title: Mouse hollow fiber encapsulated 25mg/kg Isoniazid 3 dose 6 hour replicate 1

city: Baltimore

first: Petros

last: Karakousis

address: 1550 Orleans St

institute: Johns Hopkins University School of Medicine

description: These data represent exposure of Mycobacterium tuberculosis bacilli to Isoniazid in an in-vivo hollow fiber model of dormancy.

hyb_protocol: 1ug human COT1 DNA was added to combined labeled RNA samples as a blocker. Samples were added to hybridization buffer (10XSSC, 30% formamide, 0.2% SDS), denatured at 95C for 3 minutes, and snap cooled on ice. Samples were loaded onto the slide by capillary action under a Corning lifter slip and sealed into a corning hybridization chamber with 30ul water at each as a humidifier. Samples were hybridized to the slides for 18 hours at 55C in a hybridization oven. Hybridized slides were washed for 10 minutes at room temperature in each of 2XSSC, 0.1%SDS; 1XSSC, 0.1%SDS; 1XSSC; 0.5XSSC; and rinsed for 10 seconds in DI water.

scan_protocol: fluorescence intensity data were collected with a GenePix 4000B scanner (Axon Instruments) with GenePix Pro 4.0 software. Photomultiplier tube gains were set empirically for each channel to optomize intensity and to equalize intensities for control spots on each channel.

data_processing: Genepix result files were loaded into the R statistical language using the limma package of bioconductor (www.bioconductor.org) for normalization and statistical analysis. Median spot intensities were calculated using the read.maimages function with weighted spots set to zero and normalized using the normalizeWithinArrays function with the nonlinear printtiploess normalizing algorithm and the normexp background correction algorithm with a correction factor of 50. A linear model using the lmFit function was then applied to the normalized data and a Bayesian method for determining differential expression was applied using the eBayes function.

organism: Mycobacterium tuberculosis H37Rv

source_name: 6 hour 25mg/kg INH treated hollow fiber

label_protocol: Purified RNA samples were labeled with Cy5 using the Atlas Glass RNA labelling kit from Clontech according to the manufacturers instructions.

growth_protocol: 100ul Mycobacterium tuberculosis stock culture was added to 50ml 7H9 medium supplemented with OADC, glycerol, and Tween 80 and grown at 37C to OD600 of 0.5 at 225rpm.  The culture was diluted to 10^5 cells/ml and encapsulated into a 2cm x 8mm polyvinyllidine fluoride fiber.  The fibers were implanted subcutaneously into nude immunocompetent SKH1 mice via an apical incision at the base of the skull and placed near each flank with three fibers per mouse.  The fibers were incubated in the mice for fourteen days prior to treatment.

extract_protocol: The hollow fibers were extracted from the mice and the fiber contents were pelleted by centrifugation at 1800xg for 10 minutes at 4C and resuspended in 500ul Tri Reagent (Sigma T9424) and 1/2 volume 0.1mm Silicon/Zirconia beads. Samples were alternately homogenized in a beadbeater and cooled on ice for 30 seconds and 1 minute respectively. Samples were spun at 10kxg for 10 minutes at room temperature. 200ul Chloroform was added to each samples and mixed by shaking. Samples were incubated for 15 minutes at room temperature and spun at 10kxg for 15 minutes at 4C. The aqueous phase was transferred to an equal volume of isopropanol and the RNA was precipitated overnight at -20C. The samples were spun at 12kxg for 20 minutes at 4C and washed with 1ml 70% ethanol. RNA was resuspended in 15ul DEPC treated water and analyzed by spectrophotometry.

treatment_protocol: 200ul Isoniazid was administered via a canula to a final concentration of 25mg/kg daily for three days.  Treatment ended and the hollow fibers were removed 6 hours after the third dose.

tag: Mycobacterium tuberculosis encapsulated into polyvinyllidine fluoride fibers and implanted subcutaneously in mice.  Mice were administered 25mg/kg INH by gavage daily for three days fourteen days after implantation.  Hollow fibers were extracted 6 hours after the third dose.

source_name: 6 hour water treated hollow fiber

extract_protocol: The hollow fibers were extracted from the mice and the fiber contents were pelleted by centrifugation at 1800xg for 10 minutes at 4C and resuspended in 1ml Tri Reagent (Sigma T9424) and 1/2 volume 0.1mm Silicon/Zirconia beads. Samples were alternately homogenized in a beadbeater and cooled on ice for 30 seconds and 1 minute respectively. Samples were spun at 10kxg for 10 minutes at room temperature. 200ul Chloroform was added to each samples and mixed by shaking. Samples were incubated for 15 minutes at room temperature and spun at 10kxg for 15 minutes at 4C. The aqueous phase was transferred to an equal volume of isopropanol and the RNA was precipitated overnight at -20C. The samples were spun at 12kxg for 20 minutes at 4C and washed with 1ml 70% ethanol. RNA was resuspended in 15ul DEPC treated water and analyzed by spectrophotometry.

treatment_protocol: 200ul water was administered via a canula to a final concentration of 25mg/kg daily for three days.  Treatment ended and the hollow fibers were removed 6 hours after the third dose.

tag: Mycobacterium tuberculosis encapsulated into polyvinyllidine fluoride fibers and implanted subcutaneously in mice.  Mice were administered water by gavage daily for three days fourteen days after implantation.  Hollow fibers were extracted 6 hours after the third dose.


title: 2_040226-Hog1+hog2 hog1cy5+hog2cy3-2423 TEST-CK

status: Public on Dec 17 2007

type: RNA

city: Beijing

first: Jin

last: Zhang

address: 2#, Yuanmingyuan West Road

country: China

institute: China Agricultural University

description: To avoid dye bias, the experiments were performed in duplicate by dye swap with Cy5-dCTP first used with the test pig and Cy3-dCTP used with the control pig and then Cy3-dCTP used with the test pig and Cy5-dCTP used with the control pig.

hyb_protocol: See Pronto Universal hybridization kit Quick Reference Guide.

scan_protocol: Arrays were scanned with a ScanArray Express scanner (Parckard Bioscience, Kanata, OT，USA) with the obtained images analyzed with GenePix Pro 4.0 (Axon Instruments, Foster City, CA ) and Acuity 4.0 (Axon Instruments, Foster City, CA).

data_processing: The resulting microarray data was then normalized using the space and intensity-dependent normalization in the LOWESS program. Each gene was represented in triplicate on each slide. The intensity (median) of each spot was analyzed using the student t-test to identify the differentially expressed genes (P<0.05). Low quality spots were filtered out before the student t-test analysis. Low spots refer to stained spots with bad images or spots with the intensities (median) lower than 200 (too weak) or greater than 60000 (saturated).

molecule: total RNA

organism: Sus scrofa

source_name: control

label_protocol: Reverse transcription was done with 10 µg total RNA as the template to synthesize cDNA incorporated with flourence dye Cy3-dCTP or Cy5-dCTP. Probes were purified on a Qiagen spin column (Qiagen, Valencia, CA, USA). Mix dye-labeled cDNA together and dry dye-labeled cDNA were used for hybridization.

growth_protocol: Eight Chinese miniature pigs were used in the experiments. Four hogs and four sows, all 4 weeks old, were housed in the Nutrition and Metabolism Laboratory at the China Agriculture University. They were raised under exactly the same conditions and were fed the same diets until 8 weeks (average body weight 17 kg). They were randomly divided into 4 groups with each group having two pigs with the same gender and the same parents. For the following 4 weeks, one pig in each group was fed 25 mg/kg clenbuterol twice daily in their diets as the test pig, while the other was fed the same diet without clenbuterol as the control. Then one group of hogs and one group of sows were slaughtered for analysis. These two groups are referred to as the 3 month-old pigs. The other two groups were fed with/without 50 mg/kg clenbuterol twice daily in their diets for another 4 weeks and slaughtered for analysis. These two groups are referred to as the 4 month-old pigs. Approximately 1 g biopsies were taken from the back fat adipose tissues (at the fifth lumbar vertebra level) of each pig. The adipose tissue samples were washed in sterile water, snap frozen in liquid nitrogen and stored at -80℃.

extract_protocol: Total RNA of the adipose tissue was extracted with TRIZOL reagent (Invitrogen, Gaithersburg, MD, USA) and further purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA) according to the manufacturers instructions.

treatment_protocol: The pig was fed without clenbuterol.

tag: The RNA was isolated from back fat tissue of Chinese Miniature pigs, which was 3 month-old hog.

source_name: test

treatment_protocol: The pig was fed with clenbuterol.


title: 1_040206 Hog1+hog2 hog2cy5+hog1cy3 2389 CK-TEST

data_processing: The resulting microarray data was then normalized using the space and intensity-dependent normalization in the LOWESS program [40]. Each gene was represented in triplicate on each slide. The intensity (median) of each spot was analyzed using the student t-test to identify the differentially expressed genes (P<0.05). Low quality spots were filtered out before the student t-test analysis. Low spots refer to stained spots with bad images or spots with the intensities (median) lower than 200 (too weak) or greater than 60000 (saturated).


title: 3-30-07 Calprotectin-B T0

status: Public on Dec 14 2007

city: Omaha

first: Paul

middle: M

last: Dunman

state: NE

address: 986495 Nebraska Medical Center

department: Pathology and Microbiology

country: USA

institute: University of Nebraska Medical Center

description: Biological replicate to 2-27-07 Calprotectin A T0

hyb_protocol: Affymetrix Antisense Prokaryotic

scan_protocol: Affymetrix Antisense Prokaryotic

label: biotin

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: S. aureus strain Newman, mid-log grown in Calprotectin treated RPMI medium

label_protocol: Affymetrix Antisense Prokaryotic

extract_protocol: Qiagen RNeasy Mini Prep


title: Heat Shock 1

city: Portland

first: Brad

last: Buckley

state: OR

address: 1719 SW 10th Ave

department: Biology

institute: Portland State University

hyb_protocol: cDNAs were coupled to a monoreactive fluorescent dye (either Cy3 or Cy5; Amersham) and hybridized to the microarray for 15 h at 65˚C; lowering hybridization temperature can increase detection of features with low sequence homology, so the use of a single, high hybridization temperature were used to reduce non-specific binding of probe to the arrays. Control or heat shocked samples from a given species were labeled with Cy5 dye, and were competitively hybridized against a reference sample of total RNA from the same species that was labeled with Cy3 dye.

scan_protocol: Slides were scanned on an Axon Pro 4.0 scanner

data_processing: GeneSpring software was used to convert raw data values into ratios of Cy5 to Cy3. These ratios were Lowess normalized and then each value was normalized to the average of the three control slides.

organism: Gillichthys mirabilis

source_name: Gm 4-h Heat Shock

label_protocol: Samples were converted to cDNA and labeled with either a Cy3 or Cy5 dye.

growth_protocol: Fish were maintained in recirculating aquaria at room temperature and fed trout pellets.

extract_protocol: Trizol extraction of total RNA

treatment_protocol: Fish were either maintained at a control temperature of 18C or subjected to 4 hours of exposure to 32C.

tag: Gill tissue

source_name: Reference gill tissue


title: Gm Control 1

source_name: Gm control


title: 5_040210 Hog3+Hog4 Hog4cy5+Hog3cy3 2392 ck-test

tag: The RNA was isolated from back fat tissue of Chinese Miniature pigs, which was 4 month-old hog.


title: 3-30-07 Calprotectin-C T0

description: Biological replicate to 2-27-07 Calprotectin A T0 and 3-30-07 Calprotectin-B T0

tag: S. aureus strain Newman, mid-log grown in Calprotectin treated RPMI medium


title: 3_040210 Sow1+Sow2 sow2cy5+Sow1cy3 2391 ck-test


title: 7_040210 sow3+sow4 sow4cy5+sow3cy3 2393 ck-test

tag: The RNA was isolated from back fat tissue of Chinese Miniature pigs, which was 4 month-old sow.


