title: Extraembryonic_tissue 351, source AI, cDNA labeled with dye Cy3.

status: Public on Jan 13 2012

city: Champaign

first: Robin

middle: Edward

last: Everts

address: 1201 West Gregory Drive

department: Animal Sciences

institute: UIUC

description:
The cDNA from the extraembryonic tissue RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = Extraembryonic tissue
Keywords = bovine
Keywords = AI pregnancy
Keywords = microarray

hyb_protocol: Each Cy3-labeled sample was combined with a Cy5-labeled reference, vacuum dried, and resuspended in 40 µl of ddH2O containing 10 µg of bovine Cot1 DNA, 20 µg oligo dT.  After denaturation for 3 min at 94°C and reannealing for 10 min at 60°C, 40 µl of 2x hybridization buffer (50% formamide, 10x SSC, 02% SDS) was added and the mixture was hybridized to the microarray for 40 hrs. Microarrays were subsequently washed in a series of SSC/SDS washes (1xSSC/0.2% SDS, 0.1xSS/0.2% SDS, 0.1xSSC)to remove unbound cDNA.  After washing, arrays were dried by centrifugation and stored in argon gas until scanning (max. ~1 hr).

scan_protocol: The microarray image was acquired using a GenePix 4000B scanner and analyzed using GenePix Pro 6.0 using the autobalance feature and a saturation threshold of 0.05%.

data_processing: Values are raw log2 transformed ratios, no normalizations are performed, and only GenePix flagging is performed.

organism: Bos taurus

source_name: reference standard RNA, labeled with Cy5

label_protocol: The reference RNA (10 µg) was annealed with 6 µg random N6, and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 46°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column. The cDNA was covalently coupled separately with Cy5-monoreactive dye in 50 mM sodium bicarbonate, pH 9.0. The Cy5-labeled cDNA was purified with a QIAquick PCR purification column. The labeled reference was analyzed using a spectrophotometer to assess incoproration of dyes.

extract_protocol: RNA isolation was accomplished using Trizol.

tag: reference total RNA was isolated by Trizol and consists of equal amounts total RNA extracted from EBTr, MDBK, and BL30 cell lines, and brain tissue

source_name: Extraembryonic tissue 351, type: AI, sex: female, labeled with Cy3

label_protocol: The sample RNA (10 µg) was annealed with 6 µg random N6, and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 46°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column. The cDNA was covalently coupled separately with Cy3-monoreactive dye in 50 mM sodium bicarbonate, pH 9.0. The Cy3-labeled cDNA was purified with a QIAquick PCR purification column. The labeled sample was analyzed using a spectrophotometer to assess incoproration of dyes.

tag: Extraembryonic tissue total RNA isolated by Trizol


title: PeripheralBlood_DBA_Proband_1475 [Omni1-Quad]

status: Public on Jan 15 2012

type: genomic

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

country: USA

institute: University of Arkansas for Medical Sciences

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2C01-1475

hyb_protocol: Standard Illumina Infinium HD protocol

scan_protocol: Standard Illumina scanning protocol on S101 BeadArray reader

data_processing:
Intensity data were extracted in Genome Studio (v2010.3); SNPs with GenTrain score <0.15 were not called.
Gtype:  genotype of this SNP for the sample; Score: GenTrain score indicating how well sample clustered for this locus;  Theta: the allelic intensity ratio; B Allele Freq: B allele frequency calculated as theta value for a SNP corrected for cluster position; Log R ratio: normalized intesity ratio for sample marker relative to values of the surrounding clusters

label: C-Bio; A-DNP

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Infinium HD protocol

extract_protocol: DNA is extracted from WBC pelleted from peripheral blood  after RBC lysis in 0.15M NH4Cl.  WBC are lysed overnight at 55 °C in WBC lysis solution (Qiagen), and protein precipitated and spun at 4 °C in protein precipitation solution (Qiagen).  DNA is preciptated in ethanol, pelleted and resuspended in 10mM Tris EDTA.

tag: gender

value: Female

tag: tissue

value: Peripheral Blood

tag: relationship to proband

value: Proband

tag: dba phenotype

value: DBA


title: PeripheralBlood_DBA_Proband_412 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1A02-412


title: Extraembryonic_tissue 260_2M, source AI, cDNA labeled with dye Cy5.

type: RNA

state: IL

description:
The cDNA from the extraembryonic tissue RNA and the reference standard was coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = Extraembryonic tissue
Keywords = bovine
Keywords = AI pregnancy
Keywords = microarray

hyb_protocol: Each Cy5-labeled sample was combined with a Cy3-labeled reference, vacuum dried, and resuspended in 40 µl of ddH2O containing 10 µg of bovine Cot1 DNA, 20 µg oligo dT.  After denaturation for 3 min at 94°C and reannealing for 10 min at 60°C, 40 µl of 2x hybridization buffer (50% formamide, 10x SSC, 02% SDS) was added and the mixture was hybridized to the microarray for 40 hrs. Microarrays were subsequently washed in a series of SSC/SDS washes (1xSSC/0.2% SDS, 0.1xSS/0.2% SDS, 0.1xSSC)to remove unbound cDNA.  After washing, arrays were dried by centrifugation and stored in argon gas until scanning (max. ~1 hr).

scan_protocol: The microarray image was acquired using a GenePix 4000B scanner and analyzed using GenePix Pro 6.0 using the autobalance feature and a saturation threshold of 0.05%. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).

molecule: total RNA

source_name: Extraembryonic_tissue 260_2M, type: AI, sex: Female, labeled with Cy5

label_protocol: The RNA (10 µg) was annealed with 6 µg random N6, and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 46°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.  The cDNA was covalently coupled with Cy5-monoreactive dye in 50 mM sodium bicarbonate, pH 9.0. The Cy5-labeled cDNA was purified with a QIAquick PCR purification column. Each labeled sample was analyzed using a spectrophotometer to assess dye incorporation.

tag: Extraembryonic tissue total RNA was isolated by Trizol

source_name: reference standard RNA, labeled with Cy3

label_protocol: The RNA (10 µg) was annealed with 6 µg random N6, and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 46°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column. The cDNA was covalently coupled Cy3-monoreactive dye in 50 mM sodium bicarbonate, pH 9.0. The Cy3-labeled cDNA was purified with a QIAquick PCR purification column. Each labeled reference was analyzed using a spectrophotometer to assess dye incorporation.


title: Extraembryonic_tissue 260_1M, source AI, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 260_1M, type: AI, sex: Female, labeled with Cy5


title: Extraembryonic_tissue 351, source AI, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 351, type: AI, sex: Female, labeled with Cy5


title: NOD.Pan.CD45 #1

status: Public on Jan 14 2012

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Gender: female; Age: 10 weeks; Isolation: FACS of CD45+ cells from pancreas; Strain: NOD

hyb_protocol: BioArray High Yield RNA transcript labeling T7 kit (Enzo Life Sciences)

scan_protocol: Standard Affymetrix protocol

data_processing: Standard RMA normalization (RMA-bg adjustment, quantile normalization, median polish probeset summarization) using Affymetrix Power Tools. Output on 2^ scale.

label: biotin

organism: Mus musculus

source_name: pancreatic CD45+ cells

label_protocol: biotin

extract_protocol: TriZol

tag: strain

value: WT NOD

value: female

tag: age

value: 10 week

tag: cell type

value: FACS of CD45+ cells from pancreas

tag: mri t2 value


title: PeripheralBlood_DBA_Proband_999 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1C02-999

value: Male


title: Extraembryonic_tissue 260_2M, source AI, cDNA labeled with dye Cy3.

source_name: Extraembryonic tissue 260_2M, type: AI, sex: female, labeled with Cy3


title: Extraembryonic_tissue 260_1M, source AI, cDNA labeled with dye Cy3.

source_name: Extraembryonic tissue 260_1M, type: AI, sex: female, labeled with Cy3


title: Extraembryonic_tissue 196, source NT, cDNA labeled with dye Cy3.

description:
The cDNA from the extraembryonic tissue RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = Extraembryonic tissue
Keywords = bovine
Keywords = NT pregnancy
Keywords = microarray

source_name: Extraembryonic tissue 196, type: NT, sex: female, labeled with Cy3


title: Extraembryonic_tissue 187_1M, source AI, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 187_1M, type: AI, sex: Female, labeled with Cy5


title: PeripheralBlood_DBA_Proband_2302 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1A01-2302


title: PeripheralBlood_DBA_Proband_1269 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2B01-1269


title: Extraembryonic_tissue 187_2M, source AI, cDNA labeled with dye Cy3.

source_name: Extraembryonic tissue 187_2M, type: AI, sex: female, labeled with Cy3


title: PeripheralBlood_DBA_Proband_924 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3B2-924


title: Extraembryonic_tissue 196, source NT, cDNA labeled with dye Cy5.

description:
The cDNA from the extraembryonic tissue RNA and the reference standard was coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = Extraembryonic tissue
Keywords = bovine
Keywords = NT pregnancy
Keywords = microarray

source_name: Extraembryonic_tissue 196, type: NT, sex: Female, labeled with Cy5


title: Extraembryonic_tissue 187_1M, source AI, cDNA labeled with dye Cy3.

source_name: Extraembryonic tissue 187_1M, type: AI, sex: female, labeled with Cy3


title: Extraembryonic_tissue 202, source NT, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 202, type: NT, sex: Female, labeled with Cy5


title: Extraembryonic_tissue 86, source NT, cDNA labeled with dye Cy3.

source_name: Extraembryonic tissue 86, type: NT, sex: female, labeled with Cy3


title: Extraembryonic_tissue 187_2M, source AI, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 187_2M, type: AI, sex: Female, labeled with Cy5


title: Extraembryonic_tissue 177, source NT, cDNA labeled with dye Cy3.

source_name: reference standard RNA, labeled with Cy5

source_name: Extraembryonic tissue 177, type: NT, sex: female, labeled with Cy3


title: PeripheralBlood_DBA_Proband_727 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1G01-727


title: Extraembryonic_tissue 86, source NT, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 86, type: NT, sex: Female, labeled with Cy5


title: Extraembryonic_tissue 177, source NT, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 177, type: NT, sex: Female, labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Extraembryonic_tissue 202, source NT, cDNA labeled with dye Cy3.

source_name: Extraembryonic tissue 202, type: NT, sex: female, labeled with Cy3


title: Extraembryonic_tissue 83, source AI, cDNA labeled with dye Cy3.

