title: Vibrio vulnificus SmcR biofilm cell transcriptome analysis 3

city: Seoul

first: Seung Min

last: Kim

address: 1 Gwanakro

institute: Seoul National University

description: WT-3 vs. KS15-3

hyb_protocol: 1) Activate slide in pre-Hybridization buffer for 30-60 min at 42°C. 2) Wash the slide with D.W.. 3) Dry the slide with centrifugation (700 rpm) for 5 min. 4) Add the 35 µl of hybridization buffer into the dried labeled sample tube. 5) Denaturation (95°C, 5min). 6) Centrifuge for 2 min at 11,000 rpm. 7) Mix two labeled samples well. 8) Attach the MAUI lid (heating 65°C). 9) Inject the labeled samples.  10) Sealing.  11) Mix in Lid + slide MAUI Hybridization system (42°C, 16 hrs).

scan_protocol: After hybridization, the arrays were washed, dried and scanned using Axon’s GenePix 4000B DNA microarray scanner and GenePix Pro 6.0 (Axon Instruments, Foster City, CA).

data_processing: Data from three independent experiments were normalized and then analyzed using the Agilent's GeneSpring Software.

organism: Vibrio vulnificus

source_name: wild-type biofilm cell

label_protocol: Reactions were performed with an GT's methods and Invitrogen's Bioprime DNA labeling kit (Invitrogen, Austin, TX) according to the manufacturer's procedures with 20 µg of total RNA. The equal amounts of the labeled cDNA were combined.

growth_protocol: The V. vulnificus strains were grown in fresh Defined minimal medium for Vibrio fischeri (50 mM Tris-HCl (pH7.2), 50 mM MgSO4, 10 mM CaCl2, 300 mM NaCl, 10 mM KCl, 0.333 mM K2HPO4, 18.5 mM NH4Cl, 32.6 mM Glycerol).

extract_protocol: Total cellular RNA from the V. vulnificus strains grown for 15 hr was isolated using an RNeasy® Mini Kit (Qiagen, Valencia, CA) and any residual DNA was removed using DNase I (NEB, Ipswich, MA).

tag: genotype/variation

value: wild type

source_name: smcR mutant biofilm cell

value: smcR mutant


title: C002_Control_F_87

status: Public on Dec 31 2011

type: RNA

city: Stevenage

first: Julie

last: Huxley-Jones

state: Hertfordshire

address: Gunnels Wood Road

department: Computational Biology

country: United Kingdom

institute: GlaxoSmithKline Pharmaceuticals

hyb_protocol: For each batch, 10ug total RNA was processed to Biotin-labeled cRNA and hybridized to HG-U133_Plus_2.0 GeneChips in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,).

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and fluorescence intensity for each feature of the array was obtained by using GeneChip Operating Software (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Brain BA22 post-mortem control

extract_protocol: Total RNA was extracted from frozen BA22 using a Polytron type homogenizer (YellowLine DI 25 Basic) and TriZol reagent (Invitrogen, Paisley, UK) in a ratio of 1 ml of TriZol to 20 mg of tissue. RNA was further purified using RNeasy mini-columns (Qiagen, Valencia, CA, USA) including on-column DNAse-1 step and elution in water. Although pH was analysed in brain lysates using a pH meter, this was not considered to be rigorous enough to exclude or include samples and instead the RNA integrity number (RIN) was used to assess the quality of the RNA as the primary inclusion criterion. The quantity of extracted RNA was determined by spectrophotometry and quality was assessed using an Agilent 2100 Bioanalyzer (South Plainfield, NJ, USA) to determine the RIN. Based on the RIN, samples were classified into three quality groups—pass (RIN >7.0); borderline (RIN 6.0–7.0); fail (RIN<6.0). Following classification, there were 41 pass (RIN range of samples 7.0–9.0: average=7.7), 16 borderline (RIN range of samples 6.0–6.9; average=6.4) and 5 fail samples. Samples in the fail category were excluded from the study, and the remaining samples were randomized into four batches, containing an equal number of schizophrenic/control and male/female samples, for target generation and hybridization.

tag: gender

value: Female

tag: age

tag: post-mortem delay

tag: ph

tag: disease state

value: control

tag: tissue

value: superior temporal cortex (Brodmann Area 22, BA22)


title: Vibrio vulnificus SmcR biofilm cell transcriptome analysis 2

country: South Korea

description: WT-2 vs. KS15-2


title: Vibrio vulnificus SmcR biofilm cell transcriptome analysis 1

description: WT-1 vs. KS15-1


title: Blood genomic DNA in patient with gastric cancer HRGC-19

type: genomic

city: daejeon

first: Tae-Wook

last: Kang

address: 111 Gwahangno, Yuseong-gu

institute: KRIBB

hyb_protocol: Standard Affymetrix protocol (The labeled DNA was hybridized to a Genomic-Wide Human SNP Array 6.0 for 16-18 hours in a rotating oven at 50℃ and 60 rpm.)

scan_protocol: Standard Affymetrix protocol (The SNP Array 6.0 was scanned with the Affymetirx GeneChip Scanner 3000 using Affymetrix GeneChip Operating Software (GCOS; version 1.4))

data_processing:
Standard Affymetrix protocol (Signal intensity data was analyzed by the Dynamic Model (DM) algorithm. A contrast QC of greater than or equal to 0.4 should be used to determine whether a sample should be repeated or used for downstream ananlysis.)
Standard Affymetrix protocol (Genotypes were called by the Affymetrix Genotyping Console Software (GTC; version 3.0.1) based on the Birdseed version 2 algorithm.

molecule: genomic DNA

source_name: Blood DNA in patient with gastric cancer

label_protocol: Standard Affymetrix protocol (The fragmented DNA was labeled using DNA Labeling Reagent and TdT enzyme for 4.25 hours at 37℃.)

extract_protocol: Genomic DNA was extracted from blood samples using the Qiagen DNeasy Kit according to standard instructions.

value: gastric cancer

value: female

value: blood

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-20

tag: disease state

tag: gender

tag: tissue

tag: tsi, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-16

value: male

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: E.grandis_Clone A_Ramet 2_Leaf

city: Porto Alegre

first: Giancarlo

last: Pasquali

state: RS

address: Av. Bento Gonçalves, 9500 - Pr. 43.431 - Lab. 212

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: G02 - Total RNA extracted from mature leaf blades of 4-years-old, field-grown Eucalyptus grandis tree, genotype A, ramet 2, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

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

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

data_processing: The raw data (.ftr file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Eucalyptus grandis

source_name: mature leaf blades, field-grown tree

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

growth_protocol: Differentiating xylem tissues and mature leaves were collected from 4-year-old, field-grown E. grandis and E. globulus trees located at Aracruz Celulose S.A. (Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil).

extract_protocol: Total RNA was extracted using the PureLink Reagent (Invitrogen) according to manufacturer´s miniprep protocol.

treatment_protocol: Xylem was collected by scraping the exposed vascular tissue after the removal of the 0.5-1 cm-tick stem bark. Two lines of genetically unrelated matrixes were chosen for both species and each line was represented by two clones (biological duplicates), therefore completing 4 xylem samples for E. grandis, and 4 xylem samples for E. globulus. From both clones of one of the E. grandis  lines, mature leaves were also collected. To minimize the proportion of primary xylem mainly located in the main veins of leaves, only leaf blades without the central vein of mature leaves were used for this study. Tissue samples were immediately frozen in liquid nitrogen and stored at -80 °C.

tag: genotype

value: E. grandis clone A

tag: clonal individual

value: Ramet 2


title: E.grandis_Clone A_Ramet 1_Leaf

description: G01 - Total RNA extracted from mature leaf blades of 4-years-old, field-grown Eucalyptus grandis tree, genotype A, ramet 1, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

value: Ramet 1


title: JSC-1

status: Public on Dec 30 2011

city: Pittsburgh

first: Lindsay

middle: Renee

last: Dresang

state: PA

address: 5117 Centre Ave, Hillman Cancer Res. Pav. 1.8

department: Cancer Virology Program

country: USA

institute: University of Pittsburgh

description: JSC-1: KSHV-positive, EBV-positive

hyb_protocol: Equal masses of Cy3- and Cy5-labeled samples were co-hybridized to microarrays.

scan_protocol: Scanned on an Agilent G2505B scanner.  Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction software (version 9.1.3.1) was used to generate normalized, background subtracted signal values ([g/r]ProcessedSignal).  These values were used for log ratios of Cy3 to Cy5: Log10 (gProcessedSignal / rProcessedSignal).  Saturated flag information was maintained for downstream analysis.  LIMMA in-array analysis was performed using triplicate features per unique probe sequence after normalizing to Cy3 and Cy5 signal values to mean signal values of cellular housekeeping genes (ACTA1, GAPDH, and TUBA1B).  The P-values for differential expression between the two channels are computed with Limma using the three triplicate probes per feature, and then adjusted for multiple testing according to Benjamini and Hochberg’s false discovery rate method (Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. JR Statist Soc B 1995, 57(1):289-300).  Only adjusted P-values are indicated with the raw data, while the remaining calculations are available in the supplement of the associated article.  Cross-array LIMMA analysis is also reported in the supplement of the associated article.

organism:
Homo sapiens
human gammaherpesvirus 4
Human gammaherpesvirus 8

source_name: JSC-1: KSHV-positive, EBV-positive Primary Effusion Lymphoma

label_protocol: 150 ng of RNA was reverse transcribed with an oligo d(T) promoter primer into cDNA using the Agilent Quick Amp Kit, Two Color per manufacturer's protocol.  The cDNA was then transcribed into cRNA containing Cy3 or Cy5 using Agilent T7 RNA polymerase.

growth_protocol: Cells were grown in Roswell Park Memorial Institute formulation 1640 media with 10% fetal bovine serum.  Growth medium is supplemented with 200 U/mL penicillin and 200 μg/mL streptomycin.  Cells were grown at 37 °C with a 5% CO2 humidified atmosphere.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) as described [Chomczynski P, Sacchi N: The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987, 162(1):156-159].  RNA was precipitated using the nucleating agent linear acrylamide (Ambion, Austin, TX) as described [Gaillard C, Strauss F: Ethanol precipitation of DNA with linear polyacrylamide as carrier. Nucleic Acids Res 1990, 18(2):378].  RNA samples were treated with Turbo DNase (Ambion, Austin, TX) to remove contaminating genomic DNA as per manufacturer's instructions.

treatment_protocol: No additional treatments

tag: cell type

tag: cell line

tag: treatment

value: Untreated = standard tissue culture conditions

tag: replicate

tag: array

source_name: BJAB: EBV-negative, KSHV-negative Burkitt Lymphoma

value: BJAB


title: BC-1

description: BC-1: KSHV-positive, EBV-positive

source_name: BC-1: KSHV-positive, EBV-positive Primary Effusion Lymphoma

value: EBV-negative, KSHV-negative Burkitt Lymphoma


title: BC-1 tech rep

description: BC-1: KSHV-positive, EBV-positive, technical replicate

value: KSHV-positive, EBV-positive Primary Effusion Lymphoma


title: BC-1 lytic tech rep

description: BC-1: KSHV-positive, EBV-positive, lytic, technical replicate

value: Lytic-induction = tissue culture medium supplemented with 20ng/mL 12-O-tetradecanoylphorbol-13-acetate (TPA) + 0.25mM sodium butyrate (NaB) for 48hrs


title: BC-1 lytic

description: BC-1: KSHV-positive, EBV-positive, lytic


title: MCF-7 cells, biological rep2

city: Columbus

first: Pei-Yin

last: Hsu

state: OH

address: BRT836, 460W 12th Ave

institute: OSU

description: Gene expression data from MCF-7 Ctrl-2 sample.

