Samples and Data < E-GEOD-10114 < Browse < ArrayExpress

E-GEOD-10114 - Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

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Source Name
GSM245281 1
GSM245281 1
GSM245281 2
GSM245281 2
GSM245282 1
GSM245282 1
GSM245282 2
GSM245282 2
GSM245283 1
GSM245283 1
GSM245283 2
GSM245283 2
GSM245284 1
GSM245284 1
GSM245284 2
GSM245284 2
GSM245285 1
GSM245285 1
GSM245285 2
GSM245285 2
GSM245286 1
GSM245286 1
GSM245286 2
GSM245286 2
GSM245949 1

Characteristics [Organism]	Term Source REF	Term Accession Number	Comment [Sample_characteristics]	Comment [Sample_description]	Comment [Sample_source_name]	Protocol REF	Extract Name	Material Type	Protocol REF	Labeled Extract Name	Label	Material Type	Protocol REF	Protocol REF	Hybridization Name	Array Design REF	Comment [Array Design URI]	Protocol REF	Factor Value [BIOSOURCEPROVIDER]	Scan Name	Comment [ArrayExpress FTP file]	Protocol REF	Comment [Derived ArrayExpress FTP file]
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample undiluted	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample undiluted	P-GSE10114-9	GSM245281 extract 1	genomic_DNA	P-GSE10114-10	GSM245281 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245281	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245281_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.8.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.2.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample undiluted	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample undiluted	P-GSE10114-9	GSM245281 extract 1	genomic_DNA	P-GSE10114-10	GSM245281 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245281	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245281_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.8.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.2.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA sample undiluted cells	P-GSE10114-11	GSM245281 extract 2	genomic_DNA	P-GSE10114-12	GSM245281 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245281	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245281_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.8.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.2.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA sample undiluted cells	P-GSE10114-11	GSM245281 extract 2	genomic_DNA	P-GSE10114-12	GSM245281 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245281	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245281_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.8.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.2.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample amplified by LM-PCR	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample diluted	P-GSE10114-9	GSM245282 extract 1	genomic_DNA	P-GSE10114-10	GSM245282 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245282	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245282_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample amplified by LM-PCR	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample diluted	P-GSE10114-9	GSM245282 extract 1	genomic_DNA	P-GSE10114-10	GSM245282 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245282	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245282_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA	P-GSE10114-11	GSM245282 extract 2	genomic_DNA	P-GSE10114-12	GSM245282 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245282	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245282_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA	P-GSE10114-11	GSM245282 extract 2	genomic_DNA	P-GSE10114-12	GSM245282 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245282	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245282_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample amplified by LM-PCR	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample	P-GSE10114-9	GSM245283 extract 1	genomic_DNA	P-GSE10114-10	GSM245283 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245283	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245283_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample amplified by LM-PCR	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample	P-GSE10114-9	GSM245283 extract 1	genomic_DNA	P-GSE10114-10	GSM245283 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245283	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245283_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA	P-GSE10114-11	GSM245283 extract 2	genomic_DNA	P-GSE10114-12	GSM245283 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245283	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245283_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA	P-GSE10114-11	GSM245283 extract 2	genomic_DNA	P-GSE10114-12	GSM245283 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245283	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245283_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample undiluted	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample undiluted	P-GSE10114-9	GSM245284 extract 1	genomic_DNA	P-GSE10114-10	GSM245284 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245284	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245284_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.4.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample undiluted	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample undiluted	P-GSE10114-9	GSM245284 extract 1	genomic_DNA	P-GSE10114-10	GSM245284 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245284	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245284_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.4.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA	P-GSE10114-11	GSM245284 extract 2	genomic_DNA	P-GSE10114-12	GSM245284 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245284	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245284_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.4.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA	P-GSE10114-11	GSM245284 extract 2	genomic_DNA	P-GSE10114-12	GSM245284 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245284	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245284_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.4.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample undiluted	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample undiluted	P-GSE10114-9	GSM245285 extract 1	genomic_DNA	P-GSE10114-10	GSM245285 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245285	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245285_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample undiluted	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample undiluted	P-GSE10114-9	GSM245285 extract 1	genomic_DNA	P-GSE10114-10	GSM245285 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245285	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245285_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA sample undiluted cells	P-GSE10114-11	GSM245285 extract 2	genomic_DNA	P-GSE10114-12	GSM245285 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245285	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245285_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA sample undiluted was fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA sample undiluted cells	P-GSE10114-11	GSM245285 extract 2	genomic_DNA	P-GSE10114-12	GSM245285 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245285	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245285_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.7.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample amplified by LM-PCR	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample	P-GSE10114-9	GSM245286 extract 1	genomic_DNA	P-GSE10114-10	GSM245286 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245286	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245286_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.9.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.2.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Spike in DNA sample amplified by LM-PCR	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Spike in DNA sample	P-GSE10114-9	GSM245286 extract 1	genomic_DNA	P-GSE10114-10	GSM245286 LE 1	Cy5	unknown	P-GSE10114-13	P-GSE10114-14	GSM245286	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245286_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.9.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.2.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA	P-GSE10114-11	GSM245286 extract 2	genomic_DNA	P-GSE10114-12	GSM245286 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245286	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245286_635.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.9.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.2.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	Control DNA	Spike in DNA was amplified by LM-PCR, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.	Control DNA	P-GSE10114-11	GSM245286 extract 2	genomic_DNA	P-GSE10114-12	GSM245286 LE 2	Cy3	unknown	P-GSE10114-13	P-GSE10114-14	GSM245286	A-GEOD-4559	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-4559	P-GSE10114-15	not specified	GSM245286_532.pair	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.9.zip	P-GSE10114-1	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.2.zip
Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	spike-in	For each replicate array, we labeled 1Âµg of spike-in sample and 1Âµg of control sample. The Bioprime Plus Array CGH labeling Module (Invitrogen Catolog number 18095-014) was used. The spike-in was labeled with the red channel dye (Alexa Fluor-647) and the control was labeled with the green channel dye (Alexa Fluor-555) in two of the replicates. A dye swap was performed for the third replicate. These samples were then competitively hybridized to three replicate 244k arrays from Agilent, (AMADID 25150451). We hybridized the samples to the arrays using the Agilent Array CGH protocol, with some modifications. Briefly, labeled DNA was combined with Cot-1 DNA, blocking reagent, and hybridization buffer. The hybridizations were carried out at 60Â°C. The arrays were scanned using an Agilent dual laser scanner, and the images were processed using Agilent Feature Extraction Software.	Roche gDNA + spike		GSM245949 extract 1	genomic_DNA	P-GSE10114-16	GSM245949 LE 1	Alexa 647	unknown	P-GSE10114-17	P-GSE10114-18	GSM245949	A-GEOD-6189	http://www.ebi.ac.uk/aerep/result?queryFor=PhysicalArrayDesign&aAccession=A-GEOD-6189	P-GSE10114-19	not specified	GSM245949.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.raw.6.zip	P-GSE10114-2	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-10114/E-GEOD-10114.processed.1.zip

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E-GEOD-10114 - Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets