title: Day 5 differentiated H1

status: Public on Dec 03 2010

type: mixed

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

country: USA

institute: University of Wisconsin

description:
The second channel (genomic DNA) served as common reference across the experiments.
DAY5_72159

hyb_protocol: Array hybridization and washes were performed according to NimbleGen’s recommended protocol.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner and the PMT settings were followed by NimbleGen array manual.

data_processing: 1. Image extraction: NimbleScan provided by NimbleGen is used to extract signal data from image files (*.TFF). Signal meansurements were saved in .pair files.  2. Normalization: Signal intensities from RNA and gDNA samples are normalized with Robust Multiple-chip Analysis (RMA) algorithm (Irizarry et al., 2003) separately. A median-adjusted ratio is calculated for each gene by dividing its signal intensity from the RNA sample by the sum of the corresponding signal intensity from the gDNA sample and median signal intensity of all genes from the gDNA channel.

molecule: total RNA

organism: Homo sapiens

source_name: differentiated H1, day 5

label_protocol: Amino Allyl labeling method.

growth_protocol: H1 were maintained on irradiated MEFs (Amit et al. Dev. Biol. 2000; 271:278). Differentiation was induced by transferring H1 cells on OP9 stromal cells (Vodyanik et al: Blood 2005; 105:617-626). Mouse cells (MEFs, OP9) were depleted by magnetic sorting (Vodyanik, Slukvin: Curr Ptotoc Cell Biol 2007; 36:23.6.1-23.6.28); the purity of H1 and H1-derived cells used for analysis was >99%.  H1-derived APLNR+ cells were isolated by magnetic sorting and cultured in the semisolid colony-forming culture to generate mesenchymal colonies, from which MSC lines were derived.

extract_protocol: Total RNA was extracted using the RiboPure kit (Ambion, Austin, TX) and treated with DNAse (Ambion).

treatment_protocol: The media for H1 hESC maintenance, colony-forming culture and MSC propagation contained 10-20 ng/ml basic fibroblast growth factor (FGF2). The differentiation medium for H1 hESC/OP9 cocultures contained 10% fetal bovine serum (FBS).

tag: cell line

tag: time of differentiation

value: 5 days

tag: differentiation state

value: differentiated

molecule: genomic DNA

source_name: undifferentiated H1

extract_protocol: Genomic DNA was extracted using the phenol/chloroform extraction method.

tag: cell type

value: embryonic stem cells

value: undifferentiated


title: Day 6 differentiated H1

description:
The second channel (genomic DNA) served as common reference across the experiments.
DAY6_74154

source_name: differentiated H1, day 6

value: 6 days


title: Day 3 differentiated H1

description:
The second channel (genomic DNA) served as common reference across the experiments.
DAY3_61032

source_name: differentiated H1, day 3

value: 3 days


title: Day 4 differentiated H1

description:
The second channel (genomic DNA) served as common reference across the experiments.
DAY4_61779

source_name: differentiated H1, day 4

value: 4 days


title: Day 7 differentiated H1

description:
The second channel (genomic DNA) served as common reference across the experiments.
DAY7_74308

source_name: differentiated H1, day 7

value: 7 days


title: Day 1 differentiated H1

description:
The second channel (genomic DNA) served as common reference across the experiments.
DAY1_60366

source_name: differentiated H1, day 1

value: 1 day


title: H1-derived MSCs passage 5

description:
The second channel (genomic DNA) served as common reference across the experiments.
Mp5

source_name: H1-derived MSCs passage 5

value: H1-derived MSCs

value: passage 5


title: Day 3 H1-derived cores

description:
The second channel (genomic DNA) served as common reference across the experiments.
H1d3cores

source_name: Day 3 H1-derived cores

value: H1-derived cores


title: Day 2 H1-derived MB colonies

description:
The second channel (genomic DNA) served as common reference across the experiments.
M-colonies

source_name: Day 2 H1-derived MB colonies

value: H1-derived MB colonies

value: 2 days


title: Day 2 differentiated H1

description:
The second channel (genomic DNA) served as common reference across the experiments.
DAY2_100013

source_name: differentiated H1, day 2


title: Day 3 H1-derived HB colonies

description:
The second channel (genomic DNA) served as common reference across the experiments.
H-colonies

source_name: Day 3 H1-derived HB colonies

value: H1-derived HB colonies


title: Day 3 H1-derived APLNR- cells

description:
The second channel (genomic DNA) served as common reference across the experiments.
H1d3minus1

source_name: Day 3 H1-derived APLNR- cells

value: H1-derived APLNR- cells


title: H1-derived MSCs passage 1

description:
The second channel (genomic DNA) served as common reference across the experiments.
Mp1

source_name: H1-derived MSCs passage 1

value: passage 1


title: Undifferentiated H1

description:
The second channel (genomic DNA) served as common reference across the experiments.
H1

source_name: Undifferentiated H1


title: Day 2 H1-derived cores

description:
The second channel (genomic DNA) served as common reference across the experiments.
H1d2cores

source_name: Day 2 H1-derived cores


title: Day 3 H1-derived APLNR+ cells

description:
The second channel (genomic DNA) served as common reference across the experiments.
H1d3plus1

source_name: Day 3 H1-derived APLNR+ cells

value: H1-derived APLNR+ cells


title: NAO2

status: Public on Dec 01 2010

type: RNA

city: Bethesda

first: Alexandre

last: Kuhn

state: MD

address: 35 Convent Dr

department: NIA

institute: NIH

description: RNA mixture

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label: Biotin

organism: Rattus norvegicus

source_name: Brain

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers’ protocols

tag: tissue

value: Brain

tag: mixed rna

value: N (fraction 0.5, sample N2), A (fraction 0.25, sample A4), O (fraction 0.25, sample O4)


title: Undifferentiated H1

description:
The second channel (genomic DNA) served as common reference across the experiments.
ES_60303

source_name: undifferentiated H1

value: embryonic stem cells

value: undifferentiated


title: NAO1

description: RNA mixture

value: N (fraction 0.5, sample N1), A (fraction 0.25, sample A1), O (fraction 0.25, sample O2)


title: Day 2 H1-derived APLNR- cells

description:
The second channel (genomic DNA) served as common reference across the experiments.
H1d2minus1

source_name: Day 2 H1-derived APLNR- cells


title: NA3-1

description: RNA mixture

value: N (fraction 0.75, sample N1), A (fraction 0.25, sample A1)


title: NA1-1

description: RNA mixture

value: N (fraction 0.25, sample N1), A (fraction 0.75, sample A1)


title: NAOM1

description: RNA mixture

value: N (fraction 0.5, sample N1), A (fraction 0.2, sample A1), O (fraction 0.2, sample O2), M (fraction 0.1, sample M2)


title: NA3-2

description: RNA mixture

value: N (fraction 0.75, sample N2), A (fraction 0.25, sample A4)


title: Day 2 H1-derived APLNR+ cells

description:
The second channel (genomic DNA) served as common reference across the experiments.
H1d2plus1

source_name: Day 2 H1-derived APLNR+ cells


title: M1

description: Primary culture from cerebral cortices of rat P1 pups

value: Primary microglial culture (M)


title: M3


title: NA2-2

description: RNA mixture

value: N (fraction 0.5, sample N2), A (fraction 0.5, sample A4)


title: A4

value: Primary astrocytic culture (A)


title: O1

value: Primary oligodendrocytic culture (O)


title: NA2-1

description: RNA mixture

value: N (fraction 0.5, sample N1), A (fraction 0.5, sample A1)


title: O2


title: M2


title: M4

description: RNA mixture


title: A3


title: NAOM2

description: RNA mixture

value: N (fraction 0.5, sample N2), A (fraction 0.2, sample A4), O (fraction 0.2, sample O4), M (fraction 0.1, sample M3)


title: NA1-2

description: RNA mixture

value: N (fraction 0.25, sample N2), A (fraction 0.75, sample A4)


title: O3


title: A1


title: N4

value: Primary neuronal culture (N)


title: A2

value: Brain


title: N1


title: O4


title: N2


title: preCC.OR2558m

city: Bar Harbor

first: Ricardo

middle: Alejandro

last: Verdugo

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

hyb_protocol: Standard Affymetrix hybridization protocol onto GeneChip® Mouse Gene 1.0 ST Arrays (1,102,500 probes; Affymetrix) for 16 hours at 45°C. Staining and washing using the Fludics Station 450 instrument (Affymetrix)

scan_protocol: Standard Affymetrix scanning protocol with GeneChip(R) 3000 laser confocal slide scanner.

data_processing: RMA with the affy package from Bioconductor. Log2 transformation. Rank-z (normal score) transformation applied at the probeset level.

label: biotin

organism: Mus musculus

source_name: mouse, preCC, male, liver

label_protocol: Biotin is added with an Affymetrix Labeling Reagent

growth_protocol: Mice were weaned at 3 weeks of, housed in age and sex matching cages with five or less animals per cage. All animals were fed a standard Purina Formulab Chow 5008 diet.  Animals were transported to UNC at 9 to 11 weeks of age and euthanized at 12 to 15 weeks of age after a three week protocol that included alcohol exposure and exercise interventions.

extract_protocol: Total RNA was isolated according to the manufacturer’s protocol, following reverse transcription with random primers-T7 primers, double stranded cDNA was synthesized with the GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara, Ca).

treatment_protocol: Eight founder strins were intercrossed, the F1s were outcrossed, and 220 funnels of brother-sister mating were created. One anmal per funnel was profiled at generation G2:F5 to G2:F12

value: liver

tag: scananimal

tag: scanstrain

tag: slideno

tag: sampleid

tag: genechipid

tag: hybdate

tag: batch

tag: slot

tag: hyborder

tag: strain

tag: sacdate


title: N3


title: preCC.OR1114m


title: preCC.OR878m


title: preCC.OR1639m


title: preCC.OR712m


title: preCC.OR291m


title: preCC.OR305m


title: preCC.OR3030m


title: 46 day-old transgenic plants (Arabidopsis C24 background, inducible overexpression) DEX-induced plants, biological rep1

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

hyb_protocol: performed by Atlas Biolabs

scan_protocol: performed by Atlas Biolabs

data_processing: The data were analyzed with GCRMA (Wu et al., 2004).

organism: Arabidopsis thaliana

source_name: 46 day-old transgenic plants; 5h DEX-induced (30µM) plants, biological rep1

label_protocol: Labling procedure performed using MessageAmpTM II-Biotin Enhanced Kit

growth_protocol: Transgenic plants were grown in soil and germinated under controlled condition in a growth chamber with a 16-h day lenght provided by fluorescent light at 80 or 120 µmol m2- s1- and a days/night temperature of 20/16 C°  and relative humidity 60/75%.

extract_protocol: RNA extraction performed using Rneasy Plant MiniKit (Qiagene)

treatment_protocol: 46 days-old transgenic Arabidopsis rosette were sprayed with 30µM DEX for 5 hours and then whole rosettes were carefully harvested. As control, 46 days-old transgenic Arabidopsis rosette were sprayed with 0.05% ethanol (mock) for 5 hours.