hyb_protocol: cRNA were hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays

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

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

source_name: MCF-7 cells

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

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

value: breast cancer cell line

value: ERa-positive


title: BJAB

description: BJAB: EBV-negative, KSHV-negative


title: MCF-7 cells, biological rep1

description: Gene expression data from MCF-7 Ctrl-1 sample.


title: BCBL-1

description: BCBL-1: KSHV-positive, EBV-negative

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: BCBL-1: KSHV-positive, EBV-negative Primary Effusion Lymphoma


title: Blood genomic DNA in patient with gastric cancer HRGC-18

tag: disease state

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: MutuIII

description: MutuIII: EBV-positive, KSHV-negative

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: MutuIII: EBV-positive, KSHV-negative Burkitt Lymphoma

tag: cell type

value: MutuIII


title: E.grandis_Clone A_Ramet 1_Xylem

description: G03 - Total RNA extracted from the vascular tissues of the trunk of 4-years-old, field-grown Eucalyptus grandis tree, genotype A, ramet 1, planted at Hortoflorestal Barbanegra, Eldorado do Sul, RS, Brazil.

source_name: trunk vascular tissue (xylem), 4-years-old, field-grown tree

tag: genotype

tag: clonal individual


title: Blood genomic DNA in patient with gastric cancer HRGC-14

tag: gender

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-11

tag: disease state

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-15

tag: gender

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-10

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-8

tag: disease state

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-13

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity

tag: saha, raw drug sensitivity


title: Blood genomic DNA in patient with gastric cancer HRGC-9

tag: gender

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity


title: Blood genomic DNA in patient with gastric cancer HRGC-17

tag: tissue

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: Blood genomic DNA in patient with gastric cancer HRGC-12

tag: disease state

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity


title: Blood genomic DNA in patient with gastric cancer HRGC-7

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity


title: European-American ID80

city: Montreal

first: luis

last: Barreiro

state: Quebec

address: 3175 Chemin de la Côte Sainte-Catherine

country: Canada

institute: luis

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: GenomeStudio software

label: C-Bio and A-DNP

source_name: Blood

label_protocol: standard Illumina protocol

extract_protocol: DNA from each of the blood donors was extracted using the PureGene DNA extraction kit.

tag: gender

value: Male

tag: ethnicity

value: European-American

tag: ID


title: Blood genomic DNA in patient with gastric cancer HRGC-4

value: gastric cancer

tag: tissue

tag: tax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: saha, raw drug sensitivity

tag: saha.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: pxd, raw drug sensitivity

tag: pxd.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cg2, raw drug sensitivity


title: European-American ID83


title: European-American ID74


title: Blood genomic DNA in patient with gastric cancer HRGC-6

tag: disease state

tag: tsi, raw drug sensitivity

tag: tsi.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: fu, raw drug sensitivity

tag: fu.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: oxa, raw drug sensitivity

tag: cg2.30, binary data (i.e. >= 30 or < 30) at 30% cutoff


title: European-American ID91

tag: gender


title: European-American ID90

tag: ethnicity


title: European-American ID86

tag: ID


title: Blood genomic DNA in patient with gastric cancer HRGC-5

tag: tissue

tag: oxa.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: dtax, raw drug sensitivity

tag: dtax.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: cdp, raw drug sensitivity

tag: cdp.30, binary data (i.e. >= 30 or < 30) at 30% cutoff

tag: tax, raw drug sensitivity


title: European-American ID84


title: European-American ID87


title: European-American ID73


title: European-American ID81


title: European-American ID85


title: European-American ID88


title: European-American ID75


title: European-American ID78


title: European-American ID72


title: European-American ID77


title: European-American ID82


title: European-American ID59


title: European-American ID70


title: European-American ID69


title: European-American ID68


title: European-American ID20


title: European-American ID53


title: European-American ID55


title: European-American ID71


title: European-American ID57


title: European-American ID44


title: European-American ID54


title: European-American ID46


title: European-American ID41


title: European-American ID49


title: European-American ID42


title: European-American ID51


title: European-American ID30


title: European-American ID43


title: European-American ID47


title: European-American ID40


title: European-American ID31


title: European-American ID32


title: European-American ID50


title: European-American ID45


title: European-American ID38


title: European-American ID33


title: European-American patient 10 00676(053)

city: Oklahoma City

first: Joshua

middle: O.

last: Ojwang

state: OK

address: 825 NE 13th Street

department: Arthritis and Immunology

institute: Oklahoma Medical Research Foundation

description: Total RNA was isolated using Trizol (Invitrogen)

hyb_protocol: The microarrays were hybridized a fluorescent dye using miRXplore Microarray product (Miltenyi Biotec)and the kit contains 850 human precursor miRNAs. The miRNA labeling protocol employ Cy5 dye (Amersham Pharmacia Biotech) for dyeing. In general, control sampes are labeled with Hy3 and experimental samples are labeled with Hy5.

scan_protocol: The hybridized slides were scanned (Agilent Technologies)

data_processing: Mean signal and mean local background intensities were obtained for each spot of microarray image using ImaGene software (Biodiscovery) Low-qualities spots were flagged and excluded from data analysis. The unflagged spots were analyzed with the PIQOR Analyzer software (Lowess, Miltenyi Biotec). The net signal intensity, data normalization (miRControl3 method; Miltenyi Biotec), and calculation of the Hy5/Hy3 ratios for the species of interest is recorded.

source_name: Female (Controls)

label_protocol: MiRNA were labaled using 2 micrograms of total RNA and Exiqon miRCURY labeling Kit (Miltenyi Biotec) according to the manufacturers' instructions.

extract_protocol: Two to 10 microgram of total RNA were isolated from cell suspension of 1 million EBV-transformed B cells from idividual lines using Trizol-based (Invitrogen) method according to the manufacturers' instrcuctions. The concentration and quatity of RNA were measured by UV absorbance at 260 and 280 nm and checked by gel electrophoresis. RNA samples were quality checked via the Agilent 2100 Bioanalyzer (Agilent Technologies). The results of the Bioanalyzer run were visualized in a gel image and electropherogram. The RNA integrity Number (RIN) was between 7.2 and 10.

tag: sample type

value: Female (Controls)

value: female

tag: cell type

value: PBMC

tag: disease state

value: control

source_name: Female (Cases)

value: Female (Cases)

value: EBV transformed B cell

value: lupus nephritis


title: European-American ID52

value: blood


title: European-American patient 9 00676(072)


title: European-American ID29


title: European-American patient 4 00676(067)


title: European-American patient 5 00676(068)


title: European-American patient 7 00676(070)


title: European-American ID39


title: European-American patient 6 00676(069)


title: European-American patient 3 00676(066)


title: European-American ID24


title: European-American ID28


title: European-American patient 2 00676(065)


title: European-American patient 8 00676(071)


title: African-American patient 10 00676(063)

value: African-American


title: African-American patient 8 00676(061)


title: African-American patient 6 00676(058)


title: European-American patient 1 00676(064)


title: African-American patient 9 00676(062)


title: European-American ID13


title: African-American patient 7 00676(060)


title: European-American ID26


title: European-American ID27


title: African-American patient 4 00676(056)


title: European-American ID25


title: African-American patient 2 00676(054)


title: European-American ID16


title: African-American patient 3 00676(055)


title: European-American ID17


title: African-American patient 1 00676(052)


title: European-American ID11


title: European-American ID23


title: European-American ID14


title: VRK1-deficent mutant rep4

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

description: Biological replicate 4 of 4

hyb_protocol: Standard Agilent procedures.

scan_protocol: Scanned on Agilent Scanner G2505B US45103124 using one color settings, and images were quantified using Agilent Feature Extraction Software v. 9.5.3.1

data_processing: Agilent Feature Extraction Software v. 9.5.3.1 with protocol GE1-v1_95  was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: testes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was labelled from 0.5 µg total RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by purification with RNeasy Mini Kit (Qiagen) and quantification by Nano Drop 100 spectrophotometer.

extract_protocol: Total RNA was prepared from testes of postnatal day 8 using the Trizol reagent (Invitrogen) following the manufacturer's instructions.

value: male

value: testis

tag: genotype

value: VRK1-deficent mutant


title: Wild type rep2

description: Biological replicate 2 of 4

value: wild type


title: European-American ID22


title: VRK1-deficent mutant rep3

description: Biological replicate 3 of 4


title: VRK1-deficent mutant rep2

description: Biological replicate 2 of 4


title: Wild type rep1

description: Biological replicate 1 of 4


title: Wild type rep3

description: Biological replicate 3 of 4


title: VRK1-deficent mutant rep1

description: Biological replicate 1 of 4


title: African-American patient 5 00676(057)


title: Wild type rep4

description: Biological replicate 4 of 4


title: European-American ID10


title: European-American ID12


title: European-American ID9


title: European-American ID3


title: European-American ID6


title: European-American ID2


title: European-American ID4


title: European-American ID5


title: European-American ID8


title: Rab25 FBS treated 2

city: Houston

first: Kwai Wa

last: Cheng

address: 1515 Holcombe Blvd.

department: Systems Biology

institute: UT-MD Anderson Cancer Center

description: A2780 Rab25 F2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 48C on Affy. GeneChips were washed and stained on the Affymetrix High-throughput array platform

scan_protocol: GeneChips were scanned using the Affymetrix High Throughput (HT) scanner. The software program then converts these .dat files into mini .cel files and then into composite cel files where the information is analyzed in the Affymetrix GCOS 1.2 software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. RMA with default parameters was used to create a final gene expression data. We used BRB array Tool V.3 to create the RMA and log 2 value.

source_name: Rab25, 24h FBS expt 2

growth_protocol: pcDNA or Rab25 transfected cells were maintained in 5% RPMI 1640

extract_protocol: Cells were collected after two-washings with PBS. The cell pellets were immediately frozen in liquid nitrogen, and stored until use. Total RNA was extracted using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Cells were serum straved for 8h before addition of growth factor EGF (10ng/ml) , IGF (10ng/ml), TGF beta (5ng/ml) and FBS (5%) for 8h (expt 1) or 24h (expt 2)

tag: cell line


title: Rab25 IGF treated 1

description: A2780 Rab25 I1

source_name: Rab25, 24h IGF expt 1


title: Rab25 TGF beta treated 2

description: A2780 Rab25 T2

source_name: Rab25, 24h TGF expt 2


title: Rab25 FBS treated 1

description: A2780 Rab25 F1

source_name: Rab25, 24h FBS expt 1


title: Rab25 IGF treated 2

description: A2780 Rab25 I2

source_name: Rab25, 24h IGF expt 2


title: Rab25 EGF treated 2

description: A2780 Rab25 E2

source_name: Rab25, 24h EGF expt 2


title: 60% breast cancer cell line HCC38 genomic DNA, 40% paired B lymphoblastoid cell line HCC38-BL genomic DNA

city: Boston

first: Qiyuan

last: Li

address: 44 Binney Street

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm.

