title: KASUMI-1, Isotype control detected miRNAs, biological rep2

description: Isotype control detected miRNAs

source_name: synthetic miRNA pool (universal reference)

value: 1 fmol of each of 771 synthetic miRNAs were pooled and labeled


title: KASUMI-1, Isotype control detected miRNAs, biological rep1

status: Public on Sep 11 2013

type: RNA

city: Düsseldorf

first: Pablo

last: Landgraf

address: Moorenstraße 5

department: Clinic of Pediatric Oncology, Hematology and Clinical Immunology

country: Germany

institute: Heinrich-Heine University Düsseldorf

description: Isotype control detected miRNAs

hyb_protocol: The corresponding Cy3 and Cy5 labled miRNAs were combined and hybridized overnight (16 hours, 42°C) to a miRXplore microarray (MACS molecular Miltenyi Biotec) using an a-Hyb Hybridization Station (MACS molecular Miltenyi Biotec). The microarrays were washed five times with distilled water (at room temperature) and dried with compressed, dry air.

scan_protocol: miRXplore microarrays were scanned using the Axon GenePix 4200A Microarray Scanner

data_processing: Microarray image analysis and ratio-based normalisation of the microarray data was conducted using the software package GenePix Pro 6.1 (Molecular Devices). Data was filtered with respect to background-subtracted signal intensity, signal to noise ratio and spot diameter. Local background was subtracted from the signal to obtain the net signal intensity and the ratio of both fluorescent labels. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity of the miRNAs derived from the samples of interest was two-fold the mean background value. The mean ratios of all probes were normalized to the median of the ratios detected for the spiked 18 synthetic RNA oligonucleotides reverse complement to miRControl 3 probes. Signal intensities of miRNAs without the corresponding miRNA in the synthetic miRNA pool were divided by the mean value of signal intensities of all detected miRNAs in the pool.

molecule: total RNA

organism: synthetic construct

label_protocol: miRNAs were 3' end labeled using a truncated and mutated RNA ligase Rnl2(1-249)K227Q

extract_protocol: The 4 Ago antibodies were obtained from our cooperation partner Prof. Dr. Gunter Meister from University Regensburg and were manufactured in house. TRIzol extraction of Ago- / isotype control-associated and total RNA was performed according to the manufacturer's instructions.

tag: reference

organism: Homo sapiens

source_name: KASUMI-1 cell line, 4'-thiouridine and UV treated

tag: tissue

value: human acute myeloid leukemia

tag: genotype

value: cells carry the t(8;21) AML1-ETO fusion gene

tag: age

value: cells were harvested after 48 - 72 h

tag: rna subtype

value: unspecific bound miRNAs of isotype control


title: KASUMI-1, Ago4-associated miRNAs, biological rep2

description: Identification of Ago4-associated miRNAs

value: Ago4-associated miRNAs


title: KASUMI-1, Ago4-associated miRNAs, biological rep1


title: hONS cells_HP1-treated_ 2h, biological rep 4

city: North Ryde

first: Megan

last: Osmond-McLeod

address: 11 Julius Avenue

country: Australia

institute: CSIRO

description: Gene expression data from HP1-treated hONS cells at 2h

hyb_protocol: Following fragmentation, ~600-700 ng of single-stranded DNA were hybridised on Affymetric 1.0 ST human gene arrays (17 h, 45˚C, 60 rpm) in an Affymetrix 640 GeneChip® Hybridization Oven. GeneChips were washed and stained in an Affymetrix GeneChip® Fluidics Station 450.

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

data_processing: The data was processed and analysed using Matlab Bioinformatics and Statistical toolboxes. RMA was used as the normalisation method. In-house tools were used to remove batch effects and control for false discovery.

label: Biotin

source_name: HP1-treated hONS cells at 2h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User Manual, Affymetrix).

growth_protocol: hONS cells derived from adult olfactory mucosa were propagated as adherent monolayers in DMEM/F12 (1:1, Gibco) containing 10% FBS, at 37˚C, 10% CO2.

extract_protocol: Total RNA was extracted from cells using the NucleoSpin® RNA II kit (Macherey Nagel, Scientifix) following manufacturer’s instructions.

treatment_protocol: Cells were treated with medium containing 25ug/ml of ZnO nanoparticles (Nanosun, Z-COTE, HP1 or MAX), or medium containing no nanoparticles (untreated) and incubated at 37˚C, 10% CO2 for 2h or 6h.

tag: cell type

value: hONS

tag: treatment

value: 25ug/ml of ZnO nanoparticles (HP1)

tag: incubated


title: Praz_female_15day_rep3Praz_G39F_D15_3

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

description: Gene expression data from liver samples of female CD1 mice treated with Prazosin up to 15 days.

hyb_protocol: cRNA synthesis, target hybridization, washing, staining and subsequent probe array scanning was done according to the manufacturer's instructions (3'IVT Express Kit User Manual Affymetrix)

scan_protocol: Scanner 3000 7G; Software GCOS (Genechip Operating Software) version 1.4.0

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

label: biotin

organism: Mus musculus

source_name: Prazosin, female mice, 15 days

label_protocol: Labeling according to 3'IVT Express Kit User Manual Affymetrix

growth_protocol: CD-1 male and female mice were orally treated with a set of genotoxic carcinogens (CIDB, DMN and MDA), nongenotoxic carcinogens (DCB, PB and PBO), non-hepatocarcinogens (CFX, Nif, Praz and Prop) and a group of undefined compounds (CPA, Wy-14643 and TAA) over a period of 3 and 14 days.

extract_protocol: Liver tissue was homogenized and RNA isolation was performed with Qiazol extraction (Qiagen, Hilden,Germany).

treatment_protocol: After 3 and 14 days of compound treatment mice were anaesthetized in isoflurane and exsanguinated from the heart and subjected to necropsy. The left lateral liver lobe was extracted and snap frozen under -80°C conditions.

tag: gender

value: female

tag: strain

value: CD-1 mouse

value: Liver

value: Prazosin

tag: time

value: 15 days


title: Praz_female_4day_rep5Praz_G37F_D4_5

description: Gene expression data from liver samples of female CD1 mice treated with Prazosin up to 4 days.

source_name: Prazosin, female mice, 4 days

value: 4 days


title: hONS cells_HP1-treated_ 6h, biological rep 3

description: Gene expression data from HP1-treated hONS cells at 6h

source_name: HP1-treated hONS cells at 6h


title: hONS cells_HP1-treated_ 2h, biological rep 1


title: KASUMI-1, Ago3-associated miRNAs, biological rep3

description: Identification of Ago3-associated miRNAs

value: Ago3-associated miRNAs


title: TAA_male_4day_rep1TAA_G57M_D4_1

description: Gene expression data from liver samples of male CD1 mice treated with Thioacetamid up to 4 days.

source_name: Thioacetamid, male mice, 4 days

value: male

value: Thioacetamid


title: hONS cells_HP1-treated_ 2h, biological rep 2


title: KASUMI-1, Ago4-associated miRNAs, biological rep3

value: 1 fmol of each of 771 synthetic miRNAs were pooled and labeled


title: Praz_female_15day_rep5Praz_G39F_D15_5


title: hONS cells_Z-COTE-treated_ 2h, biological rep 3

description: Gene expression data from Z-COTE-treated hONS cells at 2h

source_name: Z-COTE-treated hONS cells at 2h

value: 25ug/ml of ZnO nanoparticles (Z-COTE)


title: Praz_female_15day_rep1Praz_G39F_D15_1


title: Praz_female_15day_rep2Praz_G39F_D15_2


title: PBO_male_15day_rep3PBO_G50M_D15_3

description: Gene expression data from liver samples of male CD1 mice treated with Piperonyl-butoxide up to 15 days.

source_name: Piperonyl-butoxide, male mice, 15 days

value: Piperonyl-butoxide


title: Praz_female_15day_rep4Praz_G39F_D15_4


title: Praz_female_4day_rep3Praz_G37F_D4_3


title: Praz_female_4day_rep4Praz_G37F_D4_4


title: hONS cells_HP1-treated_ 2h, biological rep 3


title: Praz_female_4day_rep6Praz_G37F_D4_6


title: Prop_female_15day_rep4Prop_G34F_D15_4

description: Gene expression data from liver samples of female CD1 mice treated with Propranolol up to 15 days.

source_name: Propranolol, female mice, 15 days

value: Propranolol


title: Prop_female_15day_rep5Prop_G34F_D15_5


title: hONS cells_Z-COTE-treated_ 2h, biological rep 4


title: Praz_female_4day_rep2Praz_G37F_D4_2


title: Praz_female_4day_rep1Praz_G37F_D4_1


title: Prop_female_15day_rep3Prop_G34F_D15_3


title: hONS cells_Z-COTE-treated_ 2h, biological rep 1


title: KASUMI-1, Ago3-associated miRNAs, biological rep1

value: human acute myeloid leukemia

value: cells carry the t(8;21) AML1-ETO fusion gene

value: cells were harvested after 48 - 72 h


title: KASUMI-1, Ago3-associated miRNAs, biological rep2


title: KASUMI-1, Ago2-associated miRNAs, biological rep3

description: Identification of Ago2-associated miRNAs

value: Ago2-associated miRNAs


title: KASUMI-1, Ago2-associated miRNAs, biological rep2


title: KASUMI-1, Ago2-associated miRNAs, biological rep1


title: hONS cells_Z-COTE-treated_ 2h, biological rep 2

value: hONS


title: hONS cells_Nanosun-treated_ 2h, biological rep 4

description: Gene expression data from Nanosun-treated hONS cells at 2h

source_name: Nanosun-treated hONS cells at 2h

value: 25ug/ml of ZnO nanoparticles (Nanosun)


title: Prop_female_15day_rep1Prop_G34F_D15_1

value: female

value: CD-1 mouse

value: Liver


title: KASUMI-1, Ago1-associated miRNAs, biological rep2

description: Identification of Ago1-associated miRNAs

value: Ago1-associated miRNAs


title: Prop_female_4day_rep3Prop_G32F_D4_3

description: Gene expression data from liver samples of female CD1 mice treated with Propranolol up to 4 days.

source_name: Propranolol, female mice, 4 days

value: 4 days


title: KASUMI-1, Ago1-associated miRNAs, biological rep1


title: Prop_female_4day_rep5Prop_G32F_D4_5


title: Prop_female_4day_rep4Prop_G32F_D4_4


title: hONS cells_Nanosun-treated_ 2h, biological rep 1


title: Prop_female_4day_rep2Prop_G32F_D4_2


title: hONS cells_unntreated_ 2h, biological rep 4

description: Gene expression data from untreated hONS cells at 2h

source_name: Untreated hONS cells at 2h


title: KASUMI-1, Ago1-associated miRNAs, biological rep3


title: Prop_female_4day_rep6Prop_G32F_D4_6


title: hONS cells_unntreated_ 2h, biological rep 3


title: Nif_female_15day_rep3Nif_G31F_D15_3

description: Gene expression data from liver samples of female CD1 mice treated with Nifedipine up to 15 days.

source_name: Nifedipine, female mice, 15 days

value: Nifedipine

value: 15 days


title: Nif_female_15day_rep1Nif_G31F_D15_1


title: Nif_female_15day_rep5Nif_G31F_D15_5


title: hONS cells_Nanosun-treated_ 2h, biological rep 2


title: Nif_female_15day_rep4Nif_G31F_D15_4


title: Nif_female_4day_rep6Nif_G29F_D4_6

description: Gene expression data from liver samples of female CD1 mice treated with Nifedipine up to 4 days.

