title: Expression microarray with 5-aza-2'-deoxycytidine-treated Caco-2

city: Daejeon

first: sunwoo

address: 829 tamnip-dong, yuseong-gu

country: South Korea

institute: Genomictree,Inc.

hyb_protocol: All labeled probes were mixed into hybridization solution (3XSSC, 0.1% SDS, 50% formamide), and introduced on a 17K cDNA microarray. Array was hybridized at 42C in a waterbath for 16hrs.

scan_protocol: Axon scanner following manufacturer's instructions.

data_processing: GPR file, obtained from GenePixPro 6.0, was normalized with LOWESS using the GeneSpring 7.3.1 program.

source_name: untreated Caco-2

label_protocol: During reverse-transcription, using Cy3-dUTP, labeled cDNA were synthesized.

extract_protocol: TRIZOL reagent (Invitrogen)

source_name: DAC-treated Caco-2

label_protocol: During reverse-transcription, using Cy5-dUTP, labeled cDNA were synthesized.

value: 5-aza-2'-deoxycytidine (DAC)


title: TU_HuntsmanCancerCenter_TredeLab_fish2

status: Public on Dec 27 2011

type: genomic

city: Boston

first: Charles

last: Lee

state: MA

address: 221 Longwood Ave., EBRC-422

department: Pathology

country: USA

institute: Brigham and Women's Hospital/Harvard Medical School

description: Tu Reference vs. Tu Test

hyb_protocol: Labeled Reference and Test samples were combined with hybridization buffer, as described in the standard Agilent protocol, and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential in Buffer 1 and Buffer 2. Buffere 3 was not used as the scanner is in an ozone hood.

scan_protocol: Scanned on an Agilent G2505C scanner. At 2 micorns.

data_processing: Normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

molecule: genomic DNA

organism: Danio rerio

source_name: Tubingen Reference, Whole animal homogenate

label_protocol: Samples were labeled using the standard Agilent array CGH protocol with the following modifications: our experiments used 1 ug of heat denatured DNA (5 minutes at 95°C) per labeling reaction in place of the 1 ug of restriction enzyme-digested DNA, as indicated in the standard protocol. Reference samples were labeled with Cy3-dCTP and Test Samples were labeled with Cy5-dCTP.

growth_protocol: Laboratory animals were raised using standard IACUC approved methods. Native fish were captured and shipped from Bangladesh to the University of Exeter where they were raised using standarad approved culture methods

extract_protocol: standard phenol:chloroform isolation

tag: strain

value: Tubingen

source_name: Tu Test, Utah2, Whole animal homogenate


title: TU_HuntsmanCancerCenter_TredeLab_fish1

description: Tu Reference vs. Tu Test

source_name: Tu Test, Utah1, Whole animal homogenate


title: Expression microarray with 1416T colon tissue

type: RNA

data_processing: GPR file, obtained from GenePixPro 6.0, was normalized with LOWESS using the GeneSpring 7.3.1 program. An additional 'per gene normalization' was performed, in which the data for a given gene were normalized to the median expression level of that gene across all 10 samples.

molecule: total RNA

organism: Homo sapiens

source_name: total RNAs from 11 human cell lines

tag: sample type

value: reference

tag: cell line

value: 11 human cell lines mixed in equal quantities

source_name: tumor tissue of 1416 colorectal cancer patient

tag: tissue

value: tumor colon

tag: disease state

value: colorectal cancer

tag: patient


title: Ezh2-/- MEP from BM

city: Chiba

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

country: Japan

institute: Graduate School of Medicine, Chiba University

description: Gene expression data of MEP from Ezh2-/- BM

hyb_protocol: 1,650 ng of the labeled cRNA was hybridized to Agilent Whole Mouse Genome 4x44k array Ver.2, Design ID: 026655. The process of hybridization and washing was performed using a Hi-RPM Gene Expression Hybridization Kit (Large) (Agilent Technologies) and a Gene Expression Wash Pack  (Agilent Technologies) respectively.

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

organism: Mus musculus

source_name: Ezh2-/- MEP from BM

label_protocol: 250 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent Technologies), amplified and labeled with Cyanine 3 using a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, which generated single-color labeled cRNA.

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

tag: cell type

value: erythrocyte/megakaryocyte progenitor from bone marrow

tag: genotype

tag: age

value: adult

tag: genetic background


title: AB_Purdue_FreemanLab_fishFemale9

description: AB Reference vs. AB Test

source_name: AB Reference, Whole animal homogenate

value: AB

source_name: AB Test, JenFemale9, Whole animal homogenate


title: TU_HuntsmanCancerCenter_TredeLab_fish4

description: Tu Reference vs. Tu Test

source_name: Tu Test, Utah4, Whole animal homogenate


title: EV-2

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

description: No additional description available for sample: EV-2

hyb_protocol: Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).

scan_protocol: The gene chip was scanned using a confocal laser scanner (Affymetrix).

data_processing: The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.

label: biotin

source_name: iPrEC cell line transfected with the empty vector, sample: EV-2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA,  and then  transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.

growth_protocol: Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin

extract_protocol: Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.

tag: type

value: Cell culture

value: iPrEC

value: Transfection control


title: AB_Purdue_FreemanLab_fishFemale8

description: AB Reference vs. AB Test

source_name: AB Test, JenFemale8, Whole animal homogenate


title: Mut-2

description: No additional description available for sample: Mut-2

source_name: iPrEC cell line transfected with the mutant USP2A, sample: Mut-2

value: Expression of mutant USP2A


title: AB_Purdue_FreemanLab_fishFemale10

description: AB Reference vs. AB Test

source_name: AB Test, JenFemale10, Whole animal homogenate


title: AB_Purdue_FreemanLab_fishMale2

description: AB Reference vs. AB Test

source_name: Native Test, Site1 Fish6, Caudal fin clip

value: Native Population-Bangladesh


title: AB_DanaFarber_LookLab_fish7

description: AB Reference vs. AB Test

source_name: AB Test, DF7, Whole animal homogenate


title: AB_Purdue_FreemanLab_fishMale6

description: AB Reference vs. AB Test

source_name: AB Test, JenMale6, Whole animal homogenate


title: AB_Purdue_FreemanLab_fishFemale1

description: AB Reference vs. AB Test

source_name: AB Test, JenFemale1, Whole animal homogenate


title: WT-1

description: No additional description available for sample: WT-1

source_name: iPrEC cell line transfected with the wild-type USP2A, sample: WT-1

value: Expression of wild-type USP2A


title: AB_Purdue_FreemanLab_fishMale7

description: AB Reference vs. AB Test

source_name: AB Test, JenMale7, Whole animal homogenate


title: AB_DanaFarber_LookLab_fish9

description: AB Reference vs. AB Test

source_name: AB Test, DF9, Whole animal homogenate


title: Expression microarray with 9100T colon tissue

source_name: total RNAs from 11 human cell lines

source_name: tumor tissue of 9100 colorectal cancer patient


title: TU_HuntsmanCancerCenter_TredeLab_fish3

description: Tu Reference vs. Tu Test

source_name: Tubingen Reference, Whole animal homogenate

source_name: Tu Test, Utah3, Whole animal homogenate


title: Mut-1

description: No additional description available for sample: Mut-1

source_name: iPrEC cell line transfected with the mutant USP2A, sample: Mut-1


title: AB_Purdue_FreemanLab_fishFemale3

description: AB Reference vs. AB Test

source_name: AB Reference, Whole animal homogenate

source_name: AB Test, JenFemale3, Whole animal homogenate


title: Expression microarray with 7949T colon tissue

source_name: tumor tissue of 7949 colorectal cancer patient


title: AB_DanaFarber_LookLab_fish8

description: AB Reference vs. AB Test

source_name: AB Test, DF8, Whole animal homogenate


title: Wild-type MEP from E14.5 fetal liver

description: Gene expression data of MEP from wild-type E14.5 fetal liver

source_name: Wild-type MEP from E14.5 fetal liver

value: erythrocyte/megakaryocyte progenitor from fetal liver

value: wild type


title: Expression microarray with 9102T colon tissue

source_name: tumor tissue of 9102 colorectal cancer patient


title: AB_DanaFarber_LookLab_fish6

description: AB Reference vs. AB Test

source_name: AB Test, DF6, Whole animal homogenate


title: AB_DanaFarber_LookLab_fish10

description: AB Reference vs. AB Test

source_name: AB Test, DF10, Whole animal homogenate


title: AB_Purdue_FreemanLab_fishFemale2

description: AB Reference vs. AB Test

source_name: AB Test, JenFemale2, Whole animal homogenate


title: Hybrid_Strain_Male9

description: Hybrid Reference vs. Hybrid Male9

source_name: Hybrid Strain Adult, Whole animal homogenate

extract_protocol: Trizol simultaneous extraction of DNA and RNA

value: Hybrid Strain (AB x unknown)

source_name: Hybrid Male9, Whole Animal Homogenate


title: Expression microarray with 9100N colon tissue

source_name: non-tumor tissue of 9100 colorectal cancer patient

value: non-tumor colon


title: Expression microarray with 5337T colon tissue

source_name: total RNAs from 11 human cell lines

value: reference

source_name: tumor tissue of 5337 colorectal cancer patient


title: Hybrid_Strain_Male8

description: Hybrid Reference vs. Hybrid Male8

source_name: Hybrid Male8, Whole Animal Homogenate


title: CP_Mut2

description: No additional description available for sample: CP_Mut2

source_name: iPrEC cell line transfected with the mutant USP2A, sample: CP_Mut2


title: Hybrid_Strain_Male5

description: Hybrid Reference vs. Hybrid Male5

source_name: Hybrid Male5, Whole Animal Homogenate


title: Ezh2-/- MEP from E14.5 fetal liver

description: Gene expression data of MEP from Ezh2-/- E14.5 fetal liver

source_name: Ezh2-/- MEP from E14.5 fetal liver


title: CP_Mut1

description: No additional description available for sample: CP_Mut1

source_name: iPrEC cell line transfected with the mutant USP2A, sample: CP_Mut1


title: AB_DanaFarber_LookLab_fish5

description: AB Reference vs. AB Test

source_name: AB Reference, Whole animal homogenate

source_name: AB Test, DF5, Whole animal homogenate


title: CP_WT2

description: No additional description available for sample: CP_WT2

source_name: iPrEC cell line transfected with the wild-type USP2A, sample: CP_WT2


title: Ewing cell line TC252

type: mixed

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

description:
Hy5: 000760_042_1b.txt
Hy3: 000760_042_2b.txt

hyb_protocol: Fluorescently labeled samples were hybridized overnight to miRXploreTM Microarrays using the a-HybTM Hybridization Station.

