title: 13415240 - RIL 136 vs RIL 183

hyb_protocol: RIL 183 Cy5 / RIL 136 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: 13415386 - RIL 118 vs RIL 359

status: Public on Jun 05 2009

type: RNA

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: WP3 : Biodiversity of seed traits : state of the art

hyb_protocol: RIL 359 Cy5 / RIL 118 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 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

molecule: total RNA

organism: Arabidopsis thaliana

source_name: RIL 359

label_protocol: labelling Cy3 and Cy5 direct, 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: silique and seed - Media : soil (growth chamber) Hygrometry : 65% Temperature : 25degreeC Light : long day (5h-21h, harvest at 13h)

treatment_protocol: no treatment

tag: ecotype

value: arabidopsis thaliana (ril bay-0 x shahdara)

tag: age

value: 10 days after pollinisation

source_name: RIL 118

value: 10 days after pollination


title: High MK bulked F2 vs. Low MK bulked F2 Replicate 4

city: Rehovot

first: Imri

last: Ben-Israel

address: P.O box 12

department: Institute of Plant Sciences and Genetics in Agriculture

country: Israel

institute: Hebrew University

description:
Technical replicate (Dye swap) 2
Solanum lycopersicum var M82 X  Solanum habrochaites f. glabratum (accession PI126449)

hyb_protocol: The labeled aRNA samples were hybridized on to a Custom Tomato Gene Expression 4x44k (AMADID:19003). 825ng of cy3 labeled  samples and 825ng of cy5 labeled samples were pooled, fragmented and hybridized and data from these channels were used for comparison to test hybridizations of respective channels.  Fragmentation of labeled aRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

scan_protocol: Scanned on an Agilent G2565AA scanner. Hybridized arrays were scanned at 5μm resolution on an Agilent Microarray Scanner, Model G2565BA

data_processing: Feature extracted data was analyzed using GeneSpring Gx v 7.3.1 software from Agilent. The normalization was done using GeneSpring GX using the recommended Per Spot and Per Chip:Intensity dependent (Lowess) normalization. Fold change (log2 ratio) for each of the experiment were generated from Lowess normalized signals.

organism: Solanum lycopersicum x Solanum habrochaites

source_name: Tomato leaf trichomes

label_protocol: The  samples for Gene expression were labeled using Agilent Low RNA Input Linear amplification Kit (Part number:5184-3523).  Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 42°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for aRNA generation. aRNA was generated by in vitro transcription and Cy5 CTP(Agilent) for test samples was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled aRNA was cleaned up and quality assessed for yields and specific activity

growth_protocol: Plants were growth  in a net house during summer  in 15 litters pots.

extract_protocol: Qiagene RNeasy Plant Mini Kit,  following manufacturer's instructions

tag: mk levels

value: Low MK bulked F2 plants

tag: tissue

value: leaf trichome

source_name: Tomato leafe trichomes

value: High MK bulked F2 plants


title: 13415237 - RIL 349 vs RIL 173

hyb_protocol: RIL 173 Cy5 / RIL 349 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 173

source_name: RIL 349


title: 13415238 - RIL 180 vs RIL 309

hyb_protocol: RIL 309 Cy5 / RIL 180 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 309

source_name: RIL 180


title: 13415234 - RIL 267 vs RIL 170

hyb_protocol: RIL 170 Cy5 / RIL 267 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 170

source_name: RIL 267


title: 13415235 - RIL 173 vs RIL 349

hyb_protocol: RIL 349 Cy5 / RIL 173 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: High MK bulked F2 vs. Low MK bulked F2 Replicate 3

description:
Biological replicate 2
Solanum lycopersicum var M82 X  Solanum habrochaites f. glabratum (accession PI126449)


title: High MK bulked F2 vs. Low MK bulked F2 Replicate 1

description:
Biological replicate 1
Solanum lycopersicum var M82 X  Solanum habrochaites f. glabratum (accession PI126449)


title: 13415230 - RIL 170 vs RIL 267

hyb_protocol: RIL 267 Cy5 / RIL 170 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: Lymphocytes_non-radiated2 (002)

city: Las Palmas de Gran Canaria

first: Luis

last: Henriquez

state: Las Palmas

address: C/ Dr. Pasteur s/n

country: Spain

institute: University of Las Palmas de Gran Canaria

description: no additional information

hyb_protocol: Then mixed with 40 µl of the hybridization buffer supplied by the Pronto System (Corning). The labeled probe mix was added to the array and placed in a sealed hybridization chamber (Corning, NY) for 15–18 h at 65 C, after which the array was washed and dried.

scan_protocol: The arrays were scanned immediately using a GenePix scanner (Axon Instruments, Union City, CA).

data_processing: Image analysis was performed using the GenePix Pro 6.0 software (Axon Instruments). Automatic flagging was used to localize absent or very weak spots (<2 times above background), which were excluded from analysis. Fluorescence (Cy5/Cy3) ratios were normalized using the LOWESS (Locally Weighted Scatter Plot Smoother) method in the Acuity 4.0 software package (Molecular Devices, Union City, CA)

organism: Homo sapiens

source_name: Peripheral Blood Lymphocytes from Advanced Breast Cancer Patients

label_protocol: Total lymphocyte RNA (5 µg) was treated with deoxyribonuclease I (Promega) according to the manufacturer’s instructions and was labeled by reverse transcription in the presence of Cy5-CTP using the Pronto labeling kit (Corning). An equal amount of the Universal human RNA reference (Stratagene, La Jolla, CA) was labeled with Cy3-CTP, mixed with the Cy5-labeled target and purified.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: gender

value: female

tag: mean age

value: 58.5 years

tag: grade of acute and late toxicity to radiotherapy

tag: protocol

value: ex vivo non-radiated

source_name: Universal reference RNA comprising 10 different cell lines (Cat# 740000)

tag: control

value: Universal reference RNA (Stratagene)


title: Lymphocytes_non-radiated1 (007)

description: no additional information


title: 13415225 - RIL 186 vs RIL 271

hyb_protocol: RIL 271 Cy5 / RIL 186 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 271

source_name: RIL 186


title: 13415229 - RIL 234 vs RIL 187

hyb_protocol: RIL 187 Cy5 / RIL 234 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 187

source_name: RIL 234


title: Lymphocytes_non-radiated0 (010)

description: no additional information


title: 13415227 - RIL 271 vs RIL 186

hyb_protocol: RIL 186 Cy5 / RIL 271 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: 13415223 - RIL 214 vs RIL 175

hyb_protocol: RIL 175 Cy5 / RIL 214 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 175

source_name: RIL 214


title: Lymphocytes_non-radiated (003)

description: no additional information


title: 13415228 - RIL 187 vs RIL 234

hyb_protocol: RIL 234 Cy5 / RIL 187 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: Lymphocytes_non-radiated (006)

description: no additional information


title: 13415222 - RIL 175 vs RIL 214

hyb_protocol: RIL 214 Cy5 / RIL 175 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: Lymphocytes_non-radiated (008)

description: no additional information


title: Lymphocytes_non-radiated (001)

description: no additional information


title: Lymphocytes_non-radiated (011)

description: no additional information


title: Lymphocytes_non-radiated (005)

description: no additional information


title: Lymphocytes_non-radiated (009)

description: no additional information


title: Lymphocytes_non-radiated (004)

description: no additional information


title: 13415221 - RIL 256 vs RIL 232

hyb_protocol: RIL 232 Cy5 / RIL 256 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 232

source_name: RIL 256


title: Lymphocytes_non-radiated (012)

description: no additional information


title: 13415220 - RIL 232 vs RIL 256

hyb_protocol: RIL 256 Cy5 / RIL 232 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: Lymphocytes_2Gy-radiated2 (202)

description: no additional information

value: ex vivo 2Gy-radiated


title: Lymphocytes_2Gy-radiated0 (210)

description: no additional information


title: Lymphocytes_2Gy-radiated1 (207)

description: no additional information


title: Lymphocytes_2Gy-radiated (203)

description: no additional information


title: 13415218 - RIL 176 vs RIL 199

hyb_protocol: RIL 199 Cy5 / RIL 176 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 199

source_name: RIL 176


title: Lymphocytes_2Gy-radiated (211)

description: no additional information


title: Lymphocytes_2Gy-radiated (206)

description: no additional information


title: Lymphocytes_2Gy-radiated (204)

description: no additional information


title: Lymphocytes_2Gy-radiated (212)

description: no additional information


title: Lymphocytes_2Gy-radiated (201)

description: no additional information


title: Lymphocytes_2Gy-radiated (209)

description: no additional information


title: Lymphocytes_2Gy-radiated (205)

description: no additional information


title: 13415217 - RIL 199 vs RIL 176

hyb_protocol: RIL 176 Cy5 / RIL 199 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: 13415210 - RIL 19 vs RIL 334

hyb_protocol: RIL 334 Cy5 / RIL 19 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: RIL 334

source_name: RIL 19


title: 13415214 - RIL 334 vs RIL 19

hyb_protocol: RIL 19 Cy5 / RIL 334 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: Lymphocytes_2Gy-radiated (208)

description: no additional information


title: Renal Cell Carcinoma 990060B

status: Public on Jun 04 2009

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

country: USA

institute: Vanderbilt

description:
Gene expression data from Human RCC sample
RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell histopathology

hyb_protocol: Tumor sample RNA and reference RNA were hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core

scan_protocol: Agilent gene chips were scanned on an Agilent scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. UNC Microarry Database software was used.