source_name: Nifedipine, female mice, 4 days


title: hONS cells_Nanosun-treated_ 2h, biological rep 3


title: Prop_female_4day_rep1Prop_G32F_D4_1


title: hONS cells_unntreated_ 2h, biological rep 2


title: Nif_female_15day_rep2Nif_G31F_D15_2


title: Nif_female_4day_rep5Nif_G29F_D4_5


title: mouse_lung_cRaf_F_Rep 6

city: Trento

first: Valerio

last: Del Vescovo

state: Trentino Alto Adige

address: via delle Regole 101

department: CIBIO - Centre for Integrative Biology

country: Italy

institute: University of Trento

description: miRNA expression profile from female mouse, lung tumor, overexpressing cRaf, replicate 6

hyb_protocol: The samples were then hybridized to Affymetrix GeneChip miRNA array that contained 722 and 690 mouse mature and pre-miRNA, respectively using a protocol recommended by the manufacturer (http://media.affymetrix.com/support/downloads/manuals/flashtag_user_guide.pdf).

scan_protocol: The expression signals were processed and normalized by the quantile method using the miRNA QC Tool version 1.0.33.0 (Affymetrix), which was also used to check the quality of the labelling and hybridization (http://media.affymetrix.com/support/technical/datasheets/miRNA_2_datasheet.pdf).

source_name: mouse, lung, cRaf overexpressing, female, Replicate 6

label_protocol: From each lung 200 ng of total RNA was isolated and prepared for labeling of miRNA with the FlashTag Biotin HSR Procedure (Genisphere, Hatfield, PA, USA) according to the manufacturer’s instructions (http://media.affymetrix.com/support/downloads/manuals/mirna_flashtag_manual.pdf).

extract_protocol: Total RNA-extraction was performed with the RNeasy Micro Kit (RNeasy MicroKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction.

treatment_protocol: SP-C/c-raf transgenic mice were obtained from the laboratory of Prof. Ulf Rapp (University of Würzburg, Germany). Lung tissue from n=6 male and n=6 females SP-C/c-Raf transgenic mice (aged 4–6 months) and n= 6 male and n= 6 female normal lung tissue from type mice (aged 4-6 months) were sacrificed and the lung tissues were immediately frozen on dry ice and stored at - 80° until further analysis.From each frozen lung tissue 10-mm thick sections were prepared and transferred on polyethylene napthalate foil-covered slides (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). The sections were fixed in methanol/acetic acid and stained in hematoxylin. The desired cells were microdissected using the PALM MicroLaser systems (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany) and collected in an adhesive cap (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). Microdissected cells were resuspended in a guanidine isothiocyanate containing buffer (RLT buffer from RNeasy MikroKit, Qiagen, Santa Clarita, CA, USA) with 10 ml/ml ß-mercaptoethanol to ensure isolation of intact RNA.

value: lung adenocarcinoma

tag: genotype/variation

value: cRaf overexpressing


title: Nif_female_4day_rep3Nif_G29F_D4_3


title: mouse_lung_cRaf_F_Rep 5

description: miRNA expression profile from female mouse, lung tumor, overexpressing cRaf, replicate 5

data_processing: The expression signals were processed and normalized by the quantile method using the miRNA QC Tool version 1.0.33.0 (Affymetrix), which was also used to check the quality of the labelling and hybridization (http://media.affymetrix.com/support/technical/datasheets/miRNA_2_datasheet.pdf).

source_name: mouse, lung, cRaf overexpressing, female, Replicate 5


title: mouse_lung_cRaf_F_Rep 4

description: miRNA expression profile from female mouse, lung tumor, overexpressing cRaf, replicate 4

source_name: mouse, lung, cRaf overexpressing, female, Replicate 4


title: Nif_female_4day_rep4Nif_G29F_D4_4


title: Nif_female_4day_rep1Nif_G29F_D4_1


title: mouse_lung_cRaf_F_Rep 3

description: miRNA expression profile from female mouse, lung tumor, overexpressing cRaf, replicate 3

source_name: mouse, lung, cRaf overexpressing, female, Replicate 3


title: CFX_female_15day_rep6CFX_G27F_D15_6

description: Gene expression data from liver samples of female CD1 mice treated with Cefuroxime up to 15 days.

source_name: Cefuroxime, female mice, 15 days

value: Cefuroxime


title: tumor 1 from female F2

city: Jerusalem

first: Reba

last: Condiotti

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah Medical Center

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

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

data_processing: Array data were normalized by the GCRMA algorithm using Affymetrix Expression Console. Data were transformed to log 2 scale and a threshold of 5 was applied.

source_name: HCC from FIV-transduced female mouse

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

growth_protocol: Pregnant mice (16 days gestation) were anaesthetized using isoflurane. Fetuses were removed from the womb and FIV-based viral particles were administered to the yolk sac vein of each fetus. The fetuses were then returned to the womb and were delivered naturally. Mice were kept under normal conditions until they were sacrificed.

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

treatment_protocol: Liver tissue and tumors were flash frozen in liquid nitrogen and stored at -80 degrees until RNA extraction.

value: MF-1 outbred

value: 273 days

value: liver tumor

tag: fiv-transduced

value: yes

tag: mouse developed tumors


title: tumor 2 from female F1

value: 484 days


title: hONS cells_unntreated_ 2h, biological rep 1

value: hONS


title: Nif_female_4day_rep2Nif_G29F_D4_2


title: tumor-free, FIV-transduced female F3

source_name: liver from FIV-transduced female mouse that did not develop tumors

value: 715 days

value: liver

value: no


title: CFX_female_15day_rep5CFX_G27F_D15_5

value: female

value: CD-1 mouse

value: Liver


title: CFX_female_15day_rep4CFX_G27F_D15_4


title: CFX_female_15day_rep2CFX_G27F_D15_2


title: mouse_lung_cRaf_F_Rep 2

description: miRNA expression profile from female mouse, lung tumor, overexpressing cRaf, replicate 2

source_name: mouse, lung, cRaf overexpressing, female, Replicate 2


title: non-tumorous tissue surrounding tumors from female F1

source_name: liver from FIV-transduced female mouse that developed tumors


title: CFX_female_15day_rep1CFX_G27F_D15_1


title: CFX_female_15day_rep3CFX_G27F_D15_3


title: tumor 2 from female F2


title: CFX_female_4day_rep5CFX_G25F_D4_5

description: Gene expression data from liver samples of female CD1 mice treated with Cefuroxime up to 4 days.

source_name: Cefuroxime, female mice, 4 days

value: 4 days


title: CFX_female_4day_rep4CFX_G25F_D4_4


title: CFX_female_4day_rep2CFX_G25F_D4_2


title: mouse_lung_WT_F_Rep 2

description: miRNA expression profile from female mouse lung WT replicate 2

source_name: mouse, lung, wild type, Female, Replicate 2

value: wild type


title: tumor-free, FIV-transduced female F4

value: 341 days


title: non-tumorous tissue surrounding tumors from female F2


title: CFX_female_4day_rep3CFX_G25F_D4_3


title: mouse_lung_cRaf_F_Rep 1

description: miRNA expression profile from female mouse, lung tumor, overexpressing cRaf, replicate 1

source_name: mouse, lung, cRaf overexpressing, female, Replicate 1

value: lung adenocarcinoma

value: cRaf overexpressing


title: mouse_lung_WT_F_Rep 3

description: miRNA expression profile from female mouse lung WT replicate 3

source_name: mouse, lung, wild type, Female, Replicate 3


title: mouse_lung_WT_F_Rep 1

description: miRNA expression profile from female mouse lung WT replicate 1

source_name: mouse, lung, wild type, Female, Replicate 1


title: normal liver, untransduced female

description: F-control

source_name: liver from untransduced female mouse

value: MF-1 outbred

value: unknown

value: unknown, liver


title: tumor 1 from female F1

value: liver tumor

value: yes


title: mouse_lung_cRaf_M_Rep 6

description: miRNA expression profile from male mouse, lung tumor, overexpressing cRaf, replicate 6

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 6

value: male


title: mouse_lung_cRaf_M_Rep 5

description: miRNA expression profile from male mouse, lung tumor, overexpressing cRaf, replicate 5

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 5


title: mouse_lung_cRaf_M_Rep 4

description: miRNA expression profile from male mouse, lung tumor, overexpressing cRaf, replicate 4

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 4


title: normal liver, untransduced male

description: M-control

source_name: liver from untransduced male mouse


title: CMC_female_15day_rep5CMC_G23F_D15_5

description: Gene expression data from liver samples of female CD1 mice treated with Carboxymethyl cellulose up to 15 days.

source_name: Carboxymethyl cellulose, female mice, 15 days

value: Carboxymethyl cellulose

value: 15 days


title: CMC_female_15day_rep4CMC_G23F_D15_4


title: CMC_female_15day_rep3CMC_G23F_D15_3


title: CMC_female_15day_rep2CMC_G23F_D15_2


title: CFX_female_4day_rep1CFX_G25F_D4_1

value: Cefuroxime


title: CMC_female_15day_rep1CMC_G23F_D15_1

value: female


title: CMC_female_4day_rep5CMC_G22F_D4_5

description: Gene expression data from liver samples of female CD1 mice treated with Carboxymethyl cellulose up to 4 days.

source_name: Carboxymethyl cellulose, female mice, 4 days

value: CD-1 mouse


title: CMC_female_4day_rep6CMC_G22F_D4_6

value: Liver


title: mouse_lung_cRaf_M_Rep 3

description: miRNA expression profile from male mouse, lung tumor, overexpressing cRaf, replicate 3

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 3


title: tumor 2 from male M1

source_name: HCC from FIV-transduced male mouse

value: 433 days


title: tumor-free, FIV-transduced male M2

source_name: liver from FIV-transduced male mouse that did not develop tumors

value: 677 days

value: liver

value: no


title: CMC_female_4day_rep3CMC_G22F_D4_3

value: 4 days


title: mouse_lung_cRaf_M_Rep 2

description: miRNA expression profile from male mouse, lung tumor, overexpressing cRaf, replicate 2

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 2

value: lung adenocarcinoma

value: cRaf overexpressing


title: mouse_lung_cRaf_M_Rep 1

description: miRNA expression profile from male mouse, lung tumor, overexpressing cRaf, replicate 1

source_name: mouse, lung, cRaf overexpressing, Male, Replicate 1


title: tumor 1 from male M1

value: MF-1 outbred


title: CMC_female_4day_rep2CMC_G22F_D4_2


title: non-tumorous tissue surrounding tumors from male M1

source_name: liver from FIV-transduced male mouse that developed tumors


title: CMC_female_4day_rep1CMC_G22F_D4_1


title: CMC_female_4day_rep4CMC_G22F_D4_4


title: Praz_male_15day_rep3Praz_G39M_D15_3

description: Gene expression data from liver samples of male CD1 mice treated with Prazosin up to 15 days.

source_name: Prazosin, male mice, 15 days

value: Prazosin


title: Praz_male_15day_rep6Praz_G39M_D15_6


title: mouse_lung_WT_M_Rep 1

description: miRNA expression profile from male mouse lung WT replicate 1

source_name: mouse, lung, wild type, Male, Replicate 1

value: wild type


title: mouse_lung_WT_M_Rep 2

description: miRNA expression profile from male mouse lung WT replicate 2

source_name: mouse, lung, wild type, Male, Replicate 2

value: male


title: Praz_male_15day_rep4Praz_G39M_D15_4


title: Praz_male_15day_rep5Praz_G39M_D15_5


title: SAE 12494978 Prep. 3/2002 L.p. Cy5 t24 vs. Prep. 3/2002 uninfected Cy3

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

institute: Institute for Biochemistry 1

description: DNA microarrays containing 5,423 non-redundant ESTs from the D. discoideum cDNA project (Urushihara et al., 2004), partial sequences of 450 selected genes, probes of the SpotReport-10 Array Validation System (Stratagene, La Jolla, USA) and appropriate positive and negative controls were produced in-house using standard protocols. Briefly, probes were amplified by two 100µl PCR reactions in 96-well microtiter plates using standard primers (M13F2: 5’-GTAAAACGACGGCCAGTG-3’, M13R2: 5’-C6-Aminolink-ACCATGATTACGCCAAGC-3’) for the cloned ESTs and gene-specific primers for the selected genes and the positive controls. After analysis by agarose gel electrophoresis (10µl of each reaction), the two reactions were combined, precipitated, solubilised in 11µl 25% DMSO, 1µl separated again by agarose gel electrophoresis and evaluated (Farbrother et al., 2002). Probes were transferred with the proteineer dp pipetting robot (Bruker, Germany) into 384-well microarray plates with cylindrical wells (Abgene, Hamburg, Germany) and printed onto UltraGaps slides (Corning, New York, USA) at 18°C and 45% humidity with a BioRobotics MicroGrid 600 microarray robot (Genomic Solutions, Huntingdon, UK) using MicroSpot 2500 microarraying pins. Each probe was spotted in duplicate, positive and negative controls were spotted 6, 24, 192 or 286 times and the SpotReport controls 96 times. The microarray is composed of three grids with 16 subarrays each and 14,620 spots in total. The complete microarray dataset is available at GEO, accession number GPL1972.

hyb_protocol: Cy3 and Cy5 labelled targets were mixed, ethanol precipitated and dissolved in 65 µl of hybridisation buffer (Noegel et al., 1985) with 500 µg/ml Fish sperm DNA (Roche, Mannheim, Germany) and 2 µM Oligo dA 18-mer. The hybridisation mix was heated to 80 °C for 10 min, applied to the microarray under a cover-slip and incubated in a hybridisation chamber (Corning, New York, USA) for 15 hours at 37°C. Post-hybridisation washes were performed twice with 2x SSC, 0.1% SDS and once with 0.1x SSC, 0.1% SDS for 5 min each, five times with 0.1x SSC and once with with 0.01x SSC for 5 sec each and dried by centrifugation at 235xg for 5 min. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

scan_protocol: Signal detection was performed with the ScanArray 4000XL confocal laser scanner (PerkinElmer Life Sciences, Wellesley, USA). Images for Cy3 and Cy5 were obtained, spots were detected and quantified with ScanArray Express v2.2 (PerkinElmer Life Sciences), then manually inspected and if necessary corrected. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

data_processing:
For each individual comparison, 19 microarrays were hybridised and analysed. Two image pairs were produced per microarray slide, one with high laser intensity so that signals for most probes and also some saturated signals were obtained and a second one with lower laser intensity so that none of the signals was saturated. This way the dynamic range of the measurement was expanded. To handle the import and export of microarray data to different analysis programs an Excel Add-In, Array tools, was programmed in Visual Basic. Upon import of two data files of the same microarray scanned with different laser powers, the saturated spots of the high laser power scan were replaced by non-saturated spots from the low laser power scan. In addition, the import also performed data filtering by flagging SpotReport controls, negative controls, empty spots, spots where only spotting solution was printed and spots whose intensities were below or equal to zero as "Bad". Fluorescence ratios were normalised by LOWESS-normalisation using R1.6.2 (BioConductor, http://www.bioconductor.org/). The normalized M values (M = log2 (Intensityexperiment/Intensitycontrol) were transferred into a new worksheet for significance analysis of microarrays (SAM) analysis (Tusher et al., 2001). At the transfer all probes spotted in higher replicates were reduced to double spots by averaging. Furthermore, all probes that were flagged "Found" in less than half of the spots, were excluded from SAM analysis. Differentially regulated genes were identified using the one-class SAM method calculating 1000 permutations. The SAM program not only identifies the differentially regulated genes, but also predicts the number of false positives. These are the genes that are falsely reported as differentially expressed. This feature was used in all microarray experiments to set the significance level such, that the 90th percentile of the false discovery rate (FDR) was minimal.
See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

organism: Dictyostelium discoideum

label_protocol: Fairplay indirect labelling kit

extract_protocol: RNA was isolated using the protocol for the isolation of cytoplasmic RNA of the RNeasy mini kit (Qiagen AG).

tag: strain/background

value: Legionella pneumophila JR32

tag: time point

value: 24h post infection

source_name: Prep. 3/2002, uninfected


title: SAE 12494977 Prep. 3/2002 L.p. Cy5 t24 vs. Prep. 3/2002 uninfected Cy3


title: Praz_male_15day_rep1Praz_G39M_D15_1

value: 15 days


title: mouse_lung_WT_M_Rep 3

description: miRNA expression profile from male mouse lung WT replicate 3

source_name: mouse, lung, wild type, Male, Replicate 3


title: SAE 12494974 Prep. 3/2002 L.p. Cy3 t24 vs. Prep. 3/2002 uninfected Cy5


title: Praz_male_4day_rep5Praz_G37M_D4_5

description: Gene expression data from liver samples of male CD1 mice treated with Prazosin up to 4 days.

source_name: Prazosin, male mice, 4 days


title: Praz_male_4day_rep4Praz_G37M_D4_4


title: Praz_male_4day_rep3Praz_G37M_D4_3


title: Praz_male_4day_rep2Praz_G37M_D4_2


title: Praz_male_4day_rep6Praz_G37M_D4_6


title: SAE 12494973 Prep. 3/2002 L.p. Cy3 t24 vs. Prep. 3/2002 uninfected Cy5


title: Prop_male_15day_rep5Prop_G34M_D15_5

description: Gene expression data from liver samples of male CD1 mice treated with Propranolol up to 15 days.

source_name: Propranolol, male mice, 15 days

value: Propranolol


title: Praz_male_15day_rep2Praz_G39M_D15_2

value: CD-1 mouse


title: SAE 127 Prep. 3/2002 L.p. Cy5 t24 vs. Prep. 3/2002 uninfected Cy3


title: SAE 128 Prep. 3/2002 L.p. Cy5 t24 vs. Prep. 3/2002 uninfected Cy3


title: Prop_male_15day_rep6Prop_G34M_D15_6

value: Liver


title: Praz_male_4day_rep1Praz_G37M_D4_1


title: Prop_female_15day_rep2Prop_G34F_D15_2

description: Gene expression data from liver samples of female CD1 mice treated with Propranolol up to 15 days.

source_name: Propranolol, female mice, 15 days

value: female


title: Prop_male_4day_rep5Prop_G32M_D4_5

description: Gene expression data from liver samples of male CD1 mice treated with Propranolol up to 4 days.

source_name: Propranolol, male mice, 4 days


title: Prop_male_15day_rep3Prop_G34M_D15_3


title: Prop_male_15day_rep1Prop_G34M_D15_1


title: MSC plus FaDu CM day 7

city: Riyadh

first: Nehad

middle: M

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

description:
MSC plus FaDu CM
Gene expression on MSCs exposed to FaDu CM (day 7)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2× Hi-RPM Hybridization Buffer (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome GE 4x44K v2 Microarray chip for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters. Data were Percentile-shift normalized using Agilent GeneSpring X software.

source_name: MSC_FaDu CM

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cells were grown in DMEM 4.5g/l glucose supplemented with 10% fetal bovine serum, 1% NEAA, 1% L-glutamine, 100 mg/l penicillin, and 100 mg/l streptomycin

extract_protocol: RNA was extracted using Roche MagNA Pure automated nucleic acid purification system. RNA quantity and quality were measured using the NanoDrop 2000 spectrophotometer.

treatment_protocol: Control MSC were grown in normal DMEM while MSC plus FaDu CM cells were grown in FaDu CM medium for 7 days at 37°C and 5% CO2. Medium was replaced every 3-4 days.

tag: cell line

value: hMSC-TERT

value: bone marrow mesenchymal stem cells

tag: exposed to

value: tumor conditioned medium (CM) from FaDu hypo pharyngeal cancer cell line


title: SAE 12650158 Prep. 2 8/2003 L.p. Cy5 t24 vs. Prep. 2 8/2003 uninfected Cy3

source_name: Prep. 2 8/2003, uninfected

label_protocol: Fairplay indirect labelling kit.


title: 1B_rep3

city: Brest

first: soizic

last: garaud

address: 2 avenue Foch

country: France

institute: Laboratory of Immunology and Immunotherapy

description: Gene expression in Jok-E1B

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent dual-laser Microarray scanner( G2565AA) using one color scan setting for 4x44k array slides,

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cell line

label_protocol: Thirteen μg of mRNA was reverse-transcribed and fluorescence-labelled using the one colour cyanine 3-CTP RNA Quick Amplification kit based on the manufacturer's instructions (Agilent Technologies). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cells were maintained in RPMI-1640 containing 10% FCS, antibiotics, and 0.5mg/ml G418

extract_protocol: Total RNA was extracted by the QIAGEN RNeasy kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: transfection

value: cytoplasmic E1B isoform


title: Control MSC day 7

description:
Control MSC
Gene expression on control MSCs (day 7)

value: normal DMEM (control)


title: Nif_male_15day_rep5Nif_G31M_D15_5

description: Gene expression data from liver samples of male CD1 mice treated with Nifedipine up to 15 days.

source_name: Nifedipine, male mice, 15 days

tag: tissue

value: Nifedipine


title: 1B_rep2

description: Gene expression in Jok-E1B


title: Prop_male_4day_rep4Prop_G32M_D4_4

value: 4 days


title: Ctrl_rep2

description: Gene expression in untransfected Jok-1

value: control


title: Prop_male_15day_rep4Prop_G34M_D15_4


title: Prop_male_4day_rep3Prop_G32M_D4_3


title: Nif_male_15day_rep3Nif_G31M_D15_3


title: Prop_male_4day_rep6Prop_G32M_D4_6


title: 1A_rep3

description: Gene expression in Jok-E1A

value: membrane isoform of CD5 (E1A)


title: Prop_male_4day_rep2Prop_G32M_D4_2

value: male


title: Ctrl_rep3

description: Gene expression in untransfected Jok-1


title: Prop_male_15day_rep2Prop_G34M_D15_2


title: Prop_male_4day_rep1Prop_G32M_D4_1


title: Nif_male_15day_rep4Nif_G31M_D15_4


title: SAE 12650155 Prep. 1 8/2003 L.p. Cy3 t24 vs. Prep. 1 8/2003 uninfected Cy5

source_name: Prep. 1 8/2003, uninfected

value: Legionella pneumophila JR32


title: SAE 126 Prep. 3/2002 L.p. Cy3 t24 vs. Prep. 3/2002 uninfected Cy5

value: 24h post infection


title: 1A_rep2

description: Gene expression in Jok-E1A


title: SAE 12523200 Prep. 2 7/2003 L.p. Cy5 t24 vs. Prep. 2 7/2003 uninfected Cy3

source_name: Prep. 2 7/2003, uninfected


title: SAE 12650156 Prep. 1 8/2003 L.p. Cy5 t24 vs. Prep. 1 8/2003 uninfected Cy3


title: SAE 12650157 Prep. 2 8/2003 L.p. Cy3 t24 vs. Prep. 2 8/2003 uninfected Cy5


title: SAE 12523199 Prep. 1 7/2003 L.p. Cy5 t24 vs. Prep. 1 7/2003 uninfected Cy3

source_name: Prep. 1 7/2003, uninfected


title: 1A_rep1

description: Gene expression in Jok-E1A


title: Nif_male_4day_rep6Nif_G29M_D4_6

description: Gene expression data from liver samples of male CD1 mice treated with Nifedipine up to 4 days.

source_name: Nifedipine, male mice, 4 days


title: Ctrl_rep1

description: Gene expression in untransfected Jok-1


title: Nif_male_4day_rep4Nif_G29M_D4_4


title: SAE 12522860 Prep. 2 7/2003 L.p. Cy3 t24 vs. Prep. 2 7/2003 uninfected Cy5


title: CFX_male_15day_rep6CFX_G27M_D15_6

description: Gene expression data from liver samples of male CD1 mice treated with Cefuroxime up to 15 days.

source_name: Cefuroxime, male mice, 15 days

value: Cefuroxime

value: 15 days


title: CMC_female_15day_rep6CMC_G23F_D15_6

description: Gene expression data from liver samples of female CD1 mice treated with Carboxymethyl cellulose up to 15 days.

source_name: Carboxymethyl cellulose, female mice, 15 days

value: CD-1 mouse

value: Carboxymethyl cellulose


title: SAE 12519736 Prep. 2 5/2003 L.p. Cy5 t24 vs. Prep. 2 5/2003 uninfected Cy3

source_name: Prep. 2 5/2003, uninfected


title: Nif_male_4day_rep2Nif_G29M_D4_2

value: Liver


title: 1B_rep1

description: Gene expression in Jok-E1B


title: SAE 12519735 Prep. 2 5/2003 L.p. Cy3 t24 vs. Prep. 2 5/2003 uninfected Cy5


title: Nif_male_4day_rep5Nif_G29M_D4_5


title: Nif_male_15day_rep1Nif_G31M_D15_1


title: CFX_male_15day_rep5CFX_G27M_D15_5


title: CFX_male_15day_rep2CFX_G27M_D15_2


title: CFX_male_15day_rep1CFX_G27M_D15_1


title: ExVivoBlood_48hr_2Gy_rep5

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

country: USA

institute: Columbia University

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded, and only features flagged as Positive and Significant (above background) were included.

source_name: Peripheral Blood 48hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color QuickAmp kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the PerfectPure Blood RNA Purification kit (5 Prime, Inc.) following the manufacturer’s recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both alpha- and beta- globin. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 3 ml aliquots of blood were exposed at a rate of 0.82 Gy per minute to 0, 0.5, 2, 5 or 8 Gy gamma-rays using a Gammacell-40 137Cs irradiator, then incubated as above for 48 hours prior to RNA extraction.

value: female

tag: age

value: 28 years

value: Peripheral Blood


title: ExVivoBlood_48hr_8Gy_rep5


title: Nif_male_15day_rep2Nif_G31M_D15_2


title: ExVivoBlood_48hr_0Gy_rep5


title: Nif_male_4day_rep3Nif_G29M_D4_3


title: Nif_male_4day_rep1Nif_G29M_D4_1


title: ExVivoBlood_48hr_5Gy_rep5


title: Leaves_by MU_rep3

city: Gainesville

first: Jeffrey

middle: B.

last: Jones

state: FL

address: 1453 Fifield Hall

department: Plant Pathology

institute: University of Florida

description:
Sweet orange_MU-3
Sweet orange (C. sinensis) Valencia
Gene expression data of sweet orange at 120 h post infiltration of Xcc306 mutant strain with pthA4 gene deletion.

hyb_protocol: A total of 300 ng of labeled cDNA for each sample was hybridized with rotation at 45°C for 16 hours to the Affymetrix GeneChip Citrus Genome Array. The arrays were washed and stained using a GeneChip® Hybridization Wash and Stain kit (Affymetrix, Inc) on an Affymetrix Fluidics Station 450 accroding to user's manual.

scan_protocol: The arrays were scanned using a a GeneChip® 7G Scanner (Affymetrix, Inc).

data_processing: Statistical tests were performed using BioConductor statistical software, open source software based on the R programming language (http://www.bioconductor.org/). Robust Multichip Analysis (RMA) approach was used for normalizing the raw data. Differential expression analysis was carried out using a linear modeling approach and the empirical Bayes statistics as implemented in the Limma package.

organism: Citrus sinensis

source_name: Sweet orange leaves inoculated with Xcc306 mutant with pthA4 gene deleted (MU) at 120 hpi

label_protocol: Labeling was performed using a GeneChip 3'IVT Express kit (Affymetrix, Inc). Brifely, cDNA was generated from 250 ng of the total RNA through in vitro transcription; the modified cDNA was labeled with biotin and labeled cDNA was purified and fragmented following the manufacturer's instructions.

growth_protocol: The plants were kept in a quarantine glasshouse with temperature of 28 ± 2 °C,16 h light and 40-60% humidity. Strains of Xanthomonas were grown at 28 °C in nutrient agar (NA). The leaf samples were wrapped with aluminum foil and put in liquid nitrogen immediately, then were kept in -80°C freezer.

extract_protocol: RNA extraction was performed by using RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Brifely, the leaf tissue was ground in liquid nitrogen, buffer RLT was added to the powder and mixed, suspension was centrifuged with the spin column, clear lysate was collected, ethanol was added to precipitate RNA, suspension was centrifuged in RNeasy spin column, pellet was saved and washed with buffer RW1 and buffer RPE, then pellet was dissolved in RNase-free water.

treatment_protocol: The plants were inoculated at the concentration of 5 X 10^8 cfu/ml using syringe with needle.

value: young leaves

value: inoculation of Xcc306 with pthA4 gene deletion

value: 120 hours post inoculation


title: SAE 12523356 Prep. 1 7/2003 L.p. Cy3 t24 vs. Prep. 1 7/2003 uninfected Cy5


title: Leaves_by MU_rep2

description:
Sweet orange_MU-2
Sweet orange (C. sinensis) Valencia
Gene expression data of sweet orange at 120 h post infiltration of Xcc306 mutant strain with pthA4 gene deletion.


title: CFX_male_15day_rep4CFX_G27M_D15_4


title: SAE 12519734 Prep. 1 5/2003 L.p. Cy5 t24 vs. Prep. 1 5/2003 uninfected Cy3

source_name: Prep. 1 5/2003, uninfected


title: SAE 12519733 Prep. 1 5/2003 L.p. Cy3 t24 vs. Prep. 1 5/2003 uninfected Cy5


title: CFX_male_4day_rep6CFX_G25M_D4_6

description: Gene expression data from liver samples of male CD1 mice treated with Cefuroxime up to 4 days.

source_name: Cefuroxime, male mice, 4 days

value: 4 days


title: CFX_male_4day_rep5CFX_G25M_D4_5


title: CFX_male_4day_rep1CFX_G25M_D4_1


title: CMC_male_15day_rep3CMC_G23M_D15_3

description: Gene expression data from liver samples of male CD1 mice treated with Carboxymethyl cellulose up to 15 days.

source_name: Carboxymethyl cellulose, male mice, 15 days


title: ExVivoBlood_48hr_5Gy_rep4

value: 25 years


title: ExVivoBlood_48hr_0.5Gy_rep5


title: CFX_male_4day_rep2CFX_G25M_D4_2


title: CMC_male_15day_rep6CMC_G23M_D15_6


title: Leaves_by WT_rep3

description:
Sweet orange_WT-3
Sweet orange (C. sinensis) Valencia
Gene expression data of sweet orange at 120 h post infiltration of Xcc306 wild type strain.

source_name: Sweet orange leaves inoculated with Xcc306 wild type (WT) at 120 hpi

value: inoculation of Xcc306 wild type


title: ExVivoBlood_48hr_2Gy_rep4


title: ExVivoBlood_48hr_8Gy_rep4


title: CMC_male_15day_rep4CMC_G23M_D15_4

value: male


title: CFX_male_4day_rep3CFX_G25M_D4_3


title: CMC_male_15day_rep2CMC_G23M_D15_2


title: Leaves_by MU_rep1

description:
Sweet orange_MU-1
Sweet orange (C. sinensis) Valencia
Gene expression data of sweet orange at 120 h post infiltration of Xcc306 mutant strain with pthA4 gene deletion.


title: CMC_male_15day_rep5CMC_G23M_D15_5


title: CMC_male_4day_rep6CMC_G22M_D4_6

description: Gene expression data from liver samples of male CD1 mice treated with Carboxymethyl cellulose up to 4 days.

source_name: Carboxymethyl cellulose, male mice, 4 days


title: CMC_male_15day_rep1CMC_G23M_D15_1


title: ExVivoBlood_48hr_0Gy_rep4


title: ExVivoBlood_24hr_8Gy_rep5

source_name: Peripheral Blood 24hr

value: 23 years


title: CMC_male_4day_rep5CMC_G22M_D4_5


title: ExVivoBlood_24hr_0.5Gy_rep5


title: ExVivoBlood_48hr_8Gy_rep3


title: Leaves_by WT_rep1

description:
Sweet orange_WT-1
Sweet orange (C. sinensis) Valencia
Gene expression data of sweet orange at 120 h post infiltration of Xcc306 wild type strain.


title: ExVivoBlood_24hr_5Gy_rep5


title: ExVivoBlood_48hr_0.5Gy_rep4


title: CMC_male_4day_rep2CMC_G22M_D4_2


title: ExVivoBlood_48hr_2Gy_rep3


title: CIDB_male_4day_rep1CIDB_G67M_D4_1

description: Gene expression data from liver samples of male CD1 mice treated with C.I. Direct Black up to 4 days.

source_name: C.I. Direct Black, male mice, 4 days

value: C.I. Direct Black


title: ExVivoBlood_48hr_0.5Gy_rep3


title: Leaves_by WT_rep2

description:
Sweet orange_WT-2
Sweet orange (C. sinensis) Valencia
Gene expression data of sweet orange at 120 h post infiltration of Xcc306 wild type strain.


title: DMN_male_15day_rep1DMN_G72M_D15_1

description: Gene expression data from liver samples of male CD1 mice treated with Dimethylnitrosamine up to 15 days.

source_name: Dimethylnitrosamine, male mice, 15 days

value: Dimethylnitrosamine


title: ExVivoBlood_24hr_2Gy_rep5


title: ExVivoBlood_24hr_0Gy_rep5


title: ExVivoBlood_48hr_5Gy_rep3


title: DMN_male_15day_rep3DMN_G72M_D15_3

value: 15 days


title: CMC_male_4day_rep3CMC_G22M_D4_3

value: CD-1 mouse


title: ExVivoBlood_48hr_8Gy_rep2

value: 30 years


title: DMN_male_15day_rep2DMN_G72M_D15_2

value: Liver


title: ExVivoBlood_24hr_0.5Gy_rep4

value: female

value: 46 years


title: ExVivoBlood_24hr_5Gy_rep4

value: Peripheral Blood


title: CMC_male_4day_rep1CMC_G22M_D4_1

value: Carboxymethyl cellulose


title: CO_male_4day_rep2CO_G64M_D4_2

description: Gene expression data from liver samples of male CD1 mice treated with Corn oil up to 4 days.

source_name: Corn oil, male mice, 4 days

value: Corn oil


title: ExVivoBlood_24hr_8Gy_rep4


title: CO_male_4day_rep1CO_G64M_D4_1


title: CO_male_4day_rep3CO_G64M_D4_3


title: ExVivoBlood_48hr_0Gy_rep3


title: Tnfr2-deficient glomeruli, TNF-stimulated, rep2

city: Munich

first: Volker

last: Vielhauer

address: Ziemssenstr. 1

department: Medizinische Klinik IV, Nephrologisches Zentrum

institute: Klinikum der Universität München, Ludwig-Maximilans-University Munich

description: Gene expression data from Tnfr2-/- glomeruli after TNF stimulation in vitro

hyb_protocol: cRNA hybridization on Affymetrix Mouse Genome 430 2.0 arrays was performed according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix)

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software (GCOS1.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: isolated glomeruli of C57Bl/6J male Tnfr2-/- mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Glomeruli were isolated from 6 to 8 week male C57BL/6J wild-type, Tnfr1-, Tnfr2-, and Tnfr1/Tnfr2-double deficient mice after perfusion with magnetic M-450 tosylactivated Dynabeads, collagenase digestion of harvested kidneys and isolation of intact glomeruli containing trapped Dynabeads in a magnetic particle concentrator.

extract_protocol: Total RNA from TNF-stimulated glomeruli was prepared using RNeasy Mini Kit (Qiagen)

treatment_protocol: 5,000 glomeruli isolated from male C57BL/6J wild-type and Tnfr-deficient mice were serum starved and subsequently stimulated with 50 ng/ml murine TNF for 12 hours.