scan_protocol: Fluorescence signals of the hybridized miRXploreTM Microarrays were detected using a laser scanner from Agilent (Agilent Technologies). Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software (BioDiscovery, Los Angeles, CA, USA).

data_processing: Mean local background was subtracted from the mean signal to obtain the net signal intensity and the ratio of Hy5/Hy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalized using the calibration oligos. Low-quality spots were flagged and excluded from data analysis. Unflagged spots were analyzed with the PIQOR(TM) Analyzer software.

source_name: Ewing sarcoma cell line

label_protocol: Sample labeling was performed according to the miRXploreTM User manual.

extract_protocol: Total RNA was isolated using Trifast (Peqlab) according to the manufacturer’s recommendations.

value: Ewing sarcoma cells

tag: tumor/normal

value: tumor

molecule: other

organism: synthetic construct

source_name: miRXplore Universal Reference

value: Control pool of synthetic miRNAs


title: Hybrid_Strain_Female9

description: Hybrid Reference vs. Hybrid Female9

source_name: Hybrid Female9, Whole Animal Homogenate


title: AB_DanaFarber_LookLab_fish1

description: AB Reference vs. AB Test

source_name: AB Test, DF1, Whole animal homogenate


title: AB_DanaFarber_LookLab_fish4

description: AB Reference vs. AB Test

source_name: AB Test, DF4, Whole animal homogenate


title: AB_DanaFarber_LookLab_fish3

description: AB Reference vs. AB Test

source_name: AB Test, DF3, Whole animal homogenate


title: Hybrid Strain Male9

description: Hybrid Reference vs. Hybrid Male9

source_name: Hybrid Strain Adult, Whole animal homogenate

value: Hybrid Strain (AB X unknown)

source_name: Hybrid Male9, Whole Animal Homogenate


title: Ewing cell line A673

description:
Hy5: 000760_041_1b.txt
Hy3: 000760_041_2b.txt


title: Expression microarray with 1416N colon tissue

source_name: total RNAs from 11 human cell lines

value: 11 human cell lines mixed in equal quantities

source_name: non-tumor tissue of 1416 colorectal cancer patient

value: colorectal cancer


title: hpMSC sample 2

description:
Hy5: 000760_040_1b.txt
Hy3: 000760_040_2b.txt

source_name: human pediatric mesenchymal stem cells

value: pediatric mesenchymal stem cells

value: normal


title: CP_EV1

description: No additional description available for sample: CP_EV1

source_name: iPrEC cell line transfected with the empty vector, sample: CP_EV1

value: Cell culture

value: iPrEC

value: Transfection control


title: Expression microarray with 9102N colon tissue

source_name: non-tumor tissue of 9102 colorectal cancer patient


title: Expression microarray with 7949N colon tissue

source_name: non-tumor tissue of 7949 colorectal cancer patient


title: Wild-type MEP from BM

description: Gene expression data of MEP from wild-type BM

source_name: Wild-type MEP from BM

value: erythrocyte/megakaryocyte progenitor from bone marrow

value: adult


title: Expression microarray with 5337N colon tissue

source_name: non-tumor tissue of 5337 colorectal cancer patient


title: hpMSC sample 1

description:
Hy5: 000760_039_1b.txt
Hy3: 000760_039_2b.txt


title: Hybrid Strain Male8

description: Hybrid Reference vs. Hybrid Male8

source_name: Hybrid Male8, Whole Animal Homogenate


title: Hybrid_Strain_Female8

description: Hybrid Reference vs. Hybrid Female8

source_name: Hybrid Female8, Whole Animal Homogenate


title: Hybrid_Strain_Female7

description: Hybrid Reference vs. Hybrid Female7

source_name: Hybrid Female7, Whole Animal Homogenate


title: EV-1

description: No additional description available for sample: EV-1

source_name: iPrEC cell line transfected with the empty vector, sample: EV-1


title: Hybrid_Strain_Female4

description: Hybrid Reference vs. Hybrid Female4

source_name: Hybrid Female4, Whole Animal Homogenate


title: Boiler Bay High zone, plot 4, Pooled RNA from gill sample A-E_1 hr Recovery

status: Public on Dec 25 2011

city: Columbia

first: Sean

middle: P

last: Place

state: SC

address: 715 Sumter St.

department: Biological Sciences

institute: University of South Carolina

description: Biological replicate 4 of 5:Boiler Bay High zone 1 hr Recovery vs. Pooled Reference RNA

hyb_protocol: Samples were brought to a final volume of 45 µl in 25 mM Hepes, 0.75 mg/ml tRNA (Sigma, St. Louis MO, USA), 3X SSC, and 0.2% SDS. Samples were boiled for 1 min, allowed to cool to room temperature, and then applied to microarray slides. Hybridizations were conducted overnight at 65°C in hybridization chambers (Genetix, Boston, MA, USA).

scan_protocol: Scanned on a AXON GenePix 4000B scanner. The ratio of Cy5 to Cy3 fluorescence was quantified using GenePix Pro 4.0 software

data_processing: background subtracted, LOWESS normalized data obtained from median log2 ratio of processed 635 signal /532 signal

organism: Mytilus californianus

source_name: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels

label_protocol: 10 µg of total RNA was reverse transcribed to cDNA using anchored oligo(dT15) primers and amino-allyl dUTP. Single stranded cDNA was labeled by indirect coupling of the aa-dUTP substituded cDNA with 5 ul cyanine monoreactive dye (GE Healthcare)

extract_protocol: Total RNA extracted from 100 mg of gill tissue using Trizol (Invitrogen) following manufacturer's instructions. Total RNA was further cleaned using spin columns (Ambion) as described in Place et al., 2008

treatment_protocol: Gill tissue was sampled from individuals and immediately frozen on dry ice.

value: gill

source_name: Field collected gill tissue, Boiler Bay, OR population

tag: origin

tag: recovery time


title: Boiler Bay High zone, plot 5, Pooled RNA from gill sample A-E_1 hr Recovery

description: Biological replicate 5 of 5:Boiler Bay High zone 1 hr Recovery vs. Pooled Reference RNA

value: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels

value: Field collected gill tissue, Boiler Bay, OR population


title: Boiler Bay High zone, plot 3, Pooled RNA from gill sample A-E_1 hr Recovery

description: Biological replicate 3 of 5:Boiler Bay High zone 1 hr Recovery vs. Pooled Reference RNA


title: BJ RiPS derived mesenchymal progenitor cells_2 [HG-U133_Plus_2]

city: NYC

first: Tim

middle: D

last: Ahfeldt

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
Gene Expression
H0042777.CEL

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using the BioConductor affy package in R. RMA background correction was applied to probe intensities followed by quantile normalization. Probe set intensities were summarized from individual probes (excluding mismatch probes) using median polished. Gene level intensities were generated by mapping probe sets to refseq annotations. Probe sets that did not map to refseq annotations were not considered in further analyses. Probe Sets mapping to the same genes were median collapsed by gene symbol. Final normalized data was generated by median centering each array after the prior processing.

source_name: BJ RiPS derived mesenchymal progenitor cells_rep2

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA from human cell lines or human fat was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturers’ instructions. RNA quality was assessed using an Aglient Bioanalyzer

value: MPC


title: HUES 8 derived mesenchymal progenitor cells_1 [HG-U133_Plus_2]

description:
Gene Expression
H0042780.CEL

source_name: HUES 8 derived mesenchymal progenitor cells_rep1


title: HUES 2 derived mesenchymal progenitor cells_2 [HG-U133_Plus_2]

description:
Gene Expression
H0042779.CEL

source_name: HUES 2 derived mesenchymal progenitor cells_rep2


title: ADSV derived mesenchymal progenitor cells_rep_2 [HG-U133_Plus_2]

description:
Gene Expression
H0042775.CEL

source_name: ADSV derived mesenchymal progenitor cells_rep2


title: AB_DanaFarber_LookLab_fish2

description: AB Reference vs. AB Test

source_name: AB Reference, Whole animal homogenate

value: AB

source_name: AB Test, DF2, Whole animal homogenate


title: BJ RiPS derived mesenchymal progenitor cells_1 [HG-U133_Plus_2]

description:
Gene Expression
H0042776.CEL

source_name: BJ RiPS derived mesenchymal progenitor cells_rep1


title: Boiler Bay High zone, plot 2, Pooled RNA from gill sample A-E_1 hr Recovery

description: Biological replicate 2 of 5:Boiler Bay High zone 1 hr Recovery vs. Pooled Reference RNA


title: HUES 2 derived mesenchymal progenitor cells_1 [HG-U133_Plus_2]

description:
Gene Expression
H0042778.CEL

source_name: HUES 2 derived mesenchymal progenitor cells_rep1


title: HUES 8 derived mesenchymal progenitor cells_2 [HG-U133_Plus_2]

description:
Gene Expression
H0042781.CEL

source_name: HUES 8 derived mesenchymal progenitor cells_rep2


title: ADSV derived mesenchymal progenitor cells_rep_1 [HG-U133_Plus_2]

description:
Gene Expression
H0042774.CEL

source_name: ADSV derived mesenchymal progenitor cells_rep1


title: Boiler Bay mid zone, plot 5, Pooled RNA from gill sample A-E_1 hr Recovery