source_name: mRNA from Renal Clear Cell Carcinoma

label_protocol: Tumor sample RNA and reference RNA was labelled by UNC Lineberger Comprehensive Cancer Center Genomics Core

growth_protocol: Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility

extract_protocol: RNA was extracting with Qiagen RNeasy kit.

tag: Organism Part

value: Kidney

tag: BioSourceType

value: Frozen Sample

tag: BioSource Provider

value: University of North Carolina

source_name: Perou lab reference RNA

value: Cancer cell lines


title: XX vs OVCAR core #53

type: genomic

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39770.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: genomic DNA

source_name: XX - normal female genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: XX - normal female genomic DNA

source_name: OVCAR core #53

tag: tissue type

value: OVCAR core #53


title: XX vs OVCAR core #25

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39754.gif

source_name: OVCAR core #25

value: OVCAR core #25


title: XX vs OVCAR core #37

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38636.gif

source_name: OVCAR core #37

value: OVCAR core #37


title: XX vs OVCAR core #28

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38349.gif

source_name: OVCAR core #28

value: OVCAR core #28


title: XX vs OVCAR core #19

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38347.gif

source_name: OVCAR core #19

value: OVCAR core #19


title: XX vs OVCAR core #11

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39756.gif

source_name: OVCAR core #11

value: OVCAR core #11


title: XX vs OVCAR core #62

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38618.gif

source_name: OVCAR core #62

value: OVCAR core #62


title: XX vs OVCAR core #15

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39749.gif

source_name: OVCAR core #15

value: OVCAR core #15


title: XX vs OVCAR core #58

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39771.gif

source_name: OVCAR core #58

value: OVCAR core #58


title: XX vs OVCAR core #24

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38348.gif

source_name: OVCAR core #24

value: OVCAR core #24


title: XX vs OVCAR core #10

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38828.gif

source_name: OVCAR core #10

value: OVCAR core #10


title: XX vs OVCAR core #33

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39761.gif

source_name: OVCAR core #33

value: OVCAR core #33


title: XX vs OVCAR core #6

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39746.gif

source_name: OVCAR core #6

value: OVCAR core #6


title: XX vs OVCAR core #2

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38190.gif

source_name: OVCAR core #2

value: OVCAR core #2


title: XX vs OVCAR core #32

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39760.gif

source_name: OVCAR core #32

value: OVCAR core #32


title: XX vs OVCAR core #40

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39765.gif

source_name: OVCAR core #40

value: OVCAR core #40


title: XX vs OVCAR core #8

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38276.gif

source_name: XX - normal female genomic DNA

value: XX - normal female genomic DNA

source_name: OVCAR core #8

value: OVCAR core #8


title: XX vs OVCAR core #49

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38614.gif

source_name: OVCAR core #49

value: OVCAR core #49


title: XX vs OVCAR core #47

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39767.gif

source_name: OVCAR core #47

value: OVCAR core #47


title: Renal Cell Carcinoma 970185B

description:
Gene expression data from Human RCC sample
RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell histopathology

source_name: mRNA from Renal Clear Cell Carcinoma

value: Kidney

value: Frozen Sample

value: University of North Carolina

source_name: Perou lab reference RNA

value: Cancer cell lines


title: XX vs OVCAR core #30

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37982.gif

source_name: OVCAR core #30

value: OVCAR core #30


title: Renal Cell Carcinoma 980206B


title: XX vs OVCAR core #27

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39758.gif

source_name: OVCAR core #27

value: OVCAR core #27


title: XX vs OVCAR core #52

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39769.gif

source_name: OVCAR core #52

value: OVCAR core #52


title: XX vs OVCAR core #9

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39747.gif

source_name: OVCAR core #9

value: OVCAR core #9


title: Renal Cell Carcinoma 077085B


title: XX vs OVCAR core #26

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39755.gif

source_name: OVCAR core #26

value: OVCAR core #26


title: CCSP-/-, 12 hours post LPS, Replicate 3

city: Durham

first: Barry

middle: R

last: Stripp

state: NC

address: 106 Research Drive, DUMC Box 103000

institute: Duke University

description: Replicate 3 of 3.

hyb_protocol: According to manufacturer's suggested protocol, University of Pittsburgh Cancer Center, Clinical genomics facility.

data_processing: Raw data were log2 transformed and normalized by the geometric mean across all groups.

label: Biotin

organism: Mus musculus

source_name: Lung, knock-out, 12h post LPS

extract_protocol: Phenol Chloroform, (Chomczynski and sacchi 1987).

treatment_protocol: WT or CCSP-/- mice were exposed to LPS aerosol for 1.5, 6, or 12 hours and RNA isolated from the left lung for microarray analysis.  WT and CCSP-/- unexposed mice were used as control.  For additional information, please refer to the published manuscript:  Pubmed ID:  19423773.

tag: strain

tag: genotype

value: CCSP -/-

value: lung

value: male


title: CCSP-/-, 12 hours post LPS, Replicate 2

description: Replicate 2 of 3.

scan_protocol: According to manufacturer's suggested protocol, University of Pittsburgh Cancer Center, Clinical genomics facility.


title: XX vs OVCAR core #14

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39748.gif

source_name: OVCAR core #14

value: OVCAR core #14


title: CCSP-/-, 12 hours post LPS, Replicate 1

description: Replicate 1 of 3.

label_protocol: According to manufacturer's suggested protocol, University of Pittsburgh Cancer Center, Clinical genomics facility.


title: CCSP-/-, 6 hours post LPS, Replicate 3

description: Replicate 3 of 3.

source_name: Lung, knock-out, 6h post LPS


title: Renal Cell Carcinoma 071191B


title: Renal Cell Carcinoma 071073B


title: Renal Cell Carcinoma 070988B


title: XX vs OVCAR core #22

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38829.gif

value: XX - normal female genomic DNA

source_name: OVCAR core #22

value: OVCAR core #22


title: XX vs OVCAR core #57

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38637.gif

source_name: OVCAR core #57

value: OVCAR core #57


title: Renal Cell Carcinoma 070894B


title: CCSP-/-, 6 hours post LPS, Replicate 2

description: Replicate 2 of 3.


title: Renal Cell Carcinoma 070847B


title: XX vs OVCAR core #5

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39745.gif

source_name: OVCAR core #5

value: OVCAR core #5


title: XX vs OVCAR core #17

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39750.gif

source_name: XX - normal female genomic DNA

source_name: OVCAR core #17

value: OVCAR core #17


title: XX vs OVCAR core #20

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39757.gif

source_name: OVCAR core #20

value: OVCAR core #20


title: CCSP-/-, 6 hours post LPS, Replicate 1

description: Replicate 1 of 3.


title: XX vs OVCAR core #23

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39753.gif

source_name: OVCAR core #23

value: OVCAR core #23


title: CCSP-/-, 1.5 hours post LPS, Replicate 3

description: Replicate 3 of 3.

