title: SH_AG_42928_24h_2.5uM_BP2_DF

description: 24h DMSO v 24h 2.5 BaP BP1 DF

source_name: sh-HepG2 24hr 2.5uM BaP B(hepg2 24h 2.5 bap)

extract_protocol: Cell pellets were collected and total RNA extracted using the Qiagen RNeasy Mini Kit protocol (RNeasy Mini Handbook, Qiagen, UK). After addition of lysis buffer (RLT, Qiagen) samples were homogenized using QIAshredders (Qiagen).

source_name: sh-HepG2 24h DMSO B(hepg2 24h dmso)


title: SH_AG_41268_6h_2.5_BaP_BP1_DF

status: Public on Dec 30 2008

type: RNA

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: 6h DMSO v 6h 2.5 BaP exp.1 DF

hyb_protocol: Hybridization and washing were performed according to the Agilent manual.

scan_protocol: Scanner: Axon4000A. Voltage: 100%

data_processing: Regions were used for normalizing samples 1-32. To account for dye swap, the signal channel and control channel measurements for sample(s) 1, 3, 5, 7, 9-10, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32 were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

molecule: total RNA

organism: Homo sapiens

source_name: sh-HepG2 6hr 2.5uM BaP A(hepg2 6h 2.5 bap)

label_protocol: Labelling and hybridization was carried out according to the Agilent manual for microarrays with minor modifications. Total RNA (0.5 ug) was transcribed into cDNA and labelled with either Cyanine 5 (Cy5) or Cyanine 3 (Cy3). If dye-incorporation was above 7 pmol/µg RNA, 2 µg of BaP treated-cRNA and 2 µg DMSO control-cRNA were applied on the Agilent Human 1A (V2) Oligo Microarray.

tag: tissue type

value: tumor

source_name: sh-HepG2 6h DMSO A(hepg2 6h dmso)


title: SH_AG_41267_24h_2.5uM_BP2

description: 24h DMSO v 24h 2.5 BaP BP2


title: SH-3000100881_6h_3_BaP_BP1

description: 6h DMSO v 6h 3BaP exp.1

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 μl hybridisation mix (19 μl Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150μl aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

scan_protocol: Scanner: Axon4000A. Voltage: 3.55 and 3.65. Resolution (micrometers): 10.

source_name: MS-HepG2 6 h DMSO BP1(6 h DMSO BP1)

label_protocol: Total RNA (4 μg) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences, UK) using the Invitrogen Indirect cDNA Labelling Kit protocol (Invitrogen, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 μg Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.

extract_protocol: Total RNA was isolated and purified from the Trizol fraction with the RNeasy Mini Kit (Qiagen Westburg bv., Leusden, The Netherlands).

source_name: MS-HepG2 6 h 3 uM BaP BP1(6 h 3 uM BaP BP1)


title: SH-3000100487_24h_2.5_BaP_BP1_DF

description: 24 h DMSO v 24 h 2.5 BaP exp.1 DF

scan_protocol: Scanner: Axon4000A. Voltage: 4.05 and 4.39. Resolution (micrometers): 10.

source_name: sh-HepG2 24h DMSO A(hepg2 24h dmso)

source_name: sh-HepG2 24hr 2.5uM BaP A(hepg2 24h 2.5 bap)


title: SH-3000100486_6h_2.5_BaP_BP2

description: 6 h DMSO v 6 h 2.5 BaP exp.2

scan_protocol: Scanner: Axon4000A. Voltage: 4.06 and 3.84. Resolution (micrometers): 10.

source_name: sh-HepG2 6h DMSO B(hepg2 6h dmso )

source_name: sh-HepG2 6hr 2.5uM BaP B(hepg2 6h 2.5um bap )


title: SH_AG_42926_6h_2.5uM_BP2_DF

description: 6h DMSO v 6h 2.5 BaP BP2 DF


title: SH-AG_41264_6h_2.5_BaP_ BP1 #2

description: 6h DMSO v 6h 2.5 BaP exp.1

scan_protocol: Scanner: Axon4000A. Voltage: 100%. Resolution (micrometers): ?.


title: SH-3000100878_24h_3_BaP_BP1_DF

description: 24h DMSO v 24h 3 BaP exp.1 DF

scan_protocol: Scanner: Axon4000A. Voltage: 3.71 and 3.59. Resolution (micrometers): 10.

source_name: MS-HepG2 24 h 3 uM BaP BP1(24 h 3 uM BaP BP1)

source_name: MS-HepG2 24 h DMSO BP1(25 h DMSO BP1)


title: KM_AG_38779_6h_3uM_BP1 #2

description: 6h DMSO v 6h 3 BaP BP1


title: SH_AG_41266_24h_2.5uM_BP1

description: 24 h DMSO v 24h 2.5 BaP exp.1


title: SH-3000100485_6h_2.5_BaP_BP2_DF

description: 6h DMSO v 6h 2.5 BaP exp.2 DF

scan_protocol: Scanner: Axon4000A. Voltage: 4.15 and 3.81. Resolution (micrometers): 10.


title: SH-3000100488_24h_ 2.5_BaP_BP1

description: 24h DMSO v 24 h 2.5 BaP exp.1

scan_protocol: Scanner: Axon4000A. Voltage: 4.07 and 3.79. Resolution (micrometers): 10.


title: SH-3000100489_6h_2.5uM_BP1

description: 6 h DMSO v 6 h 2.5 BaP Exp.1

scan_protocol: Scanner: Axon4000A. Voltage: 4 and 3.71. Resolution (micrometers): 10.


title: msg5 f.alpha

status: Public on Dec 31 2008

city: Madrid

first: Maria

last: Molina

state: Madrid

address: Plaza Ramon y Cajal s/n

department: Microbiologia II Fcc Farmacia

country: Spain

institute: Universidad Complutense de Madrid

description: Image analysis and data segmentation were done using GenePix Pro software 5.0 (Axon Instruments) obtaining a txt file to proceed with the data analysis.

hyb_protocol: Treated and control cDNA labeled with different dyes are mixed, dried in speed vac and resuspended in hybridation solution: 50% Formamide, 6x SSC, 0.5% SDS, 5x Denhardt´s, 20 microgrammes PolyA (Sigma) and salmon sperm (Gibco) 100 microgrammes/ml. Hybridation of slides with labeled cDNA is carried out for 18 hours at 42ºC in a fluidic station LucideaTM SlidePro (Amersham Biosciences) followed by several washes and drying of slides.

scan_protocol: Microarrays were scanned using GenePix 4000B scanner (Axon Instruments) at 5 micron/píxel, using laser excitation between 550 and 700 PMT and 100% laser power.

data_processing:
Filtering of low neat intensity and inconsistent spot data was followed by Lowess normalization and calculation of ratios. Statistical t-student test was carried out to determine the significance of the induction and repression ratios.
The Data table represents results condensed from four microarrays (coming from two different biological samples labeled using dye swapping strategy).

label: Cy3, Cy5

organism: Saccharomyces cerevisiae

label_protocol: Labelling with Cy3 or Cy5 groups of the corresponding cDNA was achieved using CyScribeTM Post-Labelling kit (Amersham Biosciences) incubating the samples in the dark for two hours. Fluorocrome incorporation was measured using espectophotometer.

growth_protocol: msg5 delta strain was grown on YPD overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 4h. At this point time 0 begins. Cells were collected after 90 minutes of growth, frozen at -80 °C and processed for RNA extraction.

extract_protocol: Saccharomyces cerevisiae total RNA was extracted by mechanical disruption following the instructions of RNeasy Midi kit manufacturer (QIAGEN). Total concentration of RNA obtained was measured at 260 nm and sample quality was checked using RNA Nano Labchips in a Bioanalyzer 2100B (Agilent Technologies, Palo Alto, CA). cDNA synthesis and incorporation of aminoallyl nucleotides is carried out by retrotranscription from 25-30 microgrames of total RNA using Amersham Bioscienceskit .

treatment_protocol: growth at conditions 24 °C 200rpm

tag: msg5 strain (control condition)

source_name: msg5 factor alpha 90 min

growth_protocol: msg5 delta strain was grown on YPD overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 4h. At this point time 0 begins. Cells were collected after 90 minutes of growth under treatment with 50mM of factor alpha , frozen at -80 °C and processed for RNA extraction.

tag: msg5 strain factor alpha 50 mM (experimental condition)


title: SH_AG_42927_24h_2.5uM_BP1_DF

description: 24h DMSO v 24h 2.5 BaP exp.1 DF


title: SH-3000100484_24h_2.5_BaP_BP2

description: 24h DMSO v 24h 2.5 BaP exp.2

scan_protocol: Scanner: Axon4000A. Voltage: 4.09 and 3.79. Resolution (micrometers): 10.


title: KM_AG_47352_6h_3uM_BP2

description: 6h DMSO v 6h 3 BaP BP2

source_name: MS -HepG2 6 h DMSO BP2(6 h DMSO BP2)

source_name: MS-HepG2 6 h 3 uM BaP BP2(6 h 3 uM BaP BP2)


title: MeJA, 0h vs 12h, biol rep 1, tech rep 1

status: Public on Jan 01 2009

city: Pretoria

first: Bridget

middle: Genevieve

last: Crampton

address: PO Box 395

country: South Africa

institute: CSIR Biosciences

description: Biological replicate 1, technical replicate 1

hyb_protocol: Probes were prepared by combining selected Cy3 and Cy5 labelled samples, which were then dried in a vacuum desiccator, and resuspended in 45 µl hybridisation buffer [50% formamide, 25% hybridisation buffer (Amersham Biosciences), 25% deionised water].  Probes were denatured at 92ºC for 5 min.The glass slide was initially incubated in pretreatment solution (3.5X SSC; 0.2% SDS; 1% bovine serum albumin) without probe at 60ºC for 20 min.  Thereafter, the slide was placed in a HybUP hybridisation chamber (NB Engineering, Pretoria, South Africa) with the denatured probe solution at 42ºC for 16 h.  After hybridisation, slides were washed for 4 min at 42ºC with 1 X SSC/0.2% SDS, 0.1 X SSC/0.2% SDS (twice) followed by three washes in 0.1 X SSC for 1 min at room temperature.  Slides were rinsed with distilled water, and dried by centrifugation (2000Xg for 2 min).

