title: 2002-01-10_2399-70

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 70 min

tag: Yeast yox1 mutant cell cycle-time point 70 min


title: 2002-01-10_2399-115

status: Public on Sep 30 2007

type: RNA

city: Seattle

first: Tata

last: Pramila

state: WA

address: 1100, Fairview Avenue N

department: Basic Sciences

country: USA

institute: FHCRC

description: Yeast yox1 mutant cell cycle

data_processing: log10 ratio of medians[(F635-B635)/(F532-BF532)], normalized

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast yox1mutant cell cycle-time point 115 min

treatment_protocol: Cells were arrested with alpha factor,and released into YEPD to get a synchronized population. Cells were sampled every 10 min after relase.

tag: Yeast yox1 mutant cell cycle-time point 115 min

source_name: Yeast (wild type) asynchronous culture

treatment_protocol: Cells were grown overnight to an OD of 0.6 in YEPD

tag: Yeast (wild type) asynchronous culture


title: 2002-01-10_2399-105

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 105 min

tag: Yeast yox1 mutant cell cycle-time point 105 min


title: 2002-01-04_2399-55

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 55 min

tag: Yeast yox1 mutant cell cycle-time point 55 min


title: 2002-01-10_2399-120

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 120 min

tag: Yeast yox1 mutant cell cycle-time point 120 min


title: 2002-01-04_2399-50

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 50 min

tag: Yeast yox1 mutant cell cycle-time point 50 min


title: Kidney Cortex, 10 week old male rat, diabetic (Kidney_10WOM_DM_Rep1)

city: Omaha

first: Pascale

middle: Hammond

last: Lane

state: NE

address: 982169 Nebraska Medical Center

department: Pediatrics

institute: University of Nebraska

description: All labeling, hybridization, and scanning were performed in the microarray core facility of the University of Nebraska Medical Center

hyb_protocol: Per Affymetrix instructions

scan_protocol: GeneChip Scanner 3,000 6G per Affymetrix instructions

data_processing: Images were analyzed using GCOS imaging software.  Quality metric parameters including noise level, background, and the efficiency of reverse transcription were ascertained for all hybridizations.  Data sets passing the stringent quality recommendations were normalized using the GCOS software, and the raw intensity values exported for further analysis

label: Biotin

organism: Rattus norvegicus

label_protocol: cRNA probes were biotinylated in a core facility

extract_protocol: Aurum Total RNA Mini Kit (BioRAd Laboratories, Hercules, CA)

treatment_protocol: Injected with streptozocin, 65 mg/kg iv, at 4 weeks of age; insulin palmitate vehicle pellet placed 3 days later; ad lib food and water; blood glucose 350-450 mg/dl for 6 weeks

tag: Sprague Dawley rat, male, diabetic from 4-10 weeks of age; kidney cortex


title: 2002-01-04_2399-45

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 45 min

tag: Yeast yox1 mutant cell cycle-time point 45 min


title: 2002-01-10_2399-95

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 95 min

tag: Yeast yox1 mutant cell cycle-time point 95 min


title: 2002-01-04_2399-40

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 40 min

tag: Yeast yox1 mutant cell cycle-time point 40 min


title: 2002-01-04_2399-20

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 20 min

tag: Yeast yox1 mutant cell cycle-time point 20 min


title: 2001-08-15_2399-120

description: Yeast yox1 mutant cell cycle


title: 2002-01-10_2399-100

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 100 min

tag: Yeast yox1 mutant cell cycle-time point 100 min


title: 2002-01-10_2399-90

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 90 min

tag: Yeast yox1 mutant cell cycle-time point 90 min


title: 2002-01-10_2399-65

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 65 min

tag: Yeast yox1 mutant cell cycle-time point 65 min


title: 2001-08-16_2399-115

description: Yeast yox1 mutant cell cycle


title: 2002-01-04_2399-25

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 25 min

tag: Yeast yox1 mutant cell cycle-time point 25 min


title: 2001-08-16_2399-105

description: Yeast yox1 mutant cell cycle


title: 2002-01-04_2399-35

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 35 min

tag: Yeast yox1 mutant cell cycle-time point 35 min


title: 2002-01-10_2399-10

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 10 min

tag: Yeast yox1 mutant cell cycle-time point 10 min


title: 2001-12-27_M-5

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 5 min

tag: Yeast yox1 mutant cell cycle-time point 5 min


title: 2001-08-16_2399-110

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 110 min

tag: Yeast yox1 mutant cell cycle-time point 110 min

tag: Yeast (wild type) asynchronous culture


title: 2001-12-27_M-15

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 15 min

tag: Yeast yox1 mutant cell cycle-time point 15 min

source_name: Yeast (wild type) asynchronous culture


title: 2001-08-16_2399-95

description: Yeast yox1 mutant cell cycle


title: 2001-08-15_2399-50

description: Yeast yox1 mutant cell cycle


title: 2001-08-16_2399-100

description: Yeast yox1 mutant cell cycle


title: 2001-08-16_2399-90

description: Yeast yox1 mutant cell cycle


title: 2001-08-16_2399-60

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 60 min

tag: Yeast yox1 mutant cell cycle-time point 60 min


title: 2001-08-16_2399-70

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 70 min

tag: Yeast yox1 mutant cell cycle-time point 70 min


title: 2001-12-27_M-0

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 0 min

tag: Yeast yox1 mutant cell cycle-time point 0 min


title: 2001-08-15_2399-40

description: Yeast yox1 mutant cell cycle


title: 2001-08-15_2399-55

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 55 min

tag: Yeast yox1 mutant cell cycle-time point 55 min


title: 2002-01-04_2399-30

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 30 min

tag: Yeast yox1 mutant cell cycle-time point 30 min


title: 2001-08-16_2399-75

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 75 min

tag: Yeast yox1 mutant cell cycle-time point 75 min


title: 2001-08-16_2399-65

description: Yeast yox1 mutant cell cycle


title: 2001-08-16_2399-85

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 85 min

tag: Yeast yox1 mutant cell cycle-time point 85 min


title: 2001-08-16_2399-80

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 80 min

tag: Yeast yox1 mutant cell cycle-time point 80 min


title: 2001-08-15_2399-25

description: Yeast yox1 mutant cell cycle


title: 2001-08-15_2399-5

description: Yeast yox1 mutant cell cycle


title: 2001-08-15_2399-0

description: Yeast yox1 mutant cell cycle


title: 2001-08-15_2399-35

description: Yeast yox1 mutant cell cycle


title: 2001-08-15_2399-15

description: Yeast yox1 mutant cell cycle


title: 2001-08-15_2399-45

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 45 min

tag: Yeast yox1 mutant cell cycle-time point 45 min


title: 2001-08-15_2399-30

description: Yeast yox1 mutant cell cycle


title: 2001-08-15_2399-20

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 20 min

tag: Yeast yox1 mutant cell cycle-time point 20 min


title: wt 240 minutes growth rep3

status: Public on Aug 15 2007

city: Albany

first: Robert

last: Osuna

state: NY

address: 1400 Washington Avenue

department: Biology

institute: University at Albany

description: Gene expression data from MG1655 wildtype after 240 minutes of growth in LB medium

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

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

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.

label: biotin

organism: Escherichia coli

source_name: Escherichia coli MG1655 wt grown 240 minutes

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: Saturated E. coli cultures were diluted in LB toan OD.of  0.05 OD600, grown at 37 degrees Celsius

extract_protocol: MasterPure RNA purification Kit per manufacturers protocol

treatment_protocol: Cells were grown in LB at 37 degrees celsius with shaking for 240 minutes

tag: wildtype Escherichia coli

tag: 240 minutes growth  in LB


title: wt 90 minutes growth rep3

description: Gene expression data from MG1655 wildtype after 90 minutes of growth in LB medium

source_name: Escherichia coli MG1655 wt grown 90 minutes

treatment_protocol: Cells were grown in LB at 37 degrees celsius with shaking for 90 minutes

tag: 90 minutes growth  in LB


title: wt 240 minutes growth rep2

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.  Data from this sample were collected using Affy Ecoli anti-sense chip (2001; platform ID GPL4940), but because the analysis software failed to recognize the correct platform, we reformatted the data to match the newer (and mostly equivalent) platform GPL199 (Affy Ecoli anti-sense chip version 2, 2002).  Because, however, not all of the probes on the new platform were present on the old platform, data for some probes were unavailable and labeled in the 'remapped' dataset as 'NULL' to indicate they were missing.  While the following data are therefore formatted using ID_REFs that match GPL199, the CEL file contains the raw data (not 'remapped') and thus corresponds to the actual array used (GPL4940, Ecoli antisense chip, 2001).


title: wt 90 minutes growth rep2


title: wt 150 minutes growth rep3

description: Gene expression data from MG1655 wildtype after 150 minutes of growth in LB medium

source_name: Escherichia coli MG1655 wt grown 150 minutes

treatment_protocol: Cells were grown in LB at 37 degrees celsius with shaking for 150 minutes

tag: 150 minutes growth  in LB


title: wt 150 minutes growth rep2

growth_protocol: Saturated E. coli cultures were diluted in LB to an OD.of  0.05 OD600, grown at 37 degrees Celsius


title: wt 360 minutes growth rep2

description: Gene expression data from MG1655 wildtype after 360 minutes of growth in LB medium

source_name: Escherichia coli MG1655 wt grown 360 minutes

treatment_protocol: Cells were grown in LB at 37 degrees celsius with shaking for 360 minutes

tag: 360 minutes growth  in LB


title: Lungs from Rosa26-Foxm1 mice 12 weeks after MCA/BHT treatment

status: Public on Sep 28 2007

city: Chicago

first: Tanya

last: Kalin

state: IL

address: 5841 S. Maryland Ave.

department: Medicine

institute: University of Chicago

description: Pooled lung tissue from three Rosa26-Foxm1 mice treated with tumor inducible MCA/BHT

hyb_protocol: Microarray hybridization (using twenty micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.

scan_protocol: Chemiluminescence detection, imaging, auto gridding, and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1.0.3.

data_processing: Signal intensities across microarrays were normalized using the quantile-quantile method (www.bioconductor.org).

label: DIG-UTP

organism: Mus musculus

source_name: left lung lobes from three Rosa26-Foxm1 mice treated with MCA/BHT

label_protocol: 1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT Kit V2.0.

