express a shRNA that knockdown the expression of the gene CHD8. Expression of the shRNA is induced upon addition of doxycycline.


title: WT-Cy3 vs WT-CoCl2-Cy5 - repeat 2 - mAdbID:72575

description: mAdb experiment ID: 72575

scan_protocol: Creator: GenePix Pro 6.0.0.74 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.99;; 3.68 Temperature: 30.78

source_name: WT Control - Cy3

source_name: CoCl2 Treated WT - Cy5


title: WT-Cy5 vs WT-CoCl2-Cy3 - repeat 2 - mAdbID:72576

description: mAdb experiment ID: 72576

scan_protocol: Creator: GenePix Pro 6.0.0.74 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.99;; 3.7 Temperature: 31.06


title: WT-Cy3 vs WT-CoCl2-Cy5 - repeat 3 - mAdbID:72627

description: mAdb experiment ID: 72627

scan_protocol: Creator: GenePix Pro 6.0.0.74 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 3;; 3.69 Temperature: 30.9


title: C33KD2_with doxycycline_2

description: No further information

treatment_protocol: Cells cultured during 48 hours with doxycycline.


title: WT-Cy3 vs WT-CoCl2-Cy5 - repeat 4 - mAdbID:74064

description: mAdb experiment ID: 74064

scan_protocol: Creator: GenePix Pro 6.0.0.74 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.99;; 2.88 Temperature: 32


title: WT-Cy5 vs WT-CoCl2-Cy3 - repeat 1 - mAdbID:71926

description: mAdb experiment ID: 71926

scan_protocol: Creator: GenePix Pro 6.0.0.74 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.94;; 3.36 Temperature: 26.3


title: WT-Cy3 vs WT-CoCl2-Cy5 - repeat 1 - mAdbID:71925

description: mAdb experiment ID: 71925

scan_protocol: Creator: GenePix Pro 6.0.0.74 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.94;; 3.49 Temperature: 25.5


title: E12.5 XX Gata4ki/ki gonad-mesonephros

city: Hanover

first: Sergei

middle: G

last: Tevosian

state: NH

address: 7400 Hinman Box

department: Genetics

institute: Dartmouth Medical School

description: Gonad-mesonephric complexes from E12.5 XX Gata4ki/ki embryos

hyb_protocol: Biotinylated cRNA products were hybridized to Affymetrix GeneChip mouse arrays for 16 h at 40°C in a Gene Chip Hybridization oven 640 using the manufacturer's hybridization buffer (Affymetrix).

scan_protocol: After hybridization, the arrays were washed and stained using the Fluidics Station 450 (Affymetrix). Chips were scanned with the 7G Affymetrix Gene Scanner (Affymetrix) according to manufacturer's recommendation.

data_processing: MAS5.0 algorithm

source_name: E12.5 XX Gata4ki/ki gonad-mesonephros

label_protocol: Synthesized cRNA were labeled during transcription (Megascript system; Ambion) with biotin-11–cytidine triphosphate and biotin-16–uridine triphosphate (Enzo Diagnostics).

extract_protocol: Total RNA isolated from the 6 pairs of Gata4ki/ki complexes using RNeasy Mini kit (Qiagen). Total RNA quantity was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc.)

treatment_protocol: Gonad-mesonephric complexes were dissected from E12.5 XX Gata4ki/ki embryos

tag: Age

tag: Tissue

value: Gonad-mesonephros


title: C33KD2_without doxycycline_1

description: No further information

source_name: C33KD2 cells without doxycycline


title: WT-Cy5 vs WT-CoCl2-Cy3 - repeat 4 - mAdbID:74065

description: mAdb experiment ID: 74065

scan_protocol: Creator: GenePix Pro 6.0.0.74 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.87;; 2.87 Temperature: 31.15


title: Nasopharyngeal carcinoma common reference 22

status: Public on Apr 21 2009

city: Shanghai

first: xuping

last: fu

country: China

institute: Institute of Genetics, Fudan University

description: nasopharyngeal carcinoma versus nasopharyngeal phlogistic tissue reference

hyb_protocol: The probe was dissolved in 20 ml of hybridization solution (5xSSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide). Microarrays were pre-hybridized with a hybridization solution containing 0.5 mg/ml of denatured salmon sperm DNA at 421C for 6 h. Fluorescent probe mixtures were denatured at 951C for 5 min and then applied onto the pre-hybridized chip under a cover glass. Chips were hybridized at 421C for 15–17 h. Next, the hybridized chips were each washed at 601C for 10 min in solutions of 2xSSC and 0.2% SDS, 0.1xSSC and 0.2% SDS, 0.1xSSC and then dried at room temperature.

scan_protocol: The chips were scanned with a ScanArray 4000 (GSI Lumonics, Bellerica, MA, USA) at two wavelengths, 635 and 532 nm, to detect emission from both Cy5 and Cy3, respectively. The acquired images were analyzed using GenePix Pro 3.0 software.

data_processing: Value is the normalized ratio of the median of Channel 1 (635 nm) to Channel 2 (532 nm) using LOWESS strategy

source_name: nasopharyngeal carcinoma

label_protocol: The fluorescent cDNA probes were prepared through reverse transcription of the isolated mRNAs and then purified. The RNA samples from nasopharyngeal carcinoma patients were labeled with Cy5-dUTP.

extract_protocol: All nasopharyngeal carcinoma specimens were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and then were homogenized in TRIzol (GibcoBRL, Grand Island, NY). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol for 2 hours at 4°C. Pellet the RNA by centrifugation for 10min at 4°C in a microcentrifuge. Carefully pour off the isopropanol without dislodging the RNA pellet. Remove all of the residual isopropanol with a pipet and dissolve RNA in Milli-Q H2O.