title: Oxygen depleted 6 hour 1ug/ml INH treated replicate 3

state: MD

department: Medicine

description: These data represent a long term dose of a high concentration (10x MIC) of isoniazid to oxygen depleted cultures in-vitro.

source_name: 6 hour 1ug/ml INH treated oxygen depleted culture

growth_protocol: 100ul Mycobacterium tuberculosis stock culture was added to 50ml Dubose tween albumin broth with methylene blue and grown at 37C to OD600 of 0.5 at 225rpm. The cultures were then diluted to 10^4 cfu/ml and transferred to a 23ml test tube with sufficient volume to leave a 0.5vol head space. The cultures were stoppered and incubated upright at 37C without shaking but with gentle stirring to keep the culture homogeneous but not disturb the air/liquid interface. Hypoxia and entry into growth stage NRP2 was indicated by color change of the methylene blue to clear. Treatment started the day after color change.

extract_protocol: treated culture was pelleted by centrifugation at 1800xg for 10 minutes at 4C and resuspended in 1ml Tri Reagent (Sigma T9424) and 1/2 volume 0.1mm Silicon/Zirconia beads. Samples were alternately homogenized in a beadbeater and cooled on ice for 30 seconds and 1 minute respectively. Samples were spun at 10kxg for 10 minutes at room temperature. 200ul Chloroform was added to each samples and mixed by shaking. Samples were incubated for 15 minutes at room temperature and spun at 10kxg for 15 minutes at 4C. The aqueous phase was transferred to an equal volume of isopropanol and the RNA was precipitated overnight at -20C. The samples were spun at 12kxg for 20 minutes at 4C and washed with 1ml 70% ethanol. RNA was resuspended in 15ul DEPC treated water and analyzed by spectrophotometry.

treatment_protocol: 100ul Isoniazid was added via a 23G needle to a final concentration of 1ug/ml and incubated for 6 hours prior to RNA extraction.

tag: Mycobacterium Tuberculosis H37Rv grown to log phase, transferred to progressive hypoxia model, and treated with 1ug/ml Isoniazid for 6 hours.

source_name: 6 hour water treated oxygen depleted culture

treatment_protocol: 100ul water was added via a 23G needle to a final concentration of 1ug/ml and incubated for 6 hours prior to RNA extraction.

tag: Mycobacterium Tuberculosis H37Rv grown to log phase, transferred to progressive hypoxia model, and treated with water for 6 hours.


title: Mouse hollow fiber encapsulated 25mg/kg Isoniazid 3 dose 6 hour replicate 2

tag: Mycobacterium tuberculosis encapsulated into polyvinyllidine fluoride fibers and implanted subcutaneously in mice. Mice were administered 25mg/kg INH by gavage daily for three days fourteen days after implantation. Hollow fibers were extracted 6 hours after the third dose.

tag: Mycobacterium tuberculosis encapsulated into polyvinyllidine fluoride fibers and implanted subcutaneously in mice. Mice were administered water by gavage daily for three days fourteen days after implantation. Hollow fibers were extracted 6 hours after the third dose.


title: 4_040227 Sow1+Sow2 sow1cy5+Sow2cy3 2417 test-ck


title: Oxygen depleted 6 hour 1ug/ml INH treated replicate 2


title: 8_040227 sow3+sow4 sow3cy5+sow4cy3 2421 test-ck

hyb_protocol: see Pronto Universal hybridization kit Quick Reference Guide

data_processing:
The resulting microarray data was then normalized using the space and intensity-dependent normalization in the LOWESS program.
Each gene was represented in triplicate on each slide. The intensity (median) of each spot was analyzed using the student t-test to identify the differentially expressed genes (P<0.05). Low quality spots were filtered out before the student t-test analysis. Low spots refer to stained spots with bad images or spots with the intensities (median) lower than 200 (too weak) or greater than 60000 (saturated).

tag: The RNA was isolated from back fat tissue of Chinese Miniature pigs, which was 4 month-old femal pig.

tag: The RNA was isolated from back fat tissue of Chinese Miniature pigs, which was 4 month-old female pig.


title: 6_040227 Hog3+Hog4 Hog3cy5+Hog4cy3 p3cy5 2419 test-ck


title: 2-27-07 Mn-A T0

source_name: S. aureus strain Newman, mid-log grown in RPMI lacking Mn


title: Mouse hollow fiber encapsulated 25mg/kg Isoniazid 3 dose 6 hour replicate 3


title: Oxygen depleted 6 hour 1ug/ml INH treated replicate 1

data_processing: Genepix result files were loaded into the R statistical language using the limma package of bioconductor (www.bioconductor.org) for normalization and statistical analysis. Median spot intensities were calculated using the read.maimages function with weighted spots set to zero and normalized using the normalizeWithinArrays function with the nonlinear printtiploess normalizing algorithm and the normexp background correction algorithm with a correction factor of 50. A linear model using the lmFit function was then applied to the normalized data and a Bayesian method for determining differential expression was applied using the eBayes function

growth_protocol: 100ul Mycobacterium tuberculosis stock culture was added to 50ml Dubose tween albumin broth with methylene blue and grown at 37C to OD600 of 0.5 at 225rpm. The cultures were then diluted to 10^4 cfu/ml and transferred to a 23ml test tube with sufficient volume to leave a 0.5vol head space.  The cultures were stoppered and incubated upright at 37C without shaking but with gentle stirring to keep the culture homogeneous but not disturb the air/liquid interface.  Hypoxia and entry into growth stage NRP2 was indicated by color change of the methylene blue to clear.  Treatment started the day after color change.


title: 2-22-07 WT-A T0

source_name: S. aureus strain Newman, mid-log grown in RPMI medium + metals


title: Log phase 2 hour 1ug/ml INH treated KatG knockout replicate 3

description: These data represent a long term dose of a high concentration (10x MIC) of isoniazid to log phase cultures of KatG deletion mutant in-vitro.

source_name: 6 hour 1ug/ml INH treated log phase KatG knockout culture

growth_protocol: 100ul Mycobacterium tuberculosis KatG knockout stock culture was added to 50ml 7H9 medium supplemented with OADC, glycerol, and Tween 80 and grown at 37C to OD600 of 0.5 at 225rpm.

treatment_protocol: 100ul Isoniazid was added to a final concentration of 1ug/ml and incubated for 6 hours prior to RNA extraction.

tag: Mycobacterium Tuberculosis H37Rv with KatG deletion grown to log phase and treated with 1ug/ml Isoniazid for 6 hours.

source_name: 6 hour water treated log phase KatG knockout culture

label_protocol: Purified RNA samples were labeled with Cy3 using the Atlas Glass RNA labelling kit from Clontech according to the manufacturers instructions.

growth_protocol: 100ul Mycobacterium tuberculosis KatG deletion stock culture was added to 50ml 7H9 medium supplemented with OADC, glycerol, and Tween 80 and grown at 37C to OD600 of 0.5 at 225rpm.

treatment_protocol: 100ul water was added and incubated for 6 hours prior to RNA extraction.

tag: Mycobacterium Tuberculosis H37Rv with KatG deletion grown to log phase and treated with water for 6 hours.


title: Tb Control 1

organism: Trematomus bernacchii

source_name: Tb control 1

treatment_protocol: Fish were either maintained at a control temperature of -1.8C or subjected to either 4 hours of exposure to 4C, 4 hours of 4C and 2 h recovery at -1.8C, or 4 hours at 4C and 4 h recovery at -1.8C.


title: Log phase 2 hour 1ug/ml INH treated KatG knockout replicate 1

description: These data represent a long term dose of a high concentration (10x MIC) of isoniazid to log phase KatG deletion cultures in-vitro.


title: Log phase 2 hour 1ug/ml INH treated replicate 2

description: These data represent a short term dose of a high concentration (10x MIC) of isoniazid to log phase cultures in-vitro.

source_name: 2 hour 1ug/ml INH treated log phase culture

growth_protocol: 100ul Mycobacterium tuberculosis stock culture was added to 50ml 7H9 medium supplemented with OADC, glycerol, and Tween 80 and grown at 37C to OD600 of 0.5 at 225rpm.

treatment_protocol: 100ul Isoniazid was added to a final concentration of 1ug/ml and incubated for 2 hours prior to RNA extraction.

tag: Mycobacterium Tuberculosis H37Rv grown to log phase and treated with 1ug/ml Isoniazid for 2 hours.

source_name: 2 hour water treated log phase culture

treatment_protocol: 100ul water was added and incubated for 2 hours prior to RNA extraction.

tag: Mycobacterium Tuberculosis H37Rv grown to log phase and treated with water for 2 hours.


title: Nutrient starved 2 hour 1ug/ml INH treated replicate 1

description: These data represent a long term dose of a high concentration (10x MIC) of isoniazid to nutrient starved cultures in-vitro.

source_name: 6 hour 1ug/ml INH treated nutrient starved culture

growth_protocol: 100ul Mycobacterium tuberculosis KatG knockout stock culture was added to 50ml 7H9 medium supplemented with OADC, glycerol, and Tween 80 and grown at 37C to OD600 of 0.5 at 225rpm.  The cultures were then pelleted by centrifugation at 1800xg at room temperature and washed twice with 50ml PBS.  The pellet was resuspended in 50ml PBS with 0.05% Tween 80 and placed in a non-shaking 37C incubator.

tag: Mycobacterium Tuberculosis H37Rv grown to log phase, transfered into PBS, and treated with 1ug/ml Isoniazid for 6 hours.

source_name: 6 hour water treated nutrient starved culture

growth_protocol: 100ul Mycobacterium tuberculosis KatG deletion stock culture was added to 50ml 7H9 medium supplemented with OADC, glycerol, and Tween 80 and grown at 37C to OD600 of 0.5 at 225rpm.  The cultures were then pelleted by centrifugation at 1800xg at room temperature and washed twice with 50ml PBS.  The pellet was resuspended in 50ml PBS with 0.05% Tween 80 and placed in a non-shaking 37C incubator.

tag: Mycobacterium Tuberculosis H37Rv grown to log phase, transferred to PBS, and treated with water for 6 hours.


title: Nutrient starved 2 hour 1ug/ml INH treated replicate 2

tag: Mycobacterium Tuberculosis H37Rv grown to log phase, transfered into PBS, and treated with water for 6 hours.


title: monolayer_3T3_Vector_transduced, replicate 2

city: Boston

first: Zhe

last: Li

state: MA

department: Division of Hematology/Oncology

institute: Children's Hospital Boston

description: Gene expression data from control 3T3 cells

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to MOE 430A chips. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The raw CEL files were imported into dChip and normalized with dChip.

organism: Mus musculus

source_name: empty retroviral vector transduced NIH 3T3 cells

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

extract_protocol: Total RNAs were extracted by using Trizol following the manufacturar's instruction.

tag: 3T3 cells growing as a monolayer


title: monolayer_3T3_Vector_transduced, replicate 1


title: Log phase 2 hour 1ug/ml INH treated replicate 1

hyb_protocol: 1ug human COT1 DNA was added to combined labeled RNA samples as a blocker.  Samples were added to hybridization buffer (10XSSC, 30% formamide, 0.2% SDS), denatured at 95C for 3 minutes, and snap cooled on ice.  Samples were loaded onto the slide by capillary action under a Corning lifter slip and sealed into a corning hybridization chamber with 30ul water at each as a humidifier.  Samples were hybridized to the slides for 18 hours at 55C in a hybridization oven.  Hybridized slides were washed for 10 minutes at room temperature in each of 2XSSC, 0.1%SDS; 1XSSC, 0.1%SDS; 1XSSC; 0.5XSSC; and rinsed for 10 seconds in DI water.