source_name: Extraembryonic tissue 83, type: AI, sex: female, labeled with Cy3


title: Extraembryonic_tissue 63, source NT, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 63, type: NT, sex: Female, labeled with Cy5


title: Extraembryonic_tissue 63, source NT, cDNA labeled with dye Cy3.

source_name: Extraembryonic tissue 63, type: NT, sex: female, labeled with Cy3


title: Embryonic_Disk 351, source AI, cDNA labeled with dye Cy5.

description:
The cDNA from the embryonic disk RNA and the reference standard was coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = Embryonic_Disk
Keywords = bovine
Keywords = AI pregnancy
Keywords = microarray

source_name: Embryonic_Disk 351, type: AI, sex: Female, labeled with Cy5

tag: Embryonic Disk total RNA was isolated by Trizol


title: Embryonic_Disk 351, source AI, cDNA labeled with dye Cy3.

description:
The cDNA from the embryonic disk RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = Embryonic Disk
Keywords = bovine
Keywords = AI pregnancy
Keywords = microarray

source_name: Embryonic Disk 351, type: AI, sex: female, labeled with Cy3

tag: Embryonic Disk total RNA isolated by Trizol


title: Extraembryonic_tissue 83, source AI, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 83, type: AI, sex: Female, labeled with Cy5


title: Embryonic_Disk 187_2, source AI, cDNA labeled with dye Cy3.

source_name: Embryonic Disk 187_2, type: AI, sex: female, labeled with Cy3


title: Embryonic_Disk 196, source NT, cDNA labeled with dye Cy3.

description:
The cDNA from the embryonic disk RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = Embryonic Disk
Keywords = bovine
Keywords = NT pregnancy
Keywords = microarray

source_name: Embryonic Disk 196, type: NT, sex: female, labeled with Cy3


title: Embryonic_Disk 196, source NT, cDNA labeled with dye Cy5.

description:
The cDNA from the embryonic disk RNA and the reference standard was coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner dual-laser confocal scanner and images were processed using GenePix 6.0 (Axon Instruments, Inc., CA).
Keywords = Embryonic_Disk
Keywords = bovine
Keywords = NT pregnancy
Keywords = microarray

source_name: Embryonic_Disk 196, type: NT, sex: Female, labeled with Cy5


title: Embryonic_Disk 260_1, source AI, cDNA labeled with dye Cy3.

source_name: Embryonic Disk 260_1, type: AI, sex: female, labeled with Cy3


title: Embryonic_Disk 202, source NT, cDNA labeled with dye Cy5.

source_name: Embryonic_Disk 202, type: NT, sex: Female, labeled with Cy5


title: Extraembryonic_tissue 43, source NT, cDNA labeled with dye Cy3.

source_name: reference standard RNA, labeled with Cy5

source_name: Extraembryonic tissue 43, type: NT, sex: female, labeled with Cy3


title: Embryonic_Disk 260_1, source AI, cDNA labeled with dye Cy5.

source_name: Embryonic_Disk 260_1, type: AI, sex: Female, labeled with Cy5


title: Embryonic_Disk 202, source NT, cDNA labeled with dye Cy3.

source_name: Embryonic Disk 202, type: NT, sex: female, labeled with Cy3


title: Extraembryonic_tissue 43, source NT, cDNA labeled with dye Cy5.

source_name: Extraembryonic_tissue 43, type: NT, sex: Female, labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Embryonic_Disk 187_2, source AI, cDNA labeled with dye Cy5.

source_name: Embryonic_Disk 187_2, type: AI, sex: Female, labeled with Cy5


title: Embryonic_Disk 187_1, source AI, cDNA labeled with dye Cy3.

source_name: Embryonic Disk 187_1, type: AI, sex: female, labeled with Cy3


title: Embryonic_Disk 86, source NT, cDNA labeled with dye Cy3.

source_name: Embryonic Disk 86, type: NT, sex: female, labeled with Cy3


title: Embryonic_Disk 63A1, source NT, cDNA labeled with dye Cy5.

source_name: Embryonic_Disk 63A1, type: NT, sex: Female, labeled with Cy5


title: Embryonic_Disk 63A2, source NT, cDNA labeled with dye Cy3.

source_name: Embryonic Disk 63A2, type: NT, sex: female, labeled with Cy3


title: Embryonic_Disk 43, source NT, cDNA labeled with dye Cy3.

source_name: Embryonic Disk 43, type: NT, sex: female, labeled with Cy3


title: E3_96h

city: Luxembourg

first: Antony

last: Le Bechec

address: 162a avenue de la faïencerie

department: Life sciences research unit

country: Luxembourg

institute: University of Luxembourg

hyb_protocol: The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments. hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (Gao et al., 2004; Zhu et al., 2007). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2hPO4, 6 mM EDTA, ph 6.8) containing 25% formamide at 34 °C. Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596 Zhu, Q., hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (Bolstad et al., 2003). For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values. Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

source_name: MCF7_SNAI1_Not induced_96h

label_protocol: After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining.

growth_protocol: Cells were grown at 37°C, under 5% CO2 atmosphere. Non-induced MCF7-Tet-Off SNAI1 cells were cultured in DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 10% fetal bovine serum, L-Glutamine, penicillin and streptomycin, G418 (100ug/ml), hygromycin (200ug/ml) and tetracycline (1,5ug/ml). For SNAI1 induction tetracycline was removed from the culture media.

extract_protocol: Total RNAs were extracted using Trizol as recommended by manufacturer (Invitrogen).

treatment_protocol: The tet-off (tetracycline-repressed) MCF-7-SNAI1 cell lines were established. SNAI1 expression in MCF7 stably transfected cells was induced by removing tetracyclin from culture media according to the procedure recommended by BD biosciences Clontech Company (Protocol PT13001-1). To carry out the transcriptional analysis in temporal manner after SNAI1 induction in MCF7-SNAI1 cells, induction of cell was performed at each time point studied. See Vetter and Le Béchec et al. (2009) for more information.

tag: cell line

value: breast cancer cells

tag: genotype/variation

tag: conditional expression of snai1

value: Not induced

tag: time point

value: Induced


title: Embryonic_Disk 83, source AI, cDNA labeled with dye Cy3.

tag: reference total RNA was isolated by Trizol and consists of equal amounts total RNA extracted from EBTr, MDBK, and BL30 cell lines, and brain tissue

source_name: Embryonic Disk 83, type: AI, sex: female, labeled with Cy3


title: Embryonic_Disk 83, source AI, cDNA labeled with dye Cy5.

source_name: Embryonic_Disk 83, type: AI, sex: Female, labeled with Cy5


title: Embryonic_Disk 63A2, source NT, cDNA labeled with dye Cy5.

source_name: Embryonic_Disk 63A2, type: NT, sex: Female, labeled with Cy5


title: Embryonic_Disk 43, source NT, cDNA labeled with dye Cy5.

source_name: Embryonic_Disk 43, type: NT, sex: Female, labeled with Cy5


title: E3_48h

source_name: MCF7_SNAI1_Not induced_48h


title: E3_12h

source_name: MCF7_SNAI1_Not induced_12h


title: E3_24h

source_name: MCF7_SNAI1_Not induced_24h


title: E3_72h

source_name: MCF7_SNAI1_Not induced_72h


title: Embryonic_Disk 86, source NT, cDNA labeled with dye Cy5.

source_name: Embryonic_Disk 86, type: NT, sex: Female, labeled with Cy5


title: Embryonic_Disk 187_1, source AI, cDNA labeled with dye Cy5.

source_name: Embryonic_Disk 187_1, type: AI, sex: Female, labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: E3_8h

source_name: MCF7_SNAI1_Not induced_8h


title: Embryonic_Disk 63A1, source NT, cDNA labeled with dye Cy3.

source_name: reference standard RNA, labeled with Cy5

source_name: Embryonic Disk 63A1, type: NT, sex: female, labeled with Cy3


title: E3_4h

source_name: MCF7_SNAI1_Not induced_4h


title: Control-3

city: Philadelphia

first: xin

last: wu

state: PA

address: 3850 baltimore Ave,

department: Animal Biology

institute: School of Veterinary Medicine, University of Pennsylvania

description: Biological replicate 3 of 5. Nature born mouse

hyb_protocol: Follow the standard steps of Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis and Operated by Microarray Core of Unversity of Pennsylvania

data_processing:
Agilent feature extraction files were imported into Partek Genomics Suite v6.5. Signals were processed from extracted green (Cy3) and red (Cy5) for each position on each array. Loess normalization per array-position was applied, which resulted in normalized intensities for each experimental sample vs. the pooled reference DNA (Cy3 labeled). Inter-sample variation was visualized using PCA ≥ observed gender difference as the only defined attribute that separated the samples. Grossly, Cryopreserved ICSI-derived progeny vs. Control wild-type progeny, did not separate samples, and no gross differences were observed for all chromosomes from plotted averages of probe intensities for Cryopreserved ICSI-derived progeny vs. Control wild-type progeny (smoothed over 9 probes). 2-way anova (factors were Cryopreserved ICSI-derived progeny vs. Control wild-type progeny, and sex) was applied for all probes and generated a t-statistic for the pairwise-contrast between Cryopreserved ICSI-derived progeny vs. Control wild-type progeny.
For detection of significant regions differentiating Cryopreserved vs. Control, no regions were found to have detectable difference at default parameters (pval ≤ 0.01, fragment length 300, min 10 probes, 10% high and low excluded).

source_name: nature born mouse

growth_protocol: Viable progeny produced from 14 year ago cryopreserved germ cells

extract_protocol: A small piece of mouse liver was used to isolate genomic DNA. Tissue was incubated with proteinase K overnight, then DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA).

treatment_protocol: Three groups of DNA were collected for CGH as pooled reference DNA. Specifically, DNA, in equal amounts, from adult mice of C57BL/6, SJL and DBA strains were pooled as the pooled reference DNA. DNA from adult, wild-type ZFLacZ progeny was collect as Control wild-type DNA; DNA from ZFLacZ progeny derived from cryopreserved testis cells via ICSI was collected as Cryopreserved ICSI-derived DNA.