label: Biotin

source_name: Triple-negative breast cancer cell line HCC38, paired B lymphoblastoid cell line HCC38-BL

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Triple negative invasive ductal carcinoma


title: Rab25 EGF treated 1

description: A2780 Rab25 E1

source_name: Rab25, 24h EGF expt 1


title: Rab25 Control 2-2

description: A2780 Rab25 C4

source_name: Rab25, 8h serum straved control 2, expt 2


title: Rab25 Control 2-1

description: A2780 Rab25 C3

source_name: Rab25, 8h serum straved control 1, expt 2


title: 20% breast cancer cell line HCC38 genomic DNA, 80% paired B lymphoblastoid cell line HCC38-BL genomic DNA

description: Hybridized to 250K_Nsp


title: 100% paired B lymphoblastoid cell line HCC1143-BL genomic DNA

description: Hybridized to 250K_Nsp

source_name: Paired B lymphoblastoid cell line HCC1143-BL


title: 40% breast cancer cell line HCC38 genomic DNA, 60% paired B lymphoblastoid cell line HCC38-BL genomic DNA

description: Hybridized to 250K_Nsp


title: 80% breast cancer cell line HCC38 genomic DNA, 20% paired B lymphoblastoid cell line HCC38-BL genomic DNA

description: Hybridized to 250K_Nsp


title: 100% paired B lymphoblastoid cell line HCC38-BL genomic DNA

description: Hybridized to 250K_Nsp

source_name: Paired B lymphoblastoid cell line HCC38-BL


title: 80% breast cancer cell line HCC1143 genomic DNA, 20% paired B lymphoblastoid cell line HCC1143-BL genomic DNA

description: Hybridized to 250K_Nsp

source_name: Triple-negative breast cancer cell line HCC1143, paired B lymphoblastoid cell line HCC1143-BL


title: pcDNA TGF beta treated 2

description: A2780 pcDNA T2

source_name: pcDNA, 24h TGF expt 2


title: 40% breast cancer cell line HCC1143 genomic DNA, 60% paired B lymphoblastoid cell line HCC1143-BL genomic DNA

description: Hybridized to 250K_Nsp


title: pcDNA TGF beta treated 1

description: A2780 pcDNA T1

source_name: pcDNA, 24h TGF expt 1


title: European-American ID7

source_name: Blood

value: Male


title: 100% breast cancer cell line HCC38 genomic DNA

description: Hybridized to 250K_Nsp

source_name: Triple-negative breast cancer cell line HCC38


title: 100% breast cancer cell line HCC1143 genomic DNA

description: Hybridized to 250K_Nsp

source_name: Triple-negative breast cancer cell line HCC1143


title: 60% breast cancer cell line HCC1143 genomic DNA, 40% paired B lymphoblastoid cell line HCC1143-BL genomic DNA

description: Hybridized to 250K_Nsp


title: pcDNA FBS treated 2

description: A2780 pcDNA F2

source_name: pcDNA, 24h FBS expt 2


title: pcDNA EGF treated 1

description: A2780 pcDNA E1

source_name: pcDNA, 24h EGF expt 1


title: pcDNA FBS treated 1

description: A2780 pcDNA F1

source_name: pcDNA, 24h FBS expt 1


title: telencephalon from marine population LITC animal #5

city: Palo Alto

first: Haili

last: Zhang

state: CA

address: 279 Campus Dr. Beckman Center

department: Developmental Biology

institute: Stanford University

description:
Tel_LITC#5
Biological replicate 5 of 5 marine population LITC from British Columbia.

hyb_protocol: Fluorescently labeled samples were hybridized to the array using the Agilent Two-Color Microarray-Based Gene Expression analysis protocol.

scan_protocol: Arrays were scanned at the Stanford Functional Genomic Facility using an Agilent G2505B DNA microarray scanner. Images were quantified using Agilent Feature Extraction software version 9.5.

data_processing: Within-array LOESS normalization of the log2(Red mean signal/Green mean signal) values was performed using the limma package of Bioconductor 2.4, without background correction.

organism: Gasterosteus aculeatus

source_name: telencephalon, marine population LITC

label_protocol: RNA was reverse transcribed into cDNA and then Cy5- or Cy3-labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

extract_protocol: Total RNA was extracted using the MELT total nucleotide isolation system from Ambion.

value: telencephalon

tag: population

tag: age

value: 1.5 years old

source_name: whole embryo, freshwater population BEPA

value: whole embryo

value: freshwater population BEPA from Alaska

value: 7 days post-hatch

value: reference


title: Rab25 Control 1-1

description: A2780 Rab25 C1

source_name: Rab25, 8h serum straved control 1, expt 1


title: pcDNA Control 2-2

description: A2780 pcDNA C4

source_name: pcDNA, 8h serum straved control 2, expt 2


title: pcDNA Control 2-1

description: A2780 pcDNA C3

source_name: pcDNA, 8h serum straved control 1, expt 2


title: pcDNA EGF treated 2

description: A2780 pcDNA E2

source_name: pcDNA, 24h EGF expt 2


title: telencephalon from marine population LITC animal #4

description:
Tel_LITC#4
Biological replicate 4 of 5 marine population LITC from British Columbia.

tag: gender

value: female


title: telencephalon from marine population LITC animal #2

description:
Tel_LITC#2
Biological replicate 2 of 5 marine population LITC from British Columbia.


title: pcDNA Control 1-1

description: A2780 pcDNA C1

source_name: pcDNA, 8h serum straved control 1, expt 1


title: pcDNA IGF treated 1

description: A2780 pcDNA I1

source_name: pcDNA, 24h IGF expt 1


title: telencephalon from freshwater population FTC animal #5

description:
Tel_FTC#5
Biological replicate 5 of 5 freshwater population FTC from Washington State.

source_name: telencephalon, freshwater population FTC


title: 20% breast cancer cell line HCC1143 genomic DNA, 80% paired B lymphoblastoid cell line HCC1143-BL genomic DNA

description: Hybridized to 250K_Nsp

source_name: Triple-negative breast cancer cell line HCC1143, paired B lymphoblastoid cell line HCC1143-BL


title: telencephalon from marine population LITC animal #3

description:
Tel_LITC#3
Biological replicate 3 of 5 marine population LITC from British Columbia.


title: pcDNA Control 1-2

description: A2780 pcDNA C2

source_name: pcDNA, 8h serum straved control 2, expt 1


title: telencephalon from freshwater population FTC animal #4 male

description:
Tel_FTC#4
Biological replicate 4 of 5 freshwater population FTC from Washington State.


title: telencephalon from freshwater population FTC animal #2

description:
Tel_FTC#2
Biological replicate 2 of 5 freshwater population FTC from Washington State.


title: telencephalon from marine population LITC animal #1

description:
Tel_LITC#1
Biological replicate 1 of 5 marine population LITC from British Columbia.


title: A2780Dxl vs A2780 reverse labelling replicate 4

city: Sudbury

first: Baoqing

last: Guo

state: ON

address: 41 Ramsey Lake Road

department: Tumor Biology

institute: Advanced Medical Research Institute of Canada

description: technical replicate 8 of 8

hyb_protocol: Microarray hybridization process was conducted as per description by Agilent Two-clour Microarray-based gene expression Analysis

scan_protocol: After hybridization, the microarray slides were scanned by using an Agilent G2505C scanner as discribed in Agilent manual.

data_processing:
Images were quantified and background subtraction was performed using Agilent Feature Extraction Software (version A.9_5_3).
Normalized log2 ratio (Cy5/Cy3) was used to represent the ratio of test/reference. Data analysis was done using Partek Genomic suite after feature extraction.  A 3-way ANOVA model was performed by using Method of Moments (Eisenhart, 1947) as outlined below for both MCF-7 and A2780 cells:  Model: Yijkl = μ + (Cell lines)i+Dyesj+Arraysk+ εijkl  Where Yijkl represents the lth observation on the ith Cell lines jth Dyes kth Arrays   μ is the common effect for the whole experiment.  εijkl represents the random error present in the lth observation on the ith Cell lines jth Dyes kth Arrays. The errors εijkl are assumed to be normally and independently distributed with mean 0 and standard deviation δ for all measurements. Arrays is a random effect.    Fold changes of the differentially expressed genes between drug resistant and parental cells were calculated and genes with more than two-fold difference were selected with FDR at either 0.05 or 0.01. (Tamhane, Ajit C., & Dunlop, Dorothy D. 2000)

source_name: human ovarian cancer cells

label_protocol: Agilent 4×44k oligonucleotide arrays (Agilent, Product #: G4112F.) were used in our microarray experiments to compare the expression of genes between drug-selected docetaxel resistant cells and its parental cells. 500 ng of RNA  was used. Labelling was done using the Quick Amp labeling kit (Agilent, #5190-0444) as described in Agilent manual.

growth_protocol: Cells were grown in tissue culture flucks with DMEM H21 medium at 37C with 5% of CO2, and subcultured when cell density reached 80-90% confluence.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen), and quantity and quality were assessed using Agilent BioAnalyizer. 3 separate isolations with RIN at 10 were pooled together for labelling.

treatment_protocol: Cell were cultured and selected for survival in increasing doses of docetaxel as previously described (Guo B, Villeneuve DJ, Hembruff SLet al. Breast Cancer Res Treat. 2004;85(1):31-5126;27).  MCF-7 cells selected to docetaxel concentrations of  5.00nM (dose 10, MCF-7Txt10), and A2780 cells selected to terminally tolerated dose at 405 nM of docetacel were used in this microarray study.

tag: cell lines

value: docetaxel sensitive

value: docetaxel resistant


title: telencephalon from freshwater population FTC animal #3

description:
Tel_FTC#3
Biological replicate 3 of 5 freshwater population FTC from Washington State.


title: pectoral muscle from marine population LITC animal #5

description:
PecMuscle_LITC#5
Biological replicate 4 of 4 marine population LITC from British Columbia.

source_name: pectoral muscle, marine population LITC

value: pectoral muscle


title: A2780Dxl vs A2780 reverse labelling replicate 3

description: technical replicate 7 of 8


title: A2780Dxl vs A2780 reverse labelling replicate 1

description: technical replicate 5 of 8


title: A2780Dxl vs A2780 forward labelling replicate 4

description: technical replicate 4 of 8


title: A2780Dxl vs A2780 reverse labelling replicate 2

description: technical replicate 6 of 8


title: pectoral muscle from marine population LITC animal #3

description:
PecMuscle_LITC#3
Biological replicate 2 of 4 marine population LITC from British Columbia.


title: pectoral muscle from marine population LITC animal #4

description:
PecMuscle_LITC#4
Biological replicate 3 of 4 marine population LITC from British Columbia.


title: pectoral muscle from freshwater population FTC animal #4 male

description:
PecMuscle_FTC#4
Biological replicate 4 of 5 freshwater population FTC from Washington State.

source_name: pectoral muscle, freshwater population FTC


title: telencephalon from freshwater population FTC animal #1

description:
Tel_FTC#1
Biological replicate 1 of 5 freshwater population FTC from Washington State.


title: pectoral muscle from marine population LITC animal #1

description:
PecMuscle_LITC#1
Biological replicate 1 of 4 marine population LITC from British Columbia.


