title: Wild type (15 month) vs wild type (2.5 month)_VP_R2

status: Public on Dec 16 2010

city: Smithville

first: Dean

middle: G

last: Tang

state: TX

address: 1808 Park road 1C

department: Carcinogenesis

institute: U.T M. D. Anderson Cancer Center

description: The current array analysis was carried out to study the changes in the gene expression profile of 15 month old wild type mice ventral prostate (VP) compared to 2.5 month old wild type mice VP.

hyb_protocol: Manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF

scan_protocol: Scanning and data acquisition were performed using Agilent scanner and feature extraction software version A.7.5.1 (www.agilent.com).

data_processing: The data was acquired using Agilent's feature extraction software (version A.7.5.1) with inbuilt Lowess normalization feature and Logratio algorithms, for details visit www.agilent.com

source_name: Wild type (2.5 month old) mice ventral prostate

label_protocol: labeling was done according to manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF

extract_protocol: Total RNA was extracted from combined ventral prostates of three 2.5 month old wild type mice after mincing with Biopulverizer (Biospec products) and using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

value: ventral prostate

value: 2.5 month old

tag: genetic background

value: FVB

tag: genotype

value: wild type

source_name: Wild type (15 month old) mice ventral prostate

extract_protocol: Total RNA was extracted from combined ventral prostates of three 15 month old wild type mice after mincing with Biopulverizer (Biospec products) and using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

value: 15 month old


title: Blood-Ctrl-2248-rep1

status: Public on Jul 31 2010

type: genomic

city: University of Sydney

first: Roger

last: Pamphlett

address: Blackburn Bld

country: Australia

institute: University of Sydney

description: Affy 6.0 Ctrl Blood

data_processing:
Data processed using Affymetrix Command Console software and Affymetrix Genotyping Console 3.0.2 software using the Birdseed version 2 algorithm and default settings.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Ctrl Blood

label_protocol: According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia), Affymetrix dsDNA terminal label.

extract_protocol: Genomic DNA was extracted from leukocytes using the phenol chloroform method or Qiamp blood kits (Qiagen Pty Ltd, Doncaster, Vic, Australia), hair using the phenol chloroform method, and from sperm using Pure Sperm 100 kits (Nidacom, Gothenburg, Sweden).

tag: study #

value: Study 3 (Trio)

tag: trio #

value: Trio 12 / Father

tag: twin #

tag: twin info

tag: gender

value: M

tag: phenotype

value: Ctrl


title: Blood-Ctrl-2114-rep1

description: Affy 6.0 Ctrl Blood

hyb_protocol: According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)

value: Trio 11 / Father


title: Blood-MND-2215-rep1

description: Affy 6.0 MND Blood

scan_protocol: According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)

source_name: MND Blood

value: Trio 12 / Child

value: F

value: MND


title: Blood-Ctrl-2247-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 12 / Mother


title: Blood-Ctrl-2123-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 10 / Father


title: Blood-MND-2113-rep1

description: Affy 6.0 MND Blood

value: Trio 11 / Child


title: Blood-Ctrl-2115-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 11 / Mother


title: Blood-Ctrl-1931-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 6 / Mother


title: Blood-Ctrl-0834-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 2 / Father


title: Blood-Ctrl-1948-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 9 / Father


title: Blood-MND-1522-rep1

description: Affy 6.0 MND Blood

value: Trio 6 / Child


title: Blood-Ctrl-1912-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 8 / Father


title: Blood-Ctrl-0896-rep1

description: Affy 6.0 Ctrl Blood

value: Study 3 (Trio)

value: Trio 3 / Mother


title: Blood-Ctrl-2124-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 10 / Mother


title: Blood-Ctrl-1840-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 7 / Father

value: M

value: Ctrl


title: Blood-MND-1910-rep1

description: Affy 6.0 MND Blood

value: Trio 10 / Child


title: Blood-Ctrl-0834-rep2

description: Affy 6.0 Ctrl Blood

value: Trio 2 / Father Replicate


title: Blood-Ctrl-1841-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 7 / Mother

value: F


title: Blood-Ctrl-1686-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 5 / Father


title: Blood-Ctrl-0835-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 2 / Mother


title: Blood-MND-1685rep1

description: Affy 6.0 MND Blood

value: Trio 5 / Child

value: MND


title: Blood-MND-1483-rep1

description: Affy 6.0 MND Blood

value: Trio 7 / Child


title: Blood-Ctrl-1421-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 4 / Father


title: Blood-Ctrl-1687-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 5 / Mother


title: Blood-MND-0895-rep1

description: Affy 6.0 MND Blood

value: Study 3 (Trio)

value: Trio 3 / Child


title: Blood-Ctrl-1932-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 6 / Father


title: Blood-Ctrl-0909-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 3 / Father


title: Blood-Ctrl-1422-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 4 / Mother


title: Blood-MND-1982-rep1

description: Affy 6.0 MND Blood

value: Trio 9 / Child

value: M


title: Blood-Ctrl-0707-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 1 / Mother

value: Ctrl


title: Blood-MND-0833-rep1

description: Affy 6.0 MND Blood

value: Trio 2 / Child

value: F


title: Blood-MND-0705-rep1

description: Affy 6.0 MND Blood

value: Trio 1 / Child


title: Blood-MND-1417-rep1

description: Affy 6.0 MND Blood

value: Study 2 (Twin) and 3 (Trio)

value: Trio 4 / Child

value: Twin 2

value: Dizygotic Discordant for MND


title: Blood-Ctrl-1957-rep1

description: Affy 6.0 Ctrl Blood

value: Study 2 (Twin)

value: Twin 7

value: Monozygotic Discordant for MND


title: Blood-Ctrl-0708-rep1

description: Affy 6.0 Ctrl Blood

value: Study 3 (Trio)

value: Trio 1 / Father


title: Hair-MND-1900-rep1

description: Affy 6.0 MND Hair

source_name: MND Hair

value: Twin 4

value: MND


title: Blood-Ctrl-1955-rep1

description: Affy 6.0 Ctrl Blood

value: Twin 6

value: M


title: Blood-MND-1900-rep1

description: Affy 6.0 MND Blood


title: Blood-Ctrl-1914-rep1

description: Affy 6.0 Ctrl Blood

value: Twin 3

value: Monozygotic Control

value: Ctrl


title: Blood-MND-1900-rep2

description: Affy 6.0 MND Blood

value: Twin 4 Replicate


title: Blood-Ctrl-1467-rep1

description: Affy 6.0 Ctrl Blood


title: Blood-Ctrl-1927-rep1

description: Affy 6.0 Ctrl Blood

value: Twin 5


title: Blood-Ctrl-1901-rep2

description: Affy 6.0 Ctrl Blood


title: Hair-Ctrl-1467-rep1

description: Affy 6.0 Ctrl Hair

source_name: Ctrl Hair


title: Blood-MND-1954-rep1

description: Affy 6.0 MND Blood


title: Blood-MND-0574-rep1

description: Affy 6.0 MND Blood

value: Twin 1

value: Monozygotic Concordant for MND


title: Blood-MND-1956-rep1

description: Affy 6.0 MND Blood

value: F


title: Blood-MND-0573-rep1

description: Affy 6.0 MND Blood

value: Study 2 (Twin)


title: Blood-Ctrl-0640-rep1

description: Affy 6.0 Ctrl Blood

value: Trio 8 / Mother


title: Hair-Ctrl-1914-rep1

description: Affy 6.0 Ctrl Hair


title: Sperm-MND-1900-rep1

description: Affy 6.0 MND Sperm

source_name: MND Sperm

value: Monozygotic Discordant for MND


title: Hair-Ctrl-1901-rep1

description: Affy 6.0 Ctrl Hair


title: Blood-Ctrl-1901-rep1

description: Affy 6.0 Ctrl Blood


title: Blood-MND-2146-rep1

description: Affy 6.0 MND Blood

value: Study 1 (Somatic)


title: Brain-MND-2146-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)

source_name: MND Brain (Brodmann area 46)


title: Blood-Ctrl-2006-rep1

description: Affy 6.0 Ctrl Blood

value: Study 3 (Trio)

value: Trio 9 / Mother


title: Blood-MND-0639rep1

description: Affy 6.0 MND Blood

value: Trio 8 / Child

value: MND


title: Blood-Ctrl-1418-rep1

description: Affy 6.0 Ctrl Blood

value: Twin 2

value: Dizygotic Discordant for MND


title: Blood-Ctrl-1928-rep1

description: Affy 6.0 Ctrl Blood

value: Monozygotic Control

value: M


title: Blood-MND-1895-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-1895-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-PD-1938-rep1

description: Affy 6.0 PD Brain (Brodmann area 46)

source_name: PD Brain (Brodmann area 46)

value: PD


title: Brain-PD-1939-rep1

description: Affy 6.0 PD Brain (Brodmann area 46)


title: Brain-Ctrl-1913-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)

source_name: Ctrl Brain (Brodmann area 46)

value: Ctrl


title: Brain-Ctrl-1742-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-PD-1827-rep1

description: Affy 6.0 PD Brain (Brodmann area 46)


title: Brain-PD-1831-rep1

description: Affy 6.0 PD Brain (Brodmann area 46)


title: Brain-PD-1823-rep1

description: Affy 6.0 PD Brain (Brodmann area 46)


title: Brain-Ctrl-1741-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-PD-1829-rep1

description: Affy 6.0 PD Brain (Brodmann area 46)


title: Blood-MND-1690-rep1

description: Affy 6.0 MND Blood


title: Brain-Ctrl-1683-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-PD-1893-rep1

description: Affy 6.0 PD Brain (Brodmann area 46)


title: Brain-PD-1816-rep1

description: Affy 6.0 PD Brain (Brodmann area 46)


title: Brain-PD-1891-rep1

description: Affy 6.0 PD Brain (Brodmann area 46)