value: ZFLacZ progeny

value: male

value: liver

source_name: Pooled Reference DNA

tag: reference source

value: DNA, in equal amounts, from adult mice of C57BL/6, SJL, and DBA strains

tag: tissue source


title: Control-1

description: Biological replicate 1 of 5. Nature born mouse

scan_protocol: Follow the standard steps of Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis and Operated by Microarray Core of Unversity of Pennsylvania

tag: gender

tag: tissue


title: E2_96h

source_name: MCF7_SNAI1_Not induced_96h


title: Control-5

description: Biological replicate 5 of 5. Nature born mouse

label_protocol: Follow the standard steps of Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis and Operated by Microarray Core of Unversity of Pennsylvania


title: E2_72h


title: E2_48h


title: Control-4

description: Biological replicate 4 of 5. Nature born mouse


title: Control-2

description: Biological replicate 2 of 5. Nature born mouse


title: OT2162-5

description: Biological replicate 5 of 5. ICSI-derived mouse

source_name: ICSI-derived mouse

value: ZFLacZ progeny derived from cryopreserved testis cells via ICSI

tag: strain background

value: ♂ (ZFLacZ sperm) x ♀ (DBA x C57BL/6 oocyte), where the ZFLazZ transgenic mice were originally generated from an SJL x C57BL/6 background.


title: E2_12h


title: E2_8h


title: E2_24h


title: OT2162-3

description: Biological replicate 3 of 5. ICSI-derived mouse


title: OT2162-2

description: Biological replicate 2 of 5. ICSI-derived mouse


title: OT2162-1

description: Biological replicate 1 of 5. ICSI-derived mouse


title: E2_4h


title: E1_96h


title: E1_4h


title: E1_8h


title: E1_12h


title: E1_48h


title: E1_72h


title: E13.5_wildtype_Pax9_Mes_2

first: Joshua

middle: WK

last: Ho

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

description: Dental Mesenchyme isolated from the mandible using LCM

hyb_protocol: Illumina protocol for the cRNA samples and NuGEN's modified Illumina hybridization protocol for the LCM generated cDNA samples.

scan_protocol: Illumina protocol

data_processing: lumi R package using the log2 transformation and robust spline normalization. Furthermore, we used R package comBat to remove batch effect that were introduced due to using microarray data generated by cRNA and cDNA

label: Biotin-Labeled cDNA

source_name: Mouse LCM, E13.5_Mes

label_protocol: NuGEN Illumina Bead Array Application Note: Uracil Glycolsylase treated, and Hydrazine biotinylated according to manufacturers instructions. Standard Illumina total RNA labeling protocol.

extract_protocol: Picopure RNA Isolation Kit, Molecular Devices, LCM generated profiles.  Rneasy Qiagen RNA extraction for the hand dissected profiles separated by Dispase.

value: Dental Mesenchyme

tag: tooth

value: First lower molar

tag: developmetal stage

tag: strain source

value: Harvard Medical School

tag: hybridizing molecule

value: cDNA


title: E13.5_Pax9_null_Mes_2

tag: strain


title: E13.5_Pax9_null_Epi_2

description: Dental Epithelium isolated from the mandible using LCM

source_name: Mouse LCM, E13.5_Epi

value: Dental Epithelium


title: E13.5_wildtype_Pax9_Mes_1


title: E13.5_Pax9_null_Epi_1


title: E13.5_wildtpye_Pax9_Epi2


title: E13.5_Pax9_null_Mes_1


title: E13.5_wildtype_Pax9_Mes_3


title: E13.5_wildtpye_Pax9_Epi3


title: E13.5_Pax9_null_Mes_3


title: E13.5_Msx1_null_Mes_3


title: E13.5_Msx1_null_Epi_1


title: E13.5_wildtype_Msx1_Mes_2


title: E13.5_Pax9_null_Epi_3


title: E13.5_Msx1_null_Mes_1


title: E13.5_Msx1_null_Mes_2


title: E13.5_wildtype_Msx1_Mes_1


title: E13.5_Msx1_null_Epi_2


title: E13.5_wildtype_Msx1_Epi_3


title: E13.5_wildtpye_Pax9_Epi1


title: E13.5_Msx1_null_Epi_3


title: E13.5_wildtype_Msx1_Epi_2


title: E1_24h

tag: cell type


title: E13.5_wildtype_Msx1_Mes_3


title: E13.0_intact_culture_Epi_2

description: Dental Epithelium isolated by hand using Dispase

source_name: Mouse Hand Dissected, E13_Epi

value: Charles River Laboratories

value: cRNA


title: E13.0_i-Gsk3b_Epi_2


title: E13.0_i-Gsk3b_Epi_1


title: E13.0_Shh_Epi_1


title: E13.0_Shh_Epi_2


title: OT2162-4

description: Biological replicate 4 of 5. ICSI-derived mouse

value: female


title: E13.0_Bmp4_Epi_2


title: E13.0_Fgf8_Epi_2


title: E13.0_intact_culture_Epi_3


title: E13.0_Fgf8_Epi_1


title: E13.0_Bmp4_Epi_3


title: E13.0_intact_culture_Epi_1


title: E13.0_Bmp4_Epi_1


title: E13.5_wildtype_Msx1_Epi_1


title: E10.0_intact_culture_Mes_2

source_name: Mouse Hand Dissected, E10_Mes


title: E13.0_isolated_Epi_3


title: E10.0_intact_culture_Mes_1


title: E10.0_isolated_Mes_3


title: E13.0_Fgf8_Epi_3


title: E10.0_intact_culture_Mes_3


title: E13.0_Shh_Epi_3


title: E13.0_i-Gsk3b_Epi_3


title: E10.0_i-Gsk3b_Mes_1


title: E10.0_isolated_Mes_1


title: E10.0_i-Gsk3b_Mes_3


title: E10.0_Shh_Mes_3


title: E10.0_Shh_Mes_2


title: E10.0_isolated_Mes_2


title: E13.0_isolated_Epi_1


title: E13.0_isolated_Epi_2


title: E10.0_i-Gsk3b_Mes_2


title: E10.0_Bmp4_Mes_3


title: E10.0_Fgf8_Mes_3


title: E10.0_Fgf8_Mes_1


title: E10.0_Bmp4_Mes_2


title: E10.0_Fgf8_Mes_2


title: E10.0_Shh_Mes_1


title: E13_Mes_2

source_name: Mouse Hand Dissected, E13_Mes


title: E11_Mes_2

source_name: Mouse Hand Dissected, E11_Mes


title: E13_Mes_1


title: E11_Epi_1

source_name: Mouse Hand Dissected, E11_Epi


title: E10_Epi_2

source_name: Mouse Hand Dissected, E10_Epi


title: E10.0_Bmp4_Mes_1


title: E14.5_EK_3

source_name: Mouse LCM, E14.5_Epi


title: E14.5_EK_2


title: E11_Epi_2


title: E13_Epi_2


title: E11_Mes_1


title: E10_Epi_1


title: E13_Epi_1


title: E14.5_EK_1


title: E13.5_Epi_3


title: E13.0_Mes_3

source_name: Mouse LCM, E13.0_Mes


title: E13.5_Mes_2


title: E13.0_Mes_2


title: E13.5_Mes_3


title: E13.5_Mes_1


title: E10_Mes_1


title: E10_Mes_2


title: E13.0_Epi_3

source_name: Mouse LCM, E13.0_Epi


title: E13.5_Epi_2


title: E12.5_Epi_1

source_name: Mouse LCM, E12.5_Epi


title: E13.0_Mes_1


title: E13.0_Epi_2


title: E13.5_Epi_1


title: E12.5_Epi_3


title: E12.5_Mes_1

source_name: Mouse LCM, E12.5_Mes


title: E12.5_Epi_2


title: E12.0_Mes_3

source_name: Mouse LCM, E12.0_Mes


title: E12.0_Mes_1


title: E12.5_Mes_3


title: E13.0_Epi_1


title: E12.0_Epi_3

source_name: Mouse LCM, E12.0_Epi


title: E12.0_Mes_2


title: E12.0_Epi_1


title: E11.5_Mes_3

source_name: Mouse LCM, E11.5_Mes


title: E11.5_Mes_2


title: E12.5_Mes_2


title: E12.0_Epi_2


title: E11.5_Epi_3

source_name: Mouse LCM, E11.5_Epi


title: yeast-wildtype-03

city: Suwon-si

first: ga

middle: hee

last: shin

address: Gosaek-dong

country: South Korea

institute: Insilicogen

description: Analyzed unique probe was 906 genes.

hyb_protocol: Hybridization is performed with 5 μg of a labeled target sample per one CustomArray™ 4x2K microarray. Hybridizations were performed for 16 h at 45_C with gentle rotation. Thereafter, the arrays were washed (i) 6X SSPE, 0.05% Tween -20 for 5 min; (ii) 3X SSPE, 0.05% Tween -20 for 1 min; and (iii) 0.5X SSPE, 0.05% Tween -20 for 1 min; (iv) 2X PBS, 0.1% Tween -20 for 1 min. Biotin-labeled, performed for 30min with gentle rotation. Thereafter, the arrays were washed (i) 2X PBS, 0.1% Tween -20 for 1min; (ii) 2X PBS for 1 min. Lay the LifterSlip™ at an angle onto the microarray so that it is centered over the semiconductor area. First touch the Imaging Solution with one side of the LifterSlip™, then slowly lower the slip down, taking care not to introduce air bubbles.

scan_protocol: Hybridized microarrays were scanned PMT 500~700, Pixel size 5, Focus position 130, using a GenePix 4000B microarray scanner (Axon Instruments, Union City).

data_processing: After data extraction, the median of three or four replicate spots for each probe was calculated. Probes with missing value, signal value greater than 1 and signal value lesser than 60,000(saturation value) were excluded.The log-transformed fluorescent signal were calculated background-subtracted median intensity values. These data were used to perform Median (Global)  normalization before statistic analysis.

organism: Saccharomyces cerevisiae

source_name: wild type strain

label_protocol: The MessageAmp™ II-Biotin Enhanced (Ambion , Cat #1791, USA) Single Round aRNA Amplification Kit is based on the RNA amplification protocol developed in the laboratory of James Eberwine (Van Gelder et al. 1990). The procedure consists of reverse transcription with an oligo(dT) primer bearing a T7 promoter using ArrayScript™, a reverse transcriptase (RT) engineered to produce higher yields of first strand cDNA than wild type enzymes. ArrayScript catalyzes the synthesis of virtually full-length cDNA, which is the best way to ensure production of reproducible microarray samples. The cDNA then undergoes second strand synthesis and clean-up to become a template for in vitro transcription in a reaction containing biotin-modified UTP and T7 RNA Polymerase. To maximize biotin-labeled aRNA yield, an optimized mixture of biotin-labeled and unlabeled NTPs are supplied with kit, and Ambion’s proprietary MEGAscript ® in vitro transcription (IVT) technology is used to generate hundreds to thousands of antisense RNA copies of each mRNA in a sample.