scan_protocol: Washed slides were scanned with a Genepix™ 4000B scanner (Axon Instruments, Foster City, CA, USA).  Separate images were acquired for each fluorophore at a resolution of 10 μm per pixel.

data_processing: Scanned images (tiff images) were imported into GenePix Pro 5.0 (Axon Instruments), and fluorescence intensity in both red (CyanineTM-5 dye) and green (CyanineTM-3 dye) channels for each spot was quantified.  Grids were predefined and manually adjusted to ensure optimal spot recognition, and spots with dust or locally high background were flagged as bad.  Fluorescence data from a total of 12 slides were imported into limmaGUI (linear models for microarray data Graphical User Interface) (Wettenhall and Smyth, 2004) in the R computing environment where data was normalised (within array global loess normalisation and between array quantile normalisation), and linear models were fitted in order to contrast post treatment expression values with the non-treated sample (time = 0 h). Differentially expressed genes for each treatment were defined as those with a fold-change (expression ratio) greater than or equal to two between a particular time point and t=0, and were significant at P ≤ 0.05 (moderated t test as implemented in limmaGUI with Bonferonni correction for multiple testing (Wettenhall and Smyth 2004).

organism: Cenchrus americanus

source_name: MeJA-treated leaves, 0 hpt

label_protocol: 15 µg total RNA was reverse transcribed using SuperScript™II (Invitrogen) in the presence of 6 µg random hexamers (Invitrogen), 1 ug oligo(dT)20 (Invitrogen), and 1 X aminoallyl-dNTP labelling mix (0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, 0.2 mM aminoallyl-dUTP).  Reactions were incubated at 42ºC overnight.  Thereafter, RNA was hydrolysed at 65ºC for 15 min by the addition of 0.2 N NaOH and 0.1 mM EDTA.  Tris, pH7.4 (0.3 M) was added to neutralise the reaction before cDNA was purified using a modified Qiaquick PCR Purification kit (Qiagen) protocol. Manufacturer’s instructions were followed except that columns were washed with phosphate wash buffer (5 mM KPO4, pH 8.5 in 80% ethanol), and cDNA was eluted in 4 mM KPO4, pH 8.5.  cDNA samples were vacuum dried and resuspended in 4.5 µl 0.1 M sodium carbonate buffer (Na2CO3), pH 9.0, to which an equal volume of NHS-Cy dye (Amersham BioSciences, Little Chalfont, UK) (prepared in DMSO) was added.  The dye coupling reaction was incubated for 1 h in the dark at room temperature.  Thirty five microlitres 100 mM sodium acetate, pH 5.2 was added to neutralise the reaction, and uncoupled dye was removed by purifying the sample using a Qiaquick PCR purification kit (Qiagen) according to the manufacturer’s instructions.

growth_protocol: Pearl millet seeds (line ICML12) were surface sterilised, germinated on half strength Murashige and Skoog medium for one week, transferred to vermiculite in seedling trays, and grown for six weeks at constant temperature (25°C) and 85% relative humidity.

extract_protocol: Total RNA was isolated from leaves using Qiazol Lysis Reagent according to the manufacturer's instructions.

treatment_protocol: Seven week plants were sprayed until runoff with 500 uM MeJA in 0.1% ethanol, 0.1% Tween 20.  Leaf tissue was harvested 0, 12, 24 and 48 h post treatment.

tag: Pearl millet line ICML12 = P7

source_name: MeJA-treated leaves, 12 hpt


title: SH-3000100483_24h_2.5_BaP_BP2_DF

description: 24h DMSO v 24h 2.5 BaP exp.2 DF

scan_protocol: Scanner: Axon4000A. Voltage: 4.22 and 3.78. Resolution (micrometers): 10.

source_name: sh-HepG2 24hr 2.5uM BaP B(hepg2 24h 2.5 bap)


title: SH_AG_41265_6h_2.5uM_BP2

description: 6h DMSO v 6h 2.5 BaP BP2


title: MZ_124_GFP_neg3, biological replicate 3

status: Public on Dec 25 2008

city: Cambridge

first: Alena

last: Shkumatava

state: MA

address: 9 Cambridge Center

department: Bartel Lab

country: USA

institute: Whitehead Institute/MIT

description: Gene expression data from GFP-negative cells from the rest of the body

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Danio rerio

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Zebrafish embryos were incubated at 28C in the E3 soluion

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

tag: non-CNS cells

tag: Mzdicer mutant zebrafish embryos, 14-16 somites


title: MZ_124_GFP_neg1, biological replicate 1


title: MZ_124_GFP_pos2, biological replicate 2

description: Gene expression data from GFP-positive CNS cells

tag: CNS cells


title: wt_124_GFP_pos2, biological replicate 2

tag: wild-type zebrafish embryos, 16 hpf


title: MZ_124_GFP_pos1, biological replicate 1


title: MZ_124_GFP_neg2, biological replicate 2


title: wt_124_GFP_neg3, biological replicate 3


title: SH-3000100482_6h_2.5_BaP BP1_DF

description: 6 h DMSO v 6 h 2.5 BaP exp.1 DF

scan_protocol: Scanner: Axon4000A. Voltage: 4.04 and 3.77. Resolution (micrometers): 10.


title: SH-3000100479_24h_3_BaP_BP2

description: 24h DMSO v 24h BaP exp.2

scan_protocol: Scanner: Axon4000A. Voltage: 3.88 and 3.57. Resolution (micrometers): 10.

source_name: MS-HepG2 24 h DMSO BP2(24 h DMSO BP2 )

source_name: MS-HepG2 24 h 3 uM BaP BP2(24 h 3 uM BaP BP2)


title: wt_124_GFP_pos3, biological replicate 3


title: SH-3000100478_24h_3_BaP_BP2_DF

description: 24h DMSO v 24h 3 BaP exp.2 DF

scan_protocol: Scanner: Axon4000A. Voltage: 3.46 and 3.31. Resolution (micrometers): 10.


title: SH-3000100481_6h_3_BaP_BP2

description: 6h DMSO v 6h 3 BaP exp.2

scan_protocol: Scanner: Axon4000A. Voltage: 3.48 and 3.7. Resolution (micrometers): 10.


title: SH-3000100430_6h_3_BaP_BP2_DF

description: 6h DMSO v 6h 3 BaP exp.2 DF

scan_protocol: Scanner: Axon4000A. Voltage: 3.48 and 3.71. Resolution (micrometers): 10.


title: wt_124_GFP_neg1, biological replicate 1


title: wt_124_GFP_neg2, biological replicate 2


title: wt_206_GFP_neg3, biological replicate 3

tag: non-muscle cells


title: wt_124_GFP_pos1, biological replicate 1


title: SVEC 4-10 response to extract of diesel engine particulate, replicate #2, dye-reversal

status: Public on Dec 15 2008

city: Honolulu

first: John

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

description: Murine endothelial responses to 24 hours of exposure to a methanol extract of diesel engine particulate matter (Cat. #2975, U.S. National Institutes of Standards and Technology, Gaithersburg, MD).  The diesel  engine particulate was extracted into pure methanol under sonication, filtered, centrifuged, dried under air, and re-dissolved into dimethyl sulfoxide.

hyb_protocol: cDNA probes were combined, purified and hybridized for 14 h at 42° C in a total volume 35 ul of a hybridization solution containing 25% formamide, 3 X SSC, 0.2% SDS, 1 ug of murine Cot1 DNA, 4ug of polyA RNA, and 4 ug of tRNA. Stringency washing at room temperature was sequentially performed for ten minutes in each of the following solutions: 2X SSC containing 0.1% SDS, 0.1X SSC containing 0.1% SDS, and finally, 0.1X SSC

scan_protocol: Slides were scanned using a Molecular Devices 4000B and the images analyzed with Genepix and Acuity software from Molecular Devices(CA)

data_processing:
The GPR data was uploaded to Acuity software from Molecular Devices, normalized by ratio of medians. Filtered to mark Genepix flags.
Log2 fold change of median value of experimental/control.

organism: Mus musculus

source_name: SVEC 4-10 exposed 24 hours to control vehicle dimethyl sulfoxide 1.5% (v/v)

label_protocol: 2 ug of cDNA was labeled with Cy dye sulfo-NHS active dye according to manufacturer's instructions.

growth_protocol: Cultures were incubated in standard culture condition of DMEM with 10% FBS and sub-passaged 1:5 every week during culture period.

extract_protocol: SVEC 4-10 total cellular RNA was extracted and purified with Trizol (Invitrogen) followed by RNEASY columns.  100 ng was subjected to amplification with Ovation Amino Allyl sytem (Nugen, CA) to generate amplified cDNA.

treatment_protocol: Treatment consisted of 24 hours of exposure to 1.5% DMSO whilst cultures were incubated under standard culture condition of DMEM with 10% FBS in a humidified incubator @ 37 degrees C with 5% carbon dioxide.

tag: SVEC 4-10 cell from ATCC (Bethesda, MD). This cultured line derived from murine lymphatic endothelium was originally transformed with SV40 T-antigen. Cells were at 75% confluence at initiation of treatment.

source_name: SVEC 4-10 exposed 24 hours to extract of diesel engine particulate at 50 ug/ml and 1.5% dimethyl sulfoxide

label_protocol: cDNA labeled with Cy dye sulfo-NHS active dye according to manufacturer's instructions.

treatment_protocol: Treatment consisted of 24 hours of exposure to 1.5% DMSO along with 50 ug/ml of an extract of diesel engine particulate, performed whilst cultures were incubated under standard culture condition of DMEM with 10% FBS in a humidified incubator @ 37 degrees C with 5% carbon dioxide.


title: wt_206_GFP_neg2, biological replicate 2


title: MZ_124_GFP_pos3, biological replicate 3


title: SVEC 4-10 response to extract of diesel engine particulate, replicate #1

tag: SVEC 4-10 cell from ATCC (Bethesda, MD).  This cultured line derived from murine lymphatic endothelium was originally transformed with SV40 T-antigen.  Cells were at 75% confluence at initiation of treatment.


title: wt_206_GFP_pos1, biological replicate 1

description: Gene expression data from GFP-positive muscle cells

tag: muscle cells


title: wt_206_GFP_pos2, biological replicate 2


title: wt_206_GFP_pos3, biological replicate 3


title: In vivo aortic endothelial responses to diesel exhaust in Apo E (-/-) mice, 1000 ug/m3, replicate #1

description: Murine endothelial responses within Apo E (-/-) mice due to dilute diesel exhaust at 1000 ug/ cubic meter.

source_name: Aortic endothelium from Apo E (-/-) control mice

growth_protocol: Standard maintenance in vivarium.

extract_protocol: FACS sorting was utilized to obtain endothelium rendered fluorescent due to expression of GFP under control of Tie 2. RNA representing 10,000 endothelial cells was subjected to amplification with Ovation Amino Allyl sytem (Nugen, CA) to generate amplified cDNA.

treatment_protocol: Mice were exposed 30 days to filtered air as controls for 30 days.

tag: ApoE (-/-) and Tie2 GFP mice (strain name B6.129P2-Apoetm1Unc/J [stock #002052] and Tg(TIE2GFP)287Sato [stock #003658], from Jackson Labs, Bar Harbor, ME) were interbred and genetically selected to obtain Tie2 GFP/ ApoE (-/-) mice on an approximately 1:1 mixed genetic background of C57Bl/6 and FVB/N. Males, age 4 months at start of exposure.

source_name: Aortic endothelium from Apo E(-/-) mice exposed 30 days to 1000 ug/m3 of dilute diesel exhaust

treatment_protocol: Mice were exposed 30 days to diesel exhaust diluted to 1000 ug per cubic meter (with HEPA-filtered air) for 4 hours/day, 5 days/week, for 30 days.


title: wt_206_GFP_neg1, biological replicate 1


title: In vivo aortic endothelial responses to diesel exhaust in Apo E (-/-) mice, 1000 ug/m3, replicate #2, dye-reversal


title: hMSCs ctrl_2

city: Houston

first: Philippe

middle: M

last: Campeau

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Control cells

hyb_protocol: Phalanx Hybridization Protocol

scan_protocol: Phalanx scanning protocol

data_processing: Quantile normalization

source_name: human primary bone marrow mesenchymal stromal cells

label_protocol: AminoAllyl aRNA labeling. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP was used to conjugate the purified aRNA with the NHS-CyDye.

growth_protocol: Growth in MEM alpha medium with 20% FBS, passaged q 3 days.

extract_protocol: Cells homogenized with Qiashredder homogenizer, RNA extracted with RNeasy Mini Kit. RNA verified with NanoDrop ND-1000, Agilent RNA 6000 Nano Assay and agarose electrophoresis.

treatment_protocol: Untreated

tag: From patient 294

tag: 69 year old female

tag: Obtained after informed consent during orthopedic hip surgery

tag: Protocol approved by the ethics committee of the Montreal Jewish General Hospital


title: In vivo aortic endothelial responses to diesel exhaust in wild-type mice, 1000 ug/m3, replicate #2, dye-reversal

description: Murine endothelial responses to dilute diesel exhaust at 1000 ug/ cubic meter.

hyb_protocol: cDNA probes were combined, purified and hybridized for 14 h at 42° C in a total volume 35 ul of a hybridization solution containing 25% formamide, 3 X SSC, 0.2% SDS, 1 ug of murine Cot1 DNA, 4ug of  polyA RNA, and 4 ug of tRNA. Stringency washing at room temperature was sequentially performed for ten minutes in each of the following solutions: 2X SSC containing 0.1% SDS, 0.1X SSC containing 0.1% SDS, and finally, 0.1X SSC.

scan_protocol: Slides were scanned using a Molecular Devices 4000B and the images analyzed with Genepix and Acuity software from Molecular Devices(CA).

source_name: Aortic endothelium from wild-type control mice

tag: Mice were Tg(TIE2GFP)287Sato [stock #003658] from Jackson Labs, Bar Harbor, ME. Males, age 4 months.

source_name: Aortic endothelium from mice exposed 30 days to 1000 ug/m3 of dilute diesel exhaust

extract_protocol: FACS sorting was utilized to obtain endothelium rendered fluorescent due to expression of GFP under control of Tie 2.  RNA representing 10,000 endothelial cells was subjected to amplification with Ovation Amino Allyl sytem (Nugen, CA)  to generate amplified cDNA.  cDNA  labeled with Cy dye sulfo-NHS active dye according to manufacturer's instructions.

treatment_protocol: Mice were exposed 30 days to diesel exhaust diluted to 1000 ug per cubic meter (with HEPA-filtered air) for 4 hours/day,  5 days/week, for 30 days.


title: mMSCs CBE_2

description: CBE treated

source_name: Murine bone marrow mesenchymal stromal cells

growth_protocol: Growth in DMEM HG medium with 10% FBS, passaged q 2 days.

treatment_protocol: Treated with Conduritol B epoxide (CBE) at 100 micromolar for 5 days

tag: Strain


title: 293T cells ctrl_1

description: Control cells

source_name: 293T cells

growth_protocol: Growth in DMEM HG medium, passaged q 2 days.

treatment_protocol: untreated

tag: Human Embryonic Kidney 293 cells which also contains the SV40 Large T-antigen.


title: hMSCs CBE_1

description: CBE treated

source_name: Human primary bone marrow mesenchymal stromal cells


title: mMSCs CBE_1

description: CBE treated


title: Brain_Normal_M_122E

status: Public on Dec 10 2008

city: Cleveland

first: Girish

last: Hiremath

state: OH

address: 9500 Euclid Avenue

department: Neurosurgery

institute: Cleveland Clinic

hyb_protocol: cRNA was quantified using a nanodrop spectrophotometer and the cRNA quality (size distribution) was further analyzed on a 1% agarose gel. cRNA was hybridized to the Illumina RatRef-12 v1 Expression BeadChip using standard protocols (provided by Illumina, San Diego, CA). Individual hybridizations were performed on each sample, and no pooling of samples took place.

scan_protocol: Scan and Imaging procedures adhered strictly to standard protocols provided by Illumina, San Diego, CA.

data_processing: The summarized data from the raw microarray data were log2 transformed and processed with background correction, quantile normalization and variance stabilization (Bolstad et al, 2003). Quality control analyses were applied to detect the outlier samples.

organism: Rattus norvegicus

source_name: rat brain cortex, control, 60days

label_protocol: 250 ng of RNA was reverse transcribed into cRNA and biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: This animal was housed in the animal care facilities of Cleveland Clinic and was exposed to 12 hour light/dark cycles with free access to food and water.

extract_protocol: This animal was sacrificed and its brain was quickly isolated into RNAlater (Ambion, Austin, TX) and stored in -80C until extraction. Frozen brain slices stored in RNAlater were thawed on ice, and cortex and hippocampal regions were separated. Only cortex was used, this tissue was homogenized using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA extraction was then performed using a commercially available kit followed by a DNAse digestion step (Qiagen RNEasy Mini Kit, and Qiagen RNAse Free DNAse set, respectively, Valencia, CA).

treatment_protocol: Non-irradiated group of animals (controls).

value: Sprague-Dawley;

tag: Gender

value: Male;

tag: Age

value: 60 days;

tag: Tissue

value: cortex of rat brain


title: 293T cells CBE_2

description: CBE treated

tag: Human Embryonic Kidney 293 cells which also contain the SV40 Large T-antigen.


title: In vivo aortic endothelial responses to diesel exhaust in wild-type mice, 300 ug/m3, replicate #1

description: Murine endothelial responses to dilute diesel exhaust.

label_protocol: cDNA  labeled with Cy dye sulfo-NHS active dye according to manufacturer's instructions.

extract_protocol: FACS sorting was utilized to obtain endothelium rendered fluorescent due to expression of GFP under control of Tie 2.  RNA representing 10,000 endothelial cells was subjected to amplification with Ovation Amino Allyl sytem (Nugen, CA)  to generate amplified cDNA.

source_name: Aortic endothelium from mice exposed 30 days to 300 ug/m3 of dilute diesel exhaust

treatment_protocol: Mice were exposed 30 days to diesel exhaust diluted to 300 ug per cubic meter (with HEPA-filtered air) for 4 hours/day,  5 days/week, for 30 days.


title: Brain_Normal_F_122C

value: Female;


title: mMSCs ctrl_1

description: Control cells


title: In vivo aortic endothelial responses to diesel exhaust in Apo E (-/-) mice, 300 ug/m3, replicate #2, dye-reversal

description: Murine endothelial responses within Apo E (-/-) mice due to dilute diesel exhaust at 300 ug/ cubic meter.

source_name: Aortic endothelium from Apo E(-/-) mice exposed 30 days to 300 ug/m3 of dilute diesel exhaust

treatment_protocol: Mice were exposed 30 days to diesel exhaust diluted to 300 ug per cubic meter (with HEPA-filtered air) for 4 hours/day, 5 days/week, for 30 days.


title: mMSCs ctrl_2

description: Control cells


title: In vivo aortic endothelial responses to diesel exhaust in wild-type mice, 300 ug/m3, replicate #2, dye reversal

hyb_protocol: cDNA probes were combined, purified and hybridized for 14 h at 42° C in a total volume 35 ul of a hybridization solution containing 25% formamide, 3 X SSC, 0.2% SDS, 1 ug of murine Cot1 DNA, 4ug of polyA RNA, and 4 ug of tRNA. Stringency washing at room temperature was sequentially performed for ten minutes in each of the following solutions: 2X SSC containing 0.1% SDS, 0.1X SSC containing 0.1% SDS, and finally, 0.1X SSC.

data_processing: The GPR data was uploaded to Acuity software from Molecular Devices, normalized by ratio of medians. Filtered to mark Genepix flags. Log2 fold change of median value of experimental/control.

extract_protocol: FACS sorting was utilized to obtain endothelium rendered fluorescent due to expression of GFP under control of Tie 2. RNA representing 10,000 endothelial cells was subjected to amplification with Ovation Amino Allyl sytem (Nugen, CA) to generate amplified cDNA. cDNA labeled with Cy dye sulfo-NHS active dye according to manufacturer's instructions.


title: hMSCs CBE_2

description: CBE treated

tag: From patient 294, a 69 year old female. Obtained after informed consent during orthopedic hip surgery. Protocol approved by the ethics committee of the Montreal Jewish General Hospital.