title: Brain-Ctrl-1678-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1677-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1674-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1675-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1744-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1672-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1682-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1676-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-MND-1690-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-Ctrl-1740-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1673-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-MND-1665-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-Ctrl-1669-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-MND-1568-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-Ctrl-1680-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1667-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1679-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-MND-1438-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1568-rep1

description: Affy 6.0 MND Blood


title: Blood-MND-1438-rep1

description: Affy 6.0 MND Blood


title: Blood-MND-1267-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-1188-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1221-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-1221-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1140-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-1095-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1665-rep1

description: Affy 6.0 MND Blood


title: Brain-Ctrl-1168-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-MND-1267-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1188-rep1

description: Affy 6.0 MND Blood


title: Brain-Ctrl-1169-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Blood-MND-1082-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-1140-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1095-rep1

description: Affy 6.0 MND Blood


title: Brain-Ctrl-1167-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-Ctrl-1105-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Blood-MND-1083-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-1100-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-1083-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-1082-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-1062-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1081-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-1041-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1062-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-1081-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-1011-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-1003-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1003-rep1

description: Affy 6.0 MND Blood


title: Brain-Ctrl-0989-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-1041-rep1

description: Affy 6.0 MND Blood


title: Brain-Ctrl-0984-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Blood-MND-1016-rep1

description: Affy 6.0 MND Blood


title: Blood-MND-1011-rep1

description: Affy 6.0 MND Blood


title: Brain-Ctrl-0986-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: Brain-MND-0914-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-0870-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-0974-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-0899-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-0914-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-0868-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-0862-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-0899-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-0766-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-0844-rep1

description: Affy 6.0 MND Blood


title: TSWV_PrimerD_sequanase

status: Public on Jun 30 2010

type: RNA

city: Beijing

first: Yongjiang

last: Zhang

country: China

description: Tomato spotted wilt virus sample extracted from Datura stramonium. Reversely transcribed the RNA with PrimerD and synthesized the second strand with Sequenase. The product was labeled by Klenow polymerase with Cy3-CTP.

hyb_protocol: Cy3-labeled DNA fragments, pre-heated for 10 min at 80¡æ, were added to the microarray for hybridization for 16 hr at 42¡æ. Slides were washed for 4 min at 42¡æ with 2¡ÁSSC, 0.2% SDS and then washed for 4 min at 42¡æ with 0.2¡ÁSSC.

scan_protocol: The microarrays were scanned with LuxScan 3.0 (CapitalBio, China). Microarray images acquisition and signal analysis were performed using LuxScan 3.0 software.

data_processing: The signal intensity of the probes was corrected by subtracting background intensity from the feature intensity. The value in the sample table is the mean signal intensity of the replicated spots.

molecule: total RNA

organism: Orthotospovirus tomatomaculae

growth_protocol: Standard virus samples were collected from the Chinese Academy of Inspection and Quarantine (Beijing, China) and American Type Culture Collection (Manassas, VA). These viruses were used to infect plant hosts. After the plant hosts showed disease symptoms, the leaves were collected.

extract_protocol: Genomic RNA was extracted from host leaf and plant samples using TRIzol reagent (Invitrogen, CA) following the manufacture¡¯s protocols. RNA was purified by using the NucleotideSpin RNA clean-up (MN, Germany).

tag: virus

value: Tomato spotted wilt virus

tag: host

value: Datura stramonium


title: PVX_100

institute: Chinese Academy of Inspection and Quarantine

description: Potato virus X sample extracted from Chenopodium quinoa. RNA was diluted by 100 times before microarray hybridization.

organism: Potato virus X

label_protocol: First-strand reverse transcription to cDNA was initiated with a nonamer random primer. The amplified cDNA product was purified with the NucleotideSpin Extract II (MN, Germany). Cy3-dCTP was incorporated into the purified cDNA product with nonamer random primer using the Klenow fragment of DNA polymerase I.

extract_protocol: Genomic RNA was extracted from host leaf and plant samples using TRIzol reagent (Invitrogen, CA) following the manufacture¡¯s protocols. RNA was purified by using the NucleotideSpin RNA clean-up (MN, Germany). RNA was diluted by 100 times before microarray hybridization.

value: Potato virus X

value: Chenopodium quinoa


title: Blood-MND-0862-rep1

description: Affy 6.0 MND Blood


title: TSWV_PrimerD

description: Tomato spotted wilt virus sample extracted from Datura stramonium. PrimerD was used to reversely transcribe the RNA. The product was labeled by Klenow polymerase with Cy3-CTP.


title: TSWV

description: Tomato spotted wilt virus sample extracted from Datura stramonium


title: PVX_10

description: Potato virus X sample extracted from Chenopodium quinoa. RNA was diluted by 10 times before microarray hybridization.

extract_protocol: Genomic RNA was extracted from host leaf and plant samples using TRIzol reagent (Invitrogen, CA) following the manufacture¡¯s protocols. RNA was purified by using the NucleotideSpin RNA clean-up (MN, Germany). RNA was diluted by 10 times before microarray hybridization.


title: TaraxacumOfficinale

description: Taraxacum officinale sample used to testify the performance of the microarray.

organism: Taraxacum officinale

value: Taraxacum officinale


title: Brain-MND-0844-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Brain-MND-1016-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: TRSV

description: Tobacco ringspot virus sample extracted from Nicotiana tabacum

organism: Tobacco ringspot virus

value: Tobacco ringspot virus

value: Nicotiana tabacum


title: Blood-MND-0794-rep1

description: Affy 6.0 MND Blood

value: Study 1 (Somatic)

value: F


title: ZinniaElegans

description: Zinnia elegans sample used to testify the performance of the microarray.

organism: Zinnia elegans

value: Zinnia elegans


title: PVX

description: Potato virus X sample extracted from Chenopodium quinoa


title: Brain-Ctrl-0987-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)


title: PanaxNotoginseng

description: Unknown virus sample extracted from Panax notoginseng

organism: unidentified

value: Unknown virus

value: Panax notoginseng


title: PNRSV

description: Prunus necrotic ringspot virus sample extracted from Cucumis sativus

organism: Prunus necrotic ringspot virus

value: Prunus necrotic ringspot virus

value: Cucumis sativus


title: ToRSV

description: Tomato ringspot virus sample extracted from Tetragonia expansa

organism: Tomato ringspot virus

value: Tomato ringspot virus

value: Tetragonia expansa


title: Blood-MND-0556-rep1

description: Affy 6.0 MND Blood

value: M

value: MND


title: Blood-MND-0766-rep1

description: Affy 6.0 MND Blood


title: PPV

description: Plum pox virus sample extracted from Chenopodium quinoa

organism: Plum pox virus

value: Plum pox virus


title: Brain-MND-0556-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: Blood-MND-0754-rep1

description: Affy 6.0 MND Blood


title: Brain-MND-0794-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: TMV

description: Tobacco mosaic virus sample extracted from Nicotiana tabacum

organism: Tobacco mosaic virus

value: Tobacco mosaic virus


title: SBMV

description: Southern bean mosaic virus sample extracted from Phaseolus vulgaris

organism: Southern bean mosaic virus

value: Southern bean mosaic virus

value: Phaseolus vulgaris


title: ArMV

description: Arabis mosaic virus sample extracted from Chenopodiun amaranticolor

organism: Arabis mosaic virus

value: Arabis mosaic virus

value: Chenopodiun amaranticolor


title: Blood-MND-0329-rep1

description: Affy 6.0 MND Blood

value: Study 1 (Somatic)


title: Brain-MND-0329-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: TAX577014

status: Public on Jun 24 2010

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, (3) background corrected intensity value <0 signal units. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Prior to normalization only oligonucleotide probes without cross-hybridization to other genomic regions or transcripts were selected. Normalization was performed using block (print tip) based lowess. After normalization, a probe presence filter was applied to select only probes with suffcient presence, followed by imputation of missing values using weighted nearest-neighbor imputation (WENNI). Probes were subsequently merged on probe identifier and row-centered across the entire data set.

source_name: Breast tumor

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions from 5ug of total RNA using the Corning Pronto Plus System 6 kit as described (PMID:17334996).

extract_protocol: Total RNA from fresh frozen breast tumor tissue was extracted using Trizol reagent (Invitrogen) followed by the RNeasy Midi Purification kit (Qiagen). RNA concentrations were measured using a Nanodrop (NanoDrop Technologies). RNA integrity was determined by an Agilent Bioanalyzer.

tag: tissue

value: Breast tumor

tag: hu subtype

tag: familial status

value: sporadic

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: genomic subtype

tag: brca status

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status

value: negative

source_name: Stratagene Universal reference RNA

tag: reference

value: Stratagene Universal reference RNA


title: TAX577485


title: TAX577001


title: TAX577049

value: familial

value: brcax


title: TAX577422


title: TAX577462

value: LumB


title: Blood-MND-0539-rep1

description: Affy 6.0 MND Blood

tag: study #

tag: trio #

tag: twin #

tag: twin info

tag: gender

tag: phenotype


title: Brain-MND-0754-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)

value: F


title: TAX577515

tag: tissue

tag: hu subtype

tag: familial status

tag: er

tag: osbin


title: Brain-MND-0539-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)

value: M


title: Blood-MND-0311-rep1

description: Affy 6.0 MND Blood

value: MND


title: TAX577490

tag: os

tag: pgr

tag: primary

tag: grade

tag: genomic subtype


title: TAX577331

value: Basal

tag: brca status

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: Brain-MND-0311-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)

tag: study #

tag: trio #

tag: twin #

tag: twin info

tag: gender


title: BPMV

description: Bean pod mottle virus sample extracted from Glycine max

organism: Bean pod mottle virus

tag: virus

value: Bean pod mottle virus

tag: host

value: Glycine max


title: TAX577002

tag: tissue

tag: hu subtype

tag: familial status

tag: er

tag: osbin

tag: os


title: Brain-Ctrl-0985-rep1

description: Affy 6.0 Ctrl Brain (Brodmann area 46)

tag: phenotype

value: Ctrl


title: TAX577088

tag: pgr

tag: primary

tag: grade

tag: genomic subtype

tag: brca status

tag: pam50 classification

tag: pam50 correlation


title: TAX577033

tag: brca1 methylation status

tag: reference


title: Blood-Ctrl-1839-rep1

description: Affy 6.0 Ctrl Blood

tag: study #

value: Coriell GM10851

tag: trio #

tag: twin #

tag: twin info

tag: gender


title: Brain-MND-0302-rep1

description: Affy 6.0 MND Brain (Brodmann area 46)


title: TAX577420

tag: tissue

tag: hu subtype

tag: familial status

tag: er

tag: osbin


title: TAX577435

tag: os

tag: pgr

tag: primary

tag: grade


title: Blood-MND-0974-rep1

description: Affy 6.0 MND Blood

tag: phenotype


title: Blood-MND-0302-rep1

description: Affy 6.0 MND Blood


title: TAX577015

tag: genomic subtype

tag: brca status

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status


title: TAX577032

value: Normal

tag: reference


title: TAX577042


title: TAX577053


title: Blood-MND-0870-rep1

description: Affy 6.0 MND Blood

tag: study #

value: Study 1 (Somatic)

tag: trio #

tag: twin #

tag: twin info

tag: gender


title: TAX577040

tag: tissue

value: Breast tumor

tag: hu subtype

tag: familial status

tag: er

tag: osbin


title: TAX577031

tag: os

tag: pgr

tag: primary

tag: grade


title: TAX577048

tag: genomic subtype

tag: brca status

tag: pam50 classification

tag: pam50 correlation


title: TAX577013

tag: brca1 methylation status

tag: reference


title: TAX577436


title: TAX577306


title: TAX577354


title: TAX577034


title: TAX577302

value: sporadic


title: TAX577281


title: TAX577047


title: Blood-Ctrl-1838-rep1

description: Affy 6.0 Ctrl Blood

tag: study #

value: Coriell GM15510

tag: trio #

tag: twin #

tag: twin info

tag: phenotype


title: TAX577461

tag: tissue

tag: hu subtype

tag: familial status

tag: er

value: negative

value: Stratagene Universal reference RNA


title: TAX577022

value: familial

tag: osbin

tag: os

tag: pgr

tag: primary

value: brcax


title: TAX577043

tag: grade

tag: genomic subtype

tag: brca status

tag: pam50 classification


title: TAX577290

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: TAX577446


title: Blood-MND-0868-rep1

description: Affy 6.0 MND Blood

tag: study #

tag: trio #

tag: twin #

tag: twin info

tag: gender

value: F


title: TAX577052

tag: tissue

tag: hu subtype

tag: familial status

tag: er


title: TAX577305

tag: osbin

tag: os

tag: pgr

tag: primary


title: TAX577544

tag: grade

tag: genomic subtype

tag: brca status

tag: pam50 classification


title: TAX577417

tag: pam50 correlation

tag: brca1 methylation status

tag: reference


title: TAX577522

value: LumB


title: TAX577214

value: LumA


title: TAX577304


title: TAX577129

value: other


title: TAX577353

value: Basal

value: Basal-complex


title: TAX577128


title: TAX577036

value: nonClassified


title: TAX577492


title: TAX577148


title: TAX577012


title: TAX577455


title: TAX577153


title: TAX577259


title: TAX577338


title: TAX577172


title: TAX577399


title: TAX577343


title: TAX577038


title: TAX577287


title: TAX577412


title: TAX577018


title: TAX577390


title: TAX577429


title: TAX577339


title: TAX577330


title: TAX577122


title: TAX577380


title: TAX577452


title: TAX577284


title: TAX577571


title: TAX577411

value: positive


title: TAX577329


title: TAX577276

value: Normal


title: TAX577371


title: TAX577362


title: TAX577360


title: TAX577379


title: TAX577345


title: TAX577386


title: TAX577370


title: TAX577375


title: TAX577372


title: TAX577347


title: TAX577357


title: TAX577346


title: TAX577335


title: TAX577408


title: TAX577406


title: TAX577365


title: TAX577351


title: TAX577403


title: TAX577332


title: TAX577361


title: TAX577377


title: TAX577367


title: TAX577009


title: TAX577425


title: TAX577396


title: TAX577497


title: TAX577495


title: TAX577265


title: TAX577369


title: TAX577404


title: TAX577496


title: TAX577359


title: TAX577413


title: TAX577263


title: TAX577368


title: TAX577525

value: Luminal-complex


title: TAX577449

value: Breast tumor


title: TAX577376

value: sporadic


title: TAX577409


title: TAX577337


title: TAX577378


title: TAX577008


title: TAX577279


title: TAX577171


title: TAX577407


title: TAX577395


title: TAX577570


title: TAX577426


title: TAX577068


title: TAX577070


title: TAX577325


title: TAX577044


title: TAX577218


title: TAX577352


title: TAX577117


title: TAX577166


title: TAX577159


title: TAX577195


title: TAX577164


title: TAX577228


title: TAX577162


title: TAX577573


title: TAX577307


title: TAX577500


title: TAX577198


title: TAX577057


title: TAX577005


title: TAX577197


title: TAX577179


title: TAX577170


title: TAX577207


title: TAX577233


title: TAX577188


title: TAX577465


title: TAX577204


title: TAX577499


title: TAX577235


title: TAX577313


title: TAX577139


title: TAX577545

value: Unclassified


title: TAX577524


title: TAX577200


title: TAX577124


title: TAX577199


title: TAX577423

value: negative


title: TAX577439

value: Stratagene Universal reference RNA


title: TAX577421


title: TAX577549


title: TAX577114


title: TAX577553


title: TAX577161

value: familial


title: TAX577010

value: brcax


title: TAX577055


title: TAX577225


title: TAX577567


title: TAX577062


title: TAX577212


title: TAX577453


title: TAX577182


title: TAX577441


title: TAX577203


title: TAX577503


title: TAX577511


title: TAX577456


title: TAX577457


title: TAX577183


title: TAX577488


title: TAX577458


title: TAX577447


title: TAX577231


title: TAX577194


title: TAX577479


title: TAX577577


title: TAX577556


title: TAX577424


title: TAX577181


title: TAX577184


title: TAX577433


title: TAX577191


title: TAX577249


title: TAX577432


title: TAX577541


title: TAX577469


title: TAX577466


title: TAX577470


title: TAX577230


title: TAX577201


title: TAX577253


title: TAX577260


title: TAX577196


title: TAX577076


title: TAX577454


title: TAX577073


title: TAX577475


title: TAX577174


title: TAX577316


title: TAX577061


title: TAX577209


title: TAX577145


title: TAX577569


title: TAX577060


title: TAX577187


title: TAX577069


title: TAX577314

value: Luminal-simple


title: TAX577189

value: LumB


title: TAX577322


title: TAX577116

value: LumA


title: TAX577210


title: TAX577193


title: TAX577064


title: TAX577059


title: TAX577108


title: TAX577554


title: TAX577112


title: TAX577093


title: TAX577135


title: TAX577222


title: TAX577242


title: TAX577546


title: TAX577324


title: TAX577221


title: TAX577555


title: TAX577256


title: TAX577125


title: TAX577543


title: TAX577220


title: TAX577529


title: TAX577552


title: TAX577119


title: TAX577098


title: TAX577091


title: TAX577240


title: TAX577219


title: TAX577097


title: TAX577547


title: TAX577158


title: TAX577252


title: TAX577286


title: TAX577226


title: TAX577113


title: TAX577508


title: TAX577150


title: TAX577476


title: TAX577224


title: TAX577268


title: TAX577510


title: TAX577563


title: TAX577257


title: TAX577178


title: TAX577134


title: TAX577297

value: amplifier


title: TAX577444

value: other


title: TAX577107


title: TAX577143


title: TAX577323


title: TAX577442


title: TAX577175


title: TAX577542


title: TAX577137


title: TAX577471


title: TAX577261

value: Basal


title: TAX577484

value: nonClassified


title: TAX577557


title: TAX577550


title: TAX577478


title: TAX577111


title: TAX577539


title: TAX577560


title: TAX577472


title: TAX577300


title: TAX577519


title: TAX577531


title: TAX577215


title: TAX577566


title: TAX577536


title: TAX577216


title: TAX577173


title: TAX577350

value: positive


title: TAX577448


title: TAX577205


title: TAX577394


title: TAX577364


title: TAX577303

value: Normal


title: TAX577227


title: TAX577430


title: TAX577289


title: TAX577104


title: TAX577149


title: TAX577234


title: TAX577275


title: TAX577151


title: TAX577237


title: TAX577438

value: Luminal-complex


title: TAX577186

value: Breast tumor


title: TAX577011

value: sporadic


title: TAX577358


title: TAX577163


title: TAX577072


title: TAX577045


title: TAX577527

value: Unclassified


title: TAX577285


title: TAX577211

value: mixed


title: TAX577274

value: Stratagene Universal reference RNA


title: TAX577576

value: familial


title: TAX577565

value: brcax


title: TAX577574

value: negative


title: TAX577518


title: TAX577133


title: TAX577236

value: LumB


title: TAX577136

value: LumA


title: TAX577190


title: TAX577526


title: TAX577208


title: TAX577535

value: Luminal-simple


title: TAX577572

value: amplifier


title: TAX577473


title: TAX577564


title: TAX577387

value: Basal


title: TAX577477

value: nonClassified


title: TAX577483


title: TAX577155


title: TAX577443

value: other


title: TAX577505


title: TAX577450

value: Normal


title: TAX577243


title: TAX577277


title: TAX577223


title: TAX577327


title: TAX577298


title: TAX577320


title: TAX577334

value: positive


title: TAX577393

value: Breast tumor


title: TAX577388

value: sporadic


title: TAX577538

value: Luminal-complex

value: Unclassified


title: TAX577575

value: mixed

value: Stratagene Universal reference RNA


title: TAX577152


title: TAX577024


title: TAX577016


title: TAX577530


title: TAX577486


title: TAX577548


title: TAX577147


title: TAX577192


title: TAX577066


title: TAX577067


title: TAX577087


title: TAX577039

value: familial

value: brcax


title: c58-6h-DexDox-II

status: Public on May 07 2010

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

hyb_protocol: The chips were stained and washed in an Affymetrix fluidic station 450S.