scan_protocol: fluorescence intensity data were collected with a GenePix 4000B scanner (Axon Instruments) with GenePix Pro 4.0 software.  Photomultiplier tube gains were set empirically for each channel to optomize intensity and to equalize intensities for control spots on each channel.

extract_protocol: treated culture was pelleted by centrifugation at 1800xg for 10 minutes at 4C and resuspended in 1ml Tri Reagent (Sigma T9424) and 1/2 volume 0.1mm Silicon/Zirconia beads.  Samples were alternately homogenized in a beadbeater and cooled on ice for 30 seconds and 1 minute respectively.  Samples were spun at 10kxg for 10 minutes at room temperature.  200ul Chloroform was added to each samples and mixed by shaking.  Samples were incubated for 15 minutes at room temperature and spun at 10kxg for 15 minutes at 4C.  The aqueous phase was transferred to an equal volume of isopropanol and the RNA was precipitated overnight at -20C.  The samples were spun at 12kxg for 20 minutes at 4C and washed with 1ml 70% ethanol.  RNA was resuspended in 15ul DEPC treated water and analyzed by spectrophotometry.


title: Log phase 2 hour 1ug/ml INH treated KatG knockout replicate 2


title: Log phase 6 hour 1ug/ml INH treated replicate 2

description: These data represent a long term dose of a high concentration (10x MIC) of isoniazid to log phase cultures in-vitro.

source_name: 6 hour 1ug/ml INH treated log phase culture

tag: Mycobacterium Tuberculosis H37Rv grown to log phase and treated with 1ug/ml Isoniazid for 6 hours.

source_name: 6 hour water treated log phase culture

tag: Mycobacterium Tuberculosis H37Rv grown to log phase and treated with water for 6 hours.


title: monolayer_3T3_EN_transduced, sample 2, replicate 2

description: Gene expression data from EN-transduced 3T3 cells

source_name: ETV6-NTRK3 transduced NIH 3T3 cells


title: Malaria patient 155

status: Public on Dec 13 2007

city: Bronx

first: Johanna

middle: Patricia

last: Daily

state: NY

address: 1301 Morris Park Avenue, Price Center

department: Medicine (Infectious Disease)

institute: Albert Einstein College of Medicine

description: gene expression data from RING stage found in patient peripheral blood

hyb_protocol: 15ug of the purified cRNA were fragmented and incubated on the array for 16 hrs in a gene chip hybridization oven at 45°C.  Samples were then removed and arrays were washed and stained with streptavidin phycoerythrin conjugate following Affymetrix protocols.

scan_protocol: Arrays were scanned with an emission wavelength of 560nm at 3um resolution using a confocal scanner(Affymetrix), and the signal intensity for each sequence feature on the array was determined using the Microarray Suite 5 (Affymetrix).

data_processing: Each transcript was assigned a relative expression unit (EU) using MOID used as previously reported. (See Y. Zhou and R. Abagyan, Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis, BMC Bioinformatics 3 (1), 3:2002). After background was subtracted, the average intensity of genes between the 30th and 90th percentiles were normalized to 200 expression units across all samples, to allow comparison. These are reported as raw expression units.

organism: Plasmodium falciparum

source_name: peripheral blood

label_protocol: Eight micrograms of total RNA was used for cDNA synthesis. An oligodT primer containing a phage T7 promoter at its 5’ end was used to prime the cDNA synthesis reaction following the manufacturer’s protocol (Invitrogen). The second strand of cDNA was then synthesized and double strand cDNA were purified using QIAquick purification kit (Qiagen). The faction of double strand cDNA was used for the synthesis of Biotin-Labeled cRNA (using ENZO BioArray High Yield RNA Transcript Labeling Kit) – IVT Reaction. The collected cRNA was cleaned up using the QIAGEN RNeasy mini kit following the manufacturer’s instruction.

growth_protocol: Patients with symptomatic malaria, P. falciparum identified on thin smear and parasitemia >1% were enrolled in Velingara, Senegal. After informed consent was obtained, patients underwent venipuncture and one to two blood tubes (10-20 ml) coated with K3EDTA was collected. Tri-reagent BD (Molecular Research Center, Cincinnati, OH) was added within five to ten minutes after blood collection.

extract_protocol: Blood samples containing Plasmodium falciparum in Tri-Reagent were shipped to Boston in liquid nitrogen, thawed at room temperature and total RNA was isolated according to the manufacturer’s protocol (Tri reagent BD). Specifically 3 volumes of Tri-Reagent BD was added to 1 volume of whole blood. Phase separation is carried out with chloroform and RNA is precipitated in isopropranol, washed in 75% ethanol and resuspended in DEPC water. Twelve samples collected in 2004 and thirty-one samples from 2005 that demonstrated sharp ribosomal bands on a denaturing agarose gel stained with ethidium bromide were selected for hybridization.

treatment_protocol: The mixture was maintained at 4°C until each evening when placed in liquid nitrogen.

tag: days ill:2


title: monolayer_3T3_EN_transduced, sample 2, replicate 1


title: Log phase 6 hour 1ug/ml INH treated replicate 1


title: monolayer_3T3_EN-KD_transduced, replicate 1

source_name: NIH 3T3 cells transduced by a kinase dead (KD) version of ETV6-NTRK3


title: Malaria patient 167

tag: days ill:1


title: Malaria patient 158

tag: Lymphotactin :4086692125


title: monolayer_3T3_EN-KD_transduced, replicate 2


title: Malaria patient 159

tag: days ill:4


title: Malaria patient 188

tag: parasitemia:

tag: days ill:.

tag: TNFa:

tag: TGFa:

tag: Tissue Factor:

tag: P-selectin:

tag: Lymphotactin :


title: Malaria patient 122

tag: days ill:3


title: Malaria patient 106


title: Malaria patient 109


title: Malaria patient 105


title: Malaria patient 147


title: monolayer_3T3_EN_transduced, sample 1, replicate 1


title: Malaria patient 104


title: Malaria patient 72


title: Malaria patient 96


title: monolayer_3T3_EN_transduced, sample 1, replicate 2


title: Malaria patient 81

tag: days ill:


title: Malaria patient 145


title: Malaria patient 102


title: Malaria patient 67


title: Malaria patient 68

tag: days ill:30


title: Malaria patient 51


title: Malaria patient 57


title: Malaria patient 46


title: Malaria patient 40


title: Malaria patient 42


title: Malaria patient 39


title: Malaria patient 28


title: Malaria patient 24

tag: kg:


title: Malaria patient 20


title: Malaria patient 19


title: Malaria patient 14


title: Malaria patient 10


title: AcH_E2_Rep1

type: genomic

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

hyb_protocol: Input and IP DNA co-hybridized to the genomic array described above for 18 hours at 42°C using a TECAN HS400 hybridization machine.

scan_protocol: GenePix 4000B scanner (Axon)

data_processing:
After filtering out the spots flagged for bad quality, the signal ratio of IP-DNA over Input-DNA was log2 transformed and normalized based on a set of control genes, as described in the array design and in the supplemental materials.
The "Upper" and "Lower" .gpr files (linked below as Supplementary files) represent the two replicate regions on the same microarray slide. The exact details of the microarray design have been published and can be found here: http://mcb.asm.org/cgi/content/full/27/14/5090?view=long&pmid=17515612

molecule: genomic DNA

organism: Homo sapiens

source_name: MCF7 cells, treated for 45 minutes with EtOH or 17beta-estradiol (E2)

label_protocol: Random priming labeling

extract_protocol: DNA immunoprecipitated (IP DNA) with specific antibodies

tag: MCF-7 breast cancer cells

extract_protocol: Input DNA


title: AcH_E2_Rep2


title: AcH_EtOH_Rep2


title: AcH_EtOH_Rep1


title: Malaria patient 12.04

tag: days ill:5


title: Malaria patient 11.04


title: Malaria patient 10.04


title: SRC_EtOH_Rep2


title: Malaria patient 16


title: SRC_E2_Rep1


title: SRC_EtOH_Rep1


title: Pol_E2_Rep2


title: Malaria patient 7.04

tag: days ill:6


title: Malaria patient 9.04


title: Pol_EtOH_Rep1


title: ER_E2_Rep2


title: ER_E2_Rep3


title: Control rep3

city: Houston

first: Wei

address: one baylor plaza, MS BCM305

institute: Baylor College of Medicine

description: Control rep3

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Model-based analysis of tiling array (MAT) chip.dfci.harvard.edu/~wli/MAT/

source_name: Human genomic DNA

label_protocol: On ice:    - Dilute DnaseI (Ambion) to appropriate amount based on optimized conditions. We do a 1:100 dilution in water and use 1ul of this for each sample. Include the buffer. Efficient digestion can be checked by running the DNA on a gel. The optimal smear should range from 50bp to 100bp. A little higher is OK.     - So, add buffer, Dnase I and buffer to final volume of 55ul.  Run the program:      37C 30 min    95C 15 min    4C hold    - Run 5ul on a gel to check for good fragmentation.  Smear should be between 50bp and 100bp, although a little larger is OK    On ice:    - Add:  13ul TdT buffer (Promega)    1ul Biotin (1mM stock)    1ul TdT (30U/ul)    50ul of fragmented DNA    -Run the program:      37C 16 hours    95C 10 min    4C hold    - Spin briefly and prepare for hybridization

extract_protocol:
To create our simulated ChIP spike-in mixture, we first randomly selected 100 cloned genomic DNA sequences (average length 497 bp) corresponding to predicted promoters in the human genome15, individually purified them, and normalized the concentrations of each preparation to 500 pg/µL (Figure 1). To create enrichment levels that ranged from 1.25- to 196-fold relative to genomic DNA (Supplemental Tables 1 and 2), we added the appropriate volume of these stock solutions to a commercial human genomic DNA preparation (Methods; Supplemental Tables 1 and 2). The clones were validated by sequencing and PCR both before and after dilution (Supplemental Methods). We prepared one clone mixture to be directly labeled and hybridized to arrays at the given concentration ("undiluted", 77 ng/µL), and a different clone mixture that was diluted such that amplification would be necessary before labeling and hybridization ("diluted", 3 ng/µL). The diluted mixture was created because all of the array platforms require microgram quantities of DNA and a typical ChIP experiment produces ~50 ng of DNA, making amplification essential for most ChIP-chip experiments. Each amplification method is known to cause under- and over-representation of certain sequences16, which we aimed to assess in this context.
After the mixtures were prepared, the clones and their relative concentrations were again validated by PCR and quantitative PCR (qPCR). Note that the while the same spike-in clones were present in the diluted and undiluted mixtures, they were used at different enrichment levels in the two samples. In each mixture, most of the selected enrichment levels were represented by 10 distinct clones. To challenge the sensitivity of the array technologies, spike-in enrichment levels were biased towards enrichment levels less than tenfold. We also prepared two samples containing genomic DNA at 77 ng/µL and 3 ng/µL respectively without any spike-ins to serve as controls. We sheared the DNA mixtures with a standard chromatin sonication procedure17.