value: rosette leaves

tag: genotype

value: C24 background


title: preCC.OR3584m


title: 46 day-old transgenic plants (Arabidopsis C24 background, inducible overexpression) DEX-induced plants, biological rep2

source_name: 46 day-old transgenic plants; 5h DEX-induced (30µM) plants, biological rep2


title: preCC.OR5344m


title: preCC.OR5426m


title: preCC.OR3011m


title: preCC.OR3549m


title: preCC.OR462m


title: 46 day-old transgenic plants (Arabidopsis C24 background, inducible overexpression) mock-induced plants, biological rep2

source_name: 46 day-old transgenic plants; 5h mock-treated plants (0.05% ethanol), biological rep2


title: preCC.OR3087m


title: preCC.OR3415m


title: preCC.OR5061m


title: preCC.OR5019m


title: preCC.OR5546m


title: preCC.OR237m


title: 46 day-old transgenic plants (Arabidopsis C24 background, inducible overexpression) mock-induced plants, biological rep1

source_name: 46 day-old transgenic plants; 5h mock-treated plants (0.05% ethanol), biological rep1


title: preCC.OR3067m


title: preCC.OR3018m


title: preCC.OR739m


title: preCC.OR167m


title: preCC.OR1524m


title: preCC.OR940m


title: preCC.OR70m


title: Participant 136

city: Maastricht

first: Dennie

last: Hebels

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

description: Non-smoker

hyb_protocol: Hybridization according to Agilent instructions on 4x44K human whole genome microarrays.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 was excited at a wavelengths of 532 nm. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 543 (Cy3), based on automatic establishment of ideal scan settings. Images were subsequently saved (resolution 5 micron, 16 bit tiff image).

data_processing: Data preparations were performed in GenePix Pro software (version 6.0, Molecular Devices) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), and flagging of spots (control spots and bad spots). One raw data file was created by GenePix Pro (a GPR file). Quantile normalization and log (base=2) transformations of spot intensities were calculated in ArrayTrack (version 3.4).

source_name: Whole blood

label_protocol: Dye-labeled cRNA (Cy3) was synthesized following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies, Amstelveen, The Netherlands).

growth_protocol: n/a --> human subjects

extract_protocol: To stabilize RNA, 0.4ml of drawn whole blood was mixed with 1.2ml RNAlater (Ambion, Naerum, Denmark) and stored at -20 °C for the first 24 hrs followed by longer term storage at -80 °C until use. Total RNA was extracted according to the manufacturer's instructions.

treatment_protocol: n/a --> non-exposed human volunteer subjects

tag: gender

value: Female

tag: age


title: Participant 135

description: Non-smoker


title: Participant 124

description: Non-smoker


title: Participant 130

description: Non-smoker


title: Participant 131

description: Non-smoker


title: Participant 123

description: Non-smoker


title: preCC.OR829m


title: preCC.OR821m


title: preCC.OR4251m


title: preCC.OR3m


title: preCC.OR792m


title: Participant 133

description: Non-smoker


title: preCC.OR822m


title: Participant 128

description: Non-smoker


title: Participant 119

description: Non-smoker


title: Participant 125

description: Non-smoker


title: Participant 141

description: Non-smoker


title: Participant 121

description: Non-smoker


title: Participant 120

description: Non-smoker


title: preCC.OR5516m


title: Participant 132

description: Non-smoker


title: preCC.OR5584m


title: Participant 118

description: Non-smoker


title: Participant 117

description: Non-smoker


title: preCC.OR5370m


title: Participant 113

description: Non-smoker


title: Participant 114

description: Non-smoker


title: preCC.OR5140m


title: preCC.OR5181m


title: Participant 112

description: Non-smoker


title: preCC.OR3513m


title: preCC.OR5252m


title: preCC.OR3571m


title: Participant 109

description: Non-smoker


title: Participant 111

description: Non-smoker


title: preCC.OR5118m


title: preCC.OR5046m


title: preCC.OR5076m


title: Participant 107

description: Non-smoker


title: Participant 110

description: Non-smoker


title: preCC.OR3327m


title: Participant 106

description: Non-smoker


title: preCC.OR5454m


title: Participant 108

description: Non-smoker


title: Participant 105

description: Non-smoker


title: preCC.OR3181m


title: preCC.OR5066m


title: Participant 104

description: Non-smoker


title: Participant 102

description: Non-smoker


title: preCC.OR3046m


title: preCC.OR3076m


title: Participant 101

description: Non-smoker


title: Participant 103

description: Non-smoker


title: preCC.OR5410m


title: preCC.OR5018m


title: preCC.OR3548m


title: preCC.OR3426m


title: preCC.OR4390m


title: preCC.OR5156m


title: preCC.OR1057m


title: preCC.OR94m


title: preCC.OR5168m


title: preCC.OR3291m


title: preCC.OR477m


title: preCC.OR3168m


title: preCC.OR2227m


title: preCC.OR896m


title: preCC.OR900m


title: preCC.OR1427m


title: preCC.OR820m


title: preCC.OR2291m


title: preCC.OR652m


title: preCC.OR867m


title: preCC.OR2489m


title: preCC.OR220m


title: preCC.OR857m


title: preCC.OR1635m


title: preCC.OR5091m


title: preCC.OR5154m


title: preCC.OR3612m


title: preCC.OR3140m


title: preCC.OR3232m


title: preCC.OR2020m


title: preCC.OR3066m


title: preCC.OR5513m


title: preCC.OR3080m


title: preCC.OR3410m


title: preCC.OR1566m


title: preCC.OR3041m


title: preCC.OR3370m


title: preCC.OR4179m


title: preCC.OR5030m


title: preCC.OR549m


title: preCC.OR3007m


title: preCC.OR3389m


title: preCC.OR79m


title: preCC.OR5528m


title: preCC.OR3401m


title: preCC.OR3061m


title: preCC.OR3019m


title: preCC.OR3489m


title: preCC.OR3564m


title: preCC.OR5291m


title: preCC.OR5087m


title: preCC.OR3515m


title: preCC.OR1200m


title: preCC.OR4445m


title: preCC.OR4010m


title: preCC.OR157m


title: preCC.OR1516m


title: preCC.OR3443m


title: preCC.OR467m


title: preCC.OR941m


title: preCC.OR4559m


title: preCC.OR1626m


title: preCC.OR380m


title: preCC.OR692m


title: preCC.OR799m


title: preCC.OR2533m


title: preCC.OR1119m


title: preCC.OR779m


title: preCC.OR1246m


title: preCC.OR2041m


title: preCC.OR5232m


title: preCC.OR3546m


title: preCC.OR409m


title: preCC.OR190m


title: preCC.OR2390m


title: preCC.OR2168m


title: preCC.OR559m


title: preCC.OR3091m


title: preCC.OR3594m


title: preCC.OR5612m


title: preCC.OR113m


title: preCC.OR5067m


title: preCC.OR3078m


title: preCC.OR5515m


title: preCC.OR3154m


title: preCC.OR5308m


title: preCC.OR5489m


title: preCC.OR5415m


title: preCC.OR3358m


title: preCC.OR3528m


title: preCC.OR3252m


title: preCC.OR489m


title: preCC.OR5401m


title: preCC.OR5130m


title: preCC.OR3156m


title: preCC.OR2662m


title: preCC.OR914m


title: preCC.OR205m


title: preCC.OR5480m


title: preCC.OR381m


title: preCC.OR1234m


title: preCC.OR937m


title: preCC.OR4650m


title: preCC.OR4410m


title: preCC.OR1237m


title: lhcbdsRNA-3c

city: Fredericton

first: Denise

last: Clark

state: NB

address: 10 Bailey Drive

department: Biology

country: Canada

institute: University of New Brunswick

description:
gene expression after 4 days
lhcbdsRNA-3c

hyb_protocol: 1.65 ug of labeled cRNA was fragmented for 30 min and applied to Agilent microarrays 4x44K format (G2519F) and hybridized for 17 hrs at 65 C in the Agilent hybridization oven, and washed with Agilent wash buffers

scan_protocol: Agilent DNA Microarray Scanner at 5um resolution

data_processing: Agilent Feature extraction 9.1 software.  Intensities per spot had their local background subtracted.  A step of spatial detrending was done using negative control spots across the whole array and subtracting a surface fit from the data.  Then data were loaded into GeneSpring 7.3 and all raw values below 5 were set to 5.  The data were normalized to the median, so that intensities were divided by the median of all intensities.

organism: Drosophila melanogaster

source_name: S2 cells+lhcb dsRNA

label_protocol: RNA was linearly amplified and labeled with Cy3, and labeled cRNA quantity and specific activity were assessed with the NanoDrop ND-1000 (Thermo Scienctific).

growth_protocol: S2-6 cells were obtained from the Drosophila Genetics Resources Center and cultured in Schneider cell meda (Invitrogen) supplemented with 10% FBS (Invitrogen)

extract_protocol: Trizol (Invitrogen)

treatment_protocol: dsRNA treatment followed the protocol of Maiato et al (2003) Biol. Proced. Online 5:153-161.

tag: cell type

value: S2 cells

tag: protocol

value: control (non-specific RNAi)

tag: RNAi name

value: lhcb dsRNA


title: ade2dsRNA-2a

description:
gene expression after 4 days
ade2dsRNA-2a

source_name: S2 cells+ade2 dsRNA2

value: RNAi-mediated knockdown of ade2 (ade2 RNAi)

value: ade2 dsRNA2


title: ade2dsRNA-1b

description:
gene expression after 4 days
ade2dsRNA-1b

source_name: S2 cells+ade2 dsRNA1

value: ade2 dsRNA1


title: lhcbdsRNA-3b

description:
gene expression after 4 days
lhcbdsRNA-3b


title: preCC.OR41m

tag: tissue

tag: scananimal


title: ade2dsRNA-1c

description:
gene expression after 4 days
ade2dsRNA-1c


title: ade2dsRNA-2b

description:
gene expression after 4 days
ade2dsRNA-2b


title: preCC.OR538m

tag: scanstrain

tag: slideno


title: 72 hour-treated TG2 knockout NB4, biological rep2

city: Debrecen

first: Krisztian

last: Csomos

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

description:
3KD2
Gene expression data from 72 hour ATRA-differentiated TG2 knockout NB4.

hyb_protocol: 10 ug of ss cDNA was fragmented and labeled with biotin, and hybridized for 16 hr at 45C on the GeneChip 1.0 ST Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Affymetrix CEL files were imported into GeneSpring GX11 Software (Agilent). The RMA16 algorithm was used for probe summarization and then median normalization was performed.

source_name: NB4 cell line, TG2 knockout, ATRA, 72hr

label_protocol: Biotinylated ss cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA using the WT Expression kit (Ambion).

growth_protocol: The NB4 cell line (purchased from DSMZ GmbH) was cultured in RPMI 1640 Medium (Sigma) supplemented with (10% v/v) fetal bovine serum (FBS) (Sigma), 2 mM glutamine (Sigma), 100 U/mL penicillin and 100 µg/mL streptomycin solution (Sigma).

extract_protocol: RNeasy mini kit was used to extract total RNA (according to the manufacturer's instructions).

treatment_protocol: Differentiation of NB4 cells was induced at 1 x 100,000 cells/mL by administration of 1 µM ATRA (Sigma) for 0, 48 or 72 hours.

tag: cell line

value: TG2 knockout

tag: treatment

value: all-trans-retinoic acid (ATRA)

tag: time

value: 72 hours

tag: biological replicate


title: 72 hour-treated TG2 knockout NB4, biological rep1

description:
3KD1
Gene expression data from 72 hour ATRA-differentiated TG2 knockout NB4.


title: 48 hour-treated TG2 knockout NB4, biological rep3

description:
2KD3
Gene expression data from 48 hour ATRA-differentiated TG2 knockout NB4.

source_name: NB4 cell line, TG2 knockout, ATRA, 48hr

value: 48 hours


title: 72 hour-treated TG2 knockout NB4, biological rep3

description:
3KD3
Gene expression data from 72 hour ATRA-differentiated TG2 knockout NB4.


title: 48 hour-treated TG2 knockout NB4, biological rep2

description:
2KD2
Gene expression data from 48 hour ATRA-differentiated TG2 knockout NB4.


title: 48 hour-treated wild-type NB4, biological rep1

description:
2N1
Gene expression data from 48 hour ATRA-differentiated wild-type NB4.

source_name: NB4 cell line, wild-type, ATRA, 48hr

value: wild-type


title: Untreated wild-type NB4, biological rep2

description:
0N2
Gene expression data from undifferentiated wild-type NB4.