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.

data_processing: The analysis of exon microarrays was based on a custom CDF (CEL definition file) that allowed generating expression intensities of transcripts by summarizing the intensity signals of the individual oligonucleotide probes on the microarray targeting a particular transcript. In brief, the sequences of the >5 million 25nt-long oligonucleotide probes on the Affymetrix Exon array (HuEx-1.0-st v2) were aligned to the genomic DNA sequence from Ensembl (version 52_36n). For all probes with a single complete alignment and no additional alignments with up to 1 miss match we determined whether the alignment was within the exon boundaries of a gene.  Probes with sequences with a G/C content >18 were excluded from the analysis. Exon boundaries and transcript definitions were taken from the Ensembl core database for all known protein- and non-coding transcript and from the ASTD database (version 1.1) for all potential isoforms of a gene. Preprocessing and all further data analyses were performed in R (version 2.8.0) using packages from Bioconductor (version 2.3)  and the custom CDF file described above. The raw signal intensities where preprocessed using the GCRMA algorithm, where the “background probes” were used to predict the non-specific binding potential of the oligonucleotide probes. After preprocessing, the transcript with the highest variance across all samples was selected for further analysis as representative for a given gene.

label_protocol: Total RNA was depleted of ribosomal RNA and transcribed into cDNA using T7-promoter-tagged hexamer primers. Antisense RNA was produced by T7-polymerase and transcribed into cDNA using random priming in the presence of dUTP which was used to enzymatically fragment the cDNA.

growth_protocol: Cultured under standard conditions (37°C, 5% CO2, saturated humidity).

extract_protocol: Total RNA was extracted.

treatment_protocol: To determine ZBTB16 response genes, C7H2-2C8-ZBTB16#19 and #58 cells (expressing ZBTB16 in a doxycycline-dependent manner) were cultured in duplicates in the absence (set A) or presence (set B) of 400ng/ml doxocycline for 2h, 6h or 24h. Total RNA was prepared and 1.5 µg RNA subjected to expression profiling on Exon 1.0 microarrays (total of 24 arrays) as detailed previously [17683]. To assess the effect of ZBTB16 on the GC response, the above cell lines were cultured for 24h in the absence (set C) or presence (set D) of 200ng/ml doxycycline and subsequently exposed to 10-8M dexamethasone for 6h and 24h and expression-profiled as above resulting in a total of 15 arrays.

tag: cell ine

tag: treatment

value: DexDox

tag: time [h]

tag: experiment nr

value: II

tag: clone nr


title: c58-24h-DexDox-III

value: III


title: c58-xh-Dox-II

value: Dox


title: c58-24-EtOH-I

value: I


title: c19-6h-DexDox-III


title: c58-6-Dox-II


title: c58-24h-DexDox-I


title: c58-24h-Dex-II

value: Dex


title: c58-24-Dox-I


title: c58-6-Dox-I


title: c19-24h-DexDox-III


title: c19-24h-DexDox-II


title: c19-24h-Dex-II


title: c58-24h-Dex-III


title: c58-6h-Dex-III


title: c19-6h-DexDox-II


title: TAX577427

tag: tissue

tag: hu subtype

value: Basal

tag: familial status

tag: er


title: c58-24-EtOH-II


title: c58-2-Dox-I


title: c19-6h-Dex-III


title: c19-6h-Dex-II


title: c58-6-EtOH-I


title: c58-24-Dox-II


title: c58-2-EtOH-II


title: c58-6h-DexDox-III


title: c58-2-EtOH-I


title: c19-24h-Dex-III


title: c19-24h-Dox-II


title: Whole Blood Chamber Control 4_5529

status: Public on Apr 25 2010

city: Tübingen

first: Gabriel

last: Willmann

address: Schleichstrasse 12-16

country: Germany

institute: University Eye Hospital and Centre for Ophthalmology Tübingen

description: Whole Blood was drawn from V. Cava.

hyb_protocol: 15 micrograms of labeled cRNA from whole blood was fragmented, and 10ug was hybridized to Affymetrix Mouse 430 2.0 GeneChip arrays for 18-24h (Affymetrix Inc.). Gene chip was washed and stained with streptavidin-phycoerythrin.

scan_protocol: The chip was scanned at 6um resolution with Agilant model G2500A Gene Array scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.

data_processing:
Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. In addition, raw intensities for each probe set were stored in electronic formats by the GeneChip operating system 1.1 (Affymetrix) for GC-RMA analysis in PARTEK software later on.
NOTE: RMA data currently unavailable. Sample data table reports CHP data.

label: Biotin

organism: Mus musculus

source_name: Whole Blood

label_protocol: Three microliter total RNA was used for each sample to obtain linearly amplified labeled cRNA by using GeneChip® One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA, USA) as described by manufacturer. Briefly, total RNA was used to generate double-stranded cDNA with the T7-oligo (dT) primer. This double-stranded cDNA was used in vitro transcription and biotin labeling steps. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280nm. All the cRNA 260/280 ratios were between 1.9 and 2.1. Quality control of the labeled cRNA products was assessed by performing 1µg labeled cRNA on 2% agarose gel to see similar RNA smear type.

extract_protocol: Total RNA was isolated and purified from 100ul of whole blood with the Mouse Ribopure-Blood RNA Isolation Kit (Ambion, Austin, Texas, USA) according to manufacturers instructions.

tag: stress

value: control


title: Whole Blood Chamber Hypoxia 1_5531

description: Whole Blood was drawn from V. Cava.

extract_protocol: Total RNA was isolated and purified from 500ul of whole blood with the Mouse Ribopure-Blood RNA Isolation Kit (Ambion, Austin, Texas, USA) according to manufacturers instructions.

treatment_protocol: At the beginning of the experiment mice were divided into two groups, control (room condition) and hypoxic (hypoxic condition). For conditioning, the hypoxic group was exposed to lower levels of hypoxia, in a specially designed and hermetically closed hypoxic chamber, using a special gas mixing system Pegas 4000 MF (Columbus Instruments, Ohio, USA). The oxygen level was decreased from 21% to 8% over a period of 14 days. Animal’s weight and food intake were monitored daily. Food and water were changed daily during the course of the experiment. Before and after the experiments the hematocrit was monitored by taking blood from the tail vein of control and hypoxic animals. After 15 days animals were euthanized using CO2 after whole blood extraction from V. Cava for further analysis.

value: normobaric hypoxia


title: c58-6-EtOH-II


title: Whole Blood Chamber Hypoxia 4_5536

description: Whole Blood was drawn from V. Cava.


title: Whole Blood Chamber Hypoxia 3_5535

description: Whole Blood was drawn from V. Cava.


title: c58-2-Dox-II


title: c19-2h-EtOH-III


title: Whole Blood Chamber Control 3_5527

description: Whole Blood was drawn from V. Cava.


title: c19-24h-EtOH-II


title: c19-6h-EtOH-I


title: Whole Blood Chamber Hypoxia 2_5533

description: Whole Blood was drawn from V. Cava.


title: c19-24h-Dox-I


title: c19-6h-EtOH-II


title: c19-2h-Dox-III


title: c19-24h-EtOH-I


title: c19-2h-Dox-II


title: Whole Blood chamber Control 1_5525

description: Whole Blood was drawn from V. Cava.


title: c19-2h-EtOH-II


title: c19-6h-Dox-II


title: Subject #20_replicate_2_direct

status: Public on Apr 20 2010

city: New York

first: Juan

last: Ruano

state: NY

address: 1230 York ave

country: USA

institute: Rockefeller University

hyb_protocol: Differentially labeled aRNA samples were cohybridized on microarray slides. Hybridization was carried out using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions. Briefly, 825 ng of each fluorescent-labeled aRNA sample was mixed with blocking reagent and fragmentation buffer and incubated 30 min at 60º. Hybridization was done at 65°C for 17 h at continuous rotation of the hybridization chambers according to the Agilent manual. Slides were disassembled and washed in solutions I and II, and dried using a nitrogen-filled air gun before scanning.

scan_protocol: Microarray images were obtained by scanning each slide using a Gene Pix 4000B scanner (Axon Instruments, Union City, CA). Image quantitation was performed using Agilent Feature Extraction Software v9.5 (Agilent Technologies Inc., Santa Clara, CA, USA).

data_processing: For the Agilent oligonucleotide arrays, the background adjusted signals (BGSubSignal) calculated by the Agilent Feature Extraction Software (v9.5) were used, filtered on the flag IsWellAboveBG. Log2 dye swaped (red/green) mean-centered signal ratio data were within-array and between-array normalized by lowess and quantile methods respectively, both implemented in the R Limma package (GLP).