extract_protocol: Total RNA was isolated using RNA STAT-60 Reagent (TEL-TEST, INC., Friendswood, TX) with modifications to remove DNA using the Qiagen RNAeasy columns and DNaseI Kit (Qiagen, Valencia, CA). RNA was stored at –70C in RNase-free H2O. Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturers procedures (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Rosa26-Foxm1 mice were injected intraperitoneally (i.p.) with one dose of 3-methylcholanthrene (MCA; 15 µg/g mouse weight), followed by six weekly i.p. injections of butylated hydroxytoluene (BHT; the first dose was 150 µg/g mouse weight, and subsequent doses were 200 µg/g mouse weight)

tag: pooled left lung lobes from three Rosa26-Foxm1 mice 12 weeks after MCA/BHT treatment


title: fis 360 minutes growth rep3

description: Gene expression data from MG1655 fis::kan  after 360 minutes of growth in LB medium

source_name: Escherichia coli MG1655 fis::kan grown 360 minutes

tag: fis  Escherichia coli


title: fis 240 minutes growth rep3

description: Gene expression data from MG1655 fis::kan  after 240 minutes of growth in LB medium

source_name: Escherichia coli MG1655 fis::kan grown 240 minutes


title: fis 360 minutes growth rep2


title: wt 150 minutes growth rep1


title: wt 360 minutes growth rep3


title: fis 90 minutes growth rep3

description: Gene expression data from MG1655 fis::kan  after 90 minutes of growth in LB medium

source_name: Escherichia coli MG1655 fis::kan grown 90 minutes


title: wt 90 minutes growth rep1


title: wt 240 minutes growth rep1


title: 2001-08-15_2399-10

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 10 min

tag: Yeast yox1 mutant cell cycle-time point 10 min

source_name: Yeast (wild type) asynchronous culture

tag: Yeast (wild type) asynchronous culture


title: wt 360 minutes growth rep1


title: fis 150 minutes growth rep3

description: Gene expression data from MG1655 fis::kan  after 150 minutes of growth in LB medium

source_name: Escherichia coli MG1655 fis::kan grown 150 minutes


title: fis 150 minutes growth rep2


title: fis 240 minutes growth rep2


title: Lung WT mice 12 weeks after MCA/BHT treatment

description: Pooled lung tissue from tree  wild type FVB/N mice treated with tumor inducible MCA/BHT

source_name: left lung lobes from three mice pooled

treatment_protocol: Wild type FVB/N mice were injected intraperitoneally (i.p.) with one dose of 3-methylcholanthrene (MCA; 15 µg/g mouse weight), followed by six weekly i.p. injections of butylated hydroxytoluene (BHT; the first dose was 150 µg/g mouse weight, and subsequent doses were 200 µg/g mouse weight)

tag: Strain

value: FVB/N

tag: Gender

value: male

tag: Tissue

value: lung


title: B6 26months-1

status: Public on Aug 31 2007

city: Baltimore

first: vikas

last: misra

state: MD

address: 615 N. Wolfe street, E6609

department: Environmental health sciences

institute: Johns Hopkins University School of public health

description: B6 Lung gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 10 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affy GeneChip« Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets B6 18/26 months x 3 sets B6 2 months comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

source_name: B6 26m-1 Lung

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: no growth protocol

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

treatment_protocol: no treatment

tag: C57BL/6J mouse strain (NIA)  gender- male, age- 26 months, n = 1, # of tissue = 1 tissue

value: Lung


title: fis 90 minutes growth rep1


title: fis 150 minutes growth rep1


title: fis 240 minutes growth rep1


title: fis 360 minutes growth rep1


title: fis 90 minutes growth rep2


title: Mutant Histone H3 K4,36,79R 9 hr replicate 2

status: Public on Aug 01 2007

city: Pullman

first: John

middle: J.

last: Wyrick

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Mutant yeast strain Histone H3 K4,36,79R 9 hr

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0. Data has been normalized using exogenous spiked controls (DapX, LysX, PheX, ThrX, TrpX)

source_name: Yeast RNA

label_protocol: Approximately 20 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Cells were grown in selective media containing galactose until mid-log phase, and then shifted to selective media containing glucose for 9 hours. Cells were harvested at OD600 of 0.5-0.7. Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

tag: AMY102 9 hr (mutant Histone H3 K4,36,79R)


title: Wild-type for H3 K4,36,79R 9 hr replicate 2

description: Wild-type yeast strain - control for 9 hr mutant data set

tag: AMY101 9 hr (wild-type Histone H3)


title: Wild-type for H3 K4,36,79R 9 hr replicate 1


title: Mutant Histone H3 K4,36,79R 6 hr replicate 2

description: Mutant yeast strain Histone H3 K4,36,79R 6 hr

extract_protocol: Cells were grown in selective media containing galactose until mid-log phase, and then shifted to selective media containing glucose for 6 hours. Cells were harvested at OD600 of 0.5-0.7. Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

tag: AMY102 6 hr (mutant Histone H3 K4,36,79R)


title: Mutant Histone H3 K4,36,79R 6 hr replicate 3


title: Mutant Histone H3 K4,36,79R 9 hr replicate 1


title: Wild-type for H3 K4,36,79R 6 hr replicate 3

description: Wild-type yeast strain 6 hr

tag: AMY101 6 hr (wild-type Histone H3)


title: Wild-type for H3 K4,36,79R 0 hr replicate 1

description: Wild-type yeast strain 0 hr

extract_protocol: Cells were grown in selective media containing galactose until mid-log phase. Cells were harvested at OD600 of 0.5-0.7. Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

tag: AMY101 0 hr (wild-type Histone H3)


title: Wild-type for H3 K4,36,79R 6 hr replicate 1

description: Wild-type yeast strain 6 hr


title: Mutant Histone H3 K4,36,79R 0 hr replicate 1

description: Mutant yeast strain Histone H3 K4,36,79R 0 hr

tag: AMY102 0 hr (mutant Histone H3 K4,36,79R)


title: Mutant Histone H3 K4,36,79R 0 hr replicate 2


title: Wild-type for H3 K4,36,79R 0 hr replicate 2

description: Wild-type yeast strain 0 hr


title: Mutant Histone H3 K4,36,79R 6 hr replicate 1


title: Wild-type for H3 K4,79R replicate 2

description: Wild-type yeast strain

extract_protocol: Cells were grown in YPD media until mid-log phase. Cells were harvested at OD600 of 0.5-0.7. Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

tag: AMY139 (wild-type Histone H3)


title: Wild-type for H3 K4,36,79R 6 hr replicate 2

description: Wild-type yeast strain 6 hr


title: Wild-type for H3 K4,79R replicate 1

description: Wild-type yeast strain


title: Wild-type for H3 K4,79R replicate 3

description: Wild-type yeast strain


title: Mutant Histone H3 K4,79R replicate 2

description: Mutant yeast strain Histone H3 K4,79R

tag: AMY006 (mutant Histone H3 K4,79R)


title: Mutant Histone H3 K4,79R replicate 3

description: Mutant yeast strain Histone H3 K4,79R


title: Rice panicle WT vs. dsRNAiOsMADS2 Sample B

status: Public on Jul 31 2007

city: Bangalore

first: Shri Ram

last: Yadav

state: Karnataka

address: C. V. Raman Avenue

department: Department of Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description:
Image quality was checked with the help of-
1. Four green spots and each corner of the image
2. SpikeIn A and B control spots across the image
3. Evenness of the background in log-scale mode

hyb_protocol: Probe fragmentation: Fragmentation reaction was as- cRNA Cy3 750 ng,cRNA Cy5 750 ng,Blocking agent 50 ul,Water variable, 25 X fragmentation buffer,10 ul to 250 ul total volume. Incubate at 60C for 30 mins. Add 250 ul of 2X hybridization buffer. Use 490 ul for each slide and hybridize at 65C for 17 hrs at 5 rpm speed.

scan_protocol: Washing was done according to Agilent’s instructions using wash buffer 1 followed by wash buffer 2. Slides were scanned using Agilent DNA Microarray Scanner (G2565BA).

data_processing: The TIFF image was used to extract raw and processed data using Agilent’s Feature Extraction software (FE v8.1). The normalization was done using GeneSpring GX version 7.2 using the recommended Per Spot and Per Chip: Intensity dependent (Lowess) normalization. Number of non-control spots with ratio 0.25 and below were considered as down regulated spots.

organism: Oryza sativa

source_name: WT rice TP309 panicles

label_protocol: cDNA was synthesized from tortal RNA by RT-PCR and was used as templete for Cy3 lebeled cRNA synthesis using T7 dependent in vitro transcription system.

extract_protocol: Total RNA was isolated from WT rice panicles using Tri Reagent (Sigma) and purified by RNeasy cleanup kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.

tag: Rice TP309; wild type panicles undergoing floral organ specification and differentiation

source_name: Transgenic rice panicles knock down for OsMADS2

label_protocol: cDNA was synthesized from tortal RNA by RT-PCR and was used as templete for Cy5 lebeled cRNA synthesis using T7 dependent in vitro transcription system.

extract_protocol: Total RNA was isolated from OsMADS2 knock down rice panicles using Tri Reagent (Sigma) and purified by RNeasy cleanup kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.

tag: Transgenic rice panicles of similar developmental stage to WT where a transcription regulator, OsMADS2 has been knocked down by double stranded RNA interference


title: Mutant Histone H3 K4,79R replicate 1

description: Mutant yeast strain Histone H3 K4,79R


title: ash1^22_wing_discs_Rep3

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

country: Spain

institute: Universitat de Barcelona

description: Total RNA from w1118;+;+ wing imaginal discs was pooled and used as a common reference against ash2I1, ash2112411 and ash122/ash122F2A. Four microarrays were hybridized for each experiment in biological replicate pairs, such that the total RNA from the sample used as a starting material came from different extractions. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

hyb_protocol: Samples were diluted in 2X Hybridization Buffer #5185-5973(Agilent Technologies) and hybridization was carried out at 60ºC for 18 hours with a G2534A SureHyb Chamber in a G2545A Hybridization Oven (Agilent Technologies).

scan_protocol: GenePix Results (GPR) data files were obtained for each microarray with an Axon 4000B scanner and GenePix Pro 6 (Axon Instruments, Inc).

data_processing: GPR files were analyzed with Limma package from BioConductor (Gentleman et al., 2004; Genome Biol 5, R80; Smyth, 2004; Statistical Applications in Genetics and Molecular Biology 3, Article 3) using the same criteria. Data was background corrected with the "normexp" method and normalized with OLIN (Futschik and Crompton, 2005; Bioinformatics 21, 1724-1726). Spots not fulfilling the quality thresholds (based on spot size, foreground versus background signals, saturation, coincidence between differently calculated ratio measures and R2 of regression ratio) were eliminated from further analysis.

organism: Drosophila melanogaster

label_protocol: 1.5ug total RNA were amplified and indirectly labelled with Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc). Fragmentation was done with RNA Fragmentation Reagents #8740(Ambion, Inc).

growth_protocol: All Drosophila strains and crosses were kept on standard media with 0.025% bromophenol blue at 25ºC.

extract_protocol: Wing imaginal discs were dissected in PBS and kept in RNAlater prior to extraction with RNeasy Protect Mini Kit (QIAGEN Inc.). Quality was assessed in all samples using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies). Total RNA from w1118;+;+ wing imaginal discs was pooled and used as a common reference against ash2I1, ash2112411 and ash122/ash122F2A.