value: isolated intact glomeruli

tag: genotype

tag: background strain

value: 50 ng/ml murine TNF for 12 hours


title: CMC_male_4day_rep4CMC_G22M_D4_4

tag: treatment

value: 4 days


title: Tnfr2-deficient glomeruli, TNF-stimulated, rep3


title: CFX_male_4day_rep4CFX_G25M_D4_4

value: Cefuroxime


title: ExVivoBlood_24hr_2Gy_rep4


title: ExVivoBlood_48hr_5Gy_rep2

value: male


title: ExVivoBlood_48hr_2Gy_rep2


title: ExVivoBlood_24hr_8Gy_rep3


title: ExVivoBlood_24hr_0.5Gy_rep3


title: Tnfr1-deficient glomeruli, TNF-stimulated, rep3

description: Gene expression data from Tnfr1-/- glomeruli after TNF stimulation in vitro

source_name: isolated glomeruli of C57Bl/6J male Tnfr1-/- mouse


title: Tnfr1-deficient glomeruli, TNF-stimulated, rep1


title: ExVivoBlood_24hr_2Gy_rep3


title: ExVivoBlood_48hr_0.5Gy_rep2


title: Tnfr2-deficient glomeruli, TNF-stimulated, rep1


title: Tnfr1-deficient glomeruli, TNF-stimulated, rep2


title: Tnfr1/Tnfr2-deficient glomeruli, TNF-stimulated, rep3

description: Gene expression data from Tnfr1-/-,Tnfr2-/- glomeruli after TNF stimulation in vitro

source_name: isolated glomeruli of C57Bl/6J male Tnfr1-/-,Tnfr2-/- mouse


title: Tnfr1/Tnfr2-deficient glomeruli, TNF-stimulated, rep2


title: ExVivoBlood_24hr_5Gy_rep3


title: ExVivoBlood_48hr_0Gy_rep2


title: ExVivoBlood_24hr_0Gy_rep4


title: Wild-type glomeruli, TNF-stimulated, rep1

description: Gene expression data from wild-type glomeruli after TNF stimulation in vitro

source_name: isolated glomeruli of C57Bl/6J male wild-type mouse

value: B6 wild-type


title: Wild-type glomeruli, TNF-stimulated, rep3


title: ExVivoBlood_48hr_5Gy_rep1

value: 34 years


title: ExVivoBlood_48hr_2Gy_rep1


title: ExVivoBlood_48hr_8Gy_rep1


title: Wild-type glomeruli, TNF-stimulated, rep2


title: ExVivoBlood_24hr_0Gy_rep3


title: ExVivoBlood_48hr_0Gy_rep1


title: CFX_male_15day_rep3CFX_G27M_D15_3

description: Gene expression data from liver samples of male CD1 mice treated with Cefuroxime up to 15 days.

source_name: Cefuroxime, male mice, 15 days


title: NB4, Isotype control detected mRNAs, biological rep4

description: Isotype control detected mRNAs

hyb_protocol: Following fragmentation, aRNA was hybridized on Affymetrix Human Genome U133 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (performed by the core facility BMFZ Düsseldorf).

scan_protocol: GeneChips were scanned using the GCS 3000 from Affymetrix (performed by the core facility BMFZ, Düsseldorf).

data_processing: The data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.

source_name: NB4 cell line, 4'-thiouridine and UV treated

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from (GeneChip 3' IVT Express Kit Manual, 2008-2009, Affymetrix).

value: human acute promyelocytic leukemia

value: cells carry the t(15;17) PML-RARA fusion gene

value: cells were harvested after 48 - 72 h

tag: rna subtype

value: unspecific bound mRNAs of isotype control


title: embryo at TS27, biological rep3

city: Wuhan

first: Wenxin

last: Li

email: liwxlab@whu.edu.cn, guomx@whu.edu.cn, jinyangc13@126.com, sparkler830305@hotmail.com

state: Hubei

address: Wuhan University, Luojia Hill,Wuhan 430072,China

department: College of Life Science

country: China

institute: Wuhan Univeristy

description: Gene expression data from embryos at Theiler Stage 27

hyb_protocol: Following fragmentation, 10~15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome U133 Plus 2.0 Array in Genechip hybridization oven 640. GeneChips were washed and stained in the Affymetrix Genechip fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArrayTM scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Gene Spring Software (Agilent technologies, Santa Clara, CA, US) was used and the values in the normalized data were log2 transformed.

source_name: Mouse embryos at Theiler Stage 27

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5~10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: All mice were raised in SPF animal lab.Oocytes were obtained from each successfully supervulated mice.Females were mated with healthy F1 males for fertilized egg and post-implantation embryos collection.

treatment_protocol: Embryos of the appropriate stage were manually selected and auxiliary tissues were discarded under the dissecting scope.Selected embryos were transferred to a culture dish, rinsed with D-PBS and placed on ice in the Trizol solution (GibcoBRL).

value: dechorionated embryo

tag: developmental stage

value: Newborn mouse


title: ExVivoBlood_24hr_5Gy_rep2

tag: gender

value: 47 years


title: ExVivoBlood_24hr_8Gy_rep2

value: Peripheral Blood

tag: time


title: Tnfr1/Tnfr2-deficient glomeruli, TNF-stimulated, rep1


title: HMEC-1, biological replicate 2

city: Turku

first: Johannes

last: Keuschnigg

address: Tykistökatu 6a

country: Finland

institute: University of Turku

description:
dermal microvascular endothelial cells, immortalized by polyoma-virus
Sample name: HMEC2

hyb_protocol: Samples were processed with Affymetrix GeneChip 3’ IVT Express Kit according to manufacturer's instructions and hybridized to GeneChip Human Genome U133 plus 2.0 Array (all Affymetrix, Santa Clara, California, USA) at +45°C according to GeneChip® Expression Analysis Technical Manual (With Specific Protocols for Using the GeneChip® Hybridization, Wash and Stain Kit)

scan_protocol: GeneChip® Scanner 3000 7G with AutoLoader was used to scan the arrays

data_processing: Samples were GC-RMA normalized in Anduril bioinformatics workflow engine using R

source_name: human microvascular endothelial cell line 1

label_protocol: Labeling was performed according to protocols from Affymetrix.

growth_protocol: HMEC-1 were cultured in EBM-2 medium with EGM-2 SingleQuots (Lonza, Basel, Switzerland). TIME were cultured according to ATCC instructions (CRL-4025). Cells were subcultured after reaching ~80% confluency.

extract_protocol: Total RNA was isolated using a NucleoSpin RNA isolation kit (Macherey&Nagel, Düren, Germany)

treatment_protocol: Cells were not treated in any way

value: immortalized human microvascular endothelial cell line-1 (HMEC-1)


title: NB4, identified mRNAs of total RNA

description: Gene expression data from mRNAs of total RNA of SNB19 cells

value: total RNA


title: embryo at TS25, biological rep2

description: Gene expression data from embryos at Theiler Stage 25

source_name: Mouse embryos at Theiler Stage 25

tag: strain

value: E17 embryos


title: embryo at TS27, biological rep1


title: NB4, Isotype control detected mRNAs, biological rep3

description: Isotype control detected mRNAs


title: ExVivoBlood_24hr_8Gy_rep1

value: 38 years


title: embryo at TS23, biological rep3

description: Gene expression data from embryos at Theiler Stage 23

source_name: Mouse embryos at Theiler Stage 23

value: E15 embryos


title: ExVivoBlood_48hr_0.5Gy_rep1

source_name: Peripheral Blood 48hr

value: female


title: ExVivoBlood_24hr_2Gy_rep2

value: male


title: embryo at TS27, biological rep2


title: TIME, biological replicate 4

description:
dermal microvascular endothelial cells, immortalized by telomerase immortalization
Sample name: TIME4

source_name: telomerase immortalized microvascular endothelial cell line

value: telomerase-immortalized microvascular endothelial cell line (TIME)


title: ExVivoBlood_24hr_0Gy_rep2


title: HMEC-1, biological replicate 4

description:
dermal microvascular endothelial cells, immortalized by polyoma-virus
Sample name: HMEC4


title: HMEC-1, biological replicate 1

description:
dermal microvascular endothelial cells, immortalized by polyoma-virus
Sample name: HMEC1


title: TIME, biological replicate 2

description:
dermal microvascular endothelial cells, immortalized by telomerase immortalization
Sample name: TIME2


title: embryo at TS25, biological rep1


title: NB4, Isotype control detected mRNAs, biological rep1

description: Isotype control detected mRNAs


title: ExVivoBlood_24hr_0.5Gy_rep2


title: HMEC-1, biological replicate 3

description:
dermal microvascular endothelial cells, immortalized by polyoma-virus
Sample name: HMEC3


title: TIME, biological replicate 3

description:
dermal microvascular endothelial cells, immortalized by telomerase immortalization
Sample name: TIME3


title: TIME, biological replicate 1

description:
dermal microvascular endothelial cells, immortalized by telomerase immortalization
Sample name: TIME1


title: embryo at TS23, biological rep2


title: embryo at TS25, biological rep3


title: ExVivoBlood_24hr_5Gy_rep1


title: ExVivoBlood_24hr_0.5Gy_rep1


title: NB4, Ago4-associated mRNAs, biological rep3

description: Identification of Ago4-associated mRNAs

value: Ago4-associated mRNAs


title: NB4, Isotype control detected mRNAs, biological rep2

description: Isotype control detected mRNAs

value: human acute promyelocytic leukemia


title: NB4, Ago4-associated mRNAs, biological rep2

description: Identification of Ago4-associated mRNAs

value: cells carry the t(15;17) PML-RARA fusion gene


title: NB4, Ago4-associated mRNAs, biological rep1

description: Identification of Ago4-associated mRNAs

value: cells were harvested after 48 - 72 h


title: case7_colon,tumor_120 minutes

city: Tokyo

first: Aya

last: Yamagishi

address: 1-1-5 Sendagi Bunkyo-ku

department: department of surgery

country: Japan

institute: Nippon medical school

hyb_protocol: 1.65µg of Cy3-labeled cRNA was hybridized for 17 hours at 65˚C to an Agilent Human GE 4×44K V2 Microarray Kit with SurePrint Technology

scan_protocol: Each array was scanned with the immediately Agilent G2565CA Microarray Scanner.

data_processing: The microarray data sets were normalized by GeneSpring GX software (version 11.5, Agilent Technologies) using the Agilent FE one-color scenario. Spots that did not pass quality control procedures were flagged as Not Detected and “Compromised” . Data were normalized by Quantile method and Filtered on Expression (20.0 - 100.0)th Percentile in the Raw Data where at least 1 out of 28 samples have flags in Detected .

source_name: colorectal tumor tissue, 120 minutes after surgical removal

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Agilent Low Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Both normal and tumor tissues extracted after surgical removal and stabilized in RNAlater at 4°C overnight and stored at -20°C freezer untill RNA extraction.

extract_protocol: After homogenization, total RNA was extracted by using Rneasy kit (Qiagen,Valencia, CA,USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: location

value: rectum

value: tumor tissue

value: 120 minute


title: NB4, Ago3-associated mRNAs, biological rep3

description: Identification of Ago3-associated mRNAs

value: Ago3-associated mRNAs


title: ExVivoBlood_24hr_0Gy_rep1

source_name: Peripheral Blood 24hr

value: Peripheral Blood


title: embryo at TS21, biological rep3

description: Gene expression data from embryos at Theiler Stage 21

source_name: Mouse embryos at Theiler Stage 21

value: dechorionated embryo

value: E12.5 embryos


title: embryo at TS23, biological rep1


title: embryo at TS22, biological rep3

description: Gene expression data from embryos at Theiler Stage 22

source_name: Mouse embryos at Theiler Stage 22

value: E14 embryos


title: ExVivoBlood_6hr_2Gy_rep5

source_name: Peripheral Blood 6hr

value: 36 years


title: NB4, Ago3-associated mRNAs, biological rep2

description: Identification of Ago3-associated mRNAs


title: case6_colon,tumor_120 minutes

value: colon


title: ExVivoBlood_6hr_5Gy_rep5

value: female


title: ExVivoBlood_6hr_8Gy_rep5


title: NB4, Ago2-associated mRNAs, biological rep3

description: Identification of Ago2-associated mRNAs

value: Ago2-associated mRNAs


title: case7_colon,tumor_30 minute

source_name: colorectal tumor tissue, 30 minutes after surgical removal

value: 30 minute


title: case7_colon,tumor_0 minute

source_name: colorectal tumor tissue, 0 minute after surgical removal

value: 0 minute


title: case6_colon,tumor_30 minute


title: embryo at TS22, biological rep2


title: case7_colon,tumor_60 minute

source_name: colorectal tumor tissue, 60 minutes after surgical removal

value: 60 minute


title: case6_colon,tumor_60 minute


title: embryo at TS21, biological rep2


title: embryo at TS22, biological rep1


title: ExVivoBlood_24hr_2Gy_rep1

value: male

value: 38 years


title: embryo at TS21, biological rep1


title: NB4, Ago3-associated mRNAs, biological rep1

description: Identification of Ago3-associated mRNAs

value: human acute promyelocytic leukemia

value: cells carry the t(15;17) PML-RARA fusion gene

value: cells were harvested after 48 - 72 h


title: ExVivoBlood_6hr_0Gy_rep5


title: NB4, Ago2-associated mRNAs, biological rep2

description: Identification of Ago2-associated mRNAs


title: NB4, Ago1-associated mRNAs, biological rep2

description: Identification of Ago1-associated mRNAs

value: Ago1-associated mRNAs


title: NB4, Ago1-associated mRNAs, biological rep3

description: Identification of Ago1-associated mRNAs


title: case6_colon,tumor_0 minute

value: tumor tissue


title: embryo at TS19, biological rep2

description: Gene expression data from embryos at Theiler Stage 19

source_name: Mouse embryos at Theiler Stage 19

value: dechorionated embryo

value: E11.5 embryos


title: embryo at TS19, biological rep3


title: NB4, Ago1-associated mRNAs, biological rep1

description: Identification of Ago1-associated mRNAs


title: case5_colon,tumor_60 minute


title: ExVivoBlood_6hr_8Gy_rep4

value: 35 years

value: Peripheral Blood


title: case5_colon,tumor_0 minute

value: colon


title: NB4, Ago2-associated mRNAs, biological rep1

description: Identification of Ago2-associated mRNAs


title: case5_colon,tumor_30 minute


title: embryo at TS16, biological rep3

description: Gene expression data from embryos at Theiler Stage 16

source_name: Mouse embryos at Theiler Stage 16

value: E10 embryos


title: ExVivoBlood_6hr_2Gy_rep4

value: female


title: ExVivoBlood_6hr_0.5Gy_rep4


title: ExVivoBlood_6hr_5Gy_rep4


title: ExVivoBlood_6hr_0.5Gy_rep5

value: 36 years


title: embryo at TS19, biological rep1


title: case5_colon,tumor_120 minutes

value: 120 minute


title: case4_colon,tumor_120 minutes


title: ExVivoBlood_6hr_8Gy_rep3

value: 53 years


title: KASUMI-1, Isotype control detected mRNAs, biological rep3

description: Isotype control detected mRNAs

source_name: KASUMI-1 cell line, 4'-thiouridine and UV treated

value: human acute myeloid leukemia

value: cells carry the t(8;21) AML1-ETO fusion gene

value: unspecific bound mRNAs of isotype control


title: embryo at TS16, biological rep2


title: embryo at TS16, biological rep1


title: case4_colon,tumor_0 minute

value: male

value: 0 minute


title: KASUMI-1, Isotype control detected mRNAs, biological rep2

description: Isotype control detected mRNAs

value: cells were harvested after 48 - 72 h


title: embryo at TS13, biological rep3

description: Gene expression data from embryos at Theiler Stage 13

source_name: Mouse embryos at Theiler Stage 13

value: E8.5 embryos


title: case3_colon,tumor_120 minutes

value: rectum

value: tumor tissue


title: case2_colon,tumor_120 minutes


title: ExVivoBlood_6hr_0Gy_rep4

value: 35 years


title: ExVivoBlood_6hr_2Gy_rep3

value: Peripheral Blood


title: ExVivoBlood_6hr_0Gy_rep3


title: case3_colon,tumor_0 minute


title: case2_colon,tumor_0 minute

value: colon


title: embryo at TS11, biological rep3

description: Gene expression data from embryos at Theiler Stage 11

source_name: Mouse embryos at Theiler Stage 11

value: dechorionated embryo

value: E7.5 embryos


title: KASUMI-1, Ago4-associated mRNAs, biological rep3

description: Identification of Ago4-associated mRNAs

value: Ago4-associated mRNAs


title: ExVivoBlood_6hr_5Gy_rep3


title: KASUMI-1, Ago4-associated mRNAs, biological rep1

description: Identification of Ago4-associated mRNAs


title: ExVivoBlood_6hr_0.5Gy_rep3


title: KASUMI-1, Isotype control detected mRNAs, biological rep1

description: Isotype control detected mRNAs


title: embryo at TS13, biological rep1


title: case1_colon,tumor_120 minutes

value: 120 minute


title: KASUMI-1, Ago3-associated mRNAs, biological rep2

description: Identification of Ago3-associated mRNAs

value: Ago3-associated mRNAs


title: embryo at TS11, biological rep1


title: case1_colon,tumor_0 minute


title: embryo at TS13, biological rep2


title: ExVivoBlood_6hr_8Gy_rep2

value: female

value: 20 years


title: ExVivoBlood_6hr_2Gy_rep2


title: ExVivoBlood_6hr_5Gy_rep2


title: KASUMI-1, Ago4-associated mRNAs, biological rep2

description: Identification of Ago4-associated mRNAs

value: human acute myeloid leukemia

value: cells carry the t(8;21) AML1-ETO fusion gene


title: KASUMI-1, Isotype control detected mRNAs, biological rep4

description: Isotype control detected mRNAs

value: unspecific bound mRNAs of isotype control


title: case4_colon,normal_0 minute

source_name: colorectal normal mucosa, 0 minute after surgical removal

value: normal mucosa

value: male

value: 0 minute


title: embryo at TS11, biological rep2


title: KASUMI-1, Ago3-associated mRNAs, biological rep1

description: Identification of Ago3-associated mRNAs

value: cells were harvested after 48 - 72 h


title: KASUMI-1, identified mRNAs of total RNA

value: total RNA


title: embryo at TS09, biological rep3

description: Gene expression data from embryos at Theiler Stage 9

source_name: Mouse embryos at Theiler Stage 9

value: E6.5 embryos


title: ExVivoBlood_6hr_0.5Gy_rep2

value: Peripheral Blood


title: case3_colon,normal_120 minute

source_name: colorectal normal mucosa, 120 minutes after surgical removal

value: rectum


title: KASUMI-1, Ago3-associated mRNAs, biological rep3

description: Identification of Ago3-associated mRNAs


title: KASUMI-1, Ago2-associated mRNAs, biological rep3

description: Identification of Ago2-associated mRNAs

value: Ago2-associated mRNAs


title: ExVivoBlood_6hr_8Gy_rep1

value: 39 years


title: embryo at TS09, biological rep2

value: dechorionated embryo


title: ExVivoBlood_6hr_0Gy_rep2


title: case4_colon,normal_120 minute

value: colon

value: 120 minute


title: ExVivoBlood_6hr_5Gy_rep1


title: ExVivoBlood_6hr_2Gy_rep1


title: case1_colon,normal_120 minute


title: ExVivoBlood_6hr_0Gy_rep1


title: KASUMI-1, Ago1-associated mRNAs, biological rep2

description: Identification of Ago1-associated mRNAs

value: Ago1-associated mRNAs


title: case2_colon,normal_120 minute

value: female


title: KASUMI-1, Ago2-associated mRNAs, biological rep1

description: Identification of Ago2-associated mRNAs

value: human acute myeloid leukemia

value: cells carry the t(8;21) AML1-ETO fusion gene


title: embryo at TS01, biological rep1

description: Gene expression data from fertilized eggs.

source_name: Mouse embryos at Theiler Stage 1,fertilized eggs

value: fertilized eggs,12~14h after  coitus


title: embryo at TS01, biological rep2


title: KASUMI-1, Ago1-associated mRNAs, biological rep3

description: Identification of Ago1-associated mRNAs


title: KASUMI-1, Ago1-associated mRNAs, biological rep1

description: Identification of Ago1-associated mRNAs


title: embryo at TS01, biological rep3


title: embryo at Egg, biological rep2

description: Gene expression data from ooyvtes

source_name: Mouse oocytes

value: unfertilized eggs


title: ExVivoBlood_6hr_0.5Gy_rep1

value: male


title: case3_colon,normal_0 minute

value: normal mucosa

value: 0 minute


title: KASUMI-1, Ago2-associated mRNAs, biological rep2

description: Identification of Ago2-associated mRNAs

value: cells were harvested after 48 - 72 h


title: embryo at Egg, biological rep1

description: Gene expression data from ooyvtes


title: case2_colon,normal_0 minute


title: case1_colon,normal_0 minute


title: embryo at TS09, biological rep1

value: E6.5 embryos


title: embryo at Egg, biological rep3

description: Gene expression data from ooyvtes


title: PNP-Series3-15.6 nM

status: Public on Sep 10 2013

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Following fragmentation, biotinylated cRNA probe (25 ng/uL in 200 uL hybridizationconcktail) were hybridized for 17 hr at 45C on GeneChip Human U133 version 2 plu (GPL570) sarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (protocol FS450_0001).

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

data_processing: The data were analyzed with Affymetrix GeneChip Command Console (AGCC).  affymetrix-algorithm-name = rma-gene-default  affymetrix-algorithm-version = 1.0  program-name = Expression Console

label_protocol: Biotinylated cRNA probes were synthesized using the GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: MCF-7 cells were grown in DMEM supplemented with 5% FCS, 2 mM glutamine, and 1X Penicillin/Streptomycin.

extract_protocol: Total RNA was extracted directly from cell cultures grown on 10 cm dishes using QIAGEN RNeasy kit.

treatment_protocol: Subconfluent MCF-7 cells in 10 cm dishes were exposed to varying concentrations of xenoestrogen chemicals for exactly 48 hours and subjected to immediate isolation of total RNA. Xenoestrogen chemicals tested in this study were Bisphenol A, Diethylstilbestrol, 17alpha-ethynylestradiol, p-nonylphenol, genistein, and daidzein. Transcriptomal effects of physiological estrogen 17beta-estradiol was also examined.

tag: xenoestrogen

value: p-nonylphenol

tag: series

tag: molar concentration


title: PNP-Series3-1000 nM

tag: cell line


title: PNP-Series2-12.5 uM


title: PNP-Series2-3.125 uM


title: PNP-Series3-12.5 uM


title: PNP-Series2-250 nM


title: PNP-Series2-1000 nM


title: PNP-Series1-62.5 nM


title: PNP-Series2-25 uM


title: PNP-Series2-15.6 nM


title: PNP-Series2-control


title: PNP-Series3-6.25 uM


title: PNP-Series1-control


title: PNP-Series1- 3.125 uM


title: PNP-Series1-250 nM


title: PNP-Series1-1.95 nM


title: PNP-Series3-3.125 uM


title: PNP-Series1-12.5 uM


title: PNP-Series2-62.5 nM


title: PNP-Series1-15.6 nM


title: Gen-Series7-6 uM

value: genistein


title: Gen-Series7-0.75 uM


title: Gen-Series7-2 uM


title: Gen-Series7-8 uM


title: Gen-Series7-0.5 uM


title: Gen-Series7-4 uM


title: Gen-Series7-control


title: Gen-Series7-0.25 uM


title: Gen-Series7-0.05 uM


title: Gen-Series6-8 uM


title: Gen-Series6-6 uM


title: Gen-Series6-0.25 uM


title: Gen-Series6-0.05 uM


title: Gen-Series7-10 uM


title: Gen-Series6-0.75 uM


title: Gen-Series6-4 uM


title: Gen-Series6-3 uM


title: Gen-Series6-2 uM


title: Gen-Series5-0.1 uM


title: Gen-Series5-0.25 uM


title: Gen-Series6-10 uM


title: PNP-Series3-control


title: Gen-Series7-3 uM


title: Gen-Series6-0.5 uM


title: Gen-Series4-8 uM


title: Gen-Series4-3 uM


title: Gen-Series4-4 uM


title: Gen-Series4-0.5 uM


title: Hippocampus wild-type 2

city: Bonn

first: Dan

last: Ehninger

state: NRW

address: Ludwig-Erhard-Allee 2

institute: German Center for Neurodegenerative Diseases (DZNE)

description: 08- 789 WT

hyb_protocol: Samples were hybridized on GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Chip images were inspected and checked for proper scanning. Raw data were then imported in Expression console (Affymetrix) to verify quality criteria (poly A controls, Hybridization controls and background to noise ratio) and to perform background correction, normalization and a RMA algorithm.
affymetrix-algorithm-name = rma-exon-all : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.0.187
GeneSpring GX 10 software (Agilent) was further used for statistical evaluations and to generate clusters and heatmaps of the dataset.