extract_protocol: extraction by TRIzol RNA preperation method

value: wild type


title: yeast-ACCoverexpression-03

description: Analyzed unique probe was 906 genes.

source_name: ACC1 overexpressed wild type

value: ACC1 overexpressed wild type


title: yeast-ACCoverexpression-01

description: Analyzed unique probe was 906 genes.


title: E11.5_Mes_1


title: LmnaG609G/G609G KI #1. 461

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

hyb_protocol: The biotin-labeled cRNA was purified, fragmented, and hybridized to a GeneChip Mouse Gene 1.0 ST Array (Affymetrix).

scan_protocol: Washing and scanning were performed with a Fluidics Station 400 and GeneChip Scanner (Affymetrix).

data_processing: After scanning, raw data were processed with the RMAExpress program (http://RMAExpress.bmbolstad.com), using default settings.

source_name: Liver, LmnaG609G/G609G

label_protocol: Double-stranded cDNA was synthesized using the SuperScriptTM cDNA synthesis kit (Invitrogen). In vitro transcription was carried out with the Bioarray high-yield RNA transcript labeling kit (Enzo Diagnostics).

growth_protocol: Animals were maintained in the animal facility of the University of Oviedo. 3 knock-in and 3 wild-type female animals were killed, and total RNA was isolated from liver samples

extract_protocol: Total RNA was isolated using an RNeasy kit (Qiagen).

treatment_protocol: Animals were starved for 6 h before sacrifice

tag: genetic background

tag: genotype

value: LmnaG609G/G609G knock-in

tag: age

value: 3 mo


title: yeast-wildtype-01

description: Analyzed unique probe was 906 genes.


title: wt #2. 462

source_name: Liver, wild-type

value: wt


title: LmnaG609G/G609G KI #5. 465

value: liver


title: wt #4. 464


title: E11.5_Epi_2


title: wt #6. 466


title: LmnaG609G/G609G KI #3. 463


title: yeast-ACCoverexpression-02

description: Analyzed unique probe was 906 genes.


title: yeast-wildtype-02

description: Analyzed unique probe was 906 genes.


title: E11.5_Epi_1


title: SE1457 wild type strain after 12 hours of growth replicate 3

status: Public on Jan 12 2012

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Staphylococcus epidermidis strain SE1457 WT versus Staphylococcus epidermidis gDNA pool

hyb_protocol: A mixture of RNA from WT or DsaeRS strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing:
Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method
Microarray analysis: Hybridization fluorescence intensities were quantified using Feature Extraction software (Agilent, version 8). Feature extraction green and red signal values (g-processed and r-processed) were imported in Partek genomics suite software (Partek). Values were normalized to baseline using r-processed data as control and mean to estimate baseline (Talaat, NAR, 2002). Variance analysis of three biological replicates was processed with a false discovery rate value of 5% (P value cutoff, 0.05) and an arbitrary threshold of 3.0 fold for selecting significant differences in expression ratios.

organism: Staphylococcus epidermidis

source_name: S. epidermidis SE1457 WT

label_protocol: Incorporation during reverse transcription

growth_protocol: 4 or 12 hours growth in Tryptic Soy Broth

extract_protocol: RNAprotectTM Bacteria Reagent (Qiagen, Hilden, Germany) and immediately incubated on ice. After centrifugation for 10 min at 6.000 x g and 4°C, the supernatant was discarded and the pellet resuspended in 1 ml RLT-buffer (Qiagen) supplemented with 1 % (vol/vol) β-mercaptoethanol. Cells were disrupted in Lysing Matrix E (MP Biomedicals) using a FastPrep®-24 (MP Biomedicals, Solon, OH, USA), followed by cooling on ice for 2 min. After brief centrifugation, the supernatant was purified using RNeasy®Mini Kit. Final treatment with DNase for 1 h at 37°C and again purified with RNeasy®Mini Kit. Genomic DNA extraction: Genomic DNA from S. aureus strains was extracted using the DNeasy extraction kit (Qiagen, Hilden, Germany) following manufacturer s protocol with the following modifications: fresh colonies harvested from agar plates were washed with 500 l TE 1X and centrifuged for 10 minutes at 3 000g. Then, suspended in 200 l TE 1X with 10 l lysostaphin (Sigma; 50 g/ml final concentration) and incubated for 5 minutes at 37 C. The DNeasy protocol was then followed except for the elution step where we used 50ul RNase-DNAse-free water (Sigma).

tag: genotype/variation

tag: growth time

value: 12 hours

source_name: gDNA pool

tag: reference

value: Staphylococcus epidermidis gDNA mixture


title: SE1457 wild type strain after 12 hours of growth replicate 2


title: SE1457 wild type strain after 4 hours of growth replicate 3

value: 4 hours


title: hSFC TCDD 1nM 24h Cell 2

city: tsukuba

first: Sone

last: Hideko

state: ibaraki

department: Center for Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

description: Gene expression after 24h 1nM TCDD treatment

hyb_protocol: Sampleswere then hybridized to the G4851A SurePrint G3 Human GE 8x60Karray slides (60000 probes, Agilent Technologies).

scan_protocol: The arrays were scanned using Agilent Microarray Scanner (G2565BA, Agilent Technologies).

data_processing: The scanned images were analyzed using the standard procedures described in Agilent Feature Extraction software 9.5.3.1 (Agilent Technologies). Data analysis was performed with GeneSpring GX12.0.2 (Agilent Technologies).

source_name: human skin fibroblast cells, 24h, 1nM TCDD, Cell2

label_protocol: RNA was amplified into cRNA and labeled with Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies).

growth_protocol: hSFCs were maintained in DMEM/Ham's F-12 (048-29785, Wako, Osaka, Japan) containing 10% fetal bovine serum (FBS, Mediatech, Herndon, VA) and grown at 37°C in a 5% CO2 humidified incubator. For growth under steroid-free conditions, the cells were seeded in phenol red-free DMEM/Ham's F-12 (045-30665, Wako) containing 5% charcoal/dextran-treated FBS (Hyclone, Logan, UT). All the culture media contained 100 U/ml penicillin/streptomycin and 2 mmol/L L-glutamine (Mediatech, Herndon, VA).

extract_protocol: Total RNA was isolated from the culture cells after treated with chemicals for 24 h using an RNeasy Kit (Qiagen, Valencia, CA) in accordancewith the manufacturer’s instructions. Quantification and quality assessment of theisolated RNA samples were performed and verified using an Agilent Bioanalyzer2100 (Agilent Technologies, Palo Alto, CA)and aNanoDrop spectrophotometer (NanoDrop products, Wilmington, DE) in accordancewith the manufacturer’s instructions.

tag: congenital condition

value: hypospadias

tag: treatment

value: 1 nM TCDD

value: Skin fibroblast

value: Male


title: hSFC TCDD 1nM 24h Cell 1

source_name: human skin fibroblast cells, 24h, 1nM TCDD, Cell1

tag: gender


title: hSFC E2 0.01nM 24h Cell 2

description: Gene expression after 24h 0.01nM E2 treatment

source_name: human skin fibroblast cells, 24h, 0.01nM E2, Cell2


title: hSFC BPA 10nM 24h Cell 2

description: Gene expression after 24h 10nM BPA treatment

source_name: human skin fibroblast cells, 24h, 10nM BPA, Cell2

value: 10 nM BPA


title: SE1457 wild type strain after 12 hours of growth replicate 1


title: SE1457 saeRS mutant strain after 12 hours of growth replicate 3

description: Staphylococcus epidermidis strain SE1457DsaeRS versus Staphylococcus epidermidis gDNA pool

source_name: S. epidermidis SE1457DsaeRS

value: saeRS mutant


title: hSFC E2 0.01nM 24h Cell 1

source_name: human skin fibroblast cells, 24h, 0.01nM E2, Cell1


title: hSFC DMSO 24h Cell 1

description: Gene expression after 24h DMSO treatment

source_name: human skin fibroblast cells, 24h, DMSO, Cell1

value: DMSO


title: hSFC DMSO 24h Cell 2

source_name: human skin fibroblast cells, 24h, DMSO, Cell2


title: hSFC BPA 10nM 24h Cell 1

source_name: human skin fibroblast cells, 24h, 10nM BPA, Cell1


title: SE1457 wild type strain after 4 hours of growth replicate 2


title: hSFC TCDD 1nM 24h Cell 3

source_name: human skin fibroblast cells, 24h, 1nM TCDD, Cell3


title: SE1457 wild type strain after 4 hours of growth replicate 1


title: hSFC BPA 10nM 24h Cell 3

source_name: human skin fibroblast cells, 24h, 10nM BPA, Cell3


title: hSFC E2 0.01nM 24h Cell 3

source_name: human skin fibroblast cells, 24h, 0.01nM E2, Cell3


title: SE1457 saeRS mutant strain after 4 hours of growth replicate 3


title: SE1457 saeRS mutant strain after 12 hours of growth replicate 1


title: SE1457 saeRS mutant strain after 4 hours of growth replicate 2


title: hSFC DMSO 24h Cell 3

source_name: human skin fibroblast cells, 24h, DMSO, Cell3


title: SE1457 saeRS mutant strain after 4 hours of growth replicate 1


title: WT log vs dsrta log

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA). Images were quantified using ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA).

data_processing: scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244).

organism: Lactiplantibacillus plantarum

source_name: sampled at logarithmic growth (OD=1)

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: pH controled fermentor culture, 37 degrees, 1.5% glucose

extract_protocol: Quenching Buffer 66.7 mM HEPES (pH 6.5) 60%Methanol Extraction Mixture (Prepared in a screw-cap tube) -500 µl phenol/Chloroform -30 µl10% SDS -30 µl 3 M NaAc (pH 5.2) -500 mg glass-beads (75-150 µm) -400 µl TE buffer  1.For each sample prepare a tube with Extraction Mixture  2.Harvest cells and quench them immediately in Quenching Buffer. Add 4 volumes of Quenching Buffer ( 40°C) to 1 volume of cell culture  3.Mix and store the sample at -40°C  4.Centrifuge cells at -20°C at 9000 rpm for 10 minutes (Centrifuge RC5B)  5.Discard the supernatant; keep the cell pellet cooled and work quickly to prevent condensation of water. Transfer the pellet with a pre-cooled spatula to a screw-crap tube with Extraction Mixture  6.Mix the cell pellet thoroughly with Extraction Mixture by shaking by hand  7.Freeze the tube immediately in liquid nitrogen  8.Break cells in the Savant FastPrep FP120. Three times 40 seconds at speed 4.0 (cool cells between steps if necessary)  9.Centrifuge for 5 minutes at 4°C in an Eppendorf centrifuge at 10.000 rpm  10.Transfer 500 µl of the supernatant to a new tube. Add 400 µl chloroform (chloroform should be cooled at 4°C)  11.Centrifuge for 2 minutes in an Eppendorf centrifuge at full speed (4°C)  12.Continue with the High Pure RNA Isolation Kit from Roche (order # 1 828 665)  13.Incubate for 60 minutes with DnaseI, elute with 50 µl elution buffer   14.Store the RNA in at least 2 aliquots, one of 20 µl (for concentration and quality analysis and labelling) and one back-up of 30 µl at -80°C.

treatment_protocol: sampled at mid logarythmic and late stationary growth phase

tag: sample time

value: logarithmic growth (OD=1)

value: dsrta


title: SE1457 saeRS mutant strain after 12 hours of growth replicate 2


title: WT log vs WT log


title: dsrta stat vs dsrta stat

source_name: sampled in stationary phase

value: stationary phase


title: WT stat vs WT stat


title: WT stat vs dsrta stat


title: dsrta log vs WT log


title: dsrta log vs dsrta log


title: individual 57, T treatment

city: Stockholm

first: Johan

last: Hartman

department: Dept of Oncology and Pathology

country: Sweden

institute: Karolinska Institute

description:
57T
gene expression data from ligand treated mammospheres

hyb_protocol: Fragmented and labeled ST-cDNA was hybridized to HuGen 1.0 ST arrays and washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Preprocessing was performed in Affymetrix Expression Console (v. 1.1) using the following methods: Summarization: Median Polish (RMA), Normalization: Sketch-Quantile.

source_name: Invasive cancer_4OHT

label_protocol: Fragmentation and labeling were performed using NuGen Encore Biotin Module.

growth_protocol: Breast cancer stem cells were isolated and propagated from newly resected breast cancers. Cells forming mammospheres were used for experiment.

extract_protocol: RNA was amplified using NuGEN Ovation Pico WTA System followed by generation of ST-cDNA using WT Ovation Exon Module.

treatment_protocol: Mammospheres are treated with D (DPN), T (4OHT) or untreated (vehicle control).

tag: tissue origin

value: Invasive cancer

tag: breast cancer type

value: cells forming mammospheres

value: estrogen receptor beta inhibition by 4OHT


title: individual 84, D treatment

description:
84D
gene expression data from ligand treated mammospheres

source_name: Invasive cancer_DPN

value: estrogen receptor beta activation by DPN


title: individual 92, D treatment

description:
92D
gene expression data from ligand treated mammospheres


title: individual 69, D treatment

description:
69D
gene expression data from ligand treated mammospheres


title: individual 84, untreated

description:
84C
gene expression data from ligand treated mammospheres

source_name: Invasive cancer_untreated (vehicle control)

value: untreated (vehicle control)


title: individual 84, T treatment

description:
84T
gene expression data from ligand treated mammospheres


title: individual 57, D treatment

description:
57D
gene expression data from ligand treated mammospheres


title: individual 41, T treatment

description:
41T
gene expression data from ligand treated mammospheres

value: Ductal carcinoma in situ (DCIS)

value: unknown


title: individual 41, untreated

description:
41C
gene expression data from ligand treated mammospheres

source_name: DCIS_untreated (vehicle control)


title: individual 35, untreated

description:
35C
gene expression data from ligand treated mammospheres


title: dsrta stat vs WT stat


title: individual 35, T treatment

description:
35T
gene expression data from ligand treated mammospheres


title: individual 35, D treatment

description:
35D
gene expression data from ligand treated mammospheres


title: individual 33, T treatment

description:
33T
gene expression data from ligand treated mammospheres


title: individual 92, untreated

description:
92C
gene expression data from ligand treated mammospheres


title: individual 57, untreated

description:
57C
gene expression data from ligand treated mammospheres


title: individual 69, untreated

description:
69C
gene expression data from ligand treated mammospheres


title: individual 32, T treatment

description:
32T
gene expression data from ligand treated mammospheres


title: individual 33, untreated

description:
33C
gene expression data from ligand treated mammospheres


title: individual 32, D treatment

description:
32D
gene expression data from ligand treated mammospheres


title: individual 33, D treatment

description:
33D
gene expression data from ligand treated mammospheres


title: individual 32, untreated

description:
32C
gene expression data from ligand treated mammospheres


title: individual 92, T treatment

description:
92T
gene expression data from ligand treated mammospheres


title: P133A

city: Stanford

first: David

last: Fiorentino

state: CA

address: 900 Blake Wilbur Drive

department: Dermatology

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68146.gif

hyb_protocol: (labeled with Cy5) and amplified Human Universal Reference RNA (labeled with Cy3) (Stratagene, La Jolla, CA) were competitively hybridized to HEEBO (human exon evidence-based oligonucleotide) microarrays as described (http://www.microarray.org/sfgf/heebo.do).

scan_protocol: GenePix 4000A

data_processing: Array data were filtered based on fluorescent hybridization signal 1.5-fold over local background in either the Cy5 or the Cy3 channel and if the data were technically adequate in 80% of experiments. Array data underwent LOWESS normalization, and the data were displayed as a log2 ratio of LOWESS-normalized Cy5/Cy3 ratio (span parameter=0.4)

source_name: Stratagene Universal Human Reference

label_protocol: not provided

extract_protocol: not provided

value: Stratagene Universal Human Reference

source_name: N

extract_protocol: Poly-adenylated RNA was extracted from snap-frozen skin biopsy specimens (DM and lupus) using a two step method. First, total RNA was extracted with phenol-guanidine thiocyaniate extraction (RNAbee ,Tel-Test, Friendswood TX). Next, poly-adenylated RNA was purified using RNeasy Kit (Quiagen, Chatsworth, CA) according to the manufacturers instructions. Sample RNA and reference mRNA (Stratagene) were amplified using an Amino Allyl MessageAmp II aRNA kit (Ambion, Austin, TX).

tag: tissue

value: skin

value: 28 years

tag: organism part

value: arm

tag: disease state

value: Healthy

tag: individual

tag: Sex

value: F


title: P104

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68318.gif

source_name: C

value: 71 years

value: forearm

value: active


title: P122_06_26_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75991.gif

source_name: Primary human tissue skin

value: 53 years

value: cheek


title: P62

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68138.gif

value: 21 years

value: chest

value: inactive

value: M


title: P142b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68416.gif

value: 25 years

value: posterior neck


title: individual 41, D treatment

description:
41D
gene expression data from ligand treated mammospheres

value: Ductal carcinoma in situ (DCIS)

value: unknown

tag: cell type

value: cells forming mammospheres

value: estrogen receptor beta activation by DPN


title: P59

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68172.gif

value: Stratagene Universal Human Reference

value: skin

value: 42 years

value: upper back


title: P130a_07_02_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75999.gif

value: forearm

value: Healthy


title: P60_06_19_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75983.gif

value: 74 years

value: thigh

value: active

value: F


title: P11a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68622.gif

value: 47 years


title: P65

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68139.gif

value: 65 years

value: inactive

value: M


title: P_20

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68643.gif

source_name: C p.r.

value: finger (gottron)


title: P137c_07_02_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75995.gif

value: 28 years

value: buttock


title: P11b_06_15_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75950.gif

value: Stratagene Universal Human Reference

source_name: Primary Human Tissue Skin

value: arm


title: P89

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68336.gif

value: skin

value: 73 years


title: individual 69, T treatment

description:
69T
gene expression data from ligand treated mammospheres

value: Invasive cancer

value: cells forming mammospheres

value: estrogen receptor beta inhibition by 4OHT


title: P39

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68137.gif

source_name: B

value: 76 years

value: posterior neck


title: P25_06_15_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75951.gif

value: 23 years

value: forearm

value: Healthy

value: F


title: P59_06_19_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75955.gif

value: 42 years

value: upper back

value: active

value: M


title: P77

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68141.gif

value: Stratagene Universal Human Reference

value: 37 years

value: neck

value: inactive


title: P137a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68644.gif

value: skin

value: 28 years

value: arm


title: P129a_07_02_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76001.gif

value: 51 years


title: P25_5_21_06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68671.gif


title: P35

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68136.gif


title: P35_06_19_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75953.gif


title: P_10b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68684.gif

value: 61 years

value: posterior neck


title: P88_06_19_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75984.gif

value: 62 years

value: knee


title: P89_06_19_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75985.gif

value: 73 years

value: F


title: P142a_07_02_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75997.gif

value: 25 years

value: buttock

value: Healthy


title: P121

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68338.gif

value: Stratagene Universal Human Reference

value: 44 years

value: forearm

value: active

value: M


title: 9-1 tibia Bl6

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on the Affymetrix GeneChip Mouse Genome 430 2.0 Array followed by staining and washing in a GeneChip fluidics station 450  (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix)

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.20.0) of Bioconductor.

source_name: tibial articular cartilage and subchondral bone

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: Snap freeze in Liquid Nitrogen

extract_protocol: Samples were homogenized using the Fastprep-24 tissue-homogenizer (MP Biomedicals, Solon, OH, USA) in lysing matrix A tubes and RLT lysis buffer (RNeasy Fibrous Tissue kit (Qiagen, Chatsworth, CA, USA)). Samples were kept under pre-cooled conditions using the CryoPrep Adaptor. RNA was isolated with the RNeasy Fibrous Tissue kit (Qiagen) with proteinase K and deoxyribonuclease (DNaseI) treatment.

value: male

tag: strain

value: tibial articular cartilage/subchondral bone

value: 6 weeks

tag: genotype

value: wild-type


title: 6-1 tibia Bl6

tag: age


title: 14-tibia AC FRZB KO

value: Frzb -/-


title: 6-tibia AC FRZB KO


title: 8-1 tibia Bl6


title: 17-tibia AC FRZB KO


title: P129b_07_02_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76000.gif

value: skin

value: 51 years


title: P141b_06_26_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75994.gif

value: 22 years

value: posterior neck


title: P11b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68623.gif

value: 47 years

value: arm

value: F


title: Intestine_Ctrl_biological rep4

first: Chin

last: Chen

address: 300 Pasteur Drive

department: Pediatric Gastroenterology

institute: Stanford University School of Medicine

description: Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.

hyb_protocol: The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.

source_name: Mature proximal small intestine, first 5 cm immediately adjacent to the pylorus

label_protocol: The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.

extract_protocol: The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.

treatment_protocol: Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.

value: 6 months old

value: Pdx1flox/flox (Ctrl)

tag: litter

value: brother of the same litter


title: Intestine_KO_biological rep4

source_name: Mature proximal small intestine with intestinal epithelium-specific Pdx1 inactivation, first 5 cm immediately adjacent to the pylorus

growth_protocol: Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.

value: Pdx1flox/flox;VilCre (KO)


title: P39_06_19_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75954.gif

tag: reference

value: Stratagene Universal Human Reference

value: 76 years

value: active

value: M


title: P133a_07_02_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75996.gif

value: 28 years

value: Healthy


title: Intestine_KO_biological rep3

value: male


title: P130b_07_02_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75998.gif

value: skin

value: 53 years

value: buttock


title: P124_06_26_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75992.gif

value: 35 years

value: lower back


title: Intestine_Ctrl_biological rep2


title: P110

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68144.gif

source_name: A

value: 24 years

value: finger (gottron)

value: F


title: Intestine_KO_biological rep2

value: 6 months old

value: brother of the same litter


title: P36

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68624.gif

value: Stratagene Universal Human Reference

source_name: C r.

value: 64 years

value: dorsal hand


title: P141b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68313.gif

value: 22 years

value: posterior neck

value: M


title: P130a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68201.gif

value: forearm

value: Healthy


title: P135_06_26_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75993.gif

value: skin

value: 70 years

value: cheek


title: P66

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68140.gif

value: 35 years

value: chest

value: inactive


title: P33_06_19_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75952.gif

value: 59 years

value: arm

value: active

value: F


title: P11a_06_15_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75949.gif

value: Stratagene Universal Human Reference

value: 47 years


title: SH1000-targocil-30 min_rep3 (slide 504)

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

description:
Replicate 3
Raw data file: slide 504_CTL_Cy3_EXP_Cy5.txt
Processed data file: slide 504 log2 ratio.txt
An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus

hyb_protocol: Labelled cDNA hybridised in slides placed in  water bath for 16 h at 42 °C. Arrays then washed in 1x SSC (+0.02 % SDS)at room temperature for 2 and 5 min,  in  0.1x SSC+0.1%SDS for 5 min,  and then in 0.1x SSC for 10 min 2 times prior to drying and scanning.

scan_protocol: Arrays scanned using an Gene pix Microarray scaner, Gene pix professional, 4200A, axon Instrument scanner and Imagene version Pro 6.0 software.

data_processing:
Data analysis was carried out using Spotfinder, version 224 , MIDAS2_19, MadRalph_1.0_Final_011503 and SAM. The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. We used MIDAS software for data normalization.
Results of SAM analysis, and merging of replicate hybridizations are provided as supplementary files on the Series record.
In raw data files, channel A = Cy3 dye and channel B = Cy5 dye.

organism: Staphylococcus aureus

source_name: [EXPT] SH 1000 treated with targocil for30 min

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: An overnight S. aureus SH1000 culture was diluted (2% (v/v)) into 20 mL TSB medium in a 50 mL Erlenmeyer flask and grown at 37 °C with shaking at 200 rpm. For the targocil treatment experiments, S. aureus was grown to an OD600 ~0.4 and challenged with 8x MIC of targocil dissolved in DMSO for 30 min. Simultaneously, an equal amount of DMSO (final concentration 2% (v/v)) was added to the control culture, which was incubated along with the treated cultures. After 30 min, 5 mL aliquot was collected and used as a control for the 30 min treated culture.

extract_protocol: Bacterial cultures flushed directly into QIAGEN RNA protect before total RNA isolation using QIAGEN RNEasy Midi kit with on column DNAse digestion.

tag: agent

value: targocil

tag: time

value: 30 min

source_name: [CTL] S. aureus SH1000 treated with DMSO for 30 min

value: control


title: SH1000-targocil-30 min_rep3 (slide 556)

description:
Replicate 3
Raw data file: slide 556_CTL_Cy5_EXP_Cy3.txt
Processed data file: slide 556 log2 ratio.txt
An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus

treatment_protocol: For the targocil treatment experiments, S. aureus was grown to an OD600 ~0.4 and challenged with 8x MIC of targocil dissolved in DMSO for 30 min. Simultaneously, an equal amount of DMSO (final concentration 2% (v/v)) was added to the control culture, which was incubated along with the treated cultures. After 30 min, 5 mL aliquot was collected and used as a control for the 30 min treated culture.


title: Intestine_Ctrl_biological rep1

tag: gender

value: male

value: 6 months old

value: Pdx1flox/flox (Ctrl)

value: brother of the same litter


title: P137b_5_21_06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68627.gif

value: skin

value: 28 years

value: posterior neck

value: Healthy

value: M


title: P33_5_21_06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68672.gif

source_name: A c CA

value: 59 years

value: arm


title: Intestine_KO_biological rep1

description: Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.

value: Pdx1flox/flox;VilCre (KO)


title: SH1000-targocil-30 min_rep2 (slide 22)

description:
Replicate 2
Raw data file: slide 22_CTL_Cy5_EXP_Cy3.txt
Processed data file: slide 22 log2 ratio.txt
An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus


title: SH1000-targocil-30 min_rep2 (slide 20)

description:
Replicate 2
Raw data file: slide 20_CTL_Cy3_EXP_Cy5.txt
Processed data file: slide 20 log2 ratio.txt
An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus


title: P78

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68171.gif

value: Stratagene Universal Human Reference

value: 42 years

value: elbow

value: inactive


title: P7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68133.gif

value: 65 years

value: active

value: F


title: SH1000-targocil-30 min_rep1 (slide 15)

description:
Replicate1
Raw data file: slide 15_CTL_Cy5_EXP_Cy3.txt
Processed data file: slide 15 log2 ratio.txt
An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus

value: targocil

value: 30 min

value: control


title: P7_06_15_07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75948.gif

source_name: Primary Human Tissue from Skin

value: skin


title: SH1000-targocil-30 min_rep1 (slide 14)

description:
Replicate1
Raw data file: slide 14_CTL_Cy3_EXP_Cy5.txt
Processed data file: slide 14 log2 ratio.txt
An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus


title: P141a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68625.gif

value: 22 years


title: Intestine_Ctrl_biological rep3

value: male

value: 6 months old

value: Pdx1flox/flox (Ctrl)

value: brother of the same litter


title: aYap2

first: William

middle: T

last: Pu

address: 300 Longwood Ave

institute: Children's Hospital Boston

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affy Powertools

organism: Rattus norvegicus

source_name: P4 NRVM Ad:aYap1

label_protocol: Affy WT sense target labeling

growth_protocol: P4 Neonatal rat ventricular cardiomyocytes were cultured for 48 hours with AraC to deplete fibrobalsts. They were then treated with Ad:FLAG-YAP1 or Ad:LacZ for 48 hours in the absence of serum.

extract_protocol: Qiagen Rneasy

value: P4 neonatal rats

tag: treatment


title: aYap3


title: LacZ4

source_name: P4 NRVM Ad:LacZ

value: lacz


title: P88

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68143.gif

source_name: Stratagene Universal Human Reference

value: Stratagene Universal Human Reference

value: 62 years

value: knee

value: M


title: LacZ2


title: LacZ1


title: P79

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68142.gif

source_name: C

value: 46 years

value: neck

value: inactive


title: P134a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68415.gif

source_name: N

value: 45 years

value: posterior neck

value: Healthy


title: P103

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68464.gif

value: skin

value: 55 years

value: chest

value: active

value: F


title: second_trimester_euploid_AF_normalAFstudy_male5

status: Public on Jan 11 2012

city: Medford

first: Donna

middle: K

last: Slonim

address: 161 College Ave.

department: Computer Science

institute: Tufts University

description:
maleAF5
gene expression data from normal second trimester fetus

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.

label_protocol: Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

extract_protocol: RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA).  RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).

value: male

tag: developmental stage

value: fetus

tag: rna source

value: cell free mRNA from second trimester amniotic fluid


title: LacZ3

value: P4 neonatal rats

value: lacz


title: aYap1


title: aYap4


title: LY2 SRC1-siRNA untreated rep4

city: Dublin

first: Yuan

last: Hao

state: Ireland

address: Bioinformatics,Conway Institute, UCD

country: Ireland

institute: UCD

description: Gene expression data from endocrine resistant breast cancer cell line LY13

hyb_protocol: Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.

scan_protocol: The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.

source_name: LY2 cell line, SRC-1 siRNA untreated, biological rep4

label_protocol: Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process.  The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.

extract_protocol: RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.

treatment_protocol: siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions.  siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644  working concentration 40nM).  Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.

tag: cell line

tag: phenotype

value: Tamoxifen resistant

tag: knockdown

value: SRC-1 siRNA

value: untreated


title: LY2 control-siRNA untreated rep4

description: Gene expression data from endocrine resistant breast cancer cell line LY14

source_name: LY2 cell line, SRC-1 scrambled untreated, biological rep4

value: SRC-1 scrambled


title: LY2 control-siRNA untreated rep1

description: Gene expression data from endocrine resistant breast cancer cell line LY11

source_name: LY2 cell line, SRC-1 scrambled untreated, biological rep1


title: second_trimester_euploid_AF_normalAFstudy_female6

description:
femaleAF6
gene expression data from normal second trimester fetus

value: female


title: LY2 SRC1-siRNA untreated rep1

description: Gene expression data from endocrine resistant breast cancer cell line LY9

source_name: LY2 cell line, SRC-1 siRNA untreated, biological rep1


title: second_trimester_euploid_AF_normalAFstudy_male6

description:
maleAF6
gene expression data from normal second trimester fetus


title: second_trimester_euploid_AF_normalAFstudy_female2

description:
femaleAF2
gene expression data from normal second trimester fetus


title: second_trimester_euploid_AF_normalAFstudy_male1

description:
maleAF1
gene expression data from normal second trimester fetus


title: P129a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68145.gif

value: Stratagene Universal Human Reference

tag: tissue

value: 51 years

tag: organism part

value: posterior neck

tag: disease state

tag: individual


title: second_trimester_euploid_AF_normalAFstudy_female4

description:
femaleAF4
gene expression data from normal second trimester fetus


title: LY2 control-siRNA untreated rep2

description: Gene expression data from endocrine resistant breast cancer cell line LY12