tag: Control


title: Pol_EtOH_Rep2


title: SRC_E2_Rep2


title: ER_EtOH_Rep_1


title: ER_EtOH_Rep2


title: ER_EtOH_Rep3


title: Malaria patient 4.04


title: Malaria patient 3.04


title: Malaria patient 2.04


title: Spike-in rep3

description: Spike-in rep3

tag: Spike-in


title: Malaria patient 6.04


title: Malaria patient 8.04


title: Control rep1

description: Control rep1


title: Malaria patient 1.04

tag: Cluster 3

tag: days ill:15


title: Pol_E2_Rep1


title: Spike-in rep1

description: Spike-in rep1


title: Amplified control rep3_B1_T1

description: hybridized at Affymetrix

label_protocol: standard Affymetrix protocol

tag: Amplified control rep3


title: ER_E2_Rep1


title: Amplified control rep2_B1_T1

description: hybridized at Affymetrix

tag: Amplified control rep2


title: Malaria patient 5.04


title: Amplified spike-in rep3_B1_T1

description: hybridized at Affymetrix

tag: Amplified spike-in rep3


title: Amplified spike-in rep2_B1_T1

description: hybridized at Affymetrix

tag: Amplified spike-in rep2


title: Amplified control rep1_B1_T1

description: hybridized at Affymetrix

tag: Amplified control rep1


title: Control rep2

description: Control rep2


title: Amplified spike-in rep1_B1_T1

description: hybridized at Affymetrix

tag: Amplified spike-in rep1


title: Undiluted spike-in rep2_B2_T1

description: hybridized at Affymetrix

tag: Undiluted spike-in rep2


title: Undiluted spike-in rep3_B3_T1

description: hybridized at Affymetrix

tag: Undiluted spike-in rep3


title: Undiluted spike-in rep1_B1_T1

description: hybridized at Affymetrix

tag: Undiluted spike-in rep1


title: Undiluted control rep3_B3_T1

description: hybridized at Affymetrix

tag: Undiluted control rep3


title: Undiluted control rep2_B2_T1

description: hybridized at Affymetrix

tag: Undiluted control rep2


title: Undiluted spike-in rep3_B3

description: hybridized at Dana-Farber


title: Undiluted spike-in rep2_B2

description: hybridized at Dana-Farber


title: Undiluted control rep3_B1

description: hybridized at Dana-Farber


title: Undiluted control rep2_B2

description: hybridized at Dana-Farber


title: Undiluted control rep1_B3

description: hybridized at Dana-Farber

tag: Undiluted control rep1


title: Undiluted control rep1_B1_T1

description: hybridized at Affymetrix


title: Undiluted spike-in rep1_B1

description: hybridized at Dana-Farber


title: Spike-in rep2

description: Spike-in rep2


title: RatBrain_BV_IBN_Rep6

city: Singapore

first: Jerome

last: Boulaire

address: 31 Biopolis Way

department: Gene Delivery

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

hyb_protocol: Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.

scan_protocol: Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software

data_processing: Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 5 out of 7 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition

label: phycoerythrin

organism: Rattus norvegicus

source_name: Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of baculovirus vectors (5E7 viral particles)

label_protocol: One to 10 u of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)

extract_protocol: Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer

tag: Strain

value: Wistar

tag: Gender

value: Male

tag: Weight

tag: Age

tag: Tissue

value: Brain

tag: Treatment

value: Baculovirus vectors (5ul, 5E07 viral particles) injected stereotaxically into the striatum at tw0injection sitesAP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.


title: RatBrain_CTL_IBN_Rep4

value: PBS (5ul) injected stereotaxically into the striatum at tw0injection sitesAP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.


title: RatBrain_CTL_IBN_Rep3

source_name: Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of PBS


title: RatBrain_CTL_IBN_Rep7


title: RatBrain_CTL_IBN_Rep6

value: PBS (5ul) injected stereotaxically into the striatum at two injection sitesAP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.


title: RatBrain_BV_IBN_Rep7


title: RatBrain_BV_IBN_Rep5


title: RatBrain_CTL_IBN_Rep2


title: Log phase 6 hour 1ug/ml INH treated replicate 3

tag: Mycobacterium Tuberculosis H37Rv grown to log phase and treated with 1ug/ml Isoniazid for 6 hours.

tag: Mycobacterium Tuberculosis H37Rv grown to log phase and treated with water for 6 hours.


title: RatBrain_BV_IBN_Rep3


title: Log phase 2 hour 1ug/ml INH treated replicate 3

tag: Mycobacterium Tuberculosis H37Rv grown to log phase and treated with 1ug/ml Isoniazid for 2 hours.

tag: Mycobacterium Tuberculosis H37Rv grown to log phase and treated with water for 2 hours.


title: RatBrain_CTL_IBN_Rep5


title: WT S49_untreated_6h, biological rep1

status: Public on Dec 12 2007

city: Claremont

first: Alexander

middle: C

last: Zambon

state: CA

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

description: 6h 8-CPT-cAMP treated WT S49 cells, biological rep1

hyb_protocol: Each Affymetrix 430 A chip was hybridized to 10 µg of fragmented cRNA.

scan_protocol: Arrays were hybridized and scanned with a GeneArray Scanner (Hewlett-Packard/Affymetrix)

data_processing: Cel files were converted to signal values by gcRMA

source_name: S49 WT cells 6h treatment with 8-CPT-cAMP

label_protocol: Total cellular RNA was reverse transcribed with superscript II reverse transcriptase and an oligo-dT primer containing a T7 RNA polymerase promoter. Single stranded cDNA was converted into double-stranded cDNA (ds-cDNA) and then purified (MessageAMP aRNA Kit, Ambion, Austin, TX). Biotinylated cRNA was generated from ds-cDNA by in vitro transcription (IVT) (MessageAMP aRNA Kit, Ambion). After a further round of purification, IVT reactions yielded 30–70 µg of biotinylated cRNA, which was fragmented to ~100–base pair fragments before hybridization.

growth_protocol: D- S49 cells were grown in suspension cultures with Dulbecco's modified Eagles' medium supplemented with 10% heat-inactivated horse serum and 10 mM HEPES in a humidified atmosphere containing 10% CO2 at 37ºC. Cultures were initiated at a density of 2.5-5 x 10E5 cells/ml and carried out for the indicated times.

extract_protocol: Total cellular RNA was isolated from cells by using RNeasy mini-columns

treatment_protocol: cells were treated with 100 mM 8-CPT-cAMP for the indicated times

tag: Balb/C, Lymphoma, tumor


title: WT S49_untreated_24h, biological rep3

description: 24h 8-CPT-cAMP treated WT S49 cells, biological rep3

source_name: S49 WT cells 24h treatment with 8-CPT-cAMP


title: WT S49_untreated_time0, biological rep4

description: Untreated (time 0) WT S49 cells, biological rep4

source_name: S49 WT cells untreated


title: WT S49_untreated_2h, biological rep2

description: 2h 8-CPT-cAMP treated WT S49 cells, biological rep2

source_name: S49 WT cells 2h treatment with 8-CPT-cAMP


title: WT S49_untreated_6h, biological rep2

description: 6h 8-CPT-cAMP treated WT S49 cells, biological rep2


title: RatBrain_BV_IBN_Rep1


title: RatBrain_CTL_IBN_Rep1


title: RatBrain_BV_IBN_Rep2


title: RatBrain_BV_IBN_Rep4


title: WT S49_untreated_time0, biological rep3

description: Untreated (time 0) WT S49 cells, biological rep3


title: WT S49_untreated_2h, biological rep1

description: 2h 8-CPT-cAMP treated WT S49 cells, biological rep1


title: WT S49_untreated_6h, biological rep3

description: 6h 8-CPT-cAMP treated WT S49 cells, biological rep3


title: WT S49_untreated_24h, biological rep2

description: 24h 8-CPT-cAMP treated WT S49 cells, biological rep2


title: WT S49_untreated_24h, biological rep1

description: 24h 8-CPT-cAMP treated WT S49 cells, biological rep1


title: WT S49_untreated_time0, biological rep2

description: Untreated (time 0) WT S49 cells, biological rep2


title: WT S49_untreated_2h, biological rep3

description: 2h 8-CPT-cAMP treated WT S49 cells, biological rep3


title: D- S49_treated_24h, biological rep2

description: 24h 8-CPT-cAMP treated D- S49 cells, biological rep2

source_name: S49 D- cells 24h treatment with 8-CPT-cAMP


title: D- S49_treated_24h, biological rep1

description: 24h 8-CPT-cAMP treated D- S49 cells, biological rep1


title: D- S49_treated_24h, biological rep3

description: 24h 8-CPT-cAMP treated D- S49 cells, biological rep3


title: D- S49_treated_6h, biological rep3

description: 6h 8-CPT-cAMP treated D- S49 cells, biological rep3

source_name: S49 D- cells 6h treatment with 8-CPT-cAMP


title: D- S49_treated_2h, biological rep3

description: 2h 8-CPT-cAMP treated D- S49 cells, biological rep3

source_name: S49 D- cells 2h treatment with 8-CPT-cAMP


title: corticosterone_treated_rep10 (06SE467)

city: Leioa

first: Leyre

last: Uriguen

state: Vizcaya

address: Barrio Sarriena s/n

department: Pharmacology

country: Spain

institute: University of the Basque Country

description: comparison of corticosterone-treated and control rats with depressive-like behaviour

hyb_protocol: Samples were hybridised to Affymetrix RAE230 2.0 genechip using Affymetrix standard hybridization protocol using 15ug of biotinylated cRNA (Affymetrix Expression analysis technical manual). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The chips were scanned using an Agilent GeneArray Scanner 2500

data_processing: Feature intensity values from scanned arrays were normalised and reduced to expression summaries using RMA method and further normalised to the median of each probe

label: Biotin

source_name: FRONTOPARIETAL BRAIN CORTEX OF RATS TREATED WITH CORTICOSTERONE (18 MG/KG) FOR 14 DAYS

label_protocol: Affymetrix IVT Labeling kit

extract_protocol: Trizol Reagent Protocol

tag: Male Sprague Dawley rats (225-250 g) aged approximately two months


title: D- S49_treated_6h, biological rep2

description: 6h 8-CPT-cAMP treated D- S49 cells, biological rep2


title: corticosterone_treated_rep6 (06SE463)


title: Cortex_Control_rep7 (06SE469)

source_name: FRONTOPARIETAL BRAIN CORTEX OF RATS TREATED WITH PLACEBO FOR 14 DAYS


title: D- S49_treated_6h, biological rep1

description: 6h 8-CPT-cAMP treated D- S49 cells, biological rep1


title: corticosterone_treated_rep9 (06SE466)


title: WT S49_untreated_time0, biological rep1

description: Untreated (time 0) WT S49 cells, biological rep1


title: corticosterone_treated_rep4 (06SE460)


title: corticosterone_treated_rep3 (06SE458)


title: corticosterone_treated_rep5 (06SE462)


title: corticosterone_treated_rep7 (06SE464)


title: Cortex_Control_rep5 (06SE461)


title: Cortex_Control_rep10 (06SE472)


title: T00333353_control2

city: Rostock

first: Eik

last: Hoffmann

address: Albert-Einstein-Str. 3

department: Institute of Biological Sciences

country: Germany

institute: University of Rostock

description: uninfected/untreated control

hyb_protocol: CodeLink Expression assay protocol

scan_protocol: CodeLink Expression assay protocol

data_processing: CodeLink EXP v4.0 (http://www4.gelifesciences.com/aptrix/upp01077.nsf/Content/codelink_soft)

source_name: J774 macrophage

label_protocol: CodeLink Expression assay protocol

growth_protocol: J774.A1 cells (mouse macrophage-like cell line) were seeded onto 6-well  plates one day before the experiment. Duplicates were incubated with serum-free DME medium containing 0.01 % latex beads of 1 µm diameter coupled to the following ligands: avidin (Av), Fc fragment of mouse IgG (Fc), lipopolysaccharides from Klebsiella pneumoniae (LPS) and mannan from Saccharomyces cerevisae (Man) for 30 and 60 minutes.