title: pectoral muscle from freshwater population FTC animal #5

description:
PecMuscle_FTC#5
Biological replicate 5 of 5 freshwater population FTC from Washington State.


title: A2780Dxl vs A2780 forward labelling replicate 2

description: technical replicate 2 of 8


title: pectoral muscle from freshwater population FTC animal #3

description:
PecMuscle_FTC#3
Biological replicate 3 of 5 freshwater population FTC from Washington State.


title: pectoral muscle from freshwater population FTC animal #2

description:
PecMuscle_FTC#2
Biological replicate 2 of 5 freshwater population FTC from Washington State.


title: A2780Dxl vs A2780 forward labelling replicate 3

description: technical replicate 3 of 8


title: A2780Dxl vs A2780 forward labelling replicate 1

description: technical replicate 1 of 8


title: pectoral muscle from freshwater population FTC animal #1

description:
PecMuscle_FTC#1
Biological replicate 1 of 5 freshwater population FTC from Washington State.


title: MCF-7Txt10 vs MCF-7 forward labelling replicate 2

description: technical replicate 2 of 4

source_name: human breast adenocacinoma cancer cells


title: MCF-7Txt10 vs MCF-7 forward labelling replicate 1

description: technical replicate 1 of 4


title: Control vs 2h acetic acid treatment-replicate2

city: Valencia

first: Regina

middle: Niñoles

last: Rodenes

address: Ingeniero Fausto Elio, s/n

department: Abiotic stress

country: Spain

institute: IBMCP

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.

hyb_protocol: Labeled RNA and hybridization buffer (containing desionized fomamide, SSC, Denhardt`s solution and SDS) were applied to microarrays enclosed in Arraylt hybridization cassete (TeleChem) hybridization chambers. Hybridization was done at 37º during 16 hours.

scan_protocol: Scanned using Genepix 4000B (Axon Molecular Devices, Sunnyvale CA)

data_processing: Genepix software for preliminar normalization based in Cy5/Cy3 ratio and for eliminating spots with low intensity, or saturated in both channels. Accuity software for LOWESS normalization and for selecting only those spots with value in at least three of the four replicates. Statistical analysis using SAM (Significant analysis of variance).

organism: Arabidopsis thaliana

source_name: Control plants

label_protocol: Indirect labelling using the Amminoallyl MessageAmpTMII aRNA kit (Ambion).

growth_protocol: Plants were grown for 5 days in solid MS medium, then they were transfered to liquid MS medium for 13 days.

extract_protocol: Total RNA was extracted using phenol-chloroform and subsequent lithium precipitation. Isolated RNA was purified with the RNeasy Mininikit (Quiagen).

treatment_protocol: 18 old plants were transfered to liquid MS medium (control) or liquid MS+3,5 mM acetic acid (acetic) for 2 hours.

tag: ecotype

value: Columbia

value: 18 days old

tag: treatment

value: MS medium

value: Each sample is composed of 3 plants

tag: time

value: shoot and root

source_name: Acetic acid treated plants

value: MS+ 3,5 mM acetic acid


title: liver from marine population LITC animal #4

description:
Liver_LITC#4
Biological replicate 4 of 5 marine population LITC from British Columbia.

source_name: liver, marine population LITC

tag: tissue

value: liver


title: MCF-7Txt10 vs MCF-7 reverse labelling replicate 2

description: technical replicate 4 of 4


title: liver from marine population LITC animal #5

description:
Liver_LITC#5
Biological replicate 5 of 5 marine population LITC from British Columbia.

source_name: whole embryo, freshwater population BEPA


title: liver from marine population LITC animal #3

description:
Liver_LITC#3
Biological replicate 3 of 5 marine population LITC from British Columbia.

value: male


title: Control vs 2h acetic acid treatment-replicate1

description: Biological replicate 1 of 4. Control embryonic stem cells, untreated, harvested after several passages.

value: MS+ 3.5 mM acetic acid


title: Control vs 2h acetic acid treatment-replicate3

description: Biological replicate 3 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: Control vs 2h acetic acid treatment-replicate4

description: Biological replicate 4 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: MCF-7Txt10 vs MCF-7 reverse labelling replicate 1

description: technical replicate 3 of 4


title: liver from marine population LITC animal #2

description:
Liver_LITC#2
Biological replicate 2 of 5 marine population LITC from British Columbia.

value: 1.5 years old

value: whole embryo


title: TS2

city: Worcester

first: Michael

middle: R.

last: Green

state: MA

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description: gene expression data from ts strain after 90min at 37˚C

hyb_protocol: affymetrix GeneChip Hybridization Oven 320, FS450 fluidics stations

scan_protocol: affymetrix GeneChip Scanner 3000

data_processing: The RMA method in the oligo package from Bioconductor was used in R to summarize probe level data and to normalize the dataset to remove across array variation (Irizarry et al. 2003a,b; Bolstad et al., 2003). Log  transformed data were used in subsequent analysis and plotting.

organism: Saccharomyces cerevisiae

label_protocol: affymetrix 3'IVT express Kit

growth_protocol: YPD

extract_protocol: RNA extraction (Schmitt, 1990)

treatment_protocol: Yeast culture were shift from 30˚C to 37˚C for 60min, 90min or 120min

tag: genotype/variation

value: MATa ura3-52 lys2-801 ade2-101 trp1∆63 his3∆200 leu2∆1 tra1::HIS3+[tra1-2ts/CEN/LEU2]

tag: time point


title: WT3

description: gene expression data from wildtype after 60min at 37˚C

value: MATa ura3-52 lys2-801 ade2-101 trp1∆63 his3∆200 leu2∆1 tra1::HIS3+[TRA1/CEN/LEU2]


title: TS3

description: gene expression data from ts strain after 60min at 37˚C


title: TS1

description: gene expression data from ts strain after 120min at 37˚C


title: WT1

description: gene expression data from wildtype after 120min at 37˚C


title: liver from freshwater population FTC animal #5

description:
Liver_FTC#5
Biological replicate 4 of 4 freshwater population FTC from Washington State.

source_name: liver, freshwater population FTC

value: female

value: freshwater population BEPA from Alaska

value: 7 days post-hatch

value: reference


title: liver from freshwater population FTC animal #4 male

description:
Liver_FTC#4
Biological replicate 3 of 4 freshwater population FTC from Washington State.


title: liver from marine population LITC animal #1

description:
Liver_LITC#1
Biological replicate 1 of 5 marine population LITC from British Columbia.


title: liver from freshwater population FTC animal #2

description:
Liver_FTC#2
Biological replicate 1 of 4 freshwater population FTC from Washington State.


title: M1-D1

description: Gene expression data from wGID mutant strain

source_name: whole cell

treatment_protocol: no treatment

value: GID (gal4 interaction defective) mutant


title: hypothalamus from marine population LITC animal #4

description:
Hyp_LITC#4
Biological replicate 4 of 5 marine population LITC from British Columbia.

source_name: hypothalamus, marine population LITC

value: hypothalamus


title: M1-D2


title: WT2

description: gene expression data from wildtype after 90min at 37˚C


title: M8-D2


title: hypothalamus from marine population LITC animal #5

description:
Hyp_LITC#5
Biological replicate 5 of 5 marine population LITC from British Columbia.


title: pcDNA IGF treated 2

description: A2780 pcDNA I2

source_name: pcDNA, 24h IGF expt 2


title: hypothalamus from marine population LITC animal #3

description:
Hyp_LITC#3
Biological replicate 3 of 5 marine population LITC from British Columbia.


title: liver from freshwater population FTC animal #3

description:
Liver_FTC#3
Biological replicate 2 of 4 freshwater population FTC from Washington State.


title: WT-D1

description: Gene expression data from wild type strain

value: Wild type


title: hypothalamus from freshwater population FTC animal #5

description:
Hyp_FTC#5
Biological replicate 5 of 5 freshwater population FTC from Washington State.

source_name: hypothalamus, freshwater population FTC


title: Rab25 TGF beta treated 1

description: A2780 Rab25 T1

source_name: Rab25, 24h TGF expt 1


title: hypothalamus from marine population LITC animal #2

description:
Hyp_LITC#2
Biological replicate 2 of 5 marine population LITC from British Columbia.


title: WT-D2


title: hypothalamus from freshwater population FTC animal #1

description:
Hyp_FTC#1
Biological replicate 1 of 5 freshwater population FTC from Washington State.


title: hypothalamus from freshwater population FTC animal #4 male

description:
Hyp_FTC#4
Biological replicate 4 of 5 freshwater population FTC from Washington State.


title: SCC_FAK KO2 CD34high

city: New York

first: Markus

last: Schober

address: 1230 York Ave

institute: Rockefeller University

hyb_protocol: Mouse 430A 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using Gene Pattern (Broad Institute) and pre-processed using ExpressionFileCreator using the RMA statistical expression algorythm with background subtraction.

source_name: SCC CD34high FAK ko

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from200 ng total RNA.

treatment_protocol: Total RNAs were isolated from cells sorted directly into TrizolLS (Invitrogen).

tag: strain

value: cutaneous squamous cell carcinoma


title: Epidermal progenitor WT2

source_name: Epidermal progenitor

value: wild type

value: skin epidermis


title: SCC_TbRII/FAK dKO2 CD34high

source_name: SCC CD34high TbRII/FAK dko


title: Hair follicle bulge WT2

source_name: Hair follicle bulge

value: hair follicle bulge


title: Hair follicle bulge WT1


title: hypothalamus from freshwater population FTC animal #3

description:
Hyp_FTC#3
Biological replicate 3 of 5 freshwater population FTC from Washington State.


title: SCC_FAK KO1 CD34low

source_name: SCC CD34low FAK ko


title: heart from marine population LITC animal #4

description:
Heart_LITC#4
Biological replicate 4 of 5 marine population LITC from British Columbia.

source_name: heart atrium and ventricle, marine population LITC

value: heart atrium and ventricle


title: SCC_FAK KO2 CD34low


title: Epidermal progenitor WT1


title: SCC_TbRII/FAK dKO2 CD34low

source_name: SCC CD34low TbRII/FAK dko


title: heart from marine population LITC animal #2

description:
Heart_LITC#2
Biological replicate 2 of 5 marine population LITC from British Columbia.


title: SCC_FAK KO1 CD34high


title: heart from freshwater population FTC animal #3

description:
Heart_FTC#3
Biological replicate 3 of 5 freshwater population FTC from Washington State.

source_name: heart atrium and ventricle, freshwater population FTC


title: hypothalamus from freshwater population FTC animal #2

description:
Hyp_FTC#2
Biological replicate 2 of 5 freshwater population FTC from Washington State.


title: heart from marine population LITC animal #3

description:
Heart_LITC#3
Biological replicate 3 of 5 marine population LITC from British Columbia.

value: male


title: heart from freshwater population FTC animal #4 male

description:
Heart_FTC#4
Biological replicate 4 of 5 freshwater population FTC from Washington State.

value: 1.5 years old


title: heart from marine population LITC animal #5

description:
Heart_LITC#5
Biological replicate 5 of 5 marine population LITC from British Columbia.

value: whole embryo


title: gill from marine population LITC animal #5

description:
Gill_LITC#5
Biological replicate 5 of 5 marine population LITC from British Columbia.

