title: BW Keio mutant GadB pH7


title: BW Keio mutant SucB pH5.5

status: Public on Aug 24 2011

type: RNA

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

description:
Gene expression data from E.coli K12 at pH5.5 for 15 min
E.coli K12 mutant pH5.5 at 15 mins Adaptation

hyb_protocol: Following labelling , 80pmoles of labelled probe was hybridized for 16 hr at 42C on E.coli whole genome arrays. GeneChips were washed using Adwawash.

scan_protocol: GeneChips were scanned using the Perkin-Elmer Scanarray Scanner 4200.

data_processing: The data were analyzed with Scanarray express microarray analysis system and quantile normalization was used in R package to normalise the data.

molecule: total RNA

organism: Escherichia coli K-12

source_name: BW29113 mutant pH5.5 at 15 mins Adaptation

label_protocol: Labelled cDNA was hybridised on E.coli custom made arrays.

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

tag: E.coli K12 BW29113

tag: Keio mutant


title: BW Keio mutant GcvP pH7

description:
Gene expression data from E.coli K12 at pH7 control
E.coli K12 mutant pH7

source_name: BW29113 mutant pH7 (control)


title: hESCs after 5 days of differentiation sorted unfixed CXCR4+ cells, biological rep3

city: Stanford

first: Yuqiong

last: Pan

state: CA

address: 300 Pasteur Drive, Alway Bldg. Rm M313

department: Depts of Statistics and Genetics

country: USA

institute: Stanford University

description:
sample probe group file: HuEx-1_0-st-v2.r2.pgf
sample meta probeset file: HuEx-1_0-st-v2.na24.hg18.probeset.csv

hyb_protocol: Samples were hybridized with Affymetrix Human Exon 1.0 ST Array using Affymetrix hybridization kit materials

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: We computed gene expression indices for all the samples analyzed using the GeneBASE software. We performed background correction, probe selection, and expression index computation on all the samples, followed by quantile normalization of gene level expression values.

label: biotin

organism: Homo sapiens

source_name: unfixed, stained, sorted day 5 differentiated CXCR4+ hESCs

label_protocol: Samples were enzymatically fragmented and biotin-labeled using GeneChip Whole Transcript Sense Target Labeling Assay Manual (Affymetrix)

growth_protocol: Undifferentiated hES cells (H9 passages 40-55) were maintained on irradiated mouse embryonic fibroblast (MEF) feeders. Definitive endoderm differentiation was induced from hESCs by activin A (R&D Systems Inc.). For differentiation, hESCs were first passaged onto dishes coated with growth factor reduced Matrigel and cultured in hESC media conditioned overnight on primary MEF (CM) for 2 days. Undifferentiated hESCs samples were collected. Differentiation was carried out in RPMI 1640 supplemented with Glutamax, penicillin/streptomycin and varying concentrations of defined FBS. FBS concentrations were 0% for the first 24 h, 0.2% for the second 24 h, and 2.0% for subsequent days of differentiation. Recombinant human activin A was added to the differentiation medium at 100 ng / ml, and cells were treated for 5 days, with medium changed once at day 3.

extract_protocol: All the cells either from sorted populations or from the presorted mixtures were centrifuged at 14,000 rpm, 2 min, 4 0C to get cell pellets. Total mRNA was extracted using the Ambion Recover All nucleic acid extraction kit (optimized for fixed cells) (Applied Biosystems Ambion). Briefly, for each sample, 1.5 g of total RNA was subjected to ribosomal RNA reduction. Following rRNA reduction, double-stranded cDNA was synthesized with random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA was used as a template for amplification with T7 RNA polymerase to create antisense cRNA. Next, random hexamers were used to reverse transcribe the cRNA to produce single-stranded sense strand DNA.

treatment_protocol: Samples were collected after 3 and 5 days of differentiation.  As controls we also collected undifferentiated hESCs before the endoderm differentiation started. Cells were dissociated using 0.05% trypsin-0.53 mM EDTA at 37 0C for 3 min followed by neutralization in hESCs medium with serum. Cells were washed in staining buffer. After cells were fixed by 4% paraformaldehyde (PFA) at 4°C for 15 minutes, they were permeablized, stained with antibodies of combination of nuclear transcription factors or plus cell surface proteins, then isolated by FACS sorting. We utilized the optimized protocol to obtain the intact RNA from these cells after they were processed by the above procedures. The unsorted fixed cells and the sorted unfixed cells were also collected and analyzed  in parallel with these sorted fixed cells.

tag: differentiation stage

value: after 5 days of differentiation

tag: fixed and unfixed

value: unfixed cells

tag: sorting marker


title: hESCs after 5 days of differentiation unsorted fixed, biological rep3

source_name: fixed, stained, unsorted day 5 differentiated hESCs

value: fixed cells


title: BCL6 WT chip 2 Imatinib treated

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description: BCL6 WT CML cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: GCOS 1.3

label: Biotin

organism: Mus musculus

source_name: bone marrow, BCL6 WT, Imatinib treated

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

tag: strain

tag: age

value: 4 weeks

tag: cell culture

value: BCR-ABL1 transformed myeloid cells

tag: disease state

value: BCR-ABL1-driven CML

tag: genotype/variation

value: BCL6 WT

tag: agent

value: Imatinib


title: hESCs after 5 days of differentiation unsorted fixed, biological rep1


title: BW Keio mutant SucA pH7


title: hESCs after 3 days of differentiation sorted fixed SOX17-GATA4- cells, biological rep2

source_name: fixed, stained, sorted day 3 differentiated SOX17-GATA4- hESCs

value: after 3 days of differentiation

value: SOX17 GATA4


title: BW Keio mutant SucA pH5.5


title: BW Keio mutant SucB pH7


title: hESCs after 3 days of differentiation sorted fixed SOX17-GATA4- cells, biological rep1


title: BW Keio mutant Crp pH5.5


title: Dap12-het 76

city: Uppsala

first: Anna

last: Kiialainen

address: University Hospital, Entrance 70

department: Deapartment of Medical Sciences

country: Sweden

institute: Uppsala University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: GCOS scaling to target intensity of 100

source_name: 1 month old Dap12-deficient mouse brain

label_protocol: Affymetrix one-cycle

extract_protocol: Trizol + RNeasy

tag: midbrain of 1 month old Dap12-heterozygous C57BL6 mouse


title: Dap12-het 81


title: BW Keio mutant Crp pH7


title: BW wt pH7 C

description:
Gene expression data from E.coli K12 at pH7 control
E.coli K12 pH7 wildtype biological rep3

source_name: BW29113 pH7 wildtype (control)

tag: wildtype


title: hESCs after 3 days of differentiation unsorted fixed, biological rep1

source_name: fixed, stained, unsorted day 3 differentiated hESCs


title: Dap12-het 75


title: hESCs fixed, biological rep2

source_name: fixed, stained hESCs using the same SOX17GATA4CXCR4 protocol, without sorting

value: undifferentiated day 0


title: BW wt pH5.5 B

description:
Gene expression data from E.coli K12 at pH5.5 for 15 min
E.coli K12 pH5.5 wildtype biological rep2

source_name: BW29113 pH5.5 wildtype


title: BW wt pH5.5 C

description:
Gene expression data from E.coli K12 at pH5.5 for 15 min
E.coli K12 pH5.5 wildtype biological rep3


title: Dap12-ko 68

tag: middle brain from 1 month old Dap12-deficient C57BL6 mouse


title: Stat5 deletion in BCR-ABL1 transformed pre-B cell pMIG chip1

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

value: swiss webster

value: BCR-ABL1 transformed pre-B cells

value: BCR-ABL1-driven ALL

value: STAT5 fl/fl

tag: transduction

value: GFP only


title: Dap12-ko Ko1

tag: midbrain of 1 month old Dap12-deficient mouse brain


title: Stat5 deletion in BCR-ABL1 transformed pre-B cell pMIG chip2


title: Dap12-ko 67

tag: midbrain of Dap12-deficient C57BL6 mouse


title: Stat5 deletion in BCR-ABL1 transformed pre-B cell cre chip3

value: Cre-GFP


title: hESCs after 3 days of differentiation unsorted fixed, biological rep2


title: Stat5 deletion in BCR-ABL1 transformed pre-B cell pMIG chip3


title: hESCs fixed, biological rep1


title: BW Keio mutant RpoS pH5.5

tag: E.coli K12 BW29113


title: BW Keio mutant YcaD pH5.5

tag: Keio mutant


title: BW wt pH7 B

description:
Gene expression data from E.coli K12 at pH7 control
E.coli K12 pH7 wildtype biological rep2


title: BW wt pH7 A

description:
Gene expression data from E.coli K12 at pH7 control
E.coli K12 pH7 wildtype biological rep1


title: BW wt pH5.5 A

description:
Gene expression data from E.coli K12 at pH5.5 for 15 min
E.coli K12 pH5.5 wildtype biological rep1


title: hESCs unfixed, biological rep1

source_name: normal unfixed hESCs, published data [10], as control

tag: differentiation stage


title: ND1_VAT

status: Public on Aug 23 2011

city: Worcester

first: Timothy

middle: P

last: Fitzgibbons

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

description:
Whole tissue isolate.
Mice fed for 13 wks with normal diet.

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

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to the manufacturer'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.

source_name: Epididymal fat, normal diet

label_protocol: Ambion WT Expression Kit, Affymetrix WT Terminal Labeling Kit.

extract_protocol: RNA minilipid kit (Qiagen) using the manufacturer's protocol.

tag: tissue

value: epididymal adipose tissue (VAT)

tag: treatment

value: normal diet


title: ND3-PVAT

source_name: Perivascular fat from aortic arch, normal diet

tag: strain

value: perivascular fat from the lesser curvature of the aortic arch (PVAT)


title: HFD2-VAT

description:
Whole tissue isolate.
Mice fed for 13 wks with 45% kcal HFD.

source_name: Epididymal fat, high fat diet

value: high fat diet


title: HFD2-SAT

source_name: Inguinal subcutaneous fat, high fat diet

value: inguinal adipose tissue (SAT)


title: Dap12-wt microglia 7_12

description: wt

source_name: mouse primary microglia

label_protocol: Affymetrix two-cycle labelling kit

extract_protocol: Trizol and RNeasy

tag: C57BL6 wt


title: Dap12-wt microglia 4_5

description: wt


title: ND2-SAT

source_name: Inguinal subcutaneous fat, normal diet


title: Uninfected 1

type: other

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

state: BC

department: Michael Smith Laboratories

country: Canada

institute: The University of British Columbia

description: Metabolites

hyb_protocol: Not applicable

scan_protocol: Not applicable

data_processing:
Raw mass spectrometry data were processed using a custom-developed software package, as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140). Mass spectra were batch-processed using a custom VBA script, within the instrument vendor’s data processing software package, DataAnalysis®. First, all the raw mass spectra acquired in positive and negative ion modes were internally calibrated with the reference masses of the spiked standard compounds and a ubiquitous known contaminant, N-butylbenzensulfonamide. Monoisotopic peaks corresponding to the isotopic distribution patterns were then automatically determined and those with signal-to-noise ratios above 3 were picked. The m/z values were subsequently converted to neutral masses by subtracting 1.007276 for positive ion mode or adding 1.007276 for negative ion mode. Next, the resulting mass lists from the individual mass spectra within each paired sample group were further processed with another custom software program developed with LabVIEW® (National Instruments, Austin, USA). The first step of this program is to remove the adduct ions, e.g., (M+Na)+ and/or (M+K)+ in positive ion mode and (M+Cl)- in negative ion mode, from the mass lists based on the expected mass differences for these ions within 2 ppm. Next, the peak intensity of each unique monoisotopic neutral mass was normalized to the intra-spectrum total ion intensity. Masses observed in at least 50% of the spectra from each paired sample group were aligned into unique masses (metabolite features) from the masses that matched within 2 ppm. Finally, a two-dimensional data matrix (neutral mass vs. peak intensity) was generated for each group and saved in a tab-delimited text format. To detect metabolite differences between the different sample groups, the masses were filtered in each list for metabolites that were present on one set of samples, but not the other. Additionally, the intensities were averaged of each unique mass in each set of biological replicates and calculated the ratio between the sample groups. To assign possible metabolite identities to the masses present only in one set or showing at least 2-fold changes, the monoisotopic neutral masses of interest were queried against MassTrix (http:// masstrix.org), software designed to incorporate mass queries into metabolic pathways [21]. Masses were searched against the Mus musculus database within an error of 3 ppm.
Masses (daltons) with relative intensity are provided in the "masses_and_intensities.txt" file on the Series record.  TAR archive of raw spectral files and a readme with Sample associations are also provided there.