extract_protocol: Total RNA was isolated from J774 macrophage monolayers using Rneasy mini kit (QIAGEN).

treatment_protocol: J774.A1 were seeded onto 6-well  plates  in duplicates one day before the experiment.On the day of RNA isolation they were incubated with serum-free DME medium containing 0.01 % latex beads of 1 µm diameter coupled to the following ligands: avidin (Av), Fc fragment of mouse IgG (Fc), lipopolysaccharides from Klebsiella pneumoniae (LPS) and mannan from Saccharomyces cerevisae (Man) for 30 and 60 minutes. After incubation samples as well as untreated controls in duplicates were washed twice in PBS and total RNA was extracted using RNAeasy kit (Qiagen) following manufacturer's instructions. Each sample was  hybridized to CodeLink Mouse whole genome bioarray slides (Amersham).

tag: uninfected/untreated control


title: T00333348_60M1

description: Mannan-coated beads internalized for 60 minutes


title: Cortex_Control_rep3 (06SE457)


title: Cortex_Control_rep9 (06SE471)


title: corticosterone_treated_rep8 (06SE465)


title: Cortex_Control_rep8 (06SE470)


title: D- S49_treated_2h, biological rep2

description: 2h 8-CPT-cAMP treated D- S49 cells, biological rep2


title: T00333349_60M2

tag: Mannan-coated beads internalized for 60 minutes


title: corticosterone_treated_rep2 (06SE456)


title: T00333352_control1

description: uninfected/untreated control


title: Cortex_Control_rep4 (06SE459)


title: T00333347_30M2

description: Mannan-coated beads internalized for 30 minutes


title: Cortex_Bulbectomized_rep2

description: comparison of olfactory-bulbectomized and sham-operated rats with depressive-like behaviour

source_name: FRONTOPARIETAL BRAIN CORTEX OF OLFACTORY BULBECTOMIZED RATS


title: D- S49_treated_2h, biological rep1

description: 2h 8-CPT-cAMP treated D- S49 cells, biological rep1


title: D- S49_untreated_time0, biological rep3

description: Untreated (time 0) D- S49 cells, biological rep3

source_name: S49 D- cells untreated


title: D- S49_untreated_time0, biological rep1

description: Untreated (time 0) D- S49 cells, biological rep1


title: Cortex_Control_rep1 (06SE453)


title: T00333279_60A1

description: Avidin-coated beads internalized for 60 minutes


title: T00333338_60L2

description: LPS-coated beads internalized for 60 minutes


title: corticosterone_treated_rep1 (06SE454)


title: Cortex_Control_rep6 (05SE1760)

source_name: FRONTOPARIETAL BRAIN CORTEX OF SHAM-OPERATED RATS


title: D- S49_untreated_time0, biological rep2

description: Untreated (time 0) D- S49 cells, biological rep2


title: Cortex_Control_rep2 (06SE455)


title: Cortex_Bulbectomized_rep3


title: D- S49_untreated_time0, biological rep4

description: Untreated (time 0) D- S49 cells, biological rep4


title: Cortex_Control_rep2 (05SE1756)


title: Yeast_ESA1sup2-_rep3

first: Courtney

last: Sill

address: 715 Albany St.

department: Genetics & Genomics

institute: Boston University School of Medicine

description: ESA1 sup2-

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GS 3000 Scanner

data_processing: The data were analyzed in GCOS using the MAS 5.0 algorithm. The data was analyized using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Saccharomyces cerevisiae

source_name: yeast cell cultures: ESA1 sup2-

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Yeast cells were grown at 30 degrees Celsius in a shaking incubator overnight to saturation in 10mL of YPD complete media, yeast extract peptone, supplemented with 2% glucose.

extract_protocol: Hot phenol purification method was used to prepare the RNA. Specifically, 10mL of saturated overnight YPD cultures were resuspended in 400uL of acetate-EDTA (AE) buffer (50mM Na-acetate, pH 5.3, 10mM EDTA). 40uL of 10% sodium dodecyl sulfate (SDS) was added. The cells were vortexed before and after adding equal volumes of pre-equilibrated RT phenol. Samples were incubated at 65C for four minutes then chilled rapidly in a dry ice/EtOH bath until phenol crystals appeared. The aqueous layer was extracted with RT phenol/chloroform after centrifugation. 3M Na-acetate, pH5.3, was added to the extracted phase to a final concentration of 0.3M and 2.5 volumes of 100% EtOH was added to precipitate the RNA. After a 20 minute centrifugation, the pellet was washed with 80% EtOH then dried in a speedvac (ThermoSavant). The RNA was resuspended in 40uL of sterile water. After diluting 10-fold, the RNA was quantified by spectrophotometer (Nanodrop, ND-1000). Yields ranged from 40 to 160ug. RNA was checked by gel electrophoresis prior to microarray analysis. Samples were stored at -20C or -80C for short-term or long-term storage, respectively.

tag: single mutant


title: Cortex_Control_rep3 (05SE1757)


title: Cortex_Bulbectomized_rep5


title: T00333271_60A2

tag: Avidin-coated beads internalized for 60 minutes


title: Cortex_Control_rep4 (05SE1758)


title: Yeast_esa1-sup2-_rep3

description: esa1 sup2-

source_name: yeast cell cultures: esa1 sup2-

tag: double mutant


title: Cortex_Bulbectomized_rep1


title: Cortex_Bulbectomized_rep4


title: Cortex_Control_rep1 (05SE1755)


title: T00333274_30F2

description: Fc-coated beads internalized for 30 minutes


title: T00333342_30M1

tag: Mannan-coated beads internalized for 30 minutes


title: T00333339_60L1

tag: LPS-coated beads internalized for 60 minutes


title: T00333273_30F1

tag: Fc-coated beads internalized for 30 minutes


title: T00333269_30A1

description: Avidin-coated beads internalized for 30 minutes


title: Yeast_ESA1sup2-_rep2

description: ESA1 sup2-


title: Yeast_ESA1SUP2_rep2

description: ESA1 SUP2

source_name: yeast cell cultures: ESA1 SUP2

tag: WT


title: Yeast_esa1-sup2-_rep1

description: esa1 sup2-


title: Yeast_esa1-sup2-_rep2

description: esa1 sup2-


title: Cortex_Control_rep5 (05SE1759)


title: Cortex_reserpine_treated_rep3

description: rat model organism with depression left untreated or treated with reserpine

source_name: FRONTOPARIETAL BRAIN CORTEX OF RATS TREATED WITH ONE SINGLE DOSE OF RESERPINE 5mg/kg i.p


title: Cortex_Control_rep3 (05SE733)

source_name: FRONTOPARIETAL BRAIN CORTEX OF RATS TREATED WITH ONE SINGLE DOSE OF SALINE i.p


title: Cortex_Control_rep2 (05SE732)


title: T00333270_30A2

tag: Avidin-coated beads internalized for 30 minutes


title: Cortex_reserpine_treated_rep2


title: Cortex_reserpine_treated_rep6


title: Cortex_reserpine_treated_rep5


title: T00333193_30L1

description: LPS-coated beads internalized for 30 minutes


title: Cortex_Control_rep6 (05SE736)


title: T00333189_60F1

description: Fc-coated beads internalized for 60 minutes


title: Cortex_Control_rep4 (05SE734)


title: Yeast_ESA1SUP2_rep1

description: ESA1 SUP2


title: Cortex_reserpine_treated_rep1


title: Cortex_Control_rep1 (05SE731)


title: T00333194_30L2

tag: LPS-coated beads internalized for 30 minutes


title: Yeast_ESA1sup2-_rep1

description: ESA1 sup2-


title: Cortex_Control_rep5 (05SE735)


title: non-tumor tissue 22 (50K_Xba240_SNP)

status: Public on Dec 11 2007

first: Rameen

last: Beroukhim

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: SNP array data from a non-tumor tissue

hyb_protocol: Following fragmentation, 40 ug of cRNA were hybridized for 16 hr at 48C on GeneChip 100K Hind Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing:
Signal intensity values were obtained with dChip using invariant set normalization.
Genotypes were determined by Affymetrix Genotyping Tools Version 2.0.

source_name: non-tumor tissue

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol from 250 ng genomic DNA

extract_protocol: Extraction of genomic DNA was performed according to the Qiagen DNeasy kit instructions.

treatment_protocol: Frozen tissue was lysed and DNA purified using the Qiagen DNeasy kit

tag: non-tumor tissue tissue


title: T00333190_60F2

tag: Fc-coated beads internalized for 60 minutes


title: non-tumor tissue 19 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 20 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 23 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: Cortex_reserpine_treated_rep4


title: non-tumor tissue 21 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 17 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 86N (50K_Xba240_SNP)

description: SNP array data from a normal brain

source_name: normal brain

tag: normal brain tissue

tag: gender

value: M

tag: age

tag: survival (days):439


title: non-tumor tissue 16 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 6N (50K_Xba240_SNP)

description: SNP array data from a normal brain

tag: survival (days):3617


title: normal brain 74N (50K_Xba240_SNP)

description: SNP array data from a normal brain

tag: survival (days):430


title: non-tumor tissue 18 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 2 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 12 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 56N (50K_Xba240_SNP)

description: SNP array data from a normal brain

tag: survival (days):114


title: normal brain 8N (50K_Xba240_SNP)

description: SNP array data from a normal brain

value: F

tag: survival (days):2703


title: non-tumor tissue 1 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 4 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 13 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 9 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 14 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 15 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 84N (50K_Xba240_SNP)

description: SNP array data from a normal brain


title: normal brain 87N (50K_Xba240_SNP)

description: SNP array data from a normal brain


title: non-tumor tissue 3 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 11 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 12N (50K_Xba240_SNP)

description: SNP array data from a normal brain


title: non-tumor tissue 7 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 8 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 101N (50K_Xba240_SNP)

description: SNP array data from a normal brain


title: glioma cell line U251 (50K_Xba240_SNP)

description: SNP array data from a glioma cell line

source_name: glioma cell line

tag: glioma cell line tissue


title: non-tumor tissue 5 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 10 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 10N (50K_Xba240_SNP)

description: SNP array data from a normal brain


title: glioma cell line SNB-75 (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: glioma cell line SF-268 (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: glioma cell line U118MG (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: primary glioblastoma 106 (50K_Xba240_SNP)

description: SNP array data from a primary glioblastoma

source_name: primary glioblastoma

tag: primary glioblastoma tissue

tag: survival (days):870


title: anaplastic oligodendroglioma 6 (50K_Xba240_SNP)

description: SNP array data from a anaplastic oligodendroglioma

source_name: anaplastic oligodendroglioma

tag: anaplastic oligodendroglioma tissue

tag: survival (days):697


title: primary glioblastoma 104 (50K_Xba240_SNP)

tag: survival (days):299


title: primary glioblastoma 102 (50K_Xba240_SNP)

tag: survival (days):385


title: primary glioblastoma 103 (50K_Xba240_SNP)

tag: survival (days):670


title: primary glioblastoma 107 (50K_Xba240_SNP)

tag: survival (days):956


title: glioma cell line SF-295 (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: primary glioblastoma 105 (50K_Xba240_SNP)

tag: survival (days):756


title: non-tumor tissue 6 (50K_Xba240_SNP)

description: SNP array data from a non-tumor tissue

tag: non-tumor tissue tissue


title: glioma cell line T98G (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: primary glioblastoma 101 (50K_Xba240_SNP)

tag: gender

tag: age

tag: survival (days):863


title: primary glioblastoma 100 (50K_Xba240_SNP)

tag: survival (days):891


title: primary glioblastoma 95 (50K_Xba240_SNP)

tag: survival (days):672


title: secondary glioblastoma 15 (50K_Xba240_SNP)

