title: MDA-MB-468 (ATCC nr. HTB-137) Breast tumor cell line  MDA468_b41_s07

tag: MDA-MB-468 (ATCC nr. HTB-137) breast tumor cell line

tag: Gender

tag: adenocarcinoma, pleural effusion derived

tag: Pooled DNA from the blood of 10 normal male individuals


title: E2F1 in Daudi cell - rep1 of 2

status: Public on Apr 21 2005

type: genomic

city: San Diego

first: Chunxu

last: Qu

state: CA

department: Gene Regulation

country: USA

institute: Ludwig Institute for Cancer Research

description: Genome-wide location analysis of E2F1 binding using RenLab Hu6K array. Array ID is 271. Replicate 1 of 2.

molecule: genomic DNA

organism: Homo sapiens

source_name: Chromatin immunoprecipitated DNA using E2F1 antibody

source_name: input DNA


title: Patient#1 Blood DNA

status: Public on Jul 21 2005

city: London

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

country: United Kingdom

institute: Queen Mary University of London

description: Blood DNA for patient #1

data_processing: SNP Call

tag: #1 Blood


title: E2F1 in Daudi cell - rep2 of 2

description: Genome-wide location analysis of E2F1 binding using RenLab Hu6K array. Array ID is 272. Replicate 2 of 2.


title: TAF1 in Daudi cell - rep1 of 3

description: Genome-wide location analysis of TAF1 binding using RenLab Hu6K array. Array ID is 246. Replicate 1 of 3.

source_name: Chromatin immunoprecipitated DNA using TAF1 antibody


title: Patient #2 Blood DNA

description: Blood DNA for patient #2

tag: #2 Blood


title: Max in Daudi cell - rep5 of 5

description: Genome-wide location analysis of Max binding using RenLab Hu6K array. Array ID is 222. Replicate 5 of 5.

source_name: Chromatin immunoprecipitated DNA using Max antibody


title: RNA polymerase II in Daudi cell - rep3 of 3

description: Genome-wide location analysis of RNA polymerase II binding using RenLab Hu6K array. Array ID is 274. Replicate 3 of 3.

source_name: Chromatin immunoprecipitated DNA using RNA polymerase II antibody


title: RNA polymerase II in Daudi cell - rep2 of 3

description: Genome-wide location analysis of RNA polymerase II binding using RenLab Hu6K array. Array ID is 273. Replicate 2 of 3.


title: TAF1 in Daudi cell - rep3 of 3

description: Genome-wide location analysis of TAF1 binding using RenLab Hu6K array. Array ID is 367. Replicate 3 of 3.


title: TAF1 in Daudi cell - rep2 of 3

description: Genome-wide location analysis of TAF1 binding using RenLab Hu6K array. Array ID is 366. Replicate 2 of 3.


title: Max in Daudi cell - rep1 of 5

description: Genome-wide location analysis of Max binding using RenLab Hu6K array. Array ID is 208. Replicate 1 of 5.


title: RNA polymerase II in Daudi cell - rep1 of 3

description: Genome-wide location analysis of RNA polymerase II binding using RenLab Hu6K array. Array ID is 247. Replicate 1 of 3.


title: 1058-10 T1 bladder tumor

status: Public on Apr 15 2005

city: Aarhus N

first: Karen

last: Koed

address: Brendstrupgaardsvej

department: Dept. of Clinical Biochemistry

country: Denmark

institute: Aarhus University Hospital, Skejby Sygehus

description: genotype

source_name: tumor DNA


title: c-Myc in Daudi cell - Rep 3

description: Genome-wide location analysis of c-Myc binding using RenLab Hu6K array. Array ID is 231. Replicate 3 of 5.

source_name: Chromatin immunoprecipitated DNA using c-Myc antibody


title: c-Myc in Daudi cell - Rep 5

description: Genome-wide location analysis of c-Myc binding using RenLab Hu6K array. Array ID is 221. Replicate 5 of 5.


title: 1276-3 T1/T2 bladder tumor

description: genotype


title: 1058-3 Ta bladder tumor

description: genotype


title: 1276 blood

description: genotype

source_name: blood DNA


title: Max in Daudi cell - rep4 of 5

description: Genome-wide location analysis of Max binding using RenLab Hu6K array. Array ID is 212. Replicate 4 of 5.


title: 1058 blood

description: genotype


title: 1276-1 T1 bladder tumor

description: genotype


title: Max in Daudi cell - rep2 of 5

description: Genome-wide location analysis of Max binding using RenLab Hu6K array. Array ID is 232. Replicate 2 of 5.


title: c-Myc in Daudi cell - Rep 4

description: Genome-wide location analysis of c-Myc binding using RenLab Hu6K array. Array ID is 211. Replicate 4 of 5.


title: 1033-1 T1 bladder tumor

description: genotype


title: 1033-2 T2+ bladder tumor

description: genotype


title: 1017-3 T2+ bladder tumor

description: genotype


title: c-Myc in Daudi cell - Rep 2

description: Genome-wide location analysis of c-Myc binding using RenLab Hu6K array. Array ID is 207. Replicate 2 of 5.


title: Max in Daudi cell - rep3 of 5

description: Genome-wide location analysis of Max binding using RenLab Hu6K array. Array ID is 235. Replicate 3 of 5.


title: 1033 blood

description: genotype


title: SUM159 epithelial Breast tumor cell line  SUM159_b36_s50

status: Public on Dec 19 2005

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

hyb_protocol: Hybridization protocol available via the VUMC MACF website Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their mode value. Weighted moving average values were then calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004)  Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.).

label_protocol:
DNA labeling protocol available via the VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

growth_protocol: described in: Flanagan L, Van Weelden K, Ammerman C, Ethier SP, Welsh J., SUM-159PT cells: a novel estrogen independent human breast cancer model system., Breast Cancer Res Treat., 1999, Dec;58(3):193-204.

extract_protocol:
DNA isolation protocol available via the VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

tag: SUM159 epithelial breast tumor cell line

value: female

tag: described in

value: Flanagan L, Van Weelden K, Ammerman C, Ethier SP, Welsh J., SUM-159PT cells:a novel estrogen independent human breast cancer model system., Breast Cancer Res Treat., 1999, Dec;58(3):193-204.

source_name: male reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol


title: c-Myc in Daudi cell - Rep 1

description: Genome-wide location analysis of c-Myc binding using RenLab Hu6K array. Array ID is 206. Replicate 1 of 5.


title: 1013-3 T2+ bladder tumor

description: genotype


title: 1013-1 T1 bladder tumor

description: genotype


title: 1013 blood

description: genotype


title: 941-4 Ta bladder tumor

description: genotype


title: 941-6 T2+ bladder tumor

description: genotype


title: 1017 blood

description: genotype


title: 1017-1 T1 bladder tumor

description: genotype


title: 501-1 T1 bladder tumor

description: genotype


title: 839 blood

description: genotype


title: 501 blood

description: genotype


title: 839-2 T2+ bladder tumor

description: genotype


title: 172 blood

description: genotype


title: 941 blood

description: genotype


title: 865 blood

description: genotype


title: 172-4 T2+ bladder tumor

description: genotype


title: 501-5 T2+ bladder tumor

description: genotype


title: 365-1 T1 bladder tumor

description: genotype


title: 747-3 Ta bladder tumor

description: genotype

source_name: DNA fro tumor


title: 865-2 T1 bladder tumor

description: genotype


title: 825-3 Ta bladder tumor

description: genotype

source_name: DNA from tumor


title: 172-3 T1 bladder tumor

description: genotype


title: 365-3 T1/T2+ bladder tumor

description: genotype


title: 865-1 Ta bladder tumor

description: genotype


title: 825-5 T1 bladder tumor

description: genotype


title: 365 blood

description: genotype


title: 747-5 T1 bladder tumor

description: genotype


title: 839-1 T1 bladder tumor

description: genotype


title: 747 blood

description: genotype

source_name: DNA from blood


title: 166-9 Ta bladder tumor

description: genotype


title: 166-14 T1 bladder tumor

description: genotype


title: 166 blood

description: genotype


title: 825 blood

description: genotype


title: 166-5 Ta bladder tumor

description: genotype


title: 154-6 Ta bladder tumor

description: genotype


title: 140-8 Ta bladder tumor

description: genotype


title: 140-12 Ta bladder tumor

description: genotype


title: 112-12 T1 badder tumor

description: genotype

source_name: Tumor DNA


title: 140 blood

description: genotype


title: 154-10 T1 bladder tumor

description: genotype


title: 154-5 Ta bladder tumor

description: genotype


title: 154 blood

description: genotype


title: 112 blood

description: genotype


title: 140-16 T1 bladder tumor

description: genotype


title: 112-2 Ta bladder tumor

description: genotype


title: U-1B

status: Public on Apr 01 2005

type: RNA

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: Total RNA from U0126 (20 uM)-treated blastocyst were subjected to "GeneChip Eukaryotic Small Sample Target Labeling Assay Version II" by Affymetrix and hybridized to GeneChip Mouse Expression Array 430B

