title: Liver rosiglitazone 84µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone


title: 13852141 - pER8 25+ 1 vs pER8 25- 1

status: Public on Jan 16 2010

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Are there some genes deregulated by the p25 viral protein.

hyb_protocol: pER8 25- 1 Cy5 / pER8 25+ 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,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

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

growth_protocol: root - Media=MS255	 Temperature=21°C - 17°C	 Light=16h - 8h

treatment_protocol: Name:Induction - gene induction - compound addition,estradiol:quantity 10mM time 5hour . Bedding out of the plants from a plate to an other plate that contains the compound, and then root extraction 5 hours later.

tag: ecotype

value: columbia

tag: genome/variation

value: mutant (per8::P25-)

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

value: mutant (per8::P25+)


title: 13852145 - 25 4F 2 vs WT 4F 2

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

source_name: WT 4F 2

treatment_protocol: no treatment

value: wild type

value: mutant (p25)


title: 13852136 - 25 2F 2 vs WT 2F 2

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

source_name: WT 2F 2


title: Liver rosiglitazone 84µmol/kg biological replicate 4

city: Croissy-sur-Seine

first: Aurélie

last: Cotillard

address: 125 chemin de ronde

institute: Institut de Recherches Servier

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone

hyb_protocol: Samples were incubated at 60°C for 30 minutes and then hybridized for 17 hours at 65°C in a 10 rpm rotary oven. Slides were then washed in buffer 1 and 2, according to manufacturer’s specification.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization (GE2-v5_95_Feb07 protocol). Rosetta Resolver (v 7.1) was used for the dye-swap combination.

organism: Mus musculus

source_name: Pool of db/db control mice

label_protocol: Total RNA samples were labelled using Agilent low RNA input linear amplification Kit, according to the manufacturer's protocols. 500ng of liver and IAT total RNA were reversed transcribed by MMLV reverse transcriptase. Amplification and labelling were done by T7-polymerase transcription. Test and reference cRNA were labelled with cyanine Cy5 or Cy3-CTP dyes.

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

treatment_protocol: Per os treatment for 18 days

tag: tissue

value: Liver

tag: strain

value: BKS Cg-m+/+ Leprdb/J

source_name: db/db mouse treated with 84µmol/kg of rosiglitazone


title: Area X, singing 5hr, Replicate 6

city: Durham

first: Osceola

last: Whitney

state: NC

address: Research Drive, Bryan Research Building, Room 401E

department: Neurobiology

country: USA

institute: Duke University Medical Center

description:
Gene expression after singing
54 male zebra finch birds were isolated overnight in sound attenuation chambers on a 12/12 light:dark cycle with ad lib access to food and water.

hyb_protocol: Labeled cDNA was dried in a speed-vac and resuspended in 25ul of hybridization buffer that contained 16% formamide, and 1X Agilent Blocking buffer. Samples were then denatured at 95 degrees for 3 mins and 18uLs of each samples was loaded to each array. Each micrroarray slide contained 4 arrays (4X44K) that were hybridized using a special A4 clamp to hold Agilent 4 x 44K arrays in Maui A4 mixers. The mixer was held at 55oC for at least 20 hrs, with the humidity chamber positioned over arrays.The following day, slides were rinsed in pre-heated (42oC). They were then shaken in Agilent Wash 1 buffer solution at RT X 1min and then Agilent Wash 2 at 37C for 1min. The slides were then slowly removed from the Wash buffer to minimize droplet formation.

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000 Microarray Scanner and Agilent's Feature Extraction Software v9.5.1 using one color scan setting for 4x44k array slides (Scan resolution was 5um, Dye channel was set to 532 [Green] and PMT to 520).

data_processing: The data was normalized with variance stabilization for one-color data based on Huber et al 2002 [PMID 12169536].  Microarrays with a low percentage of probes above background and high standard deviation from the median were removed.

organism: Taeniopygia guttata

source_name: Area X, singing 5hr

label_protocol: 2.2 ugs of purified cDNA was labeled and fragmented using FL-Ovation Cy3 labeling and fragmentation kit according to the manufacturers instructions (Nugen). 2.2 ugs of purified cDNA was labeled and fragmented using FL-Ovation Cy3 labeling and fragmentation kit according to the manufacturers instructions (Nugen).   Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Picopure RNA Extraction kit (Molecular Devices, Sunnyvale, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer (Nanodrop Wilmington, DE) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). From 1.5-2ng of total RNA, amplified cDNA was prepared using the WT-Ovation Pico System (Nugen, San Carlos, CA) according to the manufacturer's instructions.

treatment_protocol: In the morning before singing or immediately after singing for 0.5, 1, 2, 3, 4, 5, 6, or 7hrs, brains were quickly dissected. For the singing groups, we used birds that sang continuously >25 bouts per 0.5 hours.

value: Brain

tag: gender

value: Male

tag: age

value: >120 days


title: 13852139 - 25 4F 1 vs WT 4F 1

hyb_protocol: WT 4F 1 Cy5 / 25 4F 1 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: WT 4F 1


title: Area X, singing 5hr, Replicate 5


title: 13852131 - 25 2F 1 vs WT 2F 1

hyb_protocol: WT 2F 1 Cy5 / 25 2F 1 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: WT 2F 1


title: 13852138 - WT 4F 1 vs 25 4F 1

hyb_protocol: 25 4F 1 Cy5 / WT 4F 1 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: FW040025_SDA_pH5_rep2

city: Hobart

first: John

middle: Phillip

last: Bowman

state: Tasmania

address: College Road, Sandy Bay

department: School of Agricultural Science

country: Australia

institute: University of Tasmania

description: Biological replicate 2 of 2

hyb_protocol: Slides were pre-hybridized in a hybridization solution [25 %, v/v, formamide, 5x SSC buffer (0.75 M NaCl, 0.075 M trisodium citrate, pH 7.0), 0.1 % SDS] containing 10 mg BSA ml–1 for 45 min at 42 °C. Slides were then rinsed twice in distilled water and air-dried. Hybridization was performed in a humid hybridization chamber at 42 °C for 16–20 h using a hybridization solution containing 0.42 µg human Cot1 DNA µl–1, 0.62 µg polyA µl–1 and 0.83 µg salmon sperm DNA µl–1. Slides were washed at room temperature in 1x SSC buffer containing 0.2 % SDS for 5 min and again in 0.1x SSC buffer containing 0.2 % SDS for 5 min. The slides were then further washed twice in 0.1x SSC buffer at room temperature for 2 min and then air-dried.

scan_protocol: Scanned using a GenePix 4000A scanner (Axon Instruments)

data_processing: Normalisation followed the method of Kort et al. 2008 (Kort, R., B. J. Keijser, M. P. M. Caspers, F. H. Schuren, and R. Montijn. 2008. Transcriptional activity around bacterial cell death reveals molecular biomarkers for cell viability. BMC Genomics 9: article no. 590.)  1. Background values subtracted  2. Raw ratio determined between Cy5 and Cy3 channels for each replicate independently  3. Weak hybridizing spots removed, including those equal or less to combined background values.  4. The raw ratios were average and the average value used to normalise the raw ratio (e.g. raw ratio/overall average ratio).  5. The normalised ratios were then coverted to log2 ratios and averaged between replicates to obtain a final value.  6. Significance was tested using one-way ANOVA analysis of log ratio values assuming a null hypothesis that the log ratio equalled 0.