description: Biological replicate 5 of 5:Boiler Bay Mid zone 1 hr Recovery vs. Pooled Reference RNA


title: Boiler Bay High zone, plot 1, Pooled RNA from gill sample A-E_1 hr Recovery

description: Biological replicate 1 of 5:Boiler Bay High zone 1 hr Recovery vs. Pooled Reference RNA


title: CP_EV2

description: No additional description available for sample: CP_EV2

source_name: iPrEC cell line transfected with the empty vector, sample: CP_EV2


title: Boiler Bay mid zone, plot 4, Pooled RNA from gill sample A-E_1 hr Recovery

description: Biological replicate 4 of 5:Boiler Bay Mid zone 1 hr Recovery vs. Pooled Reference RNA


title: Boiler Bay mid zone, plot 3, Pooled RNA from gill sample A-E_1 hr Recovery

description: Biological replicate 3 of 5:Boiler Bay Mid zone 1 hr Recovery vs. Pooled Reference RNA


title: Boiler Bay mid zone, plot 2, Pooled RNA from gill sample A-E_1 hr Recovery

description: Biological replicate 2 of 5:Boiler Bay Mid zone 1 hr Recovery vs. Pooled Reference RNA


title: Boiler Bay High zone, plot 5, Pooled RNA from gill sample A-E

description: Biological replicate 5 of 5:Boiler Bay High zone vs. Pooled Reference RNA


title: Boiler Bay mid zone, plot 1, Pooled RNA from gill sample A-E_1 hr Recovery

description: Biological replicate 1 of 5:Boiler Bay Mid zone 1 hr Recovery vs. Pooled Reference RNA


title: Hybrid Strain Male5

description: Hybrid Reference vs. Hybrid Male5

source_name: Hybrid Strain Adult, Whole animal homogenate

source_name: Hybrid Male5, Whole Animal Homogenate


title: Boiler Bay High zone, plot 4, Pooled RNA from gill sample A-E

description: Biological replicate 4 of 5:Boiler Bay High zone vs. Pooled Reference RNA


title: Boiler Bay High zone, plot 3, Pooled RNA from gill sample A-E

description: Biological replicate 3 of 5:Boiler Bay High zone vs. Pooled Reference RNA


title: Hybrid Strain Female9

description: Hybrid Reference vs. Hybrid Female9

source_name: Hybrid Female9, Whole Animal Homogenate


title: Boiler Bay mid zone, plot 4, Pooled RNA from gill sample A-E

description: Biological replicate 4 of 5:Boiler Bay Mid zone vs. Pooled Reference RNA


title: Boiler Bay High zone, plot 1, Pooled RNA from gill sample A-E

description: Biological replicate 1 of 5:Boiler Bay High zone vs. Pooled Reference RNA


title: Boiler Bay mid zone, plot 5, Pooled RNA from gill sample A-E

description: Biological replicate 5 of 5:Boiler Bay Mid zone vs. Pooled Reference RNA


title: Boiler Bay mid zone, plot 2, Pooled RNA from gill sample A-E

description: Biological replicate 2 of 5:Boiler Bay Mid zone vs. Pooled Reference RNA


title: CP_WT1

description: No additional description available for sample: CP_WT1

source_name: iPrEC cell line transfected with the wild-type USP2A, sample: CP_WT1

value: Expression of wild-type USP2A


title: Strawberry Hill High zone, plot 5, gill sample C_1h Recovery

description: Biological replicate 15 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA

source_name: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels

source_name: Field collected gill tissue, Strawberry Hill, OR population


title: Boiler Bay High zone, plot 2, Pooled RNA from gill sample A-E

description: Biological replicate 2 of 5:Boiler Bay High zone vs. Pooled Reference RNA

source_name: Field collected gill tissue, Boiler Bay, OR population


title: Strawberry Hill High zone, plot 5, gill sample B_1h Recovery

description: Biological replicate 14 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA

value: Field collected gill tissue, Strawberry Hill, OR population


title: Strawberry Hill High zone, plot 4, gill sample C_1h Recovery

description: Biological replicate 12 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Boiler Bay mid zone, plot 1, Pooled RNA from gill sample A-E

description: Biological replicate 1 of 5:Boiler Bay Mid zone vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 4, gill sample A_1h Recovery

description: Biological replicate 10 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 3, gill sample C_1h Recovery

description: Biological replicate 9 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 3, gill sample B_1h Recovery

description: Biological replicate 8 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 5, gill sample A_1h Recovery

description: Biological replicate 13 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 2, gill sample C_1h Recovery

description: Biological replicate 6 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 2, gill sample A_1h Recovery

description: Biological replicate 4 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 2, gill sample B_1h Recovery

description: Biological replicate 5 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Hybrid Strain Female4

description: Hybrid Reference vs. Hybrid Female4

value: Hybrid Strain (AB X unknown)

source_name: Hybrid Female4, Whole Animal Homogenate


title: Strawberry Hill High zone, plot 3, gill sample A_1h Recovery

description: Biological replicate 7 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 1, gill sample C_1h Recovery

description: Biological replicate 3 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Hybrid Strain Female8

description: Hybrid Reference vs. Hybrid Female8

source_name: Hybrid Female8, Whole Animal Homogenate


title: Strawberry Hill High zone, plot 1, gill sample B_1h Recovery

description: Biological replicate 2 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 3, gill sample C_1h Recovery

description: Biological replicate 9 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 1, gill sample A_1h Recovery

description: Biological replicate 1 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 2, gill sample C_1h Recovery

description: Biological replicate 6 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 4, gill sample B_1h Recovery

description: Biological replicate 11 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Hybrid Strain Female7

description: Hybrid Reference vs. Hybrid Female7

source_name: Hybrid Female7, Whole Animal Homogenate


title: Strawberry Hill Mid zone, plot 4, gill sample C_1h Recovery

description: Biological replicate 12 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 3, gill sample A_1h Recovery

description: Biological replicate 7 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 5, gill sample C_1h Recovery

description: Biological replicate 15 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 5, gill sample A_1h Recovery

description: Biological replicate 13 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 5, gill sample B_1h Recovery

description: Biological replicate 14 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 4, gill sample A_1h Recovery

description: Biological replicate 10 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 2, gill sample B_1h Recovery

description: Biological replicate 5 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 3, gill sample B_1h Recovery

description: Biological replicate 8 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 4, gill sample B_1h Recovery

description: Biological replicate 11 of 15:Strawberry Hill High zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 1, gill sample A_1h Recovery

description: Biological replicate 1 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 1, gill sample B_1h Recovery

description: Biological replicate 2 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 1, gill sample C_1h Recovery

description: Biological replicate 3 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 2, gill sample A_1h Recovery

description: Biological replicate 4 of 15:Strawberry Hill Mid zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Low zone, plot 5, gill sample B_1h Recovery

description: Biological replicate 14 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Low zone, plot 4, gill sample C_1h Recovery

description: Biological replicate 12 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Low zone, plot 5, gill sample C_1h Recovery

description: Biological replicate 15 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Low zone, plot 5, gill sample A_1h Recovery

description: Biological replicate 13 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_474

city: Brisbane

first: Krishna

middle: Bajee

last: Sriram

state: Queensland

address: Rode Road, Chermside

department: Department of Thoracic Medicine

country: Australia

institute: The Prince Charles Hospital

hyb_protocol: Purified, labelled target was added to a hybridisation mix (50 μg COT1-DNA (Invitrogen Corporation), 100 μg Yeast tRNA (Invitrogen Corporation), 50 μL 1X Control Targets (Agilent Technologies, Inc.), 1.5% SGA additive (Agilent Technologies, Inc.), 1X Hybridisation buffer (Agilent Technologies, Inc.)) to make a final volume of 500 μL. The hybridisation mix was denatured at 100C for 3 minutes, incubated at 37C for 30 minutes, then centrifuged at 14,000 x g for 1 minute before loading onto a Human Genome CGH Microarray 44B (Agilent Technologies Inc.). Hybridisation was performed for 48 hours at 65°C in a rotating oven at 10 rpm. Arrays were disassembled and washed for 5 minutes at room temperature in aCGH Wash Buffer 1 (Appendix 1, page 288) followed by 15 minutes at 37C in aCGH Wash Buffer 2 (Appendix 1, page 288). Arrays were then briefly rinsed in acetonitrile followed by Stabilization and Drying Reagent (Agilent Technologies, Inc.) before being dried and scanned in an Agilent microarray scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Lung Tissue, Tumour, Surgically resected

label_protocol: For each aCGH microarray, a tumour sample (test) was compared with a commercially available Female Genomic DNA (Promega) (reference). High molecular weight genomic DNA (0.8 μg) was digested with AluI (20 units) and RsaI (20 units) (Invitrogen Corporation) in a total volume of 13.33 μL for 2 hours at 37C followed by heat inactivation at 65C for 10 minutes. Adequacy of digestion was verified by running 0.4 μL of sample on a 1.5% agarose gel using a 1X SYBR Gold nucleic acid gel stain (Invitrogen Corporation) as described in section 2.3.1. The remaining digestion reaction was labelled using a Bioprime labelling kit (Invitrogen Corporation) according to the manufacturer's instructions in a final volume of 50 al with a modified dNTP pool containing 120 aM each of dATP, dGTP, and dCTP; 60 aM dTTP; and 60 aM Cy5-dUTP (test) or Cy3-dUTP (reference) (Amersham/GE Healthcare).

