title: PASM_1

city: Bethesda

first: Eric

last: Billings

state: MD

address: 10 Center Drive

institute: NHLBI

description: Gene expression profile of LAM Nodule from human pulmonary artery smooth muscle cell line

hyb_protocol: Following fragmentation 12 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix (HP) GeneArray Scanner G2500A.

data_processing: Microarray Suite Normalization 5.1

source_name: PASM, pulmonary-artery smooth muscle (CC-2581, Lonza) cell line

label_protocol: Arcturus RiboAMP HS Kit

growth_protocol: SmGM-2 media (Lonza)

extract_protocol: PixCell II Laser Microdissection with CapSure and PicoPure RNA collection


title: LAM_Patient_14

status: Public on Dec 31 2008

type: RNA

country: USA

description: Gene expression profile of LAM Nodule from human patient

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: Adult

tag: Tissue:LAM Nodule


title: Doxo-treated heart, biological rep3

city: Zurich

first: Michael

last: Zaugg

address: Raemistrasse 100

department: Anesthesiology

country: Switzerland

institute: Anesthesiology, University Hospital Zurich

description: Gene expression data from rat hearts perfused for 2 hours with addition of 2uM doxorubicin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Rat Genome 230 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Normalization and computation of expression values was performed using the Robust Multichip Average (RMA) algorithm.

organism: Rattus norvegicus

source_name: rat heart

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

extract_protocol: Total RNA was extracted using RNAeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Hearts from male Wistar rats (ca. 300 g) were perfused in a noncirculating Langendorff apparatus without (control; CO) or with 2  M doxorubicin (DO) during 2 hours.

tag: Wistar

tag: isolated heart, Langendorff-perfused


title: LAM_Patient_12


title: PASM_4

tag: PASM, pulmonary-artery smooth muscle (CC-2581, Lonza)


title: PASM_2


title: Control heart, biological rep2

description: Gene expression data from rat hearts perfused for 2 hours


title: LAM_Patient_11


title: PASM_6


title: Control heart, biological rep1


title: Doxo-treated heart, biological rep2


title: LAM_Patient_9


title: Control heart, biological rep4


title: Control heart, biological rep3


title: PASM_5


title: PASM_7


title: Doxo-treated heart, biological rep1


title: Melanoma_3

description: Gene expression profile of human melanoma cell line

source_name: Malme-3M, ATCC, Manassus, VA (HTB-64), human melanoma cell line

growth_protocol: DMEM, 10% FBS, ampicillin, streptomycin

tag: Male, Malme-3M, ATCC,Manassus, VA (HTB-64)


title: PASM_3


title: Melanoma_1


title: LAM_Patient_10


title: Melanoma_2


title: Melanoma_4


title: Doxo-treated heart, biological rep4


title: LAM_Patient_13


title: LAM_Patient_6


title: LAM_Patient_8


title: LAM_Patient_5


title: LAM_Patient_7


title: Human-LMD dissected breast cancer 14A

city: Sendai

first: Shuji

last: Nagasaki

state: Miyagi-ken

address: 2-1 Seiryo-machi, Aoba-ku

country: Japan

institute: Tohoku University Graduate School of Medicine

description:
Breast carcinoma were embedded in Tissue-Tek optimal cutting temperature compound(Sakura Finetechnical Co.Ltd., Tokyo, Japan) and frozen sectioned at a thickness of 8 micro mm. Approximately 5000 cells were laser transferred from the carcinoma tissue and applied to microarray analysis. Each population of the cells was estimated to be >98% homogeneous as determined by microscopic visualization of the captured cells.
Tissue estradiol concentrations were measured by liquid chromatography/electrospray tandem mass spectrometry (LC-MS/MS) analysis.

hyb_protocol: The standard protocol described in Affymetrix GeneChip expression analysis manual.

data_processing: Data processing was performed according to Affymetrix GeneChip expression analysis manual. Expression signals were extracted and normalized using MAS5.0.

source_name: human-LMD dissected breast cancer estradiol conc.:383.18pg/g

extract_protocol: Total RNA was extracted using RNeasy Mini Kit(Qiagen) according to the instruction manual

tag: Tissue:human-LMD dissected breast cancer

tag: Type:Invasive ductal carcinoma

tag: Tissue estradiol conc.:383.18pg/g


title: Human-LMD dissected breast cancer 16A

scan_protocol: The standard protocol described in Affymetrix GeneChip expression analysis manual.

source_name: human-LMD dissected breast cancer estradiol conc.:600pg/g

tag: Tissue estradiol conc.:600pg/g


title: LAM_Patient_1


title: Human-LMD dissected breast cancer 13A

source_name: human-LMD dissected breast cancer estradiol conc.:381.5pg/g

label_protocol: The standard protocol described in Affymetrix GeneChip expression analysis manual.

tag: Tissue estradiol conc.:381.5pg/g


title: Human-LMD dissected breast cancer 15A

source_name: human-LMD dissected breast cancer estradiol conc.:550pg/g

tag: Tissue estradiol conc.:550pg/g


title: Human-LMD dissected breast cancer 8A

source_name: human-LMD dissected breast cancer estradiol conc.:241.18pg/g

tag: Tissue estradiol conc.:241.18pg/g


title: EGDΔprfApPrfA /EGD glycerol Replicate 2

status: Public on Dec 01 2008

city: Würzburg

first: Regina

last: Stoll

address: Biozentrum, Am Hubland

country: Germany

institute: Lehrstuhl für Mikrobiologie

description: Biological replicate 2 of 2.

hyb_protocol: The slides were hybridized according to the manufacturers protocol (BF-BIOlabs)

scan_protocol: slides were scanned using ScanArray HT and analyzed using the Genepix Pro 6.0 software

data_processing: normalized based on the ratio of medians (Genepix Pro 6.0 software)

organism: Listeria monocytogenes

source_name: mutant strain EGDΔprfApPrfA

label_protocol: 30 µg of total RNA were primed with 9 µg Random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U SuperScript II RTase (Invitrogen), and 20 mM each dATP, dTTP, dGTP, with 16 µM dCTP, 50 nmol Cy3/Cy5-labelled dCTP

growth_protocol: bacteria were grown until OD600nm of 0.8

extract_protocol: RNA from the L. monocytogenes strains grown to an OD600 of 0.8 was extracted using the RNeasy® Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. Residual DNA was removed on a column with RNase-free DNase (QIAGEN)

treatment_protocol: L. monocytogenes strains were grown under aerobic conditions in brain heart infusion (BHI from BD Biosciences, contains 2 g dextrose/l), Luria Bertani (LB, contains 10 g/l Tryptone (Oxoid), 10 g/l NaCl, 5 g/l Bacto Yeast extract (BD Biosciences)) or a defined minimal medium (MM; MM equates MWB without any additional carbon source (Premaratne et al., 1991)) supplemented with different sugars at 37°C.

tag: Listeria monocytogenes EGD; note

value: strain EGD is distinct from EGD-e.

tag: MM with 50 mM glycerol OD600nm of 0.8

source_name: wild-type EGD strain


title: EGDΔprfApPrfA /EGD glycerol Replicate 1

description: Biological replicate 1 of 2.


title: EGDΔprfApPrfA* /EGD glycerol Replicate 2

description: Biological replicate 2 of 2.

source_name: mutant strain EGDΔprfApPrfA*


title: EGDΔprfApPrfA* /EGD glycerol Replicate 1

description: Biological replicate 1 of 2.


title: Human-LMD dissected breast cancer 7A

source_name: human-LMD dissected breast cancer estradiol conc.:40pg/g

tag: Tissue estradiol conc.:40pg/g


title: LAM_Patient_3


title: Human-LMD dissected breast cancer 11A

source_name: human-LMD dissected breast cancer estradiol conc.:325.42pg/g

tag: Tissue estradiol conc.:325.42pg/g


title: Human-LMD dissected breast cancer 12A

source_name: human-LMD dissected breast cancer estradiol conc.:358.9pg/g

tag: Tissue estradiol conc.:358.9pg/g


title: EGDΔprfApPrfA* /EGD cellobiose Replicate 1

description: Biological replicate 1 of 2.

tag: MM with 50 mM cellobiose OD600nm of 0.8


title: Human-LMD dissected breast cancer 9A

source_name: human-LMD dissected breast cancer estradiol conc.:266pg/g

tag: Tissue estradiol conc.:266pg/g


title: LAM_Patient_4

tag: Adult

tag: Tissue:LAM Nodule


title: Human-LMD dissected breast cancer 5A

source_name: human-LMD dissected breast cancer estradiol conc.:10.5pg/g

tag: Tissue estradiol conc.:10.5pg/g


title: Human-LMD dissected breast cancer 10A

source_name: human-LMD dissected breast cancer estradiol conc.:300pg/g

tag: Tissue:human-LMD dissected breast cancer

tag: Tissue estradiol conc.:300pg/g


title: Human-LMD dissected breast cancer 6A

source_name: human-LMD dissected breast cancer estradiol conc.:18.21pg/g

tag: Type:Invasive ductal carcinoma

tag: Tissue estradiol conc.:18.21pg/g


title: Human-LMD dissected breast cancer 2A

source_name: human-LMD dissected breast cancer estradiol conc.:under detection limit

tag: Tissue estradiol conc.:under detection limit


title: LAM_Patient_2


title: Human-LMD dissected breast cancer 3A

source_name: human-LMD dissected breast cancer estradiol conc.:8pg/g

tag: Tissue estradiol conc.:8pg/g


title: Human-LMD dissected breast cancer 4A

source_name: human-LMD dissected breast cancer estradiol conc.:9pg/g

tag: Tissue estradiol conc.:9pg/g


title: Human-LMD dissected breast cancer 1A


title: EGDΔprfApPrfA* /EGD cellobiose Replicate 2

description: Biological replicate 2 of 2.

tag: Listeria monocytogenes EGD; note


title: EGDΔprfApPrfA* /EGD glucose Replicate 2

description: Biological replicate 2 of 2.

tag: MM with 50 mM glucose OD600nm of 0.8


title: EGDΔprfApPrfA /EGD cellobiose Replicate 1

description: Biological replicate 1 of 2.


title: EGDΔprfApPrfA /EGD glucose Replicate 2

description: Biological replicate 2 of 2.


title: EGDΔprfApPrfA* /EGD glucose Replicate 1

description: Biological replicate 1 of 2.


title: EGDΔprfApPrfA /EGD glucose Replicate 1

description: Biological replicate 1 of 2.


title: BHI/MM Replicate 3

description: Biological replicate 3 of 3.

source_name: BHI culture

tag: OD600nm of 0.8

source_name: MM culture


title: MM/LB Replicate 2

description: Biological replicate 2 of 3.

source_name: LB culture


title: MM/LB Replicate 1

description: Biological replicate 1 of 3.


title: MM/LB Replicate 3

description: Biological replicate 3 of 3.


title: BHI/MM Replicate 1

description: Biological replicate 1 of 3.


title: BHI/LB Replicate 3

description: Biological replicate 3 of 3.


title: BHI/LB Replicate 2

description: Biological replicate 2 of 3.


title: Raji, an EBV-positive, type III Burkitt's lymphoma cell line, slide 72

city: Madison

first: Zachary

last: Pratt

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

description: The modification (label protocol) of the RNAs allows for selective amplification of RNAs with 3' hydroxyl and 5' phosphate groups.

hyb_protocol: RNAs were mixed with 1x SDS-based hybridization buffer (Genisphere, Inc.), and warmed to 70 degrees Celsius for 10 minutes.  RNAs were allowed to cool to room temperature, and then hybridized to microarray slides at 55 degrees Celsius overnight.  Slides were washed for 15 minutes in each of the following solutions pre-warmed to 55 degrees Celsius: 0.2% SDS, 2x SSC; 2x SSC; 0.2x SSC.  Slides were centrifuged to dry slides.  3DNA dendrimer (Genisphere, Inc.) was warmed to 70 degrees Celsius with 1x SDS-based hybridization buffer for 10 minutes and then allowed to cool to room temperature.  Microarray slides were hybridized with the 3DNA dendrimer, which binds the capture sequence incorporated into the RNAs during the in vitro transcription.  Microarray slides were hybridized at 42 degrees Celsius for 4 hours.  Slides were washed as after the first hybridization, but wash buffers were pre-warmed to 42 degrees Celsius.  Slides were centrifuged to dry.

scan_protocol: Slides were scanned on GenePix 4000B microarray scanner at 500 PMT, 33% laser power, 532 nm wavelength, 5 micromolar resolution.  Data image was collected in GenePix Pro 6.0.