title: hMSCs ctrl_1

description: Control cells

tag: Patient 294

tag: Female 69 years old

tag: Obtained after informed consent during orthopedia hip surgery

tag: Protocol approved by ethics committee of the Montreal Jewish General Hospital


title: Brain_CD_F_122J

source_name: rat brain cortex, irradiated, 60days

treatment_protocol: This animal was irradiated during the 17th day of gestation with 145cGy using a Cesium 137 source in a Shepherd irradiator (JL Shepherd and Associates, San Fernando, CA)


title: 293T cells CBE_1

description: CBE treated


title: In vivo aortic endothelial responses to diesel exhaust in wild-type mice, 1000 ug/m3, replicate #1


title: Brain_CD_F_122B


title: 293T cells ctrl_2

description: Control cells


title: Brain_Normal_M_122A


title: Brain_Normal_F_121K


title: Brain_Normal_M_121J


title: Brain_CD_F_121E

extract_protocol: This animal was sacrificed and the brain was quickly isolated into RNAlater (Ambion, Austin, TX) and stored in -80C until extraction. Frozen brain slices stored in RNAlater were thawed on ice, and cortex and hippocampal regions were separated. Only cortex was used, this tissue was homogenized using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA extraction was then performed using a commercially available kit followed by a DNAse digestion step (Qiagen RNEasy Mini Kit, and Qiagen RNAse Free DNAse set, respectively, Valencia, CA).


title: Brain_CD_M_121B


title: In vivo aortic endothelial responses to diesel exhaust in Apo E (-/-) mice, 300 ug/m3, replicate #1

tag: ApoE (-/-) and Tie2 GFP mice (strain name B6.129P2-Apoetm1Unc/J [stock #002052] and Tg(TIE2GFP)287Sato [stock #003658],  from Jackson Labs, Bar Harbor, ME) were interbred and genetically selected to obtain Tie2 GFP/ ApoE (-/-) mice on an approximately 1:1 mixed genetic background of C57Bl/6 and FVB/N.  Males, age 4 months at start of exposure.


title: Brain_CD_M_121C


title: Brain_Normal_M_121A


title: Brain_CD_F_121I


title: Brain_Normal_M_120K


title: Brain_Normal_M_120J


title: Brain_CD_M_120I


title: GM19207

status: Public on Dec 05 2008

city: philadelphia

first: Dustin

last: Hancks

state: PA

address: 415 curie blvd rm 515 crb

department: Genetics

institute: University of Pennsylvania

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 46 C on HG-FOCUS Array. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: HG-Fous arrays were scanned using the Affymetrix GS-2500 scanner.

data_processing: The expression data was analyzed with Affymetrix MAS 5.0, scaled to 500 and log2 transformed.  Further analysis was performed on genes defined as ‘Present’ in at least 80% of the individuals screened from one population.

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19207

label_protocol: IVT was carried out with the BioArray High Yield T7 RNA transcript labeling kit (Enzo)

growth_protocol: The cells were grown at a density of 5 x 10^5 mL in a humidified, 5% C02 incubator at 37 C in RPMI 1640 supplemented with 15% FBS, 2mM L-glutamine, 100 U/mL penicillin, and 0.1 mg/mL streptomycin.

extract_protocol: Total RNA was extracted with the RNeasy Mini-Kit (Qiagen), reverse-transcribed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen).

tag: HapMap YRI


title: Brain_CD_F_120H


title: GM19209

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19209


title: GM19210

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19210


title: GM19201

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19201


title: GM19200

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19200


title: GM19206

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19206


title: GM19193

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19193


title: GM19238

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19238


title: GM19160

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19160


title: GM19204

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19204


title: GM19203

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19203


title: GM19171

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19171


title: Brain_CD_M_120C


title: GM19239

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19239


title: GM19153

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19153


title: Brain_Normal_F_120F

source_name: rat brain cortex, control, 60days


title: GM19172

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19172


title: GM19223

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19223


title: GM19192

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19192


title: GM19222

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19222


title: GM19144

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19144


title: Ramos B cell line

status: Public on Dec 09 2008

city: Berlin

first: Marc

last: Sultan

address: Ihnestr. 73

country: Germany

institute: Max Planck Institute for molecular genetics

description: A model based analysis for tiling arrays  was applied to perform the intra-chip normalization, with the adjustment for exon arrays described by Kapur and colleagues . Quantile normalization was then applied between arrays  with Affy package in BioConductor (version 2.2) (R statistical environment, v.2.7.0) .

hyb_protocol: All probes were hybridized onto the Human Exon 1.0 ST Array (Affymetrix)  following the manufacturer's instructions

scan_protocol: Microarrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: The probe to exon assignment was done using a chip description file (HsEx10stv2_Hs_ENSE), based on Ensembl v.46 and provided as R package . Exon and gene expression were defined as the mean over probe intensities for both replicates.

source_name: Ramos B cell line

label_protocol: cDNA labeling and microarray hybridization were performed as described in GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, following manufacturer’s instructions (P/N 701880 Rev.4, www.affymetrix.com).

growth_protocol: B cells were cultured in parallel in 2*150 cm3 flasks with DMEM (penicillinstreptomycin) (Gibco) supplemented with 10% Fetal Calf Serum (FCS) (Biochrom) and Glutamax (1x) (Gibco). At passage 20 (confluent state), cells were trypsinized, washed off in PBS, pelleted and resuspended in 2 ml lysis solution RLT (Qiagen).

extract_protocol: Total RNA was then extracted from ~ 20 x 10^6 cells per sample (2*bcell samples) using RNeasy Midi extraction kit (Qiagen) by following the manufacturer s instructions. DNA was removed using the  on column digestion  protocol of the RNeasy Midi extraction kit (Qiagen). Total RNA quality was assessed by spectrophotometry (Nanodrop) and gel electrophoresis (1% agarose).

tag: Human Ramos B cell line


title: HEK293Tcells

source_name: human embryonic kidney 293T cell line

growth_protocol: HEK 293T cells were cultured in parallel in 2*150 cm3 flasks with DMEM (penicillinstreptomycin) (Gibco) supplemented with 10% Fetal Calf Serum (FCS) (Biochrom) and Glutamax (1x) (Gibco). At passage 20 (confluent state), cells were trypsinized, washed off in PBS, pelleted and resuspended in 2 ml lysis solution RLT (Qiagen).

extract_protocol: Total RNA was then extracted from ~ 20 x 10^6 cells per sample (2*HEK samples) using RNeasy Midi extraction kit (Qiagen) by following the manufacturer s instructions. DNA was removed using the  on column digestion  protocol of the RNeasy Midi extraction kit (Qiagen). Total RNA quality was assessed by spectrophotometry (Nanodrop) and gel electrophoresis (1% agarose).