source_name: LY2 cell line, SRC-1 scrambled untreated, biological rep2


title: second_trimester_euploid_AF_normalAFstudy_male4

description:
maleAF4
gene expression data from normal second trimester fetus


title: second_trimester_euploid_AF_normalAFstudy_male3

description:
maleAF3
gene expression data from normal second trimester fetus


title: second_trimester_euploid_AF_normalAFstudy_male2

description:
maleAF2
gene expression data from normal second trimester fetus


title: LY2 SRC1-siRNA untreated rep2

description: Gene expression data from endocrine resistant breast cancer cell line LY10

source_name: LY2 cell line, SRC-1 siRNA untreated, biological rep2


title: second_trimester_euploid_AF_normalAFstudy_female5

description:
femaleAF5
gene expression data from normal second trimester fetus


title: LY2 control-siRNA tamoxifen treated rep4

description: Gene expression data from endocrine resistant breast cancer cell line LY15

source_name: LY2 cell line, SRC-1 scrambled treated 120min, biological rep4

value: tamoxifen for 120 min


title: LY2 control-siRNA tamoxifen treated rep3

description: Gene expression data from endocrine resistant breast cancer cell line LY4

source_name: LY2 cell line, SRC-1 scrambled treated 120min,  biological rep3


title: LY2 control-siRNA tamoxifen treated rep1

description: Gene expression data from endocrine resistant breast cancer cell line LY6

source_name: LY2 cell line, SRC-1 scrambled treated 120min, biological rep1


title: LY2 control-siRNA tamoxifen treated rep2

description: Gene expression data from endocrine resistant breast cancer cell line LY2

source_name: LY2 cell line, SRC-1 scrambled treated 120min, biological rep2


title: second_trimester_euploid_AF_normalAFstudy_female1

description:
femaleAF1
gene expression data from normal second trimester fetus


title: LY2 SRC1-siRNA untreated rep3

description: Gene expression data from endocrine resistant breast cancer cell line LY3

source_name: LY2 cell line, SRC-1 siRNA untreated, biological rep3


title: LY2 control-siRNA untreated rep3

description: Gene expression data from endocrine resistant breast cancer cell line LY8

source_name: LY2 cell line, SRC-1 scrambled untreated, biological rep3


title: LY2 SRC1-siRNA tamoxifen treated rep1

description: Gene expression data from endocrine resistant breast cancer cell line LY5

source_name: LY2 cell line, SRC-1 siRNA treated 120mins, biological rep1

value: tamoxifen for 120 mins


title: second_trimester_euploid_AF_normalAFstudy_female3

description:
femaleAF3
gene expression data from normal second trimester fetus


title: LY2 SRC1-siRNA tamoxifen treated rep3

description: Gene expression data from endocrine resistant breast cancer cell line LY7

source_name: LY2 cell line, SRC-1 siRNA treated 120min, biological rep3


title: Human fetal colon EGF: Biological replicate 3

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

country: Canada

institute: Université de Sherbrooke

description:
Total RNA extracted using Trizol following manufacturer's instructions
aRNA amplified using TargetAmp 1-round aRNA amplification kit 103 following manufacturer's instructions (Epicentre Biotechnologies, Madison, WI)

hyb_protocol: Arabidopsis cDNA and hybridization buffer (formamide 50%, SSC 5X, SDS 0.1%) were added, and samples were applied to microarrays enclosed in hybridization chambers overnight at 42°C. After hybridization, slides were washed sequential

scan_protocol: Scanned on an ScanArray Express (Packard Bioscience).

data_processing: Images were quantified using Spotfinder 3 Software (TM4: The Microarray Software Suite: www.TM4.org). Then background subtracted data, LOWESS normalized, iterative log mean centerized were obtained from log2 of processed Red signal/processed Green signal. TIGR package software was used.

source_name: reference pool

label_protocol: 1 µg of aRNA was primed with 3 µl of 2 µg/µL hexamer random primers at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dCTP, dGTP, 200µM dTTP and 300µM aa-dUTP.

extract_protocol: Total RNA from reference pool was isolated by phenol/chloroform extraction (Trizol, Invitrogen), then amplified with TargetAmp 1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI)

value: Reference pool produced from a mixture of equimolar aliquots of RNA from Caco-2/15 cells (at -1, 10, and 25 days of confluence), proliferative HT-29 cells, SKOV3 cells, A549 cells.

source_name: human fetal colon

extract_protocol: Total RNA from human fetal colon explants cultured in the presence of EGF were isolated by phenol/chloroform extraction (Trizol, Invitrogen), then amplified with TargetAmp1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI)

value: at 19 weeks of gestation

value: human colonic explants

value: 48 hours of culture in serum-free medium containing EGF (50 ng/mL)


title: Human fetal colon EGF: Biological replicate 4

value: at 17 weeks of gestation


title: Human fetal colon EGF: Biological replicate 2

value: at 16 weeks of gestation


title: Human fetal colon control: Biological replicate 2

extract_protocol: Total RNA from human fetal ileum explants were isolated by phenol/chloroform extraction (Trizol, Invitrogen), then amplified with TargetAmp1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI)

value: 48 hours of culture in serum-free medium


title: Human fetal colon control: Biological replicate 1


title: Human fetal colon EGF: Biological replicate 1


title: Human fetal ileum EGF: Biological replicate 1

source_name: human fetal ileum

extract_protocol: Total RNA from human fetal ileum explants cultured in the presence of EGF were isolated by phenol/chloroform extraction (Trizol, Invitrogen), then amplified with TargetAmp1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI)

value: human ileal explants


title: transgenic_B.theta_rep1

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description:
Tg1
Gene expression data from human fecal isolate of Bacteroides Thetaiotaomicron

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Affymetrix human gut microbiota community GeneChip, then washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Invariantset normalization by dChip software; 4995 probe sets targeting B. Theta transcripts were processed and displayed.

organism: Bacteroides thetaiotaomicron

source_name: HLA-B27 Tg rats_B.theta (VPI-5482)

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

growth_protocol: Brain-Heart Infusion (BHI) agar and in BHI broth under strict anaerobic conditions using pre-reduced media

extract_protocol: Trizol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions

tag: strain/isolate

value: fully-sequenced human fecal isolate of B.theta (VPI-5482)

tag: host

value: germ-free HLA-B27/b2 microglobulin transgenic rat


title: transgenic_B.theta_rep3

description:
Tg3
Gene expression data from human fecal isolate of Bacteroides Thetaiotaomicron


title: non-transgenic_B.theta_rep3

description:
nTg3
Gene expression data from human fecal isolate of Bacteroides Thetaiotaomicron

source_name: non-transgenic (nTg) rats _B.theta (VPI-5482)

value: germ-free HLA-B27/b2 microglobulin non-transgenic (wild type) rat


title: non-transgenic_B.theta_rep2

description:
nTg2
Gene expression data from human fecal isolate of Bacteroides Thetaiotaomicron


title: Human fetal ileum EGF: Biological replicate 4


title: Human fetal ileum EGF: Biological replicate 2


title: Human fetal ileum EGF: Biological replicate 3


title: Human fetal ileum control: Biological replicate 3


title: Human fetal colon control: Biological replicate 3


title: Human fetal ileum control: Biological replicate 4


title: Human fetal ileum control: Biological replicate 2


title: Human fetal colon control: Biological replicate 4


title: YDFR.SC + Treated with brain-derived soluble factors

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: Gene expression of YDFR, cutaneous variant, treated with brain-derived soluble factors.

hyb_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: Only gene-level analyses was performed. RMA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.5) Copyright © 2010.

source_name: YDFR-sub-cutan variant, replicate 1

growth_protocol: Cells were grown in RPMI-1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mmol/ml L-glutamine, 0.01 M HEPES buffered saline, 100 units/ml penicillin, 0.1 mg/ml streptomycin, and 12.5 units/ml nystatin. All cells were routinely cultured in humidified air with 5% CO2 at 37°C. The cells were routinely tested for the presence of mycoplasma.

extract_protocol: Total cellular RNA was extracted using EZ-RNA, total RNA Isolation Kit (Biological Industries). RNA concentrations were determined by the absorbance at 260 nm and quality control standards were A260/A280 = 1.8 – 2.0.

treatment_protocol: Brains of BALB/c mice were harvested, minced to pieces and plated on non-tissue culture dishes in RPMI-1640 growth medium containing 5% BSA for 48 hrs. Supernatants were collected, centrifuged twice for 7 min at 1200 rpm and filtered (0.45μm, Whatman, GmbH Germany). Protein concentration was determined by Bradford reagent (Bio-Rad Laboratories GmbH Munchen, Germany).  The soluble factors present in supernatants of short-term cultures of normal mouse brain were referred here after as brain-derived soluble factors. In order to test the effect of these supernatants on human melanoma cells, 24 hrs old melanoma cell cultures were supplemented for 48 hrs with brain supernatants diluted 1:2 with growth medium. Human melanoma cells treated with growth medium alone served as control.

tag: mouse model strain

value: BALB/c

tag: cell type

value: YDFR, human melanoma brain metastasis cells

tag: malignancy stage

value: primary tumor

value: brain-derived soluble factors


title: FFA1327_BCM Mixed Dyslipidemia

city: houston

first: Ariel

last: Brautbar

address: 1 baylor plaza

institute: Baylor College of Medicine

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio v2011.1 with Genotyping module 1.9.4 (Illumina).

label: C-Bio and A-DNP

source_name: Mixed dyslipidemia_statin alone

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from peripheral blood

value: Mixed dyslipidemia

value: peripheral blood

tag: percent change in apoc3 levels

tag: treatment group

value: statin alone


title: FFA1329_BCM Mixed Dyslipidemia


title: FFA1330_BCM Mixed Dyslipidemia


title: FFA1331_BCM Mixed Dyslipidemia


title: FFA1333_BCM Mixed Dyslipidemia


title: YDFR.B3 Control

description: Gene expression of YDFR, brain metastasis variant, untreated.

scan_protocol: according to the instruction manual, as described in the Affymetrix website

source_name: YDFR-third cycle of intrcardiac inoculation, brain metastasis variant, replicate 1

value: brain metastasis

tag: treatment

value: untreated


title: YDFR.SC Control

description: Gene expression of YDFR, cutaneous variant, untreated.

label_protocol: according to the instruction manual, as described in the Affymetrix website


title: FFA1328_BCM Mixed Dyslipidemia


title: YDFR.B3 + Treated with brain-derived soluble factors

description: Gene expression of YDFR, brain metastasis variant, treated with brain-derived soluble factors.


title: Human fetal ileum control: Biological replicate 1

tag: reference

value: Reference pool produced from a mixture of equimolar aliquots of RNA from Caco-2/15 cells (at -1, 10, and 25 days of confluence), proliferative HT-29 cells, SKOV3 cells, A549 cells.