description: SNP array data from a secondary glioblastoma

source_name: secondary glioblastoma

tag: secondary glioblastoma tissue

tag: survival (days):1608


title: primary glioblastoma 97 (50K_Xba240_SNP)

tag: primary glioblastoma tissue


title: primary glioblastoma 93 (50K_Xba240_SNP)

tag: survival (days):815


title: primary glioblastoma 99 (50K_Xba240_SNP)

tag: survival (days):552


title: primary glioblastoma 88 (50K_Xba240_SNP)

tag: survival (days):479


title: primary glioblastoma 98 (50K_Xba240_SNP)

tag: survival (days):326


title: anaplastic astrocytoma 9 (50K_Xba240_SNP)

description: SNP array data from a anaplastic astrocytoma

source_name: anaplastic astrocytoma

tag: anaplastic astrocytoma tissue

tag: survival (days):2794


title: secondary glioblastoma 13 (50K_Xba240_SNP)

tag: survival (days):1342


title: primary glioblastoma 91 (50K_Xba240_SNP)

tag: survival (days):563


title: primary glioblastoma 94 (50K_Xba240_SNP)

tag: survival (days):335


title: primary glioblastoma 96 (50K_Xba240_SNP)

tag: gender

tag: survival (days):304


title: primary glioblastoma 92 (50K_Xba240_SNP)

tag: age

tag: survival (days):238


title: primary glioblastoma 87 (50K_Xba240_SNP)

tag: survival (days):439


title: primary glioblastoma 84 (50K_Xba240_SNP)

tag: survival (days):716


title: primary glioblastoma 78 (50K_Xba240_SNP)

tag: survival (days):799


title: primary glioblastoma 76 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):689


title: primary glioblastoma 86 (50K_Xba240_SNP)

tag: survival (days):636


title: secondary glioblastoma 10 (50K_Xba240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):4512


title: anaplastic astrocytoma 7 (50K_Xba240_SNP)

tag: anaplastic astrocytoma tissue

tag: survival (days):257


title: secondary glioblastoma 12 (50K_Xba240_SNP)

tag: survival (days):1770


title: primary glioblastoma 85 (50K_Xba240_SNP)

tag: survival (days):241


title: secondary glioblastoma 11 (50K_Xba240_SNP)

tag: survival (days):1334


title: primary glioblastoma 64 (50K_Xba240_SNP)

tag: gender

tag: survival (days):1427


title: secondary glioblastoma 9 (50K_Xba240_SNP)

tag: age

tag: survival (days):849


title: primary glioblastoma 75 (50K_Xba240_SNP)

tag: survival (days):883


title: primary glioblastoma 74 (50K_Xba240_SNP)

tag: survival (days):430


title: primary glioblastoma 55 (50K_Xba240_SNP)

tag: survival (days):561


title: primary glioblastoma 52 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):278


title: primary glioblastoma 56 (50K_Xba240_SNP)

tag: survival (days):114


title: secondary glioblastoma 8 (50K_Xba240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):2703


title: primary glioblastoma 48 (50K_Xba240_SNP)

tag: survival (days):494


title: primary glioblastoma 50 (50K_Xba240_SNP)

tag: survival (days):298


title: primary glioblastoma 36 (50K_Xba240_SNP)

tag: survival (days):429


title: primary glioblastoma 45 (50K_Xba240_SNP)

tag: survival (days):377


title: primary glioblastoma 47 (50K_Xba240_SNP)

tag: survival (days):130


title: primary glioblastoma 46 (50K_Xba240_SNP)

tag: gender

tag: survival (days):719


title: primary glioblastoma 43 (50K_Xba240_SNP)

tag: age

tag: survival (days):266


title: primary glioblastoma 44 (50K_Xba240_SNP)

tag: survival (days):1443


title: primary glioblastoma 41 (50K_Xba240_SNP)

tag: survival (days):37


title: primary glioblastoma 51 (50K_Xba240_SNP)

tag: survival (days):160


title: primary glioblastoma 35 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):452


title: primary glioblastoma 42 (50K_Xba240_SNP)

tag: survival (days):869


title: primary glioblastoma 38 (50K_Xba240_SNP)

tag: survival (days):63


title: primary glioblastoma 49 (50K_Xba240_SNP)

tag: survival (days):355


title: primary glioblastoma 37 (50K_Xba240_SNP)

tag: survival (days):985


title: primary glioblastoma 33 (50K_Xba240_SNP)

tag: survival (days):361


title: primary glioblastoma 40 (50K_Xba240_SNP)

tag: survival (days):447


title: primary glioblastoma 34 (50K_Xba240_SNP)

tag: survival (days):1723


title: primary glioblastoma 30 (50K_Xba240_SNP)

tag: survival (days):461


title: secondary glioblastoma 6 (50K_Xba240_SNP)

tag: secondary glioblastoma tissue

tag: gender

tag: survival (days):3617


title: primary glioblastoma 28 (50K_Xba240_SNP)

tag: age

tag: survival (days):653


title: primary glioblastoma 32 (50K_Xba240_SNP)

tag: survival (days):2003


title: primary glioblastoma 39 (50K_Xba240_SNP)

tag: survival (days):621


title: primary glioblastoma 27 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):713


title: primary glioblastoma 31 (50K_Xba240_SNP)

tag: survival (days):115


title: secondary glioblastoma 7 (50K_Xba240_SNP)


title: primary glioblastoma 54 (50K_Xba240_SNP)

tag: survival (days):88


title: glioma cell line GA-MG (50K_Xba240_SNP)

description: SNP array data from a glioma cell line

tag: glioma cell line tissue


title: glioma cell line 8-MG-BA (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: glioma cell line HS-683 (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: glioma cell line DK-MG (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: glioma cell line LN-18 (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: primary glioblastoma 90 (50K_Xba240_SNP)

tag: survival (days):125


title: primary glioblastoma 53 (50K_Xba240_SNP)

tag: survival (days):396


title: secondary glioblastoma 14 (50K_Xba240_SNP)

tag: survival (days):287


title: primary glioblastoma 29 (50K_Xba240_SNP)

tag: survival (days):535


title: glioma cell line A172 (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: anaplastic astrocytoma 8 (50K_Xba240_SNP)

tag: anaplastic astrocytoma tissue

tag: survival (days):738


title: glioma cell line M059K (50K_Xba240_SNP)

description: SNP array data from a glioma cell line


title: anaplastic astrocytoma 5 (50K_Xba240_SNP)

tag: gender

tag: survival (days):2611


title: primary glioblastoma 83 (50K_Xba240_SNP)

tag: age

tag: survival (days):311


title: primary glioblastoma 89 (50K_Xba240_SNP)


title: primary glioblastoma 82 (50K_Xba240_SNP)

tag: survival (days):417


title: anaplastic astrocytoma 6 (50K_Xba240_SNP)

tag: survival (days):1658


title: primary glioblastoma 81 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):1220


title: primary glioblastoma 80 (50K_Xba240_SNP)

tag: survival (days):166


title: anaplastic astrocytoma 4 (50K_Xba240_SNP)

tag: survival (days):284


title: primary glioblastoma 79 (50K_Xba240_SNP)

tag: survival (days):764


title: low grade mixed oligoastrocytoma 1 (50K_Xba240_SNP)

description: SNP array data from a low grade mixed oligoastrocytoma

source_name: low grade mixed oligoastrocytoma

tag: low grade mixed oligoastrocytoma tissue

tag: survival (days):3768


title: anaplastic oligodendroglioma 5 (50K_Xba240_SNP)

tag: anaplastic oligodendroglioma tissue

tag: survival (days):1580


title: primary glioblastoma 77 (50K_Xba240_SNP)

tag: survival (days):157


title: anaplastic mixed glioma 2 (50K_Xba240_SNP)

description: SNP array data from a anaplastic mixed glioma

source_name: anaplastic mixed glioma

tag: anaplastic mixed glioma tissue

tag: survival (days):738


title: primary glioblastoma 71 (50K_Xba240_SNP)

tag: gender

tag: survival (days):582


title: primary glioblastoma 70 (50K_Xba240_SNP)

tag: age

tag: survival (days):266


title: anaplastic oligodendroglioma 3 (50K_Xba240_SNP)

tag: survival (days):1768


title: primary glioblastoma 72 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):222


title: anaplastic astrocytoma 2 (50K_Xba240_SNP)

tag: anaplastic astrocytoma tissue

tag: survival (days):1156


title: primary glioblastoma 73 (50K_Xba240_SNP)

tag: survival (days):678


title: primary glioblastoma 68 (50K_Xba240_SNP)

tag: survival (days):396


title: primary glioblastoma 63 (50K_Xba240_SNP)

tag: survival (days):265


title: primary glioblastoma 67 (50K_Xba240_SNP)

tag: survival (days):534


title: primary glioblastoma 69 (50K_Xba240_SNP)

tag: survival (days):489


title: primary glioblastoma 66 (50K_Xba240_SNP)

tag: survival (days):103


title: anaplastic astrocytoma 3 (50K_Xba240_SNP)

tag: survival (days):3525


title: primary glioblastoma 65 (50K_Xba240_SNP)

tag: survival (days):195


title: primary glioblastoma 59 (50K_Xba240_SNP)

tag: gender

tag: survival (days):283


title: anaplastic astrocytoma 1 (50K_Xba240_SNP)

tag: age

tag: survival (days):1645


title: primary glioblastoma 62 (50K_Xba240_SNP)

tag: survival (days):190


title: primary glioblastoma 61 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):349


title: primary glioblastoma 57 (50K_Xba240_SNP)

tag: survival (days):199


title: primary glioblastoma 58 (50K_Xba240_SNP)

tag: survival (days):428


title: anaplastic oligodendroglioma 4 (50K_Xba240_SNP)

tag: anaplastic oligodendroglioma tissue

tag: survival (days):1172


title: primary glioblastoma 25 (50K_Xba240_SNP)

tag: survival (days):335


title: primary glioblastoma 60 (50K_Xba240_SNP)

tag: survival (days):370


title: primary glioblastoma 26 (50K_Xba240_SNP)

tag: survival (days):392


title: primary glioblastoma 21 (50K_Xba240_SNP)

tag: survival (days):436


title: primary glioblastoma 24 (50K_Xba240_SNP)

tag: survival (days):280


title: primary glioblastoma 23 (50K_Xba240_SNP)

tag: survival (days):85


title: primary glioblastoma 22 (50K_Xba240_SNP)

tag: gender

tag: survival (days):434


title: primary glioblastoma 20 (50K_Xba240_SNP)

tag: age

tag: survival (days):538


title: primary glioblastoma 16 (50K_Xba240_SNP)

tag: survival (days):404


title: secondary glioblastoma 5 (50K_Xba240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):4957


title: primary glioblastoma 13 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):545


title: primary glioblastoma 10 (50K_Xba240_SNP)

tag: survival (days):536


title: primary glioblastoma 11 (50K_Xba240_SNP)

tag: survival (days):136


title: secondary glioblastoma 2 (50K_Xba240_SNP)

tag: survival (days):2885


title: secondary glioblastoma 4 (50K_Xba240_SNP)

tag: survival (days):509


title: primary glioblastoma 5 (50K_Xba240_SNP)

tag: survival (days):225


title: primary glioblastoma 15 (50K_Xba240_SNP)

tag: survival (days):618


title: anaplastic oligodendroglioma 2 (50K_Xba240_SNP)

tag: anaplastic oligodendroglioma tissue

tag: survival (days):519


title: secondary glioblastoma 3 (50K_Xba240_SNP)

tag: gender

tag: survival (days):2975


title: primary glioblastoma 9 (50K_Xba240_SNP)

