title: Liver, PPARα (-/-), 134 mg/kg 2,4DNT, rep 5

status: Public on Jun 30 2014

type: RNA

city: Vicksburg

first: Mitchell

last: Wilbanks

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

country: USA

institute: US Army Engineer Research and Development Center

data_processing:
Gene expression assay data were analyzed using RT2 Profiler PCR Array Data Analysis software version 3.5 (SABiosciences).  The 2(DDCt) method was used to determine the relative fold change in transcript expression relative to wild-type vehicle exposed animals.  Normalization was based on the geometric mean of housekeeping genes provided in the kit. When comparisons were made between PPARα (-/-) vehicle and 2,4-DNT exposed mice,  expression values were relative to PPARα (-/-) vehicle exposed mice. Expression values were analyzed for treatment differences using Student’s T-test and were considered significantly different if P was equal to, or lower than, 0.05 and had expression values greater than 1.5 fold of the control.
Normalized values were generated by the RT2 Profiler PCR Array Data Analysis software version 3.5 using the method above.

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: liver, endurance swim

label_protocol: from liver tissues of 6 replicate mice, chosen at random from each treatment group was used to synthesize cDNA using SABiosciences (Valencia, CA) RT2 First Strand Kit according to manufacturer's instructions.

growth_protocol: C57Bl/6N and PPARα (-/-) age-matched female mice (20 g) were exposed in accordance with the Guide for Use and Care of Animals (National Research Council, 2011). Mice were housed in groups of 4 in polycarbonate shoebox cages 1 week prior to study.

extract_protocol: was extracted from about 30 mg of liver tissue which was stored in RNAlater solution (Ambion-Life Technologies, Grand Island, NY) following manufacturer’s instructions.  Tissues were homogenized in lysis buffer with a FAST Prep-24 instrument (MP Biomedicals, Santa Ana, CA) before RNA isolation with RNeasy kits (Qiagen, Valencia, CA).  concentrations were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity of  was assessed on an Agilent 2100 Bioanalyzer (Palo Alto, CA).  Criteria for acceptable RNA integrity included a RNA integrity number > 7.5 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading > 2.0.

treatment_protocol: Mice were given an oral gavage of 134 mg/kg/day 2,4-DNT or vehicle once a day for 14 days.

tag: genetic background

tag: genotype

value: PPARα (-/-)

tag: gender

value: female

tag: tissue

value: liver

tag: treatment

value: 134 mg/kg 2,4DNT


title: Liver, PPARα (-/-), 134 mg/kg 2,4DNT, rep 4


title: Liver, PPARα (-/-), 134 mg/kg 2,4DNT, rep 6


title: Liver, PPARα (-/-), 134 mg/kg 2,4DNT, rep 3


title: Liver, PPARα (-/-), 134 mg/kg 2,4DNT, rep 1


title: Liver, PPARα (-/-), vehicle, rep 6

value: vehicle


title: Liver, PPARα (-/-), 134 mg/kg 2,4DNT, rep 2


title: Liver, PPARα (-/-), vehicle, rep 4


title: Liver, wild-type, 134 mg/kg 2,4-DNT, rep 2

value: wild type


title: Liver, wild-type, 134 mg/kg 2,4-DNT, rep 3


title: Liver, PPARα (-/-), vehicle, rep 3


title: Liver, PPARα (-/-), vehicle, rep 2


title: Liver, wild-type, 134 mg/kg 2,4-DNT, rep 1


title: Liver, PPARα (-/-), vehicle, rep 1


title: Liver, wild-type, 134 mg/kg 2,4-DNT, rep 4


title: Liver, wild-type, 134 mg/kg 2,4-DNT, rep 6


title: Liver, wild-type, vehicle, rep 6


title: Liver, wild-type, vehicle, rep 5


title: Liver, PPARα (-/-), vehicle, rep 5


title: Liver, wild-type, vehicle, rep 4


title: Liver, wild-type, vehicle, rep 3


title: Liver, wild-type, 134 mg/kg 2,4-DNT, rep 5


title: Liver, wild-type, vehicle, rep 2


title: Liver, wild-type, vehicle, rep 1


title: Liver, PPARα (-/-), 134 mg/kg 2,4-DNT, rep 4


title: Liver, PPARα (-/-), 134 mg/kg 2,4-DNT, rep 6


title: Liver, PPARα (-/-), 134 mg/kg 2,4-DNT, rep 2


title: Liver, PPARα (-/-), 134 mg/kg 2,4-DNT, rep 5


title: Liver, PPARα (-/-), vehicle, rep 6


title: Liver, PPARα (-/-), vehicle, rep 2


title: Liver, PPARα (-/-), vehicle, rep 4


title: Liver, PPARα (-/-), vehicle, rep 3


title: Liver, PPARα (-/-), vehicle, rep 1


title: Liver, wild-type, vehicle, rep 6


title: Liver, wild-type, vehicle, rep 5


title: Venous blood_12 wks_enr_475

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

description: Gene expression after 12 weeks in enriched conditions in horse blood

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent HORSE-GENOPOLE Microarrays (G2514F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Equus caballus

source_name: Venous blood, 12 wks, enr, horse475

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 µg RNA using the One-Color Microarray-Based Gene Expression Analysis kit (Quick Amp Labeling, Agilent Technologies, Massy, France) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen, Courtaboeuf, France).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: Total RNA was extracted with the PAXgene Blood RNA kit (Qiagen, Courtaboeuf, France) according to the manufacturer's protocol. Total RNA quality was assessed and its concentration was measured using RNA Nano chips onto a Bioanalyser 2100 (Agilent, Boeblingen, Germany).

treatment_protocol: 5ml venous blood were collected from the 19 horses at the end of the 12 weeks treatment, using vacuum tubes which included a reagent that immediately stabilized intracellular RNA (PAXgene blood RNA system, PreAnalytiX GmbH, Hombrechtikon, Switzerland). The samples were kept at room temperature for 8 h as required for stabilizing RNA and then at -20°C until RNA extraction.

value: whole blood

value: male

tag: stress

value: enriched social and sensory condition


title: Venous blood_12 wks_enr_469

source_name: Venous blood, 12 wks, enr, horse469


title: Venous blood_12 wks_enr_473

source_name: Venous blood, 12 wks, enr, horse473


title: Venous blood_12 wks_enr_651

source_name: Venous blood, 12 wks, enr, horse651


title: Venous blood_12 wks_enr_649

source_name: Venous blood, 12 wks, enr, horse649


title: Venous blood_12 wks_imp_471

description: Gene expression after 12 weeks in impoverished conditions in horse blood

source_name: Venous blood, 12 wks, imp, horse471

value: impoverished social and sensory condition


title: Venous blood_12 wks_enr_643

source_name: Venous blood, 12 wks, enr, horse643


title: Venous blood_12 wks_imp_645

source_name: Venous blood, 12 wks, imp, horse645


title: Venous blood_12 wks_enr_646

source_name: Venous blood, 12 wks, enr, horse646


title: Venous blood_12 wks_enr_642

source_name: Venous blood, 12 wks, enr, horse642


title: Venous blood_12 wks_imp_472

source_name: Venous blood, 12 wks, imp, horse472


title: Venous blood_12 wks_enr_648

source_name: Venous blood, 12 wks, enr, horse648


title: Venous blood_12 wks_imp_470

source_name: Venous blood, 12 wks, imp, horse470


title: Venous blood_12 wks_enr_468

source_name: Venous blood, 12 wks, enr, horse468


title: Venous blood_12 wks_imp_474

source_name: Venous blood, 12 wks, imp, horse474


title: Venous blood_12 wks_imp_647

source_name: Venous blood, 12 wks, imp, horse647


title: Venous blood_12 wks_imp_476

source_name: Venous blood, 12 wks, imp, horse476


title: Venous blood_12 wks_imp_650

source_name: Venous blood, 12 wks, imp, horse650


title: Venous blood_12 wks_imp_477

source_name: Venous blood, 12 wks, imp, horse477


source_name: liver, endurance swim


title: Liver, PPARα (-/-), vehicle, rep 6


title: Liver, PPARα (-/-), vehicle, rep 5


title: Liver, PPARα (-/-), vehicle, rep 4


title: Liver, PPARα (-/-), vehicle, rep 3


title: Liver, PPARα (-/-), 134 mg/kg 2,4-DNT, rep 1


title: Liver, PPARα (-/-), vehicle, rep 2


title: Primary Tumor PCA0403

type: genomic

city: New York

first: Nikolaus

last: Schultz

state: NY

address: 1275 York Ave, Box 460

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

description: Prostate tumor PCA0403 (aCGH)

hyb_protocol: Per manufacturer's instructions

scan_protocol: Per manufacturer's instructions

data_processing: Probe-level data was subsequently normalized for local GC content with a two-stage LOESS fit.

molecule: genomic DNA

organism: Homo sapiens

source_name: tumor DNA

label_protocol: random primed (Bioprime, Invitrogen) and labeled according to manufacturer's instructions

extract_protocol: DNA was extracted using phenol/chloroform/isoamyl ethanol after proteinase K digestion

value: prostate

tag: disease status

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

tag: bcr event

value: NO

tag: metsevent

value: no

tag: dxage

tag: bxggs

tag: pretxpsa

value: LP

tag: sms

value: Negative

tag: ece

value: No

tag: svi

tag: lni

tag: pathstage

tag: pathggs

tag: surgtype

source_name: Promega reference DNA

tag: sample type

value: Promega reference DNA

value: normal


title: Primary Tumor PCA0399

description: Prostate tumor PCA0399 (aCGH)

tag: tissue


title: Primary Tumor PCA0397

description: Prostate tumor PCA0397 (aCGH)

value: RP

value: Established

value: Yes


title: Primary Tumor PCA0394

description: Prostate tumor PCA0394 (aCGH)

value: Positive


title: Primary Tumor PCA0392

description: Prostate tumor PCA0392 (aCGH)

value: YES

tag: adjradtx

value: External Beam


title: Primary Tumor PCA0401

description: Prostate tumor PCA0401 (aCGH)

tag: disease status

value: RALP

value: Focal


title: Liver, PPARα (-/-), vehicle, rep 1

tag: genetic background

tag: genotype

value: PPARα (-/-)

tag: gender

value: female

value: liver

tag: treatment

value: vehicle


title: Primary Tumor PCA0404

description: Prostate tumor PCA0404 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

tag: bcr event

tag: metsevent

value: no

tag: dxage

tag: bxggs


title: Primary Tumor PCA0396

description: Prostate tumor PCA0396 (aCGH)

value: NO

tag: pretxpsa

value: LP

tag: sms

value: Negative

tag: ece

value: Invades Capsule

value: No

tag: svi

tag: lni

value: Promega reference DNA


title: Primary Tumor PCA0402

description: Prostate tumor PCA0402 (aCGH)

tag: tissue

value: RP

value: Yes

tag: pathstage

tag: pathggs

tag: surgtype

tag: sample type

value: normal


title: Primary Tumor PCA0391

description: Prostate tumor PCA0391 (aCGH)

tag: disease status


title: Primary Tumor PCA0390

description: Prostate tumor PCA0390 (aCGH)

value: Focal


tag: genetic background

tag: genotype

value: wild type

tag: gender

tag: treatment

value: 134 mg/kg 2,4DNT


title: Primary Tumor PCA0398

description: Prostate tumor PCA0398 (aCGH)