tag: developmental stage


title: FFA1322_BCM Mixed Dyslipidemia


title: FFA1326_BCM Mixed Dyslipidemia


title: non-transgenic_B.theta_rep1

description:
nTg1
Gene expression data from human fecal isolate of Bacteroides Thetaiotaomicron


title: FFA1324_BCM Mixed Dyslipidemia


title: FFA1321_BCM Mixed Dyslipidemia


title: FFA1320_BCM Mixed Dyslipidemia


title: FFA1323_BCM Mixed Dyslipidemia


title: FFA1319_BCM Mixed Dyslipidemia


title: FFA1317_BCM Mixed Dyslipidemia


title: FFA1312_BCM Mixed Dyslipidemia


title: FFA1314_BCM Mixed Dyslipidemia


title: FFA1316_BCM Mixed Dyslipidemia


title: FFA1315_BCM Mixed Dyslipidemia


title: FFA1311_BCM Mixed Dyslipidemia


title: FFA1309_BCM Mixed Dyslipidemia


title: FFA1308_BCM Mixed Dyslipidemia


title: FFA1310_BCM Mixed Dyslipidemia


title: FFA1303_BCM Mixed Dyslipidemia


title: FFA1306_BCM Mixed Dyslipidemia


title: FFA1305_BCM Mixed Dyslipidemia


title: FFA1304_BCM Mixed Dyslipidemia


title: FFA1307_BCM Mixed Dyslipidemia


title: FFA1302_BCM Mixed Dyslipidemia


title: FFA1301_BCM Mixed Dyslipidemia


title: FFA1299_BCM Mixed Dyslipidemia


title: FFA1297_BCM Mixed Dyslipidemia


title: FFA1300_BCM Mixed Dyslipidemia


title: FFA1298_BCM Mixed Dyslipidemia


title: FFA1313_BCM Mixed Dyslipidemia


title: FFA1292_BCM Mixed Dyslipidemia


title: FFA1293_BCM Mixed Dyslipidemia


title: FFA1290_BCM Mixed Dyslipidemia


title: FFA1294_BCM Mixed Dyslipidemia


title: FFA1296_BCM Mixed Dyslipidemia


title: FFA1287_BCM Mixed Dyslipidemia


title: FFA1286_BCM Mixed Dyslipidemia


title: FFA1289_BCM Mixed Dyslipidemia


title: FFA1288_BCM Mixed Dyslipidemia


title: FFA1285_BCM Mixed Dyslipidemia


title: FFA1282_BCM Mixed Dyslipidemia


title: FFA1283_BCM Mixed Dyslipidemia


title: FFA1280_BCM Mixed Dyslipidemia


title: FFA1279_BCM Mixed Dyslipidemia


title: FFA1278_BCM Mixed Dyslipidemia


title: FFA1275_BCM Mixed Dyslipidemia


title: FFA1276_BCM Mixed Dyslipidemia


title: FFA1277_BCM Mixed Dyslipidemia


title: FFA1274_BCM Mixed Dyslipidemia


title: FFA1273_BCM Mixed Dyslipidemia


title: FFA1267_BCM Mixed Dyslipidemia


title: FFA1291_BCM Mixed Dyslipidemia


title: FFA1269_BCM Mixed Dyslipidemia


title: FFA1295_BCM Mixed Dyslipidemia


title: FFA1268_BCM Mixed Dyslipidemia


title: FFA1266_BCM Mixed Dyslipidemia


title: FFA1281_BCM Mixed Dyslipidemia


title: FFA1261_BCM Mixed Dyslipidemia


title: FFA1265_BCM Mixed Dyslipidemia


title: FFA1264_BCM Mixed Dyslipidemia


title: FFA1262_BCM Mixed Dyslipidemia


title: FFA1260_BCM Mixed Dyslipidemia


title: FFA1263_BCM Mixed Dyslipidemia


title: FFA1258_BCM Mixed Dyslipidemia


title: FFA1257_BCM Mixed Dyslipidemia


title: FFA1270_BCM Mixed Dyslipidemia


title: FFA1259_BCM Mixed Dyslipidemia


title: transgenic_B.theta_rep2

description:
Tg2
Gene expression data from human fecal isolate of Bacteroides Thetaiotaomicron


title: FFA1256_BCM Mixed Dyslipidemia


title: FFA1255_BCM Mixed Dyslipidemia


title: FFA1253_BCM Mixed Dyslipidemia


title: FFA1254_BCM Mixed Dyslipidemia


title: FFA1252_BCM Mixed Dyslipidemia


title: FFA1250_BCM Mixed Dyslipidemia


title: FFA1251_BCM Mixed Dyslipidemia


title: FFA1248_BCM Mixed Dyslipidemia


title: FFA1249_BCM Mixed Dyslipidemia


title: FFA1238_BCM Mixed Dyslipidemia


title: FFA1240_BCM Mixed Dyslipidemia


title: FFA1242_BCM Mixed Dyslipidemia


title: FFA1241_BCM Mixed Dyslipidemia


title: FFA1243_BCM Mixed Dyslipidemia


title: FFA1246_BCM Mixed Dyslipidemia


title: FFA1247_BCM Mixed Dyslipidemia


title: FFA1244_BCM Mixed Dyslipidemia


title: FFA1245_BCM Mixed Dyslipidemia


title: FFA1237_BCM Mixed Dyslipidemia


title: FFA1236_BCM Mixed Dyslipidemia


title: FFA1233_BCM Mixed Dyslipidemia


title: FFA1234_BCM Mixed Dyslipidemia


title: FFA1232_BCM Mixed Dyslipidemia


title: FFA1230_BCM Mixed Dyslipidemia


title: FFA1228_BCM Mixed Dyslipidemia


title: FFA1225_BCM Mixed Dyslipidemia


title: FFA1226_BCM Mixed Dyslipidemia


title: FFA1224_BCM Mixed Dyslipidemia


title: FFA1222_BCM Mixed Dyslipidemia


title: FFA1223_BCM Mixed Dyslipidemia


title: FFA1220_BCM Mixed Dyslipidemia


title: FFA1219_BCM Mixed Dyslipidemia


title: FFA1217_BCM Mixed Dyslipidemia


title: FFA1216_BCM Mixed Dyslipidemia


title: FFA1214_BCM Mixed Dyslipidemia


title: FFA1209_BCM Mixed Dyslipidemia


title: FFA1210_BCM Mixed Dyslipidemia


title: FFA1208_BCM Mixed Dyslipidemia


title: FFA1206_BCM Mixed Dyslipidemia


title: FFA1212_BCM Mixed Dyslipidemia


title: FFA1227_BCM Mixed Dyslipidemia


title: FFA1205_BCM Mixed Dyslipidemia


title: FFA1204_BCM Mixed Dyslipidemia


title: FFA1200_BCM Mixed Dyslipidemia


title: FFA1198_BCM Mixed Dyslipidemia


title: FFA1199_BCM Mixed Dyslipidemia


title: FFA1229_BCM Mixed Dyslipidemia


title: FFA1221_BCM Mixed Dyslipidemia


title: FFA1193_BCM Mixed Dyslipidemia


title: FFA1190_BCM Mixed Dyslipidemia


title: FFA1188_BCM Mixed Dyslipidemia


title: FFA1192_BCM Mixed Dyslipidemia


title: FFA1191_BCM Mixed Dyslipidemia


title: FFA1194_BCM Mixed Dyslipidemia


title: FFA1195_BCM Mixed Dyslipidemia


title: FFA1215_BCM Mixed Dyslipidemia


title: FFA1189_BCM Mixed Dyslipidemia


title: FFA1196_BCM Mixed Dyslipidemia


title: FFA1197_BCM Mixed Dyslipidemia


title: FFA1203_BCM Mixed Dyslipidemia


title: FFA1185_BCM Mixed Dyslipidemia


title: FFA1187_BCM Mixed Dyslipidemia


title: FFA1182_BCM Mixed Dyslipidemia


title: FFA1183_BCM Mixed Dyslipidemia


title: FFA1184_BCM Mixed Dyslipidemia


title: FFA1178_BCM Mixed Dyslipidemia


title: FFA1180_BCM Mixed Dyslipidemia


title: FFA1177_BCM Mixed Dyslipidemia


title: FFA1176_BCM Mixed Dyslipidemia


title: FFA1174_BCM Mixed Dyslipidemia


title: FFA1175_BCM Mixed Dyslipidemia


title: FFA1173_BCM Mixed Dyslipidemia


title: FFA1179_BCM Mixed Dyslipidemia


title: FFA1181_BCM Mixed Dyslipidemia


title: FFA1171_BCM Mixed Dyslipidemia


title: FFA1186_BCM Mixed Dyslipidemia


title: FFA1169_BCM Mixed Dyslipidemia


title: FFA1166_BCM Mixed Dyslipidemia


title: FFA1170_BCM Mixed Dyslipidemia


title: FFA1163_BCM Mixed Dyslipidemia


title: FFA1168_BCM Mixed Dyslipidemia


title: FFA1164_BCM Mixed Dyslipidemia


title: FFA1167_BCM Mixed Dyslipidemia


title: FFA1159_BCM Mixed Dyslipidemia


title: FFA1158_BCM Mixed Dyslipidemia


title: FFA1161_BCM Mixed Dyslipidemia


title: FFA1162_BCM Mixed Dyslipidemia


title: FFA1157_BCM Mixed Dyslipidemia


title: FFA1154_BCM Mixed Dyslipidemia


title: FFA1156_BCM Mixed Dyslipidemia


title: FFA1160_BCM Mixed Dyslipidemia


title: FFA1155_BCM Mixed Dyslipidemia


title: FFA1153_BCM Mixed Dyslipidemia


title: FFA1152_BCM Mixed Dyslipidemia


title: FFA1150_BCM Mixed Dyslipidemia


title: FFA1149_BCM Mixed Dyslipidemia


title: FFA1151_BCM Mixed Dyslipidemia


title: FFA1142_BCM Mixed Dyslipidemia


title: FFA1144_BCM Mixed Dyslipidemia


title: FFA1141_BCM Mixed Dyslipidemia


title: FFA1147_BCM Mixed Dyslipidemia


title: FFA1140_BCM Mixed Dyslipidemia


title: FFA1165_BCM Mixed Dyslipidemia


title: FFA1146_BCM Mixed Dyslipidemia


title: FFA1135_BCM Mixed Dyslipidemia


title: FFA1139_BCM Mixed Dyslipidemia