value: w1118;+;+ isogenic wt strain (Ryder, E., 2004; Genetics 167, 797-813).

tag: Stage

value: third instar larvae (bromophenol blue staged).

value: wing imaginal discs.

source_name: wing_discs_ash1^22_(EXTRACTION 2)

value: w1118;+;ash1^22/ash1^22-F2A isogenized from wt strain.


title: ash1^22_wing_discs_Rep4

extract_protocol: Wing imaginal discs were dissected in PBS and kept in RNAlater prior to extraction with RNeasy Protect Mini Kit (QIAGEN Inc.). Quality was assessed in all samples using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies).


title: 40nM T4_bisthiazolium/36 hours incubation/40nM_T4_bisthiazolium experiment

city: Riverside

first: Karine

middle: Gaelle

last: Le Roch

state: CA

address: 900 University Avenue

department: Department of Cell Biology & Neuroscience

institute: University of California

description:
40nM/36 hours incubation/40nM_T4_bisthiazolium experiment
40nM T4_bisthiazolium_ 36 hours incubation

data_processing: The data were analyzed  using the Match-Only Integral Distribution algorithm (MOID). The background noise distributions for the MOID algorithm were calculated with the probe intensities of 100 negative control genes. Background was then subtracted from each raw probe intensity probabilistically according to the above distribution. Normalization factors were determined by scaling the average intensity of genes in the range between 30 and 90 percentile to 200.

organism: Plasmodium falciparum 3D7

tag: Synchronized parasite erythrocytic cell cycle Drug added at the ring stage


description:
No drug/36 hours incubation/40nM_T4_bisthiazolium experiment
Control 36 hours


title: ash1^22_wing_discs_Rep2

source_name: wing_discs_ash1^22_(EXTRACTION 1)


title: ash1^22_wing_discs_Rep1


title: ash2112411_wing_discs_Rep4

source_name: wing_discs_ash2112411_(EXTRACTION 2)

value: w1118;+;ash2112411 isogenized from wt strain.


title: ash2112411_wing_discs_Rep2


description:
No drug/24 hours incubation/40nM_T4_bisthiazolium experiment
Control 24 hours


title: No drug/5 hours incubation/125nM_T4_bisthiazolium_bisthiazolium experiment

description:
No drug/5 hours incubation/125nM_T4_bisthiazolium experiment
5 hours control

tag: Mix population erythrocytic cell cycle


description:
No drug/30 hours incubation/40nM_T4_bisthiazolium experiment
Control 30 hours


title: 40nM T4_bisthiazolium/30 hours incubation/40nM_T4_bisthiazolium experiment

description:
40nM/30 hours incubation/40nM_T4_bisthiazolium experiment
40nM T4_bisthiazolium_ 30 hours incubation


title: ash2112411_wing_discs_Rep1

source_name: wing_discs_ash2112411_(EXTRACTION 1)

tag: Strain


title: 125nM T4_bisthiazolium/5 hours incubation/125nM_T4_bisthiazolium experiment

description:
125nM T4/5 hours incubation/125nM_T4 experiment
5 hours 125nM T4


title: ash2112411_wing_discs_Rep3


title: Rice panicle WT vs. dsRNAiOsMADS2 Sample A_SWAP


title: ash2I1_wing_discs_Rep1

extract_protocol: Wing imaginal discs were dissected in PBS and kept in RNAlater prior to extraction with RNeasy Protect Mini Kit (QIAGEN Inc.). Quality was assessed in all samples using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies). Total RNA from w1118;+;+ wing imaginal discs was pooled and used as a common reference against ash2I1, ash2112411 and ash122/ash122F2A

value: third instar larvae (bromophenol blue staged)

value: wing imaginal discs

source_name: wing_discs_ash2I1_(EXTRACTION 1)

value: w1118;+;ash2I1 isogenized from wt strain


title: ash2I1_wing_discs_Rep3

source_name: wing_discs_ash2I1_(EXTRACTION 2)

value: w1118;+;ash2I1 isogenized from wt strain.

label_protocol: 1.5ug total RNA were amplified and indirectly labelled with Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc). Fragmentation was done with RNA Fragmentation Reagents #8740 (Ambion, Inc).


title: No drug/30minutes incubation/125nM_T4_bisthiazolium_bisthiazolium experiment

description:
No drug/30minutes incubation/125nM_T4_bisthiazolium experiment
30minutes control


title: Rice panicle WT vs. dsRNAiOsMADS2 Sample A

description:
Image quality was checked with the help of-
1.	Four green spots and each corner of the image
2.	SpikeIn A and B control spots across the image
3.	Evenness of the background in log-scale mode


title: ash2I1_wing_discs_Rep2


title: ash2I1_wing_discs_Rep4

extract_protocol: Wing imaginal discs were dissected in PBS and kept in RNAlater prior to extraction with RNeasy Protect Mini Kit (QIAGEN Inc.). Quality was assessed in all samples using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies).  Total RNA from w1118;+;+ wing imaginal discs was pooled and used as a common reference against ash2I1, ash2112411 and ash122/ash122F2A.


description:
125nM_T4_bisthiazolium/30minutes incubation/125nM_T4_bisthiazolium experiment
30minutes  125nM_T4_bisthiazolium


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 5

status: Public on Jul 01 2007

city: Düsseldorf

first: Sascha

last: Raschke

address: Universitätsstraße 1

department: Klinik für Hämatologie, Onkologie und klinische Immunologie

country: Germany

institute: Heinrich-Heine Universität Düsseldorf

description: Bi-213-CD20-Rituximab irradiated primary CD19+ B-cells

hyb_protocol: Arrays were prehybridizised for 10 minutes using 140 µl MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip®  Hybridizing oven 640 (Affymetrix). After removal of the pre-hybridizing solution, the array was loaded with 250 µl of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA, 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.). Following 16-hour incubation at 45°C with permanent rotation, the hybridizing solution is removed. The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10% Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water) using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus Oligonukleotid- Arrays = Midi-euk2v3). During washing procedure the staining solution is prepared: Staining solution: 600 µl 2x Staining Buffer 540 µl dH2O 48 µl BSA 12 µl Streptavidine-Phycoerythrin-Conjugate Array was incubated with 600 µl of the staining solution after washing for 40 minutes followed by incubation with the antibody solution for 10 minutes: Antibody solution: 300 µl 2x Staining Buffer 266 4 µl dH2O 24 µl BSA 6 µl Goat IgG 3.6 µl biotinylated Anti- Streptavidin- antibody After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.

scan_protocol: The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome phycoerythrin at a wave length of 488 nm with an emission at 570 nm.

data_processing:
Using the affy package of functions of statistical scripting
language 'R' integrated into the Bioconductor project data from cel files of
each sample were normalized by variance stabilizing transformations (VSN)
Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
2002;18:96-104.

label: Biotin/Streptavidin-PE

organism: Homo sapiens

source_name: Primary CD19+ B-Cells

label_protocol:
Amplification, reverse transcription and labelling of the
sample.
For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion,
Austin, TX, USA) was used.
500 ng of isolated RNA were transcribed into cDNA.
First strand cDNA- Synthesis:
11 µl (RNA or RNA and dH2O) Sample
1 µl Oligo(dT)Primer
70°C incubation for 10 minutes, put on ice and incubated with the reaction kit
(stated below).
Reaction kit:
2 µl 10x First Strand Buffer
1 µl Ribonuclease Inhibitor
4 µl dNTP Mix
Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
Second strand cDNA- Synthesis:
63 µl Nuclease-free Water
10 µl 10x Second Strand Buffer
4 µl dNTP Mix
1 µl RNase H
For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
Incubation step at 42°C.
Purification of cDNA:
Final elution volume = 16 µl and storage for 12 h at -20°C
Labelling with in vitro transcription using biotin labelled nucleotides:
Labeling mix:
4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
Enzo Life Sciences, Farmingdale)
4 µl T7 10x reaction buffer
12 µl RNase free water
The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
added followed by an incubation period of 5 hours at 37°C. The amplified RNA
is purified and is eluted in a final volume of 96 µl.
Quality control of aRNA:
The concentration and purity of aRNA is measured using the NanoDrop ND-1000
(PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
degradation and/or contamination RNA was analyzed again using an Agilent 2100
Bioanalyzer (Agilent Technologies, Palo Alto CA).
Fragmentation:
For optimal hybridization with the complementary oligonucleodid sequences, a
fragmentation of the amplified RNA was performed.
24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
94°C for 35 minutes.

extract_protocol:
RNA of alpha irradiated K422 cells was extracted using the RNeasy
Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and
solutions are part of the kit and were applied according to the manufacturer’s instructions.
Briefly:
Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
ethanol.
700 µl suspension was put on RNeasy MinElute- column and spun down for one
minute with 10,000 rpm.
One washing step with 350 µl RW1 buffer
DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature.
2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
minutes with 10,000 rpm.
Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm.
Elution of RNA with 14 µl of RNAse free water.
Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer
(Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab
Biotechnologie
GmbH, Erlangen). Purified RNA was stored at -80°C.

treatment_protocol:
The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
Subsequently the purified Bi-213-labelled antibody was added to the immunomagnetically selected primary CD19+ B-cells.
A constant number of 1x106 CD19+ B-cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.

tag: Immunomagnetically selected from peripheral blood of healthy donor 1


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 4

tag: Immunomagnetically selected from peripheral blood of healthy donor 4


title: 40nM T4_bisthiazolium/24 hours incubation/40nM_T4_bisthiazolium experiment

description:
40nM/24 hours incubation/40nM_T4_bisthiazolium experiment
40nM T4_bisthiazolium_ 24 hours incubation


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 3


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 1

tag: Immunomagnetically selected from peripheral blood of healthy donor 3


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 3

treatment_protocol:
The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
Subsequently the purified Bi-213-labelled antibody was added to the immunomagnetically selected primary CD19+ B-cells.
A constant number of 1x106 CD19+ B-cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.

tag: Immunomagnetically selected from peripheral blood of healthy donor 2


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 2


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 7


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 4


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 2


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 5


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 6


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 7

description: untreated immunomagnetically selected primary CD19+ B-cells

treatment_protocol: untreated CD19+ B-cells


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 8


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 2


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 3

tag: Immunomagnetically selected from peripheral blood of a healthy donor


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 5

description: Bi-213-CD20-Rituximab irradiated K422 cells

source_name: Cell line Karpas 422 (K422)

label_protocol:
Amplification, reverse transcription and labelling of the
sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
Reaction kit:
2 µl 10x First Strand Buffer
1 µl Ribonuclease Inhibitor
4 µl dNTP Mix
Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
Second strand cDNA- Synthesis:
63 µl Nuclease-free Water
10 µl 10x Second Strand Buffer
4 µl dNTP Mix
1 µl RNase H
For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
Incubation step at 42°C.
Purification of cDNA:
Final elution volume = 16 µl and storage for 12 h at -20°C
Labelling with in vitro transcription using biotin labelled nucleotides:
Labeling mix:
4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
Enzo Life Sciences, Farmingdale)
4 µl T7 10x reaction buffer
12 µl RNase free water
The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
added followed by an incubation period of 5 hours at 37°C. The amplified RNA
is purified and is eluted in a final volume of 96 µl.
Quality control of aRNA:
The concentration and purity of aRNA is measured using the NanoDrop ND-1000
(PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
degradation and/or contamination RNA was analyzed again using an Agilent 2100
Bioanalyzer (Agilent Technologies, Palo Alto CA).
Fragmentation:
For optimal hybridization with the complementary oligonucleodid sequences, a
fragmentation of the amplified RNA was performed.
24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
94°C for 35 minutes.