tag: %cna (percent of  genome that is copy number altered)

tag: bcr event

value: YES

tag: metsevent

tag: dxage

tag: adjradtx

value: External Beam

value: Established


value: female

value: liver


title: Liver, PPARα (-/-), 134 mg/kg 2,4-DNT, rep 3

value: PPARα (-/-)


title: Liver, wild-type, vehicle, rep 6

value: vehicle


title: Primary Tumor PCA0393

description: Prostate tumor PCA0393 (aCGH)

value: prostate

value: prostate cancer

value: NO

value: no

tag: bxggs

tag: pretxpsa

value: RALP

tag: sms

value: Negative

tag: ece

tag: svi


tag: tissue


title: Primary Tumor PCA0400

description: Prostate tumor PCA0400 (aCGH)

value: Positive

value: Yes

tag: lni

tag: pathstage

tag: pathggs

tag: surgtype

tag: sample type

value: Promega reference DNA

value: normal


title: Primary Tumor PCA0384

description: Prostate tumor PCA0384 (aCGH)

tag: disease status

value: YES

tag: adjhormtx

value: AA, LHRH

value: LP


title: Liver, wild-type, vehicle, rep 5

tag: genetic background

tag: genotype

value: wild type

tag: gender

value: female

tag: treatment


title: Liver, wild-type, vehicle, rep 3

value: liver


title: Primary Tumor PCA0382

description: Prostate tumor PCA0382 (aCGH)

tag: %cna (percent of  genome that is copy number altered)

tag: bcr event

tag: metsevent

tag: dxage

tag: bxggs

value: Invades Capsule

value: No


title: Primary Tumor PCA0380

description: Prostate tumor PCA0380 (aCGH)

tag: tissue

value: prostate

value: prostate cancer

tag: pretxpsa

tag: sms

tag: ece

value: Focal

tag: svi


title: Primary Tumor PCA0383

description: Prostate tumor PCA0383 (aCGH)

value: NO

value: no

value: RP

tag: lni

tag: pathstage

tag: pathggs

tag: surgtype

tag: sample type


title: Primary Tumor PCA0385

description: Prostate tumor PCA0385 (aCGH)

tag: disease status

value: Negative


title: Liver, wild-type, vehicle, rep 2

tag: genetic background

tag: genotype

tag: gender

tag: treatment

value: vehicle


title: Primary Tumor PCA0387

description: Prostate tumor PCA0387 (aCGH)

tag: %cna (percent of  genome that is copy number altered)

tag: bcr event

tag: metsevent

tag: dxage

value: Yes

value: Promega reference DNA

value: normal


title: Primary Tumor PCA0381

description: Prostate tumor PCA0381 (aCGH)

tag: tissue

tag: bxggs

tag: pretxpsa

tag: sms


title: Liver, wild-type, vehicle, rep 4


title: Liver, wild-type, vehicle, rep 1


title: Primary Tumor PCA0388

description: Prostate tumor PCA0388 (aCGH)

tag: ece

tag: svi

tag: lni

tag: pathstage


title: SA564 ΔgdpS 5h of biofilm growth_rep3

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description:
Staphylococcus aureus gdpS mutant strain SA564 versus Staphylococcus aureus gDNA pool
SA564_ΔgdpS_5h_rep3

hyb_protocol: A mixture of RNA from wt or gdpS mutant strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Fluorescence intensities were quantified using Feature Extraction software (Agilent, version 8). Green and red feature data were extracted, processed, and imported into the Partek genomics suite software (Partek Incorporated. St. Louis, MO. USA). Data were normalized to baseline using red channel data as a control and mean to estimate the baseline

organism: Staphylococcus aureus

source_name: S. aureus SA564 ΔgdpS biofilm

label_protocol: Cye dye ncorporation during reverse transcription

growth_protocol: 5 hours of growth in TSB supplemented with 1% glucose in static conditions (biofilm formation) at 37°C in 6 well plates (Falcon)

extract_protocol: Supernatant was throw away and biofilms were washed twice with PBS. Then acetone/ethanol was added to the biofilms and incubated 10 minutes at RT. Biofilms were scraped and transfered to a 1.7mL test tube. Cells were washed twice with TE 1X and lysed using Lysostaphin (80µg/mL). We proceeded to RNA extraction and purification using RNeasy®Mini Kit after addition of 350µL of buffer RLT and homogeneisation with QiaShredder spin columns. Final treatment with DNase for 30 minutes at 37°C and again purified with RNeasy®Mini Kit.

treatment_protocol: No treatment

tag: strain

tag: genotype/variation

value: ΔgdpS

source_name: S. aureus gDNA pool

extract_protocol: gDNA was extracted separately from each strain using the Qiagen DNeasy kit following manufacturer recommendations. We only added a lysis step using lysostaphin prior to DNA extraction. gDNA was not extracted from biofilms, only RNA were.

tag: sample type

value: gDNA mixture contains the gDNA from each strain mapped in the microarray (UAMS-1, SA564, Newman and SA113 (RN4220))


title: SA564 ΔgdpS 5h of biofilm growth_rep1

description:
Staphylococcus aureus gdpS mutant strain SA564 versus Staphylococcus aureus gDNA pool
SA564_ΔgdpS_5h_rep1

source_name: S. aureus SA564 wt biofilm

value: wt


title: SA564 ΔgdpS 5h of biofilm growth_rep2

description:
Staphylococcus aureus gdpS mutant strain SA564 versus Staphylococcus aureus gDNA pool
SA564_ΔgdpS_5h_rep2


title: SA564 wt 5h of biofilm growth_rep3

description:
Staphylococcus aureus wt strain SA564 versus Staphylococcus aureus gDNA pool
SA564_wt_5h_rep3


title: Primary Tumor PCA0386

description: Prostate tumor PCA0386 (aCGH)

tag: disease status

tag: pathggs

tag: surgtype


title: SA564 wt 5h of biofilm growth_rep2

description:
Staphylococcus aureus wt strain SA564 versus Staphylococcus aureus gDNA pool
SA564_wt_5h_rep2


title: SA113 ΔgdpS 5h of biofilm growth_rep2

description:
Staphylococcus aureus gdpS mutant strain SA113 versus Staphylococcus aureus gDNA pool
SA113_ΔgdpS_5h_rep2

source_name: S. aureus SA113 ΔgdpS biofilm


title: Primary Tumor PCA0377

description: Prostate tumor PCA0377 (aCGH)

tag: %cna (percent of  genome that is copy number altered)

tag: bcr event

value: YES

value: Positive

value: Established


title: SA564 wt 5h of biofilm growth_rep1

description:
Staphylococcus aureus wt strain SA564 versus Staphylococcus aureus gDNA pool
SA564_wt_5h_rep1


title: Primary Tumor PCA0375

description: Prostate tumor PCA0375 (aCGH)

value: prostate

tag: metsevent

tag: survivalevent

value: Death from Other Cause

tag: dxage

value: Invades Capsule

value: No


title: Primary Tumor PCA0378

description: Prostate tumor PCA0378 (aCGH)

tag: tissue

value: prostate cancer

value: NO

value: no

tag: bxggs

tag: pretxpsa


title: Primary Tumor PCA0389

description: Prostate tumor PCA0389 (aCGH)

value: LP

tag: sms

value: Negative

tag: ece

tag: svi


title: Primary Tumor PCA0372

description: Prostate tumor PCA0372 (aCGH)

tag: adjradtx

value: External Beam

value: RP

tag: lni

tag: pathstage

value: Promega reference DNA


title: SA113 ΔgdpS 5h of biofilm growth_rep1

description:
Staphylococcus aureus gdpS mutant strain SA113 versus Staphylococcus aureus gDNA pool
SA113_ΔgdpS_5h_rep1

tag: strain

tag: genotype/variation

value: ΔgdpS

tag: sample type

value: gDNA mixture contains the gDNA from each strain mapped in the microarray (UAMS-1, SA564, Newman and SA113 (RN4220))


title: Primary Tumor PCA0370

description: Prostate tumor PCA0370 (aCGH)

tag: disease status

tag: %cna (percent of  genome that is copy number altered)

value: YES

value: Yes

tag: pathggs

tag: surgtype

value: normal


title: Primary Tumor PCA0374

description: Prostate tumor PCA0374 (aCGH)

value: prostate

tag: bcr event

tag: metsevent

tag: dxage

value: Free of tumor


title: Primary Tumor PCA0376

description: Prostate tumor PCA0376 (aCGH)

tag: tissue

tag: bxggs

tag: pretxpsa

value: Invades Capsule


title: UAMS-1 ΔgdpS 5h of biofilm growth_rep2

description:
Staphylococcus aureus gdpS mutant strain UAMS-1 versus Staphylococcus aureus gDNA pool
UAMS-1_ΔgdpS_5h_rep2

source_name: S. aureus UAMS-1 ΔgdpS biofilm


title: Primary Tumor PCA0373

description: Prostate tumor PCA0373 (aCGH)

tag: sms

tag: ece

value: No

tag: svi


title: Primary Tumor PCA0371

description: Prostate tumor PCA0371 (aCGH)

value: prostate cancer

value: Focal

tag: lni

tag: pathstage


title: UAMS-1 ΔgdpS 5h of biofilm growth_rep1

description:
Staphylococcus aureus gdpS mutant strain UAMS-1 versus Staphylococcus aureus gDNA pool
UAMS-1_ΔgdpS_5h_rep1

tag: strain

tag: genotype/variation


title: Primary Tumor PCA0379

description: Prostate tumor PCA0379 (aCGH)

tag: disease status

value: NO

value: no

tag: sample type


title: Primary Tumor PCA0365

description: Prostate tumor PCA0365 (aCGH)

tag: %cna (percent of  genome that is copy number altered)

value: Negative

tag: pathggs


title: Primary Tumor PCA0369

description: Prostate tumor PCA0369 (aCGH)

tag: bcr event

value: Established

tag: surgtype


title: Primary Tumor PCA0395

description: Prostate tumor PCA0395 (aCGH)

tag: metsevent

tag: dxage

tag: adjradtx

value: External Beam

value: LP

value: Positive


title: UAMS-1 wt 5h of biofilm growth_rep2

description:
Staphylococcus aureus wt strain UAMS-1 versus Staphylococcus aureus gDNA pool
UAMS-1_wt_5h_rep2

source_name: S. aureus UAMS-1 wt biofilm

value: wt

value: gDNA mixture contains the gDNA from each strain mapped in the microarray (UAMS-1, SA564, Newman and SA113 (RN4220))


title: Primary Tumor PCA0364

description: Prostate tumor PCA0364 (aCGH)

tag: tissue

tag: bxggs

tag: pretxpsa

value: Yes

value: Promega reference DNA


title: SA113 wt 5h of biofilm growth_rep1

description:
Staphylococcus aureus wt strain SA113 versus Staphylococcus aureus gDNA pool
SA113_wt_5h_rep1

source_name: S. aureus SA113 wt biofilm


title: SA113 wt 5h of biofilm growth_rep2

description:
Staphylococcus aureus wt strain SA113 versus Staphylococcus aureus gDNA pool
SA113_wt_5h_rep2


title: Primary Tumor PCA0368

description: Prostate tumor PCA0368 (aCGH)

value: prostate

value: RP

tag: sms

tag: ece

tag: svi

value: normal


title: Primary Tumor PCA0366

description: Prostate tumor PCA0366 (aCGH)

tag: lni

tag: pathstage


title: Primary Tumor PCA0361

description: Prostate tumor PCA0361 (aCGH)

tag: disease status

value: YES

value: No


title: Primary Tumor PCA0362

description: Prostate tumor PCA0362 (aCGH)

value: prostate cancer

tag: sample type


title: Primary Tumor PCA0367

description: Prostate tumor PCA0367 (aCGH)

tag: %cna (percent of  genome that is copy number altered)

value: NO

value: Invades Capsule


title: Primary Tumor PCA0359

description: Prostate tumor PCA0359 (aCGH)

value: no

value: Negative

value: Focal

tag: pathggs


title: UAMS-1 wt 5h of biofilm growth_rep1

description:
Staphylococcus aureus wt strain UAMS-1 versus Staphylococcus aureus gDNA pool
UAMS-1_wt_5h_rep1

tag: strain

tag: genotype/variation


title: Primary Tumor PCA0363

description: Prostate tumor PCA0363 (aCGH)

tag: bcr event

tag: metsevent

value: LP

value: Established

tag: surgtype


title: Primary Tumor PCA0358

description: Prostate tumor PCA0358 (aCGH)

tag: tissue

tag: dxage


title: Primary Tumor PCA0357

description: Prostate tumor PCA0357 (aCGH)

tag: bxggs

tag: pretxpsa


title: Primary Tumor PCA0360

description: Prostate tumor PCA0360 (aCGH)

tag: sms

tag: ece


title: Primary Tumor PCA0355

description: Prostate tumor PCA0355 (aCGH)

tag: svi

tag: lni


title: Primary Tumor PCA0354

description: Prostate tumor PCA0354 (aCGH)

tag: disease status

value: Positive

tag: pathstage


title: Primary Tumor PCA0356

description: Prostate tumor PCA0356 (aCGH)

tag: %cna (percent of  genome that is copy number altered)

value: Not Done

tag: sample type


title: Primary Tumor PCA0353

description: Prostate tumor PCA0353 (aCGH)

tag: pathggs


title: Primary Tumor PCA0348

description: Prostate tumor PCA0348 (aCGH)


title: Primary Tumor PCA0352

description: Prostate tumor PCA0352 (aCGH)

tag: adjradtx

value: External Beam

value: Yes


title: Primary Tumor PCA0350

description: Prostate tumor PCA0350 (aCGH)

value: prostate

tag: bcr event

value: Promega reference DNA


title: Primary Tumor PCA0347

description: Prostate tumor PCA0347 (aCGH)

tag: metsevent

value: normal


title: aCGH data of Ao-210k-dup

city: Noda City

first: Masahiro

last: Ogawa

state: Chiba Prefecture

address: 399 Noda

department: Research and Developmental Division

country: Japan

institute: Kikkoman Corporation

description: aCGH data of A. oryzae strain bearing a 210-kb targeted tandem chromosomal duplication

hyb_protocol: 5 ug each of the Cy-dye labeled DNAs (reference and test) were combined with 5 ug of Human Cot-1 DNA (Invitrogen). The mixture was hybridized with Agilent_017367 NISR Aspergillus oryzae 24K v.2.0 (GPL16017) using Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent Technologies). Hybridization was performed at 65ºC for 24 hours. Then, the array slides were washed with Oligo aCGH/ChIP Wash Buffer Kit (Agilent Technologies).

scan_protocol: The array slide was scanned at 5 µm resolution with an Agilent Microarray Scanner G2505B (Agilent Technologies).

data_processing: Raw microarray image files were processed using Feature Extraction Software version 9.5.1(Agilent Technologies). In this process, linear and LOWESS normalizations were carried out to remove the dye-biases of the data.

organism: Aspergillus oryzae RIB40

source_name: Aspergillus oryzae RIB40 Wild type (reference)

label_protocol: The sample genomic DNAs were sheared to approximately 500 bp using Bioruptor UCD-250HSA (Cosmo Bio). 1 μg of the fragmented genomic DNAs were labeled with Cy3 or Cy5 using Genomic DNA Labeling Kit Plus (Agilent technologies). The fragmented DNAs were mixed with random primers. The mixtures were denatured at 95ºC for 5 minutes, and then immediately cooled on ice. After addition of dNTPs, Cy3 (or Cy5)-dUTP and, Klenow fragment, the samples were incubated at 37ºC for 2 hours. The labeling reactions were stopped by heat treatment at 65 ºC for 5 min. Unincorporated nucleotides were removed from the labeled samples by filtration using Millipore Microcon YM-30 filter units, and the sample were further concentrated by YM30 filter units.

growth_protocol: Conidia of the fungal strains were inoculated into 40 ml of Polypeptone dextrin (PD) medium (polypeptone 10 g, dextrin 20 g, KH2PO4 5 g, NaNO3 1 g, MgSO4 0.5 g, casamino acid 1 g, per liter; pH 6.0), and incubated at 30°C for 3 days with shaking at 150 rpm. The mycelia were collected by filtration.

extract_protocol: The samples were frozen and ground in liquid nitrogen using a mortar and pestle. Genomic DNA of the samples were extracted using Nuclei Lysis Solution (Promega) and Protein precipitation solution (Promega). To remove the contamination of RNA, the genomic DNA samples were treated with RNaseA (Nippon Gene), and the samples were further purified by Genomic-tip 20/G column (QIAGEN).

tag: genotype/variation

value: Wild type (reference)

source_name: Aspergillus  oryzae Ao-210k-dup,a derivative of A. oryzae RIB40

value: ΔpyrG, H71::5'ΔpyrG, H160::3'ΔpyrG, duplication of 210kb region in Ch8 (H71-H160)


title: Primary Tumor PCA0349

description: Prostate tumor PCA0349 (aCGH)

tag: tissue

value: prostate cancer

value: RP

value: No

tag: surgtype


title: Primary Tumor PCA0351

description: Prostate tumor PCA0351 (aCGH)

value: NO

value: no

tag: dxage

tag: bxggs

value: Invades Capsule


title: aCGH data of Ao-700k-dup

description: aCGH data of A. oryzae strain bearing a 700-kb targeted tandem chromosomal duplication

source_name: Aspergillus  oryzae Ao-700k-dup,a derivative of A. oryzae RIB40

value: ΔpyrG, B1003::5'ΔpyrG, B1258::3'ΔpyrG, duplication of 700kb region in Chromosome2 (B1003-B1258)


title: Primary Tumor PCA0341

description: Prostate tumor PCA0341 (aCGH)

tag: pretxpsa

tag: sms

value: Negative


title: Hypothalamus_1 day of extrauterine life_Replicate 4

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

description: Gene expression in newborn hypothalamus at 1 day of life-Replicate 4

hyb_protocol: 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 X 15 K array slide (Agilent  019921), containing 8 arrays with 15,208 oligomers with a length of 60 bases corresponding to 15,208 ovine genetic sequences and hybridized at 65 °C for 17 h at 10 rpm.  After hybridization, the slides were washed for 1 minute at room temperature with Wash Buffer 1 (Agilent) and for 1 minute with 37 °C Wash buffer 2 (Agilent). After dry the excess of liquid, the slides were washed for 30 seconds in the stabilization and drying solution.

scan_protocol: The slides were scanned with an Agilent 2-dye G2505B scanner that is compatible with any 1' x 3' glass slide.

data_processing: Features were extracted with Agilent Feature extraction 9.1 software. The limma package was employed to import the raw data into R (http://www.r-project.org), perform background correction and normalize the data by the quantile normalization method. Control probes and low expressed probes were filtered out, retaining for further analysis the probes that were at least 10% brighter than the negative controls on at least four arrays.

organism: Ovis aries

source_name: hypothalamus, 1 day of extrauterine life

label_protocol: One µg of the DNase-treated RNA was labeled with Cyanine 3 (Cy3) CTP with the Agilent Quick Amp kit (5190-0442, New Castle, DE) according to their methodology, purified with the Qiagen RNeasy kit (Valencia, CA) according to Agilent’s revision of the Qiagen protocol as shown in the Quick Amp kit protocol except that the microcentrifugation spins were performed at room temperature instead of 4ºC. The resulting labeled cRNA was analyzed with the Nanodrop spectrophotometer, and the specific activities and the yields of the cRNAs were calculated. The labeled cRNA was stored at -80ºC until use.

extract_protocol: RNA was extracted from each cortex, hippocampus, hypothalamus and brainstem using Trizol (Invitrogen, Carlsbad, CA) and following the manufacturer’s directions. The RNA was resuspended in RNAsecure, and stored at -80ºC in aliquots until use. For microarray analysis 20 ug of these RNAs, were DNase treated using the Turbo RNase-free DNase kit (Ambion, Foster City, CA), the concentration determined with a Nanodrop spectrophotometer (ND-1000, ThermoFisher, Wilmington DE) and the integrity of the RNA was measured using an Agilent Bioanalyzer, 2100 model.

value: Newborn brain

tag: brain region

value: Hypothalamus

tag: developmental age

value: 1 day of life


title: Hypothalamus_1 day of extrauterine life_Replicate 3

description: Gene expression in newborn hypothalamus at 1 day of life-Replicate 3


title: Primary Tumor PCA0343

description: Prostate tumor PCA0343 (aCGH)

tag: disease status

value: YES

tag: adjhormtx

value: LHRH

value: External Beam, 3D Conformal

value: Positive

tag: ece

value: Established

value: Yes

tag: svi

tag: lni


title: Primary Tumor PCA0337

description: Prostate tumor PCA0337 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

tag: pathstage

tag: pathggs

tag: sample type

value: Promega reference DNA

value: normal


title: Hypothalamus_1 day of extrauterine life_Replicate 2

description: Gene expression in newborn hypothalamus at 1 day of life-Replicate 2

tag: tissue


title: Primary Tumor PCA0338

description: Prostate tumor PCA0338 (aCGH)

tag: bcr event

value: NO

tag: metsevent

value: no

value: RP

value: No

tag: surgtype


title: Primary Tumor PCA0345

description: Prostate tumor PCA0345 (aCGH)

tag: dxage

tag: bxggs

tag: pretxpsa

value: Negative

value: Invades Capsule


title: Primary Tumor PCA0342

description: Prostate tumor PCA0342 (aCGH)

tag: sms


title: Primary Tumor PCA0335

description: Prostate tumor PCA0335 (aCGH)

tag: disease status

value: FOCAL


title: Primary Tumor PCA0334

description: Prostate tumor PCA0334 (aCGH)

tag: survivalevent

value: Death from Other Cause

tag: adjradtx

value: Adjuvant XRT


title: Primary Tumor PCA0346

description: Prostate tumor PCA0346 (aCGH)

value: Death From Unknown Causes

tag: ece

tag: svi


title: Primary Tumor PCA0333

description: Prostate tumor PCA0333 (aCGH)

tag: %cna (percent of  genome that is copy number altered)

tag: lni


title: Primary Tumor PCA0332

description: Prostate tumor PCA0332 (aCGH)