data_processing: Background-corrected, raw-scale intensity values were obtained using GenePix Pro 6.0 (Molecular Devices) after minor manipulation to align and identify microarray probe spots.  The averages of the median intensities of quadruplicate features were normalized to the average median intensities of the small nucleolar RNAs (snoRNAs), U38B, U43, U44, and U49.

organism: human gammaherpesvirus 4

source_name: MiRNAs from Raji cell line, grown to log phase

label_protocol: For detection of miRNAs by microarray, miRNAs were amplified from total RNA isolate as previously described (47).  Briefly, miRNAs were ligated to 3’ linker (5’ AppCTG TAG GCA CCA TCA ATddC 3’, Integrated DNA Technologies) and a 5’ linker (5’ ATC GTrA rGrGrC rArCrC rUrGrA 3’, ribonucleic acids noted with an r).  The RNAs were reverse transcribed with a reverse transcription primer (5’ ATT GAT GGT GCC TAC 3’) using Superscript II (Invitrogen) and PCR amplified with forward (5’ GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG TTC TCG TGT TCC GTT TGT ACT CTA AGG TGG AAT CGT AGG CAC CTG AAA 3’) and reverse (5’ ATT GAT GGT GCC TAC AG 3’) primers.  The resulting amplicons were transcribed in vitro overnight for 12 to 16 hours using T7 Megascript (Ambion).

extract_protocol: RNA was extracted using TRIzol reagent.  MicroRNAs were precipitated with linear acrylamide.

tag: Raji is an EBV-positive, Burkitt's lymphoma cell line that exhibits a type III viral latency.  Cells were grown to log phase and then harvested for RNA isolation.


title: SavI, an EBV-positive, type I Burkitt's lymphoma cell line, slide 70

source_name: MiRNAs from SavI cell line, grown to log phase

tag: SavI is an EBV-positive, Burkitt's lymphoma cell line.  EBV in these cells exhibit a type I viral latency.  Cells were grown to log phase and then harvested for RNA isolation.


title: Recombinant Akata GFP, Burkitt's lymphoma cell line stably maintaining recombinant Akata EBV-GFP, slide 178

source_name: MiRNAs from recombinant Akata GFP cell line

tag: Akata GFP cells maintain the recombinant EBV-GFP with 500 micrograms/ml G418 selection.  Akata cells are Burkitt's lymphoma cells that have lost EBV prior to creating the recombinant cell line


title: Raji, an EBV-positive, type III Burkitt's lymphoma cell line, slide 176


title: Raji, an EBV-positive, type III Burkitt's lymphoma cell line, slide 187


title: PTLD1, an EBV-positive, post-transplant lymphoproliferative disease cell line, slide 183

source_name: MiRNAs from PTLD1 cell line, grown to log phase

tag: PTLD1 is an EBV-positive, post-transplant lymphoproliferative disease (PTLD) cell line.  The cell line is a B cell line, and exhibit a type III viral latency.  Cells were grown to log phase and harvested for RNA isolation.


title: SM-1, an EBV-positive, type I Burkitt's lymphoma cell line from an HIV-positive donor, slide 65

source_name: MiRNAs from SM-1 cell line, grown to log phase

tag: SM-1 is an EBV-positive, Burkitt's lymphoma cell line from an HIV-positive donor.  Cells exhibit a type I viral latency.  Cells were harvested during log phase growth and RNA was isolated.


title: Daudi, a type I Burkitt's lymphoma cell line, slide 189

source_name: MiRNAs from B958IID4 cell line, grown to log phase

tag: Daudi is a type I Burkitt's lymphoma cell line that spontaneously loses EBV in cell culture.  As assayed by fluorescence in situ hybridization, cells were over 80% EBV-positive at the time of harvest.  Cells were grown to log phase and then harvested for RNA isolation.


title: SM-1, an EBV-positive, type I Burkitt's lymphoma cell line from an HIV-positive donor, slide 181


title: PTLD1, an EBV-positive, post-transplant lymphoproliferative disease cell line, slide 62


title: SavI, an EBV-positive, type I Burkitt's lymphoma cell line, slide 178


title: Primary B cells, infected with B95-8 EBV, 66 hours post infection

source_name: EBV miRNAs from primary B cell infection

tag: Primary B cells were isolated from whole blood.  Cells were infected with B95-8 EBV for 4 hours, and then were harvested 66 hours post infection and RNA was isolated from the cells.


title: Primary B cells, infected with B95-8 EBV, 44 hours post infection

tag: Primary B cells were isolated from whole blood.  Cells were infected with B95-8 EBV for 4 hours, and then were harvested 44 hours post infection and RNA was isolated from the cells.


title: PTLD5, an EBV-positive, post-transplant lymphoproliferative disease cell line, slide 62

source_name: MiRNAs from PTLD5 cell line, grown to log phase

tag: PTLD5 is an EBV-positive, post-transplant lymphoproliferative disease (PTLD) cell line.  The cell line is a B cell line, and exhibit a type III viral latency.  Cells were grown to log phase and harvested for RNA isolation.


title: Primary B cells, infected with B95-8 EBV, 90 hours post infection

tag: Primary B cells were isolated from whole blood.  Cells were infected with B95-8 EBV for 4 hours, and then were harvested 90 hours post infection and RNA was isolated from the cells.


title: Primary B cells, infected with B95-8 EBV, 20 hours post infection

tag: Primary B cells were isolated from whole blood.  Cells were infected with B95-8 EBV for 4 hours, and then were harvested 20 hours post infection and RNA was isolated from the cells.


title: BHI/MM Replicate 2

description: Biological replicate 2 of 3.


title: OkuI, an EBV-positive, Wp-restricted Burkitt's lymphoma cell line, slide 177

source_name: MiRNAs from OkuI cell line, grown to log phase

tag: OkuI cells are an EBV-positive Burkitt's lymphoma cell line that is restricted to using the Wp promoter.  Cells were grown to log phase before being harvested for RNA isolation.


title: PTLD3, an EBV-positive, post-transplant lymphoproliferative disease cell line

source_name: MiRNAs from PTLD3 cell line, grown to log phase

tag: PTLD3 is an EBV-positive, post-transplant lymphoproliferative disease (PTLD) cell line.  The cell line is a B cell line, and exhibit a type III viral latency.  Cells were grown to log phase and harvested for RNA isolation.


title: OkuI, an EBV-positive, Wp-restricted Burkitt's lymphoma cell line, slide 92


title: BHI/LB Replicate 1

description: Biological replicate 1 of 3.


title: OkuI, an EBV-positive, Wp-restricted Burkitt's lymphoma cell line, slide 173


title: OkuI, an EBV-positive, Wp-restricted Burkitt's lymphoma cell line, slide 186


title: MutuIII, an EBV-positive, type III Burkitt's lymphoma cell line, slide 175

source_name: MiRNAs from MutuIII cell line, grown to log phase

tag: MutuIII is an EBV-positive, type III Burkitt's lymphoma cell line.  These cells were derived from MutuI cells.  Cells were grown to log phase and then harvested for RNA isolation.


title: MutuIII, an EBV-positive, type III Burkitt's lymphoma cell line, slide 186


title: Kem1, an EBV-positive, type I Burkitt's lymphoma cell line

source_name: MiRNAs from Kem1 cell line, grown to log phase

tag: Kem1 is an EBV-positive, type I Burkitt's lymphoma cell line.  Cells were grown to log phase prior to being harvested for RNA isolation.


title: MutuI, an EBV-positive, type I Burkitt's lymphoma cell line, slide 174

source_name: MiRNAs from MutuI cell line, grown to log phase

tag: MutuI is an EBV-positive, type I Burkitt's lymphoma cell line that spontaneously loses EBV in cell culture.  At the time of harvest, cells were over 80% EBV-positive as assayed by fluorescence in situ hybridization.  Cells were grown to log phase prior to being harvested for RNA isolation.


title: JSC-1, an EBV- and KSHV-positive primary effusion lymphoma cell line

source_name: MiRNAs from JSC-1 cell line, grown to log phase

tag: JSC-1 is an EBV- and KSHV- positive PEL.  Cells were grown to log phase prior to being harvested for RNA isolation.


title: C666-1 Nasopharyngeal carcinoma cell line, EBV-positive

source_name: MiRNAs from C666-1 cell line, grown to log phase

tag: C666-1 is a nasopharyngeal carcinoma cell line that maintains EBV without drug selection.  Cells were grown to confluency in log phase and then harvested for RNA isolation.


title: MutuIII, an EBV-positive, type III Burkitt's lymphoma cell line, slide 61


title: Daudi, an EBV-positive, Burkitt's lymphoma cell line, slide 173

source_name: MiRNAs from Daudi cell line, grown to log phase


title: Daudi, an EBV-positive, Burkitt's lymphoma cell line, slide 180


title: MutuI, an EBV-positive, type I Burkitt's lymphoma cell line, slide 61


title: GG68, an EBV-positive, type III Burkitt's lymphoma cell line, slide 174

source_name: MiRNAs from GG68 cell line, grown to log phase

tag: GG68 is a type III Burkitt's lymphoma cell line derived from P3HR-1 cells. Cells were grown to log phase prior to being harvested for RNA isolation.


title: BL-8, an EBV-positive, type I Burkitt's lymphoma cell line, slide 183

source_name: MiRNAs from BL-8 cell line, grown to log phase

tag: BL-8 is a Burkitt's lymphoma cell line from an HIV-positive donor. Cells exhibit a type I EBV latency. Cells were grown to log phase and then harvested.


title: Dante, an EBV-positive, type I Burkitt's lymphoma cell line

source_name: MiRNAs from Dante cell line, grown to log phase

tag: Dante is a type I latency Burkitt's lymphoma cell line.  Cells were grown to log phase and then harvested for RNA isolation.


title: BL-5, an EBV-positive type I Burkitt's lymphoma cell line, slide 182

source_name: MiRNAs from BL-5 cell line, grown to log phase

tag: BL-5 is a Burkitt's lymphoma cell line from an HIV-positive donor. Cells exhibit a type I EBV latency. Cells were grown to log phase and then harvested.


title: BL-8, an EBV-positive, type I Burkitt's lymphoma cell line, slide 70


title: BL-5, an EBV-positive type I Burkitt's lymphoma cell line, slide 63

tag: BL-5 is a Burkitt's lymphoma cell line from an HIV-positive donor.  Cells exhibit a type I EBV latency.  Cells were grown to log phase and then harvested.


title: EGDΔprfApPrfA /EGD cellobiose Replicate 2

description: Biological replicate 2 of 2.

source_name: mutant strain EGDΔprfApPrfA

tag: Listeria monocytogenes EGD; note

tag: MM with 50 mM cellobiose OD600nm of 0.8

source_name: wild-type EGD strain


title: Gastric Carcinoma cell line, AGS, stably maintaining recombinant Akata EBV-GFP

tag: Full length recombinant Akata EBV-GFP maintained in AGS cells with 500 micrograms/ml G418.  Cells grown to log phase.


title: B958IID4, an EBV-positive marmoset cell clone

source_name: MiRNAs from B958IID4 cell line, grown to log phase

tag: B958IID4 is a clone of a marmoset cell line that is maintained to proliferate with the B95-8 strain of EBV.  Cells were grown to log phase.


title: Akata, a type I Burkitt's lymphoma cell line maintaining EBV

source_name: MiRNAs from Akata cell line, grown to log phase

tag: Akata cells are a type I Burkitt's lymphoma cell line that spontaneously lose EBV in cell culture.  Cells were grown to log phase and harvested for RNA extraction


title: GG68, an EBV-positive, type III Burkitt's lymphoma cell line, slide 93

source_name: MiRNAs from GG68cell line, grown to log phase

tag: GG68 is a type III Burkitt's lymphoma cell line derived from P3HR-1 cells.  Cells were grown to log phase prior to being harvested for RNA isolation.


title: EBV-positive lymphoblastoid cell line 721, slide 66

source_name: 721 cells, grown to log phase

label_protocol: For detection of miRNAs by microarray, miRNAs were amplified from total RNA isolate as previously described (47).  Briefly, miRNAs were ligated to 3’ linker (5’ AppCTg TAg gCA CCA TCA ATddC 3’, Integrated DNA Technologies) and a 5’ linker (5’ ATC gTrA rgrgrC rArCrC rUrgrA 3’, ribonucleic acids noted with an r).  The RNAs were reverse transcribed with a reverse transcription primer (5’ ATT gAT ggT gCC TAC 3’) using Superscript II (Invitrogen) and PCR amplified with forward (5’ ggC CAg TgA ATT gTA ATA CgA CTC ACT ATA ggg TTC TCg TgT TCC gTT TgT ACT CTA Agg Tgg AAT CgT Agg CAC CTg AAA 3’) and reverse (5’ ATT gAT ggT gCC TAC Ag 3’) primers.  The resulting amplicons were transcribed in vitro overnight for 12 to 16 hours using T7 Megascript (Ambion).  For detection of miRNAs by microarray, miRNAs were amplified from total RNA isolate as previously described (47).  Briefly, miRNAs were ligated to 3’ linker (5’ AppCTG TAG GCA CCA TCA ATddC 3’, Integrated DNA Technologies) and a 5’ linker (5’ ATC GTrA rGrGrC rArCrC rUrGrA 3’, ribonucleic acids noted with an r).  The RNAs were reverse transcribed with a reverse transcription primer (5’ ATT GAT GGT GCC TAC 3’) using Superscript II (Invitrogen) and PCR amplified with forward (5’ GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG TTC TCG TGT TCC GTT TGT ACT CTA AGG TGG AAT CGT AGG CAC CTG AAA 3’) and reverse (5’ ATT GAT GGT GCC TAC AG 3’) primers.  The resulting amplicons were transcribed in vitro overnight for 12 to 16 hours using T7 Megascript (Ambion).

extract_protocol: Total RNA extracted using TRIzol reagent.  MicroRNAs were precipitated using linear acrylamide

tag: Lymphoblastoid cell line (LCL) maintained to proliferate with B95-8 strain of Epstein-Barr Virus.  Grown to log phase


title: EBV-positive lymphoblastoid cell line 721, slide 181

source_name: Epstein-Barr Virus lymphoblastoid cell line

extract_protocol: Total RNA extracted using TRIzol reagent.  MicroRNAs were precipitated using linear acrylamide.

tag: Lymphoblastoid (B cell) cell line maintained to proliferate with B95-8 strain of EBV.


title: Recombinant Akata GFP, Burkitt's lymphoma cell line stably maintaining recombinant Akata EBV-GFP, miRNA expression

source_name: EBV miRNA from Akata GFP, grown to log phase

tag: Akata GFP cells maintain the recombinant EBV-GFP with 500 micrograms/ml G418 selection.  Akata cells are Burkitt's lymphoma cells that have lost EBV prior to creating the recombinant cell line


title: EBV-positive lymphoblastoid cell line 721, slide 171


title: Daudi, an EBV-positive, Burkitt's lymphoma cell line, slide 102

tag: Daudi is a type I Burkitt's lymphoma cell line that spontaneously loses EBV in cell culture.  As assayed by fluorescence in situ hybridization, cells were over 80% EBV-positive at the time of harvest.  Cells were grown to log phase and then harvested for RNA isolation.


title: EBV-positive lymphoblastoid cell line 721, slide 189


title: EGD/EGD-e Replicate 3

description: Biological replicate 3 of 3.

source_name: EGD

tag: OD600nm of 0.8

organism: Listeria monocytogenes EGD-e

source_name: EGD-e


title: EGD/EGD-e Replicate 2

description: Biological replicate 2 of 3.


title: PTLD5, an EBV-positive, post-transplant lymphoproliferative disease cell line, slide 185

source_name: MiRNAs from PTLD5 cell line, grown to log phase

tag: PTLD5 is an EBV-positive, post-transplant lymphoproliferative disease (PTLD) cell line.  The cell line is a B cell line, and exhibit a type III viral latency.  Cells were grown to log phase and harvested for RNA isolation.


title: EGD/EGD-e Replicate 1

description: Biological replicate 1 of 3.


title: CTRL_3_CMP

city: Düsseldorf

first: Ingmar

last: Bruns

state: NRW

address: Moorenstr. 5

department: Hematology, Oncology and Clinical Immunology

institute: University of Düsseldorf

description: (CTRL) Healthy donor / Common Myeloid Progenitors

hyb_protocol: According to manufacturers instructions

scan_protocol: According to manufacturers instructions

data_processing: MAS 5.0, Scaling Factor 500

label: Biotin

source_name: Bone Marrow

label_protocol:
GeneChip Expression 3’-Amplification One-Cycle-Target Labeling & Control Reagents
(Affymetrix; 900493)

extract_protocol: Qiagen RNeasy micro kit (Qiagen; 74004)

tag: Common Myeloid Progenitors


title: CTRL_4_MEP

description: (CTRL) Healthy donor / Megacaryocyte-Erythrocyte Progenitors

tag: Megacaryocyte-Erythrocyte Progenitors


title: CTRL_5_CMP


title: CTRL_5_HSC

description: (CTRL) Healthy donor / Hematopoietic Stem Cells

tag: Hematopoietic Stem Cells


title: CTRL_2_MEP


title: CTRL_3_HSC


title: CTRL_5_GMP

description: (CTRL) Healthy donor / Granulocyte-Macrophage Progenitors

tag: Granulocyte-Macrophage Progenitors


title: CTRL_4_GMP


title: CTRL_2_CMP


title: CTRL_2_GMP


title: CTRL_5_MEP


title: CTRL_2_HSC


title: CTRL_1_MEP


title: CTRL_3_GMP


title: CTRL_1_GMP


title: CTRL_4_HSC


title: CTRL_1_CMP


title: PET counts from whole adult fish

city: Singapore

first: Chia

middle: Lin

last: Wei

address: 60 Biopolis Street, #02-01, Genome

country: Singapore

institute: Genome Institute Of Singapore

description: Paired End DiTags (PET) library, SDR001_177373U_29082006_nr2_v1.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Tag counts

label: not applicable

organism: Danio rerio

source_name: Whole Adult Fish

label_protocol: not applicable

tag: Strain

value: Tubingen

tag: Organ/Tissue

value: Whole Adult Fish

tag: Stage

value: 3-4 months old adult fish

tag: Sex

value: Males & Females Mixed


title: CTRL_1_HSC


title: 32 morulae from 2 female rabbits at 58Hpc after in vivo development 17MIV3Bis.p/5C2

city: JOUY EN JOSAS

first: Duranthon

last: Veronique

address: Domaine de Vilvert

department: Biologie du Développement et Reproduction

country: France

institute: INRA

description: Hybridization of labeled PCR products

hyb_protocol: Prehybridization of the nylon micro-arrays were performed in 12 ml glass tubes with 1 ml ExpressHyb Hybridization Solution (Clontech) at 68 °C during 44 hours. The all purified labelled target (50 microl) were added to the prehybridization solution and allowed to hybridyse for 24 hours at 68 °C. Washing were performed 4 times in 2X SSC, 1% SDS and once in 0.1X SSC, 0.5% SDS at 68 °C for 30 min each.

scan_protocol: Scanner:BAS-5000 Fuji - Feature extraction software: AGScan

data_processing: The initial values of the hybridised signals were obtained after image acquisition using the AGScan software. Signals from negative and positive controls on the array were then zero. Decimal log values were calculated, then normalized by the mean signal value on the array without taking into account the zero values. Transformed values from negative and positive controls on the array were then zero and then all values were normalized by standard deviation.

organism: Oryctolagus cuniculus

source_name: 32 morulae coming from 2 female rabbits picked at 58Hpc after in vivo development

label_protocol: Five hundred cDNA from PCR products were labeled with [alpha-33P] dATP (Perkin Elmer) using the Atlas SMART Probe Amplification Kit (Clontech) according to manufacturuer's instruction.cDNA labelled probes were then purified on G-50 Sephadex columns.

extract_protocol: Total RNAs were extracted from batches of embryos using the Rneasy Mini Kit (Qiagen, CA, USA) according to manufacturer's instructions. Purification procedure include a DNase I treatment (37°C, 30 min). A PCR amplification method was carried out as described by Pacheco-Trigon et al. (2002) from an aliquot of the total extract equivalent to the desired number of embryos. Briefly, total RNAs were incubated with 0,087microl diluted Tc-primer (7,35microg/ml), 0,2microl 1 mM dNTPs, 0,25microl 10% NP40, 0,25microl 0.1M DTT, 0,93microl first-strand buffer 5X, 10U RNAse inhibitor (Roche) at 65°C for 2 min, at room temperature for 3 min then cooled on ice. cDNAs were synthesised by the addition of 100U Superscript II (Invitrogen) and 1.2U AMV (Invitrogen) and incubation at 42°C for 30 min. First-strand cDNA wer poly(dG)-tailed by incubation with 0.4microl 20mM dGTP, 2microl TdT buffer 5X, 1.6 microl water and 1microl TDT enzyme (Promega) at 37°C for 1 hour. The totality of reverse transcription - tailing product(10microl) was subjected for further two rounds of PCR amplification. PCR were performed in a total volume of 50 microl using 15 units of Goldstar DNA polymerase (Eurogentec) for each round of PCR cycles. Samples were incubated at 94°C for 10 min before two rounds of PCR (18 and 18 for the first and second PCR): 94°C for 2 min; 63°C for 50 sec and 72°C for 6 min. PCR products were purified using the QIAquick PCR Purification Kit and then used for labelling.

tag: Embryo stage

value: Early morula


title: 34 morulae from 2 female rabbits at 58Hpc after in vivo development 17MIV1.p3/6D2

description: Hybridization of labeled PCR products

source_name: 34 morulae coming from 2 female rabbits picked at 58Hpc after in vivo development


title: 35 morulae from 2 female rabbits at 58Hpc after in vivo development 17MIV2ter.p2/4G2

description: Hybridization of labeled PCR products

source_name: 35 morulae coming from 2 female rabbits picked at 58Hpc after in vivo development


title: PET counts from adult gut/internal organs

description: Paired End DiTags (PET) library, DDR001_454S_350764U_31072006_nr2_v1.

source_name: Adult Gut/Internal Organs

value: Adult Gut/Internal Organs


title: PET counts from embryos

description: Paired End DiTags (PET) library, DDR002_454S_408213U_02082006_nr2_v1

source_name: Embryos

value: Embryos

value: 0-72 hours post fertilisation embryos


title: 53 4-cells embryos from 3 female rabbits at H32 pc after in vivo development 26QIV1P3/4C2

description: Hybridization of labeled PCR products

source_name: 53 4-cells embryos coming from 3 female rabbits picked at H32 pc after in vivo development

value: Four cells embryo


title: 52 4-cells embryos from 4 female rabbits at H32 pc after in vivo development 26QIV2Quatrop/5F2

description: Hybridization of labeled PCR products

source_name: 52 4-cells embryos coming from 4 female rabbits picked at H32 pc after in vivo development


title: CML_7_HSC

description: (CML) chronic myeloid leukaemia / Hematopoietic Stem Cells


title: Pool of embryos from 2 females at H32 26QIV3.p2/6H2

description: Hybridization of labeled PCR products


title: CML_6_MEP

description: (CML) chronic myeloid leukaemia / Megacaryocyte-Erythrocyte Progenitors


title: 32 morulae from 2 female rabbits at 58Hpc after in vivo development 17MIV3Bis.a/5C1

description: Hybridization of labeled antisens RNA products

hyb_protocol: Prehybridization of the nylon micro-arrays were performed in 12 ml glass tubes with 1 ml ExpressHyb Hybridization Solution (Clontech) at 68 °C during 44 hours. The all purified labelled target (50 µl) were added to the prehybridization solution and allowed to hybridyse for 24 hours at 68 °C. Washing were performed 4 times in 2X SSC, 1% SDS and once in 0.1X SSC, 0.5% SDS at 68 °C for 30 min each.

label_protocol: One µg aRNA was mixed with 1µg of random hexamers (Promega) in a volume of 50 µl then incubated at 70°C for 10 min. cDNA was synthesised by the addition of 20 µl first-strand buffer 5X, 10µl 0.1M DTT, 5µl 10 mM dNTPs (-dATP), 10µl [~-33P] dATP (Perkin Elmer), 400U Superscript II (Invitrogen) and incubation at 25°C 10 min, 42°C 50 min, 70°C 15 min. The RNA template was removed by the addition of 2 µl RNAse H and incubation at 37°C for 20min. aRNA labelled probes were then purified on G-50 Sephadex columns.

extract_protocol: Total RNAs were extracted from batches of embryos using the Rneasy Mini Kit (Qiagen, CA, USA). Purification procedure include a DNase I treatment (37°C, 30 min). In vitro transcription was carried out from an aliquot of the total extract equivalent to the desired number of embryos, using the MessageAmp aRNA Kit (Ambion) according to manufacturer's instructions.