source_name: PBMCs_total RNA_ phenol-rich virgin olive oil (397 ppm)

label_protocol: RNA samples were labeled using the SuperScript Indirect RNA Amplification System (Invitrogen Inc., Carlsbad, CA, USA) according to the manufacturer's instructions. To avoid confounding by extraneous factors, all the experiments were performed in a single batch and processed by one researcher on the same day for each step. Briefly, 1 μg of total RNA was reverse transcribed using SuperScript III Reverse Transcriptase and second strand synthesized by the DNA Polymerase I and DNA Ligase. Amplification and amino-allyl labeling were performed by T7 RNA polymerase in vitro transcription, to give amino-allyl UTP labeled RNA (aRNA). aRNA samples from PBMCs obtained after the intake of high and low phenol olive oils were labeled with Alexa Fluor 555 and Alexa Fluor 647 dyes (Invitrogen Inc., Carlsbad, CA, USA). The dye incorporation rate was assessed with a Nanodrop ND-1000 v3.5.2 spectrophotometer (Nanodrop Technology, Cambridge, UK) and was found to be between 8 and 12 pmol.μL-1.

growth_protocol: Two virgin olive oil-based breakfasts with high (398 ppm) and low (70 ppm) content of phenolic compounds were administered to all the patients following a double-blinded random crossover design in a single dosis two different mornings with a wash-out peridod of one-week between them.

extract_protocol: Venous blood samples were obtained at 0 min and 240 min after consumption of each olive oil-based breakfast. Samples from the fasting and postprandial states were collected in tubes containing 1 g EDTA/L and were stored in containers with ice and kept in the dark. Special care was taken to avoid exposure to air, light, and ambient temperature. PBMCs were isolated within 2 h after blood draw from 30 mL EDTA anticoagulated blood samples taken 4 hours after the consumption of each olive oil-based breakfast. Buffy coats were diluted 1:2 in PBS, and cells were separated in 5 mL Ficoll gradient (lymphocyte isolation solution, Rafer) by centrifugation at 2000 x g for 30 min. PBMCs were collected and washed twice with cold PBS.  Harvested PBMCs were preserved in liquid nitrogen and stored at -80ºC prior to RNA extraction. Total RNA was extracted from mononuclear cells by using of TRI Reagent (Sigma-Aldrich, Inc., St. Louis, MO, USA) and then cleanup by RNeasy MiniElute Cleanup Kit (Qiagen, Hilden, Germany). Recovered RNA was quantified using a Nanodrop ND-1000 v3.5.2 spectrophotometer (Nanodrop Technology, Cambridge, UK). RNA integrity was assessed using 1.6% agarose gel, TBE 1x. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to 18S and 28S ribosomal RNA subunits.

treatment_protocol: Prior to the first breakfast intervention, participants followed a 6-week washout period in which they were instructed to not take vitamins, soy supplements, or any drug. To eliminate the potential effect that might exist in their usual dietary habits, all subjects followed a low-fat, carbohydrate rich (CHO) diet during this period and untill the end of the study. In the 24 h before each breakfast intervention, participants were instructed to avoid consuming phenol-rich foods such as fruit or juices, wine, grape juice, chocolate, coffee, tea, olive oil, or soya, and to refrain from intense physical exercise during that period. After a 12 h fasting and following a randomized sequential crossover design with one-week washout period, participants reported to the hospital and received two fat meals consisting of 60 g of white bread, 40 mL of VOO (CANOLIVA®, Antonio Cano e Hijos™, Córdoba, Spain) with high (398 ppm) or low (70 ppm) content in phenolic compounds, and 60,000 IU of vitamin A per m2 of body surface. Olive oil with low content in phenolic compounds was obtained as a result of extraction by physical procedures of most of the phenolic compounds in the high-phenol olive oil, so that both oils kept a similar composition of the remaining macro- and micronutrients.

value: Periferal blood mononuclear cells

tag: time

value: 4 hours after olive oil intake

tag: gender

value: woman

source_name: PBMCs_total RNA_ low phenol virgin olive oil (70 ppm)


title: Subject #20_replicate_2_dye swap

description: Sub#20_rep_2_dye swap.txt


title: Subject #18_replicate_2_dye swap

description: Sub#18_rep_2_dye swap.txt


title: Subject #18_replicate_1_direct


title: Subject #20_replicate_1_dye swap

description: Sub#20_rep_1_dye swap.txt


title: Subject #19_replicate_1_direct


title: Subject #19_replicate_2_dye swap

description: Sub#19_rep_2_dye swap.txt


title: Subject #19_replicate_2_direct


title: Subject #18_replicate_2_direct


title: Subject #18_replicate_1_dye swap

description: Sub#18_rep_1_dye swap.txt


title: Subject #20_replicate_1_direct


title: Subject #17_replicate_1_direct

value: man


title: Subject #19_replicate_1_dye swap

description: Sub#19_rep_1_dye swap.txt


title: Subject #17_replicate_2_dye swap

description: Sub#17_rep_2_dye swap.txt


title: Subject #17_replicate_1_dye swap

description: Sub#17_rep_1_dye swap.txt


title: c19-6h-Dox-I


title: Subject #17_replicate_2_direct


title: Subject #15_replicate_2_dye swap

description: Sub#15_rep_2_dye swap.txt


title: Subject #16_replicate_2_dye swap

description: Sub#16_rep_2_dye swap.txt


title: Subject #12_replicate_2_dye swap

description: Sub#12_rep_2_dye swap.txt


title: Subject #13_replicate_1_direct


title: Subject #16_replicate_1_direct


title: Subject #15_replicate_2_direct


title: Subject #16_replicate_2_direct


title: Subject #14_replicate_1_direct


title: Subject #13_replicate_2_direct


title: Subject #15_replicate_1_direct


title: Subject #13_replicate_2_dye swap

description: Sub#13_rep_2_dye swap.txt


title: Subject #16_replicate_1_dye swap

description: Sub#16_rep_1_dye swap.txt


title: Subject #14_replicate_2_dye swap

description: Sub#14_rep_2_dye swap.txt


title: Subject #14_replicate_1_dye swap

description: Sub#14_rep_1_dye swap.txt


title: Subject #14_replicate_2_direct


title: Subject #10_replicate_1_direct


title: Subject #11_replicate_2_direct


title: Subject #12_replicate_1_direct


title: Subject #12_replicate_2_direct


title: Subject #10_replicate_2_direct


title: Subject #11_replicate_1_dye swap

description: Sub#11_rep_1_dye swap.txt


title: Subject #15_replicate_1_dye swap

description: Sub#15_rep_1_dye swap.txt


title: Subject #11_replicate_1_direct


title: Subject #12_replicate_1_dye swap

description: Sub#12_rep_1_dye swap.txt


title: Subject #11_replicate_2_dye swap

description: Sub#11_rep_2_dye swap.txt


title: Subject #13_replicate_1_dye swap

description: Sub#13_rep_1_dye swap.txt


title: Whole Blood Chamber Control 2_5526

description: Whole Blood was drawn from V. Cava.


title: Subject #9_replicate_2_dye swap

description: Sub#9_rep_2_dye swap.txt


title: Subject #10_replicate_2_dye swap

description: Sub#10_rep_2_dye swap.txt


title: Subject #5_replicate_2_direct


title: Subject #8_replicate_1_direct


title: Subject #9_replicate_1_direct


title: Subject #9_replicate_2_direct


title: Subject #8_replicate_2_dye swap

description: Sub#8_rep_2_dye swap.txt


title: Subject #5_replicate_2_dye swap

description: Sub#5_rep_2_dye swap.txt


title: Subject #7_replicate_1_direct


title: Subject #9_replicate_1_dye swap

description: Sub#9_rep_1_dye swap.txt


title: Subject #7_replicate_1_dye swap

description: Sub#7_rep_1_dye swap.txt


title: Subject #6_replicate_1_direct


title: Subject #4_replicate_2_dye swap

description: Sub#4_rep_2_dye swap.txt


title: Subject #8_replicate_1_dye swap

description: Sub#8_rep_1_dye swap.txt


title: Subject #4_replicate_1_direct


title: Subject #10_replicate_1_dye swap

description: Sub#10_rep_1_dye swap.txt


title: Subject #8_replicate_2_direct


title: Subject #6_replicate_2_direct


title: Subject #4_replicate_2_direct


title: Subject #6_replicate_2_dye swap

description: Sub#6_rep_2_dye swap.txt


title: Subject #3_replicate_1_dye swap

description: Sub#3_rep_1_dye swap.txt


title: Subject #5_replicate_1_dye swap

description: Sub#5_rep_1_dye swap.txt


title: Subject #7_replicate_2_dye swap

description: Sub#7_rep_2_dye swap.txt


title: Subject #2_replicate_2_dye swap

description: Sub#2_rep_2_dye swap.txt


title: Subject #4_replicate_1_dye swap

description: Sub#4_rep_1_dye swap.txt


title: Subject #3_replicate_2_dye swap

description: Sub#3_rep_2_dye swap.txt


title: Subject #6_replicate_1_dye swap

description: Sub#6_rep_1_dye swap.txt


title: Subject #3_replicate_2_direct


title: Subject #7_replicate_2_direct


title: Subject #5_replicate_1_direct


title: Subject #3_replicate_1_direct


title: Subject #2_replicate_1_dye swap

description: Sub#2_rep_1_dye swap.txt


title: Subject #1_replicate_2_dye swap

description: Sub#1_rep_2_dye swap.txt


title: Subject #2_replicate_2_direct


title: Subject #2_replicate_1_direct


title: Subject #1_replicate_1_dye swap

description: Sub#1_rep_1_dye swap.txt


title: Subject #1_replicate_1_direct


title: erStress_twins_Cauc_HB02069_500nM_thapsigargin_4h

status: Public on Mar 30 2010

city: Philadelphia

first: Renuka

last: Nayak

state: PA

address: 3516 Civic Center Blvd

institute: HHMI, University of Pennsylvania

description:
Gene expression data under ER stress from lymphoblastoid cells of twin HB02069 treated with 500nM thapsigargin.
The Family ID is REQ115 and the individual IDs are HB02069 and HB02070.
HB02069 and HB02070 are a pair of twins, but they were not obtained from Coriell.  They were obtained from HBDI.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Lymphoblastoid cell lines derived from family REQ115, member 1

label_protocol: Biotinylated cRNA were prepared according to the Ambion MessageAmp Premier RNA Amplification Kit protocol from 500 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

growth_protocol: The cells were grown at a density of 1 million cells/ ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.