tag: nasopharyngeal carcinoma

source_name: nasopharyngeal phlogistic tissue

label_protocol: The fluorescent cDNA probes were prepared through reverse transcription of the isolated mRNAs and then purified. The RNA samples from nasopharyngeal phlogistic mixed tissue were labeled with Cy3-dUTP.

extract_protocol: All nasopharyngeal phlogistic tissue were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and then were homogenized in TRIzol (GibcoBRL, Grand Island, NY). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol for 2 hours at 4°C. Pellet the RNA by centrifugation for 10min at 4°C in a microcentrifuge. Carefully pour off the isopropanol without dislodging the RNA pellet. Remove all of the residual isopropanol with a pipet and dissolve RNA in Milli-Q H2O.

tag: nasopharyngeal phlogistic tissue


title: C33KD2_without doxycycline_2

description: No further information


title: Nasopharyngeal carcinoma common reference 20


title: E12.5 gonad-mesonephros normal

description: Gonad-mesonephric complexes from E12.5 XX wild type embryos

source_name: embryonic gonad-mesonephros

extract_protocol: Total RNA isolated from the 6 pairs of wild type complexes using RNeasy Mini kit (Qiagen). Total RNA quantity was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc.)

treatment_protocol: Gonad-mesonephric complexes were dissected from E12.5 XX wild type embryos

tag: Wild-type ovary-mesonephros


title: Nasopharyngeal carcinoma common reference 16


title: Nasopharyngeal carcinoma common reference 15


title: Nasopharyngeal carcinoma common reference 21


title: Nasopharyngeal carcinoma common reference 18


title: Nasopharyngeal carcinoma common reference 19


title: transgenic, biological rep3

status: Public on Apr 30 2009

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

description: Gene expression data from renal primary epithelial cells from transgenic rats.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.1, from SAS. CustomCDF (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp) version 10 instead of CDF file from Affymetrix was used.

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Tubular epithelial cells were cultured on laminin-coated tissue culture plates and maintained in Endothelial Cell Growth Medium (PromoCell, Germany) supplemented with 2%FBS, ECGS, EGF, Hydrocortison and basic Fibroblast Factor.

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

treatment_protocol: Renal primary epithelial cells were isolated  by a sequential filtration method.

tag: SD rat


title: Nasopharyngeal carcinoma common reference 23


title: control, biological rep1

description: Gene expression data from renal primary epithelial cells from control SD rats.

source_name: renal primary epithelial cells from control  rats


title: transgenic, biological rep2

source_name: renal primary epithelial cells from transgenic rats


title: Nasopharyngeal carcinoma common reference 13


title: C33KD2_with doxycycline_1

description: No further information


title: C33KD2_without doxycycline_3

description: No further information


title: Nasopharyngeal carcinoma common reference 17


title: MG63 replicate 2

description: gene expression data from MG63 bioreplicate 2

hyb_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).

data_processing: Data from RNA expression array experiments in the form of .cel files (GCOS 1.3 software) were imported into and analysed using the Partek Genomic Suite Software (PGS). The expression array .cel files for HOB, U2OS, and MG63 (2 arrays each) were imported using PGS Gene Expression Workflow tool (subject to RMA normalization and log2 transformation). The significantly over- and under-expressed genes in U2OS and in MG63 cell lines compared to HOB were detected using 1-way ANOVA tool at p<0.01 and +/- 2-fold enrichment. Significantly over- and under-expressed regions were annotated to the corresponding genes present on the Affymetrix Gene 1.0 Array using the HuGene-1_0-st-v1.na24.hg18.transcript.csv file.

label: TdT labeling kit

extract_protocol: Total RNA from U2OS, MG63 cells and HOB was extracted using the TRIzol reagent method. Cells were washed 3 times by Phosphate Buffer Saline (PBS) and lysed in the culture vessel using TRizol (Invitrogen, Osaka, Japan). 1 ml of TRIzol was used for every 100 mm culture plates an RNase free environment. Chloroform was then added (200 µl for each 1 ml TRIzol) and the samples were centrifuged at high speed for 15 minutes at 4C. The aqueous layer was then transferred into a new tube and RNA was precipitated with iso-propanol followed by one wash using 70% ethanol. The RNA precipitate was then dissolved in 10-15 µl of RNAse free water

treatment_protocol: Cells were harvested with Tripsin (Invitrogen) as per manifacturers instructions


title: transgenic, biological rep1


title: Nasopharyngeal carcinoma common reference 6


title: Nasopharyngeal carcinoma common reference 10


title: U2OS replicate 1

description: gene expression data from U2OS bioreplicate 1

scan_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).


title: CY48_1

status: Public on Apr 09 2009

city: Bures-sur-Yvette

first: Arndt

last: Benecke

address: 35 route des Chartres

department: Integrative Biology

institute: Institut des Hautes Etudes Scientifiques & I.R.I.-CNRS

hyb_protocol: Array hybridization was performed for 16 hrs at 55 oC. Pre-Hybridization, Hybridization, antibody binding and Chemiluminescence reaction were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) following the manufacturer’s protocol (P/N 4339627).

scan_protocol: image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391). Median normalization and Probabilty for a gene to be expressed(A) were calculated with proprietary software.

label: DIG-UTP

source_name: TrHBME cells treated with TNFalpha & IFNgamma after 48H

label_protocol: Digoxigenin-UTP labeled cRNA was generated and amplified from 2 μg of total RNA from each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturer’s protocol(P/N 4365710).