title: CML_7_GMP

description: (CML) chronic myeloid leukaemia / Granulocyte-Macrophage Progenitors


title: CML_7_CMP

description: (CML) chronic myeloid leukaemia / Common Myeloid Progenitors


title: 37 in vivo developed blastocysts at H90 pc from 4 female rabbits 8BIV2.p6/6C2

description: Hybridization of labeled PCR products

source_name: 37 in vivo developped Blastocysts at H90 pc coming from 4 female rabbits

value: Expanded blastocyst


title: 35 morulae from 2 female rabbits at 58Hpc after in vivo development 17MIV2ter.a2/4G1


title: 16 in vivo developed blastocysts at H96 pc from 2 female rabbits 8Biv1.p3/5G2

description: Hybridization of labeled PCR products

source_name: 16 in vivo developped Blastocysts at H96 pc coming from 2 female rabbits


title: 34 morulae from 2 female rabbits at 58Hpc after in vivo development 17MIV1.a3/6D1


title: 60 in vivo developed blastocysts at H90 pc from 7 female rabbits 8BIV3.p2/4F2

description: Hybridization of labeled PCR products

source_name: 60 in vivo developped Blastocysts at H90 pc coming from 7 female rabbits


title: CML_6_CMP


title: CML_6_HSC


title: CML_5_MEP


title: CML_6_GMP


title: PET counts from adult brain

description: Paired End DiTags (PET) library, DDR003_454S_411102U_01082006_nr2_v1.

source_name: Adult Brain

value: Adult Brain


title: CML_5_GMP


title: CML_5_CMP


title: 53 4-cells embryos from 3 female rabbits at H32 pc after in vivo development 26QIV1a3/4C1


title: CML_5_HSC


title: 52 4-cells embryos from 4 female rabbits at H32 pc after in vivo development 26QIV2Quatroa/5F1


title: CTRL_4_CMP


title: Pool of embryos from 2 females at  H32 26QIV3.a2/6H1


title: 37 in vivo developed blastocysts at H90 pc from 4 female rabbits 8BIV2.a3/6C1


title: 60 in vivo developed blastocysts at H90 pc from 7 female rabbits 8BIV3.a2/4F1


title: CML_4_MEP


title: 16 in vivo developed blastocysts at H96 pc from 2 female rabbits 8BIV1.a3/5G1


title: PET counts from adult ovary

description: Paired End DiTags (PET) library, SDR003_346935U_27092006_nr2_v1

source_name: Adult Ovary

value: Adult Ovary

value: 3-4 months old adult females

value: Females Only


title: CML_4_CMP


title: CML_4_GMP


title: CML_3_HSC


title: CTRL_3_MEP


title: HD-NSTb vs Reference

city: MADRID

first: Luis

last: LOMBARDIA

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Molecualr Pathology Programme

country: Spain

institute: CNIO (Spanish National Cancer Center)

description: For this study, we used Agilent 44K 60-mer oligo microarray slides (Agilent Technologies), each with more than 41,000 unique human genes and transcripts represented, all with public domain annotations.

hyb_protocol: All procedures of hybridization, slide and image processing were carried out according to the manufacturer’s instructions (Two-Color Microarray-Based Gene Expression Analysis protocol). In each experiment, 825 ng of contrasting cRNA samples were fragmented at 60°C for 30 min and hybridized at 65ºC for 17hr.

scan_protocol: The slides were scanned at a resolution of 10 µm with Agilent G2565BA Microarray Scanner (Agilent Technologies).

data_processing: Signal quantification and data normalization were carried out with Feature Extraction 9.1 software (Agilent Technologies) by using default analysis parameters for 44K gene expression arrays (feature extraction protocol GE2-v4_91_2). Data of probes replicates in the array was averaged and merged.

source_name: Reference

label_protocol: RNA amplification and labelling was carried out by using the Low RNA Input Linear Amplification Kit, PLUS, Two-Color (Agilent Technologies). Briefly, for each sample 2 µg of total RNA input were amplified in two rounds of amplification by following manufacturer’s instructions. The first strand cDNA syntheses and amplification reactions were carried out by using random and T7 primers, respectively. During the 2hr in vitro transcription, Cy3- or Cy5-labeled CTP was incorporated in each amplified RNA (cRNA) from Reference and pooled samples respectively. Products of the reaction were then purified using RNAeasy mini spin column (Qiagen, Dusseldorf, Germany).

extract_protocol: Total RNA was extracted from isolated lymphocytes samples using the RNeasy Mini Kit (Quiagen Inc., Hilden, Germany). Following extraction, RNA was treated with RNase free DNase (Ambion Inc, Austin, TX). Quality of the RNA was determined with a 2100 Bioanalyzer (Agilent Technologies, Carlsbad, CA) and RNA amount was established by using a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE).

tag: Pool of equal amounts of RNA from the 9 samples of the normal group (Blood samples from healthy donors).

source_name: HD-NSTb

tag: Pool of equal amounts of total RNAs from 3 different patients with Hodgkin´s Disease who did not develop a second neoplasia.


title: CML_3_MEP


title: CML_3_CMP


title: CML_2_GMP


title: CML_2_CMP


title: HD-STb vs Reference

source_name: HD-STb

tag: Pool of equal amounts of total RNAs from 3 different patients with Hodgkin´s disease who developed a second tumor.


title: HD-NSTa vs Reference

source_name: HD-NSTa


title: CML_3_GMP

source_name: Bone Marrow


title: CML_2_MEP


title: CML_4_HSC


title: CML_2_HSC


title: Normal Nc vs Reference

source_name: Reference sample

source_name: Nc

tag: Pool of equal amounts of total RNAs from 3 different ealthy individuals.


title: CML_1_MEP


title: HD-STc vs Reference

source_name: HD-STc


title: HD-STa vs Reference

source_name: HD-STa


title: Isolate 8 Versus Reference Strain

status: Public on Nov 07 2008

type: other

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

description: comparison of clinical isolate #8 with reference strain

hyb_protocol: Agilent standard protocol 17H at 60 degrees C; Agilent proprietary Buffers

scan_protocol: Agilent scanner, 100% PMT. Images were quantified using Agilent Feature Extraction 9 Software.

data_processing: Lowess on Background subtracted value

molecule: other

organism: Rickettsia conorii str. Malish 7

source_name: Control Strain

label_protocol: Twenty nanograms of cDNA were amplified using the GenomiPhi DNA amplication kit (Amersham Biosciences, Uppsala, Sweden) and labeled with Cy3-dCTP or Cy5-dCTP dyes (Amersham Biosciences) using the BioPrime DNA labeling System (Invitrogen, Cergy-Pontoise, France). Following purification with GFX columns (Amersham Biosciences), the levels of Cy3-dCTP and Cy5-dCTP incorporation were quantified by absorbance measurement at 550 nm and 650 nm, respectively. Hybridizations were performed for 17 h at 60°C in dedicated microchambers with 75 pmol of both control or eschar samples. Stringent washings were then performed according to manufacturer’s instructions.

growth_protocol: R. conorii strain Malish 7 (ATCC, VR613) were grown in Vero cells for 48h at 32°C

extract_protocol: Total RNA extraction and purification from the eschar biopsies was carried out using the RNeasy kit (Qiagen) with some modifications. Briefly, the tissue samples removed from RNAlater were rapidly decontaminated with iodated alcohol. After 2 washings in RNase-free water, 20 mg of tissue were homogenized in RLT solution with tugsten beads and using the Mixer Mill MM300 (Qiagen). The resulting homogenate was then incubated at 55°C for 10 min with proteinase K (200 µg/ml) and centrifuged for 3 min at 10,000 x g. Supernatant containing the total RNA fraction was supplemented with ethanol and purified onto RNeasy columns according to the manufacturer’s instructions. The amount and quality of obtained RNA were determined with the microfluidic-based platform (Agilent 2100 Bioanalyzer) and using the RNA 6000 Nano Labchip kit (Agilent). Estimated amount of total RNA extracted from 20 mg eschar was around 10 µg, including 90% of eukaryotic RNAs. These contaminants were removed using the MICROBEnrich procedure (Ambion, Applied Biosystems, Courtaboeuf, France), and prokaryotic cDNA was synthesized as described by Francois et al. ( 2007)  using the M-MLV Reverse Transcriptase (Invitrogen, Cergy-Pontoise, France).

tag: Rickettsia conorii str. Malish 7

organism: Rickettsia conorii

source_name: Test Strain

tag: Rickettsia conorii clinical isolate from patient eschar


title: Normal Nb  vs Reference

source_name: Nb


title: Isolate 9 Versus Reference Strain

description: comparison of clinical isolate #9 with reference strain


title: Isolate 7 Versus Reference Strain

description: comparison of clinical isolate #7 with reference strain


title: CML_1_GMP


title: Isolate 6 Versus Reference Strain

description: comparison of clinical isolate #6 with reference strain


title: Isolate 4 Versus Reference Strain

description: comparison of clinical isolate #4 with reference strain


title: Normal Na vs Reference

growth_protocol: RNA amplification and labelling was carried out by using the Low RNA Input Linear Amplification Kit, PLUS, Two-Color (Agilent Technologies). Briefly, for each sample 2 µg of total RNA input were amplified in two rounds of amplification by following manufacturer’s instructions. The first strand cDNA syntheses and amplification reactions were carried out by using random and T7 primers, respectively. During the 2hr in vitro transcription, Cy3- or Cy5-labeled CTP was incorporated in each amplified RNA (cRNA) from Reference and pooled samples respectively. Products of the reaction were then purified using RNAeasy mini spin column (Qiagen, Dusseldorf, Germany).


title: CML_1_HSC


title: Isolate 2 Versus Reference Strain

description: comparison of clinical isolate #2 with reference strain


title: Isolate 3 Versus Reference Strain

description: comparison of clinical isolate #3 with reference strain


title: Decedent 1 HA

status: Public on Nov 01 2008

city: Mukilteo

middle: Joseph

last: Lodes

state: WA

address: 6500 Harbour Heights Pkwy, Suite 303

department: Assay Development

institute: CombiMatrix Corp

description: Nasopharyngeal swabs were submitted to the laboratory in viral transport media for immediate culture. Influenza was identified by DFA testing and the H group subtyped by a haemagglutination assay with antisera provided by the CDC. Total nucleic acid was extracted from the viral transport media and the presence of influenza A RNA was confirmed and the H group typed by real time RT-PCR

hyb_protocol: CombiMatrix 12K ECD microarrays, design 5200, were prehybridized for 10 min at 45C and hybridized for 1 hr at 45C with sample in 2x hybridization buffer (CombiMatrix).  Arrays were washed 1x with 3xSSPE with Tween 20, 2x with 2xPBS with Tween 20 and then blocked with 5x PBS/Casein (BioFX) for 5 min at RT. Arrays were labeled with Streptavidin-HRP (Sigma) for 30 min at RT and then washed 2x with 2x PBST, 2x with pH4 buffer (BioFX), and 1x with TMB substrate (BioFX).  TMB was added to the array which was scanned with CombiMatrix' ElectraSense scanner and data were analyzed with CombiMatrix Influenza analysis software.

scan_protocol: Arrays were scanned with CombiMatrix' ElectraSense scanner

data_processing: The raw probe signal intensity data for each subtype and each subgroup were averaged to make a subtype and subgroup call (CombiMatrix Influenza Analysis software)

organism: Influenza A virus

source_name: Influenza A H1

label_protocol: Two ul of total RNA was reverse-transcribed and amplified using Invitrogen's One Tube RT PCR kit with Platinum Taq and SuperScript III in the presence of biotin-14-dCTP (Invitrogen) And CombiMatrix' Influenza A primer sets (pool 1(H1+H3) and pool 2(NA))

extract_protocol: Nasopharyngeal swabs were submitted to the laboratory in viral transport media and total nucleic acid was extracted from the viral transport media with Qiagen RNeasy columns following manufacturers protocol

tag: County 1 M 0

tag: Human isolate

tag: Nasopharyngeal swab


title: Patient 18

source_name: Influenza A H1N1

tag: County 1 M-2


title: Decedent 2 HA


title: Isolate 1 Versus Reference Strain

description: comparison of clinical isolate #1 with reference strain


title: Reference 2

description: Total RNA extracted from viral cultures

tag: Human reference

tag: Culture


title: Patient 17


title: Patient 20

tag: County 1 M+2


title: Patient 15


title: Patient 16


title: Decedent 2 NA

source_name: Influenza A N1


title: Reference 1

description: Total RNA extracted from viral cultures

tag: Avian reference

tag: Avian isolate


title: Patient 19

tag: County 1 M+1


title: Patient 21

tag: County 1 M-1


title: Patient 14


title: Patient 12


title: Patient 13


title: Patient 9


title: Patient 11


title: Patient 8

tag: County 8 M-0


title: Patient 10


title: Patient 4

tag: County 4 M-2


title: Patient 7

tag: County 7 M-0


title: Patient 5

tag: County 5 M-1


title: Patient 6

tag: County 6 M-1


title: Patient 1

tag: County 1 M-6


title: Patient 3

tag: County 3 M-2


title: Myc N262 in HL60s Replicate 4 (Agilent-014706)

type: genomic

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: Biological replicate 4 of 5. Growing HL60 cells chipped with Myc N262 antibody

scan_protocol: A total of 4 ug of WGA-amplified DNA was sent for labeling to the UHN microarray center (Toronto, Canada) and was labeld and hybridized to Agilent 2x244 promoter arrays according to Manufacturer's protocols. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Microarray data was scanned using the Agilent Feature Extraction Software (v9.5) and then loaded into the R statistical environment (v2.6.2) using the limma package (v2.12.0). Array data was pre-processed using variance-stabilizing normalization, as above, with 1000 iterations to generate highly robust results on these large arrays. Pre-processing employed the vsn package (v3.2.1) again in the R statistical environment. The raw and pre-processed data were subjected to a series of quality-control measures: all arrays were included in subsequent analyses. Significance-testing employed t-tests to compare the antibody and control channels, followed by an Empirical Baye’s moderation of standard error and a false-discovery rate adjustment for multiple-testing.