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated from with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA integrity was determined using a Bioanalyzer (Agilent) instrument. Only samples with RNA integrity numbers about 10 were processed on Affymetrix chips.

tag: strain background

value: B6/SJL (for hemizygous 5xFAD mice) and C57BL/6J (for eIF2α+/S51A mice)

tag: genotype/variation

value: wild-type

value: brain; hippocampus


title: Hippocampus 5xFAD 2

description: 04- 796 TG

tag: tissue


title: Gen-Series4-12 uM


title: Gen-Series4-1 uM


title: Hippocampus wild-type 3

description: 11- 788 WT


title: Gen-Series3-2 uM


title: Gen-Series3-4 uM


title: Hippocampus eIF2α+/S51A 1

description: 05- 760 KI


title: Gen-Series4-control


title: Gen-Series3-1 uM


title: Gen-Series3-8 uM


title: Gen-Series6-control


title: Gen-Series4-2 uM


title: Hippocampus eIF2α+/S51A 2

description: 06- 1023 KI


title: Gen-Series3-16 uM


title: Gen-Series3-0.5 uM


title: Gen-Series4-16 uM


title: Hippocampus wild-type 1

description: 01- 768 WT


title: Gen-Series3-control


title: Gen-Series2-8 uM


title: Hippocampus 5xFAD 3

description: 09- 784 TG


title: Gen-Series3-3 uM


title: Hippocampus eIF2α+/S51A 3

description: 07- 798 KI


title: Hippocampus 5xFAD;eIF2α+/S51A 1

description: 03- 766 TG+KI


title: Hippocampus 5xFAD;eIF2α+/S51A 3

description: 12- 792 TG+KI


title: Hippocampus 5xFAD;eIF2α+/S51A 2

description: 10- 770 TG+KI


title: Gen-Series2-1 uM


title: Gen-Series2-control


title: Gen-Series1-12 uM


title: Gen-Series2-2 uM


title: Gen-Series2-3 uM


title: Gen-Series2-16 uM


title: Gen-Series1-3 uM


title: Gen-Series2-12 uM


title: Gen-Series5-control


title: Gen-Series1-8 uM


title: Gen-Series1-2 uM


title: Gen-Series1-0.5 uM


title: Gen-Series2-4 uM


title: Gen-Series2-0.5 uM


title: Gen-Series5-4 uM


title: Gen-Series1-16 uM


title: Gen-Series5-3 uM


title: Gen-Series5-6 uM


title: Gen-Series5-2 uM


title: Gen-Series1-4 uM


title: Gen-Series5-8 uM


title: Gen-Series1-control


title: Gen-Series5-10 uM


title: Hippocampus 5xFAD 1

description: 02- 626 TG


title: Gen-Series5-0.75 uM


title: E2-Series7-80 pM


title: Gen-Series5-0.5 uM


title: Gen-Series5-0.05 uM


title: E2-Series6-1 nM


title: E2-Series8-1 nM


title: E2-Series6-80 pM


title: E2-Series8-1 uM


title: E2-Series8-80 pM


title: E2-Series6-1 uM


title: Gen-Series5-1 uM


title: E2-Series7-100 nM


title: E2-Series7-1 nM


title: E2-Series6-10 nM


title: E2-Series8-100 nM


title: E2-Series7-1 uM


title: E2-Series5-40 pM


title: E2-Series7-control


title: E2-Series5-8 pM


title: E2-Series5-20 pM


title: E2-Series8-10 nM


title: E2-Series5-60 pM


title: E2-Series5-80 pM


title: E2-Series5-4 pM


title: E2-Series5-2 pM


title: E2-Series5-6 pM


title: E2-Series6-control


title: E2-Series8-control


title: E2-Series7-10 nM


title: E2-Series5-10 pM


title: E2-Series2-80 pM


title: E2-Series5-0.1 pM


title: E2-Series5-0.5 pM


title: E2-Series5-100 pM


title: E2-Series2-60 pM


title: E2-Series5-control


title: E2-Series2-2 pM


title: E2-Series5-0.05 pM


title: E2-Series2-40 pM


title: E2-Series2-4 pM


title: E2-Series5-1 pM


title: E2-Series2-control


title: E2-Series2-6 pM


title: E2-Series4-80 pM


title: E2-Series4-20 pM


title: E2-Series2-20 pM


title: E2-Series2-10 pM


title: E2-Series4-40 pM


title: E2-Series2-0.05 pM


title: E2-Series4-6 pM


title: E2-Series4-2 pM


title: E2-Series2-0.1 pM


title: E2-Series2-0.5 pM


title: E2-Series4-60 pM


title: E2-Series4-4 pM


title: E2-Series2-1 pM


title: E2-Series4-8 pM


title: E2-Series2-100 pM


title: E2-Series4-100 pM


title: E2-Series2-8 pM


title: E2-Series3-80 pM


title: E2-Series4-0.1 pM


title: E2-Series3-20 pM


title: E2-Series3-40 pM


title: E2-Series3-4 pM


title: E2-Series3-6 pM


title: E2-Series4-1 pM


title: E2-Series3-2 pM


title: E2-Series4-0.05 pM


title: E2-Series3-60 pM


title: E2-Series3-0.05 pM


title: E2-Series4-0.5 pM


title: E2-Series4-control


title: E2-Series3-0.5 pM


title: E2-Series1-4 pM


title: E2-Series1-80 pM


title: E2-Series3-1 pM


title: E2-Series3-control


title: E2-Series1-60 pM


title: E2-Series1-100 pM


title: E2-Series1-10 pM


title: E2-Series3-10 pM


title: E2-Series3-0.1 pM


title: E2-Series4-10 pM


title: E2-Series1-20 pM


title: E2-Series1-40 pM


title: E2-Series1-1 pM


title: E2-Series1-6 pM


title: EE2-Series5-control


title: EE2-Series3-60 pM


title: E2-Series1-control


title: EE2-Series5-10 pM


title: EE2-Series3-control


title: EE2-Series4-60 pM


title: EE2-Series3-3 pM


title: EE2-Series5-60 pM


title: EE2-Series4-10 pM


title: EE2-Series3-1 pM


title: E2-Series1-0.5 pM


title: EE2-Series3-10 pM


title: EE2-Series4-control


title: EE2-Series2-60 pM


title: EE2-Series2-10 pM


title: EE2-Series1-1 pM


title: EE2-Series2-30 pM


title: EE2-Series1-60 pM


title: EE2-Series1-30 pM


title: EE2-Series2-control


title: EE2-Series1-10 pM


title: E2-Series1-0.1 pM


title: EE2-Series2-1 pM


title: EE2-Series1-100 pM


title: EE2-Series2-100 pM


title: EE2-Series1-3 pM


title: EE2-Series2-3 pM


title: Daidzein-Series4-control

value: daidzein


title: EE2-Series1-control


title: Daidzein-Series4-4 uM


title: Daidzein-Series3-control


title: Daidzein-Series2-4 uM


title: Daidzein-Series3-3 uM


title: Daidzein-Series3-2 uM


title: Daidzein-Series4-3 uM


title: Daidzein-Series3-4 uM


title: Daidzein-Series1-3 uM


title: Daidzein-Series2-1 uM


title: Daidzein-Series1-control


title: Daidzein-Series2-2 uM


title: Daidzein-Series3-1 uM


title: Daidzein-Series2-control


title: Daidzein-Series2-3 uM


title: Daidzein-Series1-4 uM


title: Daidzein-Series4-0.5 uM


title: Daidzein-Series2-0.5 uM


title: Daidzein-Series1-1 uM


title: Daidzein-Series3-0.5 uM


title: Daidzein-Series4-2 uM


title: E2-Series1-0.05 pM


title: Daidzein-Series1-2 uM


title: DES-Series5-0.1 pM

value: diethylstilbestrol


title: Daidzein-Series4-1 uM


title: DES-Series5-0.3 pM


title: DES-Series5-0.01 pM


title: Daidzein-Series1-0.5 uM


title: DES-Series4-0.03 pM


title: DES-Series4-0.3 pM


title: DES-Series5-0.03 pM


title: DES-Series5-control


title: DES-Series4-0.1 pM


title: DES-Series3-0.3 pM


title: DES-Series34-0.1 pM


title: DES-Series3-0.01 pM


title: DES-Series3-control


title: DES-Series3-0.03 pM


title: DES-Series4-0.01 pM


title: DES-Series2-0.1 pM


title: DES-Series4-0.003 pM


title: DES-Series4-control


title: AVCM2

first: Ronald

middle: A

address: 1 Gustave Levy Pl

institute: Mount Sinai School of Medicine

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using the cubic spline algorithm available on the Illumina BeadStudio software package.

source_name: adult ventricular cardiac tissue

label_protocol: Total RNA was labeled with biotinylated nucleotides using standard protocol from the Ambion TotalPrep -96 RNA Amplification kit (a variant of the Eberwine protocol)

extract_protocol: Whole RNA was extracted from cells using Trizol and 1:4 volume of chloroform. The aqueous phase was separated using heavy phase lock gel tubes and RNA was purified using the Qiagen RNeasy mini kit according to standard protocol. All samples were verified for high quality using Agilent Bioanalyzer.

tag: stage of cardiac development

value: adult ventricular cardiac tissue

tag: age

value: 53 year old patient


title: FVCM1

description: replicate 1

source_name: fetal ventricular cardiac tissue

value: fetal ventricular cardiac tissue

value: 20 weeks


title: EVCM2

description: replicate 2

source_name: embryonic stem cell derived ventricular-like cardiomyocyte

value: 20 days post-differentiation


title: DES-Series2-0.01 pM


title: DES-Series2-0.03 pM


title: DES-Series2-0.3 pM


title: HESC1

description: replicate 1

source_name: undifferentiated human embryonic stem cell


title: AVCM1

description: replicate 1

value: 59 year old patient


title: EVCM1

description: replicate 1

value: embryonic stem cell derived ventricular-like cardiomyocyte


title: EE2-Series3-30 pM


title: EE2-Series3-100 pM


title: DES-Series2-control


title: AVCM3

description: replicate 3

value: 70 year old patient


title: DES-Series3-0.003 pM


title: DES-Series1-0.1 pM


title: HESC2

description: replicate 2

value: undifferentiated human embryonic stem cell


title: Pt33_after_drug

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Gene expression sample from Patient 33 after drug

hyb_protocol: Hybridization of labeled cRNA to the BeadChip, and washing and scanning were performed according to the Illumina BeadStation 500x manual. Essentially the amplified, biotin-labeled human cRNA samples were resuspended in a solution of Hyb E1 buffer (Illumina) and 25% (v/v) formamide at a final concentration of 25 ng/µL. 1.5 µg of each cRNA were hybridized.

scan_protocol: The arrays were scanned on the Illumina BeadArray Reader.

data_processing: The data were log2 transformed, normalised using robust spline normalisation (rsn) with Bioconductor package lumi in R and adjusted for batch effect using ComBat (http://statistics.byu.edu/johnson/ComBat/Usage.html).