extract_protocol: RNA was extracted from the cell lines using RNeasy Midi Kit (Quiagen) according to the instructions provided by the manufacturer

tag: TrHBME cell line


title: HC24_2

description: TrHBME cells treated with TNFalpha & IFNgamma and hydroxyurea after 24H


title: Nasopharyngeal carcinoma common reference 8


title: HC48_1

source_name: TrHBME cells treated with TNFalpha & IFNgamma and hydroxyurea after 48H


title: HC24_1

source_name: TrHBME cells treated with TNFalpha & IFNgamma and hydroxyurea after 24H


title: Nasopharyngeal carcinoma common reference 4


title: MG63 replicate 1

description: gene expression data from MG63 bioreplicate 1

source_name: OS cell line 1

label_protocol: Labeling, hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 4 (P/N 701880 Rev 4). (http://www.affymetrix.com/support/technical/byproduct.affx?product=hugene-1_0-st-v1).


title: HC24_5

description: TrHBME cells treated with TNFalpha & IFNgamma and hydroxyurea


title: U2OS replicate 2

description: gene expression data from U2OS bioreplicate 2

source_name: OS cell line 2


title: Nasopharyngeal carcinoma common reference 3


title: CY24_5

source_name: TrHBME cells treated with TNFalpha & IFNgamma after 24H


title: Nasopharyngeal carcinoma common reference 9


title: CY24_7

description: TrHBME cells treated with TNFalpha & IFNgamma


title: Nasopharyngeal carcinoma common reference 2


title: Nasopharyngeal carcinoma common reference 5


title: HC24_6


title: Nasopharyngeal carcinoma common reference 11


title: HC24_7


title: control, biological rep2


title: CY24_6


title: U2OS a-CGH replicate 1

description: The Agilent Human Genome CGH microarray 244A (Agilent Technologies, Inc., Palo Alto, USA) were used for the U2OS array-CGH experiments.  Three μg of Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA) and 3 μg of test genomic DNA sample were digested with AluI (5 units) and RsaI (5 units) (Promega) for a minimum of 2 hours at 37C.  Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies).  Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, the reference and sample DNA were labelled with 1.5 - 3 mM Cy3-dUTP or Cy5-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).  Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes.  The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendations; air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software. Dye-swapped duplicate experiments were carried out.

hyb_protocol: Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes.  The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendation and air dried.

scan_protocol: Arrays were scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc).

data_processing: Data were processed using Agilent’s Feature Extraction software protocol for array-CGH data

source_name: U2OS cells

label_protocol: Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, DNA was labelled with 1.5 - 3 mM Cy5-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).

extract_protocol: DNA was extracted after harvesting the cells by Trypsin (Invitrogen) followed by phenol-chloroform extraction and subsequent precipitation in 100% ethanol. DNA precipitate was washed with 70% ethanol then eluted in DNAse free water.

tag: U2OS osteosarcoma cancer cell line (ATCC # HTB-96)

source_name: Normal Human Genomic DNA

label_protocol: Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, DNA was labelled with 1.5 - 3 mM Cy3-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).

extract_protocol: Comercial DNA extracted as per manifacturers instructions - Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA)


title: HU24_5

description: TrHBME cells treated with hydroxyurea

source_name: TrHBME cells treated with hydroxyurea after 24H


title: Nasopharyngeal carcinoma common reference 7


title: HU48_1

description: TrHBME cells treated with hydroxyurea

source_name: TrHBME cells treated with hydroxyurea after 48H


title: Nasopharyngeal carcinoma common reference 1


title: CY24_1


title: HU24_6

description: TrHBME cells treated with hydroxyurea


title: Nasopharyngeal carcinoma common reference 12


title: HU24_4

description: TrHBME cells treated with hydroxyurea


title: HC48_2


title: HC48_3


title: NT24_5

description: Non-treated TrHBME cells

source_name: Non-treated TrHBME cells after 24H


title: NT24_6

description: Non-treated TrHBME cells


title: NT48_1

description: Non-treated TrHBME cells

source_name: Non-treated TrHBME cells after 48H


title: NT24_9

description: Non-treated TrHBME cells


title: NT24_3

description: Non-treated TrHBME cells


title: HC48_4


title: HU24_3

description: TrHBME cells treated with hydroxyurea


title: HC24_3


title: NT24_8

description: Non-treated TrHBME cells


title: CY48_3


title: NT24_4

description: Non-treated TrHBME cells


title: NT24_2

description: Non-treated TrHBME cells


title: NT24_7

description: Non-treated TrHBME cells


title: Nasopharyngeal carcinoma common reference 14

source_name: nasopharyngeal carcinoma


title: U2OS a-CGH replicate 2

tag: Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA)


title: NT24_1

description: Non-treated TrHBME cells


title: CY48_2


title: HC24_4


title: HU24_1

description: TrHBME cells treated with hydroxyurea


title: CY48_4


title: HU48_3

description: TrHBME cells treated with hydroxyurea


title: CY24_3


title: HU48_4

description: TrHBME cells treated with hydroxyurea


title: CY24_4


title: HU24_2

description: TrHBME cells treated with hydroxyurea


title: CY24_2


title: NT48_4

description: Non-treated TrHBME cells


title: NT48_2

description: Non-treated TrHBME cells


title: HU48_2

description: TrHBME cells treated with hydroxyurea


title: NT48_3

description: Non-treated TrHBME cells


title: JO3020 hupAB, Min Glucose, exponential phase

status: Public on Jan 01 2009

city: ORSAY

first: Jacques

last: Oberto

address: Université Paris XI, Bâtiment 409, pièce 200

department: CNRS UMR 8621

institute: Instutit de Génétique et Microbiologie

description: JO3020 (hupAB), Min Glucose, exponential phase

hyb_protocol: Biotin-labeled cDNA (2.5μg) was hybridized to E. coli antisense genome arrays (Affymetrix) at 45°C for 16 h as recommended in the GeneChip technical manual (Affymetrix).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Affymetrix .CEL files data were normalized with dChip using the array of median brightness (BS). Model method:model-base expression; background substraction: Mismatch Probe (PM/MM difference)