tag: age

tag: survival (days):541


title: primary glioblastoma 18 (50K_Xba240_SNP)

tag: survival (days):304


title: anaplastic oligodendroglioma 1 (50K_Xba240_SNP)

tag: survival (days):777


title: primary glioblastoma 19 (50K_Xba240_SNP)

tag: survival (days):853


title: primary glioblastoma 17 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):1106


title: anaplastic mixed glioma 1 (50K_Xba240_SNP)

tag: anaplastic mixed glioma tissue

tag: survival (days):2125


title: primary glioblastoma 7 (50K_Xba240_SNP)

tag: survival (days):286


title: primary glioblastoma 2 (50K_Xba240_SNP)

tag: survival (days):658


title: primary glioblastoma 8 (50K_Xba240_SNP)

tag: survival (days):882


title: secondary glioblastoma 1 (50K_Xba240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):5026


title: primary glioblastoma 4 (50K_Xba240_SNP)

tag: survival (days):99


title: primary glioblastoma 6 (50K_Xba240_SNP)

tag: gender

tag: survival (days):207


title: primary glioblastoma 12 (50K_Xba240_SNP)

tag: age

tag: survival (days):1886


title: anaplastic oligodendroglioma 7 (50K_Xba240_SNP)

tag: anaplastic oligodendroglioma tissue

tag: survival (days):558


title: primary glioblastoma 14 (50K_Xba240_SNP)

tag: survival (days):1825


title: non-tumor tissue 20 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue

tag: non-tumor tissue tissue


title: primary glioblastoma 1 (50K_Xba240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):685


title: non-tumor tissue 23 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: primary glioblastoma 3 (50K_Xba240_SNP)

tag: survival (days):1059


title: non-tumor tissue 19 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 16 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 18 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 74N (50K_Hind240_SNP)

description: SNP array data from a normal brain

tag: normal brain tissue

tag: survival (days):430


title: normal brain 86N (50K_Hind240_SNP)

description: SNP array data from a normal brain

tag: survival (days):439


title: non-tumor tissue 12 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 6N (50K_Hind240_SNP)

description: SNP array data from a normal brain

tag: survival (days):3617


title: non-tumor tissue 13 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 8 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 14 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 8N (50K_Hind240_SNP)

description: SNP array data from a normal brain

tag: survival (days):2703


title: non-tumor tissue 17 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 15 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 56N (50K_Hind240_SNP)

description: SNP array data from a normal brain

tag: survival (days):114


title: non-tumor tissue 22 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 6 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 4 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 2 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 1 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 10 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 5 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 7 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 87N (50K_Hind240_SNP)

description: SNP array data from a normal brain


title: non-tumor tissue 9 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 3 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: non-tumor tissue 21 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: glioma cell line SNB-75 (50K_Hind240_SNP)

description: SNP array data from a glioma cell line

tag: glioma cell line tissue


title: normal brain 84N (50K_Hind240_SNP)

description: SNP array data from a normal brain


title: non-tumor tissue 11 (50K_Hind240_SNP)

description: SNP array data from a non-tumor tissue


title: normal brain 101N (50K_Hind240_SNP)

description: SNP array data from a normal brain


title: glioma cell line SF-268 (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: normal brain 12N (50K_Hind240_SNP)

description: SNP array data from a normal brain


title: normal brain 10N (50K_Hind240_SNP)

description: SNP array data from a normal brain


title: glioma cell line U251 (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: glioma cell line SF-295 (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: primary glioblastoma 104 (50K_Hind240_SNP)

tag: gender

tag: survival (days):299


title: glioma cell line T98G (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: primary glioblastoma 107 (50K_Hind240_SNP)

tag: age

tag: survival (days):956


title: anaplastic oligodendroglioma 6 (50K_Hind240_SNP)

tag: anaplastic oligodendroglioma tissue

tag: survival (days):697


title: primary glioblastoma 97 (50K_Hind240_SNP)

tag: survival (days):672


title: primary glioblastoma 106 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):870


title: primary glioblastoma 95 (50K_Hind240_SNP)


title: secondary glioblastoma 15 (50K_Hind240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):1608


title: primary glioblastoma 105 (50K_Hind240_SNP)

tag: survival (days):756


title: glioma cell line U118MG (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: primary glioblastoma 103 (50K_Hind240_SNP)

tag: survival (days):670


title: primary glioblastoma 101 (50K_Hind240_SNP)

tag: survival (days):863


title: primary glioblastoma 99 (50K_Hind240_SNP)

tag: survival (days):552


title: primary glioblastoma 98 (50K_Hind240_SNP)

tag: survival (days):326


title: primary glioblastoma 86 (50K_Hind240_SNP)

tag: survival (days):636


title: primary glioblastoma 93 (50K_Hind240_SNP)

tag: gender

tag: survival (days):815


title: primary glioblastoma 102 (50K_Hind240_SNP)

tag: age

tag: survival (days):385


title: primary glioblastoma 88 (50K_Hind240_SNP)

tag: survival (days):479


title: anaplastic astrocytoma 7 (50K_Hind240_SNP)

tag: anaplastic astrocytoma tissue

tag: survival (days):257


title: primary glioblastoma 96 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):304


title: anaplastic astrocytoma 9 (50K_Hind240_SNP)

tag: survival (days):2794


title: primary glioblastoma 94 (50K_Hind240_SNP)

tag: survival (days):335


title: primary glioblastoma 92 (50K_Hind240_SNP)

tag: survival (days):238


title: secondary glioblastoma 13 (50K_Hind240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):1342


title: primary glioblastoma 87 (50K_Hind240_SNP)

tag: survival (days):439


title: primary glioblastoma 85 (50K_Hind240_SNP)

tag: survival (days):241


title: secondary glioblastoma 12 (50K_Hind240_SNP)

tag: survival (days):1770


title: primary glioblastoma 91 (50K_Hind240_SNP)

tag: gender

tag: survival (days):563


title: primary glioblastoma 84 (50K_Hind240_SNP)

tag: age

tag: survival (days):716


title: primary glioblastoma 64 (50K_Hind240_SNP)

tag: survival (days):1427


title: primary glioblastoma 55 (50K_Hind240_SNP)

tag: survival (days):561


title: primary glioblastoma 48 (50K_Hind240_SNP)

tag: survival (days):494


title: secondary glioblastoma 9 (50K_Hind240_SNP)

tag: survival (days):849


title: primary glioblastoma 78 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):799


title: primary glioblastoma 49 (50K_Hind240_SNP)

tag: survival (days):355


title: primary glioblastoma 36 (50K_Hind240_SNP)

tag: survival (days):429


title: primary glioblastoma 51 (50K_Hind240_SNP)

tag: survival (days):160


title: primary glioblastoma 45 (50K_Hind240_SNP)

tag: survival (days):377


title: primary glioblastoma 52 (50K_Hind240_SNP)

tag: survival (days):278


title: secondary glioblastoma 10 (50K_Hind240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):4512


title: secondary glioblastoma 8 (50K_Hind240_SNP)

tag: gender

tag: survival (days):2703


title: primary glioblastoma 56 (50K_Hind240_SNP)

tag: age

tag: survival (days):114


title: primary glioblastoma 47 (50K_Hind240_SNP)

tag: survival (days):130


title: primary glioblastoma 74 (50K_Hind240_SNP)

tag: survival (days):430


title: primary glioblastoma 44 (50K_Hind240_SNP)

tag: survival (days):1443


title: primary glioblastoma 50 (50K_Hind240_SNP)

tag: survival (days):298


title: primary glioblastoma 46 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):719


title: primary glioblastoma 75 (50K_Hind240_SNP)

tag: survival (days):883


title: primary glioblastoma 38 (50K_Hind240_SNP)

tag: survival (days):63


title: primary glioblastoma 42 (50K_Hind240_SNP)

tag: survival (days):869


title: primary glioblastoma 40 (50K_Hind240_SNP)

tag: survival (days):447


title: primary glioblastoma 37 (50K_Hind240_SNP)

tag: survival (days):985


title: secondary glioblastoma 11 (50K_Hind240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):1334


title: primary glioblastoma 76 (50K_Hind240_SNP)

tag: gender

tag: survival (days):689


title: primary glioblastoma 39 (50K_Hind240_SNP)

tag: age

tag: survival (days):621


title: primary glioblastoma 41 (50K_Hind240_SNP)

tag: survival (days):37


title: primary glioblastoma 43 (50K_Hind240_SNP)

tag: survival (days):266


title: primary glioblastoma 35 (50K_Hind240_SNP)

tag: survival (days):452


title: secondary glioblastoma 6 (50K_Hind240_SNP)

tag: survival (days):3617


title: secondary glioblastoma 7 (50K_Hind240_SNP)


title: primary glioblastoma 34 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):1723


title: primary glioblastoma 33 (50K_Hind240_SNP)

tag: survival (days):361


title: primary glioblastoma 29 (50K_Hind240_SNP)

tag: survival (days):535


title: primary glioblastoma 31 (50K_Hind240_SNP)

tag: survival (days):115


title: primary glioblastoma 28 (50K_Hind240_SNP)

tag: survival (days):653


title: primary glioblastoma 32 (50K_Hind240_SNP)

tag: survival (days):2003


title: primary glioblastoma 30 (50K_Hind240_SNP)

tag: survival (days):461


title: primary glioblastoma 27 (50K_Hind240_SNP)

tag: survival (days):713


title: glioma cell line M059K (50K_Hind240_SNP)

description: SNP array data from a glioma cell line

tag: glioma cell line tissue


title: anaplastic astrocytoma 8 (50K_Hind240_SNP)

tag: anaplastic astrocytoma tissue

tag: gender

tag: survival (days):738


title: glioma cell line LN-18 (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: glioma cell line A172 (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: glioma cell line HS-683 (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: primary glioblastoma 83 (50K_Hind240_SNP)

tag: age

tag: survival (days):311


title: primary glioblastoma 90 (50K_Hind240_SNP)

tag: survival (days):125


title: glioma cell line DK-MG (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: primary glioblastoma 89 (50K_Hind240_SNP)


title: primary glioblastoma 82 (50K_Hind240_SNP)

tag: survival (days):417


title: primary glioblastoma 53 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):396


title: glioma cell line GA-MG (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: anaplastic astrocytoma 6 (50K_Hind240_SNP)

tag: survival (days):1658


title: secondary glioblastoma 14 (50K_Hind240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):287


title: glioma cell line 8-MG-BA (50K_Hind240_SNP)

description: SNP array data from a glioma cell line


title: anaplastic astrocytoma 5 (50K_Hind240_SNP)

tag: survival (days):2611


title: primary glioblastoma 54 (50K_Hind240_SNP)

tag: survival (days):88


title: anaplastic astrocytoma 3 (50K_Hind240_SNP)

tag: survival (days):3525


title: anaplastic astrocytoma 4 (50K_Hind240_SNP)

tag: survival (days):284


title: primary glioblastoma 80 (50K_Hind240_SNP)

tag: survival (days):166


title: anaplastic oligodendroglioma 3 (50K_Hind240_SNP)

tag: anaplastic oligodendroglioma tissue

tag: survival (days):1768


title: primary glioblastoma 100 (50K_Hind240_SNP)

tag: gender

tag: survival (days):891


title: anaplastic astrocytoma 1 (50K_Hind240_SNP)

tag: anaplastic astrocytoma tissue

tag: age

tag: survival (days):1645


title: low grade mixed oligoastrocytoma 1 (50K_Hind240_SNP)

tag: low grade mixed oligoastrocytoma tissue

tag: survival (days):3768


title: primary glioblastoma 77 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):157


title: anaplastic oligodendroglioma 5 (50K_Hind240_SNP)