extract_protocol: A total of 300-500 mg of frozen tissue was rotor-homogenised (Polytron PT2100) and genomic DNA extracted using a salt-precipitation method or phenol chloroform method. Tissue was homogenised in 6 mL of Nucleic Lysis Buffer then incubated at 37C overnight following the addition of Proteinase K (2 mg) and 200 μL 20% sodium dodecyl sulphate (SDS). The next day, 2 mL of saturated salt solution were added and samples shaken vigorously for 1 min before centrifugation for 1 hour 45 minutes at 9,500 x g at 4C. Supernatants were transferred to new tubes and five volumes of ice-cold 100% ethanol added to precipitate DNA. A brief centrifugation for 30 seconds at 9,500 x g loosely pelleted DNA to enable removal of supernatants. DNA was then washed twice in ice- cold 70% ethanol (v/v, in water) followed by centrifugation for 2 minutes at 9,500 x g at 4C. Pellets were air-dried and resuspended in 0.5-1.0 mL of TE buffer (Appendix 1, page 288). DNA was quantified by agarose gel electrophoresis and A260/A280 spectrophotometry. High molecular weight genomic DNA was purified using a Blood and Cell Culture mini kit (Qiagen) following the manufacturer’s instructions.

tag: histology

value: Squamous cell carcinoma

tag: gender

value: Female

tag: tnm stage

value: IIIB

tag: recurrence phenotype

value: Rec

source_name: Female genomic DNA

tag: reference

value: Female Genomic DNA (Promega)


title: Strawberry Hill Low zone, plot 4, gill sample A_1h Recovery

description: Biological replicate 10 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA

tag: sample type


title: Strawberry Hill Low zone, plot 3, gill sample C_1h Recovery

description: Biological replicate 9 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA

tag: tissue


title: Strawberry Hill Low zone, plot 3, gill sample A_1h Recovery

description: Biological replicate 7 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_590

value: Male

value: IIIA


title: Strawberry Hill Low zone, plot 3, gill sample B_1h Recovery

description: Biological replicate 8 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_364

value: IIB


title: Strawberry Hill Low zone, plot 4, gill sample B_1h Recovery

description: Biological replicate 11 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_583

value: IB

value: Non-Rec


title: Strawberry Hill Low zone, plot 2, gill sample B_1h Recovery

description: Biological replicate 5 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA

value: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels

value: gill


title: Lung_Squamous cell carcinoma_Tumour_589


title: Lung_Squamous cell carcinoma_Tumour_614


title: Lung_Squamous cell carcinoma_Tumour_539

value: IV


title: Lung_Squamous cell carcinoma_Tumour_643


title: Lung_Squamous cell carcinoma_Tumour_585


title: Strawberry Hill Low zone, plot 2, gill sample C_1h Recovery

description: Biological replicate 6 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: Strawberry Hill Low zone, plot 2, gill sample A_1h Recovery

description: Biological replicate 4 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_527


title: Lung_Squamous cell carcinoma_Tumour_547

value: IIA


title: Lung_Squamous cell carcinoma_Tumour_615


title: 2G ddm1 385K_ChIP_3 rep1

city: Vienna

first: Taku

last: Sasaki

address: Dr. Bohr-gasse 3

country: Austria

institute: Gregor Mendel Institute

hyb_protocol: According to standard NimbleGen protocols (www.nimblegen.com).

scan_protocol: Used Agilent Microarray Scanner.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. This chip covers entire chromosome 5 and part of chromosome 4 of A. thaliana. Scaling is performed by subtracting the bi-weight mean for the IP/input log2 ratio values for chromosome 5 from each log2 ratio value.

organism: Arabidopsis thaliana

source_name: 5meC ChIP DNA from 2G ddm1 mutant

label_protocol: Immunoprecipitated DNA was amplified using GenomePlex Complete Whole Genome Amplification Kit (SIGMA) and purified using QIA Quick PCR Purification Kit (QIAGEN). 2μg of amplified DNA and input DNA were labeled with Cy5 and Cy3, respectively.

growth_protocol: 2G ddm1 plants were grown on soil at 22°C in 16h-8h light-dark condition

extract_protocol: Genomic DNA was isolated from leaves with the Illustra Nucleon Phytopure Genomic DNA Extraction Kits (GE Healthcare).

value: ddm1(2G-generation after plants became homozygous)

value: leaves

tag: generation

tag: chip antibody

value: anti 5meC antibody

tag: chip antibody manufacturer

value: Calbiochem

tag: chip antibody catalog #

tag: chip antibody lot#

source_name: Input DNA from 2G ddm1

value: none, input DNA


title: Strawberry Hill Low zone, plot 1, gill sample B_1h Recovery

description: Biological replicate 2 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA

value: Field collected gill tissue, Strawberry Hill, OR population


title: Strawberry Hill Low zone, plot 1, gill sample C_1h Recovery

description: Biological replicate 3 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA


title: WT 385K_ChIP_3

source_name: 5meC ChIP DNA from WT

growth_protocol: WT plants were grown on soil at 22°C in 16h-8h light-dark condition

tag: genotype

value: WT

value: control

tag: genetic background

source_name: Input DNA from WT


title: Strawberry Hill High zone, plot 5, gill sample B

description: Biological replicate 14 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 5, gill sample A

description: Biological replicate 13 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_492

tag: age

value: Squamous cell carcinoma

value: Male

value: Rec

value: Female Genomic DNA (Promega)


title: Lung_Squamous cell carcinoma_Tumour_505

value: IIB


title: 8G ddm1kyp 385K_ChIP_3

source_name: 5meC ChIP DNA from 8G ddm1 kyp double mutant

growth_protocol: 8G ddm1 kyp plants were grown on soil at 22°C in 16h-8h light-dark condition

value: ddm1 kyp(8G-generation after plants became homozygous)

source_name: Input DNA from 8G ddm1 kyp


title: Lung_Squamous cell carcinoma_Tumour_486

value: IIIA


title: Lung_Squamous cell carcinoma_Tumour_466


title: Strawberry Hill Low zone, plot 1, gill sample A_1h Recovery

description: Biological replicate 1 of 15:Strawberry Hill Low zone 1 hr recovery vs. Pooled Reference RNA

value: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels

value: gill

tag: origin


title: 8G ddm1 385K_ChIP_3 rep2

source_name: 5meC ChIP DNA from 8G ddm1 mutant

growth_protocol: 8G ddm1 plants were grown on soil at 22°C in 16h-8h light-dark condition

value: ddm1(8G-generation after plants became homozygous)

source_name: Input DNA from 8G ddm1


title: Lung_Squamous cell carcinoma_Tumour_488

value: Non-Rec


title: Lung_Squamous cell carcinoma_Tumour_482

value: IIIB


title: 8G ddm1 385K_ChIP_3 rep1

value: leaves

value: anti 5meC antibody

value: Calbiochem


title: Strawberry Hill High zone, plot 4, gill sample C

description: Biological replicate 12 of 15:Strawberry Hill High zone vs. Pooled Reference RNA

value: Field collected gill tissue, Strawberry Hill, OR population


title: Strawberry Hill High zone, plot 4, gill sample B

description: Biological replicate 11 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 3, gill sample B

description: Biological replicate 8 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: 2G ddm1 385K_ChIP_3 rep2

value: ddm1(2G-generation after plants became homozygous)

value: none, input DNA


title: Strawberry Hill High zone, plot 3, gill sample C

description: Biological replicate 9 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: Strawberry Hill High zone, plot 4, gill sample A

description: Biological replicate 10 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_475

value: Squamous cell carcinoma

value: Female


title: Strawberry Hill High zone, plot 3, gill sample A

description: Biological replicate 7 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_444

value: Male

value: Female Genomic DNA (Promega)


title: Lung_Squamous cell carcinoma_Tumour_456

value: IB

value: Rec


title: Strawberry Hill High zone, plot 2, gill sample C

description: Biological replicate 6 of 15:Strawberry Hill High zone vs. Pooled Reference RNA

value: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels


title: Strawberry Hill High zone, plot 2, gill sample B

description: Biological replicate 5 of 15:Strawberry Hill High zone vs. Pooled Reference RNA

value: gill


title: Strawberry Hill High zone, plot 2, gill sample A

description: Biological replicate 4 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_406

value: IIB


title: Lung_Squamous cell carcinoma_Tumour_436

value: Non-Rec


title: Lung_Squamous cell carcinoma_Tumour_422


title: Strawberry Hill High zone, plot 1, gill sample B

description: Biological replicate 2 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: PRIMARY FAT_2

description:
Gene Expression
Raw data file:
252800411054_201102140820_S01_GE2_105_Dec08_2_4.txt
Data column in raw data file: rProcessedSignal (AA)

hyb_protocol: 600 ng of cRNA (specific activity >10.0 pmol Cy3/5/ug cRNA) per channel per array spot (8 per slide) (cy3 and cy5 channels both utilized) was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, 1 volume of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Sureprint G3 8x60k gene expression arrays (G4858A-028004) 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)(both without Triton added).

scan_protocol: Slides were scanned immediately after washing and placement within an Agilent Ozone Barrier Slide cover (Agilent) the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 8x60k array Scan resolution 3 microns. Scanning was done in both channels and PMT is set to 100% for both Cy3\cy5 channels.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE2-105_Dec08 with the cognate G4858A-028004 grid file to obtain background subtracted and spatially detrended Processed Signal intensities. Processed Signal Intensities were expressed as a ratio to the 75th percentile value (control probes excluded) and median centered for each array and log2 transformed. Only probes tagged by Feature Extraction as above background in all constituents of a sample triplicate or duplicate set in at least one condition were considered for further analysis. After background filtering, probes values were collapsed by the GeneName column from the Feature Extraction output to condense multiple reads of the same gene. To correct for slide batch effects (each slide = 8 arrays) the R ComBat package (Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007) was employed using the universal reference (technical replicates) array on each slide upon which a universal replicate was hybridized along with each condition treating each array as a different batch.

source_name: PRIMARY FAT_rep2

label_protocol: Cyanine-3\Cyanine-5 labeled cRNA was prepared from 0.3 ug total RNA using the Two-Color Low-Input QuickAmp 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-1000 Spectrophotometer.