molecule: total RNA

organism: Mus musculus

source_name: preimplantation mouse embryo


title: U-3

description: Total RNA from U0126 (20 uM)-treated blastocyst were subjected to "Two-Cycle Target Labeling Assays" by Affymetrix and hybridized to GeneChip Mouse Genome 430 2.0 Array


title: SB-1A

description: Total RNA from SB203580 (20 uM)-treated blastocyst were subjected to "GeneChip Eukaryotic Small Sample Target Labeling Assay Version II" by Affymetrix and hybridized to GeneChip Mouse Expression Array 430A


title: U-1A

description: Total RNA from U0126 (20 uM)-treated blastocyst were subjected to "GeneChip Eukaryotic Small Sample Target Labeling Assay Version II" by Affymetrix and hybridized to GeneChip Mouse Expression Array 430A


title: SB-1B

description: Total RNA from SB203580 (20 uM)-treated blastocyst were subjected to "GeneChip Eukaryotic Small Sample Target Labeling Assay Version II" by Affymetrix and hybridized to GeneChip Mouse Expression Array 430B


title: SP-1A

description: Total RNA from SP600125 (25 uM)-treated blastocyst were subjected to "GeneChip Eukaryotic Small Sample Target Labeling Assay Version II" by Affymetrix and hybridized to GeneChip Mouse Expression Array 430A


title: SP-2

description: Total RNA from SP600125 (25 uM)-treated blastocyst were subjected to "Two-Cycle Target Labeling Assays" by Affymetrix and hybridized to GeneChip Mouse Genome 430 2.0 Array


title: SP-3


title: SB-3

description: Total RNA from SB203580 (20 uM)-treated blastocyst were subjected to "Two-Cycle Target Labeling Assays" by Affymetrix and hybridized to GeneChip Mouse Genome 430 2.0 Array


title: SB-2


title: U-2


title: corn oil control, biological rep3b

status: Public on Jun 03 2006

city: Denver

first: Linda

middle: C

last: Quattrochi

state: CO

department: Medicine

institute: University of Colorado at Denver and Health Sciences

description: Gene expression data from adult rat liver; corn oil-control; 8 h treatment

hyb_protocol: Following fragmentation, cRNA were hybridized at 45c for 16 h using a Affymetrix GeneChip Hybridization Oven 640

scan_protocol: Affymetrix GeneChip Scanner 3000

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

label: biotin

organism: Rattus norvegicus

source_name: Rattus, adult liver

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

extract_protocol: RNeasy kit, DNase I treatment on column, following manufacturer's instructions

treatment_protocol: After an overnight fast, animal received a single intraperitoneal dose of corn oil and sacrificed 8 h later

tag: Sprague-Dawley, 150-200 g


title: AURATUS goldfish genome project: slide 31-EE2 experiment

status: Public on May 31 2006

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: Additional information for microarray can be found at auratus.ca and in Martyniuk et al. (pending publishing). Gene expression profiling in the brain of male goldfish (Carassius auratus) exposed to 17α-ethinylestradiol

data_processing: The array quality filter test (AQF) (Sauer et al., 2005); The intensity-dependent Lowess normalization with span 0.4 was chosen for normalization

organism: Carassius auratus

source_name: Carassius auratus; hypothalamus; control (EtOH) EtOH for etinylestradiol experiment

tag: Hypothalmus

tag: Male adult goldfish

tag: 2-3 years of age

tag: sexually mature (March)

tag: slide 31

source_name: Carassius auratus; hypothalamus;  30ng/L EE2 for etinylestradiol experiment

tag: exposed to 30 ng/l EE2


title: SP-1B

description: Total RNA from SP600125 (25 uM)-treated blastocyst were subjected to "GeneChip Eukaryotic Small Sample Target Labeling Assay Version II" by Affymetrix and hybridized to GeneChip Mouse Expression Array 430B