source_name: NB4 cell line, wild-type, untreated

value: untreated


title: 72 hour-treated wild-type NB4, biological rep3

description:
3N3
Gene expression data from 72 hour ATRA-differentiated wild-type NB4.

source_name: NB4 cell line, wild-type, ATRA, 72hr


title: 72 hour-treated wild-type NB4, biological rep1

description:
3N1
Gene expression data from 72 hour ATRA-differentiated wild-type NB4.


title: YSBN2-chemostat_biological rep1

city: Kgs. Lyngby

first: Jie

last: Zhang

address: Kemitorvet 220

department: CFB

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station450.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R (v 2.6). The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Saccharomyces cerevisiae

source_name: YSBN2-chemostat_biological rep1

label_protocol: Labelling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

growth_protocol: strains were grown in 4 liter bioreactor at 30°C, pH 5.0 and aerobically, for batch the initial glucose concentration was 30g/l and for chemostat 7.5 g/L of glucose plus 0.3g/l of ethanol, dilution rate 0.1h-1

extract_protocol: Total RNA was isolated from frozen cell pellets using FastRNA® Pro RED kit (QBiogene, Inc, USA) according to manufacturer's instructions after partially thawing the samples on ice. RNA sample integrity and quality was assessed prior to hybridization with an Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip kit.

treatment_protocol: A volume of broth of 300-500 ml was collected by over-pressure (35-40 ml/s) directly into a plastic beaker containing excess liquid nitrogen, under vigorous manual shaking. Without allowing the frozen broth to thaw, it was crushed to small pieces, loaded into 50 ml tubes containing approximately 30 g each and stored at -80°C. Throughout the subsequent steps, until extraction, the temperature of the samples was kept within 0-4°C. The frozen broth was thawed on ice, centrifuged (5000G, 4min, 0°C) and washed once with 10 ml ice-cold buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0). The cell pellets were then re-suspended in 1.8 ml ice-cold buffer. To each sample, 1.8 ml acidic phenol/chloroform/IAA mix (Ambion) and 180 μl 10% SDS solution were added and after vortexing for 30 s the tubes were placed in a water bath at 65°C for 5 min, after which they were placed back on ice. The resulting extracts were aliquoted in screw-cap RNase-free vials, each containing the equivalent to approximately 24 mg DW and stored at -80°C until distribution.

value: prototrophic FY ho::Ble/ho::HphMX4

tag: growth protocol

value: glucose-limited chemostat

tag: biological rep


title: 72 hour-treated wild-type NB4, biological rep2

description:
3N2
Gene expression data from 72 hour ATRA-differentiated wild-type NB4.


title: CEN.PK 113-7D_chemostat_biological rep2

source_name: CEN.PK 113-7D_chemostat_biological rep2

tag: strain

value: CEN.PK 113-7D

value: CEN.PK Mat a prototrophic


title: CEN.PK 113-7D_chemostat_biological rep1

source_name: CEN.PK 113-7D_chemostat_biological rep1

tag: genotype


title: 48 hour-treated wild-type NB4, biological rep2

description:
2N2
Gene expression data from 48 hour ATRA-differentiated wild-type NB4.


title: Untreated TG2 knockout NB4, biological rep1

description:
0KD1
Gene expression data from undifferentiated TG2 knockout NB4.

source_name: NB4 cell line, TG2 knockout, untreated


title: 48 hour-treated TG2 knockout NB4, biological rep1

description:
2KD1
Gene expression data from 48 hour ATRA-differentiated TG2 knockout NB4.


title: CEN.PK 113-7D_batch_biological rep1

source_name: CEN.PK 113-7D_batch_biological rep1

value: aerobic batch


title: CEN.PK 113-7D_batch_biological rep2

source_name: CEN.PK 113-7D_batch_biological rep2


title: YSBN2-chemostat_biological rep3

source_name: YSBN2-chemostat_biological rep3


title: 48 hour-treated wild-type NB4, biological rep3

description:
2N3
Gene expression data from 48 hour ATRA-differentiated wild-type NB4.


title: ade2dsRNA-1a

description:
gene expression after 4 days
ade2dsRNA-1a

value: S2 cells


title: YSBN2-chemostat_biological rep2

source_name: YSBN2-chemostat_biological rep2


title: Untreated wild-type NB4, biological rep3

description:
0N3
Gene expression data from undifferentiated wild-type NB4.


title: Untreated TG2 knockout NB4, biological rep2

description:
0KD2
Gene expression data from undifferentiated TG2 knockout NB4.


title: CEN.PK 113-7D_chemostat_biological rep3

source_name: CEN.PK 113-7D_chemostat_biological rep3


title: lhcbdsRNA-3a

description:
gene expression after 4 days
lhcbdsRNA-3a

source_name: S2 cells+lhcb dsRNA

value: control (non-specific RNAi)


title: Untreated TG2 knockout NB4, biological rep3

description:
0KD3
Gene expression data from undifferentiated TG2 knockout NB4.


title: CaSki HPV(+), methylation

type: genomic

city: Ann Arbor

first: Jung

last: Kim

state: MI

address: 1420 Washington Heights

institute: University of Michigan

description:
7465
HPV(+) SCC cell line sample.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to the Illumina Infinium Human Methylation27 Beadchip using the standard Illumina protocol.

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

data_processing: DNA methylation levels are reported for each locus using BeadStudio software, which provides estimates of the percent methylation for each probe site, termed beta values. However, rather than using these beta values, we developed and implemented our own novel normalization strategy. Our normalization method was developed to correct for the non-linear relationship between beta values from red versus green-labeled sites, while NOT affecting the overall distribution of % methylation in CpG island sites and non-CpG island sites for each sample. Our normalization consists of the following steps, and was implemented using R statistical environment and Bioconductor. First, for each sample, obtain the raw signal levels for methylated (unbisulfite converted) and unmethylated (bisulfate converted) probes that are in a CpG island separately for green and red-labeled probes. Second, perform quantile normalization for the red versus green CpG island probes for each sample separately. Next, repeat this type of quantile normalizations for the non-CpG island probes. Since the number of red and green-labeled probes differ, NA values were added to the set containing fewer probes to allow the use of the normalize.quantiles function in R/Bioconductor software. The signal levels for CpG and non-CpG islands are then recombined, and the normalized beta values are defined as B/(A+B), where B = the quantile-normalized intensity for methylated DNA, and A = the quantile-normalized intensity for unmethylated DNA. Once the normalized beta values are calculated, we used an empirical Bayesian moderated T-test to assess the significance between the percent methylation in HPV(+) versus HPV(-) samples.

source_name: DNA from SCC cell line, HPV(+)

label_protocol: Standard Illumina protocol.

growth_protocol: HPV(+) and HPV(-) SCC cell lines were cultured to near confluence in ventilated 75cm2 cell culture flasks in DMEM (Gibco) supplemented with 20% fetal bovine serum (FBS) and prophylactic antibiotics. At 90-95% confluence, the cells were photographed through a 20x objective lens, and then harvested with Trypsin/EDTA. Total cell counts for each flask were obtained using a Coulter Particle Counter (Beckman Coulter). Trypsin was neutralized with culture media containing 2% FBS, and cell pellets were washed with sterile phosphate-buffered saline (PBS), pH 7.4, prior to digestion for nucleic acid isolation.

extract_protocol: DNA was isolated using a modified protocol for the QiaAmp DNA Mini Kit for Blood and Body Fluids (Qiagen, Valencia, CA). In brief, ≤5 million cells were suspended in 200uL of PBS to which 20uL of Proteinase K (Qiagen) was added. A 5mm stainless steel bead was added to each tube and cells were simultaneously disrupted and homogenized with 2 bursts at 15Hz, 20 seconds each, in a TissueLyser II (Qiagen). Following homogenization, 20uL of RNase A (Qiagen) was added to each tube. After the addition of RNase A, DNA isolation was carried out as per manufacturer’s instructions for processing blood and body fluids with spin column technology. Genomic DNA was eluted in 100uL final volume of nuclease-free water, pre-warmed to 40°C.

treatment_protocol: Bisulfite conversion was carried out on 600ng of DNA using the manufacturer’s protocol (EZ DNA Methylation-Direct Kit, Zymo Research Corp., Orange, CA).

value: CaSki

value: female genital squamous cell carcinoma

tag: tissue derivation

value: cervix

tag: hpv status

value: positive

tag: gender

value: female


title: CEN.PK 113-7D_batch_biological rep3

source_name: CEN.PK 113-7D_batch_biological rep3


title: Untreated wild-type NB4, biological rep1

description:
0N1
Gene expression data from undifferentiated wild-type NB4.


title: YSBN2-batch_biological rep3

source_name: YSBN2-batch_biological rep3


title: YSBN2-batch_biological rep1

source_name: YSBN2-batch_biological rep1


title: CaSki HPV(+), expression

description: Gene expression data from SCC HPV(+) cell line.

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 at the University of Michigan Affymetrix Core facility using the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader at the University of Michigan Affymetrix Core facility.

data_processing: Raw data was preprocessed and normalized using RMA.  Differential expression and significance was assessed using Intensity-Based Moderated T-statistic (IBMT). Analysis was performed using R and Bioconductor.

source_name: RNA from SCC cell line, HPV(+)

label_protocol: Biotinylated aRNA were prepared according to the Ambion Premier kit protocol from 250 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

extract_protocol: The cells were harvested at near confluence with trypsin/EDTA, counted, and washed. Nucleic acids were isolated using the RNEasy Mini Kit (Qiagen, Valencia, CA).

tag: cell type

tag: age


title: SCC74A HPV(-), expression

description: Gene expression data from HNSCC HPV(-) cell line.

source_name: RNA from HNSCC cell line, HPV(-)

value: head and neck squamous cell carcinoma (HNSCC)

value: tongue

value: negative

value: male


title: YSBN2-batch_biological rep2

source_name: YSBN2-batch_biological rep2


title: Adip_TNF_Ins_rep 2

status: Public on Nov 30 2010

city: Groton

first: Shelley

last: des Etages

state: CT

address: Eastern Point Road

institute: Pfizer Inc.

hyb_protocol: The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®.  The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on a GeneChip® Scanner 3000.

data_processing: All of the array files were normalized using the Robust Multi-Array Average (RMA) method

source_name: hMSC adipocytes, 24h TNF, 5 h insulin, buoyant fraction

label_protocol: cDNA was synthesized using 1-2 ug of high quality total RNA.   Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix.  cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix.  cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively.  The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel.

growth_protocol: Human mesenchymal stem cells were purchased from Lonza and cultured in basal media (Lonza PT3238) with mesenchymal stem cell growth supplement (Lonza PT4105).  Cells were seeded at a density of 5000 cells/cm2.  At confluence, the cells were differentiated into adipocytes using the adipogenic differentiation kit (Lonza PT3004).  The total differentiation process took 19 days, with 14 days of induction and 5 days of maintenance.  All media were from Lonza, except that the insulin concentration (in both induction and maintenance media) was adjusted to 120 pM.  Mature adipocytes were subjected to 1% formaldehyde cross-linking for 10 minutes at room temperature and neutralized with 0.125M glycine for 5 minutes.  Cells were then treated with Accutase and scraped.  The preparation was centrifuged for 25 minutes at 15°C at 3500 rpm.  The adipocytes, formed as a white layer (anti-pellet) at the meniscus, were harvested and snap-frozen in liquid nitrogen.

extract_protocol: Frozen cells were resuspended in Qiagen RLT buffer and total RNA isolated using the Qiagen RNeasy Kit.

treatment_protocol: On Day 19 of differentiation, cells were treated with 0 or 10ng/ml TNF and incubated for 24hrs. Cells then underwent a 5 hr serum starvation followed by teatment with 0 or 20nM insulin for 2 hrs.  At the end of the incubation, cells were harvested ( mixed) or fractioanted into adipocyte ( buiyant) and stromal (pelleted) fractions and subjected to RNA isolation.