label: Not applicable

molecule: other

source_name: Gallbladder

label_protocol: Not applicable

extract_protocol: To extract metabolites from gallbladders, 2 ml of chloroform:methanol (2:1) was added to each sample. Tissues were then homogenized using a tungsten bead and a Mixer Mill MM 301 (Retsch, Haan, Germany). The samples were then transferred to ice, and 1 ml of cold H2O was added. The samples were centrifuged at 3250 x g for 10 minutes at 4°C. The upper phase was discarded, and another 500 µl of cold H2O was added. The samples were centrifuged again at 3250 x g for 10 minutes at 4°C. The upper phase was discarded, and the lower phase was transferred to a new glass tube and dried under N2 gas. All extracts were kept at -80˚C until further use.

treatment_protocol: Oral infection with 3-8x10^7 Salmonella enterica serovar Typhimurium

tag: gender

value: Female

tag: infection status

value: uninfected


title: ND2-PVAT


title: SseL-infected 3

description: Metabolites

value: SseL infected


title: HFD1_SAT


title: ND3-SAT


title: HFD1_BAT

source_name: Interscapular brown fat, high fat diet

value: interscapular brown adipose (BAT)


title: HFD2-PVAT

source_name: Perivascular fat from aortic arch, high fat diet


title: SseL-infected 2

description: Metabolites


title: SseL-infected 1

description: Metabolites


title: Wildtype-infected 3

description: Metabolites

value: wildtype infected


title: HFD1_PVAT


title: Wildtype-infected 2

description: Metabolites


title: Wildtype-infected 1

description: Metabolites


title: Uninfected 3

description: Metabolites


title: Uninfected 2

description: Metabolites


title: HFD3-BAT


title: HFD1_VAT


title: Retentostat at T16, Biological replicate 2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: Glucose-limited anaerobic retentostat. Samples were taken 16 days after switching from chemostat to retentostat. At that time-point the mu max was approx. 0.0011 h-1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Saccharomyces Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions.

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

organism: Saccharomyces cerevisiae

source_name: Retentostat after 16 days of cultivation, replicate #2

label_protocol: Probe preparation were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 micrograms of total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100

growth_protocol: The prototrophic laboratory strain Saccharomyces cerevisiae CEN.PK113-7D (MATa MAL2-8c SUC2, obtained from Dr P. Kötter, Frankfurt, Germany) was used in the present study. Stock cultures were prepared from a shake flask culture on YPD medium (Sherman, 1991, Meth.Enzymol., 194: 3-21.) grown to stationary phase, by addition of glycerol (20 % v.v-1) and storage of 2 ml aliquots in sterile vials at -80 °C. Pre-cultures for retentostat cultivation were made by inoculating a frozen stock culture in 500 ml shake-flasks with 100 ml synthetic medium (Verduyn et al., 1992, Yeast, 8: 501-517.) at pH 6 with 2 % glucose. Anaerobic glucose-limited retentostats with a dilution rate of 0.025 h-1 and a working volume of 1.4 litre were operated as described previously (Boender et al., 2009, Appl.Environ.Microbiol., 75: 5607-5614.). Duplicate retentostat cultures were started from independent anaerobic, glucose-limited chemostat cultures grown at the same dilution rate. Retentostat cultivation was started when macroscopic measurements (culture dry weight and specific carbon-dioxide production rate) changed by less than 2% during two consecutive volume changes, by redirecting the effluent through an AppliSense Sample Filter assembly (0.22 µm pore size, Applikon, Schiedam, The Netherlands) instead of through the standard effluent tube. The synthetic medium was supplemented with 50 g.l-1 of glucose and 1.5 ml.l-1 of a 20 % (wt.wt-1) solution of the antifoaming agent Struktol J673 (Schill and Seilacher AG, Hamburg, Germany). Culture purity was routinely checked by phase-contrast microscopy and by plating on glucose-containing synthetic medium with 20 mM LiCl (Daran-Lapujade et al., 2009, FEMS Yeast Res., 9: 782-792.).

extract_protocol: For each array, total RNA was extracted from a single tube using the hot-phenol method (Schmitt et al., 1990, Nucleic Acids Res., 18: 3091–3092).

treatment_protocol: 50 to 100 ml of culture broth was sampled directly from the chemostat into a beaker containing 200 ml of liquid nitrogen.  With vigorous stirring, the sample froze instantly.  The frozen sample was then broken into small fragments and transferred to 50 ml centrifuge tubes.  These were thawed at room temperature, returned regularly to ice to ensure the temperature was maintained as close to zero as possible.  The volume corresponding to 120 mg of cells were spun down (5000 rpm at 0°C for 4 min), resuspended in 2 ml ice-cold AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0) and aliquotted into 5 eppendorfs. The tubes were immediately placed in a waterbath for 5 min at 65°C, vortexed then stored at -80°C.

value: CEN.PK113-7D (MATa MAL2-8c SUC2)

tag: culture age (days)

tag: specific growth rate (h-1)


title: Retentostat at T22, Biological replicate 1

description: Glucose-limited anaerobic retentostat. Samples were taken 22 days after switching from chemostat to retentostat. At that time-point the mu max was approx. 0.00063 h-1

source_name: Retentostat after 22 days of cultivation, replicate #1


title: Retentostat at T16, Biological replicate 1

source_name: Retentostat after 16 days of cultivation, replicate #1


title: ND3-VAT


title: Retentostat at T22, Biological replicate 2

source_name: Retentostat after 22 days of cultivation, replicate #2


title: Stat5 deletion in BCR-ABL1 transformed pre-B cell cre chip2

value: swiss webster

tag: age

value: 4 weeks

tag: cell culture

tag: disease state

tag: genotype/variation


title: Dap12-ko microglia 10

data_processing: GCOS scaling to target intensity 100

label_protocol: Affymetrix two-cycle kit

tag: C57BL6 Dap12-deficient


title: HFD2-BAT


title: Retentostat at T9, Biological replicate 2

description: Glucose-limited anaerobic retentostat. Samples were taken 9 days after switching from chemostat to retentostat. At that time-point the mu max was approx. 0.0024 h-1

source_name: Retentostat after 9 days of cultivation, replicate #2


title: HFD3-VAT


title: ND1_SAT


title: Retentostat at T9, Biological replicate 1

source_name: Retentostat after 9 days of cultivation, replicate #1


title: Chemostat T0, Biological replicate 1

description: Glucose-limited anaerobic chemostat at mu (=dilution rate) of  0.025 h-1 . Samples were taken at steady-state

source_name: Chemostat culture used as time point 0, replicate #1


title: Chemostat T0, Biological replicate 3

description: Glucose-limited anaerobic chemostat. Samples were taken at steady-state

source_name: Chemostat culture used as time point 0, replicate #3


title: hESCs unfixed, biological rep3

source_name: normal unfixed hESCs, published data [10], as control

value: undifferentiated day 0

tag: fixed and unfixed

value: unfixed cells


title: hESCs unfixed, biological rep2


title: ND2-BAT

source_name: Interscapular brown fat, normal diet


title: Chemostat T0, Biological replicate 2

source_name: Chemostat culture used as time point 0, replicate #2


title: Retentostat at T2, Biological replicate 1

description: Glucose-limited anaerobic retentostat. Samples were taken 2 days after switching from chemostat to retentostat. At that time-point the mu max was approx. 0.0084 h-1

source_name: Retentostat after 2 days of cultivation, replicate #1


title: ND2-VAT

source_name: Epididymal fat, normal diet


title: ND3-BAT


title: HFD3-SAT

source_name: Inguinal subcutaneous fat, high fat diet


title: Retentostat at T2, Biological replicate 2

source_name: Retentostat after 2 days of cultivation, replicate #2


title: Dap12-wt microglia 6

description: wt

source_name: mouse primary microglia


title: ND1_PVAT

source_name: Perivascular fat from aortic arch, normal diet


title: Stat5 deletion in BCR-ABL1 transformed pre-B cell cre chip1

value: BCR-ABL1 transformed pre-B cells

value: BCR-ABL1-driven ALL

value: STAT5 fl/fl

tag: transduction


title: time: 24 h - treatment: PEG - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 0.1 Hoaglands with full strength micronutrients. Experimental time 0 was at approximately 9 am. . Development stage: [4 weeks after pruning 2 year old plants to 4 nodes]. Part of organism: [shoot tips to 4th leaf including leaves, stem, tendrils, buds]. Treatment application type: [other::peg].

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Vitis vinifera

source_name: time: 24 h - treatment: PEG

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description: plants were grown in a green housewith supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30).Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponicdrip system with LECA (lightweight expanded clay aggregate), and a nutrientsolution of modified 0.1 Hoaglands with full strength micronutrients.Experimental time 0 was at approximately 9 am.

extract_protocol: RNeasy Midi

tag: time point

value: PEG

tag: organism part

tag: development stage

value: A vegetative growth PO:0007134

tag: growth media

value: hydroponic drip 0.1 hoagland


title: HFD3-PVAT

source_name: Perivascular fat from aortic arch, high fat diet

tag: strain

tag: tissue

value: perivascular fat from the lesser curvature of the aortic arch (PVAT)

tag: treatment

value: high fat diet


title: ND1_BAT

value: normal diet


title: Primary_Chronic, rep5

city: Atlanta

first: Erin

last: West

state: GA

address: 1510 Clifton Rd NE RRC room G211

institute: Emory University

hyb_protocol: 5 ug was hybridized following standard Nugen/Affymetrix protocols.

scan_protocol: Scanned with Affymetrix using AGCC v. 1.1.

data_processing: Analyzed on Affymetrix Expression Console v. 1.1 using a GC-RMA normalization algorithm producing log base 2 results.

source_name: Splenic primary effector CD8 T cells, day 8 post-chronic infection

label_protocol: 1st and 2nd strand synthesis, followed by Spia amplification using the Nugen WT pico kit to generate cDNA.  Fragmentation and biotinylation using Nugen cat# 4200 following standard Nugen/Affymetrix protocols.

extract_protocol: Spleen cells were isolated and sorted using a BD Biosciences Aria cell sorter. RNA was isolated using the Qiagen RNeasy kit according to the standard manufacturer's protocol including the optional on-column DNase treatment.

value: P14 TCR transgenic

value: spleen

tag: cell type

value: CD8 T cells

tag: cd8 t cell effector type

value: primary

tag: lcmv infection type

value: chronic


title: Secondary_Chronic, rep4

source_name: Splenic secondary effector CD8 T cells, day 8 post-chronic infection

value: secondary


title: Secondary_Acute, rep3

source_name: Splenic secondary effector CD8 T cells, day 8 post-acute infection

value: acute


title: time: 24 h - treatment: PEG - rep2


title: time: 24 h - treatment: PEG - rep1


title: time: 24 h - treatment: salt - rep3

description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 1/10 Hoagland's with full strength micronutrients. Experimental time 0 was at approximately 9 am. . Development stage: [4 weeks after pruning 2 year old plants to 4 nodes]. Part of organism: [shoot tips to 4th leaf including leaves, stem, tendrils, buds]. Treatment application type: [other::salt].

source_name: time: 24 h - treatment: salt

growth_protocol: Growth Description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 1/10 Hoagland's with full strength micronutrients. Experimental time 0 was at approximately 9 am.