tag: human embryonic kidney 293T cell line


title: GM19143

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19143


title: GM19159

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19159


title: GM19152

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19152


title: GM19138

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19138


title: GM19128

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19128


title: GM19116

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19116


title: GM19127

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19127


title: GM19141

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19141


title: GM19093

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19093


title: GM19102

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19102


title: GM19137

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19137


title: GM19130

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19130


title: GM18913

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18913


title: GM19099

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19099


title: GM19092

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19092


title: GM18912

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18912


title: GM18871

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18871


title: GM18858

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18858


title: GM19131

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19131


title: GM19101

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19101


title: GM18861

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18861


title: GM19119

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19119


title: GM18859

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18859


title: GM19140

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19140


title: GM18856

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18856


title: GM18862

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18862


title: GM18870

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18870


title: GM18855

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18855


title: GM19098

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM19098


title: GM18853

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18853


title: GM18852

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18852


title: GM18523

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18523


title: GM18517

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18517


title: GM18505

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18505


title: GM18522

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18522


title: GM18507

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18507


title: GM18504

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18504


title: GM18508

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18508


title: GM17199

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17199

tag: HapMap AFA


title: GM17195

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17195


title: GM18501

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18501


title: GM17200

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17200


title: GM17190

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17190


title: GM17192

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17192


title: GM17189

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17189


title: GM17193

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17193


title: GM17194

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17194


title: GM17182

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17182


title: GM18502

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18502


title: GM17198

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17198


title: GM17191

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17191


title: GM17183

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17183


title: GM17181

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17181


title: GM17196

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17196


title: GM17197

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17197


title: GM17179

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17179


title: GM17180

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17180


title: GM17188

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17188


title: GM17185

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17185


title: GM17184

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17184


title: GM18516

source_name: Lymphoblastoid Cell Lines (LCL), YRI, GM18516


title: GM17187

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17187


title: GM17162

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17162


title: GM17177

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17177


title: GM17161

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17161


title: GM17163

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17163


title: GM17160

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17160


title: GM17176

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17176


title: GM17157

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17157


title: GM17159

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17159


title: GM17178

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17178


title: GM17145

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17145


title: GM17149

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17149


title: GM17155

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17155


title: GM17156

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17156


title: GM17148

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17148


title: GM17142

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17142


title: GM17147

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17147


title: GM17140

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17140


title: GM17139

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17139


title: GM17150

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17150


title: GM17154

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17154


title: GM17138

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17138


title: GM17143

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17143


title: GM17137

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17137


title: GM17158

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17158


title: GM17144

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17144


title: GM17136

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17136


title: GM17141

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17141


title: GM17134

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17134


title: GM17126

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17126


title: GM17125

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17125


title: GM17135

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17135


title: GM17132

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17132


title: GM17127

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17127


title: GM17128

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17128


title: GM17133

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17133


title: GM17122

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17122


title: GM17118

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17118


title: GM17121

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17121


title: GM17116

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17116


title: GM17130

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17130


title: GM17131

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17131


title: GM17114

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17114


title: GM17115

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17115


title: GM17124

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17124


title: GM17113

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17113


title: GM17119

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17119


title: GM17129

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17129


title: GM17111

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17111


title: GM17123

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17123


title: GM17117

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17117


title: GM17110

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17110


title: GM17120

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17120


title: GM17146

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17146


title: GM17108

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17108


title: GM17109

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17109


title: GM12891

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12891

tag: HapMap CEU


title: GM12892

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12892


title: GM17102

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17102


title: GM17106

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17106


title: GM17103

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17103


title: GM17105

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17105


title: GM12875

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12875


title: GM12872, Technical replicate

description: GM12872, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12872


title: GM12875, Technical replicate

description: GM12875, Technical replicate


title: GM17112

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17112


title: GM17104

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17104


title: GM12815

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12815


title: GM12873, Technical replicate

description: GM12873, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12873


title: GM12763, Technical replicate

description: GM12763, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12763


title: GM12813, Technical replicate

description: GM12813, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12813


title: GM12814, Technical replicate

description: GM12814, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12814


title: GM12812, Technical replicate

description: GM12812, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12812


title: GM12872


title: GM12873


title: GM12874

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12874


title: GM12815, Technical replicate

description: GM12815, Technical replicate


title: GM17107

source_name: Lymphoblastoid Cell Lines (LCL), AFA, GM17107


title: GM12812


title: GM12813


title: GM12874, Technical replicate

description: GM12874, Technical replicate


title: GM12763


title: GM12762, Technical replicate

description: GM12762, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12762


title: GM12762


title: GM12814


title: GM12751

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12751


title: GM12750

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12750


title: GM12760, Technical replicate

description: GM12760, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12760


title: GM12761

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12761


title: GM12751, Technical replicate

description: GM12751, Technical replicate


title: GM12750, Technical replicate

description: GM12750, Technical replicate


title: GM12264

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12264


title: GM12154

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12154


title: GM12146, Technical replicate

description: GM12146, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12146


title: GM12717

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12717


title: GM12155

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12155


title: GM12156, Technical replicate

description: GM12156, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12156


title: GM12716

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12716


title: GM12760


title: GM12761, Technical replicate

description: GM12761, Technical replicate


title: GM12248

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12248


title: GM12248, Technical replicate

description: GM12248, Technical replicate


title: GM12156


title: GM12249, Technical replicate

description: GM12249, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12249


title: GM12236

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12236


title: GM12239

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12239


title: GM12154, Technical replicate

description: GM12154, Technical replicate


title: GM12239, Technical replicate

description: GM12239, Technical replicate


title: GM12057

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12057


title: GM12145

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12145


title: GM11993, Technical replicate

description: GM11993, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11993


title: GM11994

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11994


title: GM12146


title: GM12236, Technical replicate

description: GM12236, Technical replicate


title: GM11995

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11995


title: GM12005

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12005


title: GM12144, Technical replicate

description: GM12144, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12144


title: GM12234

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12234


title: GM12043

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12043


title: GM12145, Technical replicate

description: GM12145, Technical replicate


title: GM11993


title: GM12004

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12004


title: GM12043, Technical replicate

description: GM12043, Technical replicate


title: GM12056

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12056


title: GM11995, Technical replicate

description: GM11995, Technical replicate


title: GM12249


title: GM12144


title: GM12044, Technical replicate

description: GM12044, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12044


title: GM12044


title: GM11994, Technical replicate

description: GM11994, Technical replicate


title: GM12003

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12003


title: GM12006

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM12006


title: GM11882, Technical replicate

description: GM11882, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11882


title: GM11881, Technical replicate

description: GM11881, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11881


title: GM11992

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11992


title: GM11882


title: GM11881


title: GM07357, Technical replicate

description: GM07357, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM07357


title: GM07056, Technical replicate

description: GM07056, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM07056


title: GM11829

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11829


title: GM11831

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11831


title: GM07034, Technical replicate

description: GM07034, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM07034


title: GM07034


title: GM07000

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM07000


title: GM11992, Technical replicate

description: GM11992, Technical replicate


title: GM07022

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM07022


title: GM07345, Technical replicate

description: GM07345, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM07345


title: GM06994, Technical replicate

description: GM06994, Technical replicate

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM06994


title: GM07000, Technical replicate

description: GM07000, Technical replicate


title: GM07357


title: GM07055

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM07055


title: GM07022, Technical replicate

description: GM07022, Technical replicate


title: GM07345


title: GM11832

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11832


title: GM11830

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11830


title: GM07056


title: GM07055, Technical replicate

description: GM07055, Technical replicate


title: GM11839

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11839


title: GM06993

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM06993


title: GM06994


title: GM06993, Technical replicate

description: GM06993, Technical replicate


title: GM11840

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM11840


title: GM06985

source_name: Lymphoblastoid Cell Lines (LCL), CEU, GM06985


title: GM06985, Technical replicate

description: GM06985, Technical replicate


title: 13192009 - LAR_48h_T vs LAR_48h_C

status: Public on Dec 01 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

description: Analyse the transcriptome of plants of Arabidopsis thaliana developping a localized acquired resistance and a hypersensitive response. The goal is to identify genes inducing LAR and/or HR.

hyb_protocol: LAR_48h_C Cy5 / LAR_48h_T Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

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

growth_protocol: leaf - 21° (day) and 19°C (night), Photoperiod: 8h/16h. Hygrometry : 70%

treatment_protocol: no treatment

tag: Arabidopsis thaliana (col-0)  - dev.stage (Boyes et al. Plant Cell 2001):boyes = 3.9

treatment_protocol: Name:Pseudomonas syringae_48h - pathogen - pathogen infection,pseudomonas syringae pv. tomato dc3000:quantity 5e-07cfu/ml time 48hour . The bacteria contains the avrRpm1 avirulence gene. Leaves were double-inoculated with a seringe on the abaxial side (apical and basal zones)Name: - pathogen - pathogen infection,pseudomonas syringae pv. tomato dc3000:quantity 10mM time 48hour . Control. Leaves were double-inoculated with a seringe on the abaxial side (apical and basal zones)


title: 13192072 - HR-6h-C vs HR-6h-T

hyb_protocol: HR-6h-T Cy5 / HR-6h-C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - Earth Day : 21°, 8h Night : 19°C 16h Hygrometry : 70%

treatment_protocol: Name:Pseudomonas syringae_06h - pathogen - pathogen infection,pseudomonas syringae pv. tomato dc3000:quantity 5e-07cfu/ml time 6hour . The bacteria contains the avrRpm1 avirulence gene. Leaves were double-inoculated with a seringe on the abaxial side (apical and basal zones)

tag: Arabidopsis thaliana (col-0)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

treatment_protocol: Name:MgCl2_06h - pathogen - pathogen infection,pseudomonas syringae pv. tomato dc3000:quantity 10mM time 6hour . Control. Leaves were double-inoculated with a seringe on the abaxial side (apical and basal zones)


title: 13192004 - LAR_06h_C vs LAR_06h_T

hyb_protocol: LAR_06h_T Cy5 / LAR_06h_C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Glia SOD1G93Atg rep2

status: Public on Dec 04 2008

first: Gabriella

middle: Lutz

last: Boulting

address: 7 Divinity Ave. rm 423

department: Stem Cell and Regenerative Biology

institute: Harvard University

hyb_protocol: Standard procedure outlined by the  Illumina TotalPrep RNA Amplification Kit.

scan_protocol: Arrays were read by Illumina Bead Array Reader. Analysis was done using the Illumina Bead Studio Program.

data_processing: Average' Normalization setting was used in BeadStudio

source_name: Glia from pup transgenic for SOD1G93A_replicate2

extract_protocol: P1-P3 mouse pups transgenic for SOD1G93A, SOD1WT or non-transgenic pups were sacrificed by using an approved method of euthanasia. Under a dissection microscope, the parenquima were isolated and the meninges were carefully stripped away with fine forceps. The tissue was then dissected into small pieces and transferred to a solution containing 12ml of HBSS, 1.5 ml of trypsin (GIBCO) and 1% DNAse (Sigma) and incubated at 37ºC for 15 min, swirling the mixture periodically. The supernatant containing the dissociated cells was collected and 3ml of serum was added to inhibit the trypsin.   Cells were then centrifuged at 1000 rpm for 5 min, resuspended in Glia medium: (Minimun Essential Medium with Earl’s salts (GIBCO), D-(+)-Glucose 20% (Sigma), Penicillin-streptomycin (GIBCO), 10% Horse Serum (GIBCO)) and plated at the concentration of 80,000 cells per mL in T75 flasks (Falcon).


title: 13192007 - LAR_24h_T vs LAR_24h_C

hyb_protocol: LAR_24h_C Cy5 / LAR_24h_T Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:MgCl2_24h - pathogen - pathogen infection,pseudomonas syringae pv. tomato dc3000:quantity 10mM time 24hour . Control. Leaves were double-inoculated with a seringe on the abaxial side (apical and basal zones)

treatment_protocol: Name:Pseudomonas syringae_24h - pathogen - pathogen infection,pseudomonas syringae pv. tomato dc3000:quantity 5e-07cfu/ml time 24hour . The bacteria contains the avrRpm1 avirulence gene. Leaves were double-inoculated with a seringe on the abaxial side (apical and basal zones)


title: 13192008 - LAR_48h_C vs LAR_48h_T

hyb_protocol: LAR_48h_T Cy5 / LAR_48h_C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Glia nontransgenic rep2

description: B6SJL 2Gur/J

source_name: Glia from nontransgenic pup_replicate2

label_protocol: Standard procedure outlined by the  Illumina TotalPrep RNA Amplification Kit.


title: 13192006 - LAR_24h_C vs LAR_24h_T

hyb_protocol: LAR_24h_T Cy5 / LAR_24h_C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Glia WTSOD1tg rep2

source_name: Glia from pup transgenic for WT SOD1_replicate2


title: 13192071 - HR-6h-T vs HR-6h-C

hyb_protocol: HR-6h-C Cy5 / HR-6h-T Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Glia SOD1G93Atg rep3

source_name: Glia from pup transgenic for SOD1G93A_replicate3


title: Glia nontransgenic rep3

description: B6SJL 2Gur/J

source_name: Glia from nontransgenic pup_replicate3


title: Glia WTSOD1tg rep1

source_name: Glia from pup transgenic for WT SOD1_replicate1


title: Glia nontransgenic rep1

description: B6SJL 2Gur/J

source_name: Glia from nontransgenic pup_replicate1


title: YF15D3; Lausanne Cohort

city: Montréal

first: Bastian

middle: Robert

last: Angermann

state: Quebec

address: 264 René-Lévesque Est

country: Canada

institute: Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CR-CHUM) Saint-Luc

description: In the Lausanne Cohort 11 donors were enrolled vaccinated with Stamail, wohle blood was sampled on days 0,3 and 7.

hyb_protocol: The biotinylated cRNA was hybridized onto Illumina Human RefSeq-8 BeadChips v2 at 58oC for 20 hours.