source_name: gill filament, marine population LITC

value: gill filament


title: SCC_TbRII/FAK dKO1 CD34low


title: SCC_TbRII KO2 CD34low

source_name: SCC CD34low TbRII ko


title: heart from marine population LITC animal #1

description:
Heart_LITC#1
Biological replicate 1 of 5 marine population LITC from British Columbia.

source_name: whole embryo, freshwater population BEPA


title: heart from freshwater population FTC animal #5

description:
Heart_FTC#5
Biological replicate 5 of 5 freshwater population FTC from Washington State.


title: heart from freshwater population FTC animal #1

description:
Heart_FTC#1
Biological replicate 1 of 5 freshwater population FTC from Washington State.


title: heart from freshwater population FTC animal #2

description:
Heart_FTC#2
Biological replicate 2 of 5 freshwater population FTC from Washington State.


title: SCC_TbRII/FAK dKO1 CD34high


title: SCC_TbRII KO2 CD34high

source_name: SCC CD34high TbRII ko


title: SCC_TbRII KO1 CD34high


title: SCC_WT2 CD34high

source_name: SCC CD34high WT

value: TbRII(fl/fl)


title: SCC_TbRII KO1 CD34low


title: SCC_WT2 CD34low

source_name: SCC CD34low WT


title: gill from marine population LITC animal #4

description:
Gill_LITC#4
Biological replicate 4 of 5 marine population LITC from British Columbia.

value: female


title: gill from marine population LITC animal #3

description:
Gill_LITC#3
Biological replicate 3 of 5 marine population LITC from British Columbia.

value: freshwater population BEPA from Alaska


title: gill from marine population LITC animal #2

description:
Gill_LITC#2
Biological replicate 2 of 5 marine population LITC from British Columbia.

value: 7 days post-hatch


title: SCC_WT1 CD34high


title: gill from freshwater population FTC animal #4 male

description:
Gill_FTC#4
Biological replicate 4 of 5 freshwater population FTC from Washington State.

source_name: gill filament, freshwater population FTC

value: reference


title: gill from freshwater population FTC animal #3

description:
Gill_FTC#3
Biological replicate 3 of 5 freshwater population FTC from Washington State.


title: gill from marine population LITC animal #1

description:
Gill_LITC#1
Biological replicate 1 of 5 marine population LITC from British Columbia.


title: SCC_WT1 CD34low


title: eye from marine population LITC animal #5

description:
Eye_LITC#5
Biological replicate 5 of 5 marine population LITC from British Columbia.

source_name: eye, marine population LITC

value: eye


title: gill from freshwater population FTC animal #1

description:
Gill_FTC#1
Biological replicate 1 of 5 freshwater population FTC from Washington State.


title: M8-D1

description: Gene expression data from wGID mutant strain

source_name: whole cell

value: GID (gal4 interaction defective) mutant


title: gill from freshwater population FTC animal #5

description:
Gill_FTC#5
Biological replicate 5 of 5 freshwater population FTC from Washington State.


title: mouse_Thalamus_time_point_6hr_after_reoxygenation_replicate3

city: Sacramento

first: Huichun

last: Xu

address: 2805 50th Street

institute: University of California at Davis

description: mouse Thalamus,time point_6hr_after_reoxygenation,replicate3

hyb_protocol: Fragmented cRNA (15 ug) was hybridized overnight at 45C to Affymetrix GeneChip Mouse Genome 430 2.0 Array

scan_protocol: Hybridization was detected using a confocal laser scanner (Affymetrix)

data_processing: The data were analyzed with GCOS 1.3 using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

treatment_protocol: Adult C57BL/6 male mice were exposed to systemic preconditioning hypoxia (8% O2 ) for 3 hr and allowed to recover in normoxia for 24 hr. The mouse brains were removed and dissected into individual brain regions at multiple time points during the 3hr hypoxia and subsequent 24hr reoxygenation periods.

value: 8-9 weeks

value: brain

tag: brain region

value: Thalamus

tag: treatment protocol

value: hypoxia, followed by variable-length normoxia


title: mouse_Thalamus_time_point_12hr_after_reoxygenation_replicate3

description: mouse Thalamus,time point_12hr_after_reoxygenation,replicate3


title: mouse_Thalamus_time_point_3hr_after_reoxygenation_replicate3

description: mouse Thalamus,time point_3hr_after_reoxygenation,replicate3


title: mouse_Thalamus_time_point_hypoxia_3hr_replicate3

description: mouse Thalamus,time point_hypoxia_3hr,replicate3

value: hypoxia


title: mouse_Thalamus_time_point_24hr_after_reoxygenation_replicate3

description: mouse Thalamus,time point_24hr_after_reoxygenation,replicate3


title: mouse_Thalamus_time_point_1hr_after_reoxygenation_replicate3

description: mouse Thalamus,time point_1hr_after_reoxygenation,replicate3


title: gill from freshwater population FTC animal #2

description:
Gill_FTC#2
Biological replicate 2 of 5 freshwater population FTC from Washington State.

tag: sample type


title: mouse_Thalamus_time_point_hypoxia_1hr_replicate3

description: mouse Thalamus,time point_hypoxia_1hr,replicate3


title: eye from marine population LITC animal #1

description:
Eye_LITC#1
Biological replicate 1 of 5 marine population LITC from British Columbia.


title: eye from marine population LITC animal #3

description:
Eye_LITC#3
Biological replicate 3 of 5 marine population LITC from British Columbia.


title: eye from marine population LITC animal #4

description:
Eye_LITC#4
Biological replicate 4 of 5 marine population LITC from British Columbia.


title: mouse_Thalamus_time_point_0hr_replicate3

description: mouse Thalamus,time point_0hr,replicate3

value: control


title: mouse_Thalamus_time_point_6hr_after_reoxygenation_replicate2

description: mouse Thalamus,time point_6hr_after_reoxygenation,replicate2


title: eye from freshwater population FTC animal #4 male

description:
Eye_FTC#4
Biological replicate 4 of 5 freshwater population FTC from Washington State.

source_name: eye, freshwater population FTC

value: male


title: eye from freshwater population FTC animal #5

description:
Eye_FTC#5
Biological replicate 5 of 5 freshwater population FTC from Washington State.

value: 1.5 years old


title: eye from freshwater population FTC animal #3

description:
Eye_FTC#3
Biological replicate 3 of 5 freshwater population FTC from Washington State.

value: whole embryo


title: eye from marine population LITC animal #2

description:
Eye_LITC#2
Biological replicate 2 of 5 marine population LITC from British Columbia.


title: eye from freshwater population FTC animal #2

description:
Eye_FTC#2
Biological replicate 2 of 5 freshwater population FTC from Washington State.


title: mouse_Thalamus_time_point_1hr_after_reoxygenation_replicate2

description: mouse Thalamus,time point_1hr_after_reoxygenation,replicate2


title: hypothalamus from marine population LITC animal #1

description:
Hyp_LITC#1
Biological replicate 1 of 5 marine population LITC from British Columbia.

source_name: hypothalamus, marine population LITC

value: hypothalamus


title: mouse_Thalamus_time_point_12hr_after_reoxygenation_replicate2

description: mouse Thalamus,time point_12hr_after_reoxygenation,replicate2


title: mouse_Thalamus_time_point_24hr_after_reoxygenation_replicate2

description: mouse Thalamus,time point_24hr_after_reoxygenation,replicate2


title: mouse_Thalamus_time_point_3hr_after_reoxygenation_replicate2

description: mouse Thalamus,time point_3hr_after_reoxygenation,replicate2


title: mouse_Thalamus_time_point_hypoxia_3hr_replicate2

description: mouse Thalamus,time point_hypoxia_3hr,replicate2


title: eye from freshwater population FTC animal #1

description:
Eye_FTC#1
Biological replicate 1 of 5 freshwater population FTC from Washington State.


title: mouse_Thalamus_time_point_0hr_replicate2

description: mouse Thalamus,time point_0hr,replicate2


title: RIT patient 3, post RIT 7 weeks

city: Dallas

first: Laurie

middle: S

last: Davis

state: TX

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina protocol using Whole Genome Gene Expression Direct Hybridization

scan_protocol: Standard Illumina scanning protocol using Bead Array Reader

data_processing: The data were normalized and analyzed using Illumina Inc. BeadStudio version 1.5.0.34 and Agilent GeneSpring 7.3.1 (Agilent technologies)

source_name: RIT patient 3, post RIT 7 weeks

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit (AMIL1791) for Illumina arrays

extract_protocol: RNA was extracted from PBMC with Trizol reagent and stored at -80oC. Samples underwent DNase I treatment and extraction with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Whole blood was immediately processed by ficoll gradient centrifugation, washed in PBS and total RNA collected.