organism: Listeria monocytogenes

source_name: BHI broth, pH 5.0

label_protocol: RNA was converted to cDNA and post-labelled with Cy5 (red) and Cy3 (green) fluorescent dyes using the SuperScript Indirect cDNA Labelling System (Invitrogen).

growth_protocol: Controls grown to exponential growth phase (at 25 C) in brain-heart infusion broth (Oxoid), unadjusted pH (pH 7.3) or adjusted to pH 5 (with HCl). Flasks shaken in a watherbath at 100 rpm per minute.

extract_protocol: All cultures were pelleted at 4000 rpm for 10 min and then suspended in 3 ml Bacterial RNA Protect reagent (Qiagen) for 15 min with constant agitation followed by centrifugation and storage at -80 C. Cells were defrosted and underwent a 2–3 h (25 °C) enzymic treatment in TE buffer (10 mM Tris/HCl, 1 mM disodium EDTA, pH 7.5) containing 20 mg lysozyme ml–1 and 10 mg proteinase K ml–1. Cells were fully lysed by bead beating using 0.1 mm zirconium-silica sand in RNAeasy MIDI RNA extraction kit (Qiagen) lysis buffer containing 0.1 % β-mercaptoethanol. RNA was then extracted and purified using the RNAeasy kit and subsequently stored at –80 °C. RNA quality and quantity was assessed with the Agilent Technologies bioanalyser 2100 and RNA LabChip.

treatment_protocol: Test cultures grown to exponential growth phase (at 25 C) in brain-heart infusion broth (Oxoid), adjusted to pH 5 (with HCl) (mildly acidic stress treatment) or or ammended with 21 mM sodium diacetate and adjusted to pH 5.0. Flasks shaken in a watherbath at 100 rpm per minute.

source_name: BHI broth, pH 5.0+21mM SDA


title: Liver rosiglitazone 84µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone


title: 13852135 - WT 2F 2 vs 25 2F 2

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


title: Area X, singing 5hr, Replicate 3


title: EGD_SDA_pH5_rep2

description: Biological replicate 2 of 4

value: EGD


title: 13852130 - WT 2F 1 vs 25 2F 1

hyb_protocol: 25 2F 1 Cy5 / WT 2F 1 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: EGD_SDA_pH5_rep3

description: Biological replicate 3 of 4


title: EGD_SDA_pH5_rep1

description: Biological replicate 1 of 4


title: Area X, singing 5hr, Replicate 2


title: Liver rosiglitazone 28µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone

source_name: db/db mouse treated with 28µmol/kg of rosiglitazone


title: Area X, singing 5hr, Replicate 1


title: Liver rosiglitazone 84µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone


title: Area X, singing 5hr, Replicate 4


title: FW040025_pH5_pH7_rep4

description: Biological replicate 4 of 4

source_name: BHI broth, pH 7.3


title: Area X, singing 4hr, Replicate 5

source_name: Area X, singing 4hr


title: Liver rosiglitazone 28µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Area X, singing 4hr, Replicate 4


title: FW040025_pH5_pH7_rep2

description: Biological replicate 2 of 4


title: FW040025_pH5_pH7_rep3

description: Biological replicate 3 of 4


title: EGD_SDA_pH5_rep4

description: Biological replicate 4 of 4


title: FW040025_SDA_pH5_rep1

description: Biological replicate 1 of 2


title: Liver rosiglitazone 84µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone


title: FW040025_pH5_pH7_rep1

description: Biological replicate 1 of 4


title: Area X, singing 7hr, Replicate 3

source_name: Area X, singing 7hr


title: Liver rosiglitazone 28µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Area X, singing 4hr, Replicate 3


title: EGD_pH5_pH7_rep4

description: Biological replicate 4 of 4


title: EGD_pH5_pH7_rep3

description: Biological replicate 3 of 4


title: EGD_pH5_pH7_rep2

description: Biological replicate 2 of 4


title: Liver rosiglitazone 28µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Liver rosiglitazone 28µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Area X, singing 4hr, Replicate 2


title: EGD_pH5_pH7_rep1

description: Biological replicate 1 of 4


title: Constitutively active STAT3 cell line 3, replicate 1

status: Public on Jan 15 2010

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

hyb_protocol: For the hybridization step the samples are applied to the arrays and assembled into the BeadChip Hyb Chamber. The BeadChip is hybridized at 58°C overnight, and then washed the following day.

scan_protocol: Scanning was performed using Illumina Beadarray scanner

data_processing: Raw expression data were obtained with BeadStudio, version 3.1.7. Normalization was performed with the lumi package of Bioconductor and  default parameters

label: biotin

source_name: Tumor-derived cell line 3, constitutively active STAT3

label_protocol: RNA amplification and labelling were performed using the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: Cells were cultured in RPMI 1360 supplemented with  FCS 20%, 2 mM Glutamax, 100 U/ml Pennicillin, 100 ug/ml Streptomycin and mainteined at 37°C in a 5% CO2 atmosphere

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) followed by purification on a Qiagen RNAeasy midi column

tag: genotype

value: Constitutively active STAT3


title: TRP-1 CD4+ T Cells from LN of Mice Undergoing Tumor Treatment Compared to Naïve TRP-1 CD4+ T Cells

city: Baltimore

first: Paul

middle: Andrew

last: Antony

state: MD

address: 10 South Pine Street

department: Program in Molecular Microbiology and Immunology

institute: University of Maryland School of Medicine

description: TRP-1 CD4+ T cells from LN of mice undergoing tumor treatment compared to naïve TRP-1 CD4+ T cells.

hyb_protocol: Fragmentation was carried out by incubating at 60oC for 30 minutes and stopped by adding equal volume of 2x GE Hi- RPM hybridization buffer (Agilent Technologies). Agilent 4X44K Whole Mouse Genome Array (G4122F) with 41,534 unique probes was used. Fragmented targets were added onto a microarray, assembled into a hybridization chamber (Agilent Technologies) and hybridized at 60oC for 17 hours in a hybridization oven with rotation. Hybridized microarrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: Sample amplification and labeling procedures were carried out using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The cDNA was used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-labeled CTPs. The labeled cRNA was purified using RNeasy micro kit (Qiagen) and followed by quantification of both concentrations of cRNA and dye labeled.

extract_protocol: Total RNA extracted using RNA isolation kits from Qiagen.

treatment_protocol: 2 x 10^5 sorted TRP-1 CD4+ T cells were transferred i.v. into tumor-bearing RAG-/- hosts on day 7-10 after tumor challenge, and ~1 x 10^6 CD4+ T cells were isolated 1 week later by flow sorting from pooled lymph nodes.