value: salt


title: Primary_Chronic, rep2


title: Primary_Acute, rep4

source_name: Splenic primary effector CD8 T cells, day 8 post-acute infection


title: Secondary_Chronic, rep3


title: time: 24 h - treatment: salt - rep1


title: Dap12-ko microglia 3_11


title: Primary_Chronic, rep3


title: time: 24 h - treatment: salt - rep2


title: Primary_Chronic, rep4


title: Secondary_Chronic, rep2


title: Secondary_Acute, rep1


title: Primary_Acute, rep3


title: Dap12-ko microglia 2_8

source_name: mouse primary microglial cells


title: Primary_Chronic, rep1


title: Primary_Acute, rep2


title: Secondary_Acute, rep2


title: Primary_Acute, rep1


title: HdhQ111/HdhQ111 cerebellum at 3~10 weeks biological rep 1

city: Boston

first: Jong-Min

last: Lee

state: MA

address: 185 Cambridge Street

department: Center for Human Genetic Reseaarch

institute: Massachusetts General Hospital

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: gcRMA log2 scale

label_protocol: Affymetrix protocol

extract_protocol: Trizol extraction and Qiagen mini coulmn clean-up

tag: hdh genotype

value: cerebellum

tag: age

value: 3~10 weeks


title: time: 24 h - treatment: unstressed - rep2

description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 1/10 Hoagland's with full strength micronutrients. Experimental time 0 was at approximately 9 am. . Development stage: [4 weeks after pruning 2 year old plants to 4 nodes]. Part of organism: [shoot tips to 4th leaf including leaves, stem, tendrils, buds]. Treatment application type: [No Treatment].

source_name: time: 24 h - treatment: unstressed

value: unstressed


title: time: 24 h - treatment: unstressed - rep1


title: HdhQ111/HdhQ111 cerebellum at 3~10 weeks biological rep 2


title: HdhQ111/HdhQ111 cerebellum at 3~10 weeks biological rep 3


title: Hdh+/Hdh+ cerebellum at 3~10 weeks biological rep 1

description: Hdh+/Hdh+ cerebellum at 3~10 weeks


title: time: 8 h - treatment: cold (5 C) - rep3

description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 0.1 Hoagland with full strength micronutrients. Experimental time 0 was at approximately 9 am. . Development stage: [4 weeks after pruning 2 year old plants to 4 nodes]. Part of organism: [shoot tips to 4th leaf including leaves, stem, tendrils, buds]. Treatment application type: [temperature shock].

source_name: time: 8 h - treatment: cold (5 C)

growth_protocol: Growth Description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 0.1 Hoagland with full strength micronutrients. Experimental time 0 was at approximately 9 am.

value: 8 h

value: cold (5 C)


title: Secondary_Chronic, rep1


title: time: 8 h - treatment: PEG - rep2

source_name: time: 8 h - treatment: PEG

value: PEG

value: A vegetative growth PO:0007134

value: hydroponic drip 0.1 hoagland


title: HdhQ111/HdhQ111 striatum at 3~10 weeks biological rep 3

description: HdhQ111/HdhQ111 striatum at 3~10 weeks

value: striatum


title: Hdh+/Hdh+ cerebellum at 3~10 weeks biological rep 3

description: Hdh+/Hdh+ cerebellum at 3~10 weeks


title: time: 24 h - treatment: unstressed - rep3


title: Hdh+/Hdh+ cerebellum at 3~10 weeks biological rep 2

description: Hdh+/Hdh+ cerebellum at 3~10 weeks


title: Hdh+/Hdh+ striatum at 3~10 weeks biological rep 1

description: Hdh+/Hdh+ striatum at 3~10 weeks


title: time: 8 h - treatment: cold (5 C) - rep2


title: HdhQ111/HdhQ111 striatum at 3~10 weeks biological rep 1

description: HdhQ111/HdhQ111 striatum at 3~10 weeks


title: time: 8 h - treatment: PEG - rep3


title: HdhQ111/HdhQ111 striatum at 3~10 weeks biological rep 2

description: HdhQ111/HdhQ111 striatum at 3~10 weeks


title: time: 8 h - treatment: salt - rep3

source_name: time: 8 h - treatment: salt


title: time: 8 h - treatment: cold (5 C) - rep1


title: time: 8 h - treatment: PEG - rep1


title: Effects of ER stress ion gene expression in LCLs, 2d

city: Pittsburgh

first: Adam

last: Rosendorff

state: PA

address: 530 45th Street, 3rd Fl, Bay 9

department: Pathology

institute: University of Pittsburgh

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: RMA, Expression Console

source_name: LCLs

label_protocol: Standard Affymetrix Protocol

extract_protocol: Trizol

value: LCL

value: DMSO

tag: time


title: MASPIN-S3

city: CHAPEL HILL

first: PILAR

last: BLANCAFORT

state: NORTH CAROLINA

address: 4009 MASON FARM RD

department: PHARMACOLOGY

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

description: C_RMF:Cell Line:MDA-MB-231 transduced ATF-126 and treated with Doxycycline inducible vector

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

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

source_name: [control RNA] MDA-MB-231 RNA

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

extract_protocol: Qiagen Rneasy Kit

tag: cell line

tag: protocol

value: control

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

value: transduced with ATF-126 and treated with Doxycycline


title: Hdh+/Hdh+ striatum at 3~10 weeks biological rep 2

description: Hdh+/Hdh+ striatum at 3~10 weeks


title: MASPIN-S4

description: C_RMF:ell Line:MDA-MB-231 transduced ATF-126 and treated with Doxycycline inducible vector

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


title: Effects of ER stress on gene expression in LCLs 2b

value: TG


title: Hdh+/Hdh+ striatum at 3~10 weeks biological rep 3

description: Hdh+/Hdh+ striatum at 3~10 weeks


title: MASPIN-S2

description: C_RMF:Cell Line:MDA-MB-231 transduced with ATF-126 inducible vector

source_name: MDA-MB-231 transduced with ATF-126

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

value: transduced with ATF-126


title: time: 8 h - treatment: salt - rep2


title: MASPIN-S1

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


title: Effects of ER stress on gene expression in LCLs 2c


title: MASPIN-3

description: C_RMF:Cell Line:MDA-MB-231 transduced with Control inducible vector and treated with Doxycycline

source_name: MDA-MB-231 transduced with Control and treated with Doxycycline

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


title: MASPIN-4

description: C_RMF:Cell Line:MDA-MB-231 transduced with Control  inducible vector and treated with Doxycycline

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

value: transduced with Control and treated with Doxycycline


title: Effects of ER stress on gene expression in LCLs 2a


title: Effects of ER stress on gene expression in LCLs 1d


title: Effects of ER stress on gene expression in LCLs 1b


title: MASPIN CONTROLS

description: C_RMF:Cell Line:MDA-MB-231 transduced with Control  inducible vector

source_name: MDA-MB-231 transduced with Control

value: transduced with Control


title: Liver_highdose2_sample4

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

institute: Chalmers University of Technology

description: See Cuklev et al 2010 for further information.

hyb_protocol: Prehybridization was performed at room temperature for 15 min with a prehybridization buffer (25 mL 2 ×MES hybridization buffer and 1% BSA in 50ml DEPC H2O). Fragmented cRNA (6 µg/array) was dissolved in hybridization buffer (final concentration: 5X SSPE (Ambion® Inc.), 20% formamide, 0.5 mg BSA/mL, 0.1X TE, 0.1 mg human Cot-1 DNA (Invitrogen Carlsbad, CA), 0.01% Tween 20). Samples were denaturated for 3 min at 95 °C and hybridized to the biochips at 45 °C for 16 h, followed by a first washing step at 25 °C with 6 ×SSPE and a second washing step at 45 oC with 0.5× SSPE. Fluorescence-staining was achieved by incubating the arrays with 5 µg/mL streptavidin R-phycoerythrin conjugate (SAPE) (Invitrogen) diluted in 6×SSPE containing 2 mg BSA/ml at 25 °C for 15 min. Signal amplification was performed using biotinylated a-streptavidin antibodies (Vector Laboratories, Burlingame, CA) followed by an additional incubation with SAPE.

scan_protocol: Signals were detected using the internal CCD-camera system of the Geniom One instrument and quantified using the Geniom Wizard software. Integration times were between 390–620 ms, determined automatically by the instrument software.

data_processing:
The microarray data was imported into the statistical language R 2.10.1 (www.r-project.org) and analyzed in Bioconductor 2.5 [34]. The raw gene expression values were normalized by quantile-quantile normalization [35] and then log2-transformed.
Each of the four raw data files contain the raw data for eight arrays. Please see readme.txt file for the Sample-raw data file associations.

organism: Oncorhynchus mykiss

source_name: Liver, high dose aquarium 2, sample 4

label_protocol: Biotinylated aRNA was synthesized using MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion® Inc., Austin, TX) and quantity and quality was assessed.

extract_protocol: Homogenization of the frozen liver tissue was carried out using Tissuelyser (Qiagen, Hilden, Germany) and total hepatic RNA was isolated using QIAcube and RNeasy® Plus Mini Kit (Qiagen). The RNA quantity and quality was assessed by Experion automated electrophoresis (Bio-Rad, Hercules, CA) and spectophotometric measurements (Nanodrop 1000, NanoDrop Technologies, Wilmington, DE).

tag: gender

value: juvenile

value: liver

value: hepatocytes


title: MASPIN-2

description: C_RMF:Cell Line:MDA-MB-231 transduced with Control inducible vector

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


title: MDA-MB-231 ATF-126 + DOX vs MDA-MB-231 empty vector

description: C_RMF:Cell Line:MDA-MB-231 transduced ATF-126 inducible vector and treated with Doxycycline

source_name: MDA-MB-231 transduced ATF-126 and treated with Doxycycline


title: time: 8 h - treatment: unstressed - rep2

source_name: time: 8 h - treatment: unstressed

value: 8 h

value: unstressed


title: time: 4 h - treatment: PEG - rep2

source_name: time: 4 h - treatment: PEG

value: 4 h

value: PEG


title: time: 8 h - treatment: unstressed - rep1

value: A vegetative growth PO:0007134

value: hydroponic drip 0.1 hoagland


title: Effects of ER stress on gene expression in LCLs 1c

value: LCL


title: time: 8 h - treatment: salt - rep1

value: salt


title: time: 4 h - treatment: PEG - rep1


title: Effects of ER stress on gene expression in LCLs, 15

value: SAL


title: time: 4 h - treatment: cold (5 C) - rep3

source_name: time: 4 h - treatment: cold (5 C)

value: cold (5 C)


title: time: 4 h - treatment: cold (5 C) - rep2


title: Liver_intermediatedose2_sample4

source_name: Liver, intermediate dose aquarium 2, sample 4


title: time: 4 h - treatment: PEG - rep3


title: MDA-MB-231 EMPTY vs MDA-MB-231 empty vector

value: control


title: Effects of ER stress on gene expression in LCLs 1a

value: TG


title: Effects of ER stress on gene expression in LCLs 14


title: Liver_lowdose2_sample4

source_name: Liver, low dose aquarium 2, sample 4


title: Liver_highdose1_sample4

source_name: Liver, high dose aquarium 1, sample 4


title: Effects of ER stress on gene expression in LCLs 16.

value: TG+SAL


title: time: 4 h - treatment: cold (5 C) - rep1


title: MDA-MB-231 ATF-126 vs MDA-MB-231 empty vector

value: transduced with ATF-126


title: time: 4 h - treatment: salt - rep3

source_name: time: 4 h - treatment: salt


title: Liver_control2_sample4

source_name: Liver, control aquarium 2, sample 4

value: juvenile


title: Effects of ER stress on gene expression in LCLs 13

extract_protocol: Standard Affymetrix

value: DMSO


title: Effects of ER stress on gene expression in LCLs 12


title: Liver_intermediatedose1_sample4

source_name: liver, intermediate dose aquarium 1, sample 4

value: liver

value: hepatocytes


title: time: 1 h - treatment: cold (5 C) - rep3

source_name: time: 1 h - treatment: cold (5 C)

value: 1 h


title: Liver_highdose2_sample3

source_name: Liver, high dose aquarium 2, sample 3


title: time: 1 h - treatment: cold (5 C) - rep1


title: time: 4 h - treatment: salt - rep1

value: 4 h


title: time: 8 h - treatment: unstressed - rep3

value: 8 h

value: unstressed


title: Liver_control1_sample4

source_name: Liver, control aquarium 1, sample 4


title: Liver_lowdose1_sample4

source_name: Liver, low dose aquarium 1, sample 4


title: time: 4 h - treatment: unstressed - rep1

source_name: time: 4 h - treatment: unstressed

value: A vegetative growth PO:0007134

value: hydroponic drip 0.1 hoagland


title: Liver_lowdose2_sample3

source_name: Liver, low dose aquarium 2, sample 3


title: Effect of ER stress on gene expression in LCLs 10

source_name: LCLs

value: LCL


title: Effects of ER stress on gene expression in  LCLs 7

value: SAL


title: time: 1 h - treatment: cold (5 C) - rep2

value: cold (5 C)


title: Liver_control2_sample3

source_name: Liver, control aquarium 2, sample 3


title: Effect of ER stress on gene expression in LCLs 6


title: Effects of ER stress on gene expression in LCLs 9


title: time: 4 h - treatment: unstressed - rep2


title: Liver_highdose1_sample3

source_name: Liver, high dose aquarium 1, sample 3


title: Liver_intermediatedose2_sample3

source_name: Liver, intermediate dose aquarium 2, sample 3


title: time: 4 h - treatment: unstressed - rep3

description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 1/10 Hoagland's with full strength micronutrients. Experimental time 0 was at approximately 9 am. . Treatment application type: [No Treatment].