value: Blood

tag: cell type

value: PBMC

tag: condition

value: Allergic patient


title: mouse_Thalamus_time_point_hypoxia_1hr_replicate2

description: mouse Thalamus,time point_hypoxia_1hr,replicate2


title: RIT patient 3, post RIT 1 week

source_name: RIT patient 3, post RIT 1 week


title: RIT patient 3, pre RIT

source_name: RIT patient 3, pre RIT


title: mouse_Thalamus_time_point_6hr_after_reoxygenation_replicate1

description: mouse Thalamus,time point_6hr_after_reoxygenation,replicate1


title: mouse_Thalamus_time_point_3hr_after_reoxygenation_replicate1

description: mouse Thalamus,time point_3hr_after_reoxygenation,replicate1


title: RIT patient 2, post RIT 4 months

source_name: RIT patient 2, post RIT 4 months


title: RIT patient 2, post RIT 7 weeks

source_name: RIT patient 2, post RIT 7 weeks


title: Rab25 Control 1-2

description: A2780 Rab25 C2

source_name: Rab25, 8h serum straved control 2, expt 1

tag: cell line


title: mouse_Thalamus_time_point_12hr_after_reoxygenation_replicate1

description: mouse Thalamus,time point_12hr_after_reoxygenation,replicate1


title: RIT patient 2, post RIT 1 week

source_name: RIT patient 2, post RIT 1 week


title: RIT patient 3, post RIT 4 months

source_name: RIT patient 3, post RIT 4 months


title: mouse_Thalamus_time_point_24hr_after_reoxygenation_replicate1

description: mouse Thalamus,time point_24hr_after_reoxygenation,replicate1


title: RIT patient 1, post RIT 5 months

source_name: RIT patient 1, post RIT 5 months


title: mouse_Thalamus_time_point_hypoxia_3hr_replicate1

description: mouse Thalamus,time point_hypoxia_3hr,replicate1


title: RIT patient 2, pre RIT

source_name: RIT patient 2, pre RIT


title: mouse_striatum_time_point_12hr_after_reoxygenation_replicate3

description: mouse striatum,time point_12hr_after_reoxygenation,replicate3

value: striatum


title: mouse_striatum_time_point_3hr_after_reoxygenation_replicate3

description: mouse striatum,time point_3hr_after_reoxygenation,replicate3


title: RIT patient 1, pre RIT

source_name: RIT patient 1, pre RIT


title: mouse_Thalamus_time_point_0hr_replicate1

description: mouse Thalamus,time point_0hr,replicate1


title: RIT patient 1, post RIT 4 months

source_name: RIT patient 1, post RIT 4 months


title: mouse_striatum_time_point_6hr_after_reoxygenation_replicate2

description: mouse striatum,time point_6hr_after_reoxygenation,replicate2


title: mouse_striatum_time_point_24hr_after_reoxygenation_replicate3

description: mouse striatum,time point_24hr_after_reoxygenation,replicate3


title: mouse_striatum_time_point_hypoxia_3hr_replicate3

description: mouse striatum,time point_hypoxia_3hr,replicate3


title: RIT patient 1, post RIT 7 weeks

source_name: RIT patient 1, post RIT 7 weeks


title: RIT patient 1, post RIT 1 week

source_name: RIT patient 1, post RIT 1 week


title: mouse_Thalamus_time_point_hypoxia_1hr_replicate1

description: mouse Thalamus,time point_hypoxia_1hr,replicate1


title: mouse_Thalamus_time_point_1hr_after_reoxygenation_replicate1

description: mouse Thalamus,time point_1hr_after_reoxygenation,replicate1


title: mouse_striatum_time_point_hypoxia_1hr_replicate3

description: mouse striatum,time point_hypoxia_1hr,replicate3


title: mouse_striatum_time_point_1hr_after_reoxygenation_replicate3

description: mouse striatum,time point_1hr_after_reoxygenation,replicate3


title: mouse_striatum_time_point_24hr_after_reoxygenation_replicate2

description: mouse striatum,time point_24hr_after_reoxygenation,replicate2


title: mouse_striatum_time_point_3hr_after_reoxygenation_replicate2

description: mouse striatum,time point_3hr_after_reoxygenation,replicate2


title: mouse_striatum_time_point_1hr_after_reoxygenation_replicate2

description: mouse striatum,time point_1hr_after_reoxygenation,replicate2


title: mouse_striatum_time_point_hypoxia_1hr_replicate2

description: mouse striatum,time point_hypoxia_1hr,replicate2


title: mouse_striatum_time_point_12hr_after_reoxygenation_replicate2

description: mouse striatum,time point_12hr_after_reoxygenation,replicate2


title: mouse_striatum_time_point_hypoxia_3hr_replicate2

description: mouse striatum,time point_hypoxia_3hr,replicate2


title: mouse_striatum_time_point_6hr_after_reoxygenation_replicate3

description: mouse striatum,time point_6hr_after_reoxygenation,replicate3


title: mouse_striatum_time_point_0hr_replicate3

description: mouse striatum,time point_0hr,replicate3


title: mouse_striatum_time_point_0hr_replicate2

description: mouse striatum,time point_0hr,replicate2


title: mouse_striatum_time_point_6hr_after_reoxygenation_replicate1

description: mouse striatum,time point_6hr_after_reoxygenation,replicate1


title: mouse_striatum_time_point_12hr_after_reoxygenation_replicate1

description: mouse striatum,time point_12hr_after_reoxygenation,replicate1


title: mouse_striatum_time_point_24hr_after_reoxygenation_replicate1

description: mouse striatum,time point_24hr_after_reoxygenation,replicate1


title: mouse_striatum_time_point_3hr_after_reoxygenation_replicate1

description: mouse striatum,time point_3hr_after_reoxygenation,replicate1


title: mouse_striatum_time_point_hypoxia_3hr_replicate1

description: mouse striatum,time point_hypoxia_3hr,replicate1


title: mouse_Pons and Medulla_time_point_6hr_after_reoxygenation_replicate3

description: mouse Pons and Medulla,time point_6hr_after_reoxygenation,replicate3

value: Pons and Medulla


title: mouse_striatum_time_point_1hr_after_reoxygenation_replicate1

description: mouse striatum,time point_1hr_after_reoxygenation,replicate1


title: mouse_striatum_time_point_hypoxia_1hr_replicate1

description: mouse striatum,time point_hypoxia_1hr,replicate1


title: mouse_Pons and Medulla_time_point_3hr_after_reoxygenation_replicate3

description: mouse Pons and Medulla,time point_3hr_after_reoxygenation,replicate3


title: mouse_striatum_time_point_0hr_replicate1

description: mouse striatum,time point_0hr,replicate1


title: mouse_Pons and Medulla_time_point_24hr_after_reoxygenation_replicate3

description: mouse Pons and Medulla,time point_24hr_after_reoxygenation,replicate3


title: OSCC cell line Sa3

city: miyazaki city

first: kentarou

last: nagai

state: miyazaki

department: Miyazaki university

country: Japan

institute: biochemistry

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: oral squamous cell carcinoma cell line Sa3

extract_protocol: DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

treatment_protocol: Samples were extracted in the center of tumor, not dissected.

value: oral squamous cell carcinoma cell line


title: OSCC cell line HSC3

source_name: oral squamous cell carcinoma cell line HSC3


title: mouse_Pons and Medulla_time_point_12hr_after_reoxygenation_replicate3

description: mouse Pons and Medulla,time point_12hr_after_reoxygenation,replicate3


title: OSCC sample23

source_name: oral squamous cell carcinoma tissue 23

value: oral squamous cell carcinoma tissue


title: OSCC cell line SAS

source_name: oral squamous cell carcinoma cell line SAS

value: SAS


title: OSCC cell line HSC2

source_name: oral squamous cell carcinoma cell line HSC2


title: OSCC sample16

source_name: oral squamous cell carcinoma tissue 16


title: OSCC cell line HSC4

source_name: oral squamous cell carcinoma cell line HSC4


title: OSCC sample22

source_name: oral squamous cell carcinoma tissue 22

tag: age/sex

tag: Stage

value: Ⅱ

tag: region

value: floor of mouth

tag: clinical stage

tag: differentiation

value: well differentiated


title: mouse_Pons and Medulla_time_point_1hr_after_reoxygenation_replicate3

description: mouse Pons and Medulla,time point_1hr_after_reoxygenation,replicate3

tag: age

value: 8-9 weeks

value: brain

value: hypoxia, followed by variable-length normoxia


title: OSCC cell line Ca9-22

source_name: oral squamous cell carcinoma cell line Ca9-22


title: OSCC cell line HSQ89

source_name: oral squamous cell carcinoma cell line HSQ89


title: OSCC sample14

source_name: oral squamous cell carcinoma tissue 14


title: OSCC sample15

source_name: oral squamous cell carcinoma tissue 15

value: Ⅲ

value: gingiva-buccal


title: OSCC sample11

source_name: oral squamous cell carcinoma tissue 11

value: tongue

value: moderately


title: mouse_Pons and Medulla_time_point_hypoxia_3hr_replicate3

description: mouse Pons and Medulla,time point_hypoxia_3hr,replicate3

value: hypoxia

tag: time


title: OSCC sample13

source_name: oral squamous cell carcinoma tissue 13

value: gingiva


title: OSCC sample18

source_name: oral squamous cell carcinoma tissue 18

value: Ⅳ

value: lower gingiva


title: OSCC sample10

source_name: oral squamous cell carcinoma tissue 10

value: Ⅰ


title: mouse_Pons and Medulla_time_point_0hr_replicate3

description: mouse Pons and Medulla,time point_0hr,replicate3

tag: tissue

value: Pons and Medulla

value: control


title: mouse_Pons and Medulla_time_point_6hr_after_reoxygenation_replicate2

description: mouse Pons and Medulla,time point_6hr_after_reoxygenation,replicate2


title: mouse_Pons and Medulla_time_point_3hr_after_reoxygenation_replicate2

description: mouse Pons and Medulla,time point_3hr_after_reoxygenation,replicate2


title: OSCC sample17

source_name: oral squamous cell carcinoma tissue 17

value: oral squamous cell carcinoma tissue

value: Ⅱ


title: mouse_Pons and Medulla_time_point_1hr_after_reoxygenation_replicate2

description: mouse Pons and Medulla,time point_1hr_after_reoxygenation,replicate2


title: OSCC sample8

source_name: oral squamous cell carcinoma tissue 8

value: verrucos


title: mouse_Pons and Medulla_time_point_12hr_after_reoxygenation_replicate2

description: mouse Pons and Medulla,time point_12hr_after_reoxygenation,replicate2

value: 8-9 weeks


title: mouse_Pons and Medulla_time_point_24hr_after_reoxygenation_replicate2

description: mouse Pons and Medulla,time point_24hr_after_reoxygenation,replicate2

value: brain


title: Cardiomyocytes-Ad-β-catenin-GFP, biological rep2

city: Beijing

first: junjie

last: li

address: #5 Dong Dan San Tiao

country: China

institute: PUMC

description: Gene expression data from neonatal rat cardiomyocytes infected with Ad-β-catenin-GFP

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip rat 230 2.0 Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with GeneSpring GX 11.0 Software using RMA algorithm.

organism: Rattus norvegicus

source_name: Neonatal rat cardiomyocytes infected with Ad-β-catenin-GFP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Primary cardiomyocytes were prepared by enzymatic disassociation of 1- to 2-day old Sprague-Dawley rats, the isolated cardiomyocytes resuspended in fresh DMEM/F12 (HyClone) containing 10% FBS and 1% penicillin-streptomycin were plated into the Laminin (Sigma) precoated dishes (Corning) and incubated for 24 h at 37 ℃.

extract_protocol: Extraction of total RNA was performed using TRIzol according to the manufacturer's instructions.

treatment_protocol: Cardiomyocytes were infected with GFP control or β-catenin adenovirus and cultured with serum-free DMEM/F12 for 24 hours.

value: ventricular myocardium

value: Sprague-Dawley

value: 1- to 2-day old

tag: infection

value: Ad-β-catenin-GFP


title: mouse_Pons and Medulla_time_point_hypoxia_3hr_replicate2

description: mouse Pons and Medulla,time point_hypoxia_3hr,replicate2


title: mouse_Pons and Medulla_time_point_hypoxia_1hr_replicate2

description: mouse Pons and Medulla,time point_hypoxia_1hr,replicate2


title: OSCC sample9

source_name: oral squamous cell carcinoma tissue 9

value: gingiva-buccal

value: moderately


title: OSCC sample7

source_name: oral squamous cell carcinoma tissue 7

value: tongue

value: well differentiated


title: OSCC sample6

source_name: oral squamous cell carcinoma tissue 6

value: buccal


title: Cardiomyocytes-Ad-GFP, biological rep1

description: Gene expression data from neonatal rat cardiomyocytes infected with Ad-GFP

source_name: Neonatal rat cardiomyocytes infected with Ad-GFP

value: Ad-GFP


title: mouse_Pons and Medulla_time_point_hypoxia_1hr_replicate3

description: mouse Pons and Medulla,time point_hypoxia_1hr,replicate3

value: Pons and Medulla

value: hypoxia


title: Buffer control spleen, uninfected, rep2

city: Bangi

first: Sheila

last: Nathan

state: Selangor

address: Jalan Universiti

department: Faculty of Science & Technology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

description:
Biological replicate 2
4203008022_H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: BeadStudio version 1.0 (Illumina, USA) software was used to generate signal intensity values from the scans. The average normalization recommended by the BeadStudio software was used to rescale the difference in overall intensity to the median average intensity for all samples across multiple arrays and chips.