source_name: Lung, knock-out, 1.5h post LPS


title: Renal Cell Carcinoma 067115B

source_name: mRNA from Renal Clear Cell Carcinoma

value: Kidney

value: Frozen Sample

value: University of North Carolina

source_name: Perou lab reference RNA

value: Cancer cell lines


title: XX vs OVCAR core #31

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39759.gif

source_name: OVCAR core #31

value: OVCAR core #31


title: Renal Cell Carcinoma 061507B


title: XX vs OVCAR core #59

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39772.gif

source_name: OVCAR core #59

value: OVCAR core #59


title: CCSP-/-, 1.5 hours post LPS, Replicate 2

description: Replicate 2 of 3.

value: CCSP -/-


title: CCSP-/-, 1.5 hours post LPS, Replicate 1

description: Replicate 1 of 3.

value: lung


title: XX vs OVCAR core #3

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38191.gif

source_name: Ovcar core #3

value: OVCAR core #3


title: XX vs OVCAR core #55

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38617.gif

source_name: OVCAR core #55

value: OVCAR core #55


title: Renal Cell Carcinoma 067149B

description:
Gene expression data from Human RCC sample
RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell histopathology


title: XX vs OVCAR core #36

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39763.gif

value: XX - normal female genomic DNA

source_name: OVCAR core #36

value: OVCAR core #36


title: XX vs OVCAR core #51

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38615.gif

source_name: OVCAR core #51

value: OVCAR core #51


title: XX vs OVCAR core #60

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39773.gif

source_name: OVCAR core #60

value: OVCAR core #60


title: XX vs OVCAR core #34

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38350.gif

source_name: OVCAR core #34

value: OVCAR core #34


title: Renal Cell Carcinoma 067116B


title: CCSP-/-, Control, Replicate 3

description: Replicate 3 of 3.

source_name: Lung, knock-out, control

value: male


title: XX vs OVCAR core #39

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38830.gif

source_name: OVCAR core #39

value: OVCAR core #39


title: XX vs OVCAR core #46

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39766.gif

source_name: XX - normal female genomic DNA

source_name: OVCAR core #46

value: OVCAR core #46


title: CCSP-/-, Control, Replicate 2

description: Replicate 2 of 3.


title: XX vs OVCAR core #7

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38275.gif

source_name: OVCAR core #7

value: OVCAR core #7


title: XX vs OVCAR core #50

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39768.gif

source_name: OVCAR core #50

value: OVCAR core #50


title: XX vs OVCAR core #38

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39764.gif

source_name: OVCAR core #38

value: OVCAR core #38


title: XX vs OVCAR core #13

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38345.gif

source_name: OVCAR core #13

value: OVCAR core #13


title: Patient 20

city: Leiden

first: Marloes

last: van Kester

address: Einthovenweg 20

department: Dermatology

country: Netherlands

institute: Leiden University Medical Center

description: Patient 20

hyb_protocol: Labelled test and reference samples were pooled and precipitated in the presence of Cot1 DNA (Invitrogen, Breda, The Netherlands). DNA pellet was dissolved in hybridisation mixture. Sample was hybridized for 20 hours followed post-hybridisation washes and drying of slides by using an automated hybridisation station (Tecan Benelux BVBA, Giesen, The Netherlands).

scan_protocol: Scanned on an Genepix 4100A scanner. Images were quantified using Genepix Pro 4.1 software.

data_processing: Within this software, spots in which the reference DNA intensity was either below five times the average of the background or presented more than 3% saturated pixels were excluded from further analyses. The test/reference ratios were normalized for the median of the ratios of all features. The triplicates of the features were averaged in a homemade routine developed in Microsoft Excel 2000, and spots outside the 20% confidence interval of the average of the replicate were excluded. Only those targets presenting at least two spots within 20% confidence interval of their average were used. Unbalances of the targets were determined based on log2 ratios of the average of their replicates, and we considered sequences as amplified or deleted when outside the ±0.3 range.

source_name: PBMCs of Sézary patient

label_protocol: overnight random prime labelling reaction (BioPrime Random Prime labelling Kit, Invitrogen, Breda, The Netherlands)

extract_protocol: DNA was isolated from 1 x 10^7 Ficoll purified lymphocytes with the Genomic-tips 20/G kit (Qiagen).

value: PBMCs

source_name: reference DNA

value: Gender mismatched pooled reference DNA


title: Patient 18

description: Patient 18


title: Patient 19

description: Patient 19


title: Patient 17

description: Patient 17


title: CCSP-/-, Control, Replicate 1

description: Replicate 1 of 3.

value: CCSP -/-

value: lung


title: Patient 16

description: Patient 16


title: Renal Cell Carcinoma 050913B

source_name: mRNA from Renal Clear Cell Carcinoma

value: Kidney

value: Frozen Sample

value: University of North Carolina

source_name: Perou lab reference RNA

value: Cancer cell lines


title: Wild-type, 12 hours post LPS, Replicate 2

description: Replicate 2 of 3.

source_name: Lung, wild-type, 12h post LPS

value: wild-type


title: Patient 15

description: Patient 15


title: Wild-type, 12 hours post LPS, Replicate 3

description: Replicate 3 of 3.


title: XX vs OVCAR core #4

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39744.gif

value: XX - normal female genomic DNA

source_name: OVCAR core #4

value: OVCAR core #4


title: XX vs OVCAR core #41

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38547.gif

source_name: OVCAR core #41

value: OVCAR core #41


title: XX vs OVCAR core #16

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38346.gif

source_name: OVCAR core #16

value: OVCAR core #16


title: Renal Cell Carcinoma 047216B


title: Patient 13

description: Patient 13


title: Patient 14

description: Patient 14


title: Renal Cell Carcinoma 047200B


title: Patient 12

description: Patient 12


title: Wild-type, 12 hours post LPS, Replicate 1

description: Replicate 1 of 3.

value: male


title: XX vs OVCAR core #54

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38616.gif

source_name: OVCAR core #54

value: OVCAR core #54


title: Wild-type, 6 hours post LPS, Replicate 3

description: Replicate 3 of 3.

source_name: Lung, wild-type, 6h post LPS


title: Renal Cell Carcinoma 047288B


title: Patient 10

description: Patient 10


title: Patient 9

description: Patient 9


title: Renal Cell Carcinoma 061159B


title: Patient 8

description: Patient 8


title: Renal Cell Carcinoma 047034B


title: Patient 7

description: Patient 7

source_name: CD4+ T cells of Sézary patient

value: CD4+ T cells


title: XX vs OVCAR core #35

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39762.gif

source_name: XX - normal female genomic DNA

source_name: OVCAR core #35

value: OVCAR core #35


title: Wild-type, 6 hours post LPS, Replicate 1

description: Replicate 1 of 3.


title: Renal Cell Carcinoma 040116B


title: Renal Cell Carcinoma 037011B


title: Wild-type, 6 hours post LPS, Replicate 2

description: Replicate 2 of 3.


title: Patient 6

description: Patient 6

value: PBMCs


title: Renal Cell Carcinoma 020519B


title: gura_fum_oxy_2b

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

description: total RNA was amplified using the Ambion MessageAmp II- Bacteria kit for polyadenylation and subsequent amplification of total RNA. aRNA was ethanol precipitated and resuspended in nuclease-free water to a total concentration of ~1 ug/ul.

hyb_protocol: Combimatrix 100ul cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner.