value: Positive

value: Not Done

tag: pathstage

tag: pathggs


title: Hypothalamus_145 days of gestational life_Replicate 4

description: Gene expression in fetal hypothalamus at 145 days of gestation-Replicate 4

source_name: hypothalamus, 145 days of gestational life

tag: tissue

value: Fetal brain

tag: brain region

value: Hypothalamus

tag: developmental age

value: 145 days of fetal age


title: Hypothalamus_145 days of gestational life_Replicate 3

description: Gene expression in fetal hypothalamus at 145 days of gestation-Replicate 3


title: Primary Tumor PCA0340

description: Prostate tumor PCA0340 (aCGH)

value: prostate

value: prostate cancer

tag: bcr event

tag: metsevent

tag: surgtype

tag: sample type

value: Promega reference DNA


title: Hypothalamus_145 days of gestational life_Replicate 1

description: Gene expression in fetal hypothalamus at 145 days of gestation-Replicate 1


title: Hypothalamus_1 day of extrauterine life_Replicate 1

description: Gene expression in newborn hypothalamus at 1 day of life-Replicate 1

value: Newborn brain

value: 1 day of life


title: Hypothalamus_130 days of gestational life_Replicate 4

description: Gene expression in fetal hypothalamus at 130 days of gestation-Replicate 4

source_name: hypothalamus, 130 days of gestational life

value: 130 days of fetal age


title: Hypothalamus_145 days of gestational life_Replicate 2

description: Gene expression in fetal hypothalamus at 145 days of gestation-Replicate 2


title: Primary Tumor PCA0336

description: Prostate tumor PCA0336 (aCGH)

value: NO

value: no

tag: dxage

tag: bxggs

tag: pretxpsa

value: RP

tag: sms

value: Negative

value: No

value: normal


title: Primary Tumor PCA0344

description: Prostate tumor PCA0344 (aCGH)

tag: disease status

tag: ece


title: Primary Tumor PCA0329

description: Prostate tumor PCA0329 (aCGH)

tag: %cna (percent of  genome that is copy number altered)

value: Focal

value: Yes

tag: svi


title: Primary Tumor PCA0328

description: Prostate tumor PCA0328 (aCGH)

value: YES

tag: adjhormtx

value: LHRH

value: Invades Capsule

tag: lni

tag: pathstage


title: Primary Tumor PCA0331

description: Prostate tumor PCA0331 (aCGH)

tag: tissue

value: prostate

value: Positive

tag: pathggs


title: Hypothalamus_130 days of gestational life_Replicate 2

description: Gene expression in fetal hypothalamus at 130 days of gestation-Replicate 2

value: Fetal brain

tag: brain region

value: Hypothalamus

tag: developmental age


title: Primary Tumor PCA0339

description: Prostate tumor PCA0339 (aCGH)

value: prostate cancer

tag: bcr event

tag: metsevent

value: Established

tag: surgtype

value: Promega reference DNA


title: Hypothalamus_130 days of gestational life_Replicate 1

description: Gene expression in fetal hypothalamus at 130 days of gestation-Replicate 1

value: 130 days of fetal age


title: Primary Tumor PCA0327

description: Prostate tumor PCA0327 (aCGH)

value: NO

value: no

tag: dxage

tag: bxggs

value: RP

tag: sample type


title: Hypothalamus_120 days of gestational life_Replicate 4

description: Gene expression in fetal hypothalamus at 120 days of gestation-Replicate 4

source_name: hypothalamus, 120 days of gestational life

value: 120 days of fetal age


title: Hypothalamus_120 days of gestational life_Replicate 3

description: Gene expression in fetal hypothalamus at 120 days of gestation-Replicate 3


title: Primary Tumor PCA0324

description: Prostate tumor PCA0324 (aCGH)

tag: disease status

tag: pretxpsa

tag: sms

value: Negative

value: FOCAL

value: normal


title: Hypothalamus_100 days of gestational life_Replicate 4

description: Gene expression in fetal hypothalamus at 100 days of gestation-Replicate 4

source_name: hypothalamus, 100 days of gestational life

value: 100 days of fetal age


title: Hypothalamus_120 days of gestational life_Replicate 1

description: Gene expression in fetal hypothalamus at 120 days of gestation-Replicate 1


title: Primary Tumor PCA0325

description: Prostate tumor PCA0325 (aCGH)

source_name: tumor DNA

tag: %cna (percent of  genome that is copy number altered)

tag: ece

value: Yes

tag: svi


title: Hypothalamus_100 days of gestational life_Replicate 3

description: Gene expression in fetal hypothalamus at 100 days of gestation-Replicate 3


title: Hypothalamus_100 days of gestational life_Replicate 2

description: Gene expression in fetal hypothalamus at 100 days of gestation-Replicate 2


title: Primary Tumor PCA0323

description: Prostate tumor PCA0323 (aCGH)

value: prostate

value: YES

tag: adjhormtx

value: LHRH

tag: adjradtx

value: External Beam

tag: lni

tag: pathstage

source_name: Promega reference DNA


title: Primary Tumor PCA0326

description: Prostate tumor PCA0326 (aCGH)

tag: tissue

value: prostate cancer

value: Positive

tag: pathggs


title: Hypothalamus_80 days of gestational life_Replicate 4

description: Gene expression in fetal hypothalamus at 80 days of gestation-Replicate 4

source_name: hypothalamus, 80 days of gestational life

value: Fetal brain

tag: brain region

value: Hypothalamus

tag: developmental age

value: 80 days of fetal age


title: Hypothalamus_80 days of gestational life_Replicate 3

description: Gene expression in fetal hypothalamus at 80 days of gestation-Replicate 3


title: Primary Tumor PCA0321

description: Prostate tumor PCA0321 (aCGH)

tag: bcr event

value: NO

tag: metsevent

value: no

tag: dxage

value: Invades Capsule

value: No

tag: surgtype

value: Promega reference DNA


title: Hypothalamus_100 days of gestational life_Replicate 1

description: Gene expression in fetal hypothalamus at 100 days of gestation-Replicate 1


title: Primary Tumor PCA0322

description: Prostate tumor PCA0322 (aCGH)

tag: disease status

tag: bxggs

tag: pretxpsa

value: RP

value: Negative

value: Established

tag: sample type

value: normal


title: Hypothalamus_130 days of gestational life_Replicate 3

description: Gene expression in fetal hypothalamus at 130 days of gestation-Replicate 3

value: 130 days of fetal age


title: HF_Rosi_Apex_278

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

institute: TNO

hyb_protocol: We have used standard Illumina hybridisation protocol. The amount of biotinylated cRNA that was hybridized onto the MouseRef-8 Expression BeadChip was 750 ng

scan_protocol: Illumina’s Genomestudio v1.1.1 software with the default settings advised by Illumina, was used for Gene Expression analysis. All the quality control data of this BeadChip were within specifications of the microarray service provider (Service XS, Leiden, the Netherlands).

data_processing:
Probe-level, background subtracted expression values were used as input for GeneSpring GX11 software (Agilent), which was used for normalization of data; threshold signals below the value of 5 were set at 5. To be considered expressed, the signal detection p-value of the probe had to be lower than 0.01 in at least 1 of 48 experiments. 15505 probes fulfilled these criteria. Differential expression of probes was assessed using unpaired moderated t-test (LIMMA) via The Remote Analysis Computation for gene Expression data (RACE) suite at http://race.unil.ch
Pipeline for illumina arrays (www.arrayanalysis.org) was used to normalize data. Differential expression of probes was assessed using unpaired moderated t-test (LIMMA) via The Remote Analysis Computation for gene Expression data (RACE) suite at http://race.unil.ch

label: Biotin

source_name: mouse heart

label_protocol: The Illumina® TotalPrep™ RNA Amplification Kit (Ambion, art. No. AM-IL1791) was used to synthesize biotin labeled cRNA starting with 500 ng total RNA. Concentration of the labeled cRNA was measured using the Nanodrop spectrophotometer.

extract_protocol: Total RNA was extracted from individual hearts (n=8 hearts per group, 48 samples in total) using glass beads and RNAzol (Campro Scientific, Veenendaal, The Netherlands).

tag: strain

value: LDL-/-

tag: gender

value: male

tag: treatment

value: high fat + rosiglitazone

value: heart

tag: genetic background


title: Hypothalamus_120 days of gestational life_Replicate 2

description: Gene expression in fetal hypothalamus at 120 days of gestation-Replicate 2

value: Fetal brain

value: 120 days of fetal age


title: Hypothalamus_80 days of gestational life_Replicate 1

description: Gene expression in fetal hypothalamus at 80 days of gestation-Replicate 1

value: Hypothalamus

value: 80 days of fetal age


title: Hippocampus_1 day of extrauterine life_Replicate 4

description: Gene expression in newborn hippocampus at 1 day of life-Replicate 4

source_name: hippocampus, 1 day of extrauterine life

value: Newborn brain

value: Hippocampus

value: 1 day of life


title: Hypothalamus_80 days of gestational life_Replicate 2

description: Gene expression in fetal hypothalamus at 80 days of gestation-Replicate 2


title: Primary Tumor PCA0320

description: Prostate tumor PCA0320 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

value: NO

value: no

tag: sms

value: Positive

tag: ece

value: Yes

tag: svi

tag: lni

tag: pathstage

value: Promega reference DNA


title: HF_Rosi_Apex_275

value: LDL-/-

value: male

tag: tissue


title: HF_Rosi_Apex_277

value: high fat + rosiglitazone

value: heart


title: Hippocampus_1 day of extrauterine life_Replicate 3

description: Gene expression in newborn hippocampus at 1 day of life-Replicate 3

tag: brain region

tag: developmental age


title: Primary Tumor PCA0318

description: Prostate tumor PCA0318 (aCGH)

tag: disease status

tag: bcr event

tag: metsevent

tag: survivalevent

value: Death from Ampullary Cancer

tag: dxage

value: RP

value: Negative

value: No

tag: pathggs

tag: surgtype

value: normal


title: HF_Rosi_Apex_273

tag: strain

tag: gender

tag: treatment

tag: genetic background


title: Hippocampus_145 days of gestational life_Replicate 4

description: Gene expression in fetal hippocampus at 145 days of gestation-Replicate 4

source_name: hippocampus, 145 days of gestational life

value: Fetal brain

value: Hippocampus

value: 145 days of fetal age


title: Hippocampus_145 days of gestational life_Replicate 3

description: Gene expression in fetal hippocampus at 145 days of gestation-Replicate 3


title: HF_Pio_Apex_285

value: high fat + pioglitazone


title: Primary Tumor PCA0317

description: Prostate tumor PCA0317 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

value: YES

value: yes

value: Death From Unknown Causes

tag: bxggs

tag: pretxpsa

tag: adjchemotx

tag: adjhormtx

value: AA,LHRH,HORM

tag: adjradtx

value: External Beam

tag: sms

tag: ece

value: Established

tag: svi

tag: sample type


title: HF_Pio_Apex_287

value: LDL-/-

value: male

tag: tissue

value: heart


title: HF_Rosi_Apex_274

value: high fat + rosiglitazone


title: HF_Pio_Apex_284


title: Hippocampus_145 days of gestational life_Replicate 2

description: Gene expression in fetal hippocampus at 145 days of gestation-Replicate 2