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

growth_protocol: The five bacterial strains (JO2057, JO2081, JO2083, JO3020 and MW30) were grown in 100ml LB 0.5% NaCl, M9 minimal glucose or M9 minimal glycerol at 200 rpm in New Brunswick laboratory shaker in 2liter flasks. The typical doubling time, observed in exponential phase in LB, was 40min for JO2057, JO2081, JO2083, MW30 and 75 min for JO3020. After growth curve calibration, the various growth phase sample were collected at the following cell densities: exponential phase: OD600 0.6-0.7; transition: 2.2-2.5 and stationary: 4.6-4.8 (3.0 for hupAB).

extract_protocol: Seven mililiter of phenol/water were added before incubating 10 min at 67°C with occasional stirring. The samples were cooled on ice and spun 10 min at 5000 rpm at 4°C. The aqueous phase was separated and extracted again once the same way and then once with phenol/chloroform (v/v 1:1). One tenth of the volume of 4M NaCl and 2.5 volumes of cold ethanol were then added to the aqueous phase. The tubes were left at -20°C for two hours then spun at 8500rpm at 4°C. The pellet was washed with 70% ethanol, dried under vacuum and resuspened in 300l sterile water and transferred to an eppendord tube. An amount of 34.5l Qiagen RDD buffer and 9.37l of RNase free DNase I (Qiagen) were added. After 15min at room temperature, the tubes were mixed by inversion and deproteinized as shown above with 300l phenol/H2O at room temperature. The RNA was then precipitated with 37.5µl NaCl 4M and 823µl cold ethanol. After 2 hours at -20°C, the tubes were centrifuged 30min at 10,000G at 4°C, the pellets were then washed with 70% ethanol then dried under vacuum and resuspended in 60µl sterile water. The RNAs were stored at -20°C.

treatment_protocol: A culture volume of 7ml was mixed with the same volume of boiling 2% SDS, 4mM EDTA and heated at 100°C for 3 to 5 minutes then vortexed. At this stage, the extract was either processed further or stored at -20°C.

tag: JO3020 (hupAB)

tag: exponential phase


title: JO3020 hupAB, Min Glycerol exponential phase

description: JO3020 (hupAB), Min Glycerol exponential phase


title: JO3020 hupAB, LB, exponential phase, repetition1

description: JO3020 (hupAB), LB, exponential phase

source_name: JO3020 (hupAB), exponential phase, repetition1


title: JO3020 hupAB, Min Glucose, stationary phase

description: JO3020 (hupAB), Min Glucose, stationary phase

tag: stationary phase


title: MW30 rpoS, LB, stationary phase

description: MW30 (rpoS), LB, stationary phase

source_name: MW30 (rpoS), LB, stationary phase

tag: MW30 (rpoS)


title: JO3020 hupAB, Min Glycerol stationary phase

description: JO3020 (hupAB), Min Glycerol stationary phase


title: JO2057 WT, Min Glucose, stationary phase

description: JO2057 (WT), Min Glucose, stationary phase


title: JO2057 WT, Min Glycerol, exponential phase

description: JO2057 (WT), Min Glycerol, exponential phase


title: JO2057 WT, Min Glycerol, stationary phase

description: JO2057 (WT), Min Glycerol, stationary phase


title: MW30 rpoS, LB, exponential phase

description: MW30 (rpoS), LB, exponential phase

source_name: MW30 (rpoS), LB, exponential phase


title: JO3020 hupAB, LB, stationary phase, repetition2

description: JO3020 (hupAB), LB, stationary phase

source_name: JO3020 (hupAB), stationary phase, repetition2


title: JO3020 hupAB, LB, exponential phase, repetition2

description: JO3020 (hupAB), LB, exponential phase

source_name: JO3020 (hupAB), exponential phase, repetition2


title: JO2083 hupB, LB, transition phase

description: JO2083 (hupB), LB, transition phase

source_name: JO2083 (hupB), transition phase

tag: JO2083 (hupB)

tag: transition phase


title: JO2057 WT, Min Glucose, exponential phase

description: JO2057 (WT), Min Glucose, exponential phase


title: JO2083 hupB, LB, exponential phase

description: JO2083 (hupB), LB, exponential phase

source_name: JO2083 (hupB), exponential phase


title: JO2083 hupB, LB, stationary phase

description: JO2083 (hupB), LB, stationary phase

source_name: JO2083 (hupB), stationary phase


title: JO3020 hupAB, LB, stationary phase, repetition1

description: JO3020 (hupAB), LB, stationary phase

source_name: JO3020 (hupAB), stationary phase, repetition1


title: JO3020 hupAB, LB, transition phase

description: JO3020 (hupAB), LB, transition phase

source_name: JO3020 (hupAB), transition phase


title: JO2057 WT, LB, stationary phase, repetition2

description: JO2057 (WT), LB, stationary phase

source_name: JO2057 (WT), stationary phase, repetition2


title: JO2081 hupA, LB, stationary phase

description: JO2081 (hupA), LB, stationary phase

source_name: JO2081 (hupA), stationary phase

tag: JO2081 (hupA)


title: JO2057 WT, LB, exponential phase, repetition2

description: JO2057 (WT), LB, exponential phase

source_name: JO2057 (WT), exponential phase, repetition2


title: JO2057 WT, LB, exponential phase, repetition1

description: JO2057 (WT), LB, exponential phase

source_name: JO2057 (WT), exponential phase, repetition1


title: Adult_DMSO-treated_24h_5ml/kg_rep3

first: Yuriy

middle: O.

last: Alekseyev

state: MA

address: 77 Massachusetts ave, bldg. 56-686

department: BE

description: Adult mice were treated i.p. with a single dose of DMSO (5 ml/kg) and sacrificed 24h after treatment