value: Adipocyte

tag: treatment 1

value: 10 ng/ml TNF

tag: treatment 2

value: 20 nM Insulin


title: Strom_TNF_rep 1

source_name: hMSC adipocytes, 24 hrs TNF,  pelleted fraction

value: Stromal


title: Adip_TNF_Ins_rep 1


title: Adip_TNF_rep 1

source_name: hMSC adipocytes, 24 hrs TNF,  buoyant fraction


title: Mixed_TNF_Ins_rep 1

source_name: hMSC adipocytes, 24h TNF, 5 h insulin

value: mixed adipocyte and stromal


title: SCC4 HPV(-), methylation

description:
7462
HPV(-) HNSCC cell line sample.

source_name: DNA from HNSCC cell line, HPV(-)


title: Mixed_TNF_Ins_rep 2


title: SCC47 HPV(+), methylation

description:
7463
HPV(+) HNSCC cell line sample.

source_name: DNA from HNSCC cell line, HPV(+)


title: SCC74A HPV(-), methylation

description:
7464
HPV(-) HNSCC cell line sample.


title: Strom_TNF_rep 2


title: Adip_Ins_rep 2

source_name: hMSC adipocytes, 5 hrs insulin, buoyant fraction


title: SCC47 HPV(+), expression

description: Gene expression data from HNSCC HPV(+) cell line.

source_name: RNA from HNSCC cell line, HPV(+)


title: Mixed_TNF_rep 1

source_name: hMSC adipocytes, 24h TNF


title: Strom_Ins_rep 1

source_name: hMSC adipocytes, 5 hrs insulin, pelleted fraction


title: Strom_TNF_Ins_rep 2

source_name: hMSC adipocytes, 24h TNF, 5 h insulin, pelleted fraction


title: Mixed_Ins_rep 2

source_name: hMSC adipocytes, 5 hrs insulin


title: Strom_rep 2

source_name: hMSC adipocytes, pelleted fraction


title: SCC4 HPV(-), expression


title: Strom_Ins_rep 2


title: Strom_TNF_Ins_rep 1


title: Strom_rep 1


title: VI29_NGT

status: Public on Nov 29 2010

first: Florence

last: van Tienen

department: Genetics and Cell biology

description: Gene expression data of muscle from control subject C14

hyb_protocol: A mixture of cDNA and added hybridization controls was hybridized on Affymetrix HG-U133 Plus 2.0 chips, followed by staining and washing steps in the Affymetrix GeneChip fluidics station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with R, a free software program for statistical computing and graphics. Normal linear regression models were used to asses significantly differentially expressed genes between patients and controls.

source_name: skeletal muscle vastus lateralis

label_protocol: 150ng muscle RNA was reverse transcribed into cDNA and amplified in a two-round amplification according to the manufacturer's protocol (Affymetrix)

extract_protocol: Total RNA was isolated using the TRIzol reagent and purified with the Rneasy clean-up kit (Qiagen)

treatment_protocol: After biopsy, the muscle samples were immediately frozen in liquid nitrogen.

tag: group

value: NGT

tag: bmi


title: VE02_IGT

description: Gene expression data of muscle from control subject C11

value: IGT


title: Adip_TNF_rep 2


title: TM18_IGT

description: Gene expression data of muscle from control subject C8


title: Adip_Ins_rep1


title: TI05_NGT

description: Gene expression data of muscle from control subject C7


title: VH05_T2DM_T52

description: Gene expression data of muscle from control subject C13

value: T2DM T52


title: Mixed_TNF_rep 2


title: PO14_IGT

description: Gene expression data from muscle of patient P477


title: SL01_T2DM_T52

description: Gene expression data of muscle from control subject C3


title: Adip_rep 1

source_name: hMSC adipocytes, buoyant fraction


title: SW17_IGT

description: Gene expression data of muscle from control subject C5


title: Adip_rep 2


title: Mixed_Ins_rep 1


title: Mixed_rep 1

source_name: hMSC adipocytes


title: VH05_T2DM_T0

description: Gene expression data of muscle from control subject C12

value: T2DM T0


title: VB09_NGT

description: Gene expression data of muscle from control subject C9


title: NW30_NGT

description: Gene expression data of muscle from control subject C15


title: Mixed_rep 2


title: KA06_T2DM_T0


title: HO07_IGT


title: OP10_IGT

description: Gene expression data from muscle of patient P423


title: SL01_T2DM_T0

description: Gene expression data from muscle of patient P509


title: GO32_NGT


title: HO02_T2DM_T0

description: Gene expression data of muscle from control subject C4


title: GO11_T2DM-T0


title: GR31_NGT


title: SL22_IGT


title: ON04_NGT

description: Gene expression data of muscle from control subject C16


title: NI24_IGT


title: MR23_NGT


title: GA01_IGT


title: HO02_T2DM_T52


title: KR10_T2DM_T0


title: DO15_IGT


title: ME11_NGT


title: HE08_T2DM_T52


title: HE08_T2DM_T0


title: EN04_T2DM_T0


title: GL33_NGT


title: EN04_T2DM_T52


title: EI03_T2DM_T0


title: EI03_T2DM_T52


title: DE25_NGT


title: BL21_IGT

description: Gene expression data from muscle of patient P55


title: KR10_T2DM_T52


title: CA07_T2DM_T0

description: Gene expression data from muscle of patient P194


title: CA07_T2DM_T52


title: BE16_NGT

description: Gene expression data from muscle of patient P54


title: GBM_37_CD133sp

status: Public on Nov 21 2010

city: new york

first: Viviane

last: Tabar

state: NY

address: 411 east 67th street

department: neurosurgery

institute: MSKCC

hyb_protocol: 15ug of labeled cRNA were hybridized on the human U133-plus2 arrays

scan_protocol: according to Affymetrix manufacturer

data_processing: Overall intensity was targetted to 500.Signal intensities were generated using GCOS1.4

source_name: Brain tumor

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

extract_protocol: Total RNA was extracted by absolutely RNA nanoprep or RNAeasy Kits  according to the manufacturer's instructions.

value: Female

tag: cell source

value: brain GBM tumor

value: CD133+ cell


title: BA26_IGT

description: Gene expression data from muscle of patient P38


title: GBM_37_DN


title: GBM_37_CD144sp

value: CD144+ cell


title: GBM_15_DN

source_name: brain tumor

value: Male


title: GBM_15_CD144sp


title: GBM_37_DP


title: GBM_15_DP


title: GBM_15_CD133sp


title: Hospital-acquired isolate n°4 (M9) vs reference strain Mu50 rep1

status: Public on Nov 15 2010

city: Brussels

middle: Luis

last: De Mendonca

address: Route de Lennik 808

department: Microbiology

country: Belgium

institute: ULB - Hôpital Erasme

description: Samples were hybridized to StaphVar arrays containing 1326 60mer oligonucleotide probes (Eurogentec, Seraing, Belgium).

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 3.5xSSC, SDS 0.1%, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Prior to hybridization, fluorescent labeled DNA fragments were mixed to achieve a final 90µL volume of hybridization solution (3.4XSSC, SDS 0.3% and single stranded salmon sperm DNA 0.01%), denatured for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, microarrays were successively washed in 2XSCC-SDS 0.03% solution (twice) at 60°C, 2XSSC at 60°C, 1XSCC at room temperature and 0.2XSCC, each time for 2 min. They were dried by centrifugation at 800 rpm for 10 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and fluorescence intensities of each spot were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing:
Data processing was achieved as described by Saunders et al (Saunders NA, Underwood A, Kearns AM and Hallas G. 2004. A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus. Microbiology, 3763-3771).
Briefly, for each individual spot, two ratios were calculated:
The first one (VALUE) was calculated by the signal intensity of the spot to the median of negative control signal intensities. Spots were scored as "negative" when the VALUE was less than 3. Spots presenting a ratio superior or equal to 3 were processed further as follows:
The backgrounds were first subtracted from each individual spot for the test and the reference strains. The second one (Ratio_2) was the ratio of test strain intensity to Mu50 intensity (reference strain) normalized against the median ratio obtained for the positive controls (n=4). The spots were scored as "positive" when the Ratio_2 values were above 0.25. In the opposite, spots were scored as "negative" when the Ratio_2 values were below 0.1, and "indeterminate" for Ratio_2 values ranging between 0.1-0.25.

organism: Staphylococcus aureus

source_name: Isolate n°4 (M9)

label_protocol: Prior to labeling, 4 µg of genomic DNA were digested by Sau3AI (New Englands Biolabs, Hitchin, UK) and purified by the MinElute Reaction kit as described by the manufacturer (Qiagen). Fluorescent labeling was performed by random priming with the Bioprime DNA labeling kit (Invitrogen, Merelbeke, Belgium) with a final concentration of non-fluorescent nucleotides of 0.12 mM for dATP, dCTP, dGTP and 0.06 mM for dTTP. To each labeling reaction mixture, fluorescent nucleotide analogs (Cy5-dUTP; Amersham, Gent, Belgium) were added to a final concentration of 0.06 mM. Reactions were stopped by addition of 5 µL of 0.5 M EDTA pH 8.0 and cleaned up with the MinElute Reaction kit as described by the manufacturer (Qiagen).

growth_protocol: Prior to DNA extraction, strains were grown in brain-heart infusion medium at 37°C until optical density at 600 nm reached 1

extract_protocol: Genomic DNA was isolated using DNeasy Tissue Kit according to the manufacturer instructions (Qiagen)

treatment_protocol: No treatment

tag: sample type

value: Hospital-acquired Methicillin resistant Staphylococcus aureus recovered in Belgium

source_name: Reference strain Mu50

label_protocol: Prior to labeling, 4 µg of genomic DNA were digested by Sau3AI (New Englands Biolabs, Hitchin, UK) and purified by the MinElute Reaction kit as described by the manufacturer (Qiagen). Fluorescent labeling was performed by random priming with the Bioprime DNA labeling kit (Invitrogen, Merelbeke, Belgium) with a final concentration of non-fluorescent nucleotides of 0.12 mM for dATP, dCTP, dGTP and 0.06 mM for dTTP. To each labeling reaction mixture, fluorescent nucleotide analogs (Cy3-dUTP; Amersham, Gent, Belgium) were added to a final concentration of 0.06 mM. Reactions were stopped by addition of 5 µL of 0.5 M EDTA pH 8.0 and cleaned up with the MinElute Reaction kit as described by the manufacturer (Qiagen).

value: Sequenced Hospital acquired methicillin resistant Staphylococcus aureus


title: Hospital-acquired isolate n°1 (M8) vs reference strain Mu50 rep2

source_name: Isolate n°1 (M8)


title: Sprouting Vs NonSprouting, aged, day21_rep3 747_21

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: SproutingVsNonSprouting, day21_rep3

hyb_protocol: Purified labeled Cy-3 and Cy-5 labeled cDNA were combined and hybridized to the Agilent Whole Rat Genome Oligo Microarray Kit G4131A containing more than 41,000 gene probes. All samples were labeled with both dyes and hybridized on arrays using a dye-swap design.

scan_protocol: Agilent Scanner (G2565AA), according to Agilent protocol

data_processing: Image analysis performed with Agilent Feature Extraction software. Array data analysis was in the R computing environment and using Bioconductor packages The Cy3 and Cy5 log-intensities for each spot were summarized as M and A-values and normalized for dye-bias and spatial effects using Loess normalization.

source_name: LCM-captured neurons after stroke

label_protocol: The amplified RNA was labeled by reverse transcriptase using the indirect amino-allyl labeling (Cy Dye™ Post-Labeling Reactive Dye Packs, Amersham RPN5661). The labeled cDNA samples were separated from unincorporated dye labeled nucleotides (QIAquick spin columns,Qiagen).