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work. Background signal was calculated from a set of negative control spots incorporated into the array. As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest. To avoid this issue the negative control spots were ranked according to their total intensity. The average of the lowest 30% was calculated. Background signal was calculated as this mean + 2 standard deviations. The background signal was then subtracted from the total intensity for each spot. Probes whose signal was not greater than zero after background subtraction were omitted from further analysis. For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3) LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes. Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001. Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1. Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2. Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3. Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geotalea uraniireducens

source_name: Acetate as Electron Donor and Fumarate as Electron Acceptor - oxygen treated

label_protocol: Micromax ASAP direct labeling of 10 ug aRNA

extract_protocol: For reference see:In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl Environ Microbiol. 2004 Dec;70(12):7251-9. PMID: 15574924

tag: Geobacter uraniumreducens was grown in steady-state chemostats with acetate as the electron donor and fumarate as the electron acceptor, and chemostats were treated with oxygen.

label_protocol: Micromax ASAP direct labeling of 10ug aRNA

tag: Geobacter uraniumreducens was grown in steady-state chemostats with acetate as the electron donor and fumarate as the electron acceptor.


title: gura_fum_oxy_3a

source_name: Acetate as Electron Donor and Fumarate as Electron Acceptor


title: gura_fum_oxy_3b


title: Wild-type, 1.5 hours post LPS, Replicate 2

description: Replicate 2 of 3.

source_name: Lung, wild-type, 1.5h post LPS


title: Patient 5

description: Patient 5

value: Gender mismatched pooled reference DNA


title: gura_fum_oxy_2a


title: Patient 3

description: Patient 3


title: Patient 2

description: Patient 2


title: Wild-type, 1.5 hours post LPS, Replicate 3

description: Replicate 3 of 3.


title: gura_fum_oxy_1a


title: Wild-type, Control, Replicate 2

description: Replicate 2 of 3.

source_name: Lung, wild-type, control


title: gura_fum_oxy_1b


title: Wild-type, 1.5 hours post LPS, Replicate 1

description: Replicate 1 of 3.


title: Patient 4

description: Patient 4


title: Patient 1

description: Patient 1

source_name: PBMCs of Sézary patient


title: Renal Cell Carcinoma 010140B1

description:
Gene expression data from Human RCC sample
RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell histopathology


title: Renal Cell Carcinoma 000356B


title: Renal Cell Carcinoma 010106BAR


title: Wild-type, Control, Replicate 3

description: Replicate 3 of 3.


title: Renal Cell Carcinoma 010106B1


title: Wild-type, Control, Replicate 1

description: Replicate 1 of 3.


title: Renal Cell Carcinoma 057288B


title: XX vs OVCAR core #18

description:
Simple annotation: aCGH, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39751.gif

source_name: OVCAR core #18

value: OVCAR core #18


title: SLN:1918 - B - mAdbID:39959

status: Public on Jun 03 2009

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 39959

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133A/B GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MA S 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: polyA RNA

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
FastTrack 2.0 mRNA Isolation Kit
Extraction method: oligo dt cellulose
Other: mRNA was extracted using the FastTrack 2.0 mRNA Isolation Kit according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

value: Lymph node

tag: disease state

value: Follicular Lymphoma

tag: individual

tag: clinical info

value: Follow up status:dead

value: Follow up years:9.95

value: Stage >2:yes

value: LDH ratio >1:no

value: Number of extranodal sites >1:yes

value: Age >60:no

value: IPI score:2

value: Immune response 1:9.54

value: Immune response 2:8.77

value: With translocation:yes


title: SLN:1904 - B - mAdbID:39859

description: mAdb experiment ID: 39859

tag: tissue

value: Follow up status:alive

value: Follow up years:7.36

value: Stage >2:no

value: Number of extranodal sites >1:no

value: IPI score:1

value: Immune response 1:9.16

value: Immune response 2:8.53


title: SLN:1912 - B - mAdbID:39956

description: mAdb experiment ID: 39956

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:0.73

value: LDH ratio >1:yes

value: Immune response 1:9.3

value: Immune response 2:9.21


title: SLN:1919 - B - mAdbID:39960

description: mAdb experiment ID: 39960

value: Follow up years:10.84

value: LDH ratio >1:NA

value: Age >60:yes

value: IPI score:NA

value: Immune response 1:9.51

value: Immune response 2:8.81


title: SLN:1905 - B - mAdbID:39860

description: mAdb experiment ID: 39860

value: Follow up years:3.68

value: Stage >2:yes

value: Number of extranodal sites >1:yes

value: Age >60:no

value: IPI score:3

value: Immune response 1:9.25

value: Immune response 2:8.38

value: With translocation:yes


title: SLN:1897 - B - mAdbID:39855

description: mAdb experiment ID: 39855

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:9.63

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: IPI score:1

value: Immune response 1:9.02

value: Immune response 2:8.33


title: SLN:1916 - B - mAdbID:39958

description: mAdb experiment ID: 39958

value: Follow up years:11.61

value: LDH ratio >1:yes

value: IPI score:2

value: Immune response 1:9.22

value: Immune response 2:8.49


title: SLN:1900 - B - mAdbID:39857

description: mAdb experiment ID: 39857

value: Follow up years:7.38

value: Stage >2:no

value: Age >60:no

value: Immune response 1:9.13

value: Immune response 2:8.26


title: SLN:1898 - B - mAdbID:39856

description: mAdb experiment ID: 39856

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:5.2

value: Stage >2:yes

value: Age >60:yes

value: IPI score:NA

value: Immune response 1:8.82

value: Immune response 2:8.25

value: With translocation:yes


title: SLN:1910 - B - mAdbID:39954

description: mAdb experiment ID: 39954

value: Follow up years:13.84

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: IPI score:1

value: Immune response 1:9.36

value: Immune response 2:8.72


title: SLN:1906 - B - mAdbID:39861

description: mAdb experiment ID: 39861

value: Follow up status:dead

value: Follow up years:2.35

value: LDH ratio >1:yes

value: IPI score:3

value: Immune response 1:8.04

value: Immune response 2:8.69


title: SLN:1913 - B - mAdbID:39957

description: mAdb experiment ID: 39957

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:2.57

value: Stage >2:no

value: Age >60:no

value: Immune response 1:9.77

value: Immune response 2:8.51

value: With translocation:no


title: SLN:1907 - B - mAdbID:39873

description: mAdb experiment ID: 39873

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Age >60:yes

value: IPI score:1

value: Immune response 1:8.11

value: Immune response 2:8.21

value: With translocation:yes


title: SLN:1896 - B - mAdbID:39854

description: mAdb experiment ID: 39854

value: Follow up years:12.03

value: Immune response 1:9.8

value: Immune response 2:8.56


title: SLN:1890 - B - mAdbID:39852

description: mAdb experiment ID: 39852

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:3.03

value: Stage >2:yes

value: LDH ratio >1:yes

value: IPI score:2

value: Immune response 1:9.29

value: Immune response 2:9.05


title: SLN:1894 - B - mAdbID:39853

description: mAdb experiment ID: 39853

value: Follow up years:11.37

value: LDH ratio >1:no

value: Number of extranodal sites >1:yes

value: Age >60:no

value: Immune response 1:9.01

value: Immune response 2:8.64


title: Wild-type, biological rep. 1

city: New Delhi

first: Akhilesh

middle: Kumar

last: Tyagi

state: Delhi

address: Benito Juarez Road

department: Plant Molecular Biology

country: India

institute: University of Delhi South Campus,  Benito Juarez Road  India

description: Gene espression data of 15 days old rice shoot in wild-type plants

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using Avadis 4.2 prophetic software (Strandgenomics, Bangalore, India)

organism: Oryza sativa Indica Group

source_name: 15 days old rice shoot unstressed

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA

growth_protocol: Seedlings were raised on MS medium without antibiotic selection for 15 days.

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

treatment_protocol: Untreated seedlings were used for shoot tissue

tag: cultivar

value: Pusa Basmati 1

value: 15 days old rice shoot

tag: genotype/variation

value: wildtype


title: Transgenic line 22, biological rep. 2

description: Gene espression data of 15 days old rice shoot in codA expressing transgenic line22

value: transgenic


title: Wild-type, biological rep. 3


title: Wild-type, biological rep. 2


title: Transgenic line 22, biological rep. 3


title: SLN:1888 - B - mAdbID:39851

description: mAdb experiment ID: 39851

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:15.08

value: Number of extranodal sites >1:no

value: IPI score:1

value: Immune response 1:9.83

value: Immune response 2:8.97

value: With translocation:yes


title: Transgenic line 4, biological rep. 3

description: Gene espression data of 15 days old rice shoot in codA expressing transgenic line4