title: Effect of ER stress on gene expression in LCLs 4


title: hMSC-Tert20_differentiated_21days_replicate2

city: Oslo

first: Heidi

middle: Maria

last: Namløs

address: PO Box 4953 Nydalen

department: Institute for cancer research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

description: The hMSC-Tert20 cells were seeded in multiple 24-well plates (Thermo Fisher Scientific, Rockford, IL, USA) at a density of 40 000 cells/well. The following day, adipogenesis was initiated by replacing the normal medium with adipocyte induction medium containing 1 µM Dexamethasone (Decadron, Haarlem, The Netherlands), 0.5 mM iso-butyl-methyl-xanthine and 50 µM Indomethacine (both from Sigma-Aldrich, St. Louis, MO, USA). Cells were exposed to adipocyte induction medium which was replaced twice a week for up to 21 days.

hyb_protocol: The miRNA microarray experiments were performed using in-house spotted amino silane coated CMT UltraGAPS slides (Corning Life Sciences, Corning, NY, USA) produced at the Norwegian Microarray Consortium (www.microarray.no), University of Oslo. Each slide contained two independent arrays printed using the mirVana Probe Set v1, consisting of probes corresponding to 384 human, rat and mouse miRNAs (Life Technologies). Each probe was printed in triplicate and the slides were UV-crosslinked to immobilize the double stranded probes. All hybridizations, except for 0h, 8h and 32h, were performed twice using LifterSlips (Thermo Fisher Scientific) and manual hybridization cassettes (Arrayit, Sunnyvale, CA, USA) submerged in water.

scan_protocol: Microarrays were scanned using an Agilent Technology G2505B scanner.

data_processing:
The arrays were scanned and the data was processed and filtered as previously described (Prasmickaite et al., 2006). The expression of each miRNA at a given time point was calculated as a ratio relative to its level on day 0.
To avoid zero or negative values in the ratio calculations, spots with background-subtracted intensity less than the standard deviation of the local background in one of the channels were assigned the value of the standard deviation.
The spot was retained if the new value was less than the value in the other channel. Spots with background-subtracted intensity less than 1.5 times the standard deviation of the local background in both channels were excluded (=threshold).
Log2-transformed ratios were normalized using a global median ratio algorithm. The data was filtered to only include miRNAs with a value above threshold in at least 5 of the 9 time points.

label_protocol: The Array900 miRNA Direct Kit was used to label and hybridize enriched miRNAs (150 ng) as described by the manufacturer (Genisphere Inc, Hatfield, PA, USA).

growth_protocol: hMSC-Tert20 and 293 HEK cells (ATCC number CRL-1573) were cultured in DMEM (Cat. no. 10313-039, Life Technologies, Carlsbad, CA, USA) supplemented with 10 % FBS (PAA Laboratories, Pasching, Austria), GlutaMAX, penicillin (100 U/ml) and streptomycin (100 µg/ml) (all from Life Technologies) at 37 °C and 5 % CO2.

extract_protocol: Total RNA was extracted with TRIzol solution (Life Technologies) from cells at various time points during adipogenesis (0, 8, 24, 32, 48 and 72 hours, and 7, 14 and 21 days). Small RNAs (< 40 nucleotides) including mature miRNAs were enriched from the total RNA samples using the flashPAGE Fractionator System, and subsequently purified using the flashPAGE Reaction Clean-Up Kit according to the manufacturer (Life Technologies).

treatment_protocol: See Sample, description

value: 21 days

tag: cell line source

value: hMSC-Tert20 undergoing adipogenesis 21 days

source_name: hMSC-Tert20_0 hours

value: 0 hours


title: hMSC-Tert20_differentiated_21days_replicate1


title: hMSC-Tert20_differentiated_14days_replicate2

value: 14 days

value: hMSC-Tert20 undergoing adipogenesis 14 days


title: Liver_intermediatedose1_sample3

source_name: liver, intermediate dose aquarium 1, sample 3

value: juvenile


title: Effect of ER stress on gene expression in LCLs 3


title: hMSC-Tert20_differentiated_7days_replicate2

value: 7 days

value: hMSC-Tert20 undergoing adipogenesis 7 days


title: time: 1 h - treatment: salt - rep2

source_name: time: 1 h - treatment: salt

tag: time point

value: 1 h

value: salt


title: Liver_intermediatedose2_sample2

source_name: Liver, intermediate dose aquarium 2, sample 2

value: liver

value: hepatocytes


title: Effects of ER stress on gene expression in LCLs 5

value: DMSO


title: Effects of ER stress on gene expression in LCLs 8

value: TG+SAL


title: time: 1 h - treatment: PEG - rep2

source_name: time: 1 h - treatment: PEG

value: PEG

tag: organism part

value: A vegetative growth PO:0007134

value: hydroponic drip 0.1 hoagland


title: Effect of ER stress on gene expression in LCLs 2

value: LCL

value: TG


title: time: 1 h - treatment: PEG - rep3

tag: development stage


title: time: 1 h - treatment: salt - rep3

tag: growth media


title: time: 1 h - treatment: salt - rep1


title: Liver_lowdose2_sample2

source_name: Liver, low dose aquarium 2, sample 2


title: time: 1 h - treatment: unstressed - rep3

source_name: time: 1 h - treatment: unstressed

value: unstressed


title: Liver_highdose2_sample2

source_name: Liver, high dose aquarium 2, sample 2


title: hMSC-Tert20_differentiated_14days_replicate1

value: 14 days

value: 0 hours


title: Liver_lowdose1_sample3

source_name: liver, low dose aquarium 1, sample 3

value: juvenile


title: time: 1 h - treatment: PEG - rep1


title: Liver_highdose1_sample2

source_name: Liver, high dose aquarium 1, sample 2


title: Liver_intermediatedose1_sample2

source_name: liver, intermediate dose aquarium 1, sample 2


title: Liver_control1_sample3

source_name: Liver, control aquarium 1, sample 3


title: hMSC-Tert20_differentiated_7days_replicate1

value: 7 days


title: hMSC-Tert20_differentiated_72hours_replicate2

value: 72 hours

value: hMSC-Tert20 undergoing adipogenesis 72 hours


title: Effect of ER stress on gene expression in LCLs 1


title: time: 1 h - treatment: unstressed - rep1

value: 1 h


title: hMSC-Tert20_differentiated_48hours_replicate1

value: 48 hours

value: hMSC-Tert20 undergoing adipogenesis 48 hours


title: hMSC-Tert20_differentiated_48hours_replicate2


title: Liver_control2_sample2

source_name: Liver, control aquarium 2, sample 2

value: liver

value: hepatocytes


title: hMSC-Tert20_differentiated_72hours_replicate1


title: time: 0 h - treatment: unstressed - rep2

source_name: time: 0 h - treatment: unstressed

value: 0 h


title: time: 0 h - treatment: unstressed - rep3

value: A vegetative growth PO:0007134


title: hMSC-Tert20_differentiated_24hours_replicate2

value: 24 hours

value: hMSC-Tert20 undergoing adipogenesis 24 hours


title: Liver_highdose2_sample1

source_name: Liver, high dose aquarium 2, sample 1


title: hMSC-Tert20_differentiated_32hours_replicate1

value: 32 hours

value: hMSC-Tert20 undergoing adipogenesis 32 hours


title: Liver_lowdose1_sample2

source_name: Liver, low dose aquarium 1, sample 2


title: hMSC-Tert20_differentiated_24hours_replicate1


title: hMSC-Tert20_differentiated_8hours_replicate1

value: 8 hours

value: hMSC-Tert20 undergoing adipogenesis 8 hours


title: Liver_intermediatedose2_sample1

source_name: Liver, intermediate dose aquarium 2, sample 1

value: juvenile


title: hMSC-Tert20_undifferentiated

description: The hMSC-Tert20 cells were seeded in multiple 24-well plates (Thermo Fisher Scientific, Rockford, IL, USA) at a density of 40 000 cells/well.

value: 0 hours

value: hMSC-Tert20 undifferentiated

source_name: hMSC-Tert20_0 hours


title: Liver_lowdose2_sample1

source_name: Liver, low dose aquarium 2, sample 1


title: Liver_control2_sample1

source_name: Liver, control aquarium 2, sample 1


title: Brown seed coat, biological rep3

city: Ottawa

first: Nikola

last: Kovinich

state: Ontario

address: 960 Carling

department: Bioprocesses

institute: Agriculture and Agri-Food Canada

description: Gene expression data from brown seed coat

hyb_protocol: Labelled aRNA was hybridized to GeneChip Soybean Genome Arrays as described by the manufacturer (Affymetrix).

scan_protocol: GeneChips were scanned as described by the manufacturer (Affymetrix).

data_processing: Statistical analyses of data for the identification of differentially regulated genes were performed using FlexArray software (M. Blazejczyk and associates; Genome Quebec, Montreal) that uses R and Bio-Conductor (Gentleman et al., 2004). The raw data was adjusted for background signal, and normalized across all GeneChips using the Robust Multi-array Average (RMA) method (Irizarry et al., 2003). To identify differentially expressed genes, the SAM algorithm, which minimizes variation across arrays and incorporates an estimate of false discovery rate (FDR) (Benjamini and Hochberg, 1995), was used. Only genes with a fold change >2 or <0.5 and a P value <0.01 were considered to be differentially expressed.

organism: Glycine max

source_name: Brown soybean seed coat var. Clark 300 - 400 mg fresh seed weight stage of seed development

label_protocol: 100 ng of total RNA was in vitro transcribed for 16 h using the GeneChip 3’IVT Express Kit (Affymetrix, http://www.affymetrix.com).

growth_protocol: Black (iRT) soybean (G. max (L.) Merr.) variety Clark (PI547438) and the nearly isogenic brown (irT) soybean (PI 547475) seeds were surface-sterilized in 2% triton/70% EtOH–H2O (7:3, v/v) for 5 min on a mixer wheel, rinsed three times with EtOH, dried, and germinated in autoclaved vermiculite in a Conviron E15 cabinet under 16/8 h light (590 μE m2 s)/dark at 25 °C and 20 °C, respectively. Plants were fertilized twice weekly with N:P:K 35-5-10 (1% w/v). After 12 days, seedlings were transplanted to autoclaved soil and 34 days later the photoperiod was changed to 12 h light/12 h dark to encourage reproductive development.

extract_protocol: Total RNA was isolated from pigmented soybean seed coats as described previously (Wang and Vodkin, 1994).

treatment_protocol: No treatment.