extract_protocol: Total RNA was isolated from captured cells and subjected to two rounds of T7 amplification.

treatment_protocol: Two different fluorescent conjugates of the tracer cholera toxin B (CTb), CTb-Alexa 488 and CTb-Alexa 647 (Molecular Probes), were sequentially injected into peri-infarct cortex at the sites of post-stroke axonal sprouting using a picospritzer pressure injection system. After survival periods of 7 days and 21 days (separate cohorts of animals), CTb-647 was injected exactly within CTb-488 injection site. Seven days after the second tracer injection, laser capture microdissection (LCM) was used to capture ~300 neurons for each cell type.

tag: animal #

tag: animal age

value: 2 yr

value: Sprouting neuron

tag: time point

value: Day 21

value: Non-Sprouting neuron


title: Sprouting Vs NonSprouting, aged, day21_rep5_dye swap 744_21s

description: SproutingVsNonSprouting, day21_rep5_dye swap


title: Hospital-acquired isolate n°1 (M8) vs reference strain Mu50 rep1


title: Sprouting Vs NonSprouting, aged, day21_rep4_dye swap 742_21s

description: SproutingVsNonSprouting, day21_rep4_dye swap


title: Sprouting Vs NonSprouting, aged, day21_rep4 742_21

description: SproutingVsNonSprouting, day21_rep4


title: Sprouting Vs NonSprouting, aged, day21_rep5 744_21

description: SproutingVsNonSprouting, day21_rep5


title: Sprouting Vs NonSprouting, aged, day7_rep5_dye swap 758_7s

description: SproutingVsNonSprouting, day7_rep5_dye swap

value: Day 7


title: Sprouting Vs NonSprouting, aged, day21_rep1 749_21

description: SproutingVsNonSprouting, day21_rep1


title: Sprouting Vs NonSprouting, aged, day7_rep4_dye swap 757_7s

description: SproutingVsNonSprouting, day7_rep4_dye swap


title: Sprouting Vs NonSprouting, aged, day7_rep3 756_7

description: SproutingVsNonSprouting, day7_rep3


title: Sprouting Vs NonSprouting, aged, day21_rep3_dye swap 747_21s

description: SproutingVsNonSprouting, day21_rep3_dye swap


title: Sprouting Vs NonSprouting, aged, day7_rep2 754_7

description: SproutingVsNonSprouting, day7_rep2


title: Sprouting Vs NonSprouting, aged, day7_rep4 757_7

description: SproutingVsNonSprouting, day7_rep4


title: Sprouting Vs NonSprouting, aged, day21_rep2 746_21

description: SproutingVsNonSprouting, day21_rep2


title: Sprouting Vs NonSprouting, aged, day21_rep2_dye swap 746_21s

description: SproutingVsNonSprouting, day21_rep2_dye swap


title: Hospital-acquired isolate n°4 (M9) vs reference strain Mu50 rep2


title: Sprouting Vs NonSprouting, aged, day21_rep1_dye swap 749_21s

description: SproutingVsNonSprouting, day21_rep1_dye swap


title: Sprouting Vs NonSprouting, aged, day7_rep1_dye swap 752_7s

description: SproutingVsNonSprouting, day7_rep1_dye swap


title: Sprouting Vs NonSprouting, aged, day7_rep1 752_7

description: SproutingVsNonSprouting, day7_rep1


title: Sprouting Vs NonSprouting, aged, day7_rep3_dye swap 756_7s

description: SproutingVsNonSprouting, day7_rep3_dye swap


title: Hospital-acquired isolate n°34 (M66) vs reference strain Mu50 rep2

source_name: Isolate n°34 (M66)


title: Hospital-acquired isolate n°34 (M66) vs reference strain Mu50 rep1


title: Hospital-acquired isolate n°13 (M59) vs reference strain Mu50 rep2

source_name: Isolate n°13 (M59)


title: Hospital-acquired isolate n°27 (M39) vs reference strain Mu50 rep2

source_name: Isolate n°27 (M39)


title: Hospital-acquired isolate n°13 (M59) vs reference strain Mu50 rep1


title: Hospital-acquired isolate n°3 (M50) vs reference strain Mu50 rep2

source_name: Isolate n°3 (M50)


title: Sprouting Vs NonSprouting, aged, day7_rep5 758_7

description: SproutingVsNonSprouting, day7_rep5


title: Hospital-acquired isolate n°17 (M63) vs reference strain Mu50 rep2

source_name: Isolate n°17 (M63)


title: Hospital-acquired isolate n°3 (M50) vs reference strain Mu50 rep1


title: Sprouting Vs NonSprouting, young, day21_rep4_dye swap 21_4b

value: 2 mo


title: Sprouting Vs NonSprouting, young, day21_rep1_dye swap 21_1b


title: Hospital-acquired isolate n°17 (M63) vs reference strain Mu50 rep1


title: Sprouting Vs NonSprouting, young, day21_rep5_dye swap 21_5b


title: Hospital-acquired isolate n°10 (M49) vs reference strain Mu50 rep1

source_name: Isolate n°10 (M49)


title: Hospital-acquired isolate n°10 (M49) vs reference strain Mu50 rep2


title: Sprouting Vs NonSprouting, young, day21_rep3_dye swap 21_3b


title: Sprouting Vs NonSprouting, young, day21_rep4 21_4

description: SproutingVsNonSprouting, day21_rep4


title: Sprouting Vs NonSprouting, young, day21_rep3 21_3

description: SproutingVsNonSprouting, day21_rep3


title: Sprouting Vs NonSprouting, young, day21_rep5 21_5

description: SproutingVsNonSprouting, day21_rep5


title: Hospital-acquired isolate n°12 (M37) vs reference strain Mu50 rep1

source_name: Isolate n°12 (M37)


title: Sprouting Vs NonSprouting, aged, day7_rep2_dye swap 754_7s

description: SproutingVsNonSprouting, day7_rep2_dye swap


title: Sprouting Vs NonSprouting, young, day21_rep2_dye swap 21_2b


title: Sprouting Vs NonSprouting, young, day21_rep2 21_2

description: SproutingVsNonSprouting, day21_rep2


title: Hospital-acquired isolate n°27 (M39) vs reference strain Mu50 rep1


title: Hospital-acquired isolate n°12 (M37) vs reference strain Mu50 rep2


title: Hospital-acquired isolate n°7 (M32) vs reference strain Mu50 rep2

source_name: Isolate n°7 (M32)


title: Hospital-acquired isolate n°16 (M34) vs reference strain Mu50 rep2

source_name: Isolate n°16 (M34)


title: Hospital-acquired isolate n°16 (M34) vs reference strain Mu50 rep1


title: Hospital-acquired isolate n°33 (M2) vs reference strain Mu50 rep2

source_name: Isolate n°33 (M2)


title: Hospital-acquired isolate n° 7 (M32) vs reference strain Mu50 rep1


title: Hospital-acquired isolate n°26 (M27) vs reference strain Mu50 rep2

source_name: Isolate n°26 (M27)


title: Hospital-acquired isolate n° 18 (M22) vs reference strain Mu50 rep2

source_name: Isolate n° 18 (M22)


title: Hospital-acquired isolate n° 18 (M22) vs reference strain Mu50 rep1

source_name: Isolate n°18


title: Hospital-acquired isolate n°19 (M29) vs reference strain Mu50 rep2

source_name: Isolate n°19 (M29)


title: Sprouting Vs NonSprouting, young, day7_rep4 7_4

description: SproutingVsNonSprouting, day7_rep4


title: Hospital-acquired isolate n°33 (M2) vs reference strain Mu50 rep1

source_name: Reference strain Mu50


title: Hospital-acquired isolate n°14 (M24) vs reference strain Mu50 rep1

source_name: Isolate n°14 (M24)

source_name: Reference stain Mu50


title: Sprouting Vs NonSprouting, young, day21_rep1 21_1

description: SproutingVsNonSprouting, day21_rep1

source_name: LCM-captured neurons after stroke


title: Hospital-acquired isolate n°19 (M29) vs reference strain Mu50 rep1


title: Hospital-acquired isolate n°2 (M1) vs reference strain Mu50 rep2

source_name: Isolate n°2 (M1)


title: Sprouting Vs NonSprouting, young, day7_rep4_dye swap 7_4b


title: Sprouting Vs NonSprouting, young, day7_rep5 7_5

description: SproutingVsNonSprouting, day7_rep5


title: Livestock-associated isolate n° 50 (AU3) vs reference strain Mu50 rep1

source_name: Isolate n°50 (AU3)

value: Livestock-associated Methicillin resistant Staphylococcus aureus recovered in Belgium


title: Sprouting Vs NonSprouting, young, day7_rep5_dye swap 7_5b


title: Hospital-acquired isolate n°14 (M24) vs reference strain Mu50 rep2


title: Livestock-associated isolate n°50 (AU3) vs reference strain Mu50 rep2

source_name: Isolate n° 50 (Au3)


title: Hospital-acquired isolate n°26 (M27) vs reference strain Mu50 rep1


title: Sprouting Vs NonSprouting, young, day7_rep3 7_3

description: SproutingVsNonSprouting, day7_rep3


title: Livestock-associated isolate n°44 (C48) vs reference strain Mu50 rep1

source_name: Isolate n°44 (C48)


title: Hospital-acquired isolate n°2 (M1) vs reference strain Mu50 rep1


title: Sprouting Vs NonSprouting, young, day7_rep3_dye swap 7_3s


title: Hospital-acquired isolate n°15 (M15) vs reference strain Mu50 rep1

source_name: Isolate n°15 (M15)


title: Hospital-acquired isolate n°5 (M18) vs reference strain Mu50 rep1

source_name: Isolate n°5 (M18)


title: Livestock-associated isolate n°44 (C48) vs reference strain Mu50 rep2


title: Sprouting Vs NonSprouting, young, day7_rep2_dye swap 7_2s


title: Hospital-acquired isolate n°5 (M18) vs reference strain Mu50 rep2


title: Hospital-acquired isolate n°32 (M12) vs reference strain Mu50 rep1

source_name: Isolate n°32 (M12)


title: Sprouting Vs NonSprouting, young, day7_rep2 7_2

description: SproutingVsNonSprouting, day7_rep2


title: Sprouting Vs NonSprouting, young, day7_rep1 7_1

description: SproutingVsNonSprouting, day7_rep1


title: Hospital-acquired isolate n°32 (M12) vs reference strain Mu50 rep2


title: Sprouting Vs NonSprouting, young, day7_rep1_dye swap 7_1s


title: Hospital-acquired isolate n°15 (M15) vs reference strain Mu50 rep2


title: Livestock-associated isolate n°37 (C14) vs reference strain Mu50 rep2

source_name: Isolate n°37 (C14)


title: Hospital-acquired isolate n°6 (M10) vs reference strain Mu50 rep1

source_name: Isolate n°6 (M10)


title: Livestock-associated isolate n°38 (S543) vs reference strain Mu50 rep2

source_name: Isolate n°38 (S543)


title: Livestock-associated isolate n°37 (C14) vs reference strain Mu50 rep1


title: Hospital-acquired isolate n°6 (M10) vs reference strain Mu50 rep2


title: Livestock-associated isolate n°38 (S543) vs reference strain Mu50 rep1


title: Livestock-associated isolate n°36 (S488) vs reference strain Mu50 rep2

source_name: Isolate n°36 (S488)


title: Livestock-associated isolate n°45 (S417) vs reference strain Mu50 rep1

source_name: Isolate n°45 (S417)


title: Livestock-associated Isoalte n°36 (S488) vs reference strain Mu50 rep1


title: Livestock-associated isolate n°46 (S413) vs reference strain Mu50 rep1

source_name: Isolate n°46 (S413)