scan_protocol: Fluorescent array images were collected with Illumina BeadStation 500GX scanner fluorescent scanner and image intensity data were extracted using Illumina BeadStudio version 3 software.

data_processing: Illuma probe data were exported from BeadStudio as raw data and were screened for quality.  Samples failing chip visual inspection and control examination were removed. The R software was used to quantile normalize the probe intensities, and to minimum-replace (surrogate-replacement policy) values below background using the mean background vale of the probe controls rounded up to the rearest power of 2, determined from the microarray quality controls to reduce noise and reduce "over-inflated" expression ratios in subsequent steps.

source_name: Whole Blood, Non stimulated, Day 3

label_protocol: Total RNA as amplified and labeled using the Illumina TotalPrep RNA Amplication kit which is based on the Eberwine amplification protocol. It involves a first cDNA synthesis step followed by in vitro transcription of cRNA.

extract_protocol: Total RNA was purified using RNA extraction kits from Qiagen.  Quantification was performed using NanoDrop Technologies spectrophotometer and RNA quality was assessed using the Experion automated electrophoresis system from Bio-Rad.

tag: Vaccinated Volunteer :YF15; Gender;F


title: Glia SOD1G93Atg rep1

source_name: Glia from pup transgenic for SOD1G93A_replicate1


title: Glia WTSOD1tg rep3

source_name: Glia from pup transgenic for WT SOD1_replicate3


title: YF21D7; Lausanne Cohort

source_name: Whole Blood, Non stimulated, Day 7

tag: Vaccinated Volunteer :YF21; Gender;F


title: 13192005 - LAR_06h_T vs LAR_06h_C

hyb_protocol: LAR_06h_C Cy5 / LAR_06h_T Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: YF20D7; Lausanne Cohort

tag: Vaccinated Volunteer :YF20; Gender;F


title: YF21D3; Lausanne Cohort


title: YF21BL; Lausanne Cohort

source_name: Whole Blood, Non stimulated, Day 0

tag: Non Vaccinated Volunteer :YF21; Gender;F


title: YF14D7; Lausanne Cohort

tag: Vaccinated Volunteer :YF14; Gender;F


title: YF20BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF20; Gender;F


title: YF19D7; Lausanne Cohort

tag: Vaccinated Volunteer :YF19; Gender;F


title: YF20D3; Lausanne Cohort


title: YF19BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF19; Gender;F


title: YF15BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF15; Gender;F


title: YF18D3; Lausanne Cohort

tag: Vaccinated Volunteer :YF18; Gender;F


title: YF16BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF16; Gender;F


title: YF18D7; Lausanne Cohort


title: YF16D3; Lausanne Cohort

tag: Vaccinated Volunteer :YF16; Gender;F


title: YF16D7; Lausanne Cohort


title: YF18BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF18; Gender;F


title: YF14D3; Lausanne Cohort

tag: Vaccinated Volunteer :YF14;; Gender;F


title: YF17BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF17; Gender;F


title: YF17D3; Lausanne Cohort

tag: Vaccinated Volunteer :YF17; Gender;F


title: YF14BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF14; Gender;F


title: YF13D7; Lausanne Cohort

tag: Vaccinated Volunteer :YF13; Gender;F


title: YF10D7; Lausanne Cohort

tag: Vaccinated Volunteer :YF10; Gender;M


title: YF19D3; Lausanne Cohort


title: YF17D7; Lausanne Cohort


title: YF13D3; Lausanne Cohort


title: YF12D3; Lausanne Cohort

tag: Vaccinated Volunteer :YF12; Gender;F


title: YF15D7; Lausanne Cohort

tag: Vaccinated Volunteer :YF15; Gender;F


title: YF13BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF13; Gender;F


title: YF020_NS_3; Montreal Cohort

description: The Montreal Cohort enrolled 15 donors, and sampled whole blood pre vaccination with the Sanofi-Pasteur YF17D-204 YF-VAX vaccine, and on days 3,7,10,14,28,60,365 post vaccination.

source_name: Whole Blood, Non stimulated, Day3

tag: Vaccinated Volunteer

value: YF020;  Gender:F;  Age:31


title: YF12BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF12; Gender;F


title: YF10BL; Lausanne Cohort

tag: Non Vaccinated Volunteer :YF10; Gender;M


title: F9 cells Ezh2 chip on chip replicate 2

type: genomic

city: New York

first: Raphael

middle: F

last: Margueron

state: NY

address: 522 first Ave

department: Biochemistry

institute: NYU Langone medical center

description: Ezh2 genome-wide binding profiles in F9 cells by chip on chip

hyb_protocol: Hybridization onto the mouse promoter array, which includes 244K features distributed onto two slides (Agilent –G4490), washing and scanning were carried out according to the manufacturers instructions.

scan_protocol: According to Agilent Scanning Software

data_processing: Log ratios were calculated by the Agilent Feature Extraction software and automatically underwent Lowess normalization.

molecule: genomic DNA

source_name: Input for mouse Ezh2 chromatin immunoprecipitation

label_protocol: Input samples were amplified by LMPCR and 1 microgram of LM-PCR product was labeled with Cy3 using Invitrogen CHG kit (18095-011). Labelling reaction were cleaned up by invitrogen bind and elute CGH columns (18095-011).

growth_protocol: F9 cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: F9 cells were cross-linked by addition of formaldehyde (to 1% final concentration). Cross-linking was allowed to proceed at room temperature for 10 min and was terminated with glycine (final concentration 0.125 m). Cells were washed with PBS. Cells were collected by centrifugation and were rocked in buffer containing 50 mm HEPES (pH 7.5), 140 mm NaCl, 1 mm EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and protease inhibitors (1 mm AEBSF, 10 μg/ml aprotinin, 1 μg/ml leupeptin, 1 μg/ml pepstatin A), at 4°C for 10 min. Cells were collected by centrifugation at 4K rpm for 10 min, and the resulting pellet was resuspended in 200 mm NaCl, 1 mm EDTA, 0.5 mm EGTA, 10 mm Tris (pH 8), and protease inhibitors and incubated 10 min at room temperature. Nuclei were collected by centrifugation at 4K rpm for 10 min, resuspended in sonication buffer (1 mm EDTA, 0.5 mm EGTA, 10 mm Tris at pH 8, and protease inhibitors), and sonicated on ice to an average length of 350 bp

tag: The F9 murine teratoma cell line (obtained from ATCC)

source_name: IP for mouse Ezh2 chromatin immunoprecipitation

label_protocol: IP samples were amplified by LMPCR and 1 microgram of LM-PCR product was labeled with Cy5 using Invitrogen CHG kit (18095-011). Labelling reaction were cleaned up by invitrogen bind and elute CGH columns (18095-011).