value: Seed coat (testa)

tag: genotype

value: brown (irT)

value: transition stage of seed development (300 – 400 mg fresh seed weight)


title: Black seed coat, biological rep3

description: Gene expression data from black seed coat

source_name: Black soybean seed coat var. Clark 300 - 400 mg fresh seed weight stage of seed development

tag: tissue

value: black (iRT)


title: Liver_highdose1_sample1

source_name: Liver, high dose aquarium 1, sample 1

value: liver


title: Brown seed coat, biological rep1


title: Brown seed coat, biological rep2


title: time: 1 h - treatment: unstressed - rep2

source_name: time: 1 h - treatment: unstressed

value: 1 h

tag: treatment

value: unstressed

value: hydroponic drip 0.1 hoagland


title: Liver_lowdose1_sample1

source_name: liver, low dose aquarium 1, sample 1

tag: cell type

value: hepatocytes


title: Liver_intermediate1_sample1

source_name: liver, intermediate dose aquarium 1, sample 1


title: time: 4 h - treatment: salt - rep2

description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 1/10 Hoagland's with full strength micronutrients. Experimental time 0 was at approximately 9 am. . Development stage: [4 weeks after pruning 2 year old plants to 4 nodes]. Part of organism: [shoot tips to 4th leaf including leaves, stem, tendrils, buds]. Treatment application type: [other::salt].

source_name: time: 4 h - treatment: salt

value: 4 h

value: salt

value: A vegetative growth PO:0007134


title: Liver_control1_sample1

hyb_protocol: Prehybridization was performed at room temperature for 15 min with a prehybridization buffer (25 mL 2 ×MES hybridization buffer and 1% BSA in 50ml DEPC H2O). Fragmented cRNA (6 µg/array) was dissolved in hybridization buffer (final concentration: 5X SSPE (Ambion® Inc.), 20% formamide, 0.5 mg BSA/mL, 0.1X TE, 0.1 mg human Cot-1 DNA (Invitrogen Carlsbad, CA), 0.01% Tween 20). Samples were denaturated for 3 min at 95 °C and hybridized to the biochips at 45 °C for 16 h, followed by a first washing step at 25 °C with 6 ×SSPE and a second washing step at 45 oC with 0.5× SSPE. Fluorescence-staining was achieved by incubating the arrays with 5 µg/mL streptavidin R-phycoerythrin conjugate (SAPE) (Invitrogen) diluted in 6×SSPE containing 2 mg BSA/ml at 25 °C for 15 min. Signal amplification was performed using biotinylated α-streptavidin antibodies (Vector Laboratories, Burlingame, CA) followed by an additional incubation with SAPE.

source_name: liver, control aquarium 1, sample 1


title: C-PTC-mut LB05-261 312137

status: Public on Aug 22 2011

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
C-PTC-mut S vs C-PTC-mut L
Date:2007/04/25

hyb_protocol: Agilent : 700.0 ng at 48 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : vsn, Intraslide norm. : none, Background norm. : none, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: C-PTC-mut S

label_protocol: Invitrogen - Ulysis

extract_protocol: MirVana

tag: label

value: C-PTC-mut S

tag: extract

tag: sample

tag: subject

value: Thyroid

tag: disease

value: safe (CPTC-mut)

source_name: C-PTC-mut L

value: C-PTC-mut L

value: lesional (CPTC-mut)


title: ADENOMA LB05-137 312175

description:
ADENOMA.1S vs ADENOMA.1L
Date:2007/05/09

value: safe (adenoma)

value: lesional (adenoma)


title: ADENOMA LB05-177 311971

description:
ADENOMA.2S vs ADENOMA.2L
Date:2007/05/04


title: FT-UMP LB05-095 312135

description:
FT-UMP.2S vs FT-UMP.2L
Date:2007/05/09

value: safe (FTUMP)

value: lesional (FTUMP)


title: C-PTC-mut LB05-261 312173

description:
C-PTC-mut L vs C-PTC-mut S
Date:2007/04/25


title: Effects of ER stress on gene expression in LCLs 11

source_name: LCLs

value: LCL

value: SAL

tag: time


title: WDT-UMP LB05-126 312167

description:
WDT-UMP 1S vs WDT-UMP 1L
Date:2007/04/25

source_name: WDT-UMP 1S

value: WDT-UMP 1S

value: safe (WDTUMP)

source_name: WDT-UMP 1L

value: WDT-UMP 1L

value: lesional (WDTUMP)


title: FV-PTC LB05-310 312170

description:
FV-PTC 2S vs FV-PTC 2L
Date:2007/04/25

source_name: FV-PTC 2S

value: FV-PTC 2S

value: safe (FVPTC)

source_name: FV-PTC 2L

value: FV-PTC 2L

value: lesional (FVPTC)


title: ADENOMA LB05-177 312136

description:
ADENOMA.2L vs ADENOMA.2S
Date:2007/04/25

value: Thyroid


title: FV-PTC LB05-091 312134

description:
FV-PTC 1S vs FV-PTC 1L
Date:2007/05/09

source_name: FV-PTC 1S

value: FV-PTC 1S

source_name: FV-PTC 1L

value: FV-PTC 1L


title: FV-PTC LB05-310 312171

description:
FV-PTC 2L vs FV-PTC 2S
Date:2007/04/25


title: FTC LB05-113 312133

description:
FTC S vs FTC L
Date:2007/05/09

source_name: FTC S

value: FTC S

value: safe (FTC)

source_name: FTC L

value: FTC L

value: lesional (FTC)


title: FTC LB07-183 334403

description:
FTC.5 L vs FTC.5S
Date:2007/12/05

source_name: FTC.5 L

value: FTC.5 L


title: ADENOMA LB05-137 312174

description:
ADENOMA.1L vs ADENOMA.1S
Date:2007/04/25

value: lesional (adenoma)

value: safe (adenoma)


title: Black seed coat, biological rep2

source_name: Black soybean seed coat var. Clark 300 - 400 mg fresh seed weight stage of seed development

value: Seed coat (testa)

value: black (iRT)

value: transition stage of seed development (300 – 400 mg fresh seed weight)


title: FT-UMP LB06-435 311980

description:
FT-UMP.6S vs FT-UMP.6L
Date:2007/05/10

value: safe (FTUMP)

value: lesional (FTUMP)


title: WDT-UMP LB05-126 312166

description:
WDT-UMP 1L vs WDT-UMP 1S
Date:2007/04/25

value: WDT-UMP 1L

value: lesional (WDTUMP)

value: WDT-UMP 1S

value: safe (WDTUMP)


title: Black seed coat, biological rep1


title: FT-UMP LB05-095 312131

description:
FT-UMP.2L vs FT-UMP.2S
Date:2007/05/09

value: Thyroid


title: FV-PTC LB06-080 311986

description:
FV-PTC.4L vs FV-PTC.4S
Date:2007/05/09

value: lesional (FVPTC)

value: safe (FVPTC)


title: C-PTC-mut LB06-271 312049

description:
C-PTC-mut.4S vs C-PTC-mut.4L
Date:2007/05/10

value: safe (CPTC-mut)

value: lesional (CPTC-mut)


title: FTC LB06-624 334432

description:
FTC.3S vs FTC.3L
Date:2007/12/05

value: safe (FTC)

value: lesional (FTC)


title: FTC LB07-156 334439

description:
FTC.4 S vs FTC.4 L
Date:2007/12/05

source_name: FTC.4 S

value: FTC.4 S

source_name: FTC.4 L

value: FTC.4 L


title: C-PTC-wt LB06-160 311983

description:
C-PTC-wt.3L vs C-PTC-wt.3S
Date:2007/05/09

value: lesional (CPTC)

value: safe (CPTC)


title: C-PTC-mut LB06-190 311985

description:
C-PTC-mut.3L vs C-PTC-mut.3S
Date:2007/05/09


title: FTC LB06-624 334433

description:
FTC.3L vs FTC.3S
Date:2007/12/05


title: ADENOMA LB06-535 312007

description:
ADENOMA.5L vs ADENOMA.5S
Date:2007/05/10

value: lesional (adenoma)

value: safe (adenoma)


title: ADENOMA LB06-535 312008

description:
ADENOMA.5S vs ADENOMA.5L
Date:2007/05/10


title: FTC LB07-183 334431

description:
FTC.5 S vs FTC.5 L
Date:2007/12/05

source_name: FTC.5 S

value: FTC.5 S

value: FTC.5 L


title: FV-PTC LB06-080 311981

description:
FV-PTC.4S vs FV-PTC.4L
Date:2007/05/09


title: CPTC-mut LB06-271 311581

description:
CPTC-mut.4L vs CPTC-mut.4S
Date:2007/05/10

value: lesional (CPTC mut4)

value: safe (CPTC-mut4)


title: C-PTC-wt LB06-160 311982

description:
C-PTC-wt.3S vs C-PTC-wt.3L
Date:2007/05/09

value: Thyroid


title: C-PTC-mut LB06-273 312003

description:
C-PTC-mut.5S vs C-PTC-mut.5L
Date:2007/05/10


title: FTC LB07-156 334423

description:
FTC.4 L vs FTC.4 S
Date:2007/12/05


title: Liver_control1_sample2

description: See Cuklev et al 2010 for further information.

source_name: Liver, control aquarium 1, sample 2

value: juvenile

value: liver

value: hepatocytes


title: FTC LB07-183 342456

description:
FTC.5 S vs FTC.5 L
Date:2007/12/14


title: ADENOMA LB05-044 312002

description:
ADENOMA.6S vs ADENOMA.6L
Date:2007/05/10


title: FTC LB07-183 342457

description:
FTC.5 L vs FTC.5 S
Date:2008/01/03


title: ADENOMA LB06-174 311987

description:
ADENOMA.4L vs ADENOMA.4S
Date:2007/05/09


title: WDT-UMP LB04-084 311977

description:
WDT-UMP L vs WDT-UMP S
Date:2007/04/24

source_name: WDT-UMP L

value: WDT-UMP L

value: LESIONAL (WDTUMP)

source_name: WDT-UMP S

value: WDT-UMP S

value: safe (WDTUMP)


title: time: 0 h - treatment: unstressed - rep1

description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 1/10 Hoagland's with full strength micronutrients. Experimental time 0 was at approximately 9 am. . Development stage: [4 weeks after pruning 2 year old plants to 4 nodes]. Part of organism: [shoot tips to 4th leaf including leaves, stem, tendrils, buds]. Treatment application type: [No Treatment].

source_name: time: 0 h - treatment: unstressed

value: 0 h

value: unstressed

value: A vegetative growth PO:0007134

value: hydroponic drip 0.1 hoagland


title: WDT-UMP LB06-146 311988

description:
WDT-UMP.5S vs WDT-UMP.5L
Date:2007/05/09

value: lesional (WDTUMP)


title: hyperglycemia, benfotiamine, donor I

first: Hege

last: Thoresen

address: Sem Sælandsvei 3

department: School of Pharmacy

institute: University of Oslo

description: Controls for these arrays are already published in GEO: GSE19620 (Samples GSM489256-GSM489261)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: BeadStudio version 3.1.2.0 from Illumnia and the Gene Expression module 3.2.7.  Program R and Bioconductor packages.

source_name: myotubes from satellite cells from m. obliquus internus abdominis

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The cells were cultured in DMEM-Glutamax (5.5 mmol/l glucose) with 2 % FCS, 2 % Ultroser G, penicillin/streptomycin (P/S) and amphotericin B until 70-80 % confluence. Myoblast differentiation to myotubes was then induced by changing medium to DMEM-Glutamax (5.5 mmol/l glucose) with 2 % FCS, 34 pmol/l insulin, P/S and amphotericin B. Experiments were performed after 8 days of differentiation, and pre-incubation with hyperglycemia (20 mmol/l glucose) and benfotiamine (200 µM) was started after 4 days.

extract_protocol: Total RNA was prepared from primary myotubes from three donors using Agilent Total RNA isolation kit according to the supplier’s protocol (Agilent Technologies). RNA was used individually and RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 9.0).

treatment_protocol: From day 4-8 during the differentiation period the cells were treated with 5.5 mM glucose (control, normoglycemia) or 20 mM glucose (hyperglycemia). Isolation of RNA was performed on day 8.