growth_protocol: A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.

extract_protocol:
RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
GmbH, Erlangen). Purified RNA was stored at -80°C.

treatment_protocol:
The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.

tag: derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 2


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 6


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 4


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 5


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 3


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 4

treatment_protocol:
The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 1


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 2


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 4


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 3


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 1


title: Alpha-irradiated primary CD19+ B-cells with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 1


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 5


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 1


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 5

treatment_protocol:
The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 4


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 3


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 3

treatment_protocol:
The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 4


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 2


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 1


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 2


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 5


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 4

description: untreated K422 control cells

treatment_protocol: untreated control


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 1


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 3

description: untreated K422 control cells


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 5

description: untreated K422 control cells


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 1

description: untreated K422 control cells


title: Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 2

description: untreated K422 control cells


title: donor1_CD8_stage5_rep2

status: Public on Jun 30 2007

city: COLOGNE

first: Frank

last: Huebel

state: NRW

address: Stoeckheimer Weg 1

department: MACS Molecular 9

institute: Miltenyi Biotec GmbH, MACS Molecular Business Unit

description: For cell surface, a panel of titrated anti-human antibodies was added to freshly isolated PBMC for 15 min at room temperature (RT). For intracellular staining, cells were washed, permeabilised with FACSTM Permeabilisation buffer (Becton Dickinson), and incubated for 15 min at RT in the dark with antibodies for intracellular molecules (Perforin, Granzymes A and B). Cells were then washed and stored at 4°C until flow cytometry analysis or sorting was performed. Samples were analyzed on a Becton Dickinson LSRII. For cell sorting, peripheral blood mononuclear cells (PBMC) were obtained by Ficoll s

hyb_protocol: PIQOR Microarray Immunology, human, sense (Miltenyi) hybridization was performed according to the manufactures instructions using an automized hybridization machine (a-Hyb, Miltenyi Biotec). Briefly, volume of labeled sample was adjusted to 100 µl with nu

scan_protocol: Image capture and signal quantification of hybridized PIQOR(TM) microarrays were done with the ScanArrayLite4000 Microarray Scanner (PackardBiosciences) and ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned PIQOR(TM) microarrays was done using ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the Cy5/Cy3-ratio. The latter was only calculated from: (a) unflagged spots (b) showing  a fluorescent intensity in one of the two channels higher than an additional lower cutoff. This lower cutoff  is defined as twice the global background. Subsequently, the mean Cy5/Cy3-ratio of  validated spots representing the same cDNA was computed. The mean ratios were normalised using the Median method.

source_name: human blood (naïve)

label_protocol: For the generation of amplified cDNA, 1- 10000 cells were collected in 6.4 µl lysis buffer (including detergent, tRNA and Protease), the mRNA extracted using magnetic beads and transcribed into cDNA using tagged random and oligo(dT) primer. First strand c

extract_protocol: SuperAmp Service, Miltenyi

tag: Pool of three independently FACS sorted naive CD8+ T lymphocytes (CD45RA+/CCR7+/CD28+/CD27+)

source_name: human blood (highly differentiated)


title: donor2_CD4_stage1_rep2

tag: Pool of three independently FACS sorted naive CD4+ T lymphocytes (CD45RA+/CCR7+/CD28+/CD27+)

tag: FACS sorted_CD4_stage1_rep2


title: donor1_CD8_ Pool

tag: FACS sorted_CD8_ Pool


title: donor2_CD8_stage1_rep2

tag: FACS sorted_CD8_stage1_rep2


title: donor1_CD8_stage1_rep2


title: donor1_CD8_stage3_rep2


title: donor2_CD4_stage1

tag: FACS sorted_CD4_stage1


title: HUVEC control_sample B

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

description: untreated HUVEC control

hyb_protocol: 10 µg of fragmented cRNA were together with control cRNAs and grid alignment oligonucleotides hybridized under constant rotation at 45°C over night (16h) to oligonucleotide. Arrays were washed and stained (label: SAPE; Gene Chip Washing and Staining Hybridization kit, Affymetrix) using the Gene Chip Fluidics Station 450 (Affymetrix).

scan_protocol: Fluorescent signals were detected by the Affymetrix GeneChip Scanner 3000. Microarrays of this series were all scaled to a TGT value of 100.

data_processing: Microarray data were analyzed using MicroArray Suite (MAS) software (Affymetrix). First, background-adjusted raw intensities accounting for non-specific binding by removing probe sets with insignificant differences between single perfect-matching (PM) and mismatching (MM) probes were created. Single raw values were calculated for each probe set from the median of PM/MM discrimination values. Fold-changes (log ratio changes) and "change p values" based on a signed rank test were determined for each experiment. Only genes with a change p≤0.05 for up-regulated or a change p≥0.95 for down-regulated genes in at least 3 of 4 experiments and mean log ratio changes (calculated as mean of log ratio changes of all experiments with significant change p values) of at least 2.5 or -2.5 were considered.

source_name: HUVEC monolayer

label_protocol: cRNA was synthesized from cDNA and biotinylated using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY).20µg of cRNA was fragmented by heating at 94°C for 35 min in fragmentation buffer (40 mmol/L Tris-acetate, pH 8.1, 100 mmol/l Potassium acetate, 30 mmol/L Magnesium acetate).

growth_protocol: Twenty-four hours prior to addition of C. albicans, HUVEC cells were washed and placed in antibiotic-free medium.

extract_protocol: Total RNA (5 µg/experiment) from medium-stimulated controls or HUVEC exposed to C. albicans out of 4 independent experiments was prepared using RNeasy kits from Qiagen (Hilden, Germany) according to the manufacturer’s instructions. cDNA was prepared from 5 µg total RNA using the SuperScript Choice System kit (Invitrogen, Karlsruhe, Germany) with a T7-(dT)24 primer for first-strand synthesis.

treatment_protocol: HUVEC cells cultured in a 1:2 mixture of endothelial growth medium (EGM (Clonetics) and M199 medium (PAA, Cölbe, Germany) supplemented with 6.7% fetal bovine serum, gentamicin, amphotericin and Liquemin® N5000 (Roche, Grenzach-Wyhlen, Germany).

tag: human umbilical vein endothelial cells, passages 4


title: donor1_CD4_stage1


title: donor2_CD8_stage1

tag: FACS sorted_CD8_stage1


title: HUVEC candida_sample K

description: Candida infected HUVEC

growth_protocol: HUVEC were co-cultured with C. albicans blastospores (strain SC5314) for 5 h. Then total RNA was extracted and processed.

treatment_protocol: Twenty-four hours prior to addition of C. albicans, HUVEC cells were washed and placed in antibiotic-free medium. The C. albicans strain SC5314 was cultured overnight in M199 medium at pH 4.0 and 28°C to generate blastospores. Blastospores were then added to HUVEC cultures at a multiplicity of infection (MOI) of 1.

tag: human umbilical vein endothelial cells, passages 3


title: donor1_CD8_stage1


title: donor2_CD4_stage5


title: HUVEC candida_sample A

description: Candida infected HUVEC


title: donor2_CD4_stage3


title: HUVEC candida_sample D

description: Candida infected HUVEC

tag: human umbilical vein endothelial cells, passages 5


title: Jurkat vs. Raji_1000cells_FACS

description: PMID

source_name: Raji cells, immortalized human B cell line

tag: The human B-cell like Raji cell line was cultured in RPMI 1640 medium, 2 mM glutamine, 10% (v/v) fetal calf serum at 37 °C in 95%/5% air/CO2. diluted to a given cell number per microliter

source_name: Jurkat cells, immortalized human T cell line

tag: The human T-cell like Jurkat cell line was cultured in RPMI 1640 medium, 2 mM glutamine, 10% (v/v) fetal calf serum at 37 °C in 95%/5% air/CO2. diluted to a given cell number per microliter


title: donor2_CD4_stage4


title: HUVEC candida_sample B

description: Candida infected HUVEC


title: HUVEC control_sample D

description: untreated HUVEC control

tag: umbilical vein endothelial cells, passages 5


title: donor2_CD4_stage2


title: Jurkat vs. Raji_1000cells_w/oFACS_rep2

description: PMID


title: HUVEC control_sample A

description: untreated HUVEC control


title: Jurkat vs. Raji_1000cells_w/oFACS_rep1

description: PMID


title: donor1_CD4_ Pool

tag: FACS sorted_CD4_ Pool


title: donor2_CD8_stage5


title: HUVEC control_sample K

description: untreated HUVEC control


title: Jurkat vs. Raji_300cells_FACS

description: PMID


title: donor2_CD8_stage4


title: Small RNAs from Selaginella moellendorffii

type: MPSS

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

institute: Pennsylvania State University

description: Endogenous small RNAs as determined by pyrosequencing.

data_processing: no processing - value is simple the number of times that sequence was found, out of a total of 149,586 sequence reads in the sample

organism: Selaginella moellendorffii

source_name: Above-ground tissues (stems and leaves)

growth_protocol: 22 degree greenhouse, 16hrs light, 8hrs dark

extract_protocol: Total RNA was extracted using the protocol of Chang et al. (1993) Plant Mol. Biol. Rep. 11: 113-116.  Small RNAs were then purified by PAGE, reverse-transcribed, and sequencing using pyrosequencing (454 Life Sciences) as previously described by Axtell et al. (2006) Cell 127:565-577.