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Log (base 2) transformed, RMA normalized across adult DMSO-treated (n=3) and AFB1-treated (n=3) replicates (5 ml/kg, sacrificed 24 h after treatment)

source_name: Adult, DMSO-treated (5 ml/kg), sacrificed 24 hours after treatment

label_protocol: Affymetrix

extract_protocol: Qiagen RNeasy

treatment_protocol: Single i.p. treatment with 5 ml/kg of DMSO

tag: Strain

value: B6C3F1, Gender:male, Tissue:liver, Age:adult (60-80 days)


title: JO2081 hupA, LB, exponential phase

description: JO2081 (hupA), LB, exponential phase

source_name: JO2081 (hupA), exponential phase


title: Adult_DMSO-treated_24h_5ml/kg_rep1


title: JO2081 hupA, LB, transition phase

description: JO2081 (hupA), LB, transition phase

source_name: JO2081 (hupA), transition phase


title: JO2057 WT, LB, transition phase

description: JO2057 (WT), LB, transition phase

source_name: JO2057 (WT), transition phase


title: JO2057 WT, LB, stationary phase, repetition1

description: JO2057 (WT), LB, stationary phase

source_name: JO2057 (WT), stationary phase, repetition1


title: Adult_DMSO-treated_24h_5ml/kg_rep2


title: Adult_DMSO-treated_24h_rep1

description: Adult mice were treated i.p. with a single dose (10 ml/kg) of DMSO and sacrificed 24h after treatment

data_processing: Log (base 2) transformed, RMA (quantile) normalized across adult AFB1-treated (n=3) and DMSO-treated (n=3) replicates (sacrificed 24 h after treatment)

source_name: Adult, DMSO-treated, sacrificed 24 hours after treatment

treatment_protocol: Single i.p. treatment with 10 ml/kg DMSO


title: Adult_DMSO-treated_4h_rep3

description: Adult mice were treated i.p. with a single dose (10 ml/kg) of DMSO and sacrificed 4h after treatment

data_processing: Log (base 2) transformed, RMA (quantile) normalized across adult AFB1-treated (n=3) and DMSO-treated (n=3) replicates (sacrificed 4 h after treatment)

source_name: Adult, DMSO-treated, sacrificed 4 hours after treatment


title: Adult_AFB1-treated_24h_5ml/kg_rep2

description: Adult mice were treated i.p. with a single dose of AFB1 (6 mg/kg in 5 ml/kg DMSO)and sacrificed 24h after treatment

source_name: Adult, AFB1-treated (6 mg/kg in 5 ml/kg DMSO), sacrificed 24 hours after treatment

treatment_protocol: Single i.p. treatment with 6 mg/kg of Aflatoxin B1 in 5 ml/kg DMSO


title: Adult_AFB1-treated_4h_5ml/kg_rep1

description: Adult mice were treated i.p. with a single dose of AFB1 (6 mg/kg in 5 ml/kg DMSO)and sacrificed 4h after treatment

data_processing: Log (base 2) transformed, RMA normalized across adult DMSO-treated (n=3) and AFB1-treated (n=3) replicates (sacrificed 4 h after treatment)

source_name: Adult, AFB1-treated (5 ml/kg), sacrificed 4 hours after treatment


title: Adult_AFB1-treated_24h_5ml/kg_rep3


title: Adult_AFB1-treated_4h_5ml/kg_rep2

data_processing: Log (base 2) transformed, RMA normalized across adult DMSO-treated (n=3) and AFB1-treated (n=3) replicates (5 ml/kg, sacrificed 4 h after treatment)

source_name: Adult, AFB1-treated (6 mg/kg in 5 ml/kg DMSO), sacrificed 4 hours after treatment


title: Adult_DMSO-treated_4h_rep1

source_name: Adult, DMSO -treated, sacrificed 4 hours after treatment


title: Adult_AFB1-treated_24h_5ml/kg_rep1


title: Adult_DMSO-treated_24h_rep2


title: Adult_AFB1-treated_4h_rep3

description: Adult mice were treated i.p. with a single dose (6 mg/kg) of AFB1 and sacrificed 4h after treatment

source_name: Adult, AFB1-treated, sacrificed 4 hours after treatment

treatment_protocol: Single i.p. treatment with 6 mg/kg of Aflatoxin B1 in 10 ml/kg DMSO


title: Adult_AFB1-treated_4h_rep2

description: adult mice were treated i.p. with a single dose (6 mg/kg) of AFB1 and sacrificed 4h after treatment


title: Adult_DMSO-treated_24h_rep3

tag: Adult, DMSO-treated, sacrificed 24 hours after treatment


title: Adult_DMSO-treated_4h_5ml/kg_rep3

description: Adult mice were treated i.p. with a single dose of DMSO (5 ml/kg) and sacrificed 4h after treatment

source_name: Adult, DMSO-treated (5 ml/kg), sacrificed 4 hours after treatment


title: Adult_DMSO-treated_4h_5ml/kg_rep2


title: Adult_AFB1-treated_4h_5ml/kg_rep3


title: Adult_AFB1-treated_24h_rep1

source_name: Adult, AFB1-treated, sacrificed 24 hours after treatment


title: Adult_AFB1-treated_24h_rep2


title: Adult_AFB1-treated_24h_rep3


title: 4day_DMSO-treated_24h_rep1

description: 4-day-old mice were treated i.p. with a single dose (10 ml/kg) of DMSO and sacrificed 24h after treatment

data_processing: Log (base 2) transformed, RMA (quantile) normalized across 4-day-old AFB1-treated (n=3) and DMSO-treated (n=3) replicates (sacrificed 24 h after treatment)

source_name: 4-day-old, DMSO-treated, sacrificed 24 hours after treatment

extract_protocol: Affymetrix

value: B6C3F1, Gender:male, Tissue:liver, Age:4 days


title: 4day_DMSO-treated_24h_rep3


title: Adult_AFB1-treated_4h_rep1


title: 4day_DMSO-treated_24h_rep2


title: 4day_AFB1-treated_24h_rep2

description: 4-day-old mice were treated i.p. with a single dose (6 mg/kg) of AFB1 and sacrificed 24h after treatment