molecule: genomic DNA

source_name: DNA chipped using a polyclonal antibody directed against the N-terminal 262 residues of Myc

growth_protocol: HL60 (ATCC) cells were maintained in alpha-MEM with 10% FBS.

extract_protocol: Exponentially growing HL60 cells were cross-linked with 1% formaldehyde for 10 minutes at 37 °C. The crosslinking reaction was quenched by addition of glycine to a final concentration of 0.125 M for 5 minutes, followed by two washes with phosphatebuffered saline (PBS). Cells were resuspended in cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% [v/v] NP40, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then pelleted (5000 rpm, 5 minutes, 4 °C). The pellet was resuspended in 1 mL of nuclei lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice.  The sample was then sonicated using 11 pulses (setting high, 26 seconds per pulse, 26 seconds on ice between pulses) from a Model Diagenode BioRuptor Sonicator (Diagenode, BioRuptor 200, UCD-200 TM-EX) to generate fragments between 500 bp and 1000 bp. Lysates were centrifuged for 10 minutes at 21,000 x g at 4 °C. Supernatants were diluted into an equal volume with IP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2mN EDTA, 16.7mM Tris-HCl pH 8.1, 0.2% Sarkosyl, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) and precleared for 30 minutes at 4 °C with protein G-PLUS agarose beads (Santa Cruz Biotechnology sc-2002). Prior to use, G-PLUS agarose beads were blocked with salmonsperm DNA at a final concentration of 50 μg/mL and rotated overnight at 4 °C. Diluted and cleared extracts corresponding to 10 x 106 HL60 cells were incubated and rotated at 4°C for approximately 12 to 16 hours with each of the following antibodies: no-antibody control, 0.7 μg normal rabbit IgG (Santa Cruz Biotechnology sc-2027), 0.7 μg N262 (Santa Cruz Biotechnology sc-764), for the N262 home-made unpurified and purified antibodies, we determined empirically, by serial dilutions, the amount of antibody to be used. 50 μL of salmon sperm DNA pre-blocked Protein G-PLUS agarose beads were added to each sample, incubated on a rotating platform at 4 °C for 3 hours. Each pellet was washed once with 1.4 mL of sonication buffer and then twice with 1.4 mL of high salt buffer (0.1% [v/v] SDS, 1% [v/v] Triton X-100, 1 mM EDTA, 50 mM HEPES, 500 mM NaCl, 0.1% [w/v] sodium deoxycholate) and then once with 1.4 mL LiCl Buffer (250 mM LiCl, 1% [v/v] NP-40, 1% [w/v] sodium deoxycholate, 1 mM EDTA, 1 mM Tris pH 8) and finally twice with 1.4 mL TE pH 8 (10 mM Tris pH8, 1 mM EDTA). For each wash, the pellets were mixed for 5 minutes at room temperature then pelleted (3000 rpm, 30 seconds, room temperature). After the last wash, the pellets were eluted in 300 μL of Elution buffer (1% [w/v] SDS, 10 mM Tris pH 8, 5 mM EDTA), incubated at 65 °C for 15 minutes, and then pelleted (3000 rpm, 3 minutes, room temperature). Crosslinks were reversed in the presence of 200 mM NaCl at 65 °C over-night and samples were treated with RNase A (Sigma R5500). After ethanol precipitation, the samples were resuspended in 100 μL of TE (10 mM Tris, pH 7.5, 1 mM EDTA), 25 μL of 5x proteinase K buffer (1.25% SDS, 50 mM Tris, pH 7.5, 25 mM EDTA), and 1.5 μL of proteinase K (Roche 1413783) and incubated at 42 °C for 2 hours. DNA was extracted from each sample using phenol:chloroform:isoamyl alcohol (25:24:1), then precipitated with 1/10th volume of 3 M sodium acetate (pH 5.3), 5 μg of glycogen, and 2 volumes of ethanol at -20 °C overnight. Pellets were collected by microcentrifugation and resuspended in 60 μL of H2O.

treatment_protocol: No treatment

tag: Cell Line

tag: Antibody

value: Myc

source_name: DNA chipped using a non-specific IgG antibody

value: IgG


title: Myc N262 in HL60s Replicate 3 (Agilent-014707)

description: Biological replicate 3 of 5. Growing HL60 cells chipped with Myc N262 antibody

hyb_protocol: A total of 4 ug of WGA-amplified DNA was sent for labeling to the UHN microarray center (Toronto, Canada) and was labeld and hybridized to Agilent 2x244 promoter arrays according to Manufacturer's protocols.


title: Myc N262 in HL60s Replicate 3 (Agilent-014706)

label_protocol: A total of 4 ug of WGA-amplified DNA was sent for labeling to the UHN microarray center (Toronto, Canada) and was labeld and hybridized to Agilent 2x244 promoter arrays according to Manufacturer's protocols.


title: Myc N262 in HL60s Replicate 2 (Agilent-014706)

description: Biological replicate 2 of 5. Growing HL60 cells chipped with Myc N262 antibody


title: Patient 2

tag: County 2 M-2

tag: Human isolate

tag: Nasopharyngeal swab


title: Myc N262 in HL60s Replicate 2 (Agilent-014707)


title: Myc N262 in HL60s Replicate 4 (Agilent-014707)


title: Myc N262 in HL60s Replicate 1 (Agilent-014707)

description: Biological replicate 1 of 5. Growing HL60 cells chipped with Myc N262 antibody


title: Myc N262 in HL60s Replicate 1 (Agilent-014706)


title: Myc N262 in HL60s Replicate 5 (Agilent-014706)

description: Biological replicate 5 of 5. Growing HL60 cells chipped with Myc N262 antibody


title: Myc N262 in HL60s Replicate 5 (Agilent-014707)


title: liver-AHRWT-cornoil-rep5

description: mouse liver, AHR wildtype, cornoil treated, 19 hours

hyb_protocol: Manufacturer's protocol

scan_protocol: Manufacturer's protocol

data_processing: Array data were loaded into the R statistical package (version 2.0.0) using the affy package (version 1.5.8; http://www.bioconductor.org) (Gautier et al., 2004) of the BioConductor open-source project (Gentleman et al., 2004). Data were investigated for spatial and distributional homogeneity, then preprocessed with a sequence-specific version of the RMA algorithm (Irizarry et al., 2003) termed GCRMA, as implemented in BioConductor (version 1.1.3).

organism: Mus musculus

source_name: liver-AHRWT-cornoil

label_protocol: Manufacturer's protocol

growth_protocol: Male Ahr–/– mice (10 weeks old) in a C57BL/6J background were obtained from The Jackson Laboratory (Bar Harbor, ME). Wild-type (Ahr+/+) male C57BL/6J mice (15 weeks old) were bred at the National Public Health Institute (Kuopio, Finland) from stock originally obtained from The Jackson Laboratory.

extract_protocol: Liver was harvested 19 h after treatment, sliced, snap-frozen, and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (QIAGEN, Valencia, CA) according to the manufacturer's instructions. DNase (QIAGEN) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry, and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Mice were given a single dose of 1000 µg/kg TCDD or corn oil vehicle by gavage. TCDD initially was dissolved in ether and added to corn oil; the ether subsequently was evaporated off. TCDD was purchased from the UFA-Oil Institute (Ufa, Russia) and was >99% pure as determined by gas chromatography-mass spectrometry.


title: Patient with CAD; patient group: control; CADi: 0 (d4067)

status: Public on Oct 31 2008

city: Basel

first: Peter

last: Grass

address: Klybeck Strasse

department: DMP

institute: Novartis

description: Gene expression analysis in patient with coronary artery disease (CADi>0) in comparison  to control patients (CADi=0)

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

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

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

source_name: Homo sapiens;tissue: blood cells

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

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

tag: tissue

value: blood cells

tag: cohort

value: pooled

tag: patient group

value: control

tag: sex

value: m

tag: age

tag: ethnicity

value: caucasian

tag: CADi


title: liver-AHRWT-cornoil-rep3


title: OAR27K 723, 3/17/06

city: Fort Collins

first: Amanda

last: Broz

state: CO

address: 1173 Campus Delivery

department: Horticulture and Lanscape Architecture

institute: Colorado State University

description: OAR27K 723, 3/17/06

hyb_protocol: Genisphere Array900

scan_protocol: Axon GenePix3.0

data_processing: GenePix Pro (gpr) and image files for each experiment were uploaded to a secure site through the Yale server where they could be accessed for analysis (http://ymd.med.yale.edu/ymd_prod/cgi-bin/gz_login.cgi).  In the preliminary   experiment, all unflagged genes were considered in the analysis without   analyzing up or down regulation between tissues, to get a general overview of   hybridization.  For each chip, flagged genes were removed from the analysis.  The average background was calculated for each dye channel (wavelength 635 and 532) and only genes having pixel counts (median minus background) over two   times the average background in at least one channel were considered. In Experiment 2 each chip was initially analyzed separately.  Flagged values and all channel values that were less than two standard deviations above the mean   background were removed from the analysis.  Ratios ((F635-B635)/(F532-B532))  of the remaining values were averaged per chip, and a correction factor was  calculated for each chip, in order to set the average of all ratios equal to  one.  Ratios were multiplied by the appropriate correction factor to globally normalize the data.  We chose oligos (array spots) that were present in all four chips for further analysis.  This raises our confidence in the data, and allows us to compare the two experimental conditions.  In addition,   normalization provided better agreement between results from the microarray   and those obtained by RT-PCR.  Replicates (two per experimental condition) were combined and the average ratios and respective standard deviations were   calculated for each oligo.  A one sample t-test was preformed to identify   oligos in which the test condition (Centaurea-Gaillardia or Centaurea-Festuca)   was significantly different from the control (Centaurea alone).  A two sample   t-test was preformed to identify oligos that were differentially regulated between experiments (Centaurea-Gaillardia and Centaurea-Festuca).  Accession numbers for each gene fitting the above criteria were used to query the TAIR (www.arabidopsis.org) database to determine function, and genes were then   grouped into functional categories based on the Kyoto Encyclopedia of Genes   and Genomics (KEGG) Orthology System (www.genome.jp/kegg/brite.html).