tag: brain region

tag: developmental age


title: Primary Tumor PCA0314

description: Prostate tumor PCA0314 (aCGH)

tag: disease status

tag: bcr event

tag: metsevent

tag: survivalevent

tag: dxage

value: AA,LHRH

value: RP

value: Negative

value: Focal

value: Yes

value: Positive

tag: lni

tag: pathstage

tag: pathggs

tag: surgtype

value: Promega reference DNA

value: normal


title: HF_Pio_Apex_283

tag: strain

tag: gender

tag: treatment

value: high fat + pioglitazone

tag: genetic background


title: Hippocampus_145 days of gestational life_Replicate 1

description: Gene expression in fetal hippocampus at 145 days of gestation-Replicate 1

value: Fetal brain

value: Hippocampus

value: 145 days of fetal age


title: HF_Apex_214

value: high fat


title: Hippocampus_130 days of gestational life_Replicate 4

description: Gene expression in fetal hippocampus at 130 days of gestation-Replicate 4

source_name: hippocampus, 130 days of gestational life

value: 130 days of fetal age


title: HF_Apex_213

value: LDL-/-

value: male


title: Hippocampus_1 day of extrauterine life_Replicate 2

description: Gene expression in newborn hippocampus at 1 day of life-Replicate 2

value: Newborn brain

value: 1 day of life


title: Hippocampus_130 days of gestational life_Replicate 3

description: Gene expression in fetal hippocampus at 130 days of gestation-Replicate 3


title: Primary Tumor PCA0316

description: Prostate tumor PCA0316 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

value: NO

value: no

tag: bxggs

tag: pretxpsa

value: RP

tag: sms

tag: ece

value: No

tag: svi

tag: sample type


title: Primary Tumor PCA0315

description: Prostate tumor PCA0315 (aCGH)

tag: tissue

tag: disease status

tag: bcr event

tag: metsevent

value: Negative

value: Invades Capsule

value: Promega reference DNA

value: normal


title: HF_Apex_211

value: heart


title: Hippocampus_130 days of gestational life_Replicate 2

description: Gene expression in fetal hippocampus at 130 days of gestation-Replicate 2

value: Fetal brain

tag: brain region

value: Hippocampus

tag: developmental age


title: Primary Tumor PCA0311

description: Prostate tumor PCA0311 (aCGH)

value: YES

value: yes

tag: dxage

tag: adjhormtx

value: AA

value: Established

value: Yes

value: Positive

tag: lni

tag: pathstage

tag: pathggs

tag: surgtype


title: Hippocampus_130 days of gestational life_Replicate 1

description: Gene expression in fetal hippocampus at 130 days of gestation-Replicate 1

value: 130 days of fetal age


title: Primary Tumor PCA0312

description: Prostate tumor PCA0312 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

value: NO

value: no

tag: bxggs

tag: pretxpsa


title: Hippocampus_120 days of gestational life_Replicate 3

description: Gene expression in fetal hippocampus at 120 days of gestation-Replicate 3

source_name: hippocampus, 120 days of gestational life

value: 120 days of fetal age


title: Primary Tumor PCA0309

description: Prostate tumor PCA0309 (aCGH)

tag: adjradtx

value: External Beam

value: RP

tag: sms

tag: ece

tag: svi

value: Negative

value: Promega reference DNA


title: HF_Apex_209

tag: strain

value: LDL-/-

tag: gender

value: male

tag: treatment

value: high fat

tag: tissue

value: heart

tag: genetic background


title: Hippocampus_120 days of gestational life_Replicate 4

description: Gene expression in fetal hippocampus at 120 days of gestation-Replicate 4

value: Fetal brain

tag: brain region

value: Hippocampus

tag: developmental age


title: Primary Tumor PCA0306

description: Prostate tumor PCA0306 (aCGH)

tag: disease status

tag: bcr event

value: YES

tag: metsevent

tag: dxage

value: Positive

value: FOCAL

value: Yes

tag: lni

tag: pathstage

tag: sample type

value: normal


title: Hippocampus_120 days of gestational life_Replicate 2

description: Gene expression in fetal hippocampus at 120 days of gestation-Replicate 2


title: Primary Tumor PCA0308

description: Prostate tumor PCA0308 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

value: no

tag: bxggs

tag: pretxpsa

tag: adjradtx

value: IMRT

tag: sms

value: Established

tag: pathggs

tag: surgtype


title: HF_Apex_205

tag: strain

tag: gender

tag: treatment

tag: tissue

tag: genetic background


title: Hippocampus_100 days of gestational life_Replicate 3

description: Gene expression in fetal hippocampus at 100 days of gestation-Replicate 3

source_name: hippocampus, 100 days of gestational life

tag: brain region

tag: developmental age

value: 100 days of fetal age


title: Hippocampus_120 days of gestational life_Replicate 1

description: Gene expression in fetal hippocampus at 120 days of gestation-Replicate 1

value: 120 days of fetal age


title: cyclopamine-3

city: Calgary

first: Sarah

middle: J

last: Childs

state: AB

address: 3330 Hospital Drive NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.31 (Roche NimbleGen, Inc.).
Z-score was then calculated by standardization (with subtraction of the average and subsequently divided by the standard deviation, SD, of each array). Changes (Z-Ratio’s) due to igu mutation or cyclopamine treatments were calculated for each gene according to the following formula: (Z_Ratio = [(Z-score_G1ave)Exp –Z-score_G1ave)Con] / SD of Z score differencesG1. . .Gn) where G1 represents the average Z score for any particular gene being tested under multiple experimental conditions (in this case, experimental versus control) and G1. . . Gn represents the aggregate measure of all of the genes. Genes with absolute Z_Ratio values of greater than or equal to 1.96 were marked as significantly differential (P < 0.05).
The Z_Ratios statistics for microarray experiments were performed using an EXCEL template as per Cheadle et al. (2003)  J Mol Diagn 5: 73-81.
supplementary file contains the following:
Zratio_WM - Zratio of average value of fo 10 mutants to fo 10 wild type sibs
Zratio_DC - Zratio of average value of embryos exposed to cyclopamine to those exposed to DMSO

organism: Danio rerio

source_name: 100 uM cyclopamine treated

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Zebrafish were maintained at in accordance with procedures approved by the University of Calgary Animal Care Committee. Embryos were generated and maintained as outlined by Westerfield (2000) The zebrafish book
Embryos were collected and maintained at 28.5⁰C in E3 buffer. Where necessary, embryos were dechorionated with 20mg/ml pronase (Sigma, St. Louis MO). Embryos were derived from igufo10, bbhm292, or Tüpfel longfin fish (Lamont RE, et al. (2010) Mech Dev 127: 159-168. and Liu J, Fraser, et al. (2007) Proc Natl Acad Sci U S A 104: 13990-13995.)

extract_protocol: RNA was isolated using the QIAGEN RNeasy Mini or Midi Kits (QIAGEN, Hilden, Germany), using 1% β- mercaptoethanol for whole embryo homogenization, and DNase I treatment.

treatment_protocol: Cyclopamine (Toronto Research Chemicals Inc., Toronto, ON) and Pim1 inhibitor II (Calbiochem, Mississauga, ON) were diluted in dimethyl sulfoxide (DMSO) to stock concentrations of 10mM and 27mM, respectively. Cyclopamine was applied at a working concentration of 100µM in E3 buffer, with controls receiving an equal dose of 1% DMSO alone. Embryos collected for microarray analysis were treated from 4-30 hpf.  We treated embryos with Pim1 inhibitor II at a concentration of 5, 10 or 20µM in combination with 100 µM of cyclopamine, applied at 24hpf, and hemorrhage was scored at 48hpf.

value: 100 uM cyclopamine treated

tag: genotype

value: wild type

value: TL

tag: age

value: 30 hpf

value: embryo


title: HF_Apex_208

value: LDL-/-

value: male

value: high fat

value: heart


title: Primary Tumor PCA0310

description: Prostate tumor PCA0310 (aCGH)

tag: disease status

tag: bcr event

value: NO

tag: metsevent

tag: dxage

value: RP

value: Negative

tag: ece

value: FOCAL

value: Yes

tag: svi

tag: lni

tag: pathstage

tag: sample type

value: Promega reference DNA

value: normal


title: fo10 mutants-3

source_name: Iguana mutants

value: Iguana mutants


title: Primary Tumor PCA0307

description: Prostate tumor PCA0307 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

value: no

tag: bxggs

tag: pretxpsa

tag: sms

value: Positive

value: Established

tag: pathggs

tag: surgtype


title: fo10 wt sibs-3

source_name: Iguana wild type siblings

tag: genotype

value: Iguana wild type siblings

tag: genetic background

value: TL

value: 30 hpf

tag: tissue

value: embryo


title: Hippocampus_100 days of gestational life_Replicate 2

description: Gene expression in fetal hippocampus at 100 days of gestation-Replicate 2

value: Fetal brain

tag: brain region

value: Hippocampus

tag: developmental age

value: 100 days of fetal age


title: Primary Tumor PCA0303

description: Prostate tumor PCA0303 (aCGH)

tag: disease status

tag: bcr event

value: NO

tag: metsevent

tag: dxage

value: RP

value: Negative

value: No


title: DMSO-3

source_name: DMSO

tag: treatment

value: DMSO

value: wild type

tag: age


title: Hippocampus_100 days of gestational life_Replicate 1

description: Gene expression in fetal hippocampus at 100 days of gestation-Replicate 1


title: DMSO-2


title: Hippocampus_80 days of gestational life_Replicate 4

description: Gene expression in fetal hippocampus at 80 days of gestation-Replicate 4

source_name: hippocampus, 80 days of gestational life

value: 80 days of fetal age


title: cyclopamine-2

value: 100 uM cyclopamine treated


title: Hippocampus_80 days of gestational life_Replicate 2

description: Gene expression in fetal hippocampus at 80 days of gestation-Replicate 2


title: HF_Pio_Apex_286

tag: strain

value: LDL-/-

tag: gender

value: male

value: high fat + pioglitazone

value: heart


title: Hippocampus_80 days of gestational life_Replicate 1

description: Gene expression in fetal hippocampus at 80 days of gestation-Replicate 1


title: Hippocampus_80 days of gestational life_Replicate 3

description: Gene expression in fetal hippocampus at 80 days of gestation-Replicate 3


title: fo10 wt sibs-2

value: Iguana wild type siblings

value: TL

value: 30 hpf


title: DMSO-1

value: embryo


title: cyclopamine-1


title: Brainstem_1 day of extrauterine life_Replicate 4

description: Gene expression in newborn brainstem at 1 day of life-Replicate 4

source_name: brainstem, 1 day of extrauterine life

value: Newborn brain

value: Brainstem

value: 1 day of life


title: Brainstem_1 day of extrauterine life_Replicate 2

description: Gene expression in newborn brainstem at 1 day of life-Replicate 2


title: Hippocampus_1 day of extrauterine life_Replicate 1

description: Gene expression in newborn hippocampus at 1 day of life-Replicate 1

value: Hippocampus


title: fo10 mutants-1

value: Iguana mutants


title: Primary Tumor PCA0302

description: Prostate tumor PCA0302 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

value: YES

value: no

tag: bxggs

tag: pretxpsa

tag: adjradtx

value: Radiation Therapy, Unspecified

value: RP

value: Positive

tag: ece

value: Established

value: Yes

tag: svi

value: Negative

tag: lni

tag: pathstage

tag: sample type

value: Promega reference DNA

value: normal


title: Primary Tumor PCA0300

description: Prostate tumor PCA0300 (aCGH)

tag: tissue

tag: disease status

tag: adjhormtx

value: AA,LHRH

tag: sms

value: Tumor present at the apical margin.