data_processing: Log (base 2) transformed, RMA normalized across 4-day-old DMSO-treated (n=3) and AFB1-treated (n=3) replicates (sacrificed 24 h after treatment)

source_name: 4-day-old, AFB1-treated, sacrificed 24 hours after treatment


title: Adaptive remodeling collateral EC gene expression N2

city: Boston

first: Peter

middle: J

last: Mack

address: 77 Avenue Louis Pasteur, NRB-752

department: Pathology

institute: Harvard Medical School

description: Transcriptional profiling was performed with endothelial cells subjected to simulated coronary collateral waveforms using an

hyb_protocol: ABI protocol

scan_protocol: ABI protocol

data_processing: ABI 1700 chemiluminescent microarray system and analyzer.  Post-processing of data with Lowess regression and Z-pool variances was performed with custom statistical software.

label: Digoxigenin

source_name: human umbilical vein endothelial cells, adaptive remodeling collateral EC gene expression N2

label_protocol: Digoxigenin labeling into the cDNA products (ABI protocol)

growth_protocol: Medium-199, 2% FBS, 2 mM L-Glutamine, 100 units/ml penicillin plus 100 m g/ml streptomycin, and 2.8 % dextran (Invitrogen)

extract_protocol: 40 µg of total RNA, extracted using Trizol (Invitrogen) and RNeasy Purication (Quiagen) according to the manufacturer’s instructions

treatment_protocol: Approximately 5e6 endothelial cells were subjected to simulated adaptive remodeling coronary collateral waveforms for 24 hr.

tag: primary human umbilical vein endothelial cells from pooled sources


title: Normal collateral EC gene expression N1

description: Transriptional profiling was performed with endothelial cells subjected to simulated coronary collateral waveforms using an in vitro system in order to characterize the effect of shear stress on vascular remodeling gene expression

source_name: human umbilical vein endothelial cells, normal collateral EC gene expression N1

treatment_protocol: Approximately 5e6 endothelial cells were subjected to simulated normal coronary collateral waveforms for 24 hr.


title: Normal collateral EC gene expression N2

source_name: human umbilical vein endothelial cells, normal collateral EC gene expression N2


title: Normal collateral EC gene expression N3

source_name: human umbilical vein endothelial cells, normal collateral EC gene expression N3


title: 4day_AFB1-treated_4h_rep1

description: 4-day-old mice were treated i.p. with a single dose (6 mg/kg) of AFB1 and sacrificed 4h after treatment

data_processing: Log (base 2) transformed, RMA (quantile) normalized across 4-day-old AFB1-treated (n=3) and DMSO-treated (n=3) replicates (sacrificed 4 h after treatment)

source_name: 4-day-old, AFB1-treated, sacrificed 4 hours after treatment

value: B6C3F1, Gender:male,  Tissue:liver, Age:4 days


title: 4day_AFB1-treated_24h_rep3


title: Adaptive remodeling collateral EC gene expression N1

source_name: human umbilical vein endothelial cells, adaptive remodeling collateral EC gene expression N1


title: 4day_DMSO-treated_4h_rep3

description: 4-day-old mice were treated i.p. with a single dose (10 ml/kg) of DMSO and sacrificed 4h after treatment

source_name: 4-day-old, DMSO-treated, sacrificed 4 hours after treatment


title: Adaptive remodeling collateral EC gene expression N3

source_name: human umbilical vein endothelial cells, adaptive remodeling collateral EC gene expression N3


title: 4day_DMSO-treated_4h_rep1


title: 4day_AFB1-treated_4h_rep3


title: 4day_untreated_4h_rep2

description: Untreated controls: mice were sacrificed at the same time as the treated mice (4h after treatment)

data_processing: Log (base 2) transformed, RMA normalized across 4-day-old (n=3) and adult (n=3) untreated replicates

source_name: 4-day-old, untreated, sacrificed 4 hours after mock-treatment

treatment_protocol: untreated


title: adult_untreated_4h_rep2

source_name: adult, untreated, sacrificed 4 hours after mock-treatment

value: B6C3F1, Gender:male,  Tissue:liver, Age:adult (60-80 days)


title: 4day_untreated_4h_rep3


title: 4day_AFB1-treated_4h_rep2


title: adult_untreated_4h_rep1


title: 4day_AFB1-treated_24h_rep1


title: 4day_untreated_4h_rep1


title: adult_untreated_4h_rep3


title: Pod vs Root TCPRR02

status: Public on Dec 31 2008

city: Lubbock

first: Kameswara Rao

last: Kottapalli

state: TX

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University

description:
Keyword = peanut
Keyword = tissue comparison

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies.

scan_protocol: Standard protocol of GenePix 4000B Microarray Scanner

data_processing: Feature Extraction software Version 9.1 from Agilent Technologies

organism: Arachis hypogaea

source_name: Root_Replication 2

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were field grown under pivot irrigation and tissue samples were harvested on 115 DAS.

extract_protocol: Total RNA was extracted using Qiagen Rneasy Plant Maxi Kit according to manufacturers protocol.

treatment_protocol: No treatment

tag: Samples from root tissues of FR458

source_name: Pod_Replication 2

tag: Samples from pod tissues of FR458


title: Pod vs Root TCPRR01

source_name: Pod_Replication 1

source_name: Root_Replication 1


title: Pod vs Stem TCPSR02

source_name: Stem_Replication 2

tag: Samples from stem tissues of FR458

source_name: pod_Replication 2


title: Pod vs Stem TCPSR01

source_name: Stem_Replication 1


title: True Ad Libitum pool

city: Lincoln

first: preston

middle: w

last: estep

address: PO Box 53

institute: Longenity Inc.