value: RAG -/-

tag: tumor

value: melanoma

value: lymph nodes

tag: cell type

value: TRP-1 CD4+ T cells

source_name: Naïve TRP-1 CD4+ T cells from Tg mice

value: naïve TRP-1 CD4+ T cells


title: Constitutively active STAT3 cell line 2, replicate 2

source_name: Tumor-derived cell line 2, constitutively active STAT3


title: TRP-1 CD4+ T Cells from Spleen of Mice Undergoing Tumor Treatment Compared to Naïve TRP-1 CD4+ T Cells

description: TRP-1 CD4+ T cells from spleen of mice undergoing tumor treatment compared to naïve TRP-1 CD4+ T cells.

treatment_protocol: 2 x 10^5 sorted TRP-1 CD4+ T cells were transferred i.v. into tumor-bearing RAG-/- hosts on day 7-10 after tumor challenge, and ~1 x 10^6 CD4+ T cells were isolated 1 week later by flow sorting from pooled spleens.

value: spleen


title: Wild-type cell line 3, replicate 2

source_name: Tumor-derived cell line 3, wild-type STAT3

value: Wild-type STAT3


title: Constitutively active STAT3 cell line 2, replicate 1


title: Constitutively active STAT3 cell line 1, replicate 1

source_name: Tumor-derived cell line 1, constitutively active STAT3


title: Wild-type cell line 2, replicate 2

source_name: Tumor-derived cell line 2, wild-type STAT3


title: Wild-type cell line 1, replicate 2

source_name: Tumor-derived cell line 1, wild-type STAT3


title: Wild-type cell line 2, replicate 1


title: Naïve TRP-1 CD4+ T Cells Compared to TRP-1 CD4+ T Cells from Spleen of Mice Undergoing Tumor Treatment

description: Naïve TRP-1 CD4+ T cells compared to TRP-1 CD4+ T cells from spleen of mice undergoing tumor treatment.


title: Constitutively active STAT3 cell line 3, replicate 2


title: KM120T

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Mad2-induced chromosome instability leads to lung tumor relapse after oncogene withdrawal

hyb_protocol: according to manufacturer

scan_protocol: according to manufacturer

data_processing: Affymetrix Microarray Suite version 5.0, total intensity targeted to 500.

source_name: lung tumor TI-KM

label_protocol: affymetrix two cycle target prep

extract_protocol: RNeasy (Qiagen)

value: lung adenocarcinoma/adenoma

value: TI-KM 129/Bl6 mixed background

value: CCSP-rtTA;TRE-KrasV12; TRE-Mad2


title: Constitutively active STAT3 cell line 1, replicate 2


title: Wild-type cell line 1, replicate 1


title: Wild-type cell line 3, replicate 1


title: K1024T

source_name: lung tumor TI-K

value: TI-K 129/Bl6 mixed background


title: KM214R

source_name: lung tumor recurrence TI-KM

value: lung adenocarcinoma/adenoma recurrence


title: KM922T


title: KM780T


title: KM1011T


title: KM907T


title: KM1010T


title: K699T


title: KM651R


title: KM33T


title: K779T


title: Liver rosiglitazone 28µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone

source_name: Pool of db/db control mice

value: Liver

value: BKS Cg-m+/+ Leprdb/J


title: KM704R


title: KM600R


title: KM737T


title: KM646R


title: KM580R


title: KM76T2


title: Naïve TRP-1 CD4+ T Cells Compared to TRP-1 CD4+ T Cells from LN of Mice Undergoing Tumor Treatment

description: Naïve TRP-1 CD4+ T cells compared to TRP-1 CD4+ T cells from LN of mice undergoing tumor treatment.


title: KM417T1


title: KM240T


title: K7545T


title: K7266T


title: K6920T


title: Mock biol_repl3

city: Denver

first: Laurel

last: Lenz

state: CO

address: 1400 Jackson St

institute: National Jewish Health

description: Gene expression from macrophages mock infected at d7 in culture.

hyb_protocol: Model 450 Fluidics Station

scan_protocol: Model GCS 3000 Gene array scanner

data_processing: CEL files were loaded into genechip operating software for normalization. Probesets with a P value were further analyzed based on comparisons of mean signal intensities using GeneSifter software (see Series GSE19374 supplementary file).

source_name: mock infected mouse bone marrow derived macrophages (MOCK_3)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bone marrow cells were isolated from female C57BL/6 mice and cultured for 6 days in DMEM/penicillin/streptomycin/10 % FCS/10 % L cell conditioned media as a source of L-CSF. They were replated overnight in antibiotic free media prior to experiment.

extract_protocol: RNA was extracted using Qiagen RNEasy mini kits with on-column DNAse treatment.

treatment_protocol: Macrophages were treated with 100 ul of PBS or 100 ul PBS containing washed, log-phase Listeria monocytogenes at a final multiplicity of 2 bacteria per cell.

value: bone marrow derived macrophages

value: female

tag: host genotype

value: C57BL/6 mouse

tag: infection

value: mock


title: hyperoxic_P12_rep1

city: Fukuoka

first: Keijiro

last: Ishikawa

address: 3-1-1  Maidashi, Higashi-ku

department: Ophthalmology

country: Japan

institute: Kyushu University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw gene expression data were summarized using the Illumina Bead Studio software. Normalization (quantile method), calculation of signal intensities and fold change  analysis between groups were performed by Genespring v 7.3

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

growth_protocol: Litters of 7-day-old [postnatal day 7 (P7)] C57BL/6N pups along with their mothers were placed in a 75 ± 2% oxygen atmosphere for 5 days and then returned to room air at age P12

extract_protocol: To extract the RNAs, retinas isolated from normal P12 mice, P12 and P12.5 hyperoxic/hypoxic exposed mice were homogenized with a Polytron homogenizer in extraction reagent, extracted with chloroform, and the aqueous phase was precipitated in isopropanol.

tag: tissue type

value: retina

value: postnatal day12


title: K6900T


title: Cecae, 24h, Salmonella challenged, probiotic treated 1h later, replicate 3

status: Public on Jan 14 2010

city: College Park

first: Tom

middle: E.

last: Porter

address: Building 142

department: Animal and Avian Sciences

institute: University of Maryland

description:
Salmonella challenged (1x10^4 cfu/ chick) and treated one h later with probiotic (1x10^6 cfu/chick)
Biological Replicate 3 of 4

hyb_protocol: The arrays were baked at 90C for 90 minutes prior to use.  Pre-treatment of slides was accomplished by incubation of slides in pre-hybridization solution (5xSSC, 0.1%SDS, and 1% BSA) for 45 min at 42C.  Slides were then dipped in 2x SSC and 0.2x SSC for 5 min each.  Slides were dried by centrifugation (5 min at 1000 x g).  An aliquot of 5 µg of labeled, purified aRNA was fragmented in 1x fragmentation buffer (Ambion, Austin, TX) for 15 min at 70C.  Stop solution was added to terminate the reaction, and samples were dried again in the SpeedVac.  Pre-warmed DIG Easy Hyb solution (Roche Diagnostics Corporation, Indianapolis, IN) was used to reconstitute the samples in a 30 µL volume.  Reference aRNA samples used within the same day were pooled and aliquoted. One reference pool (30 µL) and one sample (target) (30 µL) were mixed and 2.5 µL of 10mg/mL yeast tRNA and 2.5 µL of 10mg/mL salmon testes DNA (Sigma, St. Louis, MO) were added. The target/reference mixture (65 µL) was heated to 94C for 2 min for denaturation, cooled at room temperature, and loaded to the middle of a pre-treated slide held in a hybridization chamber (Corning #2551, Lowell, MA), which was overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). Slides were then incubated for 14-16h at 42C inside a light-tight sealed box in a water bath.  Following incubation, the cover slip was removed by flushing with wash solution #1 (1x SSC, 0.2% SDS, 0.5% DTT).   Sequential washes were as follows: Ten min at 42C in pre-warmed wash solution #1, five min at room temp in wash solution #2 (0.1x SSC, 0.2% SDS, 0.5% DTT), and one min at room temperature in wash solution #3 (0.1x SSC, 0.5% DTT).  Slides were then washed with ddH2O and dried by centrifugation.  Slides were stored in 50 mL conical tubes covered in foil in the presence of nitrogen gas until scanning.