tag: Wild-type, greenhouse grown S. moellendorffii


title: donor2_CD8_stage3


title: donor1_CD4_stage5


title: Jurkat vs. Raji_100cells_FACS

description: PMID


title: Jurkat vs. Raji_30cells_FACS

description: PMID


title: Jurkat vs. Raji_1cell_FACS

description: PMID


title: donor2_CD8_stage2


title: donor1_CD4_stage2


title: Jurkat vs. Raji_10cells_FACS

description: PMID


title: donor1_CD8_stage5


title: donor1_CD4_stage3


title: Jurkat vs. Raji_3cells_FACS

description: PMID


title: donor1_CD4_stage4


title: naive vs differentiated CD8 Tcells, donor1_10000cells_rep1

tag: FACS sorted naïve CD8+ T lymphocytes (CD45RA+/CCR7+/CD28+/CD27+)

tag: FACS sorted highly differentiated CD8+ T lymphocytes (CCR7-/CD28-/CD27-)


title: donor1_CD8_stage3

tag: Pool of three independently FACS sorted naive CD8+ T lymphocytes (CD45RA+/CCR7+/CD28+/CD27+)


title: naive vs differentiated CD8 Tcells, donor1_100cells_rep1


title: naive vs differentiated CD8 Tcells, donor1_1000cells_rep2


title: naive vs differentiated CD8 Tcells, donor1_100cells_rep2


title: donor1_CD8_stage2


title: naive vs differentiated CD8 Tcells, donor1_10cells_rep1


title: naive vs differentiated CD8 Tcells, donor2_10000cells_rep2


title: naive vs differentiated CD8 Tcells, donor1_1000cells_rep1


title: naive vs differentiated CD8 Tcells, donor1_100cells_rep3


title: naive vs differentiated CD8 Tcells, donor1_10000cells_rep2


title: naive vs differentiated CD8 Tcells, donor2_1000cells_rep2


title: naive vs differentiated CD8 Tcells, donor2_1000cells_rep1


title: naive vs differentiated CD8 Tcells, donor2_10000cells_rep1


title: naive vs differentiated CD8 Tcells, donor2_100cells_rep1


title: donor1_CD8_stage4


title: naive vs differentiated CD8 Tcells, donor2_100cells_rep3


title: naive vs differentiated CD8 Tcells, donor2_100cells_rep2


title: naive vs differentiated CD8 Tcells, donor2_10cells_rep3


title: naive vs differentiated CD8 Tcells, donor2_10cells_rep2


title: naive vs differentiated CD8 Tcells, donor2_10cells_rep1


title: Jurkat vs. Raji_10^7cell_rep2

description: PMID

label_protocol: Unamplified labeled samples were generated using the µMACS one step cDNA Labeling Kit (Miltenyi Biotec). In brief, cells were centrifuged at 300 g and resuspended in 1 mL Lysis/Binding Buffer. Lysate was sheared through a 21G needle and cleared using a Ly

extract_protocol: µMACS One-step cDNA labeling kit, Miltenyi


title: Jurkat vs. Raji_10000cell_rep1

description: PMID


title: Jurkat vs. Raji_10^7cell_rep1

description: PMID


title: Jurkat vs. Raji_10000cell_rep2

description: PMID


title: Jurkat vs. Raji_100cell_rep1

description: PMID


title: Jurkat vs. Raji_10cell_rep1

description: PMID


title: Jurkat vs. Raji_1000cell_rep2

description: PMID


title: Jurkat vs. Raji_1cell_rep1

description: PMID


title: Jurkat vs. Raji_1000cell_rep1

description: PMID


title: Jurkat vs. Raji_10cell_rep2

description: PMID


title: Jurkat vs. Raji_100cell_rep2

description: PMID


title: Jurkat vs. Raji_1cell_rep2

description: PMID


title: SA_acidshock_10min_replicate3

status: Public on Jun 29 2007

city: Aas

first: Solveig

last: Langsrud

address: Osloveien 1

country: Norway

institute: Matforsk, Norwegian Food Research Institute

description: All genes are spotted in triplicate on the slides to increase accuracy of the measured intensities.

hyb_protocol: The hybridisation of the labeled cDNA probes was performed according to protocol from TIGR (Standard operating procedure no. M008). Briefly, slides were incubated in a preheated prehybridization buffer (5x SSC [1x SSC is 0.15 M NaCl and 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 1% Bovine Serum Albumin), at 42 oC for at least one hour. After prehybridization the slides were washed in distilled water (5x 2 min in 50 ml tubes) and then in 50 ml isopropanol. The slides were dried by centrifugation at 90 x g for 12 min at room temperature. The dried Cy3- and Cy5-labeled cDNA was resuspended in 60 ul hybridization buffer (50% formamide, 5x SSC, 0.1% SDS, 300 ug Salmon Sperm DNA), denatured at 95 oC for 5 min, vortexed at low speed and heated again at 95 oC for 5 min. The sample was centrifuged briefly and applied to the prehybridized microarray under a coverslip (LifterSlip, Erie Scientific Company). The slides were placed in a waterproof hybridization chamber for hybridization in a 42 oC water bath overnight. After hybridization the slides were washed in 2x SSC buffer with 0.1% SDS (55 oC, 2 min), then washed in 0.1x SSC with 0.1% SDS buffer (room temperature, 2 min), followed by two washes in 0.1x SSC buffer (room temperature, 2 min). The slides were dried by centrifugation at 90 x g at room temperature for 12 min.

scan_protocol: Slides were scanned with the ScanArray Express 1.0 scanner (Packard BioScience), following the manufacturer’s guidelines.

data_processing: The intensities of the fluorescent spots were quantified with ImaGene 5 software (Biodiscovery Inc.). Background subtraction and normalisation were performed in GeneSpring 6.1 (Silicon Genetics).

organism: Staphylococcus aureus

source_name: Staphylococcus aureus treated

label_protocol: Total RNA was reverse transcribed by using random hexamers in the presence of aminoallyl-dUTP, followed by labeling with Cy5 monoreactive dyes (TIGR protocol, standard operating procedure no. M007). Briefly, 2 ug of total RNA and 6 ug of random hexamers (Invitrogen) in a reaction volume of 18.5 ul were denatured at 70 oC for 10 min, snap cooled on ice for 30 s and centrifuged briefly to bring down condensation. Then 6 ul of First Strand buffer (Invitrogen), 3 ul of 0.1 M dithiothreitol (DTT), 1.2 ul of 12.5 mM deoxynucleoside triphosphate-aminoallyl-dUTP labeling mix (Invitrogen) and 400 U of Superscript II reverse transcriptase (Invitrogen) was added. The labeling reaction mixture was incubated at 42 oC overnight. The first-strand synthesis reaction was stopped by adding 10 ul of 0.5 M EDTA and 10 ul of 1 M NaOH. The reaction mixture was incubated at 65 oC for 15 min, and then 25 ul of 1 M Tris-HCl (pH 7.0) was added. The removal of unincorporated aa-dUTP and free amines was performed according to the TIGR protocol with the Qiagen QIA-quick PCR purification kit. After being dried in a Speed Vac, the samples were stored at –80 oC. Coupling of aminoallyl-labeled cDNA to Cy Dye Ester (Amersham Biosciences) was done according to the TIGR protocol.

growth_protocol: Precultures of S. aureus 50583 were prepared by inoculation of frozen glycerol culture to 1 ml Tryptic Soy Broth (TSB, Oxoid) and incubation overnight at 200 rpm and 37 oC.

extract_protocol: Total RNA was extracted by using the RNeasy Protect Bacteria Mini Prep kit (Qiagen). Briefly, 1.5 ml bacterial culture was added directly to 3 ml RNA Protect Bacteria reagent, vortexed for 5 s, incubated at room temperature for 5 min and then centrifuged at 10 000 x g for 10 min at room temperature. The supernatant was discarded and the pellet resuspended in 40 ul Tris-EDTA buffer followed by addition of 50 ul lysozyme stock solution (40 mgml-1) and 10 ul lysostaphin stock solution (1mg ml-1l). The samples were incubated at 37 oC with shaking for 10 min. The manufacturer’s protocol including use of kit buffers was followed from this point. RNase-free water was added to the membrane of the RNeasy mini spin column and after 1 min incubation at room temperature the RNA was eluted by centrifugation of the column at 10 000 x g for 1 min. The concentration and purity of the total RNA were analysed with an Ultrospec 3000 spectrophotometer (Pharmacia Biotech) and the RNA 600 Nano LabChip system (Agilent Technologies).

treatment_protocol: S. aureus was inoculated in  TSB and incubated at 200 rpm and 37 oC. At an OD600 of 1.0 corresponding to 108 CFUml-1 HCl was added to directly bring the pH down to 4.5. The sample was withdrawn after 10 min and directly transferred to RNA Protect Bacteria reagent (Qiagen).

tag: S. aureus 50583 was isolated from a foodborne outbreak where the source of infection was traced to a pizza.

source_name: Staphylococcus aureus control

label_protocol: Total RNA was reverse transcribed by using random hexamers in the presence of aminoallyl-dUTP, followed by labeling with Cy3 monoreactive dyes (TIGR protocol, standard operating procedure no. M007). Briefly, 2 ug of total RNA and 6 ug of random hexamers (Invitrogen) in a reaction volume of 18.5 ul were denatured at 70 oC for 10 min, snap cooled on ice for 30 s and centrifuged briefly to bring down condensation. Then 6 ul of First Strand buffer (Invitrogen), 3 ul of 0.1 M dithiothreitol (DTT), 1.2 ul of 12.5 mM deoxynucleoside triphosphate-aminoallyl-dUTP labeling mix (Invitrogen) and 400 U of Superscript II reverse transcriptase (Invitrogen) was added. The labeling reaction mixture was incubated at 42 oC overnight. The first-strand synthesis reaction was stopped by adding 10 ul of 0.5 M EDTA and 10 ul of 1 M NaOH. The reaction mixture was incubated at 65 oC for 15 min, and then 25 ul of 1 M Tris-HCl (pH 7.0) was added. The removal of unincorporated aa-dUTP and free amines was performed according to the TIGR protocol with the Qiagen QIA-quick PCR purification kit. After being dried in a Speed Vac, the samples were stored at –80 oC. Coupling of aminoallyl-labeled cDNA to Cy Dye Ester (Amersham Biosciences) was done according to the TIGR protocol.

treatment_protocol: S. aureus was inoculated in TSB and incubated at 200 rpm and 37 oC. At an OD600 of 1.0 corresponding to 108 CFUml-1 the sample was withdrawn and directly transferred to RNA Protect Bacteria reagent (Qiagen).


title: SA_acidshock_2min_replicate3

treatment_protocol: S. aureus was inoculated in  TSB and incubated at 200 rpm and 37 oC. At an OD600 of 1.0 corresponding to 108 CFUml-1 HCl was added to directly bring the pH down to 4.5. The sample was withdrawn after 2 min and directly transferred to RNA Protect Bacteria reagent (Qiagen).


title: SA_acidshock_10min_replicate2


title: SA_acidshock_20min_replicate2

treatment_protocol: S. aureus was inoculated in  TSB and incubated at 200 rpm and 37 oC. At an OD600 of 1.0 corresponding to 108 CFUml-1 HCl was added to directly bring the pH down to 4.5. The sample was withdrawn after 20 min and directly transferred to RNA Protect Bacteria reagent (Qiagen).