description: Total RNA pool from 3 individual samples

hyb_protocol: Sample cDNA and control cDNA were mixed together with spiked controls and then the mixed sample was hybridized to the microarray surface using a Maui Hybridization System (Biomicro, Salt Lake City, UT).

scan_protocol: Microarrays were scanned at 532 nm and 635 nm wavelengths on an Axon 4000B microarray scanner (Axon Instruments, Union City, CA). Scanned data were collected and processed using GenePix 4.1 software (Axon Instruments, Union City, CA).

data_processing: Genes with median spot intensities below 50 for liver expression for both CR and HIGHCAL were culled from the data set to give a set of 9,550 genes and controls for normalization. These culled data were normalized using the CARMAweb implementation of the limma package for R. Median background was subtracted from median foreground signal using the normexp method followed by loess within-array normalization and then scale between-array normalization. To further eliminate genes near background in these normalized data we set a median expression threshold value of 90 for either CR or HIGHCAL.

source_name: Stratagene Universal Mouse Control RNA

label_protocol: 10 µg of total RNA was labeled directly during cDNA synthesis using the ChipShot labeling and cleanup system (Promega, Madison, WI). Total liver RNA was labeled with Cy3 and control RNA was labeled with Cy5.

growth_protocol: HIGH CALORIE diet consisted of two sub-groups of mice: True Ad Libitum (TAL) and Fixed High Calorie (FHC).  A total of 35 mice were fed 3 specified dietary regimens. Six mice were fed a TAL diet of which they ate as much as they desired, 12 mice were fed calorie-restricted diets of 73 kcals per week (CR), and 17 mice were fed a diet of 110 kcals per week (FHC). TAL mice consumed between 120 and 130 kcal/week. Therefore,  the approximate percent calorie reduction for each fixed-calorie diet relative to TAL is 10% to 15% for FHC and 40% to 45% for CR. Calorie reduction of CR relative to FHC is 34%.

extract_protocol: Liver pieces were homogenized in Qiagen guanidine isothiocyanate lysis buffer, and then subsequent steps were performed according to the Qiagen RNA extraction protocol.

tag: Multi-tissue pool

source_name: Liver

value: ICR (CD1)

tag: Age

value: 9 months

tag: Gender

value: Male


title: Pod vs Root TCPRR03

source_name: Pod_Replication 3

source_name: Root_Replication 3


title: Pod vs Peg TCPPR03

source_name: Peg_Replication 3

tag: Samples from peg tissues of FR458


title: Fixed High Calorie sample 8

description: Individual liver sample


title: Pod vs Peg TCPPR01

source_name: Peg_Replication 1


title: Pod vs Stem TCPSR03

source_name: Stem_Replication 3


title: True Ad Libitum sample 5

description: Individual liver sample


title: Fixed High Calorie pool 2


title: Pod vs Leaf TCPLR03

source_name: Leaf_Replication 3

tag: Samples from leaf tissues of FR458


title: Fixed High Calorie sample 5

description: Individual liver sample


title: Fixed High Calorie pool 1


title: True Ad Libitum sample 6

description: Individual liver sample


title: Fixed High Calorie sample 7

description: Individual liver sample


title: Fixed High Calorie sample 6

description: Individual liver sample


title: True Ad Libitum sample 2

description: Individual liver sample


title: Pod vs Peg TCPPR02

source_name: Peg_Replication 2


title: Fixed High Calorie sample 4

description: Individual liver sample


title: Pod vs Leaf TCPLR01

source_name: Leaf_Replication 1


title: Fixed High Calorie pool 3


title: Pod vs Leaf TCPLR02

source_name: Leaf_Replication 2


title: Fixed High Calorie sample 3

description: Individual liver sample


title: Fixed High Calorie sample 2

description: Individual liver sample


title: Fixed High Calorie sample 1

description: Individual liver sample


title: Val 2_Liver_48H_REV

city: Seattle

first: Allison

last: Mitchell

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson CRC

description: Reverse PCR amplification of the transposon

hyb_protocol: Arrays were hybridized overnight at 65C.  Wash 1: 42C for 5 minutes in 2X SSC + 0.2%SDS, Wash 2: 1 minute in 0.2X SSC +  0.1% SDS, Wash 3: 1 minute in 0.2X SSC, Wash 4 and 5: 0.05X SSC for 1 minute each; all washes were done on shaker at a moderate speed.  Spin at 1,000rpm for 5 minutes.

scan_protocol: Arrays were scanned using Axon Genepix 4000B scanner with Axon Genpix Pro 6.0 software.

data_processing: Data were extracted from Longhorn Array database where duplicate spots per gene were averaged and flagged spots were not included.  Note: Sample data table contains unfiltered data and thus different from the data used for the analysis of the study described in the paper.  Series supplementary file contains filtered data that shows on a per organ/timepoint basis with the ORF comparable across rows.

organism: Francisella tularensis subsp. novicida

source_name: Deposition Validation pool 2

label_protocol: The second, nested PCR was done to incorporate aminoallyl-dUTP and the PCR product was cleaned and labeled (deposition-Cy3, output pool-Cy5).

extract_protocol: Bacterial gDNA were extracted using Wizard genomic DNA preparation kit (Promega) then sequences flanking one side of the transposons in each pool were amplified in a two-step PCR.