title: SLN:1887 - B - mAdbID:39850

description: mAdb experiment ID: 39850

value: Follow up status:dead

value: Follow up years:5.14

value: Stage >2:no

value: LDH ratio >1:no

value: Age >60:yes

value: Immune response 1:9.47

value: Immune response 2:8.57


title: SLN:1882 - B - mAdbID:39847

description: mAdb experiment ID: 39847

value: Follow up years:8.84

value: Age >60:no

value: Immune response 1:9.43

value: Immune response 2:8.76


title: SLN:1880 - B - mAdbID:39750

description: mAdb experiment ID: 39750

value: Lymph node

value: Follicular Lymphoma

value: Follow up years:12.84

value: Stage >2:yes

value: Immune response 1:8.82

value: Immune response 2:8.35


title: SLN:1885 - B - mAdbID:39849

description: mAdb experiment ID: 39849

value: Follow up status:alive

value: Follow up years:15.49

value: Number of extranodal sites >1:no

value: IPI score:1

value: Immune response 1:9.7

value: Immune response 2:8.85

value: With translocation:yes


title: SLN:1857 - B - mAdbID:39660

description: mAdb experiment ID: 39660

value: Follow up status:dead

value: Follow up years:8.39

value: Stage >2:no

value: LDH ratio >1:no

value: Age >60:yes

value: Immune response 1:9.8

value: Immune response 2:9.14


title: HB007WX

city: Jaipur

first: Sandeep

last: Mathur

state: Rajasthan

address: JLN Marg

department: Endocrinology

institute: S.M.S.Medical College

description: no additional information

hyb_protocol: Applied Biosystems Chemiluminescence Detection kit was used for hybridising the cRNA to Applied Boisystems 1700 Human genome survey microarrays

scan_protocol: The AB 1700 Human Genome survey microarrays were scanned using Applied Biosystems 1700 Chemiluminescent Analyzer following the manufacturer's protocol

data_processing: The data was initially analysed by AB array which is a software package written in R for the quality assessment and automated statistical analysis of Applied Boisystems expression array system data. AB array provides Quality control graphical output, data integrity graphical output, statistical processing and statistical graphical output.The data is then analysed using spotfire statistical software. The data is first normalised (trim mean normalization) and samples are being grouped into controls and samples. The two groups are then compared for fold change expression and the data is then merged with the pathways wrt probe IDs and Gene IDs.

label: digoxigenin (DIG)

source_name: Omentum (visceral adipose ) tissue from diabetic subject

label_protocol: Followed one round (standard) of amplification. NanoAmp RT-IVT Labeling kit from Applied Biosystems was used to convert RNA into digoxigenin (DIG)-labeled cRNA for hybridisation to Applied Boisystems microarrays

extract_protocol: Adipose tissue was collected in RNA Later. Total RNA was extracted using Ribopure kit from Ambion.

value: type-2 diabetes mellitus


title: SLN:1884 - B - mAdbID:39848

description: mAdb experiment ID: 39848

value: Lymph node

value: Follicular Lymphoma

value: Follow up years:11.92

value: LDH ratio >1:yes

value: IPI score:2

value: Immune response 1:9.48

value: With translocation:no


title: HB00CY3

description: no additional information


title: SLN:1879 - B - mAdbID:39749

description: mAdb experiment ID: 39749

value: Follow up years:7.13

value: Stage >2:yes

value: Number of extranodal sites >1:no

value: IPI score:NA

value: Immune response 1:9.25

value: Immune response 2:8.62


title: SLN:1874 - B - mAdbID:39550

description: mAdb experiment ID: 39550

value: Follow up status:dead

value: Follow up years:3.15

value: Number of extranodal sites >1:yes

value: Age >60:no

value: Immune response 1:9.38

value: Immune response 2:8.74

value: With translocation:yes


title: HB00GAH

description: no additional information

value: type-2 diabetes mellitus


title: Patient 11

description: Patient 11

value: PBMCs

source_name: reference DNA

value: Gender mismatched pooled reference DNA


title: SLN:1876 - B - mAdbID:39548

description: mAdb experiment ID: 39548

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:15.07

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:9.59

value: Immune response 2:8.72


title: SLN:1873 - B - mAdbID:39549

description: mAdb experiment ID: 39549

value: Follow up status:dead

value: Follow up years:7.78

value: Stage >2:yes

value: LDH ratio >1:yes

value: Number of extranodal sites >1:no

value: IPI score:2

value: Immune response 1:9.39

value: Immune response 2:8.66


title: SLN:1870 - B - mAdbID:39547

description: mAdb experiment ID: 39547

value: Follow up years:6.41

value: Age >60:yes

value: Immune response 1:10.01

value: Immune response 2:9.22

value: With translocation:yes


title: HB008CZ

description: no additional information

source_name: Omentum (visceral adipose ) tissue from healthy control subject

value: control


title: HB0084U

description: no additional information


title: HB007WP

description: no additional information

value: type-2 diabetes mellitus


title: Transgenic line 4, biological rep. 2

value: Pusa Basmati 1

value: 15 days old rice shoot

value: transgenic


title: HBOOGA7

description: no additional information


title: HB008CQ

description: no additional information


title: HB007WZ

description: no additional information


title: Transgenic line 4, biological rep. 1

description: Gene espression data of 15 days old rice shoot in codA expressing transgenic line 4


title: Transgenic line 22, biological rep. 1


title: SLN:1857 - A - mAdbID:40534

description: mAdb experiment ID: 40534

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:8.39

value: Stage >2:no

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:9.8

value: Immune response 2:9.14


title: SLN:1866 - B - mAdbID:39546

description: mAdb experiment ID: 39546

value: Follow up years:10.72

value: Stage >2:yes

value: Number of extranodal sites >1:no

value: Age >60:no

value: Immune response 1:9.93

value: Immune response 2:8.94

value: With translocation:NA


title: SLN:1863 - B - mAdbID:39545

description: mAdb experiment ID: 39545

value: Follow up years:10.77

value: LDH ratio >1:yes

value: IPI score:2

value: Immune response 1:9.31

value: Immune response 2:8.85

value: With translocation:yes


title: HB007WT

description: no additional information

value: control


title: SLN:1919 - A - mAdbID:39869

description: mAdb experiment ID: 39869

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:10.84

value: Stage >2:no

value: LDH ratio >1:NA

value: Age >60:yes

value: IPI score:NA

value: Immune response 1:9.51

value: Immune response 2:8.81


title: SLN:1912 - A - mAdbID:39864

description: mAdb experiment ID: 39864

value: Follow up years:0.73

value: Stage >2:yes

value: Number of extranodal sites >1:no

value: Age >60:no

value: Immune response 1:9.3

value: Immune response 2:9.21


title: SLN:1855 - B - mAdbID:39540

description: mAdb experiment ID: 39540

value: Follow up years:9.96

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:9.31

value: Immune response 2:8.39

value: With translocation:yes


title: SLN:1916 - A - mAdbID:39866

description: mAdb experiment ID: 39866

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:11.61

value: LDH ratio >1:yes

value: IPI score:2

value: Immune response 1:9.22

value: Immune response 2:8.49


title: SLN:1850 - B - mAdbID:39496

description: mAdb experiment ID: 39496

value: Follow up status:NA

value: Follow up years:

value: Stage >2:NA

value: LDH ratio >1:NA

value: Number of extranodal sites >1:no

value: Age >60:NA

value: IPI score:NA

value: Immune response 1:9.75

value: Immune response 2:8.83

value: With translocation:no


title: SLN:1910 - A - mAdbID:39862

description: mAdb experiment ID: 39862

value: Lymph node

value: Follicular Lymphoma

value: Follow up years:13.84

value: Stage >2:yes

value: LDH ratio >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.36

value: Immune response 2:8.72

value: With translocation:yes


title: SLN:1851 - B - mAdbID:39497

description: mAdb experiment ID: 39497

value: Follow up status:dead

value: Follow up years:4.08

value: LDH ratio >1:yes

value: Age >60:yes

value: IPI score:2

value: Immune response 1:9.43

value: Immune response 2:9.01


title: SLN:1854 - B - mAdbID:39499

description: mAdb experiment ID: 39499

value: Lymph node

value: Follow up status:alive

value: Follow up years:13.81

value: Number of extranodal sites >1:no

value: Immune response 1:9.32

value: Immune response 2:8.84


title: SLN:1918 - A - mAdbID:39868

description: mAdb experiment ID: 39868

value: Follicular Lymphoma

value: Follow up years:9.95

value: Stage >2:yes

value: LDH ratio >1:no

value: Number of extranodal sites >1:yes

value: Age >60:no

value: Immune response 1:9.54

value: Immune response 2:8.77


title: SLN:1861 - B - mAdbID:39542

description: mAdb experiment ID: 39542

value: Follow up status:dead

value: Follow up years:3.19

value: IPI score:1

value: Immune response 1:9.47

value: Immune response 2:8.57

value: With translocation:yes


title: SLN:1864 - B - mAdbID:39544

description: mAdb experiment ID: 39544

value: Lymph node

value: Follow up status:alive

value: Follow up years:14.25

value: Number of extranodal sites >1:no

value: Immune response 1:9.98

value: Immune response 2:9.12


title: SLN:1862 - B - mAdbID:39543

description: mAdb experiment ID: 39543

value: Follicular Lymphoma

value: Follow up years:7.22

value: Stage >2:yes

value: LDH ratio >1:no

value: Immune response 1:8.96

value: Immune response 2:8.33


title: SLN:1841 - A - mAdbID:40371

description: mAdb experiment ID: 40371

value: Follow up status:dead

value: Follow up years:0.88

value: LDH ratio >1:yes

value: Age >60:yes

value: IPI score:2

value: Immune response 1:9.32

value: Immune response 2:9.1

value: With translocation:NA


title: SLN:1848 - B - mAdbID:39495

description: mAdb experiment ID: 39495

value: Lymph node

value: Follow up status:alive

value: Follow up years:12.52

value: Number of extranodal sites >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.76