organism: Arabidopsis thaliana

source_name: EXP

label_protocol: Genisphere Array900

growth_protocol: In April 2005, 1.5 liters of sterile 20/30 grit sand (Lane Mountain, Inc. Valley, WA) was added to the bottom of 2.4 liter pots and 1 liter of weed-free sifted soil collected in Missoula, MT was placed on top of the sand.  The pots were placed in a naturally lit greenhouse supplemented with artificial light and seeded with five seeds of Gaillardia aristata (strong competitor) or Festuca idahoensis (weak competitor), species which are both native to North American rangelands invaded by Centaurea.  Once seedlings were established they were thinned to one plant per pot.  After the natives had grown for 30 days, a single Centaurea seed collected from an invasive population in Missoula, MT was added to each pot containing native species and allowed to establish.  Centaurea seeds were also grown in pots without natives.  Plants were fertilized every three weeks with 100 mL of Miracle GrowTM solution per pot (0.34 grams 15-2-20 Miracle GrowTM per liter water), watered to near saturation, and rotated on the bench every 10 days.  Plants were harvested in September of 2005, when native plants were approximately 153 days old and C. maculosa plants were 123 days old

extract_protocol: RNeasy kit (quiagen)

treatment_protocol: Centaurea maculosa grown in competition with Festuca idahoensis

tag: Roots of Centaurea maculosa grown in competition with Festcua idahoensis

tag: This is an experimental replicate of chip 720 (2-23-06)

source_name: REF

treatment_protocol: Centaurea maculosa grown in isolation

tag: Centaurea maculosa grown alone


title: liver-AHRWT-TCDD-rep3

description: mouse liver, AHR wildtype, 1000 ug/kg TCDD treated, 19 hours

source_name: liver-AHRWT-TCDD


title: CML_7_MEP

description: (CML) chronic myeloid leukaemia / Megacaryocyte-Erythrocyte Progenitors

source_name: Bone Marrow

tag: Megacaryocyte-Erythrocyte Progenitors


title: liver-AHRWT-TCDD-rep5


title: liver-AHRWT-cornoil-rep4


title: ABRO_OAR27K-508_9-9-05

scan_protocol: Axon GenePix 3.0

data_processing: Data processing VALUE is log2 (CY5/CY3; exp/ref)

growth_protocol: Invasive Centaurea maculosa plants from Missoula, MT were grown from seed in the greenhouse for approximately six months.  Seeds were germinated in 8-cm diameter pots of soil gathered from Larimer County, CO, and soils were maintained near saturation with watering.

tag: Centaurea maculosa rosette leaf

tag: seed source

value: Missoula Montana, plant ~6 months old

tag: Centaurea maculosa root

value: Missoula Montana, plant ~6 months old (used same plant as was used for leaf tissue)


title: OAR27K 720, 2/23/06

description: OAR27K 720, 2/23/06

growth_protocol: In April 2005, 1.5 liters of sterile 20/30 grit sand (Lane Mountain, Inc. Valley, WA) was added to the bottom of 2.4 liter pots and 1 liter of weed-free sifted soil collected in Missoula, MT was placed on top of the sand.  The pots were placed in a naturally lit greenhouse supplemented with artificial light and seeded with five seeds of Gaillardia aristata (strong competitor) or Festuca idahoensis (weak competitor), species which are both native to North American rangelands invaded by Centaurea.  Once seedlings were established they were thinned to one plant per pot.  After the natives had grown for 30 days, a single Centaurea seed collected from an invasive population in Missoula, MT was added to each pot containing native species and allowed to establish.  Centaurea seeds were also grown in pots without natives.  Plants were fertilized every three weeks with 100 mL of Miracle GrowTM solution per pot (0.34 grams 15-2-20 Miracle GrowTM per liter water), watered to near saturation, and rotated on the bench every 10 days.  Plants were harvested in September of 2005, when native plants were approximately 153 days old and C. maculosa plants were 123 days old.

treatment_protocol: Grown in competition with weak competitor, Festuca

tag: Roots of Centaurea maculosa grown alone


title: Patient with CAD; patient group: case; CADi: 32 (d3776)

value: females

value: case

value: f


title: HD-NSTc vs Reference

description: For this study, we used Agilent 44K 60-mer oligo microarray slides (Agilent Technologies), each with more than 41,000 unique human genes and transcripts represented, all with public domain annotations.

source_name: Reference

tag: Pool of equal amounts of RNA from the 9 samples of the normal group (Blood samples from healthy donors).

source_name: HD-NSTc

tag: Pool of equal amounts of total RNAs from 3 different patients with Hodgkin´s Disease who did not develop a second neoplasia.


title: LnCap cells with CMV6-EBP1 vector

city: Baltimore

first: Anne

last: Hamburger

address: 655 W. Baltimore St

department: Cancer Center

institute: University of Maryland Baltimore

description: Ebp1 effets in hormone independent prostate cancer case

hyb_protocol: The cRNA pellet was resuspended in 10 l Rnase-free H2O and 10.0 g was fragmented by heat and ion-mediated hydrolysis at 95oC for 35 mins in 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc. The fragmented cRNA was hybridized for 16hr at 45oC to U133A oligonucleotide arrays (Affymetrix) containing ~39,000 full length annotated genes together with additional probe sets designed to represent EST sequences.  Arrays were washed at 25oC with 6 X SSPE (0.9M NaCl, 60 mMNaH2PO4, 6 mM EDTA + 0.01% Tween 20) followed by a stringent wash at 50oC with 100 mM MES, 0.1M [Na+], 0.01% Tween 20.  The arrays were then stained with phycoerythrein conjugated streptavidin (Molecular Probes) and the fluorescence intensities were determined using a laser confocal scanner (Hewlett-Packard).

scan_protocol: The scanned images were analyzed using Microarray software (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to constant target intensity (2500) for all arrays used.

data_processing: Data Analysis was conducted using Microarray Suite 5.0 (Affymetrix) following user guidelines.  The signal intensity for each gene was calculated as the average intensity difference, represented by [(PM - MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes

source_name: LNCap 81 cells ebp1 transfected

label_protocol:
cRNA synthesis and labeling. First and second strand cDNA were synthesized from 5-15 g of total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Gibco Life Technologies) and oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) primer according to the manufacturer’s instructions.
cRNA was synthesized labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter coupled double stranded cDNA as template and the T7 RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).  Briefly, double stranded cDNA synthesized from the previous steps were washed twice with 70% ethanol and resuspended in 22 l Rnase-free H2O. The cDNA was incubated with 4 l of 10X each Reaction Buffer, Biotin Labeled Ribonucleotides, DTT, Rnase Inhibitor Mix and 2 l 20X T7 RNA Polymerase for 5 hr at 37oC.  The labeled cRNA was separated from unincorporated ribonucleotides by passing through a CHROMA SPIN-100 column (Clontech) and precipitated at –20oC for 1 hr to overnight.

extract_protocol: RNA was extracted with TRIzol reagent.

tag: Hormone independent LNCaP C81 cells were trasnfected with a CMV6-EBP1 vector.


title: Patient with CAD; patient group: case; CADi: 32 (d4206)

tag: tissue

tag: cohort

value: others

value: afro-american


title: liver-AHRWT-TCDD-rep4


title: Patient with CAD; patient group: case; CADi: 63 (d4091)

tag: patient group

tag: sex

value: other


title: Patient with CAD; patient group: control; CADi: 0 (d4096)

tag: age

tag: ethnicity


title: liver-AHRWT-TCDD-rep6


title: Patient with CAD; patient group: control; CADi: 0 (d4095)

tag: CADi


title: OAR27K 623, 1-20-06

description: OAR27K 623, 1-20-06

extract_protocol: RNeasy kit

treatment_protocol: Roots of Centaurea maculosa grown in competition with Gaillardia aristata

tag: This is a replicate of chip 618 (12-7-05)


title: Patient with CAD; patient group: case; CADi: 32 (d4090)


title: liver-AHRWT-cornoil-rep2


title: Isolate 5 Versus Reference Strain

description: comparison of clinical isolate #5 with reference strain

source_name: Control Strain

tag: Rickettsia conorii str. Malish 7

tag: Rickettsia conorii clinical isolate from patient eschar


title: LnCap cells with CMV6 vector control

description: Ebp1 effects in hormone refractory prostate cancer

hyb_protocol: The cRNA pellet was resuspended in 10 l Rnase-free H2O and 10.0 g was fragmented by heat and ion-mediated hydrolysis at 95oC for 35 mins in 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc. The fragmented cRNA was hybridized for 16hr at 45oC to U133A oligonucleotide arrays (Affymetrix) containing ~39,000 full length annotated genes together with additional probe sets designed to represent EST sequences.  Arrays were washed at 25oC with 6 X SSPE (0.9M NaCl, 60 mMNaH2PO4, 6 mM EDTA + 0.01% Tween 20) followed by a stringent wash at 50oC with 100 mM MES, 0.1M [Na+], 0.01% Tween 20.  The arrays were then stained with phycoerythrein conjugated streptavidin (Molecular Probes) and the fluorescence intensities were determined using a laser confocal scanner (Hewlett-Packard).  The scanned images were analyzed using Microarray software (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to constant target intensity (2500) for all arrays used.  Data Analysis was conducted using Microarray Suite 5.0 (Affymetrix) following user guidelines.  The signal intensity for each gene was calculated as the average intensity difference, represented by [(PM - MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes.

source_name: Logaritmically growing cels LnCap C81 cells

label_protocol:
cRNA synthesis and labeling. First and second strand cDNA were synthesized from 5-15 ug of total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Gibco Life Technologies) and oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) primer according to the manufacturer’s instructions.
cRNA was synthesized labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter coupled double stranded cDNA as template and the T7 RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).  Briefly, double stranded cDNA synthesized from the previous steps were washed twice with 70% ethanol and resuspended in 22 l Rnase-free H2O. The cDNA was incubated with 4 ul of 10X each Reaction Buffer, Biotin Labeled Ribonucleotides, DTT, Rnase Inhibitor Mix and 2 ul 20X T7 RNA Polymerase for 5 hr at 37oC.  The labeled cRNA was separated from unincorporated ribonucleotides by passing through a CHROMA SPIN-100 column (Clontech) and precipitated at –20oC for 1 hr to overnight

extract_protocol: RNA was extracted using TRIZol reagent.

tag: Androgen independent C81 LnCap cells were transfected with a control CMV6 vector. RNA was derived from logarithmically growing cells.


title: liver-AHRWT-cornoil-rep1


title: OAR27K 618, 12-7-05

description: OAR27K 618, 12-7-05

treatment_protocol: Centaurea maulosa grown in competition with Gaillardia aristata

tag: Centaurea maculosa grown alone


title: liver-AHRWT-TCDD-rep2


title: liver-AHRWT-TCDD-rep1


title: Patient with CAD; patient group: control; CADi: 0 (d4089)


title: Patient with CAD; patient group: case; CADi: 32 (d3775)


title: Patient with CAD; patient group: control; CADi: 0 (d4144)


title: Patient with CAD; patient group: control; CADi: 0 (d4205)


title: Patient with CAD; patient group: case; CADi: 32 (d3773)


title: Patient with CAD; patient group: control; CADi: 0 (d4065)


title: Patient with CAD; patient group: control; CADi: 0 (d4143)


title: Patient with CAD; patient group: control; CADi: 0 (d4066)


title: Patient with CAD; patient group: case; CADi: 32 (d3770)


title: Patient with CAD; patient group: control; CADi: 0 (d3772)


title: Patient with CAD; patient group: case; CADi: 32 (d4138)


title: Patient with CAD; patient group: control; CADi: 0 (d3771)


title: Patient with CAD; patient group: case; CADi: 100 (d4146)


title: Patient with CAD; patient group: control; CADi: 0 (d4064)


title: Patient with CAD; patient group: control; CADi: 0 (d4145)


title: Patient with CAD; patient group: control; CADi: 0 (d4142)


title: Patient with CAD; patient group: control; CADi: 0 (d4203)


title: Patient with CAD; patient group: case; CADi: 67 (d3774)

value: asian


title: Patient with CAD; patient group: control; CADi: 0 (d4063)


title: Patient with CAD; patient group: control; CADi: 0 (d4139)


title: Patient with CAD; patient group: control; CADi: 0 (d4147)


title: Patient with CAD; patient group: case; CADi: 32 (d4148)


title: Patient with CAD; patient group: control; CADi: 0 (d4204)


title: Patient with CAD; patient group: case; CADi: 23 (d4134)


title: Patient with CAD; patient group: case; CADi: 23 (d4136)


title: Patient with CAD; patient group: control; CADi: 0 (d4135)


title: Patient with CAD; patient group: case; CADi: 48 (d4130)


title: Patient with CAD; patient group: case; CADi: 74 (d4199)


title: Patient with CAD; patient group: control; CADi: 0 (d3769)

value: hispanic


title: Patient with CAD; patient group: control; CADi: 0 (d4059)


title: Patient with CAD; patient group: case; CADi: 23 (d4137)


title: Patient with CAD; patient group: control; CADi: 0 (d3768)


title: Patient with CAD; patient group: control; CADi: 0 (d4198)


title: Patient with CAD; patient group: control; CADi: 0 (d4061)


title: Patient with CAD; patient group: control; CADi: 0 (d4129)


title: Patient with CAD; patient group: control; CADi: 0 (d4202)


title: Patient with CAD; patient group: case; CADi: 32 (d4128)


title: Patient with CAD; patient group: control; CADi: 0 (d4140)


title: Patient with CAD; patient group: case; CADi: 48 (d4131)


title: Patient with CAD; patient group: case; CADi: 32 (d4127)