tag: Bacterial DNA from lung tissue in C57/BL6 mice

source_name: 48h liver validation pool 2

tag: Bacterial DNA from liver tissue in C57/BL6 mice


title: Val 2_Liver_72H_REV

source_name: 72h liver validation pool 2


title: Val 2_Lung_48H_REV

source_name: 48h lung validation pool 2


title: Val 2_Lung_72H_REV

source_name: 72h lung validation pool 2


title: Calorie Restriction pool 2


title: Val 2_Lung_24H_REV

source_name: 24h lung validation pool 2


title: Val 2_Spleen_48H_REV

source_name: 48h spleen validation pool 2

tag: Bacterial DNA from spleen tissue in C57/BL6 mice


title: Val 2_Spleen_72H_REV

source_name: 72h spleen validation pool 2


title: Calorie Restriction pool 1

source_name: Stratagene Universal Mouse Control RNA

source_name: Liver


title: Val 1_Spleen_72H_REV

source_name: Deposition Validation pool 1

source_name: 72h spleen validation pool 1


title: Val 1_Spleen_48H_REV

source_name: 48h spleen validation pool 1


title: Pool 11_Spleen_72H_FORW

description: Forward PCR amplification of the transposon

source_name: Deposition 288-11


title: Val 1_Liver_48H_REV

source_name: 48h liver validation pool 1


title: Pool 10_Spleen_72H_FORW

source_name: Deposition 288-10


title: Val 1_Lung_72H_REV

source_name: 72h lung validation pool 1


title: Val 1_Lung_48H_REV

source_name: 48h lung validation pool 1


title: Pool 11_Spleen_48H_FORW


title: Val 1_Lung_24H_REV

source_name: 24h lung validation pool 1


title: Val 1_Liver_72H_REV

source_name: 72h liver validation pool 1


title: Calorie Restriction sample 9

description: Individual liver sample


title: Calorie Restriction sample 12

description: Individual liver sample


title: Calorie Restriction sample 3

description: Individual liver sample


title: Calorie Restriction sample 11

description: Individual liver sample


title: Calorie Restriction sample 2

description: Individual liver sample


title: Pool 10_Spleen_48H_FORW


title: Pool 9_Spleen_72H_FORW

source_name: Deposition 288-9

source_name: 72h spleen 288-9


title: Pool 7_Spleen_48H_FORW

source_name: Deposition 288-7

source_name: 48h spleen 288-7


title: Pool 7_Spleen_72H_FORW

source_name: 72h spleen 288-7


title: Pool 5_Spleen_48H_FORW

source_name: Deposition 288-5

source_name: 48h spleen 288-5


title: Pool 4_Spleen_72H_FORW

source_name: Deposition 288-4

source_name: 72h spleen 288-4


title: Pool 5_Spleen_72H_FORW

source_name: 72h spleen 288-5


title: Pool 8_Spleen_48H_FORW

source_name: Deposition 288-8

source_name: 48h spleen 288-8


title: Pool 8_Spleen_72H_FORW

source_name: 72h spleen 288-8


title: Pool 6_Spleen_48H_FORW

source_name: Deposition 288-6

source_name: 48h spleen 288-6


title: Pool 2_Spleen_72H_FORW

source_name: Deposition 288-2

source_name: 72h spleen 288-2


title: Pool 4_Spleen_48H_FORW

source_name: 48h spleen 288-4


title: Pool 9_Spleen_48H_FORW

source_name: Deposition 288-9

source_name: 48h spleen 288-9


title: Pool 6_Spleen_72H_FORW

source_name: 72h spleen 288-6


title: Calorie Restriction sample 10

description: Individual liver sample

source_name: Stratagene Universal Mouse Control RNA

source_name: Liver


title: Pool 3_Spleen_72H_FORW

source_name: Deposition 288-3

source_name: 72h spleen 288-3


title: Pool 10_Liver_72H_FORW

source_name: Deposition 288-10


title: Pool 1_Spleen_72H_FORW

source_name: Deposition 288-1

source_name: 72h spleen 288-1


title: Pool 2_Spleen_48H_FORW

source_name: 48h spleen 288-2


title: Pool 3_Spleen_48H_FORW

source_name: 48h spleen 288-3


title: Pool 11_Liver_72H_FORW

source_name: Deposition 288-11


title: Pool 8_Liver_72H_FORW

source_name: Deposition 288-8


title: Pool 8_Liver_48H_FORW


title: Pool 9_Liver_48H_FORW


title: Pool 1_Spleen_48H_FORW

source_name: 48h spleen 288-1


title: Pool 11_Liver_48H_FORW


title: Pool 10_Liver_48H_FORW


title: Pool 7_Liver_72H_FORW

source_name: Deposition 288-7


title: Pool 6_Liver_72H_FORW

source_name: Deposition 288-6


title: Pool 5_Liver_72H_FORW

source_name: Deposition 288-5


title: Pool 6_Liver_48H_FORW


title: Pool 7_Liver_48H_FORW


title: Pool 2_Liver_72H_FORW

source_name: Deposition 288-2


title: Pool 4_Liver_48H_FORW

source_name: Deposition 288-4


title: Pool 3_Liver_48H_FORW


title: Pool 3_Liver_72H_FORW


title: Pool 1_Liver_72H_FORW


title: Pool 11_Lung_72H_FORW


title: Pool 10_Lung_72H_FORW


title: Pool 1_Liver_48H_FORW


title: Pool 10_Lung_24H_FORW


title: Pool 2_Liver_48H_FORW


title: Pool 4_Liver_72H_FORW


title: Pool 9_Lung_72H_FORW

source_name: Deposition 288-9


title: Pool 11_Lung_24H_FORW


title: Pool 9_Lung_24H_FORW


title: Pool 10_Lung_48H_FORW


title: Pool 9_Lung_48H_FORW


title: Pool 8_Lung_48H_FORW


title: Pool 8_Lung_24H_FORW


title: Pool 11_Lung_48H_FORW


title: Pool 7_Lung_48H_FORW


title: Pool 8_Lung_72H_FORW


title: Pool 7_Lung_72H_FORW


title: Pool 5_Liver_48H_FORW


title: Pool 7_Lung_24H_FORW


title: Pool 6_Lung_72H_FORW


title: Pool 6_Lung_24H_FORW


title: Pool 6_Lung_48H_FORW


title: Pool 5_Lung_72H_FORW


title: Pool 5_Lung_48H_FORW