tag: cell type

value: adipose


title: Strawberry Hill High zone, plot 1, gill sample C

description: Biological replicate 3 of 15:Strawberry Hill High zone vs. Pooled Reference RNA

source_name: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels


title: Strawberry Hill High zone, plot 1, gill sample A

description: Biological replicate 1 of 15:Strawberry Hill High zone vs. Pooled Reference RNA

source_name: Field collected gill tissue, Strawberry Hill, OR population


title: Lung_Squamous cell carcinoma_Tumour_400

tag: histology


title: Lung_Squamous cell carcinoma_Tumour_382

tag: gender


title: Lung_Squamous cell carcinoma_Tumour_390

tag: tnm stage


title: Lung_Squamous cell carcinoma_Tumour_410

tag: recurrence phenotype


title: PRIMARY FAT_1

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_2_3.txt
Data column in raw data file: rProcessedSignal (AA)

source_name: PRIMARY FAT_rep1


title: ADSV_49_UNDIFF_1

description:
Gene Expression
Raw data file:
252800411052_201102140751_S01_GE2_105_Dec08_2_1.txt
Data column in raw data file: rProcessedSignal (AA)

value: MPC


title: Universal_ref_slide_53

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_2_4.txt
Data column in raw data file: rProcessedSignal (AA)

value: universal reference (Stratagene cat#740000)


title: ADSV_49_UNDIFF_2

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_2_2.txt
Data column in raw data file: rProcessedSignal (AA)


title: Lung_Squamous cell carcinoma_Tumour_388

tag: reference


title: ADSV_49_PPARG_3

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_2_1.txt
Data column in raw data file: rProcessedSignal (AA)

tag: agent


title: ADSV_49_PPARG_2

description:
Gene Expression
Raw data file:
252800411052_201102140751_S01_GE2_105_Dec08_1_4.txt
Data column in raw data file: rProcessedSignal (AA)


title: Strawberry Hill Mid zone, plot 5, gill sample C

description: Biological replicate 15 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA

tag: sample type

tag: tissue


title: Lung_Squamous cell carcinoma_Tumour_385

value: IA


title: Lung_Squamous cell carcinoma_Tumour_373


title: Strawberry Hill Mid zone, plot 5, gill sample B

description: Biological replicate 14 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA

value: Field collected gill tissue, Strawberry Hill, OR population


title: 8G ddm1kyp 385K_ChIP_2

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. This chip covers entire chromosome 3 and part of chromosome 2 and 4 of A. thaliana. Scaling is performed by subtracting the bi-weight mean for the IP/input log2 ratio values for chromosome 3 from each log2 ratio value.

value: ddm1 kyp(8G-generation after plants became homozygous)

value: leaves

tag: chip antibody

value: anti 5meC antibody

tag: generation

value: Calbiochem


title: Lung_Squamous cell carcinoma_Tumour_381

value: Squamous cell carcinoma

value: Male


title: WT 385K_ChIP_2

value: WT

value: control

tag: chip antibody manufacturer

tag: chip antibody catalog #

value: none, input DNA


title: ADSV_49_PPARG_1

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_1_4.txt
Data column in raw data file: rProcessedSignal (AA)


title: ADSV_28_UNDIFF_1

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_1_3.txt
Data column in raw data file: rProcessedSignal (AA)


title: 8G ddm1 385K_ChIP_2 rep2

tag: genotype

value: ddm1(8G-generation after plants became homozygous)

tag: chip antibody lot#


title: ADSV_28_UNDIFF_2

description:
Gene Expression
Raw data file:
252800411052_201102140751_S01_GE2_105_Dec08_1_3.txt
Data column in raw data file: rProcessedSignal (AA)


title: Strawberry Hill Mid zone, plot 4, gill sample C

description: Biological replicate 12 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA

value: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels

value: gill


title: ADSV_28_PPARG_3

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_1_2.txt
Data column in raw data file: rProcessedSignal (AA)


title: 8G ddm1 385K_ChIP_2 rep1

tag: genetic background


title: Strawberry Hill Mid zone, plot 5, gill sample A

description: Biological replicate 13 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA

tag: origin


title: 2G ddm1 385K_ChIP_2 rep1

value: ddm1(2G-generation after plants became homozygous)


title: ADSV_28_PPARG_2

description:
Gene Expression
Raw data file:
252800411052_201102140751_S01_GE2_105_Dec08_1_1.txt
Data column in raw data file: rProcessedSignal (AA)

tag: cell type

value: MPC


title: Strawberry Hill High zone, plot 5, gill sample C

description: Biological replicate 15 of 15:Strawberry Hill High zone vs. Pooled Reference RNA


title: BJRIPS_UNDIFF_3

description:
Gene Expression
Raw data file:
252800411054_201102140820_S01_GE2_105_Dec08_2_4.txt
Data column in raw data file: gProcessedSignal (Z)


title: Lung_Squamous cell carcinoma_Tumour_368

tag: age

tag: histology

value: IB

value: Non-Rec

value: Female Genomic DNA (Promega)


title: BJRIPS_UNDIFF_1

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_2_4.txt
Data column in raw data file: gProcessedSignal (Z)


title: Lung_Squamous cell carcinoma_Tumour_346

tag: gender

tag: tnm stage

value: IA

value: Rec


title: Lung_Squamous cell carcinoma_Tumour_323

tag: recurrence phenotype

tag: reference


title: Strawberry Hill Mid zone, plot 3, gill sample C

description: Biological replicate 9 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA

tag: sample type

value: Field collected gill tissue, Strawberry Hill, OR population


title: ADSV_28_PPARG_1

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_1_1.txt
Data column in raw data file: rProcessedSignal (AA)

tag: agent


title: HUES_9_UNDIFF_1

description:
Gene Expression
Raw data file:
252800411052_201102140751_S01_GE2_105_Dec08_1_3.txt
Data column in raw data file: gProcessedSignal (Z)


title: Strawberry Hill Mid zone, plot 4, gill sample A

description: Biological replicate 10 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA

tag: tissue


title: BJRIPS_PPARG_2

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_1_4.txt
Data column in raw data file: gProcessedSignal (Z)


title: Lung_Squamous cell carcinoma_Tumour_327

value: IIB


title: Lung_Squamous cell carcinoma_Tumour_305

value: Squamous cell carcinoma


title: Strawberry Hill Mid zone, plot 3, gill sample B

description: Biological replicate 8 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_460

value: Male


title: HUES_9_PPARG_2

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_1_3.txt
Data column in raw data file: gProcessedSignal (Z)


title: BJRIPS_PPARG_1

description:
Gene Expression
Raw data file:
252800411052_201102140751_S01_GE2_105_Dec08_2_3.txt
Data column in raw data file: gProcessedSignal (Z)


title: Lung_Squamous cell carcinoma_Tumour_301


title: HUES_9_PPARG_1

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_2_2.txt
Data column in raw data file: gProcessedSignal (Z)


title: Lung_Squamous cell carcinoma_Tumour_299

value: Female


title: HUES_9_UNDIFF_2

description:
Gene Expression
Raw data file:
252800411053_201102140806_S01_GE2_105_Dec08_2_3.txt
Data column in raw data file: gProcessedSignal (Z)


title: Strawberry Hill Mid zone, plot 2, gill sample C

description: Biological replicate 6 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA


title: 2G ddm1 385K_ChIP_2 rep2

value: leaves

tag: chip antibody

value: anti 5meC antibody

tag: generation

value: Calbiochem


title: Strawberry Hill Mid zone, plot 4, gill sample B

description: Biological replicate 11 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA

value: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels


title: Lung_Squamous cell carcinoma_Tumour_290


title: CC_PrimaryFATPannus.2._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_D02_646998.CEL
CC_PrimaryFATPannus(2)_8-2010

data_processing:
Data were processed using the BioConductor affy package in R. RMA background correction was applied to probe intensities followed by quantile normalization. Probe set intensities were summarized from individual probes (excluding mismatch probes) using median polished. Gene level intensities were generated by mapping probe sets to refseq annotations. Probe sets that did not map to refseq annotations were not considered in further analyses. Probe Sets mapping to the same genes were median collapsed by gene symbol. Final normalized data was generated by median centering each array after the prior processing.
probe group file: [Exon array] probe group file: HuGene-1_0-st-v1.r4.pgf/HG-U133_Plus_2.pgf
meta-probeset file: [Exon array] meta-probeset file: HuGene-1_0-st-v1.r4.mps/HG-U133_Plus_2.mps

value: adipose


title: CC_ADSV49F.undiff..3._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_C06_647070.CEL
CC_ADSV49F(undiff)(3)_8-2010


title: Strawberry Hill Mid zone, plot 3, gill sample A

description: Biological replicate 7 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA

value: gill


title: Universal_ref_slide_52

description:
Gene Expression
Raw data file:
252800411052_201102140751_S01_GE2_105_Dec08_2_4.txt
Data column in raw data file: rProcessedSignal (AA)

value: universal reference (Stratagene cat#740000)


title: Lung_Squamous cell carcinoma_Tumour_276


title: BJRIPS_UNDIFF_2

description:
Gene Expression
Raw data file:
252800411052_201102140751_S01_GE2_105_Dec08_2_4.txt
Data column in raw data file: gProcessedSignal (Z)

value: MPC


title: Strawberry Hill Mid zone, plot 2, gill sample B

description: Biological replicate 5 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_236


title: Lung_Squamous cell carcinoma_Tumour_280

value: IIIB

value: Non-Rec


title: CC_ADSV49F.undiff..2._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_C05_647088.CEL
CC_ADSV49F(undiff)(2)_8-2010


title: CC_ADSV49F.P..3._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_C03_647048.CEL
CC_ADSV49F(P)(3)_8-2010


title: CC_PrimaryFATPannus.3._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_D03_647090.CEL
CC_PrimaryFATPannus(3)_8-2010

source_name: PRIMARY FAT_rep3


title: Lung_Squamous cell carcinoma_Tumour_240

value: IB

value: Female Genomic DNA (Promega)


title: CC_PrimaryFATPannus1_8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_D01_646934.CEL
CC_PrimaryFATPannus1_8-2010