scan_protocol: GenePix 4000B microarray scanner was used to scan each slide. The image was acquired at 10 µm resolution during simultaneous scanning of two wavelengths, 532nm (green) and 635nm (red).  The PMT count ratio was adjusted to 1 during preview at low resolution scanning, and a high resolution TIFF image file was then obtained.

data_processing: Each TIFF image was further analyzed with GenePix Pro software, generating a GenePix Report (gpr) file.  GenePix report files were converted to .mev files using Express Converter software freely available from The Institute for Genomic Research (TIGR) website.  Converted files were Lowess normalized using Microarray Data Analysis System (MIDAS) software, also freely available on the TIGR website.

label: Alexa 555

organism: Gallus gallus

source_name: Pool of 2 individual rinsed cecae from 2 separate chicks

label_protocol: Dye labeling was accomplished according to the instructions for dye labeling and labeled aRNA cleanup with the Amino Allyl MessageAmpTM II aRNA Amplification Kit.  Twenty micrograms of aRNA were dried to a minimal volume (not overdryed) in a SpeedVac concentrator. The aRNA was then reconstituted in 9µL of coupling buffer and mixed with 11µL of prepared dye. Aliquots of the dye (60 µg) were dissolved in DMSO just prior to use.  aRNA with dye was incubated in the dark for one h at room temperature for coupling.  The incorporation of dye and concentration of aRNA were quantified with the NanoDrop spectrophotometer (Wilmington, DE) and incorporation efficiency was determined using the calculator available at www.ambion.com/tools/dye

growth_protocol: Cobb broiler breeder chicks were obtained from a local hatchery.  Chicks were taken to the laboratory, randomized, and assigned to one of four treatment groups.  Chicks were placed in a battery brooder at an age appropriate temperature, with individual groups on separate levels.  All chicks were given free access to water and standard chick starter ration ad libitum.

extract_protocol: Total RNA was isolated from cecae using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s protocol.  The isolated RNA was quantified using the Ribogreen RNA Quantitation Kit (Molecular Probes, Eugene, OR) and RNA quality was determined by RNA gel electrophoresis.  RNA was then amplified using the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion, Austin, TX).  One round of RNA amplification was performed using 2µg of total RNA.  In vitro transcription (IVT) was performed for 14h at 37C.  aRNA was quantified and analyzed for quality using the same methods as were used for total RNA.

treatment_protocol: Two groups of chicks were challenged with 1x10^4 cfu of Salmonella enteritica subsp. Enteritidis phage type 13A by oral gavage.  Two groups of unchallenged chicks were also orally gavaged with the vehicle alone, which was sterile saline.  One hour post-challenge, one non-challenged and one challenged group were subsequently treated with 1 x 10^6 cfu of probiotic culture by oral gavage.  The two remaining groups received the vehicle, skim milk, by oral gavage.  Chicks were returned to the battery brooder, and samples were collected at 12h and 24h post-treatment.  One cecae per chick was rinsed, pooled with another cecae, and snap frozen for RNA isolation and microarray analysis.  These were stored at -80 until RNA extraction.  The other cecae from each chick was subjected to microbiological analysis to determine the presence of Salmonella infection and enumerate the bacteria.

tag: salmonella challenge

tag: probiotic treatment

tag: time

value: 24h post-treatment

label: Alexa 647

source_name: Reference pool, 40 cecae

tag: reference

value: pool of all samples in experiment


title: K6843T


title: hyperoxic_P12_rep3


title: hypoxic_P12.5_rep3

value: postnatal day12.5


title: Cecae, 24h, Salmonella challenged, probiotic treated 1h later, replicate 2

description:
Salmonella challenged (1x10^4 cfu/ chick) and treated one h later with probiotic (1x10^6 cfu/chick)
Biological Replicate 2 of 4


title: hypoxic_P12.5_rep1


title: control_P12_rep1


title: Infected biol_repl2

description: Gene expression from macrophages infected with Listeria monocytogenes at d7 in culture.

source_name: Listeria infected mouse bone marrow derived macrophages (LM_INF_2)

value: Listeria monocytogenes strain 10403S


title: Cecae, 24h, Salmonella challenged, probiotic treated 1h later, replicate 4

description:
Salmonella challenged (1x10^4 cfu/ chick) and treated one h later with probiotic (1x10^6 cfu/chick)
Biological Replicate 4 of 4


title: Infected biol_repl1

source_name: Listeria infected mouse bone marrow derived macrophages (LM_INF_1)


title: control_P12_rep3


title: CCSP

source_name: normal lung

value: normal lung tissue

value: 129/Bl6 mixed background

value: CCSP-rtTA


title: KM434T

value: lung adenocarcinoma/adenoma

value: TI-KM 129/Bl6 mixed background

value: CCSP-rtTA;TRE-KrasV12; TRE-Mad2


title: Mock biol_repl1

source_name: mock infected mouse bone marrow derived macrophages (MOCK_1)


title: hyperoxic_P12_rep2


title: Mock biol_repl2

source_name: mock infected mouse bone marrow derived macrophages (MOCK_2)


title: hypoxic_P12.5_rep2


title: control_P12_rep2


title: Cecae, 24h, Salmonella challenged, replicate 1

description:
Salmonella challenged (1x10^4 cfu/ chick)
Biological Replicate 1 of 4


title: KM76T1


title: Cecae, 24h, Salmonella challenged, replicate 2

description:
Salmonella challenged (1x10^4 cfu/ chick)
Biological Replicate 2 of 4


title: Cecae, 24h, Salmonella challenged, replicate 4

description:
Salmonella challenged (1x10^4 cfu/ chick)
Biological Replicate 4 of 4


title: Cecae, 24h, Salmonella challenged, probiotic treated 1h later, replicate 1

description:
Salmonella challenged (1x10^4 cfu/ chick) and treated one h later with probiotic (1x10^6 cfu/chick)
Biological Replicate 1 of 4


title: Cecae, 24h, probiotic treatment, replicate 3

description:
probiotic treated (1x10^6 cfu/chick)
Biological Replicate 3 of 4

value: probiotic treated (1x10^6 cfu/chick)


title: Cecae, 24h, probiotic treatment, replicate 4

description:
probiotic treated (1x10^6 cfu/chick)
Biological Replicate 4 of 4


title: Cecae, 24h, probiotic treatment, replicate 1

description:
probiotic treated (1x10^6 cfu/chick)
Biological Replicate 1 of 4


title: Cecae, 24h, Salmonella challenged, replicate 3

description:
Salmonella challenged (1x10^4 cfu/ chick)
Biological Replicate 3 of 4


title: Cecae, 24h, probiotic treatment, replicate 2

description:
probiotic treated (1x10^6 cfu/chick)
Biological Replicate 2 of 4


title: 26-30 somites mid-foregut, biological rep2

city: Boston

first: Maria

middle: Isabel

last: Ramirez

state: MA

address: 72 E. Concord St. E603

department: Medicine

institute: Boston University School of Medicine

description: Gene expression data from mouse mid-foregut tissue at 26-30 somite stage

hyb_protocol: 10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.