tag: survival (days):1580


title: primary glioblastoma 81 (50K_Hind240_SNP)

tag: survival (days):1220


title: primary glioblastoma 66 (50K_Hind240_SNP)

tag: survival (days):103


title: primary glioblastoma 79 (50K_Hind240_SNP)

tag: survival (days):764


title: primary glioblastoma 65 (50K_Hind240_SNP)

tag: survival (days):195


title: anaplastic oligodendroglioma 4 (50K_Hind240_SNP)

tag: survival (days):1172


title: anaplastic astrocytoma 2 (50K_Hind240_SNP)

tag: survival (days):1156


title: anaplastic mixed glioma 2 (50K_Hind240_SNP)

tag: anaplastic mixed glioma tissue

tag: survival (days):738


title: primary glioblastoma 71 (50K_Hind240_SNP)

tag: gender

tag: survival (days):582


title: primary glioblastoma 63 (50K_Hind240_SNP)

tag: age

tag: survival (days):265


title: primary glioblastoma 69 (50K_Hind240_SNP)

tag: survival (days):489


title: primary glioblastoma 67 (50K_Hind240_SNP)

tag: survival (days):534


title: primary glioblastoma 60 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):370


title: primary glioblastoma 58 (50K_Hind240_SNP)

tag: survival (days):428


title: primary glioblastoma 70 (50K_Hind240_SNP)

tag: survival (days):266


title: primary glioblastoma 59 (50K_Hind240_SNP)

tag: survival (days):283


title: primary glioblastoma 57 (50K_Hind240_SNP)

tag: survival (days):199


title: primary glioblastoma 72 (50K_Hind240_SNP)

tag: survival (days):222


title: primary glioblastoma 73 (50K_Hind240_SNP)

tag: survival (days):678


title: primary glioblastoma 62 (50K_Hind240_SNP)

tag: survival (days):190


title: primary glioblastoma 68 (50K_Hind240_SNP)

tag: survival (days):396


title: primary glioblastoma 61 (50K_Hind240_SNP)

tag: survival (days):349


title: primary glioblastoma 21 (50K_Hind240_SNP)

tag: gender

tag: survival (days):436


title: primary glioblastoma 23 (50K_Hind240_SNP)

tag: age

tag: survival (days):85


title: 702_cy5_ vs_F1_cy3_2

city: Birmingham

first: Jan

middle: P

last: Dumanski

state: AL

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

description: We studied 19 pairs of monozygotic twins with either concordant or discordant phenotype using two platforms for genome-wide CNV analyses and show that CNVs exist within pairs in both groups.

hyb_protocol: The 32K slides were prehybridized in 5x SCC, 0.1% SDS at 45 ºC for at least one hour, washed with ddH20 and dried using compressed dust-free air. The dried pellets from the labeling steps were re-suspended in 50 µl of hybridization solution (50% Formamide, 4% SDS, 10 %, Dextran Sulfate, M.W. 500 000, 2 X SSC) and denatured for 5 min at 95°C, followed by incubation at 45°C for 2 h to block repetitive sequences. Subsequently, the probe mixture was applied to the slide surface, covered with a lifterslip (22x60mm, Erie Scientific, Portsmouth, NH) and hybridized at 45 °C for 20 hours in a slide chamber (Corning Inc. Life Sciences, Big Flats, NY). After hybridization the lifterslip was rinsed off using 1xPBS. Washing was performed in 25 % formamide, 2 X SSC, 0.1% SDS, at 45ºC, for 15 min, followed by 10 min in 1 X PBS at room temperature, and brief rinse in 0.2 X SSC. The array was immersed in deionized H2O and immediately dried using pressurized dust-free air.

scan_protocol: Image acquisition was performed using the GenePix 4000B scanner (Axon Instruments Inc, Union City, CA), and image analysis was carried out using the GenePixPro v6 software (Axon Instruments).

data_processing: We uploaded the GPR files from GenePix pro into a perl script called colloactor. This script links the information about clones to the array position. It also uploads the raw data to the BASE platform. These raw data files are attached as tables. Filtering and normalization was done using the LCB Data-WareHouse (dw.lcb.uu.se). The filters applied on the raw data removed spots containing more than 5% oversaturated pixels, spots with low Signal-to-Noise Ratio (SNR<3) and spots automatically and manually flagged as bad, absent or not found in GenePixPro program. Normalization was done using a print-tip loess method.

source_name: Genomic DNA isolated from twin no. 702

label_protocol: Labeling was done using 2 mcg DNA, according to the BioPrime® Array CGH Genomic Labeling System protocol supplied by the manufacturer (Invitrogen, Carlsbad, CA). We used CY3 dCTP and CY5 dCTP respectively (PA53021 and PA55021, GE Healthcare, Piscataway, NJ). The labeled DNA probes were mixed together and combined with 200 µg human Cot-1 DNA (Invitrogen, Carlsbad, CA) and dried using a vacufuge concentrator (Eppendorf, Westbury, NY).

extract_protocol: genomic DNA isolation with phenol extraction according to standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989)

tag: Peripheral blood derived DNA

tag: probable PD

source_name: Genomic DNA isolated from twin no. F1

tag: Healthy female Refernce DNA


title: primary glioblastoma 22 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):434


title: 702_cy5_ vs_F1_cy3_1


title: primary glioblastoma 24 (50K_Hind240_SNP)

tag: survival (days):280


title: secondary glioblastoma 5 (50K_Hind240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):4957


title: primary glioblastoma 17 (50K_Hind240_SNP)

tag: survival (days):1106


title: primary glioblastoma 26 (50K_Hind240_SNP)

tag: survival (days):392


title: 702_cy3_ vs_F1_cy5


title: 701_cy5_ vs_F1_cy3

source_name: Genomic DNA isolated from twin no. 701

tag: Unaffected


title: 492_cy3_ vs_F1_cy5

source_name: Genomic DNA isolated from twin no. 492


title: primary glioblastoma 25 (50K_Hind240_SNP)

tag: survival (days):335


title: 492_cy5_ vs_F1_cy3


title: primary glioblastoma 20 (50K_Hind240_SNP)

tag: survival (days):538


title: primary glioblastoma 19 (50K_Hind240_SNP)

tag: gender

tag: survival (days):853


title: 701_cy3_ vs_F1_cy5


title: primary glioblastoma 18 (50K_Hind240_SNP)

tag: age

tag: survival (days):304


title: 491_cy3_ vs_F1_cy5

source_name: Genomic DNA isolated from twin no. 491

tag: Peripheral blood derived DNA


title: 491_cy5_ vs_F1_cy3

tag: probable PD


title: 292_cy5_ vs_F1_cy3_2

source_name: Genomic DNA isolated from twin no. 292

tag: possible PD, Chronic lymphocytic leukemia

tag: Healthy female Refernce DNA


title: primary glioblastoma 16 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):404


title: 292_cy3_ vs_F1_cy5


title: primary glioblastoma 14 (50K_Hind240_SNP)

tag: survival (days):1825


title: primary glioblastoma 15 (50K_Hind240_SNP)

tag: survival (days):618


title: 291_cy5_ vs_F1_cy3

source_name: Genomic DNA isolated from twin no. 291


title: 2961_cy5_vs_2962_cy3

source_name: Genomic DNA isolated from twin no. 2961

tag: essential tremor

source_name: Genomic DNA isolated from twin no. 2962


title: 292_cy5_ vs_F1_cy3_1


title: secondary glioblastoma 4 (50K_Hind240_SNP)

tag: secondary glioblastoma tissue

tag: survival (days):509


title: primary glioblastoma 12 (50K_Hind240_SNP)

tag: survival (days):1886


title: 2961_cy3_vs_2962_cy5


title: primary glioblastoma 11 (50K_Hind240_SNP)

tag: survival (days):136


title: primary glioblastoma 13 (50K_Hind240_SNP)

tag: gender

tag: survival (days):545


title: 2041_cy5_vs_2042_cy3

source_name: Genomic DNA isolated from twin no. 2041

source_name: Genomic DNA isolated from twin no. 2042

tag: cerebrovascular parkinsonism and parkinsonism due to neuroleptics


title: secondary glioblastoma 3 (50K_Hind240_SNP)

tag: age

tag: survival (days):2975


title: primary glioblastoma 10 (50K_Hind240_SNP)

source_name: primary glioblastoma

tag: survival (days):536


title: primary glioblastoma 9 (50K_Hind240_SNP)

tag: survival (days):541


title: secondary glioblastoma 2 (50K_Hind240_SNP)

tag: survival (days):2885


title: 291_cy3_vs_F1_cy5

tag: Peripheral blood derived DNA

tag: Unaffected

tag: Healthy female Refernce DNA


title: anaplastic oligodendroglioma 1 (50K_Hind240_SNP)

source_name: anaplastic oligodendroglioma

tag: anaplastic oligodendroglioma tissue

tag: survival (days):777


title: primary glioblastoma 8 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):882


title: 2041_cy3_vs_2042_cy5

tag: probable PD


title: 931_cy3_vs_932_cy5

source_name: Genomic DNA isolated from twin no. 931

source_name: Genomic DNA isolated from twin no. 932

tag: essential tremor


title: 931_cy5_vs_932_cy3


title: primary glioblastoma 6 (50K_Hind240_SNP)

tag: gender

tag: survival (days):207


title: anaplastic oligodendroglioma 2 (50K_Hind240_SNP)

tag: survival (days):519


title: 701_cy3_vs_702_cy5


title: primary glioblastoma 5 (50K_Hind240_SNP)

tag: age

tag: survival (days):225


title: 491_cy5_vs_492_cy3


title: 1961_cy3_vs_1962_cy5_1

source_name: Genomic DNA isolated from twin no. 1961

tag: parkinsonism of unknown cause

source_name: Genomic DNA isolated from twin no. 1962


title: 701_cy5_vs_702_cy3

source_name: Genomic DNA isolated from twin no. 702


title: primary glioblastoma 4 (50K_Hind240_SNP)

tag: survival (days):99


title: 291_cy3_vs_292_cy5

tag: possible PD, Chronic lymphocytic leukemia


title: anaplastic mixed glioma 1 (50K_Hind240_SNP)

source_name: anaplastic mixed glioma

tag: anaplastic mixed glioma tissue

tag: survival (days):2125


title: anaplastic oligodendroglioma 7 (50K_Hind240_SNP)

tag: survival (days):558


title: 291_cy5_vs_292_cy3

tag: Peripheral blood derived DNA

tag: Unaffected


title: 111_cy5_vs_112_cy3

source_name: Genomic DNA isolated from twin no. 111

source_name: Genomic DNA isolated from twin no. 112


title: 111_cy3_vs_112_cy5


title: 1961_cy3_vs_1962_cy5_2


title: 631_cy5_vs_632_cy3

source_name: Genomic DNA isolated from twin no. 631

tag: lewy body dementia

source_name: Genomic DNA isolated from twin no. 632


title: 491_cy3_vs_492_cy5

source_name: Genomic DNA isolated from twin no. 491

source_name: Genomic DNA isolated from twin no. 492


title: primary glioblastoma 3 (50K_Hind240_SNP)

tag: primary glioblastoma tissue

tag: survival (days):1059


title: primary glioblastoma 7 (50K_Hind240_SNP)

tag: survival (days):286


title: primary glioblastoma 2 (50K_Hind240_SNP)

tag: gender

tag: survival (days):658


title: secondary glioblastoma 1 (50K_Hind240_SNP)

source_name: secondary glioblastoma

tag: secondary glioblastoma tissue

tag: survival (days):5026


title: primary glioblastoma 1 (50K_Hind240_SNP)

tag: age

tag: survival (days):685


title: 631_cy3_vs_632_cy5