value: Focal

tag: pathggs

tag: surgtype


title: fo10 mutants-2

tag: genotype

tag: genetic background

value: TL

tag: age

value: 30 hpf

value: embryo


title: Primary Tumor PCA0319

description: Prostate tumor PCA0319 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

tag: bcr event

value: NO

tag: metsevent

tag: dxage

tag: bxggs

value: No


title: Primary Tumor PCA0301

description: Prostate tumor PCA0301 (aCGH)

value: no

tag: survivalevent

value: Death from Other Cause

tag: pretxpsa

value: RP

tag: ece

tag: svi

tag: lni


title: Brainstem_1 day of extrauterine life_Replicate 3

description: Gene expression in newborn brainstem at 1 day of life-Replicate 3

tag: tissue

value: Newborn brain

tag: brain region

value: Brainstem

tag: developmental age

value: 1 day of life


title: fo10 wt sibs-1

value: Iguana wild type siblings


title: Brainstem_1 day of extrauterine life_Replicate 1

description: Gene expression in newborn brainstem at 1 day of life-Replicate 1


title: Brainstem_145 days of gestational life_Replicate 4

description: Gene expression in fetal brainstem at 145 days of gestation-Replicate 4

source_name: brainstem, 145 days of gestational life

value: Fetal brain

value: 145 days of fetal age


title: Brainstem_130 days of gestational life_Replicate 3

description: Gene expression in fetal brainstem at 130 days of gestation-Replicate 3

source_name: brainstem, 130 days of gestational life

value: 130 days of fetal age


title: Brainstem_130 days of gestational life_Replicate 4

description: Gene expression in fetal brainstem at 130 days of gestation-Replicate 4


title: Primary Tumor PCA0305

description: Prostate tumor PCA0305 (aCGH)

source_name: tumor DNA

tag: disease status

value: YES

tag: sms

value: Negative

tag: pathstage

tag: pathggs

tag: surgtype

tag: sample type

value: Promega reference DNA

value: normal


title: Brainstem_145 days of gestational life_Replicate 3

description: Gene expression in fetal brainstem at 145 days of gestation-Replicate 3


title: Brainstem_145 days of gestational life_Replicate 2

description: Gene expression in fetal brainstem at 145 days of gestation-Replicate 2


title: Brainstem_145 days of gestational life_Replicate 1

description: Gene expression in fetal brainstem at 145 days of gestation-Replicate 1


title: Brainstem_130 days of gestational life_Replicate 1

description: Gene expression in fetal brainstem at 130 days of gestation-Replicate 1


title: Brainstem_130 days of gestational life_Replicate 2

description: Gene expression in fetal brainstem at 130 days of gestation-Replicate 2


title: Brainstem_120 days of gestational life_Replicate 2

description: Gene expression in fetal brainstem at 120 days of gestation-Replicate 2

source_name: brainstem, 120 days of gestational life

value: 120 days of fetal age


title: Brainstem_120 days of gestational life_Replicate 4

description: Gene expression in fetal brainstem at 120 days of gestation-Replicate 4


title: Brainstem_120 days of gestational life_Replicate 3

description: Gene expression in fetal brainstem at 120 days of gestation-Replicate 3


title: Brainstem_100 days of gestational life_Replicate 3

description: Gene expression in fetal brainstem at 100 days of gestation-Replicate 3

source_name: brainstem, 100 days of gestational life

value: 100 days of fetal age


title: Brainstem_120 days of gestational life_Replicate 1

description: Gene expression in fetal brainstem at 120 days of gestation-Replicate 1


title: Brainstem_100 days of gestational life_Replicate 4

description: Gene expression in fetal brainstem at 100 days of gestation-Replicate 4


title: Brainstem_100 days of gestational life_Replicate 1

description: Gene expression in fetal brainstem at 100 days of gestation-Replicate 1


title: Brainstem_80 days of gestational life_Replicate 4

description: Gene expression in fetal brainstem at 80 days of gestation-Replicate 4

source_name: brainstem, 80 days of gestational life

value: 80 days of fetal age


title: Brainstem_100 days of gestational life_Replicate 2

description: Gene expression in fetal brainstem at 100 days of gestation-Replicate 2


title: aorta_norethisterone_acetate_rep3

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

description:
gene expresion after 90 days of treament
11_NET-A_US45103065_251486838646_S01_GE1_1100_Jul11_1_3

hyb_protocol: After fragmentation labeled cRNA was hybridized to Agilent 4x44k Whole Mouse Genome v1 Microarrays for 17 h at 65 °C according to the manufacturers´ protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Agilent Technologies)

scan_protocol: Microarray slides were scanned as described in the manufacturers´ protocol (Scanner G2505C, Agilent Technologies).

data_processing: Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 10.7.1.1 / 11.0.1.1; Agilent Technologies) using scan protocol GE1_107_Sep09 / grid 014868_D_F_20100123 (medroxyprogesterone acetate experiments) and scan protocol GE1_1100_Jul11 / grid 014868_D_F_20130207 (norethisterone acetate experiments), respectively. Data analyses were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples

source_name: aorta, norethisterone acetate

label_protocol: Synthesis of cDNA and subsequent fluorescent labeling of cRNA was performed according to the manufacturers´ protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNA

extract_protocol: Tissue samples were pulverised, immediately transferred into 1 ml of peqGOLD TriFastTM (peqlab), incubated at room temperature for 1 hour and vortexed every 10 minutes. Extraction of RNA was then performed according to the manufacturer`s instructions. Final purification of total RNA was performed according to the RNET-Asy Mini Kit RNA cleanup protocol (Qiagen)

treatment_protocol: Female ApoE-deficient mice were ovariectomized at the age of 4 - 5 weeks and two weeks later implanted subcutaneously with pellets (Innovative Research of America) constantly releasing the respective hormone (medroxyprogesterone acetate, norethisterone acetate or placebo) for 90 days. For the time of hormone substitution mice were fed a high fat diet. After 78 - 90 days of treatment mice were sacrificed and aortas removed from behind the aortic arch curvature to approximately 1 mm before the vessel-branches to the kidney and snap-frozen in liquid nitrogen.

tag: strain

tag: genotype/variation

value: ApoE deficient

tag: gender

value: female (ovariectomized)

tag: age

value: 4-5 weeks

tag: agent

value: norethisterone acetate

value: aorta

tag: diet

value: high-fat Western-type diet


title: aorta_norethisterone_acetate_rep2

description:
gene expresion after 90 days of treament
10_NET-A_US45103065_251486838647_S01_GE1_1100_Jul11_1_4


title: Primary Tumor PCA0313

description: Prostate tumor PCA0313 (aCGH)

value: prostate

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

tag: bcr event

value: NO

tag: metsevent

value: no

tag: dxage

tag: bxggs

tag: pretxpsa

value: RP

value: Positive

tag: ece

value: FOCAL

value: Yes

tag: svi

source_name: Promega reference DNA


title: aorta_norethisterone_acetate_rep4

description:
gene expresion after 90 days of treament
12_NET-A_US45103065_251486838647_S01_GE1_1100_Jul11_1_2

tag: tissue


title: Brainstem_80 days of gestational life_Replicate 3

description: Gene expression in fetal brainstem at 80 days of gestation-Replicate 3

value: Fetal brain

tag: brain region

value: Brainstem

tag: developmental age


title: Brainstem_80 days of gestational life_Replicate 1

description: Gene expression in fetal brainstem at 80 days of gestation-Replicate 1

value: 80 days of fetal age


title: aorta_norethisterone_acetate_rep1

description:
gene expresion after 90 days of treament
7_NET-A_US45103065_251486838645_S01_GE1_1100_Jul11_1_4

tag: strain

value: ApoE deficient


title: Brainstem_80 days of gestational life_Replicate 2

description: Gene expression in fetal brainstem at 80 days of gestation-Replicate 2


title: Cortex_1 day of extrauterine life_Replicate 3

description: Gene expression in newborn cortex at 1 day of life-Replicate 3

source_name: cortex, 1 day of extrauterine life

value: Newborn brain

value: Cortex

value: 1 day of life


title: aorta_N_placebo_rep3

description:
gene expresion after 90 days of treament
8_Plac_US45103065_251486838647_S01_GE1_1100_Jul11_1_3

source_name: aorta, placebo

tag: genotype/variation

value: female (ovariectomized)

value: 4-5 weeks

value: placebo

value: aorta


title: Cortex_1 day of extrauterine life_Replicate 4

description: Gene expression in newborn cortex at 1 day of life-Replicate 4


title: Cortex_1 day of extrauterine life_Replicate 2

description: Gene expression in newborn cortex at 1 day of life-Replicate 2


title: aorta_N_placebo_rep2

description:
gene expresion after 90 days of treament
5_Plac_US45103065_251486838646_S01_GE1_1100_Jul11_1_1

tag: gender

value: high-fat Western-type diet


title: aorta_medroxyprogesterone_acetate_rep4

description:
gene expresion after 90 days of treament
AM7_US45103065_251486819714_S01_GE1_107_Sep09_1_2

source_name: aorta, medroxyprogesterone acetate

tag: age

value: medroxyprogesterone acetate


title: aorta_N_placebo_rep1

description:
gene expresion after 90 days of treament
4_Plac_US45103065_251486838645_S01_GE1_1100_Jul11_1_3

tag: agent


title: aorta_M_placebo_rep4

description:
gene expresion after 90 days of treament
AP8_US45103065_251486819714_S01_GE1_107_Sep09_1_4

tag: diet


title: aorta_N_placebo_rep4

description:
gene expresion after 90 days of treament
9_Plac_US45103065_251486838647_S01_GE1_1100_Jul11_1_1


title: M_ZR75-1A774(48h)