scan_protocol: The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.

source_name: Mouse embryonic mid-foregut at 26-30 somite developmental stage

label_protocol: RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).

extract_protocol:
To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.

value: wild type

tag: development stage/age

value: embryos containing between 26 and 30 somites, E9.5


title: 26-30 somites mid-foregut, biological rep3


title: High N vs Low N rep4_B55

city: Urbana

first: Stephen

middle: Patrick

last: Moose

state: IL

address: 1201 W Gregory

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

description: High N vs Low N rep4

hyb_protocol: Hybridizations were performed overnight in custom designed cassettes in 42 degree water bath, followed by 3 washes.

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA). Used GenePix Pro 6.0 (Molecular Devices Corporation) for spotfinding.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

organism: Zea mays

source_name: B73 X Mo17

label_protocol: The Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion, Austin, TX) with Cyanine-3 and -5 (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) dyes were used to amplify and label samples.

extract_protocol: Total RNA was isolated using LS TRIzol (Invitrogen, Carlsbad, CA), digested by DNAse,  then Rneasy purification kit (Qiagen, Valencia, CA).

tag: hybrid line

value: B73 X Mo17

value: at Anthesis

value: Earshoot

tag: nitrogen condition

value: Nitrogen sufficient

tag: parental line

value: Nitrogen deficient


title: 16-20 somites mid-foregut, biological rep1

description: Gene expression data from mouse mid-foregut tissue at 16-20 somite stage

source_name: Mouse embryonic mid-foregut at 16-20 somite developmental stage

value: embryos containing between 16 and 20 somites, E8.5


title: High N vs Low N rep3_B54

description: High N vs Low N rep3


title: 21-25 somites mid-foregut, biological rep3

description: Gene expression data from mouse mid-foregut tissue at 21-25 somite stage

source_name: Mouse embryonic mid-foregut at 21-25 somite developmental stage

value: embryos containing between 21 and 25 somites, E9.0


title: 16-20 somites mid-foregut, biological rep2


title: Low N vs Low N rep4_B51

description: Low N vs Low N rep4


title: 26-30 somites mid-foregut, biological rep1


title: 21-25 somites mid-foregut, biological rep2


title: Low N vs Low N rep3_B50

description: Low N vs Low N rep3


title: High N vs Low N rep2_B53

description: High N vs Low N rep2


title: 21-25 somites mid-foregut, biological rep1


title: High N vs Low N rep1_B52

description: High N vs Low N rep1


title: 16-20 somites mid-foregut, biological rep3


title: Low N vs Low N rep2_B49

description: Low N vs Low N rep2


title: Cecae, 24h, no treatment, replicate 1

description:
no treatment
Biological Replicate 4 of 4

value: 24h post-treatment

value: pool of all samples in experiment


title: Cecae, 24h, no treatment, replicate 4

description:
no treatment
Biological Replicate 3 of 4


title: Cecae, 24h, no treatment, replicate 2

description:
no treatment
Biological Replicate 1 of 4


title: BL6/C57 mouse heart, control, rep1

first: Tobias

last: Eckle

address: 12700 E 19th Avenue

department: Anesthesiology

institute: UC Denver

description: snap frozen, left ventricle, area at risk

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

scan_protocol: After hybridization and staining, the arrays were scanned using a GCS3000 with the latest 7G upgrade

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: heart tissue, untreated controls

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

growth_protocol: male wildtype BL6/C57 mice were ordered from Jackson Laboratories. A2BAR deficient mice (BL6/C57 background) were bred in house. 12 week old male were used for the study.

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

treatment_protocol: In situ IP was performed in A2BAR-/- mice and matched littermate controls. IP consisted of 4 cycles of 5 min myocardial ischemia and 5 min reperfusion followed by 2 h of reperfusion. The area at risk was excised and shock frozen in liquid nitrogen. Controls were sham operated.

value: male

tag: strain

tag: genotype/variation

value: wildtype

value: 12 weeks


title: BL6/C57 mouse heart IP120, rep3

source_name: heart tissue treated with 4 cycles of 5 min ischemia/5 min reperfusion followed by 2 h of reperfusion

tag: gender

tag: age


title: KM973T

description: Mad2-induced chromosome instability leads to lung tumor relapse after oncogene withdrawal

source_name: lung tumor TI-KM

tag: tissue

value: lung adenocarcinoma/adenoma

value: TI-KM 129/Bl6 mixed background

tag: genome/variation


title: BL6/C57 mouse heart, control, rep2


title: BL6/C57 mouse heart, control, rep3


title: BL6/C57 mouse heart IP120, rep2


title: Cecae, 12h, Salmonella challenged, probiotic treated 1h later, replicate 4

description:
Salmonella challenged (1x10^4 cfu/ chick) and treated one h later with probiotic (1x10^6 cfu/chick)
Biological Replicate 4 of 4

value: 12h post-treatment


title: Low N vs Low N rep1_B48

description: Low N vs Low N rep1


title: Cecae, 12h, Salmonella challenged, probiotic treated 1h later, replicate 3

description:
Salmonella challenged (1x10^4 cfu/ chick) and treated one h later with probiotic (1x10^6 cfu/chick)
Biological Replicate 3 of 4


title: Salmonella Typhimurium LT2 wt strain replicate 3

city: Brno

first: Magdalena

last: Crhanova

address: Hudcova 70

department: Bacteriology

country: Czech Republic

institute: Veterinary research institute

description: Biological replicate 3 of 3

hyb_protocol: Hybridisation and posthybridisation washes were performed using Nexterion Slide 70mer Kit exactly according to the instructions of the manufacturer.

scan_protocol: Scanned on an ScanArray® Express scanner (PerkinElmer).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. PerkinElmer ScanArray® Express software was used.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Total RNA from Salmonella Typhimurium LT2 rfaC mutant strain cells

label_protocol: Approx. 5 µg of total RNA was reverse transcribed and labeled with Cyanine-3- or Cyanine-5-CTPs using LabelStarTM Array Kit (Qiagen) according to the protocol

growth_protocol: Both bacterial strains were grown for 18 hours in 20 ml Luria-Bertani Broth (LB) at 37°C without shaking. Cultures were centrifuged and used for RNA purification.