title: CC_ADSV49F.P..2._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_C02_646988.CEL
CC_ADSV49F(P)(2)_8-2010


title: Strawberry Hill Mid zone, plot 2, gill sample A

description: Biological replicate 4 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA

value: Field collected gill tissue, Strawberry Hill, OR population


title: Strawberry Hill Mid zone, plot 1, gill sample C

description: Biological replicate 3 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA


title: Strawberry Hill Mid zone, plot 1, gill sample B

description: Biological replicate 2 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA


title: CC_ADSV49F.undiff..1._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_C04_647062.CEL
CC_ADSV49F(undiff)(1)_8-2010


title: Lung_Squamous cell carcinoma_Tumour_234


title: CC_ADSV49F.P..1._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_C01_646928.CEL
CC_ADSV49F(P)(1)_8-2010


title: Strawberry Hill Mid zone, plot 1, gill sample A

description: Biological replicate 1 of 15:Strawberry Hill Mid zone vs. Pooled Reference RNA


title: Strawberry Hill Low zone, plot 5, gill sample C

description: Biological replicate 15 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_227


title: CC_ADSV28F.undiff..3._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B12_646930.CEL
CC_ADSV28F(undiff)(3)_8-2010


title: CC_ADSV28F.undiff..1._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B10_647024.CEL
CC_ADSV28F(undiff)(1)_8-2010


title: Strawberry Hill Low zone, plot 5, gill sample B

description: Biological replicate 14 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: CC_ADSV28F.undiff..2._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B11_646954.CEL
CC_ADSV28F(undiff)(2)_8-2010


title: Lung_Squamous cell carcinoma_Tumour_219

value: Rec


title: Strawberry Hill Low zone, plot 5, gill sample A

description: Biological replicate 13 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: Strawberry Hill Low zone, plot 4, gill sample C

description: Biological replicate 12 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: CC_ADSV28F.P..3._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B09_647034.CEL
CC_ADSV28F(P)(3)_8-2010


title: Strawberry Hill Low zone, plot 4, gill sample A

description: Biological replicate 10 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: Strawberry Hill Low zone, plot 4, gill sample B

description: Biological replicate 11 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: 2G ddm1 385K_ChIP_1 rep2

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. This chip covers entire chromosome 1 and part of chromosome 2 of A. thaliana. Scaling is performed by subtracting the bi-weight mean for the IP/input log2 ratio values for chromosome 1 from each log2 ratio value.

value: ddm1(2G-generation after plants became homozygous)

tag: chip antibody manufacturer

tag: chip antibody catalog #

value: none, input DNA


title: Lung_Squamous cell carcinoma_Tumour_210

value: Squamous cell carcinoma

value: Male


title: CC_ADSV28F.P..1._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B07_646976.CEL
CC_ADSV28F(P)(1)_8-2010


title: 8G ddm1 385K_ChIP_1 rep1

tag: genotype

value: ddm1(8G-generation after plants became homozygous)

value: leaves

value: anti 5meC antibody

tag: chip antibody lot#


title: CC_BJRiPSMPC.1.1.undiff..3._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B06_647112.CEL
CC_BJRiPSMPC#1.1(undiff)(3)_8-2010


title: Lung_Squamous cell carcinoma_Tumour_114

value: Female

value: IIA


title: Lung_Squamous cell carcinoma_Tumour_112

value: IIIA


title: stbC mutant

city: Taipei

first: Ke-Chuan

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

description:
Raw data file:
US22502527_251590610001_S01_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: The labeled cDNA was then pooled and hybridized to microarrays at 60° C for 17 h.

scan_protocol: Microarrays were scanned with an Agilent microarray scanner at 535 nm for Cy3-CTP and 625 nm for Cy5-CTP.

data_processing:
Scanned images were then analyzed by Feature Extraction 9.5.3 software (Agilent).
Image analysis and normalization software was used to quantify signal and background intensity for each feature and substantially normalized the data by rank-consistant LOWESS method.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Mutant Salmonella Typhimurium LB5010

label_protocol: One microgram of enriched mRNA was reverse-transcribed to cDNA with a CyScribe 1st-strand cDNA labeling kit and labeled with Cy3-CTP or Cy5-CTP.

growth_protocol: Bacterial cells were cultured on LB agar.

extract_protocol: Total RNA were harvested in TRIzole reagent and disrupted using the MagNA Lyser System.

tag: genotype/variation

value: stbC mutant

tag: culture condition

value: LB agar

source_name: Wild-type Salmonella Typhimurium LB5010

value: Wild-type


title: Strawberry Hill Low zone, plot 3, gill sample B

description: Biological replicate 8 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA

value: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels

value: gill

tag: origin


title: 8G ddm1kyp 385K_ChIP_1

value: ddm1 kyp(8G-generation after plants became homozygous)

value: Calbiochem

tag: genetic background


title: 2G ddm1 385K_ChIP_1 rep1

value: ddm1(2G-generation after plants became homozygous)


title: Lung_Squamous cell carcinoma_Tumour_201

source_name: Lung Tissue, Tumour, Surgically resected

tag: age

tag: histology

tag: gender

value: Non-Rec

value: Female Genomic DNA (Promega)


title: CC_ADSV28F.P..2._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B08_647086.CEL
CC_ADSV28F(P)(2)_8-2010

tag: cell type

value: MPC


title: WT 385K_ChIP_1

value: WT

value: control

value: none, input DNA


title: Lung_Squamous cell carcinoma_Tumour_99

value: Squamous cell carcinoma

value: Male

tag: tnm stage

value: IB

tag: recurrence phenotype

value: Rec

source_name: Female genomic DNA

tag: reference


title: CC_BJRiPSMPC.1.1.undiff..2._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B05_647108.CEL
CC_BJRiPSMPC#1.1(undiff)(2)_8-2010


title: 8G ddm1 385K_ChIP_1 rep2

value: ddm1(8G-generation after plants became homozygous)

tag: tissue

value: leaves

tag: chip antibody

value: anti 5meC antibody


title: CC_BJRiPSMPC.1.1.undiff..1._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B04_646968.CEL
CC_BJRiPSMPC#1.1(undiff)(1)_8-2010


title: Lung_Squamous cell carcinoma_Tumour_104

value: Female

value: IIB


title: 4 day old mated male vs 4 day old virgin male rep3

city: Pavia

first: Ludvik

middle: Marcus

last: Gomulski

state: PV

address: Piazza Botta 9

department: Biologia Animale

institute: University of Pavia

description: Assay for the determination of transcriptome changes due to mating status in males

hyb_protocol: Agilent Technologies

scan_protocol: Axon

data_processing: signal intensity cutoff: 100, Lowess normalization

organism: Ceratitis capitata

source_name: 4 day old virgin male

label_protocol: Agilent Technologies

extract_protocol: Qiagen

value: 4 day virgin

value: male

tag: body part

value: head

tag: strain

value: ISPRA

source_name: 4 day old mated male

value: 4 day mated


title: Strawberry Hill Low zone, plot 2, gill sample C

description: Biological replicate 6 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA

tag: sample type

value: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels

value: gill

value: Field collected gill tissue, Strawberry Hill, OR population


title: 4 day old mated male vs 4 day old virgin male rep2


title: Strawberry Hill Low zone, plot 3, gill sample C

description: Biological replicate 9 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_92

value: Squamous cell carcinoma

value: Female Genomic DNA (Promega)


title: Strawberry Hill Low zone, plot 2, gill sample B

description: Biological replicate 5 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_97

value: Male


title: Strawberry Hill Low zone, plot 2, gill sample A

description: Biological replicate 4 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: Strawberry Hill Low zone, plot 3, gill sample A

description: Biological replicate 7 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: 4 day old mated female vs 4 day old virgin female rep1

description: Assay for the determination of transcriptome due to mating status in females

source_name: 4 day old virgin female

value: female

source_name: 4 day old mated female


title: 4 day old mated female vs 4 day old virgin female rep2


title: CC_BJRiPSMPC.1.1.P..3._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B03_646980.CEL
CC_BJRiPSMPC#1.1(P)(3)_8-2010

value: MPC

tag: agent


title: CC_BJRiPSMPC.1.1.P..1._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B01_646978.CEL
CC_BJRiPSMPC#1.1(P)(1)_8-2010


title: CC_BJRiPSMPC.1.1.P..2._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_B02_647004.CEL
CC_BJRiPSMPC#1.1(P)(2)_8-2010


title: Strawberry Hill Low zone, plot 1, gill sample C

description: Biological replicate 3 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_65

value: IB

value: Non-Rec


title: Strawberry Hill Low zone, plot 1, gill sample B

description: Biological replicate 2 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: Lung_Squamous cell carcinoma_Tumour_63

value: Female


title: Lung_Squamous cell carcinoma_Tumour_64

value: IA


title: Strawberry Hill Low zone, plot 1, gill sample A

description: Biological replicate 1 of 15:Strawberry Hill Low zone vs. Pooled Reference RNA


title: 1 day old virgin male vs 4 day old virgin male rep2

description: Assay for the determination of transcriptome changes during female maturation

value: 4 day virgin

source_name: 1 day old virgin male

value: 1 day virgin


title: CC_HUES9MPC.undiff..1._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_A10_646956.CEL
CC_HUES9MPC(undiff)(1)_8-2010


title: CC_HUES9MPC.undiff..2._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_A11_647022.CEL
CC_HUES9MPC(undiff)(2)_8-2010


title: Lung_Squamous cell carcinoma_Tumour_59


title: CC_HUES9MPC.P..2._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_A08_647078.CEL
CC_HUES9MPC(P)(2)_8-2010


title: 1 day old virgin male vs 4 day old virgin male rep1

value: male

value: head


title: CC_HUES9MPC.P..3._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_A09_647064.CEL
CC_HUES9MPC(P)(3)_8-2010


title: Lung_Squamous cell carcinoma_Tumour_30


title: Lung_Squamous cell carcinoma_Tumour_50

value: IIB

value: Rec


title: 1 day old virgin female vs 4 day old virgin female rep2

value: ISPRA

source_name: 1 day old virgin female


title: 1 day old virgin female vs 4 day old virgin female rep3


title: 14227261 - wox14 B4 vs N8514 B4

status: Public on Dec 24 2011

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

country: France

institute: INRA

description: Our scope is to establish a functional link to organ initiation and development in Arabidopsis by identifying genes that are deregulated in the wox14 mutant background.