title: Patient with CAD; patient group: control; CADi: 0 (d4133)


title: Patient with CAD; patient group: control; CADi: 0 (d3767)


title: Patient with CAD; patient group: control; CADi: 0 (d4141)


title: Patient with CAD; patient group: control; CADi: 0 (d3766)


title: Patient with CAD; patient group: control; CADi: 0 (d4196)


title: Patient with CAD; patient group: control; CADi: 0 (d4057)


title: Patient with CAD; patient group: control; CADi: 0 (d4058)


title: Patient with CAD; patient group: control; CADi: 0 (d4126)


title: Patient with CAD; patient group: control; CADi: 0 (d4055)


title: Patient with CAD; patient group: case; CADi: 67 (d4200)


title: Patient with CAD; patient group: case; CADi: 32 (d4053)


title: Patient with CAD; patient group: case; CADi: 23 (d4132)


title: Patient with CAD; patient group: control; CADi: 0 (d3763)

value: native american


title: Patient with CAD; patient group: case; CADi: 32 (d4054)


title: Patient with CAD; patient group: control; CADi: 0 (d4194)


title: Patient with CAD; patient group: control; CADi: 0 (d3762)


title: Patient with CAD; patient group: case; CADi: 63 (d3764)


title: Patient with CAD; patient group: case; CADi: 63 (d4051)


title: Patient with CAD; patient group: case; CADi: 63 (d4056)


title: Patient with CAD; patient group: case; CADi: 32 (d4122)


title: Patient with CAD; patient group: control; CADi: 0 (d4125)


title: Patient with CAD; patient group: case; CADi: 48 (d4121)


title: Patient with CAD; patient group: control; CADi: 0 (d4124)


title: Patient with CAD; patient group: case; CADi: 32 (d4052)


title: Patient with CAD; patient group: case; CADi: 82 (d4195)


title: Patient with CAD; patient group: control; CADi: 0 (d4123)


title: Patient with CAD; patient group: case; CADi: 82 (d3765)


title: Patient with CAD; patient group: control; CADi: 0 (d4193)


title: Patient with CAD; patient group: case; CADi: 32 (d4197)


title: Patient with CAD; patient group: control; CADi: 0 (d4120)


title: Patient with CAD; patient group: control; CADi: 0 (d3761)


title: Patient with CAD; patient group: case; CADi: 74 (d4191)


title: Patient with CAD; patient group: case; CADi: 74 (d3759)


title: Patient with CAD; patient group: case; CADi: 74 (d4190)


title: Patient with CAD; patient group: case; CADi: 63 (d4188)


title: Patient with CAD; patient group: control; CADi: 0 (d4049)


title: Patient with CAD; patient group: case; CADi: 32 (d3760)


title: Patient with CAD; patient group: case; CADi: 32 (d4187)


title: Patient with CAD; patient group: case; CADi: 32 (d4044)


title: Patient with CAD; patient group: control; CADi: 0 (d4189)


title: Patient with CAD; patient group: control; CADi: 0 (d4119)


title: Patient with CAD; patient group: case; CADi: 23 (d4043)


title: Patient with CAD; patient group: case; CADi: 32 (d4046)


title: Patient with CAD; patient group: case; CADi: 63 (d4045)


title: Patient with CAD; patient group: control; CADi: 0 (d4047)


title: Patient with CAD; patient group: case; CADi: 74 (d4041)


title: Patient with CAD; patient group: case; CADi: 48 (d4048)


title: Patient with CAD; patient group: control; CADi: 0 (d4201)


title: Patient with CAD; patient group: control; CADi: 0 (d4038)


title: Patient with CAD; patient group: case; CADi: 63 (d4192)


title: Patient with CAD; patient group: case; CADi: 32 (d4040)


title: Patient with CAD; patient group: case; CADi: 100 (d4186)


title: Patient with CAD; patient group: case; CADi: 32 (d4184)


title: Patient with CAD; patient group: case; CADi: 56 (d4185)


title: Patient with CAD; patient group: control; CADi: 0 (d4183)


title: Patient with CAD; patient group: case; CADi: 67 (d4042)


title: Patient with CAD; patient group: case; CADi: 67 (d4039)


title: Patient with CAD; patient group: control; CADi: 0 (d4182)


title: Patient with CAD; patient group: control; CADi: 0 (d3758)


title: Patient with CAD; patient group: case; CADi: 23 (d4181)


title: Patient with CAD; patient group: control; CADi: 0 (d4180)


title: Patient with CAD; patient group: case; CADi: 63 (d4179)


title: Patient with CAD; patient group: case; CADi: 32 (d4175)


title: Patient with CAD; patient group: case; CADi: 23 (d3757)


title: Patient with CAD; patient group: case; CADi: 63 (d4178)


title: Patient with CAD; patient group: case; CADi: 42 (d4174)


title: Patient with CAD; patient group: control; CADi: 0 (d4170)


title: Patient with CAD; patient group: case; CADi: 37 (d4171)


title: Patient with CAD; patient group: case; CADi: 32 (d4173)


title: Patient with CAD; patient group: case; CADi: 42 (d4176)


title: Patient with CAD; patient group: case; CADi: 74 (d4169)


title: Patient with CAD; patient group: case; CADi: 32 (d4177)


title: Patient with CAD; patient group: case; CADi: 63 (d3910)


title: Patient with CAD; patient group: control; CADi: 0 (d3755)


title: Patient with CAD; patient group: control; CADi: 0 (d4168)


title: Patient with CAD; patient group: case; CADi: 48 (d4172)


title: Patient with CAD; patient group: control; CADi: 0 (d4167)


title: Patient with CAD; patient group: case; CADi: 100 (d4165)


title: Patient with CAD; patient group: case; CADi: 74 (d3909)


title: Patient with CAD; patient group: case; CADi: 48 (d4164)


title: Patient with CAD; patient group: control; CADi: 0 (d3905)


title: Patient with CAD; patient group: control; CADi: 0 (d4163)


title: Patient with CAD; patient group: case; CADi: 23 (d3903)


title: Patient with CAD; patient group: case; CADi: 63 (d3904)


title: Patient with CAD; patient group: case; CADi: 32 (d3902)


title: Patient with CAD; patient group: case; CADi: 67 (d3901)


title: Patient with CAD; patient group: control; CADi: 0 (d3900)


title: Patient with CAD; patient group: control; CADi: 0 (d4162)


title: Patient with CAD; patient group: control; CADi: 0 (d4037)


title: Patient with CAD; patient group: control; CADi: 0 (d3895)


title: Patient with CAD; patient group: case; CADi: 37 (d3896)


title: Patient with CAD; patient group: case; CADi: 100 (d3894)


title: Patient with CAD; patient group: control; CADi: 0 (d3899)


title: Patient with CAD; patient group: case; CADi: 32 (d3892)


title: Patient with CAD; patient group: control; CADi: 0 (d4166)


title: Patient with CAD; patient group: case; CADi: 63 (d4160)


title: Patient with CAD; patient group: case; CADi: 48 (d3754)


title: Patient with CAD; patient group: case; CADi: 100 (d4161)


title: Patient with CAD; patient group: control; CADi: 0 (d3891)


title: Patient with CAD; patient group: case; CADi: 48 (d3890)


title: Patient with CAD; patient group: case; CADi: 37 (d3897)


title: Patient with CAD; patient group: case; CADi: 42 (d3893)


title: Patient with CAD; patient group: control; CADi: 0 (d3888)


title: Patient with CAD; patient group: control; CADi: 0 (d3889)


title: Patient with CAD; patient group: case; CADi: 74 (d3886)


title: Patient with CAD; patient group: case; CADi: 42 (d4159)


title: Patient with CAD; patient group: case; CADi: 48 (d3885)


title: Patient with CAD; patient group: case; CADi: 32 (d3884)


title: Patient with CAD; patient group: case; CADi: 32 (d3883)


title: Patient with CAD; patient group: control; CADi: 0 (d3887)


title: Patient with CAD; patient group: control; CADi: 0 (d4158)


title: Patient with CAD; patient group: case; CADi: 32 (d4157)


title: Patient with CAD; patient group: case; CADi: 42 (d3942)


title: Patient with CAD; patient group: case; CADi: 74 (d3756)


title: Patient with CAD; patient group: case; CADi: 23 (d4155)


title: Patient with CAD; patient group: control; CADi: 0 (d3940)


title: Patient with CAD; patient group: control; CADi: 0 (d4154)


title: Patient with CAD; patient group: case; CADi: 48 (d3941)


title: Patient with CAD; patient group: control; CADi: 0 (d3939)


title: Patient with CAD; patient group: case; CADi: 32 (d3938)


title: Patient with CAD; patient group: case; CADi: 23 (d4151)


title: Patient with CAD; patient group: case; CADi: 48 (d4153)


title: Patient with CAD; patient group: case; CADi: 23 (d3937)


title: Patient with CAD; patient group: case; CADi: 74 (d3752)


title: Patient with CAD; patient group: case; CADi: 63 (d3933)


title: Patient with CAD; patient group: case; CADi: 32 (d3932)


title: Patient with CAD; patient group: case; CADi: 42 (d3936)


title: Patient with CAD; patient group: case; CADi: 63 (d4150)


title: Patient with CAD; patient group: case; CADi: 82 (d3753)


title: Patient with CAD; patient group: case; CADi: 32 (d4152)


title: Patient with CAD; patient group: case; CADi: 37 (d4118)


title: Patient with CAD; patient group: control; CADi: 0 (d3934)


title: Patient with CAD; patient group: case; CADi: 32 (d4117)


title: Patient with CAD; patient group: case; CADi: 63 (d4116)


title: Patient with CAD; patient group: case; CADi: 32 (d3906)


title: Patient with CAD; patient group: case; CADi: 37 (d4149)


title: Patient with CAD; patient group: case; CADi: 32 (d3930)


title: Patient with CAD; patient group: case; CADi: 48 (d4156)


title: Patient with CAD; patient group: control; CADi: 0 (d4115)


title: Patient with CAD; patient group: control; CADi: 0 (d3928)


title: Patient with CAD; patient group: case; CADi: 63 (d4114)


title: Patient with CAD; patient group: case; CADi: 63 (d3751)


title: Patient with CAD; patient group: control; CADi: 0 (d4113)


title: Patient with CAD; patient group: control; CADi: 0 (d3750)


title: Patient with CAD; patient group: control; CADi: 0 (d3927)


title: Patient with CAD; patient group: control; CADi: 0 (d3929)


title: Patient with CAD; patient group: control; CADi: 0 (d4108)


title: Patient with CAD; patient group: control; CADi: 0 (d4105)


title: Patient with CAD; patient group: control; CADi: 0 (d4107)


title: Patient with CAD; patient group: control; CADi: 0 (d3926)


title: Patient with CAD; patient group: control; CADi: 0 (d3925)


title: Patient with CAD; patient group: control; CADi: 0 (d3924)


title: Patient with CAD; patient group: control; CADi: 0 (d4102)


title: Patient with CAD; patient group: control; CADi: 0 (d4110)


title: Patient with CAD; patient group: control; CADi: 0 (d3921)


title: Patient with CAD; patient group: control; CADi: 0 (d4106)


title: Patient with CAD; patient group: control; CADi: 0 (d3920)


title: Patient with CAD; patient group: control; CADi: 0 (d4101)


title: Patient with CAD; patient group: control; CADi: 0 (d3922)


title: Patient with CAD; patient group: control; CADi: 0 (d3749)


title: Patient with CAD; patient group: control; CADi: 0 (d4104)


title: Patient with CAD; patient group: control; CADi: 0 (d3923)


title: Patient with CAD; patient group: control; CADi: 0 (d4098)


title: Patient with CAD; patient group: control; CADi: 0 (d3748)


title: Patient with CAD; patient group: control; CADi: 0 (d4099)


title: Patient with CAD; patient group: control; CADi: 0 (d3917)


title: Patient with CAD; patient group: control; CADi: 0 (d4100)


title: Patient with CAD; patient group: control; CADi: 0 (d3919)


title: _12_cy3_Anaerobic_Stationary_Phase

status: Public on Oct 10 2008

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

hyb_protocol: The two separately labeled cDNA pools  to be compared were mixed together in a hybridization solution containing 50% formamide, applied to microarrays and incubated overnight  at 50 C. Microarrays were washed using buffers of increasing stringency accordin

scan_protocol: The sample was scanned with a ScanArray 5000 Microarray Analysis System PerkinElmer Life Sciences Inc, Boston, MA and images were quantified using Microarray Imager software from Combimatrix.