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description: p53 knock down

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

extract_protocol: Qiagen Rneasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Breast Cancer Cell Line

tag: treatment

value: p53 knock down

tag: cell line


title: C_RMF:ZR751(0:1,48h)_rep1

description: wild-type p53 expression

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133

value: wild-type p53 expression


title: M_ZR75-1A774(48h)_rep1

description: p53 knock down

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135


title: Primary Tumor PCA0304

description: Prostate tumor PCA0304 (aCGH)

value: prostate

tag: disease status

value: prostate cancer

tag: %cna (percent of  genome that is copy number altered)

tag: bcr event

value: NO

tag: metsevent

value: no

tag: dxage

value: RP

tag: sms

value: Negative

value: Invades Capsule

value: No

tag: lni

tag: pathstage

tag: pathggs

tag: surgtype

tag: sample type

value: Promega reference DNA

value: normal


title: M_HMECC

description: wild-type p53 expression

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

value: HMECC


title: Cortex_130 days of gestational life_Replicate 4

description: Gene expression in fetal cortex at 130 days of gestation-Replicate 4

source_name: cortex, 130 days of gestational life

tag: tissue

value: Fetal brain

tag: brain region

value: Cortex

tag: developmental age

value: 130 days of fetal age


title: M_SUM102A774

description: p53 knock down

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: C_RMF:ZR751(0:1,48h)

description: wild-type p53 expression

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

tag: treatment


title: Cortex_145 days of gestational life_Replicate 3

description: Gene expression in fetal cortex at 145 days of gestation-Replicate 3

source_name: cortex, 145 days of gestational life

value: 145 days of fetal age


title: Cortex_145 days of gestational life_Replicate 2

description: Gene expression in fetal cortex at 145 days of gestation-Replicate 2


title: M_MCF7A774

description: p53 knock down

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

value: p53 knock down

tag: cell line


title: M_SUM102(48h)

description: wild-type p53 expression

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

value: wild-type p53 expression


title: Cortex_1 day of extrauterine life_Replicate 1

description: Gene expression in newborn cortex at 1 day of life-Replicate 1

value: Newborn brain

value: 1 day of life


title: aorta_medroxyprogesterone_acetate_rep3

description:
gene expresion after 90 days of treament
AM5_US45103065_251486819714_S01_GE1_107_Sep09_1_1

tag: strain

tag: genotype/variation

value: ApoE deficient

tag: gender

value: female (ovariectomized)

tag: age

value: 4-5 weeks

tag: agent

value: medroxyprogesterone acetate

value: aorta

tag: diet

value: high-fat Western-type diet


title: Cortex_145 days of gestational life_Replicate 1

description: Gene expression in fetal cortex at 145 days of gestation-Replicate 1


title: Cortex_130 days of gestational life_Replicate 3

description: Gene expression in fetal cortex at 130 days of gestation-Replicate 3


title: Cortex_130 days of gestational life_Replicate 2

description: Gene expression in fetal cortex at 130 days of gestation-Replicate 2


title: M_MCF7(48h)_rep2

description: wild-type p53 expression

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129


title: aorta_M_placebo_rep2

description:
gene expresion after 90 days of treament
AP4_US45103065_251486819713_S01_GE1_107_Sep09_1_4

value: placebo


title: M_HMECCA774(48h)_rep1

description: p53 knock down

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

value: HMECC


title: aorta_M_placebo_rep3

description:
gene expresion after 90 days of treament
AP7_US45103065_251486819714_S01_GE1_107_Sep09_1_3


title: M_MCF7(48h)

description: wild-type p53 expression

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128


title: Cortex_145 days of gestational life_Replicate 4

description: Gene expression in fetal cortex at 145 days of gestation-Replicate 4

value: Fetal brain


title: C_RMF:SUM102(0:1,48h)_rep2

description: wild-type p53 expression

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128


title: Cortex_130 days of gestational life_Replicate 1

description: Gene expression in fetal cortex at 130 days of gestation-Replicate 1

value: Cortex


title: aorta_M_placebo_rep1

description:
gene expresion after 90 days of treament
AP3_US45103065_251486819713_S01_GE1_107_Sep09_1_3


title: M_SUM102A774_rep1

description: p53 knock down

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131


title: M_MCF7A774_rep1

description: p53 knock down

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126


title: aorta_medroxyprogesterone_acetate_rep1

description:
gene expresion after 90 days of treament
AM1_US45103065_251486819713_S01_GE1_107_Sep09_1_1


title: aorta_medroxyprogesterone_acetate_rep2

description:
gene expresion after 90 days of treament
AM2_US45103065_251486819713_S01_GE1_107_Sep09_1_2


title: App1_Ana_rep3

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

country: China

institute: Huazhong Agricultural University

description: biological replicate 3 of 3 comparing gene expressions of Actinobacillus pleuropneumoniae cultured aerobically and anaerobically

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (Agilent). After fragmentation, 300ng of Cy5 labeled cRNA and Cy3 labeled cRNA were hybridized with the same array at 65°C, 10 rpm rotation for 17 hours. Then, the arrays were washed twice using wash buffer 1 and 2 from Gene Expression Wash Buffer Kit (Agilent).

scan_protocol: Arrays were scanned using Agilent Microarray Scanner System (G2565BA) (Agilent) with resolution of 5μm. The scanner uses 100% and 10% PTM respectively and combines the two data automatically.

data_processing:
The scanned signal intensities were normalized using Feature Extraction Software (Agilent) by Linear & LOWESS method (the default method for normalizing Agilent microarrays). Then, the normalized signal intensities were transformed into log2 values. The data submitted are normalized log2 ratio (Cy5/Cy3) representing test/reference.
For further analysis, the genes with positive signals (flags = P or M) in all the three replicates were selected. The genes with P value < 0.05 (one-way class T-test) using the software TM4 were selected as differentially expressed genes to do function analysis and experimental validations.

organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074

source_name: Actinobacillus pleuropneumoniae 4074

label_protocol: 2μg RNA was reverse-transcribed into cDNA and then transcribed into cRNA. After purified, 4μg cRNA from control sample (aerobically cultured) was labeled with Cy5 NHS ester and 4μg cRNA of test sample (anaerobically cultured) was labeled with Cy3 NHS ester (GE healthcare) respectively and purified.

growth_protocol: A. pleuropneumoniae was cultured in Tryptic Soy Broth (TSB) or on Tryptic Soy Agar (TSA) (Difco Laboratories) supplemented with 10 μg/ml of nicotinamide adenine dinucleotide (NAD) and 10% (v/v) filtered cattle serum at 37°C.

extract_protocol: Total RNA was extracted using RNA-Solv Reagent (Omega) according to the manufacturer’s instructions, then purified using QIAGEN RNeasy Mini Kit (QIAGEN).

treatment_protocol: The bacteria was cultured under aerobic condition to mid-log phase (3 hours) and then divided into two separate groups, one group was continually cultured under aerobic condition for 1 hour and the other group was cultured under anaerobic condition for 1 hour.

value: reference strain of serovar 1

tag: culture condition

value: cultured in TSB medium aerobically

value: cultured in TSB medium anaerobically


title: C_HMECC:HMECCA774MMPlasmidOnly(1:0,48h)

description: wild-type p53 expression

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: M_HMECCA774(48h)

description: p53 knock down

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

value: p53 knock down


title: Cortex_120 days of gestational life_Replicate 4

description: Gene expression in fetal cortex at 120 days of gestation-Replicate 4

hyb_protocol: 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 X 15 K array slide (Agilent  019921), containing 8 arrays with 15,208 oligomers with a length of 60 bases corresponding to 15,208 ovine genetic sequences and hybridized at 65 °C for 17 h at 10 rpm.  After hybridization, the slides were washed for 1 minute at room temperature with Wash Buffer 1 (Agilent) and for 1 minute with 37 °C Wash buffer 2 (Agilent). After dry the excess of liquid, the slides were washed for 30 seconds in the stabilization and drying solution.

source_name: cortex, 120 days of gestational life

value: 120 days of fetal age


title: App1_Ana_rep2

description: biological replicate 2 of 3 comparing gene expressions of Actinobacillus pleuropneumoniae cultured aerobically and anaerobically


title: Cortex_120 days of gestational life_Replicate 3

description: Gene expression in fetal cortex at 120 days of gestation-Replicate 3


title: Cortex_120 days of gestational life_Replicate 2

description: Gene expression in fetal cortex at 120 days of gestation-Replicate 2


title: App1_Ana_rep1

description: biological replicate 1 of 3 comparing gene expressions of Actinobacillus pleuropneumoniae cultured aerobically and anaerobically


title: Cortex_100 days of gestational life_Replicate 4

description: Gene expression in fetal cortex at 100 days of gestation-Replicate 4

source_name: cortex, 100 days of gestational life

value: 100 days of fetal age


title: Cortex_120 days of gestational life_Replicate 1

description: Gene expression in fetal cortex at 120 days of gestation-Replicate 1


title: Cortex_80 days of gestational life_Replicate 4

description: Gene expression in fetal cortex at 80 days of gestation-Replicate 4

source_name: cortex, 80 days of gestational life

value: 80 days of fetal age


title: Cortex_80 days of gestational life_Replicate 3

description: Gene expression in fetal cortex at 80 days of gestation-Replicate 3


title: Cortex_100 days of gestational life_Replicate 1

description: Gene expression in fetal cortex at 100 days of gestation-Replicate 1


title: Cortex_100 days of gestational life_Replicate 2

description: Gene expression in fetal cortex at 100 days of gestation-Replicate 2


title: Cortex_100 days of gestational life_Replicate 3

description: Gene expression in fetal cortex at 100 days of gestation-Replicate 3


title: Cortex_80 days of gestational life_Replicate 2

description: Gene expression in fetal cortex at 80 days of gestation-Replicate 2


title: Cortex_80 days of gestational life_Replicate 1

description: Gene expression in fetal cortex at 80 days of gestation-Replicate 1


title: CD8_PBS_rep3

hyb_protocol: After fragmentation labelled cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturers´ protocol.

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing: Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by GeneSprings´ ExonRMA16 algorithm after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples.

label: biotin

source_name: CD8+ T cells, PBS

label_protocol: Synthesis of cDNA and subsequent biotin labeling of cRNA was performed according to the manufacturers´ protocol (WT Plus Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and biotin labelling of cDNA.

growth_protocol: Purified primary CD8+ T cells (CD8a+ T Cell Isolation Kit II) were incubated  for 6 hours at 37 °C.

extract_protocol: Total RNA was extracted according to the manufacturers´ protocol (RNeasy Mini Kit, Qiagen).

treatment_protocol: CD8+ T cells were stimulated with anti-CD3 antibody in the presence or absence of IFN-4a. Additionally, CD8+ cells were treated with IFN-4a and PBS only, respectively.

value: spleen

tag: cell type

value: CD8+ lymphocytes


title: CD8_PBS_IFN_rep3

source_name: CD8+ T cells, PBS, IFN-4a


title: CD8_PBS_rep2


title: CD8_PBS_IFN_rep1


title: CD8_antiCD3_IFN_rep3

source_name: CD8+ T cells, anti-CD3, IFN-4a


title: CD8_PBS_rep1


title: CP-CML_354

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

description: Sample 354

hyb_protocol: Array were prepared for hybridization in the capillary flow-through chamber. Samples were applied to BeadChips and incubated overnight. After hybridization, allelic specificity was conferred by enzymatic base extension. Products were subsequently fluorescently stained.

scan_protocol: Illumina  iScan System

data_processing: GenomeStudio Genotyping (GT) Module

label: Cy3 and Cy5

source_name: chronic phase chronic myeloid leukemia (CP-CML)

label_protocol: Cy3 and Cy5; according to standard protocol

extract_protocol: DNA sample were isothermally amplified. Amplified product were then fragmented by a controlled enzymatic process.