title: Livestock-associated isolate n°47 (S318) vs reference strain Mu50 rep2

source_name: Isolate n°47 (S318)

source_name: Reference strain Mu50


title: Livestock-associated isolate n°46 (S413) vs reference strain Mu50 rep2


title: Livestock-associated isolate n°45 (S417) vs reference strain Mu50 rep2


title: Livestock-associated isolate n°40 (S262) vs reference strain Mu50 rep2

source_name: Isolate n°40 (S262)


title: Livestock-associated isolate n°51 (S231) vs reference strain Mu50 rep2

source_name: Isolate n°51 (S231)


title: Livestock-associated isolate n°43 (S256) vs reference strain Mu50 rep1

source_name: Isolate n°43 (S256)


title: Livestock-associated isolate n°40 (S262) vs referecnce strain Mu50 rep1


title: Livestock-associated isolate n°43 (S256) vs reference strain Mu50 rep2


title: Livestock-associated isolate n°47 (S318) vs reference strain Mu50 rep1


title: Livestock-associated isolate n°51 (S231) vs reference strain Mu50 rep1


title: Livestock-associated isolate n°41 (S220) vs reference strain Mu50 rep2

source_name: Isolate n°41 (S220)


title: Livestock-associated isolate n°52 (S226) vs reference strain Mu50 rep1

source_name: Isolate n°52 (S226)


title: Livestock-associated isolate n°42 (S174) vs reference strain Mu50 rep2

source_name: Isolate n°42 (S174)


title: Livestock-associated isolate n°41 (S220) vs reference strain Mu50 rep1


title: Livestock-associated isolate n°52 (S226) vs reference strain Mu50 rep2


title: Livestock-associated isolate n°48 (S143) vs reference strain Mu50 rep1

source_name: Isolate n°48 (S143)

source_name: Reference Strain Mu50


title: Livestock-associated isolate n°39 (S172) vs reference strain Mu50 rep1

source_name: Isolate n°39 (S172)


title: Livestock-associated isolate n°35 (S170) vs reference strain Mu50 rep1

source_name: Isolate n°35 (S170)


title: Livestock-associated isolate n°48 (S143) vs reference strain Mu50 rep2


title: Livestock-associated isolate n°35 (S170) vs reference strain Mu50 rep 2

source_name: Reference stran Mu50


title: Livestock-associated isolate n°39 (S172) vs reference strain Mu50 rep2


title: Livestock-associated isolate n°49 (AS5) vs reference strain Mu50 rep2

source_name: Isolate n°49 (AS5)


title: Livestock-associated isolate n°42 (S174) vs reference strain Mu50 rep1


title: Livestock-associated isolate n°49 (AS5) vs reference strain Mu50 rep1


title: hh- vs.hh+ (9th-161_homo_het)

status: Public on Nov 03 2010

city: San Francisco

first: Brian

last: Biehs

address: 505 Parnassus Ave

institute: UCSF

hyb_protocol: Cy3 and Cy5 labeld probes were combined and hybridized to arrays overnight using home-made hybridization chambers.  Arrays were thn washed using a dilution series of SDS SSC washes.

scan_protocol: Hybridized microarrays were scanned with a GenePix 4000 A Microarray Scanner (Axon Instruments, Union City, CA). Data were analyzed and displayed with Cluster and Treeview, Genepix PRO (Axon Instruments), and Microsoft Excel.

data_processing: Global means normalization for cluster analysis  were done with NOMAD. Only genes that qualified with a combined median intensity > 300 above background in both channels in at least 80% of the repeated experiments were included in the analysis. A threshold of >  0.55 of the log2-transformed ratios was chosen for all comparisons.

source_name: total RNA from hh- embryos

label_protocol: We indirectly labeled the hybridization probes by incorporation of amino-allyl modified nucleotides in a first strand cDNA reverse transcription reaction. Monofunctional Cy5 or Cy3 dye (Amersham Inc.) was subsequently coupled to the reactive residues. Independently generated samples were used for hybridizations for all experiments, and dye labeling was reversed to avoid systematic bias.

extract_protocol: Total RNA was extracted using the micro RNA extraction kit (Zymo).

tag: genotype/variation

value: hh-/hh-

source_name: total RNA from hh+ embryos

value: hh-/hh+


title: smo- vs. smo+ (10th_incyte-166)

source_name: total RNA from smo- embryos

value: smo-/smo-

source_name: total RNA from smo+ embryos

value: smo-/smo+


title: smo- vs. smo+ (10th_incyte-204)


title: ci- vs. ci+ (9th-84_ci-_ci+)

source_name: total RNA from ci- embryos

value: ci-/ci-

source_name: total RNA from ci+ embryos

value: ci-/ci+


title: hh- vs.hh+ (9th-85)


title: Da>Cim1-m4 vs. wt (10th_incyte-31)

source_name: total RNA from wt embryos

value: wt

source_name: total RNA from Da>Cim1-m4 embryos

value: UAS Da>Cimi-m4


title: Da>Cim1-m4 vs. wt (10th_incyte-44)


title: smo- vs. smo+ (10th_incyte-205)


title: ci- vs. ci+ (9th-80)

value: ci+/ci-


title: smo- vs. smo+ (10th_incyte-206)


title: ptc- vs. ptc+ (5th-245_ptc_het)

source_name: total RNA from ptc- embryos

value: ptc-/ptc-

source_name: total RNA from ptc+ embryos

value: ptc-/ptc+


title: Da>Cim1-m4 vs. wt (10th_incyte-30)


title: smo- vs. smo+ (10th_incyte-211)


title: ptc- vs. ptc+ (5th-109_het_ptc)


title: 2009 pandemic influenza H1N1-positive sample Ont-84 (Canada)

status: Public on Nov 01 2010

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

description: amplified cDNA

hyb_protocol: Microarrays were hybridized overnight according to the manufacturer's protocol (Agilent Technologies) using the Agilent Gene Expression Hybridization kit

scan_protocol: Microarrays were scanned at 2 um resolution on an Agilent DNA Microarray Scanner

data_processing: Normalized output intensities from Agilent's Feature Extraction Software were further normalized (sum of the squares of the values set to 1.0) based on the 12,361 viral probes on the array in common between the three platforms GPL10896, GPL10897 and GPL10898.

source_name: nasopharyngeal swab

label_protocol: Randomly amplified cDNA was labelled using a Cy3 or Cy5 fluorescent dye via aa-dNTP incorporation (Wang, et al, 2002; Chiu, et al, 2006; Chiu, et al, 2008)

extract_protocol: Total RNA was extracted using commercially available kits

value: nasopharyngeal swab


title: 2009 pandemic influenza H1N1-positive sample Cal-UC6 (California)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample BC-59 (Canada)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample Mex-943 (Mexico)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample BC-44 (Canada)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample Ont-69 (Canada)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample Cal-UC12 (California)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample BC-76 (Canada)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample Ont-61 (Canada)

description: amplified cDNA


title: DamCi m1-m4 C

description: replicate 3

hyb_protocol: Arrays were hybridized at Nimblegen

scan_protocol: Arrays were scanned at Nimblegen

data_processing: All analyses were performed in R v2.7.1 (R Development Core Team, 2005) unless otherwise noted.  At each tiling array feature, log ratios between the experimental and control samples were calculated and normalized using limma (Smyth, 2005), applying “loess” and “Aquantile” for normalization within arrays and between arrays, respectively (Wormald et al., 2006).

source_name: Dam alone methylated DNA from UAS Dam embryos

label_protocol: Samples were labeled at Nimblegen

growth_protocol: Embryos were collected for 2hrs and aged for an additional 4 hours at 25 degrees

extract_protocol: Genomic DNA was isolated from 2-6 hour old embryos containing DamCi or Dam transgenes using the DNeasy kit (Qiagen).

tag: developmental stage

value: embryo (stage 10-11)

value: UAS Dam Ci m1-m4

source_name: DamCi m1-m4 methylated DNA from UAS DamCi m1-m4 embryos


title: DamCiRep B

description: replicate 2

source_name: DamCiRep methylated DNA from UAS DamCiRep embryos

value: UAS Dam CiRep

tag: genotype

value: UAS Dam alone


title: DamCi m1-m4 B

description: replicate 2


title: 5 CD8

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

hyb_protocol: Standard Affymetrix 49 Format Hybridization with 15mg of fragmented cRNA

scan_protocol: Affymetrix EukGE-WS2v4

data_processing: RMAExpress

label: SAPE

source_name: Peripheral Blood

label_protocol: Ambion MessageAmp Biotin II Enhanced

growth_protocol: Peripheral Blood collected in Paxgene tubes and EDTA purple top tubes and cell subtypes separated by magnetic beads

extract_protocol: RNA was extracted using the Paxgene and Trizol RNA systems

tag: donor number

value: Control 5

value: Control Day 0

tag: cell subtype


title: 94

value: Whole Blood


title: 3 CD19

value: Control 3


title: 4 CD14

value: Control 4


title: 4 CD19


title: DamCiRep C

description: replicate 3


title: 3 CD14


title: 3 CD56


title: 4651


title: 4 CD8


title: DamCi m1-m4 A

description: replicate 1


title: 5 CD19


title: 3 CD8


title: 2 CD4

value: Control 2


title: 2 CD19


title: 5 CD14


title: 3 CD4


title: 4 CD4


title: 4674


title: 2 CD8


title: 5 CD4


title: 2 CD56


title: 4559


title: DamCiRep A

description: replicate 1


title: 1855

value: Control 1


title: 2 CD14


title: 1306 CD14

value: Week 12


title: 1305

value: Week 8


title: 1301_CD4

value: Pre-Tx


title: 1304

value: Week 4


title: 1301_PBL

value: Whole blood


title: 1301


title: 1301_8


title: 1303

value: Week 2


title: 1206-CD19_


title: 1203 CD8


title: 1204_14


title: 1205


title: 1206


title: 1203 CD4


title: 1206 CD56


title: 1204_PBL


title: 1206-CD8_


title: 1206-CD14_


title: 1206 CD19


title: 1206 CD8


title: 1203 CD19


title: 1203 CD56


title: 1202

value: Week 1


title: 1206-CD4_


title: 1206 CD14


title: 1203 CD14


title: 1204


title: 1201_8


title: 1206 CD4


title: 1204_4


title: 1201_19


title: 1203


title: 1106 CD14


title: 1103 CD14


title: 1302


title: 1104_14


title: 1003 CD19


title: 1106 CD4


title: 1201_4


title: 1201


title: 1004


title: 1005


title: 1106


title: 1105_14


title: 1103 CD8


title: 1104_PBL


title: 1102


title: 1001


title: 1 CD8


title: 1002


title: 1006


title: 1104a


title: 1104b


title: 1103


title: 1003


title: 1001_PBL


title: 1003 CD56


title: 1001_8


title: 1101


title: 1005_4


title: 1003 CD14


title: 1 CD56


title: 0706-CD4_


title: 0706-CD14_


title: 1 CD4


title: 1 CD14


title: 0706-CD8_


title: 0901_4


title: 0706 CD4


title: 706


title: 705


title: 0706 CD14


title: 704


title: 0705_4


title: 0706 CD8


title: 1 CD19


title: 0703 CD8


title: 0703 CD14


title: 0701_4


title: 0602_PBL


title: 702


title: 0706 CD19


title: 701


title: 703


title: 0702_14


title: 0701_8


title: 0703 CD4


title: 0702_PBL


title: 0602_14


title: 0702_4


title: 0601_PBL


title: 506


title: 0503 CD8


title: 0503-CD8_


title: 0601_14


title: 0504-Pax


title: 0406-CD8_


title: 0503 CD4


title: 0406-CD14_


title: 0503-CD4_


title: 0501_PBMC


title: 0503 CD14


title: 0406_4


title: 0503-CD14_


title: 0405_8


title: 406


title: 0405_PBL


title: 0406_14


title: 0501_14


title: 502


title: 0404_PBL


title: 0406-CD4_


title: 0405_14


title: 405


title: 403


title: 0503 CD56


title: IGF-1 stimulated mouse small intestinal crypt cell vs control mouse small intestinal crypt cell replicate 3

city: Davis

first: Bo

last: Lonnerdal

address: 1 Shields Ave.