data_processing: Microarray data was log 2 transformed and normalized using the standard normalization routine as implemented in JMP Genomics 3.0 (SAS Institute Inc., Cary, NC).

organism: Zymomonas mobilis

label_protocol: The purified RNA from each sample was used as the template to generate cDNA copies labeled with either Cy3-dUTP or Cy5-dUTP.

growth_protocol: Z. mobilis ZM4 was obtained from the American Type Culture Collection  and cultured in RM medium at 30 C.

extract_protocol: Samples from aerobic and anaerobic fermentors were harvested by centrifugation and the TRIzol reagent (Invitrogen) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residua

treatment_protocol: Anaerobic


title: _11_cy5_Anaerobic_Stationary_Phase


title: _12_cy5_Aerobic_Stationary_Phase

treatment_protocol: Aerobic


title: _11_cy3_Aerobic_Stationary_Phase


title: _5_cy3_Aerobic_exponential_phase


title: _6_cy3_Anaerobic_exponential_phase


title: Patient with CAD; patient group: control; CADi: 0 (d3918)


title: _5_cy5_Anaerobic_exponential_phase


title: _8_cy3_Anaerobic_Stationary_Phase


title: _7_cy3_Aerobic_Stationary_Phase


title: _10_cy3_Anaerobic_Stationary_Phase


title: _7_cy5_Anaerobic_Stationary_Phase


title: _9_cy5_Anaerobic_Stationary_Phase


title: _9_cy3_Aerobic_Stationary_Phase


title: _6_cy5_Aerobic_exponential_phase


title: _4_cy3_Anaerobic_exponential_phase


title: Patient with CAD; patient group: control; CADi: 0 (d3916)


title: Patient with CAD; patient group: control; CADi: 0 (d4097)


title: Patient with CAD; patient group: control; CADi: 0 (d3913)


title: Patient with CAD; patient group: control; CADi: 0 (d3747)


title: Patient with CAD; patient group: control; CADi: 0 (d3914)


title: _4_cy5_Aerobic_exponential_phase


title: _3_cy5_Anaerobic_exponential_phase


title: _1_cy5_Anaerobic_exponential_phase


title: _2_cy5_Aerobic_exponential_phase


title: _1_cy3_Aerobic_exponential_phase

extract_protocol: Samples from aerobic and anaerobic fermentors were harvested by centrifugation and the TRIzol reagent was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I to digest residual chromosomal DNA and subsequently


title: Psoriasis_lesion_42

status: Public on Oct 04 2008

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

institute: ETH Zurich

hyb_protocol: TaqMan™Quantitative RT-PCR

scan_protocol: TaqMan™ RT-PCR - Fluorescence

data_processing: Raw data were normalized to the cycle number (Ct) of 18S expression

label: TaqMan Probe

source_name: Human dermal tissue

label_protocol: TaqMan™Quantitative RT-PCR - FAM

extract_protocol: Total RNA was also obtained from frozen samples of 43 psoriatic skin lesions, using homogenization with a TissueLyser (Qiagen, Hilden, Germany) and RNA extraction with the Trizol reagent. Briefly, isolate total cellular RNA with 1 ml of the Trizol reagent (Invitrogen) after washing one 80-90 % confluent 10 cm culture dish with PBS. Homogenize the sample using a cell scraper and add 0.2 ml of chloroform in a 1.5 ml tube. Shake the sample vigorously for 15 seconds and allow standing for 5 minutes. Centrifuge the resulting mixture at 12,000 x g for 15 minutes at 4 degree Celsius. Transfer the aqueous phase to a fresh tube and add 0.5 ml of iso-propanol and mix. Allow the sample to stand for 5 minutes at room temperature and centrifuge at 12,000 x g for 10 minutes at 4 degrees Celsius. Remove the supernatant and wash the RNA pellet by adding 1 ml of 75% ethanol. Vortex the sample and then centrifuge at 12,000 x g for 5 minutes at 4 degrees Celsius. Remove the ethanol and briefly dry the RNA pellet for 5 minutes and add 50 micro-liter of RNAase/DNAase free water and mix by repeated pipetting until RNA pellet is fully dissolved.

tag: Tissue biopsy of chronically inflamed skin


title: Psoriasis_lesion_43


title: _10_cy5_Aerobic_Stationary_Phase


title: Psoriasis_lesion_40


title: Psoriasis_lesion_41


title: Psoriasis_lesion_32


title: Psoriasis_lesion_39


title: _3_cy3_Aerobic_exponential_phase


title: Psoriasis_lesion_36


title: Psoriasis_lesion_34


title: Psoriasis_lesion_37


title: Psoriasis_lesion_35


title: Psoriasis_lesion_30


title: Psoriasis_lesion_38


title: Psoriasis_lesion_28


title: Psoriasis_lesion_29


title: Psoriasis_lesion_27


title: _2_cy3_Anaerobic_exponential_phase


title: Psoriasis_lesion_26


title: Psoriasis_lesion_33


title: Psoriasis_lesion_25


title: Psoriasis_lesion_24


title: Psoriasis_lesion_20


title: Psoriasis_lesion_31


title: Psoriasis_lesion_19


title: Psoriasis_lesion_21


title: Psoriasis_lesion_22


title: Psoriasis_lesion_23


title: Psoriasis_lesion_18


title: Psoriasis_lesion_16


title: Psoriasis_lesion_17


title: Psoriasis_lesion_15


title: Psoriasis_lesion_14


title: 100% HUVEC

data_processing: Raw data were normalized to the cycle number (Ct) of beta-Actin expression

source_name: Human dermis

growth_protocol: Cells were propagated in endothelial cell basal medium (Cambrex Corp.; East Rutherford, NJ ) containing 20% fetal bovine serum, antibiotics, 2 mmol/L L-glutamine (Invitrogen Corp.; Carlsbad, CA), 10 µg/mL hydrocortisone acetate and 2.5  10-2 mg/ml  N-6,2’-O-dibutyryl adenosine-3,5’-cyclic monophosphate (Sigma-Aldrich; St. Louis, MO).

extract_protocol: Isolate total cellular RNA with 1 ml of the Trizol reagent (Invitrogen) after washing one 80-90 % confluent 10 cm culture dish with PBS. Homogenize the sample using a cell scraper and add 0.2 ml of chloroform in a 1.5 ml tube. Shake the sample vigorously for 15 seconds and allow standing for 5 minutes. Centrifuge the resulting mixture at 12,000 x g for 15 minutes at 4 degree Celsius. Transfer the aqueous phase to a fresh tube and add 0.5 ml of iso-propanol and mix. Allow the sample to stand for 5 minutes at room temperature and centrifuge at 12,000 x g for 10 minutes at 4 degrees Celsius. Remove the supernatant and wash the RNA pellet by adding 1 ml of 75% ethanol. Vortex the sample and then centrifuge at 12,000 x g for 5 minutes at 4 degrees Celsius. Remove the ethanol and briefly dry the RNA pellet for 5 minutes and add 50 micro-liter of RNAase/DNAase free water and mix by repeated pipetting until RNA pellet is fully dissolved.

tag: Human umbilical vein endothelial cell


title: Psoriasis_lesion_13


title: 20% of LEC and 80% of HUVEC

tag: Admixture


title: Psoriasis_lesion_10


title: Psoriasis_lesion_11


title: 50% of LEC and 50% of HUVEC


title: Psoriasis_lesion_12


title: Psoriasis_lesion_9


title: 80% of LEC and 20% of HUVEC


title: Psoriasis_lesion_7


title: Human keratinocyte cell line

description: HaCat

tag: Spontaneously transformed human keratinocyte cell line


title: 100% of LEC

tag: CD45-/CD34-/CD31+ Human Lymphatic Endothelial Cell (LEC)


title: Psoriasis_lesion_6


title: Human dermal fibroblast

description: Fibroblast

tag: Dermal derived fibroblast (IMR91)


title: Human dermal microvascular endothelial cell purchased from Science Cell

description: HDMEC (SC)

source_name: Sciencell™

tag: CD31+/Factor VIII+


title: Human dermal microvascular endothelial cell purchased from Promo Cell

description: HDMEC (PC)

source_name: Promo Cell


title: Human immortalized dermal microvascular endothelial cell line - 1


title: Psoriasis_lesion_5


title: Psoriasis_lesion_4


title: Psoriasis_lesion_3


title: Psoriasis_lesion_2


title: Psoriasis_lesion_8


title: Psoriasis_lesion_1


title: Human umbilical vein endothelial cell purchased from Promo Cell

description: HUVEC (PC)


title: Patient with CAD; patient group: control; CADi: 0 (d4109)

tag: tissue

tag: cohort

tag: patient group


title: Human dermal lymphatic endothelial cell purchased from Science Cell

description: LEC (SC)


title: Clonetics Human dermal lymphatic microvascular endothelial cell (Lonza)

description: LEC (Camb)

source_name: Lonza

tag: Factor VIII+/SMA-a-/CD31+/Podoplanin+


title: Human dermal blood vascular endothelial cell 6

source_name: Human primary dermal microvascular blood endothelial cell (BEC) isolated from neonatal human foreskin

tag: CD45-/CD34+ Human Blood Vascular Endothelial Cell (BEC)


title: Human dermal blood vascular endothelial cell 5


title: Human dermal blood vascular endothelial cell 2


title: Human dermal blood vascular endothelial cell 1


title: Human dermal lymphatic endothelial cell 7

source_name: Human primary dermal microvascular lymphatic endothelial cell (LEC) isolated from neonatal human foreskin


title: Human dermal blood vascular endothelial cell 8


title: Human dermal blood vascular endothelial cell 3


title: Human dermal blood vascular endothelial cell 7


title: Human dermal lymphatic endothelial cell 5


title: Human dermal blood vascular endothelial cell 4


title: Human dermal lymphatic endothelial cell 2


title: Human dermal lymphatic endothelial cell 6


title: Human dermal lymphatic endothelial cell 1


title: Human umbilical vein endothelial cell purchased from Science Cell

description: HUVEC (SC)


title: _8_cy5_Aerobic_Stationary_Phase


title: Human dermal lymphatic endothelial cell 3


title: Human dermal lymphatic endothelial cell 4


title: reference decay profile 1, t=40min

status: Public on Oct 01 2008

city: Rehovot

first: Ophir

last: Shalem

address: Hertzel

country: Israel

institute: Weizmann Inst.

description: Reference decay profile 1, t=40 min

data_processing: RMA algorithm followed by normalization using spiked-in RNA as explained in detail in the supplementary of the paper (Shalem et al.).

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: No treatment, 40 min following transcription inhibition

label_protocol: cDNA was prepared using poly(T) primers, labeled cRNA was prepared using the GeneChip system according to manufacturer instructions.

growth_protocol: Yeast strain Y262 (carrying a temperature-sensitive mutation in RNA polymerase II) was grown in YPD to mid-log phase in 26 degrees.

extract_protocol: Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies).

treatment_protocol: In the oxidative stress and DNA damage experiments, cells were treated with 0.3mM H2O2 or 0.1% MMS, 25 or 40 minutes prior to transcription inhibition. At time point 0, the temperature of the culture was raised to 37 degrees by adding an equal amount of medium prewarmed to 49 degrees. This step inactivated the temperature-sensitive RNA polymerase II and therefore stopped transcription. Following transcription inhibition, 10 samples were taken for each time course (0,  5 min, 10 min, 15 min, 20 min, 30 min, 40 min, 50 min, 60 min) and a technical replicate of time point zero. In the second reference decay profile, the three last time points (40 min, 50 min, and 60 min) turned out to be outliers, and thus were not used and not submitted.

tag: strain Y262


title: reference decay profile 1, t=0

description: Reference decay profile 1, t=0

hyb_protocol: GeneChip system according to manufacturer instructions.

source_name: No treatment, time 0 following transcription inhibition


title: reference decay profile 2, t=5min

description: Reference decay profile 2, t=5 min

scan_protocol: GeneChip system according to manufacturer instructions.

source_name: No treatment, 5 min following transcription inhibition


title: reference decay profile 1, t=0, replicate

description: Reference decay profile 1, t=0


title: reference decay profile 1, t=60min

description: Reference decay profile 1, t=60 min

source_name: No treatment, 60 min following transcription inhibition


title: reference decay profile 1, t=50min

description: Reference decay profile 1, t=50 min

source_name: No treatment, 50 min following transcription inhibition


title: reference decay profile 2, t=15min

description: Reference decay profile 2, t=15 min

source_name: No treatment, 15 min following transcription inhibition


title: reference decay profile 2, t=0, replicate

description: Reference decay profile 2, t=0