hyb_protocol: N8514 B4 Cy5 / wox14 B4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: stem - Media : soil  hygrometry : 65%  Temperature : 20  Light: LD 150µmol.m-2.s-1

extract_protocol: N8514 B4:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: Nossen

tag: mutant

tag: dev.stage (boyes et al. plant cell 2001)

source_name: wox14 B4

growth_protocol: stem - Media : soil  hygrometry : 65%  Temperature : 20  Light : LD 150µmol.m-2.s-1

extract_protocol: wox14 B4:5ug. (Qiagen_RNeasy.pdf)


title: 14227262 - N8514 B5 vs wox14 B5

hyb_protocol: wox14 B5 Cy5 / N8514 B5 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wox14 B5

extract_protocol: wox14 B5:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: N8514 B5:5ug. (Qiagen_RNeasy.pdf)


title: 14227260 - N8514 B4 vs wox14 B4

hyb_protocol: wox14 B4 Cy5 / N8514 B4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 1 day old virgin male vs 4 day old virgin male rep3


title: 4 day old mated male vs 4 day old virgin male rep1

description: Assay for the determination of transcriptome changes due to mating status in males

value: 4 day mated


title: 14227263 - wox14 B5 vs N8514 B5

hyb_protocol: N8514 B5 Cy5 / wox14 B5 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CC_HUES9MPC.P..1._8.2010 [HuGene-1_0-st]

description:
Gene Expression
MINTY_p_Cowen_Affy1.0ST_plate_HuGene-1_0-st-v1.r4_A07_647006.CEL
CC_HUES9MPC(P)(1)_8-2010


title: UPN72 NK-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis

city: Angers

first: Philippe

last: Guardiola

state: Maine et Loire

address: 4 rue Larrey

institute: Angers University Hospital

hyb_protocol: Hybridization on Illumina HumanHT-12 v3 Expression BeadChips and staining were performed according to Illumina’s protocol.

scan_protocol: Detection of cRNAs on microarrays using an I-Scan system were performed according to Illumina’s protocol.

data_processing: GenomeStudio 2010.3 software (Illumina Inc., San Diego, USA) and its Gene Expression Analysis Module (version 1.8.0) were used for signal extraction. No normalization was applied to the primary probe data.

source_name: Human acute myeloid leukemic cells

label_protocol: The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.

extract_protocol: Total RNAs were extracted from 10e7 thawed cells using RNEasy® Mini Kits (Qiagen Incorporation, Valencia, USA). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA) according to manufacturer recommendations. Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA).

treatment_protocol: Blasts and mononuclear cells were purified by Ficoll-Hypaque density gradient centrifugation from bone marrow or peripheral blood samples (Nygaard, Oslo, Norway). Isolated cell samples were then immediately cryopreserved.

tag: duplicates

value: no

tag: aml subtype

value: NK-AML

tag: cell source

value: Bone Marrow

tag: time point

value: Diagnosis

tag: dilution

value: Dilution 75%

tag: quality control

value: Good Quality Controls


title: UPN60 NK-AML_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis

value: Peripheral Blood

value: No dilution


title: UPN25 NK-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN73 NK-AML_Peripheral Blood_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN66 NK-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN97 NK-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN11 NK-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN74 NK-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN38 NK-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: 1 day old virgin female vs 4 day old virgin female rep1

tag: age

value: 4 day virgin

tag: gender

value: female


title: UPN19 NK-AML_Bone Marrow_No dilution_Good Quality Controls_Diagnosis


title: UPN78 NK-AML_Peripheral Blood_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN89 NK-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: BJRIPS_PPARG_3

description:
Gene Expression
Raw data file:
252800411052_201102140751_S01_GE2_105_Dec08_1_4.txt
Data column in raw data file: gProcessedSignal (Z)

tag: cell type

value: MPC


title: UPN8 NK-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN44 NK-AML_Peripheral Blood_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN96 NK-AML_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis


title: UPN1 NK-AML_Peripheral Blood_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN44 NK-AML_Peripheral Blood_Dilution 50%_Good Quality Controls_Diagnosis

value: Dilution 50%


title: UPN73 NK-AML_Peripheral Blood_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN89 NK-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN78 NK-AML_Peripheral Blood_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN66 NK-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN97 NK-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN74 NK-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN25 NK-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN11 NK-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN72 NK-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN67 inv(16)-AML_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis


title: UPN52 inv(16)-AML_Bone Marrow_No dilution_Good Quality Controls_Diagnosis


title: UPN1 NK-AML_Peripheral Blood_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN43 inv(16)-AML_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis


title: UPN87 inv(16)-AML_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis


title: UPN9 inv(16)-AML_Bone Marrow_No dilution_Good Quality Controls_Diagnosis


title: UPN36 inv(16)-AML_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis


title: UPN31 inv(16)-AML_Bone Marrow_No dilution_Good Quality Controls_Diagnosis


title: UPN79 inv(16)-AML_Bone Marrow_No dilution_Poor Quality Control_Diagnosis

value: Poor Quality Control


title: UPN8 NK-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN88 inv(16)-AML_Bone Marrow_No dilution_Good Quality Controls_Diagnosis


title: UPN37 inv(16)-AML_Peripheral Blood_No dilution_Good Quality Controls_Relapse

value: Relapse


title: UPN52 inv(16)-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN38 NK-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN23 inv(16)-AML_Bone Marrow_No dilution_Poor Quality Control_Diagnosis


title: UPN7 inv(16)-AML_Bone Marrow_No dilution_Good Quality Controls_Relapse


title: UPN37 inv(16)-AML_Bone Marrow_No dilution_Good Quality Controls_Diagnosis


title: UPN6 inv(16)-AML_Bone Marrow_No dilution_Poor Quality Control_Diagnosis


title: 4 day old mated female vs 4 day old virgin female rep3

value: head

value: ISPRA


title: UPN10 inv(16)-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN45 inv(16)-AML_Bone Marrow_No dilution_Poor Quality Control_Diagnosis


title: UPN90 inv(16)-AML_Peripheral Blood_No dilution_Poor Quality Control_Diagnosis


title: UPN45 inv(16)-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN37 inv(16)-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN37 inv(16)-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN45 inv(16)-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN52 inv(16)-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis

value: yes


title: UPN47 inv(16)-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis

value: no


title: UPN10 inv(16)-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN47 inv(16)-AML_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis

value: Dilution 90%


title: UPN52 inv(16)-AML_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis

value: Bone Marrow


title: ME-1_Cell Line 2

value: Diagnosis


title: UPN45 inv(16)-AML_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis


title: UPN52 inv(16)-AML_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis

value: Dilution 95%


title: UPN10 inv(16)-AML_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis

value: Good Quality Controls


title: UPN47 inv(16)-AML_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis


title: UPN45 inv(16)-AML_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis


title: ME-1_Cell Line


title: UPN95 t(8;21)-AML_Bone Marrow_No dilution_Good Quality Controls_Diagnosis


title: UPN26 t(8;21)-AML_Bone Marrow_No dilution_Good Quality Controls_Diagnosis


title: UPN76 t(8;21)-AML_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis

value: Peripheral Blood


title: MP.12.R1 p75KO.diabetic

first: Klemens

last: Vierlinger

address: Giefinggasse 4

department: HMD

institute: AIT

hyb_protocol: 1.65 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, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, 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 to obtain background subtracted and spatially detrended Processed Signal intensities. The Sample data table values are quantile-normalised background-substracted log2-values (using R/Bioconductor package limma).

source_name: diabetic ischemic limbs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

extract_protocol: RNeasy AllPrep column extraction (Qiagen) using the manufacturers protocols

treatment_protocol: Three day old wounds from diabetic and healthy, wildtype and p75KO mice were sampled.

tag: genotype/variation

tag: disease state

value: diabetic

tag: tissue

value: skin

value: male


title: MP.6.R3 WT.diabetic

tag: strain


title: UPN21 t(8;21)-AML_Bone Marrow_No dilution_Good Quality Controls_Diagnosis

value: No dilution


title: UPN69 t(8;21)-AML_Peripheral Blood_Dilution 75%_Good Quality Controls_Diagnosis

value: Dilution 75%


title: MP.3.R4 WT.healthy

value: healthy


title: MP.3.R2 WT.healthy


title: MP.12.R4 p75KO.diabetic


title: MP.6.R5 WT.diabetic


title: UPN69 t(8;21)-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN30 t(8;21)-AML_Peripheral Blood_No dilution_Poor Quality Control_Diagnosis

value: Poor Quality Control


title: UPN51 t(8;21)-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Relapse

value: Relapse


title: MP.3.R3 WT.healthy


title: UPN69 t(8;21)-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis

value: Dilution 50%


title: UPN69 t(8;21)-AML_Peripheral Blood_Dilution 50%_Good Quality Controls_Diagnosis


title: MP.6.R6 WT.diabetic


title: MP.6.R1 WT.diabetic


title: MP.12.R3 p75KO.diabetic


title: MP.3.R1 WT.healthy


title: UPN69 t(8;21)-AML_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis


title: UPN30 t(8;21)-AML_Peripheral Blood_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN61 t(8;21)-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN51 t(8;21)-AML_Bone Marrow_Dilution 50%_Good Quality Controls_Relapse


title: Kasumi-1_Cell Line 2

value: yes


title: UPN82 APL_Bone Marrow_No dilution_Poor Quality Control_Diagnosis

value: no

value: APL


title: UPN61 t(8;21)-AML_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis

value: Bone Marrow

value: Dilution 90%


title: UPN51 t(8;21)-AML_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis

value: Diagnosis


title: UPN51 t(8;21)-AML_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis

value: Dilution 95%

value: Good Quality Controls


title: UPN30 t(8;21)-AML_Peripheral Blood_Dilution 95%_Good Quality Controls_Diagnosis

value: Peripheral Blood


title: MP.12.R5 p75KO.diabetic

value: diabetic

value: skin


title: Kasumi-1_Cell Line

value: No dilution


title: UPN30 t(8;21)-AML_Peripheral Blood_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN30 t(8;21)-AML_Peripheral Blood_Dilution 90%_Good Quality Controls_Diagnosis


title: UPN86 APL_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis


title: UPN69 t(8;21)-AML_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis


title: UPN61 t(8;21)-AML_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis


title: UPN59 APL_Peripheral Blood_No dilution_Poor Quality Control_Diagnosis


title: UPN13 APL_Bone Marrow_No dilution_Poor Quality Control_Diagnosis


title: HCC1937_3

city: Madrid

first: Beatriz

last: Martinez

address: Calle Melchor Fernandez Almagro 3

department: Human Cancer Genetics

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

hyb_protocol: For each hybridization, 1 μg Cyanine 3 labeled cRNA (reference) and 1 μg of Cyanine 5 labeled cRNA (samples) were mixed, fragmented, and hybridized at 65°C for 17 hours to an Agilent 4 × 44 K Whole Human Genome Oligo Microarray.