extract_protocol: RNA was extracted using the Rneasy Mini-Kit (Qiagen) as per the manufacturer's instructions

treatment_protocol: 500nM thapsigargin 4 hours

tag: cell line

value: lymphoblastoid cell line

tag: family id

tag: individual id

tag: individual

value: Twin number 1

tag: agent

value: thapsigargin

tag: dose

value: 4 hours


title: erStress_twins_Cauc_HB02070_500nM_thapsigargin_4h

description:
Gene expression data under ER stress from lymphoblastoid cells of twin HB02070 treated with 500nM thapsigargin.
The Family ID is REQ115 and the individual IDs are HB02069 and HB02070.
HB02069 and HB02070 are a pair of twins, but they were not obtained from Coriell.  They were obtained from HBDI.

source_name: Lymphoblastoid cell lines derived from family REQ115, member 2

value: Twin number 2


title: Subject #1_replicate_2_direct


title: erStress_twins_Cauc_HB02069_DMSO_4h

description:
Gene expression data under ER stress from lymphoblastoid cells of twin HB02069 treated with DMSO.
The Family ID is REQ115 and the individual IDs are HB02069 and HB02070.
HB02069 and HB02070 are a pair of twins, but they were not obtained from Coriell.  They were obtained from HBDI.

treatment_protocol: DMSO 4 hours

value: DMSO


title: erStress_twins_Cauc_HB02070_DMSO_4h

description:
Gene expression data under ER stress from lymphoblastoid cells of twin HB02070 treated with DMSO.
The Family ID is REQ115 and the individual IDs are HB02069 and HB02070.
HB02069 and HB02070 are a pair of twins, but they were not obtained from Coriell.  They were obtained from HBDI.


title: Tumor_case42

status: Public on Mar 17 2010

city: Frankfurt am Main

first: Sylvia

last: Hartmann

department: Pathology

institute: University Frankfurt

description:
PTCL NOS
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

hyb_protocol: Affymetrix 500k SNP array manual

scan_protocol: Affymetrix 500k SNP array manual

data_processing: GCOS, GTYPE, CNAG, CNAT, dCHIP, BRLMM

source_name: lymph node

label_protocol: Affymetrix 500k SNP array manual

extract_protocol: Qiagen DNA Mini Kit

tag: disease state

value: tumor

value: lymph node


title: Tumor_case37


title: Tumor_case46


title: Tumor_case40


title: Tumor_case39


title: Tumor_case32


title: Tumor_case44


title: Tumor_case38


title: Tumor_case35


title: Tumor_case41


title: Tumor_case34


title: Tumor_case43


title: Tumor_case33


title: Tumor_case45


title: Tumor_case18


title: Tumor_case27


title: Tumor_case30


title: Tumor_case47


title: Tumor_case29


title: Tumor_case23


title: Tumor_case26


title: Tumor_case31


title: Tumor_case25


title: Tumor_case21


title: Tumor_case22


title: Tumor_case19


title: Tumor_case36


title: Tumor_case20


title: Tumor_case24


title: Tumor_case28


title: Tumor_case17


title: Tumor_case11


title: Tumor_case12


title: Tumor_case13


title: Tumor_case15


title: Tumor_case2


title: Tumor_case5


title: Tumor_case9


title: Tumor_case14


title: Tumor_case4


title: Tumor_case1


title: Tumor_case7


title: Tumor_case8


title: Normal_N5

description:
healthy reference
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: peripheral blood

value: normal

value: peripheral blood


title: Normal_D07-5


title: Normal_D07-7


title: Normal_D07-6


title: Tumor_case16


title: Tumor_case6


title: Tumor_case10


title: CF HI2424 vs. J2315 4, dye swap

status: Public on Dec 01 2009

city: Boston

first: Deborah

middle: R.

last: Yoder-Himes

state: MA

address: 77 Louis Pasteur Ave, 1038 NRB

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

description: Biological replicate 4 of 4.

hyb_protocol: Hybridization and washing of quadruplicate arrays including a single dye swap was performed according to the “Two-colour microarray based gene expression analysis” protocol from Agilent (version 5.5, Feb. 2007) with the following changes: for hybridization the 25x fragmentation buffer was omitted; the mix of cDNAs and 10x Blocking Agent was heat-denatured for 3 min at 98ºC and cooled to room temperature before adding the hybridization buffer; the post-hybridization microarray washing included the optional acetonitrile and Stabilization and Drying Solution (Agilent).

scan_protocol: The microarrays were scanned with the G2565 BA microarray scanner (Agilent) and the Scan Control software version A.7.0.3 Feb 2007 (Agilent). The scanning resolution was set to 5 μm and the scan region was adjusted to 61 x 21.6 mm. The Extended Dynamic Range function was switched on with 100% and 10% PMT gain settings.

data_processing: The images were analyzed with the Feature Extraction software, version 9.5.1 February 2007 (Agilent). The FE protocol used was GE2_v5_95_Feb07 with the default setting maintained.  Flagged spots were removed in GeneSpring GX 7.3.1 analysis software. GeneSpring data available on Series record.

organism: Burkholderia cenocepacia

source_name: HI2424 CF-grown cells

label_protocol: cDNA generation and labeling was performed using the CyScribe Post-Labeling kit (GE Healthcare) according to the manufacturers protocol with the following exceptions: Spike-In controls (Agilent) were included into the labeling procedure for quality control purposes; the second dilution of the Spike-In control was added to the primer annealing mix.  For primer annealing the following quantities were used: 10 μg total RNA, 2 μl random nonamers, 1 μl anchored oligo(dT), 2 μl Agilent Spike-In control, and water to 11 μl.  The cDNA purification was performed by ethanol precipitation and the labeled cDNA was purified using the CyScribe GFX purification kit. For the elution from the GFX columns, water was used instead of the elution buffer from the kit.

growth_protocol: Cells were grown in liquid cultures on shakers at 250 rpm at 37°C in respective media.  Cells were grown until the O.D.600s listed with the samples above.

extract_protocol: Total RNA was purified by the RiboPure Kit (Ambion, Austin, TX) with the following exceptions: 2 x 2 mL of fresh culture was used for each biological replicate; cells were cup-sonicated 3 x 12 seconds (90% duty cycle, 70% output cycle, W-385 sonicator, Misonix, Inc, Farmingdale, NY) on ice after resuspension in RNAwiz reagent to encourage lysis; an 1-hr incubation of the samples with DNase I was used.  RNA quality and concentration was measured using Agilent’s RNA 6000 Pico kit and 2100 Bioanalyzer machine.  Only samples with RNA integrity numbers greater than 8.0 were used for microarray experiments.

tag: growth

value: mid-log phase, OD600~1.0

tag: strain

source_name: J2315 CF-grown cells


title: Normal_N9


title: Tumor_case3


title: CF J2315 vs. HI2424 3

description: Biological replicate 3 of 4.


title: Normal_N8


title: Normal_N4


title: Normal_N2


title: Normal_D07-3


title: DirectRandom_B_3

status: Public on Nov 25 2009

city: Emeryville

first: Mario

last: Ouellet

state: CA

address: 5885 Hollis St., 4th Floor

institute: Joint BioEnergy Institute

description: no additional information

hyb_protocol: Samples were randomly distributed on 5 4-plex slides. Hybridization and washes were performed as recommended [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.] simultaneously for all arrays.

scan_protocol: Individual arrays were scanned independently using a GenePix Professional 4200A scanner (Axon Instruments), adjusting the PMT gain for each array as recommended [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.]. Image analysis was performed with the NimbleScan software and features intensities were exported as .pair files

data_processing: ArrayStar 3.0 (DNASTAR) was used for probe summarization and normalization (RMA algorithm, quantile normalization) and data analysis

organism: Saccharomyces cerevisiae

source_name: Sample B (strain EPY338)

label_protocol:
10 µg of total RNA was used as starting material regardless of the labeling method used.
1) ds-cDNA method: the labeling method was carried as recommended by NimbleGen [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.], except that the components for the ds-cDNA synthesis were purchased separately and SuperScriptIII was used for the first strand cDNA synthesis. As recommended, 4 µg of labeled ds-cDNA was used for hybridization to each array.
2) Direct Random method:  7 µg of 5’Cy3 random nonamers (TriLink Biotechnologies, San Diego, CA) were added to the total RNA for a volume of 18.5 µl, heat denatured at 70°C for 5 minutes and placed on ice immediately. The remainder of the reverse transcription reaction components (6 µl of 5X First-Strand buffer, 1.5 µl of 0.1M DTT, 1 µl of 10mM dNTPs, 2 µl of 400U/µl SuperScriptIII and 1 µl of 40U/µl RNAseOut) were added and the reaction incubated at 25°C for 5 minutes and at 42°C for 3h. Template RNA was chemically hydrolysed by addition of 1 volume of a 200 mM NaOH, 20mM EDTA solution and incubation at 65°C for 10 minutes. The hydrolysis reaction was neutralized with 1 volume of 1M HEPES and the labeled cDNA purified on a Qiaquick column (QIAGEN) following the manufacturer’s recommendations for PCR purification. 5µg of labeled cDNA was hybridized to each array.
3) Indirect method: The SuperScript Plus Indirect cDNA Labeling System (Invitrogen) was used with Alexa Fluor 555 reactive dye following the manufacturer's recommendations, except for the chemical hydrolysis of RNA and cDNA purifications, which were carried as described above for the Direct random method with the exception that the kit wash buffer in the first cDNA purification was replaced with 80% ethanol. 300ng of labeled cDNA was hybridized to each array.