title: SA_acidshock_20min_replicate1


title: SA_acidshock_5min_replicate3

treatment_protocol: S. aureus was inoculated in  TSB and incubated at 200 rpm and 37 oC. At an OD600 of 1.0 corresponding to 108 CFUml-1 HCl was added to directly bring the pH down to 4.5. The sample was withdrawn after 5min and directly transferred to RNA Protect Bacteria reagent (Qiagen).


title: SA_acidshock_10min_replicate1


title: SA_acid shock_2min_replicate2

hyb_protocol: The eluted Cy3- and Cy5-labeled samples were mixed and dried in a Speed Vac. The hybridisation of the labeled cDNA probes was performed according to protocol from TIGR (Standard operating procedure no. M008). Briefly, slides were incubated in a preheated prehybridization buffer (5x SSC [1x SSC is 0.15 M NaCl and 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 1% Bovine Serum Albumin), at 42 oC for at least one hour. After prehybridization the slides were washed in distilled water (5x 2 min in 50 ml tubes) and then in 50 ml isopropanol. The slides were dried by centrifugation at 90 x g for 12 min at room temperature. The dried Cy3- and Cy5-labeled cDNA was resuspended in 60 ul hybridization buffer (50% formamide, 5x SSC, 0.1% SDS, 300 g Salmon Sperm DNA), denatured at 95 oC for 5 min, vortexed at low speed and heated again at 95 oC for 5 min. The sample was centrifuged briefly and applied to the prehybridized microarray under a coverslip (LifterSlip, Erie Scientific Company). The slides were placed in a waterproof hybridization chamber for hybridization in a 42 oC water bath overnight. After hybridization the slides were washed in 2x SSC buffer with 0.1% SDS (55 oC, 2 min), then washed in 0.1x SSC with 0.1% SDS buffer (room temperature, 2 min), followed by two washes in 0.1x SSC buffer (room temperature, 2 min). The slides were dried by centrifugation at 90 x g at room temperature for 12 min.

label_protocol: Total RNA was reverse transcribed by using random hexamers in the presence of aminoallyl-dUTP, followed by labeling with Cy5 monoreactive dye (TIGR protocol, standard operating procedure no. M007). Briefly, 2 ug of total RNA and 6 ug of random hexamers (Invitrogen) in a reaction volume of 18.5 ul were denatured at 70 oC for 10 min, snap cooled on ice for 30 s and centrifuged briefly to bring down condensation. Then 6 ul of First Strand buffer (Invitrogen), 3 ul of 0.1 M dithiothreitol (DTT), 1.2 ul of 12.5 mM deoxynucleoside triphosphate-aminoallyl-dUTP labeling mix (Invitrogen) and 400 U of Superscript II reverse transcriptase (Invitrogen) was added. The labeling reaction mixture was incubated at 42 oC overnight. The first-strand synthesis reaction was stopped by adding 10 ul of 0.5 M EDTA and 10 ul of 1 M NaOH. The reaction mixture was incubated at 65 oC for 15 min, and then 25 ul of 1 M Tris-HCl (pH 7.0) was added. The removal of unincorporated aa-dUTP and free amines was performed according to the TIGR protocol with the Qiagen QIA-quick PCR purification kit. After being dried in a Speed Vac, the samples were stored at –80 oC. Coupling of aminoallyl-labeled cDNA to Cy Dye Ester (Amersham Biosciences) was done according to the TIGR protocol.

treatment_protocol: St. aureus was inoculated in TSB and incubated at 200 rpm and 37 oC. At an OD600 of 1.0 corresponding to 108 CFUml-1 HCl was added to directly bring the pH down to 4.5. The sample was withdrawn 2 min after addition of acid and directly transferred to RNA Protect Bacteria reagent (Qiagen).

label_protocol: Total RNA was reverse transcribed by using random hexamers in the presence of aminoallyl-dUTP, followed by labeling with Cy3 monoreactive dye (TIGR protocol, standard operating procedure no. M007). Briefly, 2 ug of total RNA and 6 ug of random hexamers (Invitrogen) in a reaction volume of 18.5 ul were denatured at 70 oC for 10 min, snap cooled on ice for 30 s and centrifuged briefly to bring down condensation. Then 6 ul of First Strand buffer (Invitrogen), 3 ul of 0.1 M dithiothreitol (DTT), 1.2 ul of 12.5 mM deoxynucleoside triphosphate-aminoallyl-dUTP labeling mix (Invitrogen) and 400 U of Superscript II reverse transcriptase (Invitrogen) was added. The labeling reaction mixture was incubated at 42 oC overnight. The first-strand synthesis reaction was stopped by adding 10 ul of 0.5 M EDTA and 10 ul of 1 M NaOH. The reaction mixture was incubated at 65 oC for 15 min, and then 25 ul of 1 M Tris-HCl (pH 7.0) was added. The removal of unincorporated aa-dUTP and free amines was performed according to the TIGR protocol with the Qiagen QIA-quick PCR purification kit. After being dried in a Speed Vac, the samples were stored at –80 oC. Coupling of aminoallyl-labeled cDNA to Cy Dye Ester (Amersham Biosciences) was done according to the TIGR protocol.

treatment_protocol: St. aureus was inoculated in TSB and incubated at 200 rpm and 37 oC. At an OD600 of 1.0 corresponding to 108 CFUml-1 a sample was withdrawn and directly transferred to RNA Protect Bacteria reagent (Qiagen).


title: SA_acidshock_5min_replicate1


title: SA_acid shock_2min_replicate1

hyb_protocol: The eluted Cy3- and Cy5-labeled samples were mixed and dried in a Speed Vac. The hybridisation of the labeled cDNA probes was performed according to protocol from TIGR (Standard operating procedure no. M008). Briefly, slides were incubated in a preheated prehybridization buffer (5x SSC [1x SSC is 0.15 M NaCl and 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 1% Bovine Serum Albumin), at 42 oC for at least one hour. After prehybridization the slides were washed in distilled water (5x 2 min in 50 ml tubes) and then in 50 ml isopropanol. The slides were dried by centrifugation at 90 x g for 12 min at room temperature. The dried Cy3- and Cy5-labeled cDNA was resuspended in 60 l hybridization buffer (50% formamide, 5x SSC, 0.1% SDS, 300 g Salmon Sperm DNA), denatured at 95 oC for 5 min, vortexed at low speed and heated again at 95 oC for 5 min. The sample was centrifuged briefly and applied to the prehybridized microarray under a coverslip (LifterSlip, Erie Scientific Company). The slides were placed in a waterproof hybridization chamber for hybridization in a 42 oC water bath overnight. After hybridization the slides were washed in 2x SSC buffer with 0.1% SDS (55 oC, 2 min), then washed in 0.1x SSC with 0.1% SDS buffer (room temperature, 2 min), followed by two washes in 0.1x SSC buffer (room temperature, 2 min). The slides were dried by centrifugation at 90 x g at room temperature for 12 min.

tag: S. aureus 50583 was isolated from a foodborne outbreak where the source of infection was traced to a pizza


title: SA_acidshock_5min_replicate2


title: SA_acidshock_20min_replicate3


title: Mother Patient 117 - Cy3:14033:13011535-Female-Male

status: Public on Jun 23 2007

type: genomic

city: Nijmegen

first: Joris

middle: Andre

last: Veltman

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: Analysis genomic DNA mother patient 117

hyb_protocol: Test and reference samples were mixed with 120 µg human Cot-1 DNA, co-precipitated and resuspended in 120 µl of a hybridization solution containing 50% formamide, 10% dextran sulfate, 2X SCC, 4% SDS and 10 µg/µl yeast tRNA. Overnight hybridization and post-hybridization washing procedures were performed using a GeneTac Hybridization Station

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4200AL fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysis software.

data_processing: The log2 transformed test over reference ratio for each clone was normalized by subtracting its local mean log2 test over reference ratio obtained by a weighted median filter (Yin and Yang 1996). This filter averages the log ratios of autosomal clones weighted by a Gaussian with its mean at the spot to be normalized and a standard deviation of one physical millimetre on the array.

molecule: genomic DNA

source_name: Mother Patient 117 - Cy3

label_protocol: Five hundred nanogram of genomic DNA was labelled by random priming with Cy3-dUTP

extract_protocol: Genomic DNA extracted from blood

tag: Genomic DNA isolated from blood

source_name: male ref pool - Cy5

label_protocol: Five hundred nanogram of genomic DNA was labelled by random priming with Cy5-dUTP