department: Nutrition

institute: University of California, Davis

hyb_protocol: Hybridization SureHyb chamber kit and Gasket slide kit (Agilent) were used to hybridize the labeled RNA for 18 h to Exiqon miRCURY LNA miRNA array V.11.0 (miRBase Sequence Database, http://microrna.sanger.ac.uk/sequences, release 11.0).

scan_protocol: Arrays were scanned on an Axon GenePix 4000B scanner

data_processing:
GPR files containing fluorescent ratios (sample/control) were generated using GenePix Pro 6.0 software. GPR files were read into R/Bioconductor [19] using the marray package. GenePix flagged spots were removed from subsequent analysis, and only unflagged human, mouse and rat probes were used for normalization and subsequent analysis. M (log2 ratios) of Cy5 to Cy3 signals were calculated for each array, and normalized by print tip loess normalization using only unflagged spots.
For each miRNA with more than 1 unflagged probe, the median of normalized M of the replicate probes was taken as its summary value for the miRNA in each array.

source_name: mouse small intestinal crypt cells

label_protocol: 300 ng of each sample was labeled with Cy5/Cy3 using miRCURY LNA microRNA array Power Labeling kit (Exiqon).

extract_protocol: Total RNA extracted with miRNeasy Mini Kit (Qiangen) according to the manufacturer's instructions

treatment_protocol: untreated

tag: passage

value: crypt cells isolated from mouse small intestine

tag: strain

source_name: mouse small intestinal crypt cells treated with 20ng/ml IGF-3

growth_protocol: The cells were resuspended with crypt culture media (Advanced DMEM/F12, GlutaMax 1:100, Hepes 10 mM, Penicillin/Streptomycin 1:100, N2 supplement 1:100, B27 supplement, retinoic acid free 1:50, mouse recombinant EGF 50 ng/ml), mouse recombinant noggin 100 ng/ml, human recombinant R-spondin1 500 ng/ml, and N-Acetylcysteine 1 μM). IGF-1 was added after cells were plated onto the cell culture plate.

treatment_protocol: 20ng/ml IGF1 (R&D Systems)


title: IGF-1 stimulated mouse small intestinal crypt cell vs control mouse small intestinal crypt cell replicate 2

growth_protocol: The cells were resuspended with crypt culture media (Advanced DMEM/F12, GlutaMax 1:100, Hepes 10 mM, Penicillin/Streptomycin 1:100, N2 supplement 1:100, B27 supplement, retinoic acid free 1:50, mouse recombinant EGF 50 ng/ml), mouse recombinant noggin 100 ng/ml, human recombinant R-spondin1 500 ng/ml, and N-Acetylcysteine 1 μM).

tag: cell type

source_name: mouse small intestinal crypt cells treated with 20ng/ml IGF-2


title: 402


title: 0306-Pax


title: 0403-CD8_


title: 0403-CD14_


title: 0303-CD4_


title: 304


title: 0206-CD8_


title: 0306-CD14_


title: 0601_4


title: 305


title: 0301-Pax


title: 0206-CD14_


title: 0206-CD19_


title: 0205-Pax


title: 0306-CD4_


title: 0303-CD14_


title: 0205_PBMC


title: 206


title: 0303-Pax


title: 0303-CD19_


title: 0306-CD8_


title: 0503-Pax


title: 0106-Pax


title: 0202-Pax


title: 0203-CD14_


title: 0206-CD4_


title: IGF-1 stimulated mouse small intestinal crypt cell vs control mouse small intestinal crypt cell replicate 1

source_name: mouse small intestinal crypt cells treated with 20ng/ml IGF-1


title: 204


title: 0103-Pax


title: 0103-CD4_


title: 0203-CD19_


title: 0203-CD4_


title: 0103-CD8_


title: Cord donor 060408A DCs RSV infected

city: Nashville

first: James

last: Crowe

state: TN

address: T2219 21st Avenue South,

department: Vanderbilt Vaccine Center

institute: Vanderbilt University Medical Center

hyb_protocol: 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.

data_processing: Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)

source_name: Umbillical cord blood dendritic cells, respiratory syncytial virus infected

label_protocol: RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.

growth_protocol: Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.

extract_protocol: Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.

treatment_protocol: Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.

tag: age

value: neonatal

tag: tissue

value: blood

tag: cell types

value: isolated conventional and plasmacytoid dendritic cells

tag: infection

value: respiratory syncytial virus infected


title: 201

value: Whole Blood


title: 0104-Pax


title: 0103-CD19_


title: 0103-CD14_


title: 0101-Pax


title: Cord donor 060408B DCs RSV infected


title: Cord donor 060408A DCs mock infected

source_name: Umbillical cord blood dendritic cells, mock infected

value: mock infected


title: 00704_4


title: 2009 pandemic influenza H1N1-positive sample Cal-UC2 (California)

description: amplified cDNA

value: nasopharyngeal swab


title: Cord donor 052808 DCs RSV infected


title: Adult donor 90 DCs mock infected

source_name: Adult dendritic cells, mock infected

value: adult


title: Adult donor 88 DCs RSV infected

source_name: Adult dendritic cells, respiratory syncytial virus infected


title: Adult donor 88 DCs mock infected


title: 2009 pandemic influenza H1N1-positive sample Mex-730 (Mexico)

description: amplified cDNA


title: Cord donor 060408B DCs mock infected


title: 2009 pandemic influenza H1N1-positive sample Ont-MT2 (Canada)

description: amplified cDNA


title: Cord donor 052808 DCs mock infected


title: 0102-Pax


title: Adult donor 34 DCs mock infected


title: seasonal influenza H3N2-positive sample (Canada)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample Mex-1225 (Mexico)

description: amplified cDNA


title: negative respiratory sample (California)

description: amplified cDNA


title: Adult donor 90 DCs RSV infected


title: Adult donor 34 DCs RSV infected


title: seasonal influenza H3N2-positive sample #2 (California)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample Mex-619 (Mexico)

description: amplified cDNA


title: respiratory syncytial virus-positive sample (California)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample Mex-956 (Mexico)

description: amplified cDNA


title: 2009 pandemic influenza H1N1-positive sample BC-1422 (Canada)

description: amplified cDNA


title: rhinovirus-positive sample #2 (California)

description: amplified cDNA


title: rhinovirus-positive sample #1 (California)

description: amplified cDNA


title: parainfluenza virus 3-positive sample (California)

description: amplified cDNA


title: parainfluenza virus 1-positive sample (California)

description: amplified cDNA


title: coronavirus-positive sample (California)

description: amplified cDNA


title: seasonal influenza H3N2-positive sample #1 (California)

description: amplified cDNA


title: seasonal influenza H1N1-positive sample #1 (California)

description: amplified cDNA


title: seasonal influenza H1N1-positive sample #2 (California)

description: amplified cDNA


title: 0404-Pax


title: 2009 pandemic influenza H1N1-positive sample Ont-MT1 (Canada)

description: amplified cDNA


title: Female PBS_rep3

status: Public on Oct 31 2010

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Female Control - replicate 3
Agilent TIFF High File: US23502387_251486824229_S01_H.tif
Agilent TIFF Low File: US23502387_251486824229_S01_L.tif

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data were obtained and processed with the Agilent Feature Extraction Software (v9.5) and the resulting data were imported into Rosetta Resolver (v7.1).

source_name: liver

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Livers were homogenized and total RNA from liver was extracted by using the RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. All samples were treated with the RNase-free DNase set (Qiagen). Samples were aliquoted and frozen at -800C.

treatment_protocol: Male and female (diestrous 1) adrenalectomized C57BL/6 mice were treated with vehicle (phosphate buffered saline) or dexamethasone (1 mg/kg i.p.) (Steraloids) on the same day. Six hours after dexamethasone treatment the liver was harvested and kept in RNAlater solution at 4oC overnight. All samples were frozen and stored at -800C

tag: gender

value: female (Diestrous 1)

value: 11 weeks, Adrenalectomized

value: liver

tag: treatment group

value: vehicle (phosphate buffered saline) for 6 hours


title: Female PBS_rep 2

description:
Female Control - replicate 2
Agilent TIFF High File: US23502387_251486824227_S01_H.tif
Agilent TIFF Low File: US23502387_251486824227_S01_L.tif


title: Male Dexamethasone 6 hr_rep 2

description:
Male Treated - replicate 2
Agilent TIFF High File: US23502387_251486824227_S01_H.tif
Agilent TIFF Low File: US23502387_251486824227_S01_L.tif

value: male

value: dexamethasone 1mg/Kg (i.p.) for 6 hours


title: Female Dexamethasone 6 hr_rep 3

description:
Female Treated - replicate 3
Agilent TIFF High File: US23502387_251486824228_S01_H.tif
Agilent TIFF Low File: US23502387_251486824228_S01_L.tif


title: Male PBS_rep1

description:
Male Control - replicate 1
Agilent TIFF High File: US23502387_251486824227_S01_H.tif
Agilent TIFF Low File: US23502387_251486824227_S01_L.tif


title: Male Dexamethasone 6 hr_rep 3

description:
Male Treated - replicate 3
Agilent TIFF High File: US23502387_251486824229_S01_H.tif
Agilent TIFF Low File: US23502387_251486824229_S01_L.tif


title: Oryza longistaminata-young leaf, biological rep3

city: beijing

first: ting

last: zhang

state: beijing

address: zhongguancun south street 12

country: China

institute: Chinese Acadamy of agricultural science

hyb_protocol: RNA from the three independent replicate samples were used for hybridization to the Affymetrix Genechips® Rice Genome Array chips, which contain probes to query 51,279 transcripts from two rice cultivars, including 48,564 japonica transcripts and 1,260 indica transcripts from Affymetrix (Santa Clara, CA).Hybridization to the arrays and quality control checks were carried out at the Company of CapitalBio Corporation, Beijing. (Affymetrix GeneChip Expression Analysis g of this fragmented target cRNA wasmTechnical Manual).

scan_protocol: standard Affymetrix protocol

data_processing: The SAM (Significant Analysis of Microarray) software was applied to identify differentially regulated genes (DRGs) between samples using the two classes unpaired method based on the empirical criterion of more than two-fold change and significant q value (FDR adjusted P value) less than 0.05. A list of known or unknown genes was generated by performing a BLASTn search (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi) from the Affymetrix website

organism: Oryza longistaminata

source_name: Oryza longistaminata, young leaf

label_protocol: Biotin labeled cRNA was produced with 5 ug of total RNA as starting material for each sample reaction.

growth_protocol: The wild rice Oryza longistaminata with long and strong rhizomes, originally collected from Niger and cultured in the greenhouse at the Institute of Food Crops, Yunnan Academy of Agricultural Sciences.

extract_protocol: Total RNA were extracted using TRIzol reagents according to the instruction and then purified and concentrated using RNeasy MinElute Cleanup kit (Qiagen).

treatment_protocol: At active tillering stage, five tissues from rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) were collected for total RNA extraction. Three independent biological replicates for each sample from individual rice plant were sampled, and all collected samples were snap-frozen in liquid nitrogen and kept in -70℃ freezer.