value: Immune response 2:8.81

value: With translocation:yes


title: SLN:1905 - A - mAdbID:39745

description: mAdb experiment ID: 39745

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:3.68

value: Stage >2:yes

value: Number of extranodal sites >1:yes

value: IPI score:3

value: Immune response 1:9.25

value: Immune response 2:8.38


title: SLN:1907 - A - mAdbID:39747

description: mAdb experiment ID: 39747

value: Lymph node

value: Follow up years:2.35

value: Stage >2:no

value: LDH ratio >1:no

value: Age >60:yes

value: Immune response 1:8.11

value: Immune response 2:8.21


title: SLN:1906 - A - mAdbID:39746

description: mAdb experiment ID: 39746

value: LDH ratio >1:yes

value: Number of extranodal sites >1:no

value: Immune response 1:8.04

value: Immune response 2:8.69


title: SLN:1913 - A - mAdbID:39865

description: mAdb experiment ID: 39865

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:2.57

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.77

value: Immune response 2:8.51

value: With translocation:no


title: SLN:1853 - B - mAdbID:39498

description: mAdb experiment ID: 39498

value: Lymph node

value: Follow up years:12.5

value: Stage >2:no

value: Immune response 1:9.28

value: Immune response 2:8.54

value: With translocation:yes


title: SLN:1846 - B - mAdbID:39494

description: mAdb experiment ID: 39494

value: Follow up status:dead

value: Follow up years:1.8

value: Stage >2:yes

value: LDH ratio >1:yes

value: Number of extranodal sites >1:no

value: IPI score:2

value: Immune response 1:9.79

value: Immune response 2:9.61


title: SLN:1845 - B - mAdbID:39493

description: mAdb experiment ID: 39493

value: Follicular Lymphoma

value: Follow up years:12.92

value: LDH ratio >1:no

value: Age >60:no

value: Immune response 1:9.89

value: Immune response 2:9.04


title: SLN:1844 - B - mAdbID:39492

description: mAdb experiment ID: 39492

value: Lymph node

value: Follow up status:alive

value: Follow up years:13.39

value: Stage >2:no

value: IPI score:1

value: Immune response 1:9.41

value: Immune response 2:8.55


title: SLN:1904 - A - mAdbID:39744

description: mAdb experiment ID: 39744

value: Follow up years:7.36

value: Number of extranodal sites >1:no

value: Immune response 1:9.16

value: Immune response 2:8.53

value: With translocation:yes


title: SLN:1900 - A - mAdbID:39742

description: mAdb experiment ID: 39742

value: Follicular Lymphoma

value: Follow up years:7.38

value: Immune response 1:9.13

value: Immune response 2:8.26


title: SLN:1842 - B - mAdbID:39491

description: mAdb experiment ID: 39491

value: Follow up years:4.56

value: Stage >2:yes

value: LDH ratio >1:NA

value: Number of extranodal sites >1:yes

value: Age >60:yes

value: IPI score:NA

value: Immune response 1:9.73

value: Immune response 2:8.87


title: SLN:1838 - B - mAdbID:39488

description: mAdb experiment ID: 39488

value: Lymph node

value: Follow up status:alive

value: Follow up years:2.54

value: Stage >2:no

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:9.9

value: Immune response 2:9.12

value: With translocation:no


title: SLN:1896 - A - mAdbID:39700

description: mAdb experiment ID: 39700

value: Follicular Lymphoma

value: Follow up years:12.03

value: Number of extranodal sites >1:no

value: Age >60:no

value: Immune response 1:9.8

value: Immune response 2:8.56


title: SLN:1894 - A - mAdbID:39699

description: mAdb experiment ID: 39699

value: Follow up status:dead

value: Follow up years:11.37

value: Stage >2:yes

value: Number of extranodal sites >1:yes

value: IPI score:2

value: Immune response 1:9.01

value: Immune response 2:8.64

value: With translocation:yes


title: SLN:1835 - B - mAdbID:39485

description: mAdb experiment ID: 39485

value: Lymph node

value: Follow up status:alive

value: Follow up years:12.49

value: LDH ratio >1:yes

value: Immune response 1:9.26

value: Immune response 2:8.83


title: SLN:1888 - A - mAdbID:39697

description: mAdb experiment ID: 39697

value: Follicular Lymphoma

value: Follow up years:15.08

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.83

value: Immune response 2:8.97


title: SLN:1898 - A - mAdbID:39702

description: mAdb experiment ID: 39702

value: Follow up years:5.2

value: Stage >2:yes

value: Age >60:yes

value: IPI score:NA

value: Immune response 1:8.82

value: Immune response 2:8.25


title: SLN:1841 - B - mAdbID:39490

description: mAdb experiment ID: 39490

value: Lymph node

value: Follow up status:dead

value: Follow up years:0.88

value: LDH ratio >1:yes

value: IPI score:2

value: Immune response 1:9.32

value: Immune response 2:9.1

value: With translocation:NA


title: SLN:1885 - A - mAdbID:39695

description: mAdb experiment ID: 39695

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:15.49

value: Stage >2:no

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.7

value: Immune response 2:8.85

value: With translocation:yes


title: SLN:1884 - A - mAdbID:39694

description: mAdb experiment ID: 39694

value: Lymph node

value: Follow up status:dead

value: Follow up years:11.92

value: Age >60:yes

value: Immune response 1:9.48

value: Immune response 2:9.14

value: With translocation:no


title: SLN:1836 - B - mAdbID:39486

description: mAdb experiment ID: 39486

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:12.24

value: Stage >2:yes

value: Immune response 1:9.55

value: Immune response 2:8.64


title: SLN:1887 - A - mAdbID:39696

description: mAdb experiment ID: 39696

value: Follow up years:5.14

value: Stage >2:no

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: IPI score:1

value: Immune response 1:9.47

value: Immune response 2:8.57


title: SLN:1829 - B - mAdbID:39481

description: mAdb experiment ID: 39481

value: Lymph node

value: Follow up years:4.11

value: LDH ratio >1:yes

value: Age >60:yes

value: IPI score:2

value: Immune response 1:9.57

value: Immune response 2:8.73

value: With translocation:yes


title: SLN:1833 - B - mAdbID:39484

description: mAdb experiment ID: 39484

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:11.95

value: Stage >2:yes

value: Age >60:no

value: Immune response 1:9.74

value: Immune response 2:8.67

value: With translocation:no


title: SLN:1897 - A - mAdbID:39701

description: mAdb experiment ID: 39701

value: Follow up years:9.63

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: IPI score:1

value: Immune response 1:9.02

value: Immune response 2:8.33


title: SLN:1882 - A - mAdbID:39693

description: mAdb experiment ID: 39693

value: Lymph node

value: Follow up status:dead

value: Follow up years:8.84

value: Stage >2:no

value: Immune response 1:9.43

value: Immune response 2:8.76


title: SLN:1890 - A - mAdbID:39698

description: mAdb experiment ID: 39698

value: Follicular Lymphoma

value: Follow up years:3.03

value: Stage >2:yes

value: LDH ratio >1:yes

value: Age >60:yes

value: IPI score:2

value: Immune response 1:9.29

value: Immune response 2:9.05

value: With translocation:yes


title: SLN:1834 - B - mAdbID:39483

description: mAdb experiment ID: 39483

value: Follow up status:alive

value: Follow up years:15.92

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.22