title: Father Patient 049 - Cy3:13335:12940361-Male-Female

description: Analysis genomic DNA father patient 049

source_name: Father Patient 049 - Cy3

source_name: female ref pool - Cy5


title: Mother Patient 065 - Cy3:14445:13011239-Female-Female

description: Analysis genomic DNA mother patient 065

source_name: Mother Patient 065 - Cy3


title: Father Patient 065 - Cy3:14440:13011238-Male-Female

description: Analysis genomic DNA father patient 065

source_name: Father Patient 065 - Cy3


title: Father Patient 013 - Cy3:11634:12940424-Male-Female

description: Analysis genomic DNA father patient 013

source_name: Father Patient 013 - Cy3


title: Father  Patient 013 - Cy3:15857:13107710-Male-Female

description: Analysis genomic DNA father patient 013

source_name: Father  Patient 013 - Cy3


title: Sister  Patient 204 - Cy3:15585:13105847-Female-Female

description: Analysis genomic DNA sister patient 204

source_name: Sister  Patient 204 - Cy3


title: Male Patient  116 - Cy3:19225:13231214-Male-Male

description: Analysis genomic DNA male patient 116

source_name: Male Patient  116 - Cy3


title: Male Patient  106 - Cy3:19482:13126790-Male-Male

description: Analysis genomic DNA male patient 106

source_name: Male Patient  106 - Cy3


title: Male Patient 106 - Cy3:13333:12942168-Male-Male

description: Analysis genomic DNA male patient 106

source_name: Male Patient 106 - Cy3


title: Father Patient 013 - Cy3:14776:12940113-Male-Female

description: Analysis genomic DNA father patient 013


title: Male Patient  801 - Cy3:22334:13401517-Male-Male

description: Analysis genomic DNA male patient 801

source_name: Male Patient  801 - Cy3


title: Male Patient 797 - Cy3:22353:13390740-Male-Male

description: Analysis genomic DNA male patient 797

source_name: Male Patient 797 - Cy3


title: Father  Patient 148 - Cy3:15460:13068089-Male-Female

description: Analysis genomic DNA father patient 148

source_name: Father  Patient 148 - Cy3


title: Male Patient  112 - Cy3:19221:13231210-Male-Male

description: Analysis genomic DNA male patient 112

source_name: Male Patient  112 - Cy3


title: Male Patient  107 - Cy3:19808:13126804-Male-Male

description: Analysis genomic DNA male patient 107

source_name: Male Patient  107 - Cy3


title: Male Patient  PN01-0012 - Cy3:20855:13231197-Male-Male

description: Analysis genomic DNA male patient PN01-0012

source_name: Male Patient  PN01-0012 - Cy3


title: Male Patient  PN01-0010 - Cy3:19918:13211891-Male-Male

description: Analysis genomic DNA male patient PN01-0010

source_name: Male Patient  PN01-0010 - Cy3

source_name: male ref pool - Cy5


title: Male Patient  PN01-0001 - Cy3:15623:13068537-Male-Male

description: Analysis genomic DNA male patient PN01-0001

source_name: Male Patient  PN01-0001 - Cy3


title: Male Patient  PN01-0002 - Cy3:15618:13105851-Male-Male

description: Analysis genomic DNA male patient PN01-0002

source_name: Male Patient  PN01-0002 - Cy3


title: Male Patient  742 - Cy3:21860:13301199-Male-Male

description: Analysis genomic DNA male patient 742

source_name: Male Patient  742 - Cy3


title: Male Patient  750 - Cy3:20824:13231110-Male-Male

description: Analysis genomic DNA male patient 750

source_name: Male Patient  750 - Cy3


title: Male Patient  744 - Cy3:21978:13302457-Male-Male

description: Analysis genomic DNA male patient 744

source_name: Male Patient  744 - Cy3


title: Male Patient  745 - Cy3:21980:13302458-Male-Male

description: Analysis genomic DNA male patient 745

source_name: Male Patient  745 - Cy3


title: Male Patient  071 - Cy5:11172:12939692-Female-Male

description: Analysis genomic DNA male patient 071

source_name: female ref pool - Cy3

source_name: Male Patient  071 - Cy5


title: Male Patient  065 - Cy5:10496:12940199-Female-Male

description: Analysis genomic DNA male patient 065

source_name: Male Patient  065 - Cy5


title: Male Patient  778 - Cy3:22260:13406050-Male-Male

description: Analysis genomic DNA male patient 778

source_name: Male Patient  778 - Cy3


title: Male Patient  199 - Cy5:13904:13011528-Female-Male

description: Analysis genomic DNA male patient 199

source_name: Male Patient  199 - Cy5


title: Male Patient  751 - Cy3:20788:13231099-Male-Male

description: Analysis genomic DNA male patient 751

source_name: Male Patient  751 - Cy3


title: Male Patient  029 - Cy5:11015:12940354-Female-Male

description: Analysis genomic DNA male patient 029

source_name: Male Patient  029 - Cy5


title: Male Patient  071 - Cy5:15613:13105848-Female-Male

description: Analysis genomic DNA male patient 071


title: Male Patient  850 - Cy3:22129:13401526-Male-Male

description: Analysis genomic DNA male patient 850

source_name: Male Patient  850 - Cy3


title: Male Patient  771 - Cy3:22121:13401532-Male-Male

description: Analysis genomic DNA male patient 771

source_name: Male Patient  771 - Cy3


title: Male Patient  755 - Cy3:21986:13302442-Male-Male

description: Analysis genomic DNA male patient 755

source_name: Male Patient  755 - Cy3


title: Male Patient  793 - Cy3:22322:13390742-Male-Male

description: Analysis genomic DNA male patient 793

source_name: Male Patient  793 - Cy3

source_name: male ref pool - Cy5


title: Male Patient  757 - Cy3:21970:13302455-Male-Male

description: Analysis genomic DNA male patient 757

source_name: Male Patient  757 - Cy3


title: Male Patient  172 - Cy5:14282:13011510-Female-Male

description: Analysis genomic DNA male patient 172

source_name: Male Patient  172 - Cy5


title: Male Patient  779 - Cy3:22270:13406049-Male-Male

description: Analysis genomic DNA male patient 779

source_name: Male Patient  779 - Cy3


title: Male Patient  802 - Cy3:22358:13390741-Male-Male

description: Analysis genomic DNA male patient 802

source_name: Male Patient  802 - Cy3


title: Male Patient  821 - Cy3:22379:13390728-Male-Male

description: Analysis genomic DNA male patient 821

source_name: Male Patient  821 - Cy3


title: Male Patient  822 - Cy3:22374:13390731-Male-Male

description: Analysis genomic DNA male patient 822

source_name: Male Patient  822 - Cy3


title: Male Patient  730 - Cy3:21851:13301210-Male-Male

description: Analysis genomic DNA male patient 730

source_name: Male Patient  730 - Cy3


title: Male Patient  739 - Cy3:21915:13302461-Male-Male

description: Analysis genomic DNA male patient 739

source_name: Male Patient  739 - Cy3


title: Male Patient  732 - Cy3:20792:13231101-Male-Male

description: Analysis genomic DNA male patient 732

source_name: Male Patient  732 - Cy3


title: Male Patient  726 - Cy3:21833:13301205-Male-Male

description: Analysis genomic DNA male patient 726

source_name: Male Patient  726 - Cy3


title: Male Patient  729 - Cy3:21837:13301209-Male-Male

description: Analysis genomic DNA male patient 729

source_name: Male Patient  729 - Cy3


title: Male Patient  833 - Cy3:22159:13406104-Male-Male

description: Analysis genomic DNA male patient 833

source_name: Male Patient  833 - Cy3


title: Male Patient  818 - Cy3:22368:13390729-Male-Male

description: Analysis genomic DNA male patient 818

source_name: Male Patient  818 - Cy3


title: Male Patient  853 - Cy3:22133:13401529-Male-Male

description: Analysis genomic DNA male patient 853

source_name: Male Patient  853 - Cy3


title: Male Patient  724 - Cy3:21796:13301214-Male-Male

description: Analysis genomic DNA male patient 724

source_name: Male Patient  724 - Cy3


title: Male Patient  720 - Cy3:21511:13301193-Male-Male

description: Analysis genomic DNA male patient 720

source_name: Male Patient  720 - Cy3


title: Male Patient  716 - Cy3:21123:13301590-Male-Male

description: Analysis genomic DNA male patient 716

source_name: Male Patient  716 - Cy3

source_name: male ref pool - Cy5


title: Male Patient  712 - Cy3:21098:13302149-Male-Male

description: Analysis genomic DNA male patient 712

source_name: Male Patient  712 - Cy3


title: Male Patient  710 - Cy3:20932:13301572-Male-Male

description: Analysis genomic DNA male patient 710

source_name: Male Patient  710 - Cy3


title: Male Patient  683 - Cy3:20428:13207954-Male-Male

description: Analysis genomic DNA male patient 683

source_name: Male Patient  683 - Cy3


title: Male Patient  697 - Cy3:20907:13231115-Male-Male

description: Analysis genomic DNA male patient 697

source_name: Male Patient  697 - Cy3


title: Male Patient  694 - Cy3:20485:13231194-Male-Male

description: Analysis genomic DNA male patient 694

source_name: Male Patient  694 - Cy3


title: Male Patient  700 - Cy3:20983:13301574-Male-Male

description: Analysis genomic DNA male patient 700

source_name: Male Patient  700 - Cy3


title: Male Patient  709 - Cy3:21004:13301573-Male-Male

description: Analysis genomic DNA male patient 709

source_name: Male Patient  709 - Cy3


title: Male Patient  660 - Cy3:20412:13207939-Male-Male

description: Analysis genomic DNA male patient 660

source_name: Male Patient  660 - Cy3


title: Male Patient  678 - Cy3:20511:13207947-Male-Male

description: Analysis genomic DNA male patient 678

source_name: Male Patient  678 - Cy3


title: Male Patient  711 - Cy3:21009:13301575-Male-Male

description: Analysis genomic DNA male patient 711

source_name: Male Patient  711 - Cy3


title: Male Patient  698 - Cy3:20978:13301486-Male-Male

description: Analysis genomic DNA male patient 698

source_name: Male Patient  698 - Cy3


title: Male Patient  687 - Cy3:20903:13231117-Male-Male

description: Analysis genomic DNA male patient 687

source_name: Male Patient  687 - Cy3


title: Male Patient  635 - Cy3:19933:13211901-Male-Male

description: Analysis genomic DNA male patient 635

source_name: Male Patient  635 - Cy3


title: Male Patient  721 - Cy3:21513:13301192-Male-Male

description: Analysis genomic DNA male patient 721

source_name: Male Patient  721 - Cy3


title: Male Patient  717 - Cy3:21509:13301191-Male-Male

description: Analysis genomic DNA male patient 717

source_name: Male Patient  717 - Cy3


title: Male Patient  669 - Cy3:20351:13207941-Male-Male

description: Analysis genomic DNA male patient 669

source_name: Male Patient  669 - Cy3


title: Male Patient  753 - Cy3:20830:13231108-Male-Male

description: Analysis genomic DNA male patient 753

source_name: Male Patient  753 - Cy3

source_name: male ref pool - Cy5


title: Male Patient  708 - Cy3:20997:13301581-Male-Male

description: Analysis genomic DNA male patient 708

source_name: Male Patient  708 - Cy3


title: Male Patient  691 - Cy3:20860:13231190-Male-Male

description: Analysis genomic DNA male patient 691

source_name: Male Patient  691 - Cy3


title: Male Patient  704 - Cy3:20480:13231196-Male-Male

description: Analysis genomic DNA male patient 704

source_name: Male Patient  704 - Cy3


title: Male Patient  716 - Cy3:21282:13302168-Male-Male

description: Analysis genomic DNA male patient 716

source_name: Male Patient  716 - Cy3


title: Male Patient  694 - Cy3:20490:13231198-Male-Male

description: Analysis genomic DNA male patient 694

source_name: Male Patient  694 - Cy3


title: Male Patient  677 - Cy3:20432:13207958-Male-Male

description: Analysis genomic DNA male patient 677

source_name: Male Patient  677 - Cy3