source_name: Buffer control spleen, uninfected

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit  for BeadChip arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: Spleen

tag: time point (hrs post-infection)

value: Buffer Control

value: BALB/c

value: 8-10 weeks old


title: mouse_Pons and Medulla_time_point_0hr_replicate2

description: mouse Pons and Medulla,time point_0hr,replicate2

tag: strain

value: 8-9 weeks

value: brain

value: control


title: OSCC sample12

source_name: oral squamous cell carcinoma tissue 12

value: oral squamous cell carcinoma tissue

value: Ⅰ


title: Cardiomyocytes-Ad-β-catenin-GFP, biological rep1

value: ventricular myocardium

value: Sprague-Dawley

value: 1- to 2-day old

value: Ad-β-catenin-GFP


title: OSCC cell line Ho1u1

source_name: oral squamous cell carcinoma cell line Ho1u1

value: oral squamous cell carcinoma cell line


title: OSCC sample5

source_name: oral squamous cell carcinoma tissue 5

value: Ⅱ

value: floor of mouth

value: Invasive


title: Buffer control liver, uninfected, rep2

description:
Biological replicate 2
4203008022_F

source_name: Buffer control liver, uninfected

value: Liver


title: mouse_Pons and Medulla_time_point_3hr_after_reoxygenation_replicate1

description: mouse Pons and Medulla,time point_3hr_after_reoxygenation,replicate1

tag: brain region

value: Pons and Medulla

value: hypoxia, followed by variable-length normoxia


title: Diabetic spleen, infected, 42 hpi, rep2

description:
Biological replicate 2
4203008022_E

source_name: Diabetic spleen, 42 hpi

value: Spleen

value: Diabetic

value: BALB/c

value: 8-10 weeks old


title: mouse_Pons and Medulla_time_point_6hr_after_reoxygenation_replicate1

description: mouse Pons and Medulla,time point_6hr_after_reoxygenation,replicate1

value: 8-9 weeks

value: brain

tag: treatment protocol


title: OSCC sample20

source_name: oral squamous cell carcinoma tissue 20

value: oral squamous cell carcinoma tissue

value: tongue

value: verrucos


title: mouse_Pons and Medulla_time_point_1hr_after_reoxygenation_replicate1

description: mouse Pons and Medulla,time point_1hr_after_reoxygenation,replicate1


title: Buffer control liver, uninfected, rep3

description:
Biological replicate 3
4203008022_G

value: Buffer Control


title: mouse_Pons and Medulla_time_point_24hr_after_reoxygenation_replicate1

description: mouse Pons and Medulla,time point_24hr_after_reoxygenation,replicate1


title: mouse_Pons and Medulla_time_point_hypoxia_1hr_replicate1

description: mouse Pons and Medulla,time point_hypoxia_1hr,replicate1

value: hypoxia


title: Diabetic liver, infceted, 16 hpi, rep3

description:
Biological replicate 3
4203008022_C

source_name: Diabetic liver, 16 hpi


title: Diabetic liver, infected, 24 hpi, rep3

description:
Biological replicate 3
4203008022_D

source_name: Diabetic liver, 24 hpi


title: mouse_Pons and Medulla_time_point_hypoxia_3hr_replicate1

description: mouse Pons and Medulla,time point_hypoxia_3hr,replicate1


title: OSCC sample1

source_name: oral squamous cell carcinoma tissue 1

value: Ⅲ

value: buccal

value: well differentiated


title: Diabetic spleen, infected, 42 hpi, rep1

description:
Biological replicate 1
4203008019_E


title: oral leukoplakia sample1

source_name: oral leukoplakia 1

value: oral leukoplakia


title: mouse_Pons and Medulla_time_point_0hr_replicate1

description: mouse Pons and Medulla,time point_0hr,replicate1

value: Pons and Medulla

value: control


title: mouse_midbrain_time_point_6hr_after_reoxygenation_replicate3

description: mouse midbrain,time point_6hr_after_reoxygenation,replicate3

value: midbrain

value: hypoxia, followed by variable-length normoxia


title: Diabetic liver, uninfected, rep3

description:
Biological replicate 3
4203008019_F

source_name: Diabetic liver, uninfected

value: Liver

value: Diabetic

value: BALB/c


title: oral leukoplakia sample5

source_name: oral leukoplakia 5


title: mouse_midbrain_time_point_24hr_after_reoxygenation_replicate3

description: mouse midbrain,time point_24hr_after_reoxygenation,replicate3

value: 8-9 weeks

value: brain


title: mouse_midbrain_time_point_3hr_after_reoxygenation_replicate3

description: mouse midbrain,time point_3hr_after_reoxygenation,replicate3


title: oral leukoplakia sample3

source_name: oral leukoplakia 3


title: oral leukoplakia sample4

source_name: oral leukoplakia 4


title: oral leukoplakia sample2

source_name: oral leukoplakia 2


title: Diabetic liver, infected, 42 hpi, rep2

description:
Biological replicate 2
4203008019_D

source_name: Diabetic liver, 42 hpi

value: 8-10 weeks old


title: mouse_midbrain_time_point_12hr_after_reoxygenation_replicate3

description: mouse midbrain,time point_12hr_after_reoxygenation,replicate3


title: Diabetic spleen, infected, 42 hpi, rep3

description:
Biological replicate 3
4203008011_H

value: Spleen


title: mouse_midbrain_time_point_1hr_after_reoxygenation_replicate3

description: mouse midbrain,time point_1hr_after_reoxygenation,replicate3


title: Diabetic spleen, infected, 16 hpi, rep3

description:
Biological replicate 3
4203008003_E

source_name: Diabetic spleen, 16 hpi


title: Diabetic liver, infected, 16 hpi, rep2

description:
Biological replicate 2
4203008003_B


title: Diabetic spleen, infected, 24 hpi, rep3

description:
Biological replicate 3
4203008003_H

source_name: Diabetic spleen, 24 hpi


title: Buffer control spleen, uninfected, rep1

description:
Biological replicate 1
4203008003_A

source_name: Buffer control spleen, uninfected

value: Buffer control


title: Diabetic spleen, infected, 16 hpi, rep2

description:
Biological replicate 2
4203008003_D


title: Diabetic liver, infected, 42 hpi, rep3

description:
Biological replicate 3
4203008011_G


title: Diabetic spleen, infected, 24 hpi, rep2

description:
Biological replicate 2
4203008003_G


title: Diabetic spleen, infected, 16 hpi, rep4

description:
Biological replicate 4
4203008019_H


title: mouse_midbrain_time_point_hypoxia_3hr_replicate3

description: mouse midbrain,time point_hypoxia_3hr,replicate3

value: hypoxia


title: Diabetic spleen, infected, 16 hpi, rep1

description:
Biological replicate 1
4203008003_C


title: Diabetic liver, infected, 24 hpi, rep2

description:
Biological replicate 2
4203008003_F


title: mouse_midbrain_time_point_0hr_replicate3

description: mouse midbrain,time point_0hr,replicate3


title: Cardiomyocytes-Ad-GFP, biological rep2

description: Gene expression data from neonatal rat cardiomyocytes infected with Ad-GFP

source_name: Neonatal rat cardiomyocytes infected with Ad-GFP

value: ventricular myocardium

value: Sprague-Dawley

value: 1- to 2-day old

value: Ad-GFP


title: Diabetic liver, infected, 16 hpi, rep1

description:
Biological replicate 1
4201061015_H


title: mouse_Pons and Medulla_time_point_12hr_after_reoxygenation_replicate1

description: mouse Pons and Medulla,time point_12hr_after_reoxygenation,replicate1

value: Pons and Medulla


title: Diabetic liver, infected, 42 hpi, rep1

description:
Biological replicate 1
4203008019_A


title: OSCC sample3

source_name: oral squamous cell carcinoma tissue 3

value: oral squamous cell carcinoma tissue

value: Ⅱ

value: tongue

value: well differentiated


title: mouse_midbrain_time_point_hypoxia_1hr_replicate3

description: mouse midbrain,time point_hypoxia_1hr,replicate3

value: midbrain


title: OSCC sample2

source_name: oral squamous cell carcinoma tissue 2

value: Ⅲ


title: Diabetic spleen, uninfected, rep3

description:
Biological replicate 3
4203008019_G

source_name: Diabetic spleen, uninfected

value: Diabetic

value: BALB/c


title: mouse_midbrain_time_point_hypoxia_3hr_replicate2

description: mouse midbrain,time point_hypoxia_3hr,replicate2

value: 8-9 weeks

value: brain


title: mouse_midbrain_time_point_6hr_after_reoxygenation_replicate2

description: mouse midbrain,time point_6hr_after_reoxygenation,replicate2

value: hypoxia, followed by variable-length normoxia


title: mouse_midbrain_time_point_12hr_after_reoxygenation_replicate2

description: mouse midbrain,time point_12hr_after_reoxygenation,replicate2


title: mouse_midbrain_time_point_3hr_after_reoxygenation_replicate2

description: mouse midbrain,time point_3hr_after_reoxygenation,replicate2


title: mouse_midbrain_time_point_24hr_after_reoxygenation_replicate2

description: mouse midbrain,time point_24hr_after_reoxygenation,replicate2


title: mouse_midbrain_time_point_1hr_after_reoxygenation_replicate2

description: mouse midbrain,time point_1hr_after_reoxygenation,replicate2


title: Diabetic spleen, uninfected, rep2

description:
Biological replicate 2
4201061015_G

value: Spleen

value: 8-10 weeks old


title: Diabetic spleen, infected, 24 hpi, rep1

description:
Biological replicate 1
4201061015_E


title: mouse_midbrain_time_point_hypoxia_1hr_replicate2

description: mouse midbrain,time point_hypoxia_1hr,replicate2

value: hypoxia


title: mouse_midbrain_time_point_6hr_after_reoxygenation_replicate1

description: mouse midbrain,time point_6hr_after_reoxygenation,replicate1


title: mouse_midbrain_time_point_3hr_after_reoxygenation_replicate1

description: mouse midbrain,time point_3hr_after_reoxygenation,replicate1


title: mouse_midbrain_time_point_0hr_replicate2

description: mouse midbrain,time point_0hr,replicate2

value: control


title: Diabetic liver, uninfected, rep2

description:
Biological replicate 2
4201061015_F

value: Liver


title: mouse_midbrain_time_point_24hr_after_reoxygenation_replicate1

description: mouse midbrain,time point_24hr_after_reoxygenation,replicate1


title: Diabetic spleen, uninfected, rep1

description:
Biological replicate 1
4201061015_C


title: Diabetic liver, infected, 24 hpi, rep1

description:
Biological replicate 1
4201061015_D


title: mouse_midbrain_time_point_1hr_after_reoxygenation_replicate1

description: mouse midbrain,time point_1hr_after_reoxygenation,replicate1


title: Diabetic liver, uninfected, rep1

description:
Biological replicate 1
4201061015_B


title: mouse_hippocampus_time_point_3hr_after_reoxygenation_replicate3

description: mouse hippocampus,time point_3hr_after_reoxygenation,replicate3

value: hippocampus


title: epithelium Alt, rep2

city: La Jolla

first: Taylor

last: Doherty

address: 9500 Gilman Dr 0635

institute: UC San Diego

description: Gene expression data from lung epithelium 24 hours after Alternaria allergen challenge