growth_protocol: 3 colonies for each strain were pre-cultured in SD-His-Met-Leu medium and used to inoculate 5 ml of YPG inducing medium [Ro et al. BMC Biotechnol 2008, 8(1):83] for induction at 30°C in culture tubes for 24h

extract_protocol: Cells were harvested by quick centrifugation and immediately frozen in liquid nitrogen, disrupted with glass beads in a bead-beater and total RNA was extracted using the RNeasy Mini kit (QIAGEN), including the on-column DNAse treatment. RNA was quantified by spectrophotometry with a Nanodrop ND-1000 and its integrity verified on a 2100 Bioanalyzer (Agilent). Equal amounts of RNA from each replicate culture were pooled for each strain.

tag: labeling method

value: direct

tag: induction time (h)


title: J2315 CF vs SE 3

description: Biological replicate 3 of 4.

source_name: J2315 SE-grown cells

value: mid-log phase, OD600~0.8


title: J2315 SE vs CF 4, dye swap

description: Biological replicate 4 of 4.


title: J2315 CF vs SE 2

description: Biological replicate 2 of 4.


title: DirectRandom_B_2

description: no additional information


title: DirectRandom_B_1

description: no additional information


title: CF J2315 vs. HI2424 2

description: Biological replicate 2 of 4.


title: J2315 CF vs SE 1

description: Biological replicate 1 of 4.


title: Normal_N7

organism: Homo sapiens

tag: tissue


title: Normal_N3


title: DirectRandom_A_2

description: no additional information

source_name: Sample A (strain EPY330)


title: DirectRandom_A_3

description: no additional information


title: DirectRandom_A_1

description: no additional information


title: Indirect_B_3

description: no additional information

value: indirect


title: Indirect_B_2

description: no additional information


title: Indirect_B_1

description: no additional information


title: Indirect_A_3

description: no additional information


title: Normal_N1


title: dscDNA_B_3

description: no additional information

value: ds-cDNA


title: Indirect_A_2

description: no additional information


title: dscDNA_B_2

description: no additional information


title: Indirect_A_1

description: no additional information


title: dscDNA_B_1

description: no additional information


title: dscDNA_A_2

description: no additional information


title: Normal_B6


title: Normal_B2


title: Normal_N10


title: Myel Progen Dnmtfl/fl Cre+, biological replicate 1

status: Public on Nov 17 2009

first: Jennifer

last: Trowbridge

address: 44 Binney St., Mayer 652

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from sorted myeloid progenitors (Lineage-c-Kit+Sca-1-) from Dnmt1fl/fl Mx-Cre mice, 4 days after poly(I)poly(C) injections, experimental sample, biological replicate 1

hyb_protocol: cRNA were hybridized overnight at 45oC on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with dChip using the default normalization method.

source_name: Dnmt1fl/fl Mx-Cre+ mouse bone marrow Lineage-c-Kit+Sca-1-

label_protocol: Purified single-stranded cRNA (5ug) was fragmented and biotin labeled with the FL-Ovation cDNA Biotin Module V2 (NuGEN) according to the manufacturer's instructions

growth_protocol: The Dnmt1fl/fl Mx-Cre mouse strain was maintained on a C57BL/6 background. Mice were used between 8-12 weeks of age. Each biological replicate (control & experimental samples) were obtained from littermates.

extract_protocol: Total RNA was extracted from cell pellets using the Rneasy Micro Kit (Qiagen), was reverse transcribed and amplified using the WT-Ovation Pico RNA Amplification System (NuGEN Technologies). Single-stranded cRNA amplification products were purified with QIAquick PCR purification kit (Qiagen).

treatment_protocol: All mice (control and experimental) were administered 7 injections of poly(I)-poly(C) (Sigma) at 25ug/kg every other day. Four days following the last poly(I)-poly(C) injection, the mice were sacrificed and the bone marrow from 4-6 mice of the same genotype were pooled. Mature hematopoietic cells were removed from the bone marrow by antibody-mediated magnetic lineage depletion. The lineage-depleted cells were then stained with fluorescence-conjugated antibodies against c-Kit, Sca-1 and CD34. Cells of the indicated surface marker combination were purified by fluorescence-activated cell sorting (FACS) on a FACSAria. Purified cells were pelleted and cell pellets were snap frozen and stored at -80oC until extraction of RNA.

value: Dnmt1fl/fl Mx-Cre

value: Bone marrow

tag: cell surface antigens


title: MPP Dnmtfl/fl Cre+, biological replicate 2

description: Gene expression data from sorted multipotent progenitors (Lineage-c-Kit+Sca-1+CD34+) from Dnmt1fl/fl Mx-Cre mice, 4 days after poly(I)poly(C) injections, experimental sample, biological replicate 2

source_name: Dnmt1fl/fl Mx-Cre+ mouse bone marrow Lineage-c-Kit+Sca-1+CD34+


title: Myel Progen Dnmtfl/fl Cre+, biological replicate 2

description: Gene expression data from sorted myeloid progenitors (Lineage-c-Kit+Sca-1-) from Dnmt1fl/fl Mx-Cre mice, 4 days after poly(I)poly(C) injections, experimental sample, biological replicate 2


title: Myel Progen Dnmtfl/fl Cre-, biological replicate 2

description: Gene expression data from sorted myeloid progenitors (Lineage-c-Kit+Sca-1-) from Dnmt1fl/fl mice, 4 days after poly(I)poly(C) injections, control sample, biological replicate 2

source_name: Dnmt1fl/fl Mx-Cre- mouse bone marrow Lineage-c-Kit+Sca-1-


title: Myel Progen Dnmtfl/fl Cre-, biological replicate 3

description: Gene expression data from sorted myeloid progenitors (Lineage-c-Kit+Sca-1-) from Dnmt1fl/fl mice, 4 days after poly(I)poly(C) injections, control sample, biological replicate 3


title: Myel Progen Dnmtfl/fl Cre-, biological replicate 1

description: Gene expression data from sorted myeloid progenitors (Lineage-c-Kit+Sca-1-) from Dnmt1fl/fl mice, 4 days after poly(I)poly(C) injections, control sample, biological replicate 1


title: Normal_B1


title: Normal_N6


title: MPP Dnmtfl/fl Cre-, biological replicate 2

description: Gene expression data from sorted multipotent progenitors (Lineage-c-Kit+Sca-1+CD34+) from Dnmt1fl/fl mice, 4 days after poly(I)poly(C) injections, control sample, biological replicate 2

source_name: Dnmt1fl/fl Mx-Cre- mouse bone marrow Lineage-c-Kit+Sca-1+CD34+


title: Normal_B5


title: LTHSC Dnmtfl/fl Cre+, biological replicate 1

description: Gene expression data from sorted long-term HSCs (Lineage-c-Kit+Sca-1+CD34-) from Dnmt1fl/fl Mx-Cre mice, 4 days after poly(I)poly(C) injections, experimental sample, biological replicate 1

source_name: Dnmt1fl/fl Mx-Cre+ mouse bone marrow Lineage-c-Kit+Sca-1+CD34-


title: MPP Dnmtfl/fl Cre-, biological replicate 1

description: Gene expression data from sorted multipotent progenitors (Lineage-c-Kit+Sca-1+CD34+) from Dnmt1fl/fl mice, 4 days after poly(I)poly(C) injections, control sample, biological replicate 1


title: MPP Dnmtfl/fl Cre+, biological replicate 1

description: Gene expression data from sorted multipotent progenitors (Lineage-c-Kit+Sca-1+CD34+) from Dnmt1fl/fl Mx-Cre mice, 4 days after poly(I)poly(C) injections, experimental sample, biological replicate 1


title: Embryonic Drosophila cells, Kc167 cells, GAF DamID after white RNAi

status: Public on Nov 05 2009

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Replicates were averaged: GAF_w.RNAi_1, GAF_w.RNAi_2

hyb_protocol: Samples were hybridized to the arrays in a volume of approximately 30 ul (5 mM TRIS, 0.5 mM EDTA, 3X SSC). The following competitors were added: 25 ug DpnI-digested Dam-fusion plasmid DNA, 100 ug yeast tRNA, 20 ug poly (dA-dT). Arrays were washed in four subsequent steps. The respective washing buffers were: 1X SSC/0.03% SDS (arrays were submerged once), 1XSSC (arrays were submerged 15 times), 0.2XSSC (20 minutes), 0.05XSSC (10 minutes).

scan_protocol: Microarrays are scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel (Red or Green), a variable resolution (5 or 10 um per pixel) and a suitable scan area.

data_processing: Scan TIFF images were processed with ImaGene 6.0.1 software (BioDiscovery) using automated grid placement with manual control and automated spot adjustment. Measurements were extracted as median spot intensities minus median background intensities. After removal of low quality (ImaGene flags), redundant or ambiguous probes, hybridization data of 9,993 probes was used for analyses, all measured ratios were log base 2-transformed and normalized to the median value of the entire array.

label: Cy3, Cy5

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-GAF, white RNAi

label_protocol: Sample labeling was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA. On day 5,  pNDamMyc-Trl (Moorman C. et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A 103, 12027-32, 2006) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: protocol

value: expressing Dam-GAF (experimental)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, white RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA. On day 5,  pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.

value: expressing Dam (control)


title: Embryonic Drosophila cells, Kc167 cells, GAF DamID after brahma RNAi

description: Replicates were averaged: GAF_brm.RNAi_1, GAF_brm.RNAi_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-GAF, brahma RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul brahma dsRNA. On day 5,  pNDamMyc-Trl (Moorman C. et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A 103, 12027-32, 2006) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, brahma RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul brahma dsRNA. On day 5,  pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.


title: CF J2315 vs. HI2424 1

description: Biological replicate 1 of 4.