title: Male Patient  676 - Cy3:20535:13207949-Male-Male

description: Analysis genomic DNA male patient 676

source_name: Male Patient  676 - Cy3


title: Male Patient  674 - Cy3:20355:13207942-Male-Male

description: Analysis genomic DNA male patient 674

source_name: Male Patient  674 - Cy3


title: Male Patient  654 - Cy3:20472:13231201-Male-Male

description: Analysis genomic DNA male patient 654

source_name: Male Patient  654 - Cy3


title: Male Patient  563 - Cy3:21112:13301589-Male-Male

description: Analysis genomic DNA male patient 563

source_name: Male Patient  563 - Cy3


title: Male Patient  568 - Cy3:20339:13211887-Male-Male

description: Analysis genomic DNA male patient 568

source_name: Male Patient  568 - Cy3


title: Male Patient  528 - Cy3:21633:13301197-Male-Male

description: Analysis genomic DNA male patient 528

source_name: Male Patient  528 - Cy3


title: Male Patient  558 - Cy3:21258:13300990-Male-Male

description: Analysis genomic DNA male patient 558

source_name: Male Patient  558 - Cy3


title: Male Patient  395 - Cy3:21972:13302460-Male-Male

description: Analysis genomic DNA male patient 395

source_name: Male Patient  395 - Cy3


title: Male Patient  461 - Cy3:21178:13302148-Male-Male

description: Analysis genomic DNA male patient 461

source_name: Male Patient  461 - Cy3


title: Male Patient  544 - Cy3:22236:13406045-Male-Male

description: Analysis genomic DNA male patient 544

source_name: Male Patient  544 - Cy3


title: Male Patient  375 - Cy3:20973:13301582-Male-Male

description: Analysis genomic DNA male patient 375

source_name: Male Patient  375 - Cy3

source_name: male ref pool - Cy5


title: Male Patient  415 - Cy3:20476:13231208-Male-Male

description: Analysis genomic DNA male patient 415

source_name: Male Patient  415 - Cy3


title: Male Patient  360 - Cy3:20424:13207952-Male-Male

description: Analysis genomic DNA male patient 360

source_name: Male Patient  360 - Cy3


title: Male Patient  372 - Cy3:20941:13301485-Male-Male

description: Analysis genomic DNA male patient 372

source_name: Male Patient  372 - Cy3


title: Male Patient  357 - Cy3:20531:13207948-Male-Male

description: Analysis genomic DNA male patient 357

source_name: Male Patient  357 - Cy3


title: Male Patient  359 - Cy3:20911:13207936-Male-Male

description: Analysis genomic DNA male patient 359

source_name: Male Patient  359 - Cy3


title: Male Patient  381 - Cy3:20874:13231236-Male-Male

description: Analysis genomic DNA male patient 381

source_name: Male Patient  381 - Cy3


title: Male Patient  445 - Cy3:21174:13302156-Male-Male

description: Analysis genomic DNA male patient 445

source_name: Male Patient  445 - Cy3


title: Male Patient  354 - Cy3:19531:13126795-Male-Male

description: Analysis genomic DNA male patient 354

source_name: Male Patient  354 - Cy3


title: Male Patient  245 - Cy3:19448:13211897-Male-Male

description: Analysis genomic DNA male patient 245

source_name: Male Patient  245 - Cy3


title: Male Patient  494 - Cy3:19867:13211898-Male-Male

description: Analysis genomic DNA male patient 494

source_name: Male Patient  494 - Cy3


title: Male Patient  362 - Cy3:20888:13231114-Male-Male

description: Analysis genomic DNA male patient 362

source_name: Male Patient  362 - Cy3


title: Male Patient  324 - Cy3:20457:13231193-Male-Male

description: Analysis genomic DNA male patient 324

source_name: Male Patient  324 - Cy3


title: Male Patient  374 - Cy3:20962:13301490-Male-Male

description: Analysis genomic DNA male patient 374

source_name: Male Patient  374 - Cy3


title: Male Patient  483 - Cy3:15825:13068088-Male-Male

description: Analysis genomic DNA male patient 483

source_name: Male Patient  483 - Cy3


title: Male Patient  361 - Cy3:20878:13207932-Male-Male

description: Analysis genomic DNA male patient 361

source_name: Male Patient  361 - Cy3


title: Male Patient  373 - Cy3:20957:13301483-Male-Male

description: Analysis genomic DNA male patient 373

source_name: Male Patient  373 - Cy3


title: Male Patient  371 - Cy3:20946:13301491-Male-Male

description: Analysis genomic DNA male patient 371

source_name: Male Patient  371 - Cy3

source_name: male ref pool - Cy5


title: Male Patient  341 - Cy3:21810:13301208-Male-Male

description: Analysis genomic DNA male patient 341

source_name: Male Patient  341 - Cy3


title: Male Patient  364 - Cy3:20884:13231116-Male-Male

description: Analysis genomic DNA male patient 364

source_name: Male Patient  364 - Cy3


title: Male Patient  262 - Cy3:21596:13300964-Male-Male

description: Analysis genomic DNA male patient 262

source_name: Male Patient  262 - Cy3


title: Male Patient  358 - Cy3:20555:13231093-Male-Male

description: Analysis genomic DNA male patient 358

source_name: Male Patient  358 - Cy3


title: Male Patient  355 - Cy3:20547:13207956-Male-Male

description: Analysis genomic DNA male patient 355

source_name: Male Patient  355 - Cy3


title: Male Patient  356 - Cy3:20539:13207953-Male-Male

description: Analysis genomic DNA male patient 356

source_name: Male Patient  356 - Cy3


title: Male Patient  167 - Cy3:19981:13211885-Male-Male

description: Analysis genomic DNA male patient 167

source_name: Male Patient  167 - Cy3


title: Male Patient  209 - Cy3:22406:13390727-Male-Male

description: Analysis genomic DNA male patient 209

source_name: Male Patient  209 - Cy3


title: Male Patient  333 - Cy3:19461:13126793-Male-Male

description: Analysis genomic DNA male patient 333

source_name: Male Patient  333 - Cy3


title: Male Patient  150 - Cy3:19235:13231212-Male-Male

description: Analysis genomic DNA male patient 150

source_name: Male Patient  150 - Cy3


title: Male Patient  066 - Cy3:21166:13302153-Male-Male

description: Analysis genomic DNA male patient 066

source_name: Male Patient  066 - Cy3


title: Male Patient  203 - Cy3:21286:13300969-Male-Male

description: Analysis genomic DNA male patient 203

source_name: Male Patient  203 - Cy3


title: Male Patient  151 - Cy3:20335:13207934-Male-Male

description: Analysis genomic DNA male patient 151

source_name: Male Patient  151 - Cy3


title: Male Patient  197 - Cy3:21154:13302155-Male-Male

description: Analysis genomic DNA male patient 197

source_name: Male Patient  197 - Cy3


title: Male Patient  041 - Cy3:21457:13302164-Male-Male

description: Analysis genomic DNA male patient 041

source_name: Male Patient  041 - Cy3


title: Male Patient  164 - Cy3:19327:13126791-Male-Male

description: Analysis genomic DNA male patient 164

source_name: Male Patient  164 - Cy3


title: Male Patient  045 - Cy3:19525:13126792-Male-Male

description: Analysis genomic DNA male patient 045

source_name: Male Patient  045 - Cy3

source_name: male ref pool - Cy5


title: Male Patient  086 - Cy3:19369:13211904-Male-Male

description: Analysis genomic DNA male patient 086

source_name: Male Patient  086 - Cy3


title: Male Patient  130 - Cy3:19998:13231207-Male-Male

description: Analysis genomic DNA male patient 130

source_name: Male Patient  130 - Cy3


title: Male Patient  759 - Cy3:22163:13406105-Male-Female

description: Analysis genomic DNA male patient 759

source_name: Male Patient  759 - Cy3

source_name: female ref pool - Cy5


title: Male Patient  041 - Cy3:21202:13300976-Male-Male

description: Analysis genomic DNA male patient 041


title: Male Patient  764 - Cy3:21240:13302169-Male-Female

description: Analysis genomic DNA male patient 764

source_name: Male Patient  764 - Cy3


title: Male Patient  645 - Cy3:17818:13118858-Male-Female

description: Analysis genomic DNA male patient 645

source_name: Male Patient  645 - Cy3


title: Male Patient  659 - Cy3:18774:13126695-Male-Female

description: Analysis genomic DNA male patient 659

source_name: Male Patient  659 - Cy3


title: Male Patient  673 - Cy3:19023:13126702-Male-Female

description: Analysis genomic DNA male patient 673

source_name: Male Patient  673 - Cy3


title: Male Patient  641 - Cy3:18264:13127180-Male-Female

description: Analysis genomic DNA male patient 641

source_name: Male Patient  641 - Cy3


title: Male Patient  653 - Cy3:18268:13127203-Male-Female

description: Analysis genomic DNA male patient 653

source_name: Male Patient  653 - Cy3


title: Male Patient  652 - Cy3:16999:13108060-Male-Female

description: Analysis genomic DNA male patient 652

source_name: Male Patient  652 - Cy3


title: Male Patient  651 - Cy3:18879:13126715-Male-Female

description: Analysis genomic DNA male patient 651

source_name: Male Patient  651 - Cy3


title: Male Patient  796 - Cy3:21784:13301215-Male-Female

description: Analysis genomic DNA male patient 796

source_name: Male Patient  796 - Cy3


title: Male Patient  643 - Cy3:18771:13126694-Male-Female

description: Analysis genomic DNA male patient 643

source_name: Male Patient  643 - Cy3


title: Male Patient  PN01-0003 - Cy3:15841:13107716-Male-Female

description: Analysis genomic DNA male patient PN01-0003

source_name: Male Patient  PN01-0003 - Cy3


title: Male Patient  146 - Cy3:21422:13300972-Male-Male

description: Analysis genomic DNA male patient 146

source_name: Male Patient  146 - Cy3


title: Male Patient  631 - Cy3:16987:13108056-Male-Female

description: Analysis genomic DNA male patient 631

source_name: Male Patient  631 - Cy3


title: Male Patient  633 - Cy3:18817:13126785-Male-Female

description: Analysis genomic DNA male patient 633

source_name: Male Patient  633 - Cy3


title: Male Patient  600 - Cy3:17360:13105515-Male-Female

description: Analysis genomic DNA male patient 600

source_name: Male Patient  600 - Cy3


title: Male Patient  599 - Cy3:17365:13105514-Male-Female

description: Analysis genomic DNA male patient 599

source_name: Male Patient  599 - Cy3


title: Male Patient  598 - Cy3:18258:13127183-Male-Female

description: Analysis genomic DNA male patient 598

source_name: Male Patient  598 - Cy3

source_name: female ref pool - Cy5


title: Male Patient  616 - Cy3:18252:13124006-Male-Female

description: Analysis genomic DNA male patient 616

source_name: Male Patient  616 - Cy3


title: Male Patient  583 - Cy3:18219:13123989-Male-Female

description: Analysis genomic DNA male patient 583

source_name: Male Patient  583 - Cy3


title: Male Patient  640 - Cy3:18290:13127192-Male-Female

description: Analysis genomic DNA male patient 640

source_name: Male Patient  640 - Cy3


title: Male Patient  599 - Cy3:17588:13105527-Male-Female

description: Analysis genomic DNA male patient 599


title: Male Patient  605 - Cy3:18260:13127184-Male-Female

description: Analysis genomic DNA male patient 605

source_name: Male Patient  605 - Cy3


title: Male Patient  578 - Cy3:16678:13105961-Male-Female

description: Analysis genomic DNA male patient 578

source_name: Male Patient  578 - Cy3


title: Male Patient  587 - Cy3:18236:13127188-Male-Female

description: Analysis genomic DNA male patient 587

source_name: Male Patient  587 - Cy3


title: Male Patient  555 - Cy3:16845:13108065-Male-Female

description: Analysis genomic DNA male patient 555

source_name: Male Patient  555 - Cy3


title: Male Patient  580 - Cy3:18254:13127182-Male-Female

description: Analysis genomic DNA male patient 580

source_name: Male Patient  580 - Cy3