extract_protocol: Total RNA was extracted using RNeasy® Mini Kit (Qiagen) following manufacturer's instructions

tag: genotype

value: rfaC mutant

source_name: Total RNA from Salmonella Typhimurium LT2 wt strain cells

value: wild type


title: Cecae, 24h, no treatment, replicate 3

description:
no treatment
Biological Replicate 2 of 4


title: Salmonella Typhimurium LT2 wt strain replicate 2

description: Biological replicate 2 of 3


title: A2BAR -/- mouse heart, control, rep2


title: Cecae, 12h, Salmonella challenged, probiotic treated 1h later, replicate 2

description:
Salmonella challenged (1x10^4 cfu/ chick) and treated one h later with probiotic (1x10^6 cfu/chick)
Biological Replicate 2 of 4


title: Cecae, 12h, Salmonella challenged, probiotic treated 1h later, replicate 1

description:
Salmonella challenged (1x10^4 cfu/ chick) and treated one h later with probiotic (1x10^6 cfu/chick)
Biological Replicate 1 of 4


title: A2BAR -/- mouse heart, control, rep3


title: Salmonella Typhimurium LT2 rfaC strain replicate 3

description: Biological replicate 3 of 3


title: A2BAR -/- mouse heart, control, rep1


title: A2BAR -/- mouse heart IP120, rep2


title: A2BAR -/- mouse heart IP120, rep3


title: Salmonella Typhimurium LT2 wt strain replicate 1

description: Biological replicate 1 of 3


title: BL6/C57 mouse heart IP120, rep1


title: Salmonella Typhimurium LT2 rfaC strain replicate 2

description: Biological replicate 2 of 3


title: Salmonella Typhimurium LT2 rfaC strain replicate 1

description: Biological replicate 1 of 3


title: Cecae, 12h, Salmonella challenged, replicate 2

description:
Salmonella challenged (1x10^4 cfu/ chick)
Biological Replicate 2 of 4


title: Cecae, 12h, Salmonella challenged, replicate 4

description:
Salmonella challenged (1x10^4 cfu/ chick)
Biological Replicate 4 of 4


title: A2BAR -/- mouse heart IP120, rep1


title: Cecae, 12h, Salmonella challenged, replicate 1

description:
Salmonella challenged (1x10^4 cfu/ chick)
Biological Replicate 1 of 4


title: Cecae, 12h, Salmonella challenged, replicate 3

description:
Salmonella challenged (1x10^4 cfu/ chick)
Biological Replicate 3 of 4


title: Basal cell carcinoma-2, Ptch1+/- Blm+/+, B205

type: genomic

city: San Francisco

first: Bing

last: Huey

state: CA

address: 1450 Third Street

department: Helen Diller Comprehensive Cancer Center

institute: University of California at San Francisco

hyb_protocol: The test and reference DNAs together with 100 ug human Cot-1 DNA were hybridized to the BAC arrays for ~48 hrs at 37C. After post-hybridization washes, the arrays were mounted in a solution containing 90% glycerol, 10% PBS and 1 uM DAPI and sealed with a cover slip.

scan_protocol: A custom built CCD camera system was used to acquire 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images (Pinkel et al., 1998). Image analysis was carried out using UCSF SPOT software (Jain et al., 2002).

data_processing: The log2ratio of the total integrated Cy3 and Cy5 intensities for each spot after background subtraction was calculated, normalized to the median log2ratio of all the clones on the array and the average of the triplicates calculated using a second custom program, SPROC. Automatic data filtering to reject data points based on low DAPI intensity, low correlation between Cy3 and Cy5 within each segmented spot and low reference/DAPI signal intensity was also carried out using SPROC. Data files were subsequently manually edited by rejecting clones for which only one spot of the triplicate survived after SPROC analysis and for which the standard deviation of the log2ratio of the triplicate was >0.2. For each tumor, the data are plotted as the mean log2ratio of the triplicate spots for each clone normalized to the genome median log2ratio. The clones are ordered by position in the genome (UCSC draft genome sequence, May 2004 freeze) beginning at chromosome 1 and ending with chromosome X.

molecule: genomic DNA

source_name: basal cell carcinoma, Ptch1+/- Blm+/+

label_protocol: The tumor genomic DNA and normal individually-matched genomic reference DNA (300 ng each) were labeled by random priming in separate 50 ul reactions to incorporate Cy3-dUTP and Cy5-dUTP, respectively.

extract_protocol: Genomic DNA was isolated from paraffin-embedded blocks (six BCC samples and five RMS samples from separate mice) by standard techniques. In addition, genomic DNA was extracted from paraffin-embedded liver tissue from each mouse to be used as the normal reference.

treatment_protocol: Tissues were paraffin embedded.

value: basal cell carcinoma

value: Ptch1+/- Blm+/+

tag: sample type

value: tumor

tag: sample source

source_name: liver, Ptch1+/- Blm+/+

value: liver

value: reference


title: Basal cell carcinoma, Ptch1+/- Blm-/-, B128

source_name: basal cell carcinoma, Ptch1+/- Blm-/-

value: Ptch1+/- Blm-/-

source_name: liver, Ptch1+/- Blm-/-


title: Basal cell carcinoma, Ptch1+/- Blm-/-, B86


title: Basal cell carcinoma-1, Ptch1+/- Blm+/+, B179


title: Basal cell carcinoma, Ptch1+/- Blm+/-, B137

source_name: basal cell carcinoma, Ptch1+/- Blm+/-

value: Ptch1+/- Blm+/-

source_name: liver, Ptch1+/- Blm+/-


title: Rhabdomyosarcoma, Ptch1+/- Blm-/-, B34

source_name: rhabdomyosarcoma, Ptch1+/- Blm-/-

value: rhabdomyosarcoma


title: Basal cell carcinoma, Ptch1+/- Blm+/-, B24


title: Cecae, 12h, no treatment, replicate 1

source_name: Pool of 2 individual rinsed cecae from 2 separate chicks

tag: salmonella challenge

source_name: Reference pool, 40 cecae

value: pool of all samples in experiment


title: Rhabdomyosarcoma, Ptch1+/- Blm+/+, B149

source_name: rhabdomyosarcoma, Ptch1+/- Blm+/+


title: Cecae, 12h, probiotic treatment, replicate 2

description:
probiotic treated (1x10^6 cfu/chick)
Biological Replicate 2 of 4

tag: probiotic treatment

value: probiotic treated (1x10^6 cfu/chick)