title: YF019_NS_0; Montreal Cohort

source_name: Whole Blood, Non stimulated, Day0

tag: Non vaccinated Volunteer

value: YF019;  Gender:F;  Age:43


title: YF10D3; Lausanne Cohort


title: F9 cells Ezh2 chip on chip replicate 1


title: YF12D7; Lausanne Cohort


title: F9 cells Ezh1 chip on chip replicate 1

description: Ezh1 genome-wide binding profiles in F9 cells by chip on chip

source_name: Input for mouse Ezh1 chromatin immunoprecipitation

source_name: IP for mouse Ezh1 chromatin immunoprecipitation


title: F9 cells Ezh1 chip on chip replicate 2


title: YF017_NS_7; Montreal Cohort

source_name: Whole Blood, Non stimulated, Day7

value: YF017;  Gender:F;  Age:22


title: YF010_NS_10; Montreal Cohort

source_name: Whole Blood, Non stimulated, Day10

value: YF010;  Gender:M;  Age:27


title: YF019_NS_7; Montreal Cohort


title: YF011_NS_14; Montreal Cohort

source_name: Whole Blood, Non stimulated, Day14

value: YF011;  Gender:F;  Age:25


title: YF012_NS_3; Montreal Cohort

value: YF012;  Gender:F;  Age:29


title: YF011_NS_28; Montreal Cohort

source_name: Whole Blood, Non stimulated, Day28


title: YF012_NS_7; Montreal Cohort


title: YF020_NS_0.2; Montreal Cohort


title: YF019_NS_3; Montreal Cohort


title: YF011_NS_10; Montreal Cohort


title: YF008_NS_28; Montreal Cohort

value: YF008;  Gender:F;  Age:23


title: YF010_NS_14; Montreal Cohort


title: YF013_NS_0; Montreal Cohort

value: YF013;  Gender:M;  Age:28


title: YF010_NS_7; Montreal Cohort


title: YF009_NS_14; Montreal Cohort

value: YF009;  Gender:F;  Age:34


title: YF009_NS_7; Montreal Cohort


title: YF008_NS_14; Montreal Cohort


title: YF005_NS_60; Montreal Cohort

source_name: Whole Blood, Non stimulated, Day60

value: YF005;  Gender:F;  Age:28


title: YF008_NS_0; Montreal Cohort


title: YF005_NS_10; Montreal Cohort


title: YF009_NS_3; Montreal Cohort


title: YF008_NS_10; Montreal Cohort


title: YF012_NS_28; Montreal Cohort


title: YF007_NS_28; Montreal Cohort

value: YF007;  Gender:F;  Age:26


title: YF007_NS_14; Montreal Cohort


title: YF012_NS_14; Montreal Cohort


title: YF004_NS_14; Montreal Cohort

value: YF004;  Gender:F;  Age:21


title: YF005_NS_7; Montreal Cohort


title: YF012_NS_10; Montreal Cohort


title: YF004_NS_10; Montreal Cohort


title: YF011_NS_0; Montreal Cohort


title: YF012_NS_0; Montreal Cohort


title: YF011_NS_7; Montreal Cohort


title: YF011_NS_60; Montreal Cohort


title: YF010_NS_0; Montreal Cohort


title: YF009_NS_60; Montreal Cohort


title: YF009_NS_28; Montreal Cohort


title: YF011_NS_3; Montreal Cohort


title: YF010_NS_28; Montreal Cohort


title: YF008_NS_3; Montreal Cohort


title: YF004_NS_60; Montreal Cohort


title: YF007_NS_0; Montreal Cohort


title: YF009_NS_0; Montreal Cohort


title: YF016_NS_28; Montreal Cohort

value: YF016;  Gender:M;  Age:23


title: YF017_NS_3; Montreal Cohort


title: YF004_NS_7; Montreal Cohort


title: YF018_NS_7; Montreal Cohort

value: YF018;  Gender:F;  Age:25


title: YF007_NS_3; Montreal Cohort


title: YF017_NS_0; Montreal Cohort


title: YF010_NS_3; Montreal Cohort


title: YF008_NS_7; Montreal Cohort


title: YF018_NS_3; Montreal Cohort


title: YF008_NS_60; Montreal Cohort


title: YF018_NS_0; Montreal Cohort


title: YF004_NS_28; Montreal Cohort


title: YF018_NS_60; Montreal Cohort


title: YF004_NS_3; Montreal Cohort


title: YF007_NS_10; Montreal Cohort


title: YF017_NS_10; Montreal Cohort


title: YF020_NS_10; Montreal Cohort


title: YF020_NS_7; Montreal Cohort


title: YF015_NS_10; Montreal Cohort

value: YF015;  Gender:M;  Age:26


title: YF014_NS_10; Montreal Cohort

value: YF014;  Gender:F;  Age:28


title: YF014_NS_14; Montreal Cohort


title: YF014_NS_3; Montreal Cohort


title: YF013_NS_7; Montreal Cohort


title: YF014_NS_7; Montreal Cohort


title: YF018_NS_14; Montreal Cohort


title: YF019_NS_10; Montreal Cohort


title: YF020_NS_0.1; Montreal Cohort


title: YF015_NS_7; Montreal Cohort


title: YF013_NS_10; Montreal Cohort


title: YF013_NS_60; Montreal Cohort


title: YF015_NS_0; Montreal Cohort


title: YF018_NS_28; Montreal Cohort


title: YF013_NS_28; Montreal Cohort


title: YF019_NS_14; Montreal Cohort


title: YF014_NS_60; Montreal Cohort


title: YF015_NS_28; Montreal Cohort


title: YF015_NS_60; Montreal Cohort


title: YF018_NS_10; Montreal Cohort


title: YF016_NS_0; Montreal Cohort


title: YF016_NS_10; Montreal Cohort


title: YF013_NS_14; Montreal Cohort


title: YF014_NS_0; Montreal Cohort


title: YF014_NS_28; Montreal Cohort


title: YF015_NS_3; Montreal Cohort


title: Patient_#5000_C3

type: protein

city: Budapest

first: József

last: Prechl

address: Pázmány Péter s. 1/C

department: Immunology Research Group

country: Hungary

institute: ELTE-MTA

hyb_protocol: Dried arrays were rinsed in PBS for 15 minutes before use, then incubated with 5 times diluted serum at 37°C for 1 hour. Sera were diluted in 5% BSA, 0.05% Tween 20 Ca and Mg supplemented Veronal buffer. Serum treated slides were washed with 0.05% Tween 20 containing PBS, then incubated in 1:5000 diluted Cy5-conjugated F(ab')2 fragment goat anti-human IgM (Jackson ImmunoResearch). Following washing in 0.05% Tween 20 containing PBS, arrays were dried and scanned.

scan_protocol: Arrays were scanned on Typhoon Trio+ imager (Amersham Bioscience) (Excitation:633nm ; Emission: 670 BP30 , PMT:410 Mode:Fluorescence, Sensitivity:Normal, FocalPlane=+3 mm). Data were analyzed with ImageQuantTL (Amersham Bioscience) software.

data_processing: Background derived from marked spots, was substracted from signal. For interassay comparison, data were normalized to the mean of two dilutions of printed anti-human IgG+IgM control material (ID_REF: #539, #571, #603, #355, #387, #419). Only data derived from slides with normalization factor between 0.4 and 2.5 were considered suitable for analysis. Based on the distribution of data normalized fluorescence intensity signals smaller than 1000 for IgM were rounded up to these values.

molecule: protein

source_name: serum

label_protocol: Labeling with fluorescent antibodies was carried out at room temperature for 30 min in 5% BSA and 0.05% Tween 20 containing PBS.

growth_protocol: Serum samples were stored at -70C

extract_protocol: Serum sample was centrifuged for 6min at 15000g for removing particles

tag: SEX

value: Female


title: Patient_#5381_C3

value: Male


title: Patient_#5415_C3


title: Patient_#6209_C3


title: Patient_#6223_C3


title: Patient_#5982_C3


title: YF016_NS_3; Montreal Cohort


title: Patient_#6311_C3


title: YF015_NS_14; Montreal Cohort


title: YF016_NS_7; Montreal Cohort


title: Patient_#3936_C3


title: Patient_#6277_C3


title: Patient_#4199_C3


title: Patient_#6248_C3


title: Patient_#4248_C3


title: Patient_#4211_C3


title: Patient_#4624_C3


title: Patient_#6196_C3


title: Patient_#4249_C3


title: Patient_#5143_C3


title: Patient_#6000_C3


title: Patient_#5066_C3


title: Patient_#6209_IgA


title: Patient_#5415_IgA


title: Patient_#5982_IgA


title: Patient_#6000_IgA


title: Patient_#5134_C3


title: Patient_#6196_IgA


title: Patient_#2988_C3


title: Patient_#3899_C3


title: Patient_#1000_C3


title: Patient_#3024_C3


title: Patient_#2000_C3


title: Patient_#3937_C3


title: Patient_#3951_C3


title: Patient_#3773_C3


title: Patient_#2989_C3


title: Patient_#6248_IgA


title: Patient_#6277_IgA


title: Patient_#6223_IgA


title: Patient_#6311_IgA


title: Patient_#3885_C3


title: Patient_#5143_IgA


title: Patient_#5381_IgA


title: Patient_#5134_IgA


title: Patient_#5000_IgA


title: Patient_#5066_IgA


title: Patient_#4248_IgA


title: Patient_#3936_IgA


title: Patient_#3024_IgA


title: Patient_#3773_IgA


title: Patient_#1000_IgA


title: Patient_#2988_IgA


title: Patient_#3899_IgA


title: Patient_#2989_IgA


title: Patient_#2000_IgA


title: Patient_#3885_IgA


title: Patient_#3937_IgA


title: Patient_#4249_IgA


title: Patient_#4199_IgA


title: Patient_#4624_IgA


title: Patient_#3951_IgA


title: Patient_#4211_IgA


title: HFF 24hpi Rep 2

city: Moscow

first: Holger

last: Hannemann

state: ID

department: MMBB

institute: University of Idaho

description: HFF 24hpi Rep2

hyb_protocol: protocols for hybridization and stripping were provided by Combimatrix.

scan_protocol: The fluorescence of each feature on the hybridized slides was read on an Axon GenePix 4200A (Axon, Sunnyvale, CA), and the raw fluorescence values were obtained using the Combimatrix MicroArray Imager

data_processing: First, a mean value was calculated for each feature on the array from the three technical replicates. Then, the variance stabilization normalization was calculated seperately for the 12 hpi and the 24 hpi values.

organism:
Homo sapiens
Human herpesvirus 5 strain Towne

source_name: human foreskin fibroblast (HFF) cell line; harvested after 24 hpi

label_protocol: Amplified RNA was labelled with Cy5 using the ULS labelling Kit for Combimatrix Arrays (Kreatech Biotechnology)

growth_protocol: Primary human foreskin fibroblast cells were grown in Eagle’s minimal essential medium (MEM, Gibco BRL) supplemented with 10% fetal bovine serum (FBS, Atlanta Biologicals), 200U/ml penicillin, 200µg/ml streptomycin, 2mM glutamine and 1.5µg/ml Amphotericin B (all Gibco BRL). The telomerase immortalized human lung fibroblast (THF) cell line was grown in DMEM/F12 (Gibco BRL) supplemented with 10% FBS, 200U/ml penicillin, 200µg/ml streptomycin and 2mM glutamine. THF derived p53-/- telomerase immortalized human fibroblasts were grown in DMEM supplemented with 7.5% FBS, 200U/ml penicillin, 200µg/ml streptomycin and 2mM glutamine (6). All cells were maintained at 37°C in a humified atmosphere containing 5% CO2.

extract_protocol: SV Total RNA Isolation Kit (Promega).RNA was amplified with the  Superscript RNA Amplification kit (Invitrogen)

treatment_protocol: Cells were synchronized in G0 by serum starvation for 60h (8), trypsinized and replated onto 100mm dishes at a density of 1x106 cells per plate for microarray and RT-PCR. Cells were then infected with the HCMV Towne strain 3 h after reseeding at an MOI of 1 for the microarray studies. Virus containing media was replaced by fresh media 3 h post infection (hpi), the cells were harvested by trypsinization after 12 or 24 hpi and the pellets were stored at -80°C until use.