value: young leaf

tag: sample type

value: Oryza longistaminata, wild rice with long and strong rhizomes

value: wild type

value: active tillering stage


title: Male Dexamethasone 6 hr_rep 1

description:
Male Treated - replicate 1
Agilent TIFF High File: US23502387_251486824229_S01_H.tif
Agilent TIFF Low File: US23502387_251486824229_S01_L.tif


title: Female PBS_rep 1

description:
Female Control - replicate 1
Agilent TIFF High File: US23502387_251486824228_S01_H.tif
Agilent TIFF Low File: US23502387_251486824228_S01_L.tif


title: Male PBS_rep 3

description:
Male Control - replicate 3
Agilent TIFF High File: US23502387_251486824228_S01_H.tif
Agilent TIFF Low File: US23502387_251486824228_S01_L.tif


title: Female Dexamethasone 6 hr_rep 1

description:
Female Treated - replicate 1
Agilent TIFF High File: US23502387_251486824228_S01_H.tif
Agilent TIFF Low File: US23502387_251486824228_S01_L.tif


title: Male Dexamethasone 6 hr_rep 3

description:
Male Treated - replicate 3
Agilent TIFF High File : US23502387_251487917405_S01_H.tif
Agilent TIFF Low File: US23502387_251487917405_S01_L.tif

source_name: isolated hepatocytes

extract_protocol: Total RNA from cells were extracted by using the RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. All samples were treated with the RNase-free DNase set (Qiagen) and were kept at -80°C until labeling and hybridization.

treatment_protocol: Livers were isolated from adult male and female Sprague-Dawley rats and digested with the collagenase perfusion method developed by Berry and Friend (J Cell Biol 43, 506-520;1969). After collagenase treatment, the liver was excised, minced in balanced salt solution, and centrifuged at 50 g for 3 min. Immediately after isolation, hepatocytes were resuspended in Williams E Medium containing penicillin (100 units/ml), streptomycin (100 mg/ml), 2 mM glutamine pH 7.4, and 10% fetal bovine serum and plated on collagen-coated 94 x 16 mm cell culture dishes and maintained for 24 hours in a 95% air–5% CO2, 37°C incubator. The medium was then changed to free serum Williams E Medium and maintained in culture for an additional 24 hours. Hepatocytes isolated from male and rats were treated with vehicle (0.01% ethanol) or dexamethasone (100 nm) for 6 hours.

value: Sprague-Dawley

value: 11 weeks

value: liver-isolated hepatocytes

value: dexamethasone (100 nm) for 6 hours


title: Oryza longistaminata-shoot internodes, biological rep2

source_name: Oryza longistaminata, shoot internodes

value: shoot internodes


title: Male PBS_rep 2

description:
Male Control - replicate 2
Agilent TIFF High File: US23502387_251486824229_S01_H.tif
Agilent TIFF Low File: US23502387_251486824229_S01_L.tif


title: Oryza longistaminata-rhizome internodes, biological rep3

source_name: Oryza longistaminata, rhizome internodes

value: rhizome internodes


title: Oryza longistaminata-shoot internodes, biological rep1


title: Oryza longistaminata-young leaf, biological rep1


title: Male Dexamethasone 6 hr_rep 1

description:
Male Treated - replicate 1
Agilent TIFF High File : US23502387_251487917404_S01_H.tif
Agilent TIFF Low File: US23502387_251487917404_S01_L.tif


title: Oryza longistaminata-rhizome internodes, biological rep2


title: Oryza longistaminata-rhizome tip, biological rep1

source_name: Oryza longistaminata, rhizome tip

value: rhizome tip


title: Male Dexamethasone 6 hr_rep 2

description:
Male Treated - replicate 2
Agilent TIFF High File : US23502387_251487917405_S01_H.tif
Agilent TIFF Low File: US23502387_251487917405_S01_L.tif


title: Oryza longistaminata-rhizome tip, biological rep2


title: Female Dexamethasone 6 hr_rep 1

description:
Female Treated - replicate 1
Agilent TIFF High File : US23502387_251487917396_S01_H.tif
Agilent TIFF Low File: US23502387_251487917396_S01_L.tif


title: Oryza longistaminata-shoot internodes, biological rep3


title: Female Dexamethasone 6 hr_rep 3

description:
Female Treated - replicate 3
Agilent TIFF High File : US23502387_251487917396_S01_H.tif
Agilent TIFF Low File: US23502387_251487917396_S01_L.tif


title: Oryza longistaminata-rhizome internodes, biological rep1


title: Oryza longistaminata-young leaf, biological rep2


title: Female Dexamethasone 6 hr_rep 2

description:
Female Treated - replicate 2
Agilent TIFF High File : US23502387_251487917396_S01_H.tif
Agilent TIFF Low File: US23502387_251487917396_S01_L.tif


title: Oryza longistaminata-rhizome tip, biological rep3


title: HCMV_24h_rep1

city: Shreveport

first: Andrew

middle: D.

last: Yurochko

state: LA

address: 1501 Kings Highway

department: Microbiology & Immunology

institute: LSUHSC-S

description: 1st replicate, 1h with DMSO in RPMI media, then HCMV added for 24h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U95Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling with a target intensity value of 2500 as normalization method.

source_name: monocytes, 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was harvested with the RNA STAT-60 isolation kit (Tel-Test Inc., Friendswood, TX), according to the manufacturer’s protocol.

value: monocyte

value: HCMV


title: Male Vehicle_rep1

description:
Male Control - replicate 1
Agilent TIFF High File : US23502387_251487917404_S01_H.tif
Agilent TIFF Low File: US23502387_251487917404_S01_L.tif

value: vehicle (0.01% ethanol) for 6 hours


title: HCMV+PP2_24h_rep3

description: 3rd replicate, 1h with PP2 in RPMI media, then HCMV added for 24h

tag: pre-treatment


title: Mock_24h_rep1

description: 1st replicate, 1h with DMSO in RPMI media, then RPMI media added for 24h

value: Mock


title: Female Vehicle_rep 2

description:
Female Control - replicate 2
Agilent TIFF High File : US23502387_251487917405_S01_H.tif
Agilent TIFF Low File: US23502387_251487917405_S01_L.tif

value: male


title: HCMV+PP2_24h_rep1

description: 1st replicate, 1h with PP2 in RPMI, then HCMV added for 24h


title: HCMV+PP2_24h_rep2

description: 2nd replicate, 1h with PP2 in RPMI media, then HCMV added for 24h


title: Oryza longistaminata-shoot tip, biological rep3

source_name: Oryza longistaminata, shoot tip

value: shoot tip


title: Female Vehicle_rep 1

description:
Female Control - replicate 1
Agilent TIFF High File : US23502387_251487917405_S01_H.tif
Agilent TIFF Low File: US23502387_251487917405_S01_L.tif


title: HCMV_24h_rep3

description: 3rd replicate, 1h with DMSO in RPMI media, then HCMV added for 24h


title: Male Vehicle_rep 2

description:
Male Control - replicate 2
Agilent TIFF High File : US23502387_251487917404_S01_H.tif
Agilent TIFF Low File: US23502387_251487917404_S01_L.tif


title: Mock_24h_rep2

description: 2nd replicate, 1h with DMSO in RPMI media, then RPMI media added for 24h


title: Male Vehicle_rep 3

description:
Male Control - replicate 3
Agilent TIFF High File : US23502387_251487917404_S01_H.tif
Agilent TIFF Low File: US23502387_251487917404_S01_L.tif


title: Mock_24h_rep3

description: 3rd replicate, 1h with DMSO in RPMI media, then RPMI media added for 24h


title: HCMV_24h_rep2

description: 2nd replicate, 1h with DMSO in RPMI media, then HCMV added for 24h


title: Oryza longistaminata-shoot tip, biological rep2


title: Oryza longistaminata-shoot tip, biological rep1


title: Female Vehicle_rep3

description:
Female Control - replicate 3
Agilent TIFF High File : US23502387_251487917396_S01_H.tif
Agilent TIFF Low File: US23502387_251487917396_S01_L.tif


title: DCs-CP3 IOWA

status: Public on Oct 20 2010

city: North Grafton

first: Hanping

last: Feng

address: 200 Westboro Rd.

institute: Tufts University

hyb_protocol: The fragmented target cRNA (20 ug) was mixed with 200 ul of hybridization cocktail (100 mM 2-morpholino-ethanesulfonic acid (MES), 1 M NaCl, 20 mM ethylenediaminetetraacetic acid, 0.01% Tween 20, 0.1 mg/ml herring sperm DNA, 500 g/ml acetylated bovine serum albumin) and hybridized to the Affymetrix chip at 45°C for 16 h in a rotisserie oven at 60 rpm. Following hybridization, the target cRNA was removed; the arrays washed in 6X SSPE at 25°C and then with 100 mM MES, 0.1 M NaCl, and 0.01% Tween 20 at 50C. The arrays were then be stained with streptavidin IgG (3 ug/ml), followed by a a second staining with streptavidin phycoerthrin and then rinsed in 100 mM MES, 0.1 M NaCl and 0.01% Tween 20 at 50°C.

scan_protocol: The arrays were scanned by using Gene Array scanner (Affymetrix, Santa Clara, Calif, USA).

data_processing:
Data was normalized using CEL files followed by RMA normalization, median polishing and the raw data filtered. The normalized array intensities were employed to compare expression intensities between samples.
Changes in gene expression were detected using Affymetrix software (Microarray Suite v5.0 and Data Mining Tool v2.0). Only significantly changed probe sets (P < 0.05) were be considered. Up regulated and down regulated genes were clustered depending upon their functions using NetAffyx Gene Ontology Mining Tool software. Data was also be analyzed using the GeneSpring Suite 7 software package.

source_name: Dendritic cells treated with C. parvum

label_protocol: Biotin-labeled cRNAs were generated using the GeneChip IVT Labeling Kit (in vitro transcription using T7 RNA polymerase at 37°C for 16 hours) in a thermal cycler. The biotinylated cRNA was subsequently treated with RNeasy clean-up kit (Qiagen) to remove any unincorporated biotinylated ribonucleotides from the cRNA samples and quantitated spectrophotometrically

extract_protocol: RNA extracted and purified with RNeasy mini kit (Qiagen).

value: Female

value: Bone marrow

value: Dendritic cells

value: C. parvum (strain Iowa)


title: DCs-CP2 IOWA


title: P90 MD to Control MSAM rep1

city: Houston

first: Richard

last: Kellermayer

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Colonic mucosa was sheared by microscope slide and flash frozen on dry ice

hyb_protocol: Hybridization of the arrays was carried out according to the Agilent Chip-on-chipmammalian protocol (version 9.1, 2006)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Probe ratios were calculated for each MD to control comparisons in each of the 4 arrays separately.

source_name: P90 Control

label_protocol: 4ug of the digested and amplified DNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Chip-on-chipmammalian protocol (version 9.1, 2006)

extract_protocol: Total DNA was extracted by standard phenol-chloroform isolation.

value: 90 postnatal days

value: colonic mucosa

tag: treatment

value: control

source_name: P90 MD

value: methyl donor diet


title: P90 MD to Control MSAM rep3


title: DCs-EC3

source_name: Dendritic cells treated with E. cuniculi

value: E. cuniculi


title: P90 MD to Control MSAM rep2


title: P90 MD to Control MSAM rep4


title: DCs-EC2


title: DCs-CP1 IOWA


title: DCs-EC1


title: P90 MD to Control Gene Expression rep3

hyb_protocol: Standard Agilent protocol

label_protocol: RNA (0.4ug) samples were processed and labelled with Cy3 and Cy5 (Quick Amp labelling kit, two color, Agilent technologies)

extract_protocol: Total RNA was extracted by Quiagen Rneasy mini kit (Cat.no.74106)


title: Nogo-A/B_KO_Lung_11

city: New Haven

first: Paulette

middle: Lee

last: Wright

address: 10 Amistad St.

department: Pharmacology

institute: Yale University

description: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu and http://www.agilent.com).

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent,).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent).

source_name: KO

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

extract_protocol: Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: lung

value: 8 wks


title: Wild-type_Lung_12

source_name: WT