title: Cecae, 12h, no treatment, replicate 3

tag: time


title: Cecae, 12h, no treatment, replicate 4

tag: reference


title: Rhabdomyosarcoma, Ptch1+/- Blm+/-, B142

source_name: rhabdomyosarcoma, Ptch1+/- Blm+/-


title: Cecae, 12h, probiotic treatment, replicate 1

description:
probiotic treated (1x10^6 cfu/chick)
Biological Replicate 1 of 4


title: Cecae, 12h, probiotic treatment, replicate 3

description:
probiotic treated (1x10^6 cfu/chick)
Biological Replicate 3 of 4


title: High N vs Low N rep1_A54

description: High N vs Low N rep1

source_name: B73 X Mo17

value: B73 X Mo17

value: at Anthesis

tag: tissue type

value: Earshoot

value: Nitrogen sufficient

value: Nitrogen deficient


title: High N vs Low N rep4_A57

description: High N vs Low N rep4

tag: hybrid line


title: Cecae, 12h, no treatment, replicate 2

value: 12h post-treatment


title: Rhabdomyosarcoma, Ptch1+/- Blm-/-, B87


title: High N vs Low N rep2_A55

description: High N vs Low N rep2

tag: nitrogen condition


title: Low N vs Low N rep4_A53

description: Low N vs Low N rep4

tag: parental line


title: High N vs Low N rep3_A56

description: High N vs Low N rep3


title: Low N vs Low N rep1_A50

description: Low N vs Low N rep1


title: Low N vs Low N rep3_A52

description: Low N vs Low N rep3


title: Low N vs Low N rep2_A51

description: Low N vs Low N rep2


title: Cecae, 12h, probiotic treatment, replicate 4

description:
probiotic treated (1x10^6 cfu/chick)
Biological Replicate 4 of 4


title: Rhabdomyosarcoma, Ptch1+/- Blm+/-, B168


title: YRI Female, NA19240, slide 19

status: Public on Jan 13 2010

city: Seoul

first: Dongwan

last: Hong

address: 28 Yeongeon-dong, Jongno-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Genomic Medicine Institute, Seoul National University College of Medicine

description: CNV discovery from NA19240 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed using wash buffer I, II (Agilent Inc.).

scan_protocol: Scanned on an Agilent G2505 Scanner.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Homo sapiens

source_name: Immortalized cell line, African Yoruban female

label_protocol: 1.5ul of genomic DNA fragmented and amplified using random primer. Cy3-dCTP and Cy5-dCTP were incorporated using the BioPrime DNA labelling kit using the manufacturer’s protocol.

growth_protocol: Cell lines were cultured under 10% FBS+standard RPMI media. No antibacterials were used.

extract_protocol: Genomic DNA was extracted using the Gentra DNA extraction kit (Qiagen).

treatment_protocol: Not treated.

tag: population

value: African Yoruban

value: female

value: HapMap

value: control

source_name: NA10851 reference

value: Caucasian

value: male


title: Chinese Female, NA19582, slide 19

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, Chinese female

value: Chinese

value: test

value: reference


title: Japanese Female, NA18997, slide 19

description: CNV discovery from NA18997 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, Japanese female

value: Japanese


title: Chinese Female, NA18552, slide 19

description: CNV discovery from NA18552 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18973, slide 19

description: CNV discovery from NA18973 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18566, slide 19

description: CNV discovery from NA18566 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: CEU Female, NA12878, slide 19

description: CNV discovery from NA12878 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Immortalized cell line, Caucasian female


title: Japanese Female, NA18951, slide 19

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18947, slide 19

description: CNV discovery from NA18947 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18999, slide 19

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK16, slide 19

description: CNV discovery from AK16 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Blood cells, Korean female

value: Korean

value: anonymous


title: Chinese Female, NA18547, slide 19

description: CNV discovery from NA18547 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18969, slide 19

description: CNV discovery from NA18969 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK14, slide 19

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK20, slide 19

description: CNV discovery from AK20 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK12, slide 19

description: CNV discovery from AK12 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18592, slide 19

description: CNV discovery from NA18592 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18526, slide 19

description: CNV discovery from NA18526 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18542, slide 19

description: CNV discovery from NA18542 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18972, slide 19

description: CNV discovery from NA18972 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK18, slide 19

description: CNV discovery from AK18 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18949, slide 19

description: CNV discovery from NA18949 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18968, slide 19

description: CNV discovery from NA18968 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18942, slide 19

description: CNV discovery from NA18942 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18564, slide 19

description: CNV discovery from NA18564 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18537, slide 19

description: CNV discovery from NA18537 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18570, slide 19

description: CNV discovery from NA18570 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK4, slide 19

description: CNV discovery from AK4 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK8, slide 19

description: CNV discovery from AK8 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK6, slide 19

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Male, AK1, slide 19

description: CNV discovery from AK1 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

source_name: Blood cells, Korean male


title: Chinese Female, NA18552, slide 18

description: CNV discovery from NA18552 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK10, slide 19

description: CNV discovery from AK10 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18537, slide 18


title: Japanese Female, NA18969, slide 18

description: CNV discovery from NA18969 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK2, slide 19

description: CNV discovery from AK2 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18997, slide 18

description: CNV discovery from NA18997 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: YRI Female, NA19240, slide 18

description: CNV discovery from NA19240 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18526, slide 18

description: CNV discovery from NA18526 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18999, slide 18

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA19582, slide 18

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18542, slide 18

description: CNV discovery from NA18542 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18972, slide 18

description: CNV discovery from NA18972 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18973, slide 18

description: CNV discovery from NA18973 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18949, slide 18

description: CNV discovery from NA18949 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18968, slide 18

description: CNV discovery from NA18968 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18566, slide 18

description: CNV discovery from NA18566 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18564, slide 18

description: CNV discovery from NA18564 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18951, slide 18

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18947, slide 18

description: CNV discovery from NA18947 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Reference HapMap sample NA07019_B05

status: Public on Mar 01 2010

city: Turku

first: Elisa

middle: Maarit

last: Närvä

address: Tykistönkatu 6

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

description: Hybridized in Finnish DNA Microarray Centre

hyb_protocol: accordingly manufactures protocol

scan_protocol: accordingly manufactures protocol

data_processing: For detecting copy number variation in the samples, we utilized Affymetrix Genotyping Console 3.0.1 and Birdseed v2-algorithm. Samples were normalized against 40 International HapMap samples for copy number variation (CNV), Loss of heterozygosity (LOH) and Single nucleotide polymorphism (SNP).

label: TdT

source_name: Reference HapMap sample NA07019_B05

label_protocol: accordingly manufactures protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: cell samples were harvested in each collaborative laboratorion, washed with PBS and sent as a frozen cell pellet to analysis laboratory. Genomic DNA was extracted using QIAamp DNA Mini Kit (Qiagen)

tag: cell type

value: reference HapMap

tag: cell line


title: Chinese Female, NA18547, slide 18

description: CNV discovery from NA18547 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.

tag: gender


title: Chinese Female, NA18570, slide 18

description: CNV discovery from NA18570 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18592, slide 18

description: CNV discovery from NA18592 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: CEU Female, NA12878, slide 18

description: CNV discovery from NA12878 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18942, slide 18

description: CNV discovery from NA18942 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK20, slide 18

description: CNV discovery from AK20 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK16, slide 18

description: CNV discovery from AK16 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK18, slide 18

description: CNV discovery from AK18 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK12, slide 18

description: CNV discovery from AK12 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK14, slide 18

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: YRI Female, NA19240, slide 17

description: CNV discovery from NA19240 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: CEU Female, NA12878, slide 17


title: Korean Male, AK1, slide 18

description: CNV discovery from AK1 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK10, slide 18

description: CNV discovery from AK10 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18999, slide 17