tag: donor

value: I

tag: condition

value: hyperglycemia

tag: agent

value: benfotiamine


title: ADENOMA LB05-044 311979

description:
ADENOMA.6L vs ADENOMA.6S
Date:2007/04/24

value: lesional (adenoma)

value: safe (adenoma)


title: normoglycemia, benfotiamine, donor III

value: III

value: normoglycemia


title: ADENOMA LB05-044 311919

description:
ADENOMA.6L vs ADENOMA.6S
Date:2007/05/10

value: Thyroid


title: hyperglycemia, benfotiamine, donor III


title: normoglycemia, benfotiamine, donor II

value: II


title: WDT-UMP LB06-146 311989

description:
WDT-UMP.5L vs WDT-UMP.5S
Date:2007/05/09


title: normoglycemia, benfotiamine, donor I


title: FTC LB07-156 342455

description:
FTC.4 S vs FTC.4 L
Date:2007/12/14

value: FTC.4 S

value: safe (FTC)

value: FTC.4 L

value: lesional (FTC)


title: hyperglycemia, benfotiamine, donor II


title: FT-UMP LB06-435 311917

description:
FT-UMP.6L vs FT-UMP.6S
Date:2007/05/10

value: lesional (FTUMP)

value: safe (FTUMP)


title: CNS PNET42 Xba1

type: genomic

city: Nottingham

first: Suzanne

last: Miller

state: Nottinghamshire

address: Queen's Medical Centre

department: Human Development

institute: Children's Brain Tumour Research Centre

description: CNS PNET42 Xba1

hyb_protocol: Affymetrix 100K Hybridisation Protocol

scan_protocol: Affymetrix 100K Scanning Protocol

data_processing: GCOS

molecule: genomic DNA

source_name: Brain Tumour, CNS PNET42 Xba1

label_protocol: Affymetrix 100K Labeling Protocol

extract_protocol: Phenol/Chloroform Isoamyl Alcohol and PLG tubes

tag: gender

value: female

tag: age

value: 148 months

tag: tumour location

value: Frontal and Parietal Lobes


title: C-PTC-wt LB05-037 311972

description:
C-PTC-wt.4L vs C-PTC-wt.4S
Date:2007/04/24

value: lesional (CPTC wt4)

tag: origin

value: thyroid

value: safe (CPTC-wt4)


title: C-PTC-wt LB05-037 311974

description:
C-PTC-wt.4S vs C-PTC-wt.4L
Date:2007/04/23


title: ADENOMA LB05-044 311975

description:
ADENOMA.6S vs ADENOMA.6L
Date:2007/04/23

value: safe (adenoma)

value: lesional (adenoma)


title: C-PTC-mut LB06-273 311916

description:
C-PTC-mut.5 L vs C-PTC-mut.5 S
Date:2007/05/10

source_name: C-PTC-mut.5 L

value: C-PTC-mut.5 L

value: lesional (CPTC mut5)

source_name: C-PTC-mut.5 S

value: C-PTC-mut.5 S

value: safe (CPTC-mut5)


title: PB8 Xba1

description: PB8 Xba1

source_name: Brain Tumour, PB8 Xba1

value: 168 months

value: Pineal


title: FTC LB05-572 312021

description:
FTC.2L vs FTC.2S
Date:2007/05/09

value: Thyroid

value: lesional (FTC)

value: safe (FTC)


title: ADENOMA LB04-068 312145

description:
ADENOMA S vs ADENOMA L
Date:2007/04/24

source_name: ADENOMA S

value: ADENOMA S

source_name: ADENOMA L

value: ADENOMA L


source_name: Blood, CNS PNET38 and CNS PNET39 Constitutional Xba1

value: male

value: 141 months


title: CNS PNET44 Xba1

description: CNS PNET44 Xba1

source_name: Brain Tumour, CNS PNET44 Xba1

value: Parietal Lobe


title: WDT-UMP LB04-084 312146

description:
WDT-UMP S vs WDT-UMP L
Date:2007/04/24

value: WDT-UMP S

value: safe (WDTUMP)

value: WDT-UMP L

value: lesional (WDTUMP)


title: CNS PNET40 Xba1

description: CNS PNET40 Xba1

source_name: Brain Tumour, CNS PNET40 Xba1

value: 142 months

value: Hemispheric and Lateral Ventricle

tag: metastasis


title: CNS PNET38 Xba1

description: CNS PNET38 Xba1

source_name: Brain Tumour, CNS PNET38 Xba1

value: Frontal Lobe


title: PB7 Xba1

description: PB7 Xba1

source_name: Brain Tumour, PB7 Xba1

value: 132 months


title: CNS PNET39 Xba1

description: CNS PNET39 Xba1

source_name: Brain Tumour, CNS PNET39 Xba1


title: ADENOMA LB05-562 312024

description:
ADENOMA.3S vs ADENOMA.3L
Date:2007/05/09

tag: tissue

value: safe (adenoma)

value: lesional (adenoma)


title: C-PTC-wt LB05-338 311957

description:
C-PTC-wt.L vs C-PTC-wt.S
Date:2007/05/09

value: Thyroid

value: lesional (CPTC wt)

value: safe (CPTC-wt)


title: ADENOMA LB05-562 312020

description:
ADENOMA.3L vs ADENOMA.3S
Date:2007/05/09


title: ADENOMA LB04-068 312144

description:
ADENOMA L vs ADENOMA S
Date:2007/04/24

value: ADENOMA L

value: ADENOMA S


title: FT-UMP LB05-329 311959

description:
FT-UMP.3S vs FT-UMP.3L
Date:2007/05/09

value: safe (FTUMP)

value: lesional (FTUMP)


title: CNS PNET36 Xba1

description: CNS PNET36 Xba1

source_name: Brain Tumour, CNS PNET36 Xba1

value: male

value: 122 months

value: Parietal Lobe


title: CNS PNET34 Xba1

description: CNS PNET34 Xba1

source_name: Brain Tumour, CNS PNET34 Xba1

value: 107 months

value: Cerebral and Posteria Fossa


source_name: Blood, CNS PNET35 and CNS PNET36 Constitutional Xba1


title: CNS PNET35 Xba1

description: CNS PNET35 Xba1

source_name: Brain Tumour, CNS PNET35 Xba1


source_name: Blood, CNS PNET33 and CNS PNET34 Constitutional Xba1


title: FTC LB05-542 311909

description:
FTC.2L vs FTC.2S
Date:2007/05/09

value: lesional (FTC)

value: safe (FTC)


title: FTC LB05-542 312023

description:
FTC.1S vs FTC.1L
Date:2007/05/09


title: wild-type neuron/embryo replicate 3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

hyb_protocol: Slides were hybridized with a mixture of Cy3 and Cy5 labeled aRNA probes. Hybridizations were performed at 63°C overnight under standard conditions (3X SSC, 0.2 mg/ml salmon sperm DNA, 25 mM HEPES, 0.25% SDS) and slides were washed at room temperature successively with 0.6X SSC/0.03% SDS and then 0.06X SSC prior to scanning.

scan_protocol: Microarray images were acquired with a GenePix 4000B scanner (Axon Instruments, Foster City, CA). For image analysis GenePix pro 6.0 software was used (Axon Instruments).

data_processing: Data files were uploaded to Acuity version 4.0 (Molecular Devices), where the raw data were log-transformed, normalized using Lowess normalization, filtered for quality spots (RgnR2[635/532]>0.5; F532median - B532 >= 150; F635median - B635 >= 150; problematic or flagged spots removed). Mean values from dye-swap experiments were used for further analysis. Oligonucleotide probes were mapped to genes and transcripts defined in Flybase (version FB2009_07, r5.20, released August 10, 2009) (http://flybase.org/) (Tweedie et al. 2009).

organism: Drosophila melanogaster

source_name: elav+ cells

label_protocol: Concentration and quality of RNA were determined on the Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA). For array analysis, labeled aRNA was prepared starting with ≤ 1 µg of total RNA using the Amino Allyl MessageAmp II aRNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) according to the manufacturer’s specifications.  5 µg amino allyl-modified aRNA was coupled with Cy dyes (CyDye Post-Labeling Reactive Dye Pack, GE Heathcare, RPN 5661). Labeling reactions were quenched with hydroxylamine, and uncoupled dye material removed with aRNA Filter Cartridges supplied in the MessageAmp II kit.  Labeled aRNA was fragmented to 60-200 nts using Ambion RNA Fragmentation Reagents (P/N AM8740) according to manufacturer’s instructions.

growth_protocol: Stage 15-16 Drosophila melanogaster embryos were collected on apple juice/agar plates at 25C.

extract_protocol: Embryos were dechorionated for 2 min in 50% bleach and rinsed well with embryo wash buffer (0.04% Triton X-100; 0.7% NaCl) and distilled water. Embryos were transferred to a 7 mL Dounce Homogenizer on ice containing 5 mL ice-cold Schneider media supplemented with 3 mM EGTA and homogenized gently with the loose pestle for 8 – 10 strokes. Debris was pelleted in a 15 mL conical tube for 3 min at 50 x g and the supernatant decanted to a fresh conical tube. Cells were pelleted at 350 x g for 5 min, resuspended in 1.5 mL cold PBS (pH 7.4) and passed through a 70 micron filter. All centrifugation steps were performed at 4ºC. Cells were stained with 7-Amino-actinomycin D (7-AAD) prior to Fluorescence Activated Cell Sorting (FACS) to identify membrane-intact live cells. Dissociated cells were sorted on a MoFlo high speed sorter (Beckman Coulter) for FACS of GFP positive cells. Gating was performed by first excluding sub-cellular debris from a plot of light scatter characteristics. Further gating on pulse width was performed to exclude undesired large particles, clusters of cells and small debris. Finally, GFP was plotted against yellow autofluorescence and single GFP positive cells were isolated for further analysis. GFP and autofluorescence were both excited with 488 nm laser light at 200 mW from a water-cooled argon ion laser (Coherent). GFP fluorescence was collected behind a 530/40 bandpass filter and autofluorescence behind a 580/30 filter on the FL1 and FL2 detectors, respectively. Approximately 150,000 to 300,000 cells were sorted for each biological sample (timed collections), with cell dissociation taking ~15 min and FACS occurring immediately following dissociation for ~0.5 – 1h. Cells were sorted directly into TriZol, and RNA was isolated and then amplified using MessageAmp II aRNA amplification kit (Ambion).

tag: developmental stage

value: stage 15-16 embryos

tag: genotype

value: P{w+mW.hs=GawB}elav[C155], P{w+mC=UAS-mCD8::GFP.L}LL4, P{ry+t7.2=hsFLP}1, w*

source_name: whole dissociated embryo cells


title: wild-type neuron/embryo replicate 2

description: This is a merged dye-swap sample


title: CNS PNET33 Xba1

description: CNS PNET33 Xba1

source_name: Brain Tumour, CNS PNET33 Xba1

value: Cerebral


title: C-PTC-wt LB06-041 311908

description:
C-PTC-wt.2L vs C-PTC-wt.2S
Date:2007/05/03

tag: label

value: Thyroid

value: lesional (CPTC wt2)

value: safe (CPTC-wt2)


title: C-PTC-wt LB06-041 312154

description:
C-PTC-wt 2S vs C-PTC-wt 2L
Date:2007/05/03

source_name: C-PTC-wt 2S

value: C-PTC-wt 2S

tag: extract

value: safe (CPTC)

source_name: C-PTC-wt 2L

value: C-PTC-wt 2L

value: lesional (CPTC)


title: CNS PNET26 Constitutional Xba1

description: CNS PNET26 Constitutional Xba1

source_name: Blood, CNS PNET26 Constitutional Xba1

value: male

value: 61 months


title: FT-UMP LB06-061 311907

description:
FT-UMP.5S vs FT-UMP.5L
Date:2007/05/03

tag: sample

value: safe (FTUMP)

value: lesional (FTUMP)