value: Immune response 2:8.72


title: SLN:1839 - B - mAdbID:39489

description: mAdb experiment ID: 39489

value: Lymph node

value: Follicular Lymphoma

value: Follow up years:4.48

value: Stage >2:no

value: Immune response 1:8.56

value: Immune response 2:8.32


title: SLN:1837 - B - mAdbID:39487

description: mAdb experiment ID: 39487

value: Follow up status:dead

value: Follow up years:0.55

value: Stage >2:yes

value: LDH ratio >1:yes

value: IPI score:2

value: Immune response 1:9.47

value: Immune response 2:8.84

value: With translocation:no


title: SLN:1879 - A - mAdbID:39650

description: mAdb experiment ID: 39650

value: Follow up years:7.13

value: Number of extranodal sites >1:no

value: Age >60:yes

value: IPI score:NA

value: Immune response 1:9.25

value: Immune response 2:8.62

value: With translocation:yes


title: SLN:1880 - A - mAdbID:39648

description: mAdb experiment ID: 39648

value: Lymph node

value: Follicular Lymphoma

value: Follow up years:12.84

value: LDH ratio >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:8.82

value: Immune response 2:8.35


title: SLN:1828 - B - mAdbID:39480

description: mAdb experiment ID: 39480

value: Follow up status:alive

value: Follow up years:11.51

value: Stage >2:yes

value: LDH ratio >1:NA

value: Immune response 1:8.99

value: Immune response 2:8.09


title: SLN:1827 - B - mAdbID:39479

description: mAdb experiment ID: 39479

value: Follow up years:3.66

value: Stage >2:no

value: Number of extranodal sites >1:no

value: Age >60:yes

value: Immune response 1:9.8

value: Immune response 2:8.84


title: SLN:1825 - B - mAdbID:39478

description: mAdb experiment ID: 39478

value: Lymph node

value: Follicular Lymphoma

value: Follow up years:2.98

value: LDH ratio >1:no

value: Immune response 1:9.46

value: Immune response 2:9.07

value: With translocation:yes


title: SLN:1876 - A - mAdbID:39476

description: mAdb experiment ID: 39476

value: Follow up status:alive

value: Follow up years:15.07

value: Stage >2:yes

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.59

value: Immune response 2:8.72


title: SLN:1719 - B - mAdbID:39377

description: mAdb experiment ID: 39377

value: Follow up status:dead

value: Follow up years:7.7

value: Stage >2:no

value: LDH ratio >1:NA

value: Number of extranodal sites >1:yes

value: IPI score:NA

value: Immune response 1:9.13

value: Immune response 2:8.5


title: SLN:1873 - A - mAdbID:39474

description: mAdb experiment ID: 39474

value: Lymph node

value: Follicular Lymphoma

value: Follow up years:7.78

value: LDH ratio >1:yes

value: Number of extranodal sites >1:no

value: IPI score:2

value: Immune response 1:9.39

value: Immune response 2:8.66


title: SLN:1864 - A - mAdbID:39470

description: mAdb experiment ID: 39470

value: Follow up status:alive

value: Follow up years:14.25

value: Stage >2:yes

value: LDH ratio >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.98

value: Immune response 2:9.12

value: With translocation:yes


title: SLN:1866 - A - mAdbID:39471

description: mAdb experiment ID: 39471

value: Lymph node

value: Follow up status:dead

value: Follow up years:10.72

value: Immune response 1:9.93

value: Immune response 2:8.94

value: With translocation:NA


title: SLN:1830 - B - mAdbID:39482

description: mAdb experiment ID: 39482

value: Follicular Lymphoma

value: Follow up years:5.65

value: Number of extranodal sites >1:no

value: Age >60:yes

value: IPI score:2

value: Immune response 1:9.01

value: Immune response 2:8.68


title: SLN:1799 - B - mAdbID:39371

description: mAdb experiment ID: 39371

value: Follow up status:alive

value: Follow up years:14.18

value: Stage >2:no

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:9.32

value: Immune response 2:8.63

value: With translocation:no


title: SLN:1862 - A - mAdbID:39468

description: mAdb experiment ID: 39468

value: Lymph node

value: Follow up status:dead

value: Follow up years:7.22

value: Stage >2:yes

value: Age >60:no

value: Immune response 1:8.96

value: Immune response 2:8.33

value: With translocation:yes


title: SLN:1810 - B - mAdbID:39281

description: mAdb experiment ID: 39281

value: Follicular Lymphoma

value: Follow up years:9.91

value: LDH ratio >1:yes

value: Number of extranodal sites >1:no

value: Age >60:yes

value: IPI score:2

value: Immune response 1:8.66

value: Immune response 2:8.41


title: SLN:1863 - A - mAdbID:39469

description: mAdb experiment ID: 39469

value: Follow up years:10.77

value: Immune response 1:9.31

value: Immune response 2:8.85


title: SLN:1853 - A - mAdbID:39404

description: mAdb experiment ID: 39404

value: Lymph node

value: Follow up status:alive

value: Follow up years:12.5

value: Stage >2:no

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:9.28

value: Immune response 2:8.54


title: SLN:1790 - B - mAdbID:39277

description: mAdb experiment ID: 39277

value: Follicular Lymphoma

value: Follow up years:1.42

value: Stage >2:yes

value: LDH ratio >1:yes

value: Number of extranodal sites >1:yes

value: IPI score:3

value: Immune response 1:9.85

value: Immune response 2:9.4

value: With translocation:yes


title: SLN:1861 - A - mAdbID:39467

description: mAdb experiment ID: 39467

value: Lymph node

value: Follow up status:dead

value: Follow up years:3.19

value: Number of extranodal sites >1:no

value: Age >60:no

value: Immune response 1:9.47

value: Immune response 2:8.57


title: SLN:1788 - B - mAdbID:39276

description: mAdb experiment ID: 39276

value: Follow up years:1

value: Stage >2:no

value: LDH ratio >1:no

value: Age >60:yes

value: IPI score:1

value: Immune response 1:9.09

value: Immune response 2:9.13

value: With translocation:no


title: SLN:1854 - A - mAdbID:39405

description: mAdb experiment ID: 39405

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:13.81

value: Stage >2:yes

value: Immune response 1:9.32

value: Immune response 2:8.84


title: SLN:1772 - B - mAdbID:39275

description: mAdb experiment ID: 39275

value: Lymph node

value: Follow up status:dead

value: Follow up years:13.64

value: LDH ratio >1:NA

value: Number of extranodal sites >1:yes

value: Age >60:no

value: IPI score:NA

value: Immune response 1:9.49

value: Immune response 2:8.49

value: With translocation:yes


title: SLN:1792 - B - mAdbID:39278

description: mAdb experiment ID: 39278

value: Follow up years:2.01

value: Number of extranodal sites >1:no

value: Immune response 1:9.33

value: Immune response 2:8.72


title: SLN:1851 - A - mAdbID:39403

description: mAdb experiment ID: 39403

value: Follicular Lymphoma

value: Follow up years:4.08

value: Stage >2:yes

value: LDH ratio >1:yes

value: Age >60:yes

value: IPI score:2

value: Immune response 1:9.43

value: Immune response 2:9.01


title: SLN:1870 - A - mAdbID:39472

description: mAdb experiment ID: 39472

value: Lymph node

value: Follow up status:dead

value: Follow up years:6.41

value: LDH ratio >1:no

value: Immune response 1:10.01

value: Immune response 2:9.22


title: SLN:1855 - A - mAdbID:39466

description: mAdb experiment ID: 39466

value: Follow up years:9.96

value: Stage >2:no

value: Number of extranodal sites >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.31