source_name: PBMC

label_protocol: Biotinylated cRNA was prepared using the Illumina RNA Amplification Kit, Catalog #1L1791 (Ambion, Inc., Austin, TX) according to the manufacturer's directions starting with ~250 ng total RNA. mRNA was converted to cDNA, followed by an amplification/labeling step mediated by T7 DNA polymerase. The cDNA and cRNA filter cartridges (Ambion) were used according to the manufacturer's instructions for RT and IVT cleanup, respectively.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer.

tag: Sex

value: Male

value: 27 years

tag: ethnicity

value: White

tag: drug regimen

value: Switchers

tag: cd4+ t cell count measurement

value: after 48 weeks

tag: cd4+ t cell count, cells/ul

tag: batch

tag: reanalysis

value: New analysis

tag: sdf file

tag: analysis

value: Patient included in analysis

tag: subject

value: antiretroviral therapy


title: DES-Series1-0.03 pM

tag: xenoestrogen

value: diethylstilbestrol

tag: series

tag: molar concentration


title: DES-Series5-0.003 pM

tag: cell line


title: Pt34_after_drug

description: Gene expression sample from Patient 34 after drug

value: 29 years

tag: treatment


title: Pt35_after_drug

description: Gene expression sample from Patient 35 after drug

value: 38 years


title: Pt32_after_drug

description: Gene expression sample from Patient 32 after drug

value: 47 years


title: Pt31_after_drug

description: Gene expression sample from Patient 31 after drug

value: 42 years


title: BPA-Series3-62.5 nM

value: Bisphenol A


title: BPA-Series3-50 uM


title: Pt29_after_drug

description: Gene expression sample from Patient 29 after drug

value: Asian


title: DES-Series1-control


title: DES-Series1-0.01 pM


title: Pt36_after_drug

description: Gene expression sample from Patient 36 after drug

value: 34 years


title: Pt27_after_drug

description: Gene expression sample from Patient 27 after drug

value: 49 years


title: Pt26_after_drug

description: Gene expression sample from Patient 26 after drug

value: Male

value: 43 years


title: DES-Series1-0.003 pM


title: Pt24_after_drug

description: Gene expression sample from Patient 24 after drug

value: 27 years

value: White

value: PI


title: BPA-Series3-15.6 nM


title: BPA-Series3-3.12 uM


title: BPA-Series3-250 nM


title: BPA-Series3-250 pM


title: DES-Series1-0.3 pM


title: Pt28_after_drug

description: Gene expression sample from Patient 28 after drug

value: 36 years

value: Switchers

value: after 48 weeks

value: New analysis


title: Pt25_after_drug

description: Gene expression sample from Patient 25 after drug

value: Patient included in analysis

value: antiretroviral therapy


title: BPA-Series3-12.5 uM


title: Pt22_after_drug

description: Gene expression sample from Patient 22 after drug

value: 37 years


title: Pt20_after_drug

description: Gene expression sample from Patient 20 after drug

value: African American


title: Pt23_after_drug

description: Gene expression sample from Patient 23 after drug

value: 54 years


title: Pt15_after_drug

description: Gene expression sample from Patient 15 after drug

value: 58 years

value: Patient dropped from analysis


title: BPA-Series3-control

description: RMA expression value derived from Expression Console software; core-exon analysis

value: Bisphenol A


title: BPA-Series3-1000 nM


title: BPA-Series1-6.25 uM


title: Pt18_after_drug

description: Gene expression sample from Patient 18 after drug

value: Male

value: 24 years

value: American Indian


title: BPA-Series1-500 pM


title: Pt21_after_drug

description: Gene expression sample from Patient 21 after drug

value: 40 years

value: Asian


title: Pt19_after_drug

description: Gene expression sample from Patient 19 after drug

value: 39 years

value: White

value: PI


title: BPA-Series1-7.81 pM


title: BPA-Series3-1.95 nM


title: Pt16_after_drug

description: Gene expression sample from Patient 16 after drug

value: 50 years

value: after 48 weeks

value: New analysis


title: BPA-Series1-62.5 nM


title: BPA-Series1-7.81 nM


title: BPA-Series1-50 uM


title: Pt17_after_drug

description: Gene expression sample from Patient 17 after drug

value: 33 years

value: Patient included in analysis

value: antiretroviral therapy


title: Pt14_after_drug

description: Gene expression sample from Patient 14 after drug


title: Pt12_after_drug

description: Gene expression sample from Patient 12 after drug

value: 19 years

value: NNRTI


title: BPA-Series1-31.25 pM

value: Bisphenol A


title: Pt10_after_drug

description: Gene expression sample from Patient 10 after drug

value: Male


title: BPA-Series1-3.91 nM


title: Pt9_after_drug

description: Gene expression sample from Patient 9 after drug

value: 28 years


title: BPA-Series1-250 pM


title: BPA-Series1-3.125 uM


title: BPA-Series1-500 nM


title: Pt7_after_drug

description: Gene expression sample from Patient 7 after drug

value: 24 years

value: African American


title: Pt13_after_drug

description: Gene expression sample from Patient 13 after drug

value: 29 years

value: Patient dropped from analysis


title: Pt8_after_drug

description: Gene expression sample from Patient 8 after drug

value: 38 years

value: White


title: Pt11_after_drug

description: Gene expression sample from Patient 11 after drug


title: Pt30_after_drug

description: Gene expression sample from Patient 30 after drug

value: 45 years

value: Switchers


title: BPA-Series1-15.6 nM


title: Pt6_after_drug

description: Gene expression sample from Patient 6 after drug

value: 42 years

value: after 48 weeks

value: New analysis


title: Pt5_after_drug

description: Gene expression sample from Patient 5 after drug

value: 52 years

value: Patient included in analysis

value: antiretroviral therapy


title: BPA-Series1-250 nM

description: RMA expression value derived from Expression Console software; core-exon analysis

value: Bisphenol A


title: BPA-Series1-125 pM


title: Pt3_after_drug

description: Gene expression sample from Patient 3 after drug

value: Male

value: 39 years

value: American Indian

value: NNRTI


title: Pt4_after_drug

description: Gene expression sample from Patient 4 after drug


title: Pt34_before_drug

description: Gene expression sample from Patient 34 before drug

value: 29 years

value: baseline


title: Pt2_after_drug

description: Gene expression sample from Patient 2 after drug

value: 36 years


title: DES-Series2-0.003 pM

value: diethylstilbestrol


title: Pt36_before_drug

description: Gene expression sample from Patient 36 before drug

value: 34 years

value: White


title: BPA-Series1-125 nM


title: BPA-Series1-25 uM


title: Pt1_after_drug

description: Gene expression sample from Patient 1 after drug

value: 31 years


title: Pt33_before_drug

description: Gene expression sample from Patient 33 before drug

value: 27 years

value: Switchers


title: BPA-Series1-12.5 uM


title: BPA-Series1-1000 nM


title: Pt35_before_drug

description: Gene expression sample from Patient 35 before drug

value: 38 years

value: New analysis


title: BPA-Series1-1.56 uM


title: BPA-Series1-31.25 nM


title: Pt32_before_drug

description: Gene expression sample from Patient 32 before drug

value: 47 years

value: Patient included in analysis


title: BPA-Series1-1.95 pM

value: Bisphenol A


title: BPA-Series1-1.95 nM


title: BPA-Series1-control


title: Pt30_before_drug

description: Gene expression sample from Patient 30 before drug

value: Male

value: 45 years


title: Pt28_before_drug

description: Gene expression sample from Patient 28 before drug


title: Pt29_before_drug

description: Gene expression sample from Patient 29 before drug

value: 42 years

value: Asian


title: BPA-Series2-6.25 uM


title: Pt25_before_drug

description: Gene expression sample from Patient 25 before drug

value: baseline


title: BPA-Series2-500 nM


title: BPA-Series2-62.5 nM


title: Human intestinal microbiota associated rat's caecum, biological rep3

city: St-Hyacinthe

first: Guillaume

last: Le Bihan

state: Québec

address: 3200 Sicotte

country: Canada

institute: GREMIP, UdM

description: Gene expression data from Escherichia coli O157:H7, strain EDL933 in the caecal content of rats associated with the human microbiota.

hyb_protocol: Following fragmentation, 1ug of cDNA were hybridized for 16 hr at 45°C on GeneChip E. coli 2.0  Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data were processed using the robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation. The EB (Wright and Simon) test was used for the fold change and the pvalue calculation,

organism: Escherichia coli O157:H7 str. EDL933

source_name: Escherichia coli O157:H7 cultivated for 6 hours in the caecal content of rats

label_protocol:
cDNA synthesis protocol: 10 µg of RNA were supplemented with 2 µL of the GeneChip® Eukaryotic Poly-A RNA Control Kit (Affymetrix, Santa Clara, CA) and converted into cDNA using SuperScript II and random hexanucleotide primers (Invitrogen, Carlsbad, CA), according to the manufacturer's instructions.
fragmentation protocol: cDNA fragmentation was performed according to the manufacturer's instructions (expression manual, prokaryotic sample and array processing, Affymetrix)
Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 2ug total cDNA (expression manual, prokaryotic sample and array processing, Affymetrix).

growth_protocol: E. coli O157:H7 was grown in 15mL falcon tubes containing 8mL of filtered rat's caecal content. Growth were performed in static condition at 37 °C for 6 hours.

extract_protocol: RNA extractions were performed using RiboPure™Bacteria Kit (Ambion, Austin, TX), according to the manufacturer's recommendations

treatment_protocol: Bacterial pellets were resuspended in 350µl RNAwiz  (Ambion, Austin, TX) and kept at -80 °C.

tag: growth protocol


title: Pt26_before_drug

description: Gene expression sample from Patient 26 before drug

tag: age

value: 43 years


title: BPA-Series2-50 uM


title: Germfree rat's caecum, biological rep3

description: Gene expression data from Escherichia coli O157:H7, strain EDL933 in the caecal content of germfree rats.

value: control


title: BPA-Series2-250 pM

description: RMA expression value derived from Expression Console software; core-exon analysis


title: BPA-Series2-3.91 pM


title: Human intestinal microbiota associated rat's caecum, biological rep1

value: in the caecal content of rats associated with the human microbiota


title: Human intestinal microbiota associated rat's caecum, biological rep2


title: Germfree rat's caecum, biological rep2


title: BPA-Series2-250 nM


title: Pt23_before_drug

description: Gene expression sample from Patient 23 before drug

tag: Sex

value: 54 years

value: White

value: PI

value: re-analysis of GSM477717


title: BPA-Series2-125 nM


title: BPA-Series2-15.6 nM


title: BPA-Series2-1000 nM


title: Pt21_before_drug

description: Gene expression sample from Patient 21 before drug

value: 40 years

tag: ethnicity

value: re-analysis of GSM477715


title: BPA-Series2-12.5 uM


title: BPA-Series2-1.95 pM


title: Pt24_before_drug

description: Gene expression sample from Patient 24 before drug

value: 27 years

tag: drug regimen

value: re-analysis of GSM477718


title: BPA-Series2-25 uM

value: Bisphenol A


title: BPA-Series2-1.95 nM


title: BPA-Series2-1.56 uM


title: BPA-Series6-62.5 nM


title: Pt19_before_drug

description: Gene expression sample from Patient 19 before drug

value: Male

value: 39 years

tag: cd4+ t cell count measurement

value: re-analysis of GSM477713

value: Patient included in analysis


title: Pt16_before_drug

description: Gene expression sample from Patient 16 before drug

value: 50 years

value: baseline

tag: cd4+ t cell count, cells/ul

value: re-analysis of GSM477710

value: Patient dropped from analysis


title: BPA-Series6-4 uM


title: BPA-Series6-8 uM


title: Germfree rat's caecum, biological rep1

value: control


title: Pt20_before_drug

description: Gene expression sample from Patient 20 before drug

value: 34 years

value: African American

tag: batch

value: re-analysis of GSM477714


title: BPA-Series6-2 uM