title: LTHSC Dnmtfl/fl Cre-, biological replicate 2

description: Gene expression data from sorted long-term HSCs (Lineage-c-Kit+Sca-1+CD34-) from Dnmt1fl/fl mice, 4 days after poly(I)poly(C) injections, control sample, biological replicate 2

source_name: Dnmt1fl/fl Mx-Cre- mouse bone marrow Lineage-c-Kit+Sca-1+CD34-


title: LTHSC Dnmtfl/fl Cre-, biological replicate 1

description: Gene expression data from sorted long-term HSCs (Lineage-c-Kit+Sca-1+CD34-) from Dnmt1fl/fl mice, 4 days after poly(I)poly(C) injections, control sample, biological replicate 1


title: LTHSC Dnmtfl/fl Cre+, biological replicate 2

description: Gene expression data from sorted long-term HSCs (Lineage-c-Kit+Sca-1+CD34-) from Dnmt1fl/fl Mx-Cre mice, 4 days after poly(I)poly(C) injections, experimental sample, biological replicate 2


title: Embryonic Drosophila cells, Kc167 cells, DSP1 DamID

description: Replicates were averaged: DSP1_1 (published previously, see GSM257299), DSP1_2 (published previously, see GSM257300), DSP1_3, DSP1_4, DSP1_5 (published previously, see GSM257301), technical replicates (same biological sample) DSP1_6a & DSP1_6b.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-DSP1

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc-DSP1 (de Wit E. et al., Global chromatin domain organization of the Drosophila genome. PLoS Genet 4(3):e1000045, 2008) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

value: expressing Dam-DSP1 (experimental)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Plasmid pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: Embryonic Drosophila cells, Kc167 cells, HP1 DamID after white RNAi

description: Replicates were averaged: HP1_w.RNAi_1, HP1_w.RNAi_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-HP1, white RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA. On day 5,  pNDamMyc-HP1 (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.

value: expressing Dam-HP1 (experimental)


title: Embryonic Drosophila cells, Kc167 cells, BEAF-32b DamID

description: Replicates were averaged: BEAF32b_1, BEAF32b_2, BEAF32b_3

source_name: Embryonic Drosophila cells, Kc167 cells, expressing BEAF-32-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length BEAF-32b was cloned into pCMycdam (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

value: expressing BEAF-32-Dam (experimental)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam


title: Embryonic Drosophila cells, Kc167 cells, Su(var)3-7 DamID after white RNAi

description: Replicates were averaged: Suvar37_w.RNAi_1, Suvar37_w.RNAi_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Su(var)3-7, white RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA. On day 5,  pNDamMyc-Su(var)3-7 (de Wit E. et al., Global chromatin domain organization of the Drosophila genome. PLoS Genet 4(3):e1000045, 2008) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.


title: Embryonic Drosophila cells, Kc167 cells, HP1 DamID after brahma RNAi

description: Replicates were averaged: HP1_brm.RNAi_1, HP1_brm.RNAi_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-HP1, brahma RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul brahma dsRNA. On day 5,  pNDamMyc-HP1 (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.


title: Embryonic Drosophila cells, Kc167 cells, Rpd3 DamID

description: Replicates were averaged: Rpd3_1, Rpd3_2, Rpd3_3, technical replicates (same biological sample) Rpd3_4a & Rpd3_4b

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Rpd3-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pC-Rpd3-MycDam (Moorman C. et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A 103, 12027-32, 2006) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

value: expressing Rpd3-Dam (experimental)


title: Embryonic Drosophila cells, Kc167 cells, Su(var)3-7 DamID after brahma RNAi

description: Replicates were averaged: Suvar37_brm.RNAi_1, Suvar37_brm.RNAi_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Su(var)3-7, brahma RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul brahma dsRNA. On day 5,  pNDamMyc-Su(var)3-7 (de Wit E. et al., Global chromatin domain organization of the Drosophila genome. PLoS Genet 4(3):e1000045, 2008) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.


title: Embryonic Drosophila cells, Kc167 cells, JRA DamID after brahma RNAi

description: Replicates were averaged: JRA_brm.RNAi_1, JRA_brm.RNAi_2, JRA_brm.RNAi_3, JRA_brm.RNAi_4

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-JRA, brahma RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul brahma dsRNA. On day 5,  pNDamMyc-Jra (Moorman C. et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A 103, 12027-32, 2006) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.

value: expressing Dam-JRA (experimental)


title: Embryonic Drosophila cells, Kc167 cells, Top1 DamID

description: Replicates were averaged: Top1_1, Top1_2, Top1_3

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Top1-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length Top1 was cloned into pCMycDam (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

value: expressing Top1-Dam (experimental)


title: Embryonic Drosophila cells, Kc167 cells, PARP DamID

description: Replicates were averaged: PARP_1, PARP_2, PARP_3

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-PARP

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length PARP was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

value: expressing Dam-PARP (experimental)


title: Embryonic Drosophila cells, Kc167 cells, Dnmt2 DamID

description: Replicates were averaged: Dnmt2_1, Dnmt2_2, Dnmt2_3

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Dnmt2

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length Dnmt2 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

value: expressing Dam-Dnmt2 (experimental)


title: Myel Progen Dnmtfl/fl Cre+, biological replicate 3

description: Gene expression data from sorted myeloid progenitors (Lineage-c-Kit+Sca-1-) from Dnmt1fl/fl Mx-Cre mice, 4 days after poly(I)poly(C) injections, experimental sample, biological replicate 3

source_name: Dnmt1fl/fl Mx-Cre+ mouse bone marrow Lineage-c-Kit+Sca-1-

growth_protocol: The Dnmt1fl/fl Mx-Cre mouse strain was maintained on a C57BL/6 background. Mice were used between 8-12 weeks of age. Each biological replicate (control & experimental samples) were obtained from littermates.


title: Embryonic Drosophila cells, Kc167 cells, Su(Hw) DamID

description: Replicates were averaged: SuHw_1, SuHw_2, SuHw_3

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Su(Hw)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length Su(Hw) was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

value: expressing Dam-Su(Hw) (experimental)


title: synthetic RNA pool vs. synthetic miRNA pool (9)

status: Public on Oct 27 2009

type: mixed

city: Bergisch Gladbach

first: Ute

last: Bissels

state: NRW

address: Friedrich-Ebert-Str. 68

department: R&D

institute: Miltenyi Biotec GmbH

description: PMID

hyb_protocol: An equimolar mixture of synthetice miRNA, with 1 to 10,000 amol of each individual miRNA and 1 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The synthetic miRNA pool consisted of 954 non redundant miRNAs sequences. Hybridization was performed using an automated hybridization machine (a-Hyb, Miltenyi Biotec). Briefly, volume of labelled sample was adjusted to 100 µl with nuclease-free water and 100 µl 2x Hybridization Solution pre-warmed at 42°C was added. After mixing, the solution was pre-heated to 60 °C for 2 min prior to application to the a-Hyb. Microarray processing in the a-Hyb was as follows: incubation in Pre-Hyb Solution for 5 min at 42°C, hybridization with the labeled RNAs for 960 min at 42°C, wash with Wash Buffer I for 1 min at 10°C (2 cycles), and  second wash with Wash Buffer II for 1 min at 10°C (2 cycles). Pump speed at all incubations was set to 1 ml/min. Microarrays were blow-dried and scanned with the ScanArray Lite (GSI Lumonics, Watertown, MA) and the Agilent DNA-Microarray Scanner.

scan_protocol: Image capture was done with Agilent DNA-Microarray Scanner (Agilent, Santa Clara, CA)

data_processing: Signal processing and quantification was done with ImaGene software version 8.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the mean of the net signal intensities of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots). Subsequently,the array data was normalized by calculating the median of the miRControl 3 present in both samples.

organism: synthetic construct

source_name: synthetic miRNA pool (miRXploreTM Universal Reference, Miltenyi Biotec)

tag: composition

value: 1 amol of each of 954 synthetic miRNAs were pooled and labelled.

molecule: other

label_protocol: 1 fmol of each of 954 synthetic miRNAs were pooled and labelld using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer

value: 1 fmol of each of 954 synthetic miRNAs were pooled and labelled.


title: Embryonic Drosophila cells, Kc167 cells, JRA DamID after white RNAi

description: Replicates were averaged: JRA_w.RNAi_1, JRA_w.RNAi_2, JRA_w.RNAi_3, JRA_w.RNAi_4

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-JRA, white RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA. On day 5,  pNDamMyc-Jra (Moorman C. et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A 103, 12027-32, 2006) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, white RNAi

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. On day 1 and 3, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA. On day 5,  pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000) and cells were again treated with dsRNA.


title: synthetic RNA pool vs. synthetic miRNA pool (8)

description: PMID

label_protocol: synthetic miRNAs were pooled and labelld using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer

value: 5 amol of each of 954 synthetic miRNAs were pooled and labelled.


title: synthetic RNA pool vs. synthetic miRNA pool (2)

description: PMID

value: 5000 amol of each of 954 synthetic miRNAs were pooled and labelled.


title: synthetic RNA pool vs. synthetic miRNA pool (5)

description: PMID

value: 100 amol of each of 954 synthetic miRNAs were pooled and labelled.


title: synthetic RNA pool vs. synthetic miRNA pool (3)

description: PMID

value: 1000 amol of each of 954 synthetic miRNAs were pooled and labelled.


title: synthetic RNA pool vs. synthetic miRNA pool (1)

description: PMID

value: 10000 amol of each of 954 synthetic miRNAs were pooled and labelled.


title: synthetic RNA pool vs. synthetic miRNA pool (4)

description: PMID

value: 500 amol of each of 954 synthetic miRNAs were pooled and labelled.


title: synthetic RNA pool vs. synthetic miRNA pool (6)

description: PMID

value: 50 amol of each of 954 synthetic miRNAs were pooled and labelled.