title: wild-type neuron/embryo replicate 1


title: CNS PNET31 Constitutional Xba1

description: CNS PNET31 Constitutional Xba1

source_name: Blood, CNS PNET31 Constitutional Xba1

value: female

value: 85 months


title: CNS PNET31 Xba1

description: CNS PNET31 Xba1

source_name: Brain Tumour, CNS PNET31 Xba1

value: Frontal Lobe


title: wild-type neuron/embryo replicate 4

value: stage 15-16 embryos


title: CNS PNET25 Xba1

description: CNS PNET25 Xba1

source_name: Brain Tumour, CNS PNET25 Xba1

value: 59 months

value: Midline and Frontal Lobe


title: CNS PNET28 Xba1

description: CNS PNET28 Xba1

source_name: Brain Tumour, CNS PNET28 Xba1

value: 71 months

value: Frontal and Parietal Lobes


title: wild-type muscle/embryo replicate 4

description: This is a merged dye-swap sample

source_name: mef2+ cells


title: CNS PNET26 Xba1

description: CNS PNET26 Xba1

source_name: Brain Tumour, CNS PNET26 Xba1


title: wild-type muscle/embryo replicate 2

description: This is a merged dye-swap sample


title: wild-type muscle/embryo replicate 3

description: This is a merged dye-swap sample


title: C-PTC-mut LB06-066 312153

description:
C-PTC-mut 2L vs C-PTC-mut 2S
Date:2007/05/03

source_name: C-PTC-mut 2L

value: C-PTC-mut 2L

tag: subject

value: Thyroid

value: lesional (CPTC-mut)

source_name: C-PTC-mut 2S

value: C-PTC-mut 2S

value: safe (CPTC-mut)


title: FT-UMP LB06-061 311906

description:
FT-UMP.5L vs FT-UMP.5S
Date:2007/05/03

tag: disease


title: CNS PNET24 Constitutional Xba1

description: CNS PNET24 Constitutional Xba1

source_name: Blood, CNS PNET24 Constitutional Xba1

value: 53 months


title: CNS PNET24 Xba1

description: CNS PNET24 Xba1

source_name: Brain Tumour, CNS PNET24 Xba1

value: Temporal and Parietal Lobes


title: FT-UMP LB05-058 312129

description:
FT-UMP.1S vs FT-UMP.1L
Date:2007/05/09

value: safe (FTUMP)


title: sgf11 muscle/wild-type muscle replicate 4

description: This is a merged dye-swap sample

source_name: sgf11-/- mef2+ cells


title: wild-type muscle/embryo replicate 1

description: This is a merged dye-swap sample


title: sgf11 muscle/wild-type muscle replicate 3

description: This is a merged dye-swap sample


title: sgf11 muscle/wild-type muscle replicate 2

description: This is a merged dye-swap sample


title: CNS PNET23 Xba1

description: CNS PNET23 Xba1

source_name: Brain Tumour, CNS PNET23 Xba1

value: 51 months


title: C-PTC-mut LB05-590 312152

description:
C-PTC-mut 1S vs C-PTC-mut 1L
Date:2007/05/03

source_name: C-PTC-mut 1S

value: C-PTC-mut 1S

source_name: C-PTC-mut 1L

value: C-PTC-mut 1L


title: PB5 Xba1

description: PB5 Xba1

source_name: Brain Tumour, PB5 Xba1

value: male

value: 24 months

value: Pineal


title: FV-PTC LB05-049 312128

description:
FV-PTC S vs FV-PTC L
Date:2007/05/09

source_name: FV-PTC S

value: FV-PTC S

value: safe (FVPTC)

source_name: FV-PTC L

value: FV-PTC L

value: lesional (FVPTC)


title: sgf11 muscle/wild-type muscle replicate 1

value: stage 15-16 embryos


title: D2214, biological rep1 [gDNA]

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

description:
Nonmucoid isolate
Bcc_D2214_1_A810_imomeira_IST_JL_(Bcc1sa520656F).CEL
B. multivorans_D2214_A

hyb_protocol: 5 µg of biotinylated DNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Analysis was carried out with DNA-Chip Analyzer 2008. First a digital mask was applied, leaving for analysis only 9281 probe sets representing B. multivorans ATCC 17616 transcripts. Then the 4 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method.Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a Perfect Match (PM)-only model. Replicate data (duplicates) for each bacterial isolate was weighted gene-wise by using inverse squared standard error as weights. An LCB cut-off of 1.5 in combination with a consistent hybridization signal above 10 in the two replicas of at least one strain was chosen, resulting in 55 genomic loci showing significantly different hybridization signals.

organism: Burkholderia multivorans

source_name: D2214 isolate with 15h growth in LB medium

label_protocol: A total of 1,5 ug of genomic DNA per sample was labeled using the Bioprime DNA labelling System (Invitrogen,Paisley, UK). Cleanup was performed using MinElute PCR Purification Kit (Qiagen, Hilden) and quality was checked on an Agilent 2100 Bioanalyser using a DNA 1000 assay

growth_protocol: D2095 and D2214 bacterial isolates were grown in 100 ml LB medium contained into 250 ml Erlenmyer flasks at 37ºC, 250 r.p.m. for 15 h

extract_protocol: Total DNA extraction was carried out using the Dneasy Blood and tissue Kit (Qiagen) by following manufacturer’s recommendation

tag: isolate


title: PB6 Xba1

description: PB6 Xba1

source_name: Brain Tumour, PB6 Xba1


title: D2214, biological rep1 [mRNA]

description: B. multivorans_D2214_J

hyb_protocol: Following fragmentation, 2 µg of end-labeled fragmented cDNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

data_processing: Scanned arrays were analyzed with Affymetrix Expression Console software. Subsequent analysis was carried out with DNA-Chip Analyzer 2008. First a digital mask was applied, leaving for analysis only the 9291 probe sets on the array representing Burkholderia multivorans ATCC 17616 transcripts. Then the 6 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a Perfect Match (PM)-only model. Replicate data (triplicates) for each bacterial isolate was weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2.

source_name: D2214 isolate with 17h growth in SM medium

label_protocol: RNA was processed for use on Affymetrix custom dual species Burkholderia arrays, according to the manufacturer’s Prokaryotic Target Preparation Assay. Briefly, 10 ug of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix, Santa Clara, CA) was used in a reverse transcription reaction with random primers (Invitrogen Life Technologies) to generate first-strand cDNA. After removal of RNA, 2 ug of cDNA were fragmented with DNase and end-labeled with biotin using terminal polynucleotidyl transferase (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, was assessed using an Agilent 2100 Bioanalyzer.

growth_protocol: D2095 and D2214 bacterial isolates were grown in 100 ml SM medium contained into 250 ml Erlenmyer flasks at 37ºC, 250 r.p.m. for 17 h

extract_protocol: Total RNA extraction was carried out using the RNeasy MiniKit (Qiagen) by following manufacturer’s recommendation

treatment_protocol: Bacterial cells were resuspended in RNAprotect bacteria reagent (Qiagen).

tag: isolate type

value: Nonmucoid


title: D2214, biological rep2 [mRNA]

description: B. multivorans_D2214_K


title: D2214, biological rep3 [mRNA]

description: B. multivorans_D2214_L


title: CNS PNET22 Xba1

description: CNS PNET22 Xba1

source_name: Brain Tumour, CNS PNET22 Xba1

value: 37 months

value: Temporal Lobe


title: D2214, biological rep2 [gDNA]

description:
Nonmucoid isolate
Bcc_D2214_2_A811_imoreira_IST_JL_(Bcc1sa520656F).CEL
B. multivorans_D2214_B


title: D2095, biological rep1 [gDNA]

description:
Mucoid isolate
Bcc_D2095_1_A808_lmoreira_IST_JL_(Bcc1sa520656F).CEL
B. multivorans_D2095_A

source_name: D2095 isolate with 15h growth in LB medium


title: D2095, biological rep2 [gDNA]

description:
Mucoid isolate
Bcc_D2095_2_A809_lmoreira_IST_JL_(Bcc1sa520656F).CEL
B. multivorans_D2095_B


title: D2095, biological rep3 [mRNA]

description: B. multivorans_D2095_I

source_name: D2095 isolate with 17h growth in SM medium

value: Mucoid


title: CNS PNET20 Xba1

description: CNS PNET20 Xba1

source_name: Brain Tumour, CNS PNET20 Xba1

value: 32 months

value: Frontal Lobe


title: FTC LB05-113 311588

description:
FTC L vs FTC S
Date:2007/05/09

source_name: FTC L

value: FTC L

value: Thyroid

value: lesional (FTC)

source_name: FTC S

value: FTC S

value: safe (FTC)


title: FV-PTC LB05-049 311585

description:
FV-PTC L vs FV-PTC S
Date:2007/05/09

value: lesional (FV-PTC)

value: safe (FV-PTC)


title: FT-UMP LB06-024 312151

description:
FT-UMP.4S vs FT-UMP.4L
Date:2007/05/03

value: safe (FTUMP)

value: lesional (FTUMP)


title: FTC LB07-156 342652

description:
FTC.4 L vs FTC.4 S
Date:2007/12/14

source_name: FTC.4 L

value: FTC.4 L

source_name: FTC.4 S

value: FTC.4 S


title: D2095, biological rep2 [mRNA]

description: B. multivorans_D2095_H


title: CNS PNET18 Xba1

description: CNS PNET18 Xba1

source_name: Brain Tumour, CNS PNET18 Xba1

value: female

value: 24 months


title: D2095, biological rep1 [mRNA]

description: B. multivorans_D2095_G


title: FT-UMP LB06-024 310493

description:
FT-UMP-L vs FT-UMP-S
Date:2007/05/03

source_name: FT-UMP-L

value: FT-UMP-L

source_name: FT-UMP-S

value: FT-UMP-S


title: hnf4KD_H9_d20_hepatic differentiated_3

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

description: The availability of pluripotent stem cells offers the possibility of using such cells to model hepatic disease and development. With this in mind, we previously established a protocol that facilitates the differentiation of both human embryonic stem cells and induced pluritpotent cells into cells with hepatocyte characteristics. The use of highly defined culture conditions and the avoidance of feeder cells or embryoid bodies allowed synchronous and reproducible differentiation to occur. The differentiation toward a hepatocyte–like fate appeared to recapitulate many of the stages normally associated with the formation of hepatocytes in vivo. In the current study we addressed the feasibility of using human pluripotent stem cells to probe the molecular mechanisms underlying human hepatocyte differentiation. We demonstrate i) that human ES cells express a number of mRNAs that characterize each stage in the differentiation process, ii) that gene expression can be efficiently depleted throughout the differentiation time course using shRNAs expressed from lentiviruses, and iii) that the nuclear hormone receptor HNF4a is essential for specification of human hepatic progenitor cells by establishing expression of the network of transcription factors that control hepatocyte cell fate.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Standard Affymetrix protocol, standard GCOS data processing produced the values in the accompanying table

source_name: WA09 human embryonic stem cells

label_protocol: Affymetrix One-Cycle Target Labeling

extract_protocol: total RNA

tag: cell type

value: WAO9 human embryonic stem cells

tag: genotype/variation

value: shRNA-mediated HNF4a knockdown

tag: growth protocol

value: subjected to a hepatic differentiation protocol

tag: time


title: CNS PNET15 Xba1

description: CNS PNET15 Xba1

source_name: Brain Tumour, CNS PNET15 Xba1

tag: gender

tag: age

value: 20 months

tag: tumour location

value: Frontal Lobe


title: FV-PTC LB05-091 311584

description:
FV-PTC.1L vs FV-PTC.1S
Date:2007/05/09

tag: tissue

value: Thyroid

tag: origin

value: thyroid

value: safe (FV-PTC.1)


title: hnf4KD_H9_d20_hepatic differentiated_2


title: hnf4KD_H9_d20_hepatic differentiated_1


title: CNS PNET14 Xba1

description: CNS PNET14 Xba1

source_name: Brain Tumour, CNS PNET14 Xba1

value: male

value: 19 months

value: Frontal and Temporal Lobes

tag: metastasis


title: CNS PNET15 Constitutional Xba1

description: CNS PNET15 Constitutional Xba1

source_name: Blood, CNS PNET15 Constitutional Xba1


title: WDT-UMP LB05-397 311910

description:
WDT-UMP.2L vs WDT-UMP.2S
Date:2007/05/09

tag: label

value: lesional (WDTUMP)

value: safe (WDTUMP)


title: FV-PTC LB05-425 312115

description:
FV-PTC.3S vs FV-PTC.3L
Date:2007/05/09

tag: extract

value: safe (FVPTC)

value: lesional (FVPTC)


title: C-PTC-wt LB05-583 312050

description:
C-PTC-wt.1S vs C-PTC-wt.1L
Date:2007/05/09

tag: sample

value: safe (CPTC)

value: lesional (CPTC)