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

source_name: Lung epithelium transcripts 24hr after Alternaria challenge

growth_protocol: Mice were housed in university vivarium and fed normal diet

extract_protocol: Airway epithelial cells obtained by bronchial brushing were lysed by multiple passages through an 18G needle. RNA was then extracted according to manufacturer’s protocol (Qiagen). Isolated epithelial RNA with sufficient purity (A260/280 = 1.97-2.12) and yield (8.99-12.66 ng/ul) was used for microarray analysis (GeneChip Mouse Gene 1.0 ST, Affymetrix).

treatment_protocol: Prior to performing epithelial brushing, BAL was performed to remove BAL cells. The bronchial brushing was performed using a sterile plastic feeding tube (Solomon Scientific) modified by removal of the rubber bulb, sanding to create roughness, and autoclaving. The tube was inserted into the right main and left main bronchus with gentle brushing and immediately placed in RNAlater (Qiagen).

value: bronchial epithelium

value: 6 weeks


title: mouse_midbrain_time_point_12hr_after_reoxygenation_replicate1

description: mouse midbrain,time point_12hr_after_reoxygenation,replicate1


title: buffer control liver, uninfected, rep1

description:
Biological replicate 1
4201061015_A

source_name: buffer control liver, uninfected

value: Buffer control


title: mouse_hippocampus_time_point_6hr_after_reoxygenation_replicate3

description: mouse hippocampus,time point_6hr_after_reoxygenation,replicate3


title: mouse_midbrain_time_point_hypoxia_3hr_replicate1

description: mouse midbrain,time point_hypoxia_3hr,replicate1


title: epithelium PBS, rep1

description: Gene expression data from lung epithelium 24 hours after control PBS challenge

source_name: Lung epithelium transcripts 24hr after PBS challenge


title: epithelium PBS, rep3


title: mouse_hippocampus_time_point_24hr_after_reoxygenation_replicate3

description: mouse hippocampus,time point_24hr_after_reoxygenation,replicate3


title: mouse_hippocampus_time_point_12hr_after_reoxygenation_replicate3

description: mouse hippocampus,time point_12hr_after_reoxygenation,replicate3


title: mouse_midbrain_time_point_0hr_replicate1

description: mouse midbrain,time point_0hr,replicate1


title: epithelium PBS, rep2


title: epithelium Alt, rep3


title: mouse_midbrain_time_point_hypoxia_1hr_replicate1

description: mouse midbrain,time point_hypoxia_1hr,replicate1


title: mouse_hippocampus_time_point_hypoxia_3hr_replicate3

description: mouse hippocampus,time point_hypoxia_3hr,replicate3


title: epithelium Alt, rep1


title: ES2, G4, M1, V48h

city: Gothenburg

first: Ali

middle: Mohaghegh

last: Harandi

address: Medicinaregatan 7A

department: Microbiology and Immunology

country: Sweden

institute: University of Gothenburg

description: Gr 4, mouse vagina, 48h

hyb_protocol: 200 ng of sample was hybridized according to Affymetrix´s recommended protocoll (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay, 701880 Rev. 5).

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix) by a Gene chip Fluidics station FS-400 and gene chip scanner 3000 7G

data_processing: Probe logarithmic Intensity Error (PLIER) with quantile normalization

label: Biotin Allonamide Triphosphate

source_name: mouse vagina, 48h post treatment

label_protocol: Labeling reaction with Biotin Allonamide Triphosphateat was performed at 37 degrees

extract_protocol: Vaginas (cut below cervix) were surgically removed at different time-points following treatment and RNA was extracted by Rneasy according to manufacturer's instructions.

treatment_protocol: Mice were given Depo Provera (long lasting progestin) subconateously prior to being administered intravaginally with either adjuvant (CpG ODN or α-GalCer) or their respective control buffers, PBS and PBS/Tween 0.5%.

tag: gender

value: female

tag: treatment

value: α-GalCer


title: ES2, G4, M2, V48h

description: Gr 4, mouse vagina, 48h


title: mouse_hippocampus_time_point_hypoxia_1hr_replicate3

description: mouse hippocampus,time point_hypoxia_1hr,replicate3


title: mouse_hippocampus_time_point_3hr_after_reoxygenation_replicate2

description: mouse hippocampus,time point_3hr_after_reoxygenation,replicate2


title: ES2, G4, M2, V24h

description: Gr 4, mouse vagina, 24h

source_name: mouse vagina, 24h post treatment


title: mouse_hippocampus_time_point_6hr_after_reoxygenation_replicate2

description: mouse hippocampus,time point_6hr_after_reoxygenation,replicate2


title: mouse_hippocampus_time_point_1hr_after_reoxygenation_replicate3

description: mouse hippocampus,time point_1hr_after_reoxygenation,replicate3


title: ES2, G4, M1, V24h

description: Gr 4, mouse vagina, 24h


title: ES1, G4, M2, V48h

description: Gr 4, mouse vagina, 48h


title: ES1, G4, M1, V48h

description: Gr 4, mouse vagina, 48h


title: ES1, G4, M2, V24h

description: Gr 4, mouse vagina, 24h


title: mouse_hippocampus_time_point_24hr_after_reoxygenation_replicate2

description: mouse hippocampus,time point_24hr_after_reoxygenation,replicate2


title: mouse_hippocampus_time_point_0hr_replicate3

description: mouse hippocampus,time point_0hr,replicate3


title: ES1, G4, M1, V24h

description: Gr 4, mouse vagina, 24h


title: mouse_hippocampus_time_point_1hr_after_reoxygenation_replicate2

description: mouse hippocampus,time point_1hr_after_reoxygenation,replicate2


title: mouse_hippocampus_time_point_12hr_after_reoxygenation_replicate2

description: mouse hippocampus,time point_12hr_after_reoxygenation,replicate2


title: mouse_hippocampus_time_point_3hr_after_reoxygenation_replicate1

description: mouse hippocampus,time point_3hr_after_reoxygenation,replicate1


title: ES2, G3, M1, V48h

description: Gr 3, mouse vagina, 48h

value: CpG ODN


title: ES2, G3, M2, V48h

description: Gr 3, mouse vagina, 48h


title: mouse_hippocampus_time_point_hypoxia_1hr_replicate2

description: mouse hippocampus,time point_hypoxia_1hr,replicate2


title: mouse_hippocampus_time_point_0hr_replicate2

description: mouse hippocampus,time point_0hr,replicate2


title: ES2, G4, M1, V4h

description: Gr 4, mouse vagina, 4h

source_name: mouse vagina, 4h post treatment


title: ES2, G3, M2, V24h

description: Gr 3, mouse vagina, 24h


title: mouse_hippocampus_time_point_hypoxia_3hr_replicate2

description: mouse hippocampus,time point_hypoxia_3hr,replicate2


title: ES1, G4, M1, V4h

description: Gr 4, mouse vagina, 4h


title: ES2, G4, M2, V4h

description: Gr 4, mouse vagina, 4h


title: mouse_hippocampus_time_point_24hr_after_reoxygenation_replicate1

description: mouse hippocampus,time point_24hr_after_reoxygenation,replicate1


title: mouse_hippocampus_time_point_6hr_after_reoxygenation_replicate1

description: mouse hippocampus,time point_6hr_after_reoxygenation,replicate1


title: mouse_hippocampus_time_point_1hr_after_reoxygenation_replicate1

description: mouse hippocampus,time point_1hr_after_reoxygenation,replicate1


title: ES1, G3, M1, V48h

description: Gr 3, mouse vagina, 48h


title: ES1, G4, M2, V4h

description: Gr 4, mouse vagina, 4h


title: mouse_hippocampus_time_point_hypoxia_1hr_replicate1

description: mouse hippocampus,time point_hypoxia_1hr,replicate1


title: ES2, G3, M2, V4h

description: Gr 3, mouse vagina, 4h


title: ES1, G3, M1, V24h

description: Gr 3, mouse vagina, 24h


title: mouse_hippocampus_time_point_hypoxia_3hr_replicate1

description: mouse hippocampus,time point_hypoxia_3hr,replicate1


title: ES2, G3, M1, V24h

description: Gr 3, mouse vagina, 24h


title: mouse_hippocampus_time_point_0hr_replicate1

description: mouse hippocampus,time point_0hr,replicate1


title: ES2, G3, M1, V4h

description: Gr 3, mouse vagina, 4h


title: ES1, G3, M2, V24h

description: Gr 3, mouse vagina, 24h


title: mouse_cerebral cortex_time_point_6hr_after_reoxygenation_replicate3

description: mouse cerebral cortex,time point_6hr_after_reoxygenation,replicate3

value: cerebral cortex


title: ES1, G3, M2, V48h

description: Gr 3, mouse vagina, 48h


title: mouse_cerebral cortex_time_point_24hr_after_reoxygenation_replicate3

description: mouse cerebral cortex,time point_24hr_after_reoxygenation,replicate3


title: mouse_cerebral cortex_time_point_3hr_after_reoxygenation_replicate3

description: mouse cerebral cortex,time point_3hr_after_reoxygenation,replicate3


title: ES1, G3, M2, V4h

description: Gr 3, mouse vagina, 4h


title: mouse_cerebral cortex_time_point_1hr_after_reoxygenation_replicate3

description: mouse cerebral cortex,time point_1hr_after_reoxygenation,replicate3


title: ES1, G3, M1, V4h

description: Gr 3, mouse vagina, 4h


title: ES2, G2, M1, V48h

description: Gr 2, mouse vagina, 48h

value: PBS/Tween 0.5%


title: ES1, G2, M2, V48h

description: Gr 2, mouse vagina, 48h


title: mouse_cerebral cortex_time_point_hypoxia_1hr_replicate3

description: mouse cerebral cortex,time point_hypoxia_1hr,replicate3

value: 8-9 weeks


title: ES1, G2, M1, V48h

description: Gr 2, mouse vagina, 48h


title: mouse_cerebral cortex_time_point_12hr_after_reoxygenation_replicate3

description: mouse cerebral cortex,time point_12hr_after_reoxygenation,replicate3

value: brain


title: ES2, G2, M1, V24h

description: Gr 2, mouse vagina, 24h


title: ES1, G2, M2, V24h

description: Gr 2, mouse vagina, 24h


title: ES2, G2, M2, V48h

description: Gr 2, mouse vagina, 48h


title: ES1, G2, M1, V24h

description: Gr 2, mouse vagina, 24h


title: ES2, G2, M2, V24h

description: Gr 2, mouse vagina, 24h


title: mouse_cerebral cortex_time_point_hypoxia_3hr_replicate3

description: mouse cerebral cortex,time point_hypoxia_3hr,replicate3


title: ES2, G2, M1, V4h

description: Gr 2, mouse vagina, 4h


title: ES1, G2, M1, V4h

description: Gr 2, mouse vagina, 4h


title: ES1, G2, M2, V4h

description: Gr 2, mouse vagina, 4h


title: ES2, G2, M2, V4h

description: Gr 2, mouse vagina, 4h


title: mouse_cerebral cortex_time_point_6hr_after_reoxygenation_replicate2

description: mouse cerebral cortex,time point_6hr_after_reoxygenation,replicate2

value: hypoxia, followed by variable-length normoxia


title: mouse_cerebral cortex_time_point_0hr_replicate3

description: mouse cerebral cortex,time point_0hr,replicate3