tag: disease state

value: Chronic phase

value: female

tag: imatinib dose (mg/day)

tag: sokal score

value: Int

tag: molecular response

value: peripheral blood

value: Leucocyte


title: CD8_antiCD3_rep2

source_name: CD8+ T cells, anti-CD3

tag: tissue


title: CP-CML_355

description: Sample 355

value: male


title: CD8_PBS_IFN_rep2


title: CNL01i-ipsc - P9

city: Los Angeles

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

description:
CNL01i-ipsc - P9
genomic DNA from cell lines

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: corneal

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

value: ips derived cell line

tag: sample condition

value: ips derived cell line; primary corneal; passage 9


title: CNL01i-ipsc on AM - differentiated

description:
CNL01i-ipsc on AM - differentiated
genomic DNA from cell lines

tag: individual

value: patient 14

value: ips derived cell line; patient 14; on AM


title: CP-CML_353

description: Sample 353

value: Low


title: Corneal Primary cell - parental

description:
Corneal Primary cell - parental
genomic DNA from cell lines

value: primary corneal parental cell line

value: primary corneal parental cell line;  no treatment


title: CD8_antiCD3_rep3


title: CD8_antiCD3_rep1


title: CD8_antiCD3_IFN_rep2


title: 16365_case_4hrs_unstimulated

city: London

first: Helen

middle: Alison

last: Fletcher

address: Keppel Street

department: IID

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86804.gif

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Illumina BeadStudio

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 4 hrs unstimulated.

label_protocol: not provided

extract_protocol: not provided

value: pbmc isolated from bcg vaccinated_case

tag: stimulation time and condition

value: 4 hrs unstimulated


title: 12748_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86801.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 4 hrs BCG stimulated.

value: 4 hrs BCG stimulated


title: 83i-ipsc on AM - differentiated

description:
83i-ipsc on AM - differentiated
genomic DNA from cell lines

value: patient 83

value: ips derived cell line; patient 83; on AM


title: 13572_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86677.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 12 hrs BCG stimulated.

value: 12 hrs BCG stimulated


title: 14106_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86726.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 4 hrs unstimulated.

value: pbmc isolated from bcg vaccinated_control


title: 14i-ipsc - P52

description:
14i-ipsc - P52
genomic DNA from cell lines

value: ips derived cell line; patient 14; passage 52


title: CNL01i-ipsc - P41

description:
CNL01i-ipsc - P41
genomic DNA from cell lines

value: ips derived cell line; primary corneal; passage 41


title: Fibroblast 14 - parental

description:
Fibroblast 14 - parental
genomic DNA from cell lines

value: fibroblast parental cell line

value: fibroblast parental cell line; patient 14; no treatment


title: CD8_antiCD3_IFN_rep1

value: spleen

value: CD8+ lymphocytes


title: CP-CML_351

description: Sample 351

value: Chronic phase

value: male

value: peripheral blood

value: Leucocyte


title: 14i-ipsc - P6

description:
14i-ipsc - P6
genomic DNA from cell lines

value: patient 14

value: ips derived cell line

value: ips derived cell line; patient 14; passage 6


title: 10656_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86703.gif

value: pbmc isolated from bcg vaccinated_case


title: CP-CML_350

description: Sample 350

value: female


title: CP-CML_352

description: Sample 352

value: Int


title: CP-CML_348

description: Sample 348


title: Fibroblast 83 - parental

description:
Fibroblast 83 - parental
genomic DNA from cell lines

value: patient 83

value: fibroblast parental cell line; patient 83; no treatment


title: CP-CML_347

description: Sample 347


title: CP-CML_346

description: Sample 346


title: CP-CML_349

description: Sample 349


title: CP-CML_345

description: Sample 345

value: Low


title: 19508_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86670.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 12 hrs BCG stimulated.

value: pbmc isolated from bcg vaccinated_control

value: 12 hrs BCG stimulated


title: 83i-ipsc - P39

description:
83i-ipsc - P39
genomic DNA from cell lines

value: ips derived cell line; patient 83; passage 39


title: 13468_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86715.gif

value: 4 hrs BCG stimulated


title: 17359_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86782.gif


title: 83i-ipsc - P13

description:
83i-ipsc - P13
genomic DNA from cell lines

value: ips derived cell line; patient 83; passage 13


title: CP-CML_343

description: Sample 343

value: Chronic phase

value: High


title: CP-CML_342

description: Sample 342

value: peripheral blood

value: Leucocyte


title: 16015_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86745.gif

source_name: PBMC isolated from BCG vaccinated_case. Stimulation time and condition: 12 hrs unstimulated.

value: 12 hrs unstimulated


title: Corneal primary cells on AM

description:
Corneal primary cells on AM
genomic DNA from cell lines

value: primary corneal cell line

value: primary corneal cell line; on AM


title: CP-CML_344

description: Sample 344

value: female


title: CP-CML_338

description: Sample 338

value: male

value: Int


title: CP-CML_341

description: Sample 341


title: CP-CML_339

description: Sample 339


title: 13187_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86707.gif

value: 4 hrs unstimulated


title: 20691_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86831.gif


title: 16890_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86791.gif

value: pbmc isolated from bcg vaccinated_case


title: CP-CML_335

description: Sample 335


title: CP-CML_336

description: Sample 336


title: CP-CML_337

description: Sample 337


title: CP-CML_332

description: Sample 332

value: Low


title: 13236_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86789.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 12 hrs unstimulated.

value: pbmc isolated from bcg vaccinated_control


title: 12406_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86796.gif


title: CP-CML_333

description: Sample 333


title: 14887_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86697.gif

value: 12 hrs BCG stimulated


title: CP-CML_331

description: Sample 331


title: 13301_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86699.gif


title: CP-CML_334

description: Sample 334


title: 13187_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86709.gif


title: CP-CML_328

description: Sample 328


title: K562 control cell

city: Jiangsu

first: Yun

last: Zhao

address: No. 1, Shizi Street

institute: Cyrus Tang Hematology Center, Soochow University

description:
Gene expression data from K562 normal cell
K562-NC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the  GeneChip® Scanner 3000: Affymetrix, P/N 00-00212.

data_processing: MAS  5.0 algorithm

source_name: K562 normal cell

label_protocol: IVT cRNA were prepared according to the standard Affymetrix protocol from 20 uL total RNA using 3' IVT Express Kit.

growth_protocol: K562 and Jurkat cells were cultured with RPMI-1640 media supplemented with 10% FBS at 5% CO2. The The control (shNC) and ZFX silence lentiviral vectors (shZFX#1 and shZFX#2) were used to infect K562 and Jurkat cells and the fluorescent cells were purified with a cell sorter. The control and ZFX silenced cells were cultured with same condition as their parental cells

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

treatment_protocol: QIAGEN RNeasy kit was used to extract RNA,  during  the  procedure  DNaseI  treatment  was  applied  as  well according  to  the  manufacturer’s  protocol  to  minimize  the  contamination  with  genomic DNA.

tag: cell line

value: control


title: CP-CML_329

description: Sample 329


title: 14379_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86833.gif


title: 13472_control_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86747.gif


title: CP-CML_325

description: Sample 325


title: K562 cell 2

description:
Gene expression data from K562 cell with shZFX#(1012)
K562-1012

source_name: K562 cell with shZFX#1(1012)

value: ZFX silencing using shZFX#1 (1012)


title: CP-CML_327

description: Sample 327

value: Chronic phase


title: K562 cell 1

description:
Gene expression data from K562 cell with shZFX#(381)
K562-381

source_name: K562 cell with shZFX#1(381)

value: ZFX silencing using shZFX#1 (381)


title: CP-CML_330

description: Sample 330

value: peripheral blood


title: 13228_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86809.gif

source_name: PBMC isolated from BCG vaccinated_control. Stimulation time and condition: 4 hrs BCG stimulated.

value: 4 hrs BCG stimulated


title: CP-CML_326

description: Sample 326

value: High

value: Leucocyte


title: 17039_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86764.gif

value: 12 hrs unstimulated


title: Jurkat control cell

description:
Gene expression data from Jurkat normal cell
Ferkat-NC

source_name: Jurkat normal cell

value: Jurkat


title: CP-CML_323

description: Sample 323

value: female


title: Jurkat cell 1

description:
Gene expression data from Jurkat cell with shZFX#(381)
FerKat-381

source_name: Jurkat cell with shZFX#1(381)


title: 19002_case_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86754.gif


title: CP-CML_321

description: Sample 321

value: male


title: CP-CML_322

description: Sample 322


title: Jurkat cell 2

description:
Gene expression data from Jurkat cell with shZFX#(1012)
FerKat-1012

source_name: Jurkat cell with shZFX#1(1012)


title: CP-CML_320

description: Sample 320

source_name: chronic phase chronic myeloid leukemia (CP-CML)


title: 22482_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86692.gif


title: CP-CML_324

description: Sample 324


title: CP-CML_317

description: Sample 317


title: 16365_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86807.gif


title: CP-CML_316

description: Sample 316


title: 19933_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86769.gif


title: CP-CML_315

description: Sample 315

value: Int


title: CP-CML_318

description: Sample 318


title: chHES-127-initial, biological rep3

city: changsha

first: Ge

last: Lin

state: hunan

address: xiangya road

department: Institute of Reproductive & Stem Cell Engineering

institute: Central South University

description:
127-P7
P4-P9 represents the initial passaged hESCs, P20-P52 represents the low-passaged hESCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner 3000 7G.

data_processing: The data were analyzed with Gcos1.4GeneChip Operating Software using Affymetrix default analysis settings.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

treatment_protocol: hESCs cultured in Standard human embryonic stem cell media amd RNA was isolated

value: Human embryonic stem cell line

tag: passage


title: CP-CML_319

description: Sample 319


title: chHES-127-low, biological rep3

description:
127-P27
P4-P9 represents the initial passaged hESCs, P20-P53 represents the low-passaged hESCs

growth_protocol: Standard human embryonic stem cell media


title: CP-CML_314

description: Sample 314


title: 17359_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86783.gif

value: pbmc isolated from bcg vaccinated_case


title: 17771_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86674.gif

value: pbmc isolated from bcg vaccinated_control


title: 17448_control_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86818.gif


title: CP-CML_312

description: Sample 312

value: Low


title: chHES-88-initial, biological rep3

description:
88-P4
P4-P9 represents the initial passaged hESCs, P20-P50 represents the low-passaged hESCs


title: CP-CML_313

description: Sample 313


title: CP-CML_311

description: Sample 311


title: 13468_case_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86717.gif

value: 12 hrs BCG stimulated


title: chHES-63-low, biological rep3

description:
63-P28
P4-P9 represents the initial passaged hESCs, P20-P49 represents the low-passaged hESCs


title: chHES-88-low, biological rep3

description:
88-P20
P4-P9 represents the initial passaged hESCs, P20-P51 represents the low-passaged hESCs


title: chHES-63-initial, biological rep3

description:
63-P5
P4-P9 represents the initial passaged hESCs, P20-P48 represents the low-passaged hESCs


title: 20426_control_4hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86679.gif


title: 15417_case_12hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86875.gif


title: 13187_control_12hrs_BCG_stimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86710.gif


title: CP-CML_309

description: Sample 309


title: 15417_case_4hrs_unstimulated

description:
Simple annotation: Antigen Stimulation, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs//86761.gif

value: 4 hrs unstimulated


title: chHES-35-initial, biological rep3

description:
35-P5
P4-P9 represents the initial passaged hESCs, P20-P46 represents the low-passaged hESCs


title: chHES-35-low, biological rep3

description:
35-P22
P4-P9 represents the initial passaged hESCs, P20-P47 represents the low-passaged hESCs


title: CP-CML_306

description: Sample 306

value: Chronic phase


title: CP-CML_305

description: Sample 305


title: CP-CML_304

description: Sample 304


title: CP-CML_308

description: Sample 308


title: CP-CML_307

description: Sample 307