scan_protocol: Microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: Agilent Feature Extraction software (version 9.5.3) was run on all array datasets using the GE2-v5_95_Feb07 protocol.  Lowess  and quantiles were applied for intra-array and between array normalization, respectively.

source_name: Universal Human Reference RNA

label_protocol: 500 ng of total RNA from samples and Universal Human Reference RNA (Stratagene, Catalog #740000) were used for amplification and labeling using the Low RNA Input Linear Amplification Kit (Agilent) following the detailed protocol described in the kit manual.

growth_protocol: Cell lines were cultured in DMEM medium supplemented with 10%FBS, 0.08% Fungizone and 100units/mL penicillin/streptomycin, and maintained at 37ºC in 5% CO2.

extract_protocol: Total RNA was extracted from cell lines using Trizol (Invitrogen) according to the instructions of the manufacturer.

tag: sample description

value: pool of total RNA from 10 human cell lines

tag: cell line

value: breast cancer cells

tag: brca1 expression


title: UPN47 inv(16)-AML_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis

value: Dilution 75%


title: HCC1937_2


title: UPN5 APL_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis


title: HCC1937_1


title: UPN50 APL_Peripheral Blood_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN48 APL_Peripheral Blood_No dilution_Good Quality Controls_Diagnosis


title: HCC1937/BRCA1, replicate3

description: BRCA1 gene is expressed.

hyb_protocol: Exiqon miRNA microarray slides containing denaturated labeled RNA in 1x hybridization buffer were hybridized at 56ºC for 16h.

scan_protocol: Slides were scanned using an Agilent array scanner set to 10μm wit 100PMT sensitivity in an ozone-free-environment. Fluorescence intensities on scanned images were quantified using Feature Extraction software (Agilent) using the modified Exiqon protocol.

data_processing: Background correction was carried out using normexp, and data was normalized using quantiles between-arrays normalization. Data processing was carried out using Bioconductor´s limma package.

label_protocol: 300ng of total RNA were treated with Calf Intestine Phosphatase and than labeled with Hy3 fluorescent dye.

growth_protocol: Cell lines were grown in 10% FBS DMEM media with 2% penicillin/streptomycin at 37ºC, 5% CO2 atmosphere and 80% humidity.

extract_protocol: Total RNA was extracted from cell pellets using Trizol following the manufacturer's recommendations.


title: HCC1937, replicate3

description: No BRCA1 expression confirmed by Western Blot.


title: UPN65 APL_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN47 inv(16)-AML_Bone Marrow_No dilution_Poor Quality Control_Diagnosis

value: Poor Quality Control


title: HCC1937, replicate2


title: BRCA1_3

value: BRCA1-transfected HCC1937


title: UPN22 APL_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN40 APL_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: BRCA1_2

value: yes


title: UPN40 APL_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis

value: no

value: Dilution 50%


title: HCC1937, replicate1


title: UPN53 APL_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis

value: APL

value: Bone Marrow


title: UPN65 APL_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis

value: Diagnosis


title: UPN53 APL_Bone Marrow_Dilution 75%_Good Quality Controls_Diagnosis


title: UPN22 APL_Bone Marrow_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN50 APL_Peripheral Blood_Dilution 50%_Good Quality Controls_Diagnosis


title: UPN22 APL_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis

value: Dilution 90%


title: BRCA1_1


title: UPN50 APL_Peripheral Blood_Dilution 95%_Good Quality Controls_Diagnosis

value: Dilution 95%

value: Good Quality Controls


title: UPN40 APL_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis


title: UPN50 APL_Peripheral Blood_Dilution 90%_Good Quality Controls_Diagnosis

value: Peripheral Blood


title: UPN53 APL_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis


title: UPN40 APL_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis


title: HCC1937/BRCA1, replicate1

description: BRCA1 gene is expressed.


title: NB4_Cell Line


title: NB4_Cell Line 2


title: Arsenic-treated rat L2 Cells C_D7 replication3

status: Public on Dec 23 2011

city: Stillwater

first: Tingting

last: Weng

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

description: Sample replication 1 of 6. L2 cells were exposed with 0.75 uM of arsenite for 0, 1, 3, 5, and 7 days (C, D1, D3, D5 and D7). The samples were arranged for hybridization using a loop design. For each paired sample, dye flip and three biological replications were performed for each sample.

hyb_protocol: The cDNAs were column-purified and mixed with 2x formamide hybridization buffer (50% formamide, 6 x SSC, 0.2% SDS) in equal volume.  The paired cDNAs were then combined in 1:1 ratio (v/v) and denatured at 80oC for 10 min.  The slide was blocked with 0.1% SDS, 1% BSA and 3 x SSC at 42oC for 40 min and hybridized with labeled cDNAs at 45oC for 48 h.  The slide was then washed and incubated with Cy-3 or Alexa 647-labeled dendrimers at 45oC for 3 h.

scan_protocol: ScanArray Express laser scanner (PerkinElmer, Boston, MA). The signal intensity for each spot was obtained from the scanned slides using GenePix 5.0

data_processing: The raw data were LOWESS normalized, the bad and weak spots were removed,  followed by one-class statistical SAM test using a false discovery rate (q value) of <0.05 to identify significantly changed genes.

organism: Rattus norvegicus

source_name: Total RNA from L2 cells treated with arsenite for 0 day labeled with Alexa546 (green).

label_protocol: Total RNA (3 ug each) were reverse-transcribed into cDNA with Alexa 546 (green)- or Alexa 647 (red)-specific primer of the 3DNA 350 expression kit (Genishere Inc., Hatfield, PA, USA), purified with Microcom YM-30 columns, and mixed with an equal amount of 2x formamide hybridization buffer (50% formamide, 6x SSC, 0.2% SDS, and 10x Denhardt solution).

growth_protocol: L2 cells (passages 30-40) were cultured in 30 or 100 mm cell culture dishes in F12 K medium supplemented with 10% of heat-inactivated FBS and antibiotics (1 x penicillin/streptomycin). When grown to 80 to 90% confluence, the cells were treated with arsenite (0-5 uM) for various times (0 to 7 days).  At the end of incubation, the cells were used for the viability assay, DNA microarray analysis and real-time PCR analysis.

extract_protocol: TRI reagents (Molecular Research Center, Cincinnati, OH, USA).

tag: Lung epithelial cell line (L2)

source_name: Total RNA from L2 cells treated with arsenite for 7 days labeled with Alexa647 (red).


title: UPN10 inv(16)-AML_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis

tag: duplicates


title: UPN53 APL_Bone Marrow_Dilution 90%_Good Quality Controls_Diagnosis

tag: aml subtype


title: Arsenic-treated rat L2 Cells D7_C replication6

source_name: Total RNA from L2 cells treated with arsenite for 7 days labeled with Alexa546 (green).

source_name: Total RNA from L2 cells treated with arsenite for 0 day labeled with Alexa647 (red).


title: Arsenic-treated rat L2 Cells D7_D5 replication5

source_name: Total RNA from L2 cells treated with arsenite for 5 days labeled with Alexa647 (red).


title: Arsenic-treated rat L2 Cells D7_C replication4


title: Arsenic-treated rat L2 Cells D5_D7 replication3

source_name: Total RNA from L2 cells treated with arsenite for 5 days labeled with Alexa546 (green).


title: Arsenic-treated rat L2 Cells C_D7 replication2


title: Arsenic-treated rat L2 Cells C_D7 replication1


title: Arsenic-treated rat L2 Cells D5_D7 replication1


title: UPN22 APL_Bone Marrow_Dilution 95%_Good Quality Controls_Diagnosis

tag: cell source


title: Arsenic-treated rat L2 Cells D5_D3 replication5

source_name: Total RNA from L2 cells treated with arsenite for 3 days labeled with Alexa647 (red).


title: Arsenic-treated rat L2 Cells D7_D5 replication4


title: Arsenic-treated rat L2 Cells D5_D3 replication6


title: Arsenic-treated rat L2 Cells D5_D7 replication2


title: Arsenic-treated rat L2 Cells D3_D1 replication5

source_name: Total RNA from L2 cells treated with arsenite for 3 days labeled with Alexa546 (green).

source_name: Total RNA from L2 cells treated with arsenite for 1 day labeled with Alexa647 (red).


title: Arsenic-treated rat L2 Cells D3_D5 replication3


title: Arsenic-treated rat L2 Cells D3_D1 replication6


title: Arsenic-treated rat L2 Cells D1_D3 replication1

source_name: Total RNA from L2 cells treated with arsenite for 1 days labeled with Alexa546 (green).