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK2, slide 18

description: CNV discovery from AK2 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18542, slide 17

description: CNV discovery from NA18542 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA19582, slide 17

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK4, slide 18

description: CNV discovery from AK4 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18973, slide 17

description: CNV discovery from NA18973 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18968, slide 17

description: CNV discovery from NA18968 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18951, slide 17

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18564, slide 17

description: CNV discovery from NA18564 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18949, slide 17

description: CNV discovery from NA18949 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK6, slide 18

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18537, slide 17

description: CNV discovery from NA18537 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK8, slide 18

description: CNV discovery from AK8 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18969, slide 17

description: CNV discovery from NA18969 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18570, slide 17

description: CNV discovery from NA18570 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18942, slide 17

description: CNV discovery from NA18942 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18552, slide 17

description: CNV discovery from NA18552 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18997, slide 17

description: CNV discovery from NA18997 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18566, slide 17

description: CNV discovery from NA18566 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18547, slide 17

description: CNV discovery from NA18547 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18947, slide 17

description: CNV discovery from NA18947 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18972, slide 17

description: CNV discovery from NA18972 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18592, slide 17

description: CNV discovery from NA18592 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18526, slide 17

description: CNV discovery from NA18526 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK20, slide 17

description: CNV discovery from AK20 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK18, slide 17

description: CNV discovery from AK18 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK14, slide 17

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Male, AK1, slide 17

description: CNV discovery from AK1 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK16, slide 17

description: CNV discovery from AK16 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK12, slide 17

description: CNV discovery from AK12 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK8, slide 17

description: CNV discovery from AK8 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK6, slide 17

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18552, slide 6


title: Korean Female, AK4, slide 17

description: CNV discovery from AK4 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: CEU Female, NA12878, slide 6

description: CNV discovery from NA12878 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK2, slide 17

description: CNV discovery from AK2 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18969, slide 6

description: CNV discovery from NA18969 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18968, slide 6

description: CNV discovery from NA18968 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: YRI Female, NA19240, slide 6

description: CNV discovery from NA19240 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18999, slide 6

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA19582, slide 6

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18564, slide 6

description: CNV discovery from NA18564 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18973, slide 6

description: CNV discovery from NA18973 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18537, slide 6

description: CNV discovery from NA18537 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK10, slide 17

description: CNV discovery from AK10 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18997, slide 6

description: CNV discovery from NA18997 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18949, slide 6

description: CNV discovery from NA18949 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18942, slide 6

description: CNV discovery from NA18942 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18570, slide 6

description: CNV discovery from NA18570 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18526, slide 6

description: CNV discovery from NA18526 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18566, slide 6

description: CNV discovery from NA18566 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18951, slide 6

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18542, slide 6

description: CNV discovery from NA18542 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18547, slide 6

description: CNV discovery from NA18547 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18972, slide 6

description: CNV discovery from NA18972 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18947, slide 6

description: CNV discovery from NA18947 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK14, slide 6

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18592, slide 6

description: CNV discovery from NA18592 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Male, AK1, slide 6

description: CNV discovery from AK1 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK12, slide 6

description: CNV discovery from AK12 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK8, slide 6

description: CNV discovery from AK8 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK18, slide 6

description: CNV discovery from AK18 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK20, slide 6

description: CNV discovery from AK20 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK4, slide 6

description: CNV discovery from AK4 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK16, slide 6

description: CNV discovery from AK16 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK6, slide 6

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK10, slide 6

description: CNV discovery from AK10 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: YRI Female, NA19240, slide 5

description: CNV discovery from NA19240 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: CEU Female, NA12878, slide 5

description: CNV discovery from NA12878 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18552, slide 5

description: CNV discovery from NA18552 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK2, slide 6

description: CNV discovery from AK2 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18949, slide 5

description: CNV discovery from NA18949 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18968, slide 5

description: CNV discovery from NA18968 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA19582, slide 5

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18564, slide 5

description: CNV discovery from NA18564 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18999, slide 5

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18951, slide 5

description: CNV discovery from NA18951 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18973, slide 5

description: CNV discovery from NA18973 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18942, slide 5

description: CNV discovery from NA18942 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18566, slide 5

description: CNV discovery from NA18566 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18969, slide 5

description: CNV discovery from NA18969 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18570, slide 5

description: CNV discovery from NA18570 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18997, slide 5

description: CNV discovery from NA18997 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18542, slide 5

description: CNV discovery from NA18542 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18537, slide 5

description: CNV discovery from NA18537 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: imiquimod3

status: Public on Jan 26 2010

city: Seattle

first: Lynn

middle: M

last: Amon

state: WA

address: 1100 Fairview, M1-C108

department: Division of Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

description: replicate 3

hyb_protocol: biotin-labeled cRNA were hybridized to Sentrix Mouse Ref-8 Expression Bead Chip v1.0a

data_processing: Trimmed mean intensities were log2 transformed and quantile normalized using affy package from Bioconductor.org.

source_name: spontaneous mammary tumor

label_protocol: labeled cRNA were generated using the Illumina TotalPrep RNA Amplification kit from Ambion (cat# IL1791)

growth_protocol: spontaneous tumors in neu transgenic mice

extract_protocol: RNA was extracted from tumors using RNAqueous4PCR kit (Ambion)

treatment_protocol: topical imiquimod

tag: strain

value: FVB/N-TgN (MMTVneu)-202Mul

tag: treatment

value: imiquimod cream


title: Japanese Female, NA18972, slide 5

description: CNV discovery from NA18972 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18947, slide 5

description: CNV discovery from NA18947 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18526, slide 5

description: CNV discovery from NA18526 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK20, slide 5

description: CNV discovery from AK20 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18547, slide 5

description: CNV discovery from NA18547 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK16, slide 5

description: CNV discovery from AK16 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: CEU Female, NA12878, slide 22

description: CNV discovery from NA12878 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18592, slide 5

description: CNV discovery from NA18592 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK4, slide 5

description: CNV discovery from AK4 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: YRI Female, NA19240, slide 22

description: CNV discovery from NA19240 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK18, slide 5

description: CNV discovery from AK18 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA19582, slide 22

description: CNV discovery from NA19582 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK14, slide 5

description: CNV discovery from AK14 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18999, slide 22

description: CNV discovery from NA18999 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK2, slide 5

description: CNV discovery from AK2 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK6, slide 5

description: CNV discovery from AK6 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK12, slide 5

description: CNV discovery from AK12 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA18552, slide 22

description: CNV discovery from NA18552 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Male, AK1, slide 5

description: CNV discovery from AK1 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: YRI Female, NA19240, slide 4


title: Japanese Female, NA18968, slide 22

description: CNV discovery from NA18968 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Japanese Female, NA18997, slide 4

description: CNV discovery from NA18997 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Chinese Female, NA19582, slide 4


title: Korean Female, AK8, slide 5

description: CNV discovery from AK8 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.


title: Korean Female, AK10, slide 5

description: CNV discovery from AK10 using NA10851 as a reference sample. 24M probes covering whole genome were distributed on 24 slides of 1.1M Agilent platform.