value: Immune response 2:8.39

value: With translocation:yes


title: SLN:1874 - A - mAdbID:39475

description: mAdb experiment ID: 39475

value: Follicular Lymphoma

value: Follow up years:3.15

value: Stage >2:yes

value: LDH ratio >1:yes

value: Number of extranodal sites >1:yes

value: IPI score:2

value: Immune response 1:9.38

value: Immune response 2:8.74


title: SLN:1768 - B - mAdbID:39274

description: mAdb experiment ID: 39274

value: Lymph node

value: Follow up status:alive

value: Follow up years:13.04

value: LDH ratio >1:NA

value: IPI score:NA

value: Immune response 1:9.42

value: Immune response 2:8.47


title: SLN:1771 - B - mAdbID:39273

description: mAdb experiment ID: 39273

value: Follow up status:dead

value: Follow up years:9.26

value: Stage >2:no

value: Number of extranodal sites >1:no

value: Age >60:yes

value: Immune response 1:9.09

value: Immune response 2:8.67


title: SLN:1797 - B - mAdbID:39280

description: mAdb experiment ID: 39280

value: Follicular Lymphoma

value: Follow up years:7.17

value: Stage >2:yes

value: LDH ratio >1:yes

value: Number of extranodal sites >1:yes

value: Age >60:no

value: IPI score:3

value: Immune response 1:9.34

value: Immune response 2:8.92

value: With translocation:yes


title: SLN:1795 - B - mAdbID:39279

description: mAdb experiment ID: 39279

value: Lymph node

value: Follow up status:dead

value: Follow up years:0.71

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:10.19

value: Immune response 2:9.27


title: SLN:1764 - B - mAdbID:39213

description: mAdb experiment ID: 39213

value: Follicular Lymphoma

value: Follow up years:0.42

value: Stage >2:no

value: LDH ratio >1:NA

value: Number of extranodal sites >1:no

value: Age >60:yes

value: IPI score:NA

value: Immune response 1:9.25

value: Immune response 2:8.87


title: SLN:1850 - A - mAdbID:39402

description: mAdb experiment ID: 39402

value: Follow up status:NA

value: Follow up years:

value: Stage >2:NA

value: Age >60:NA

value: Immune response 1:9.75

value: Immune response 2:8.83

value: With translocation:no


title: SLN:1839 - A - mAdbID:39395

description: mAdb experiment ID: 39395

value: Lymph node

value: Follow up status:alive

value: Follow up years:4.48

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:8.56

value: Immune response 2:8.32

value: With translocation:yes


title: SLN:1837 - A - mAdbID:39393

description: mAdb experiment ID: 39393

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:0.55

value: Stage >2:yes

value: LDH ratio >1:yes

value: Number of extranodal sites >1:no

value: Age >60:no

value: IPI score:2

value: Immune response 1:9.47

value: Immune response 2:8.84


title: SLN:1834 - A - mAdbID:39389

description: mAdb experiment ID: 39389

value: Lymph node

value: Follow up status:alive

value: Follow up years:15.92

value: Immune response 1:9.22

value: Immune response 2:8.72


title: SLN:1833 - A - mAdbID:39388

description: mAdb experiment ID: 39388

value: Follow up years:11.95

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:9.74

value: Immune response 2:8.67

value: With translocation:no


title: SLN:1838 - A - mAdbID:39394

description: mAdb experiment ID: 39394

value: Follicular Lymphoma

value: Follow up years:2.54

value: Stage >2:no

value: Age >60:yes

value: Immune response 1:9.9

value: Immune response 2:9.12


title: SLN:1836 - A - mAdbID:39391

description: mAdb experiment ID: 39391

value: Lymph node

value: Follow up years:12.24

value: Stage >2:yes

value: Number of extranodal sites >1:no

value: Age >60:no

value: Immune response 1:9.55

value: Immune response 2:8.64

value: With translocation:yes


title: SLN:1846 - A - mAdbID:39400

description: mAdb experiment ID: 39400

value: Follow up status:dead

value: Follow up years:1.8

value: LDH ratio >1:yes

value: IPI score:2

value: Immune response 1:9.79

value: Immune response 2:9.61


title: SLN:1835 - A - mAdbID:39390

description: mAdb experiment ID: 39390

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:12.49

value: Immune response 1:9.26

value: Immune response 2:8.83


title: SLN:1844 - A - mAdbID:39398

description: mAdb experiment ID: 39398

value: Lymph node

value: Follow up years:13.39

value: Stage >2:no

value: IPI score:1

value: Immune response 1:9.41

value: Immune response 2:8.55


title: SLN:1729 - B - mAdbID:39209

description: mAdb experiment ID: 39209

value: Follow up years:8.06

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Age >60:no

value: Immune response 1:9.35

value: Immune response 2:8.65

value: With translocation:yes


title: TS053-D14-rep3

status: Public on Jun 23 2009

city: Ibaragi

first: kohei

last: inoue

address: Sunayama

country: Japan

institute: Mitsubishi Chemical Medience Corporation

description: Biological replicate 3 of 4. Control samples were pooled.

hyb_protocol: Fragmented cRNA was obtained by heating the solution of 1× fragmentation buffer (Invitrogen), 0.75 μg of Cy3-labeled cRNA, and 0.75 μg of Cy5-labeled cRNA at 94 deg C for 15 min. 30 μl of the fragmented mixture, 46.5 μl of water, 37.5 μl of 20× SSC, 7.5 μl of 10% SDS, and 12 μl of 5× Denhardt's solution were mixed and heated at 95 deg C for 2 min. 1.5 μl of 10 mg/ml salmon sperm DNA solution and 15 μl of formamide were added and heated at 60 deg C for 3 min. 130 μl of hybridization mixture was injected into a microarray chamber and sealed. The microarray was transferred to a hybridization chamber and incubated at 60 deg C overnight with rotation at 6 rpm. After incubation, the microarray was washed for 10 min at 30 degb C in lowstringency wash buffer (5× SSC and 0.1% SDS), washed twice for 2 min at 30 deg C in high-stringency wash buffer (0.5× SSC), and finally rinsed with 0.5× SSC and 0.01% Tween20. The microarray was dried by centrifugation at 360×g for 1 min.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using GenePix Pro Software (version 4.0).

data_processing: LOWESS normalized, background subtracted data was calculated by an R package 'sma' using processed Red signal and processed Green signal.

organism: Rattus norvegicus

source_name: rat liver, control

label_protocol: Amino-allyl cRNA was synthesized from 5 μg of total RNA using the SuperScript Indirect RNA Amplification System (Invitrogen). Amino-allyl cRNA was amplified by in vitro transcription reaction for 3 h, purified using the RNeasy MinElute Kit (Qiagen), and used for the fluorescent dye coupling reaction with the Cy3 or Cy5 Post-Labeling Reactive Dye Pack (GE Healthcare). Amino-allyl cRNA from individual compound-treated rats and pooled time-matched control rats were labeled with Cy3 and Cy5, respectively.

growth_protocol: 4 week-old male Fischer 344 rats were purchased from Charles River Japan. They were housed in an air-conditioned room at 22±2 deg C and 55±15% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (CRF-1, Oriental Yeast Co.), with tap water ad libitum.

extract_protocol: Total RNA was extracted from liver using RNeasy Midi Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Each group was composed of 4 rats. At each time point for each compound, there were a group that received the test compound and a control group. Compounds were administered once daily by oral gavage at a dose of 5 ml/kg for up to 1, 3, 7, 14, or 28 days. Control animals received corresponding volumes of vehicle.

tag: gender

value: Male

tag: age

value: 5 weeks

value: Liver

tag: compound

value: Vehicle

tag: dose

tag: administration

value: gavage

tag: treatment time

value: 14 days

tag: vehicle

value: Water

source_name: rat liver, chemically-treated

value: Methapyrilene HCl

tag: treatment


title: SLN:1845 - A - mAdbID:39399

description: mAdb experiment ID: 39399

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:12.92

value: Stage >2:yes

value: IPI score:2

value: Immune response 1:9.89

value: Immune response 2:9.04


title: SLN:1717 - B - mAdbID:39205

description: mAdb experiment ID: 39205

value: Follow up years:2.01

value: Stage >2:NA

value: LDH ratio >1:yes

value: Number of extranodal sites >1:no

value: Age >60:yes

value: IPI score:NA

value: Immune response 1:9.35

value: Immune response 2:8.88

value: With translocation:yes


title: SLN:1732 - B - mAdbID:39210

description: mAdb experiment ID: 39210

value: Lymph node

value: Follow up years:0.71

value: Immune response 1:7.81

value: Immune response 2:8.59


title: SLN:1848 - A - mAdbID:39401

description: mAdb experiment ID: 39401

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:12.52

value: Stage >2:yes

value: LDH ratio >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.76

value: Immune response 2:8.81