title: THF 24hpi Rep 1

description: THF 24hpi Rep1

source_name: telomerase immortalized human foreskin fibroblast (THF) cell line; harvested after 24 hpi


title: HFF 24hpi Rep 3

description: HFF 24hpi Rep3

tag: human foreskin fibroblast (HFF) cell line


title: THF 24hpi Rep 2

description: THF 24hpi Rep2

tag: telomerase immortalized human foreskin fibroblast (THF) cell line


title: HFF 24hpi Rep 1

description: HFF 24hpi Rep1


title: p53KO 24hpi Rep 1

description: p53KO 24hpi Rep 1

source_name: p53 deficient telomerase immortalized human foreskin fibroblast )p53KO) cell line; harvested after 24 hpi


title: p53KO 24hpi Rep 2

description: p53KO 24hpi Rep 2

tag: p53 deficient telomerase immortalized human foreskin fibroblast )p53KO) cell line


title: THF 24hpi Rep 3

description: THF 24hpi Rep2


title: YF016_NS_14; Montreal Cohort


title: p53KO 24hpi Rep 3

description: p53KO 24hpi Rep 3


title: p53KO 12hpi Rep 3

description: p53KO 12hpi Rep 3

source_name: p53 deficient telomerase immortalized human foreskin fibroblast )p53KO) cell line; harvested after 12 hpi


title: THF 12hpi Rep 3

description: THF 12hpi Rep 3

source_name: telomerase immortalized human foreskin fibroblast (THF) cell line; harvested after 12 hpi


title: p53KO 12hpi Rep 2

description: p53KO 12hpi Rep 2


title: p53KO 12hpi Rep 1

description: p53KO 12hpi Rep 1


title: THF 12hpi Rep 1

description: THF 12hpi Rep1


title: Patient_#6248_IgG


title: Patient_#6277_IgG


title: Patient_#6209_IgG


title: THF 12hpi Rep 2

description: THF 12hpi Rep 2


title: Patient_#6311_IgG


title: HFF 12hpi Rep 2

description: HFF 12hpi Rep 2

source_name: human foreskin fibroblast (HFF) cell line; harvested after 12 hpi


title: Patient_#5415_IgG


title: HFF 12hpi Rep 3

description: HFF 12hpi Rep 3


title: HFF 12hpi Rep 1

description: HFF 12hpi Rep1


title: Patient_#4211_IgG


title: Patient_#4249_IgG


title: Patient_#4199_IgG


title: Patient_#4248_IgG


title: Patient_#5982_IgG


title: Patient_#6196_IgG


title: Patient_#5066_IgG


title: Patient_#6000_IgG


title: Patient_#6223_IgG


title: Patient_#3951_IgG


title: Patient_#3937_IgG


title: Patient_#3936_IgG


title: Patient_#5000_IgG


title: Patient_#4624_IgG


title: Patient_#5381_IgG


title: Patient_#5134_IgG


title: Patient_#3885_IgG


title: Patient_#3773_IgG


title: Patient_#3899_IgG


title: Patient_#5143_IgG


title: Patient_#6223_IgM


title: Patient_#6248_IgM


title: Patient_#6311_IgM


title: Patient_#6277_IgM


title: Patient_#2989_IgG


title: Patient_#1000_IgG


title: Patient_#2000_IgG


title: Patient_#3024_IgG


title: Patient_#2988_IgG


title: Patient_#4624_IgM


title: Patient_#4249_IgM


title: Patient_#3885_IgM


title: Patient_#4211_IgM


title: Patient_#3773_IgM


title: Patient_#5381_IgM


title: Patient_#4199_IgM


title: Patient_#5143_IgM


title: Patient_#3951_IgM


title: Patient_#5000_IgM


title: Patient_#3937_IgM


title: Patient_#4248_IgM


title: Patient_#6196_IgM


title: Patient_#5415_IgM


title: Patient_#3936_IgM


title: Patient_#5134_IgM


title: Patient_#6209_IgM


title: Patient_#2988_IgM


title: Patient_#5066_IgM


title: Patient_#2989_IgM


title: Patient_#6000_IgM


title: Patient_#2000_IgM


title: Patient_#1000_IgM


title: Patient_#5982_IgM


title: Patient_#3024_IgM


title: 5448R-_2_AH1_red635

city: Wollongong

first: Andrew

last: Hollands

state: NSW

address: Northfields Ave

department: School of Biological Sciences

country: Australia

institute: University of Wollongong

description: We followed a cyclic design that allowed us to compare every condition to each other at least twice, and guaranteed dye swapping to eliminate effects of non-specific binding.

hyb_protocol: Equal amounts of dendrimer-labeled cDNA from different pairs of isolates were mixed, applied to the glass microarrays, and incubated for 16 h. After this first hybridization, the arrays were washed, labeled with a mixture of Alexa Fluor 546 and Alexa Fluor 647 (Genisphere), incubated for 3 h, washed again, then scanned.

scan_protocol: GenePix 4000B scanner (Axon Instruments, Inc.)

data_processing: Values below 0.01 were set to 0.01. Each measurement was divided by the 50.0th percentile of all measurements in that sample. Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.

label: Alexa Fluor 647

organism: Streptococcus pyogenes

source_name: GAS strain 5448R-, in vivo derived 24h

label_protocol: Bacterial RNA was treated with DNase Turbo (Ambion) for 1 h to remove any genomic DNA contamination, then converted it to dendrimer-labeled cDNA using the 3DNA Array 900TM kits (Genisphere, http://www.genisphere.com/array_detection_900.html) following the manufacturer’s protocol.

extract_protocol: To obtain in vivo-derived RNA for microarray analysis, a subcutaneous murine Teflon chamber model was used. Approximately 10e8 cfu of bacteria were injected in sterile Teflon chambers that had been surgically inserted under the skin of age-matched female BALB/c mice. After 24 h, bacteria were collected, tested for purity and phenotypic homogeneity on blood agar plates and Columbia-casein agar plates, respectively. Only pure isolates with homogeneous protease activity (either positive or negative) were further selected for RNA extraction. Selected isolates recovered from Teflon chambers were centrifuged, and their pellets were washed twice in PBS, sheared with beads (QBiogene), then processed for RNA extraction according to the RNEasey protocol (Qiagen).

tag: Strain

tag: Growth condition

value: in vivo 24h (tissue cage)

tag: Mouse type

value: BALB/c female


title: 5448_4_AH14_green532

label: Alexa Fluor 546

source_name: GAS strain 5448, in vivo derived 24h


title: 5448R-_3_AH10_red635


title: 5448R-_1_AH21_green532


title: Patient_#3899_IgM


title: 5448_2_AH1_green532


title: 5448_3_AH8_red635


title: TY041035

city: Seattle

first: Derek

middle: L

last: Stirewalt

state: WA

address: 1100 Fairview Ave N, D5-112

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: For 34BM and T-cells, biotin-labeling of total RNA (5 µg) was performed as per standard Affymetrix protocol. For the 34P38NPBSC arrays, the single-stranded linear amplification protocol was used to process total RNA (100 nanograms) for the microarrays. Both protocols are described in detail in PMID14706461.

hyb_protocol: Hybridization was performed according to Affymetrix protocol.

scan_protocol: Arrays were scanned according to Affymetrix protocol.

data_processing: .DAT files were generated using GCOS 1.2.1 software (Affymetrix). CEL files were generated using MAS 5.0 softare (Affymetrix) with target signals for probe sets scaled to 500. Log2 expression values for individual probe sets were generated from .CEL files via robust multi-array average (gcRMA).

label: Biotin

source_name: Expanded T-cells

label_protocol: Target was labeled with Enzo BioArray High Yield RNA Trascript Labeling Kit (Enzo Life TEchnologies, Farmingdale, NY) according to manufacturer's protocol.

extract_protocol: Total RNA extracted using TRIzol reagent (Invitrogen, Carlsbad, CA)according to manufacturer's protocol.

tag: Expanded T-cells from 21 yo Male


title: TYPCA1011

tag: Expanded T-cells from 24 yo Female


title: TO600571

tag: Expanded T-cells from 86 yo Male


title: TYPCA0715

tag: Expanded T-cells from 23 Female


title: TO600318

tag: Expanded T-cells from 81 yo Male


title: TO600071

tag: Expanded T-cells from 76 yo Female


title: TYPCA1077


title: TO600649

label_protocol: Target was labeled with Enzo BioArray High Yield RNA Trascript Labeling Kit (Enzo Life Technologies, Farmingdale, NY) according to manufacturer's protocol.

tag: Expanded T-cells from 84 yo Male


title: TO600042

tag: Expanded T-cells from 83 yo Female


title: 5448_1_AH7_red635

data_processing: Values below 0.01 were set to 0.01. Each measurement was divided by the 50.0th percentile of all measurements in that sample.Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.


title: TO600599

tag: Expanded  T-cells from 74 yo Male


title: TY040085

tag: Expanded T-cells from 23 yo Male


title: TO600380

tag: Expanded T-cells from 75 yo Male


title: TY51128

tag: Expanded T-cells from 30 yo Female


title: TO600428

tag: Expanded T-cells from 77 yo Male


title: 34P38NPBSC000485

tag: CD34 positive CD38 negative cells from G-CSF mobilized PBSC of 53 yo Male.


title: 34P38NPBSC000497

tag: CD34 positive CD38 negative cells from G-CSF mobilized PBSC of 27 yo Male.


title: TYPCA0941


title: TO600799

tag: Expanded T-cells from 82 yo Male


title: 34P38NPBSC000500

tag: CD34 positive CD38 negative cells from G-CSF mobilized PBSC of 51 yo Male.


title: 34P38NPBSC000513

tag: CD34 positive CD38 negative cells from G-CSF mobilized PBSC of 22 yo male.


title: 34BM3488

source_name: CD34 selected bone marrow

tag: CD34 selected cells from cadaveric bone marrow of 23 yo Male.

tag: .CEL file is identical to GSM239339


title: TO600025

tag: Expanded T-cells from 85 yo Female


title: TY27949B

tag: Expanded T-cells from 26 yo Male


title: F9 cells Ezh1 chip on chip replicate 1

source_name: Input for mouse Ezh1 chromatin immunoprecipitation

tag: The F9 murine teratoma cell line (obtained from ATCC)

source_name: IP for mouse Ezh1 chromatin immunoprecipitation


title: 34BM2854

tag: CD34 selected cells from cadaveric bone marrow of 18 yo Male.

tag: .CEL file is identical to GSM239343


title: F9 cells Ezh2 chip on chip replicate 1

source_name: Input for mouse Ezh2 chromatin immunoprecipitation

source_name: IP for mouse Ezh2 chromatin immunoprecipitation


title: Day14_YF1173; VaxDesign Mimic experiment

description: PBMCs used in the assays were acquired from normal healthy donors enrolled in a VaxDesign Corporation apheresis study program (protocol CRRI 0906009). Blood collections were performed at Florida’s Blood Centers (Olrando, FL) using standard techniques.  The enriched leukocytes were isolated and cryopreserved. Human DCs were prepared as described in Gaucher et al. “Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses , J. Exp. Med XXX. After 5 days of culture with IL-4 and GM-CSF, the DCs were infected with a 1:100 dilution of the live-attenuated YF-VAX® vaccine.  After 24 hrs, 5% human AB serum was added to the media to quench the infection. Alternatively, some of the DCs we not infected.  On the sixth day, all DCs were matured with an overnight treatment of 25 ng/mL TNF- (R&D Systems).

source_name: Frozen stocks of autologous PBMCs were used as a source of lymphocytes.

treatment_protocol: Purified CD4+ T cells were co-cultured  in the Mimic System with YF17D-pulsed DCs at a ratio of 60:1 for 14 days

tag: Yellow Fever unexposed volunteer