title: PB4 Xba1

description: PB4 Xba1

source_name: Brain Tumour, PB4 Xba1

value: 15 months

value: Pineal


title: H9_d15_hepatic differentiated_2

value: WAO9 human embryonic stem cells

value: subjected to a hepatic differentiation protocol


title: CNS PNET12 Xba1

description: CNS PNET12 Xba1

source_name: Brain Tumour, CNS PNET12 Xba1

value: Cerebral and Posteria Fossa


title: H9_d15_hepatic differentiated_3


title: WDT-UMP LB05-397 312117

description:
WDT-UMP.2S vs WDT-UMP.2L
Date:2007/05/09

tag: subject

value: Thyroid


title: H9_d5_hepatic differentiated_3


title: FTC LB05-572 312029

description:
FTC.2S vs FTC.2L
Date:2007/05/09

tag: disease

value: safe (FTC)

value: lesional (FTC)


title: CNS PNET13 Xba1

description: CNS PNET13 Xba1

source_name: Brain Tumour, CNS PNET13 Xba1

value: male


title: WDT-UMP LB05-582 312026

description:
WDT-UMP.4S vs WDT-UMP.4L
Date:2007/05/09


title: C-PTC-wt LB05-583 312028

description:
C-PTC-wt.1L vs C-PTC-wt.1S
Date:2007/05/09


title: H9_d10_hepatic differentiated_1


title: H9_d10_hepatic differentiated_3


title: H9_d15_hepatic differentiated_1


title: H9_d10_hepatic differentiated_2


title: WDT-UMP LB05-582 312025

description:
WDT-UMP.4L vs WDT-UMP.4S
Date:2007/05/09


title: H9_d5_hepatic differentiated_2

source_name: WAO9 human embryonic stem cells


title: PB3 Constitutional Xba1

description: PB3 Constitutional Xba1

source_name: Blood, PB3 Constitutional Xba1

value: female

value: 13 months


title: CNS PNET10 Xba1

description: CNS PNET10 Xba1

source_name: Brain Tumour, CNS PNET10 Xba1

value: 10 months

value: Frontal Lobe


title: H9_d5_hepatic differentiated_1


title: PB4 Constitutional Xba1

description: PB4 Constitutional Xba1

source_name: Blood, PB4 Constitutional Xba1


title: PB3 Xba1

description: PB3 Xba1

source_name: Brain Tumour, PB3 Xba1


title: C-PTC-mut LB06-066 310490

description:
C-PTC-mut.2 S vs C-PTC-mut.2 L
Date:2007/05/03

source_name: C-PTC-mut.2 S

value: C-PTC-mut.2 S

value: safe (classic papillary carcinoma)

source_name: C-PTC-mut.2 L

value: C-PTC-mut.2 L

value: lesional classic papillary carcinoma)


title: C-PTC-mut LB05-590 312195

description:
C-PTC-mut.1 L vs C-PTC-mut.1 S
Date:2007/05/03

source_name: C-PTC-mut.1 L

value: C-PTC-mut.1 L

value: lesional (C-PTC- mut)

source_name: C-PTC-mut.1 S

value: C-PTC-mut.1 S

value: safe tissue (C-PTC-mut)


title: CNS PNET44 HindIII

description: CNS PNET44 HindIII

source_name: Brain Tumour, CNS PNET44 HindIII

value: Parietal Lobe


title: CNS PNET9 Xba1

description: CNS PNET9 Xba1

source_name: Brain Tumour, CNS PNET9 Xba1


title: FT-UMP LB04-008 312191

description:
FT-UMP S vs FT-UMP L
Date:2007/05/09

source_name: FT-UMP S

value: FT-UMP S

value: Thyroid

value: safe (FTUMP)

source_name: FT-UMP L

value: FT-UMP L

value: lesional (FTUMP)


source_name: Blood, CNS PNET9 and CNS PNET10 Constitutional Xba1

value: female


title: PB2 Xba1

description: PB2 Xba1

source_name: Brain Tumour, PB2 Xba1

value: male

value: 12 months

value: Pineal


title: CNS PNET42 HindIII

description: CNS PNET42 HindIII

source_name: Brain Tumour, CNS PNET42 HindIII

value: 148 months

value: Frontal and Parietal Lobes


title: FT-UMP LB04-008 312192

description:
FT-UMP L vs FT-UMP S
Date:2007/05/09


title: WDT-UMP LB05-473 312112

description:
WDT-UMP.3L vs WDT-UMP.3S
Date:2007/05/09

value: lesional (WDTUMP)

value: safe (WDTUMP)


title: FV-PTC LB05-425 312113

description:
FV-PTC.3L vs FV-PTC.3S
Date:2007/05/09

value: lesional (FVPTC)

value: safe (FVPTC)


title: healthy male M(35)

city: Toronto

first: Rosanna

last: Weksberg

address: 555 University Ave.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

description: sample: M(35); age-match to F(33)

data_processing: The data were normalised using average normalisation in BeadStudio, Methylation Module 3.2

source_name: healthy male

label_protocol: Genomic sample not directly labeled. Detection involves extension of bead-bound probe with a single fluorescent nucleotide.

extract_protocol: Genomic DNA was extracted using phenol-chloroform and Phase Lock Gel according to protocol provided by Eppendorf

treatment_protocol: Genomic DNA was sodium-bisulfite treated using Epitect Bisulfite Kit according to protocol provided by Qiagen

value: whole blood lymphocytes

tag: sex

tag: age (yrs)


title: PB8 HindIII

description: PB8 HindIII

source_name: Brain Tumour, PB8 HindIII

value: 168 months


title: PB1 Xba1

description: PB1 Xba1

source_name: Brain Tumour, PB1 Xba1

value: 6 months


title: healthy male M(16)

description: sample: M(16); age-match to F(16)


title: C-PTC-wt LB05-338 312111

description:
C-PTC-wt S vs C-PTC-wt L
Date:2007/05/09

source_name: C-PTC-wt S

value: C-PTC-wt S

value: Thyroid

value: safe (CPTC)

source_name: C-PTC-wt L

value: C-PTC-wt L

value: lesional (CPTC)


title: CNS PNET40 HindIII

description: CNS PNET40 HindIII

source_name: Brain Tumour, CNS PNET40 HindIII

value: male

value: 142 months

value: Hemispheric and Lateral Ventricle


title: healthy male M(19)

description: sample: M(19); age-match to F(21)


title: healthy male M(14)

description: sample: M(14); age-match to F(15)


title: Flag-HA-TEAD4 Duplicate 2/2 array 1

city: Illkirch

first: Celine

last: Keime

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

hyb_protocol: 5µg of Cy3 Labeled Input DNA was combined with 5µg of Cy5 ChIP-DNA and the mix was hybridized to the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent) for 40 hours at 65 degrees in the Agilent hybridization oven rotating at 20rpm. The arrays were washed and processed according to Agilent’s Mammalian ChIP-on-chip Protocol (Version 9.1, August 2006).

scan_protocol: Arrays were scanned on at 5-micron resolution using the Agilent G2505B Scanner and data were extracted using Feature Extraction software v9.1 with ChIP-v1_95_May07 protocol.

data_processing: Raw array data were processed with Agilent's ChIP Analytics software v1.3 following Agilent G4477AA ChIP Analytics 1.3 User Guide

source_name: C2C12 myoblasts

label_protocol: Input DNA (4µg) was labelled with Cy3 dye and ChIP-DNA (4µg) was labelled with Cy5 using Invitrogen’s BioPrime Array CGH Genomic Labeling System (18095-012) as detailed in the Agilent Mammalian ChIP-on-chip Protocol (Version 9.1, August 2006).

growth_protocol: C2C12 cells were cultured in DMEM with 10% FCS and differentiated by replacing growth medium with differentiation medium containing 2% horse serum

extract_protocol: Cells were crosslinked with formaldehyde 0.4% for 10 min at room temperature and the reaction was stopped by adding glycine to final concentration 0.2M for 10 minutes at room temperature. Fixed cells were rinsed twice with PBS and resuspended in lysis buffer (10 mM EDTA pH 8, 50 mM Tris-HCl pH 8, SDS 1 %). Lysate was sonicated 30 min (30 sec on / 30 sec off) in Diagenode water bath-sonicator and centrifuged at 14000 rpm for 10 min. The cleared supernatant was used immediately in ChIP experiments or stored at -80°C. ChIP was performed  by standard methods as described in the publication.

treatment_protocol: C2C12 cells were infected with a retrotiviral vector expressing Flag-HA-Tagged TEAD4 or with empty control vector and selected in the continouos presence of puromycin. Infected cell populations were then differentiated for 5 days in DMEM medium with 2% horse serum and fixed in 0.4% formaldehyde.

tag: cell line

value: C2C12 cell derived myotubes

tag: sample type

value: Flag-immunoprecipitated formaldehyde fixed chromatin

tag: antibody

value: anti-Flag

value: Formaldehyde fixed chromatin - input DNA


source_name: Blood, CNS PNET38 and CNS PNET39 Constitutional HindIII

value: 141 months


title: ADENOMA LB06-174 312187

description:
ADENOMA.4S vs ADENOMA.4L
Date:2007/05/09

value: safe (adenoma)

value: lesional (adenoma)


title: CNS PNET39 HindIII

description: CNS PNET39 HindIII

source_name: Brain Tumour, CNS PNET39 HindIII

value: Frontal Lobe


title: Flag-HA Control array 1

value: Flag-immunoprecipitated Formaldehyde fixed chromatin


title: Flag-HA-TEAD4 Duplicate 1/2 array 1


title: PB7 HindIII

description: PB7 HindIII

source_name: Brain Tumour, PB7 HindIII

value: 132 months

value: Pineal


title: WDT-UMP LB05-473 312110

description:
WDT-UMP.3S vs WDT-UMP.3L
Date:2007/05/09

value: Thyroid

value: safe (WDTUMP)

value: lesional (WDTUMP)


title: FT-UMP LB05-329 312107

description:
FT-UMP.3L vs FT-UMP.3S
Date:2007/05/09

value: lesional (FTUMP)

value: safe (FTUMP)


source_name: Blood, CNS PNET35 and CNS PNET36 Constitutional HindIII

value: male

value: 122 months


title: healthy male M(12)

description: sample: M(12); age-match to F(12)

value: whole blood lymphocytes


title: healthy male M(10)

description: sample: M(10); age-match to F(10)


title: healthy male M(7)_2

description: sample: M(7)_2; age-match to F(8)_2


title: slide 11 - Hyp Quin

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

institute: University of Ottawa

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline, and;
2)  0.6% saline (control) or quinpirole (LY 171555) 2 ug/g in 0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #11

hyb_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

scan_protocol: Microarrays were scanned at full speed 10 micron resolution using the ScanArray 5000 XL system (Packard Biosciences/PerkinElmer) using both red and blue lasers. Images were obtained with ScanArray Express software using automatic calibration sensitivity varying PMT gain (PMT starting at 65% for Cy5 and 70% for Cy3) with fixed laser power at 80% and the target intensity set for 90%.

data_processing: Microarray images were analyzed using QuantArray (Packard Biosciences/PerkinElmer) and raw signal intensity values were obtained for duplicate spots of genes. Normalization was performed using LOWESS and GPA methods.

organism: Carassius auratus

source_name: control

extract_protocol: RNA was isolated with the TRIzol reagent (Invitrogen, Burlington, ON, Canada) per the manufacturer's protocol.  Samples were treated with DNase on-column in an RNeasy Mini Plus kit (Qiagen, Mississauga, ON, Canada).  RNA quantity was evaluated using the NanoDrop.  RNA integrity was evaluated using the BioAnalyzer (Agilent);   RIN for each sample was > 8.4.

tag: Sexually mature (mid-May) female adult goldfish received 2 injections at 5 uL/g body weight:

tag: 1) 0.1% DMSO in 0.6% saline, and;

tag: 2) 0.6% saline

tag: Hypothalamus tissue was extracted 5h post-injection.

source_name: quinpirole 2 ug/g

tag: 2) quinpirole (LY 171555) 2 ug/g in 0.6% saline


title: healthy male M(7)_1

description: sample: M(7)_1; age-match to F(8)_1

tag: tissue