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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
GSM245949 2
GSM245950 1
GSM245950 2
GSM245951 1
GSM245951 2
GSM248654 1
GSM248654 2
GSM248657 1
GSM248657 2
GSM248666 1
GSM248666 2
GSM248996 1
GSM248996 1
GSM248997 1
GSM248997 1
GSM248998 1
GSM248998 1
GSM248999 1
GSM248999 1
GSM249000 1
GSM249000 1
GSM249001 1
GSM249001 1
GSM249002 1
GSM249003 1
GSM249004 1
GSM249005 1
GSM249006 1
GSM249007 1
GSM249008 1
GSM249009 1
GSM249010 1
GSM249011 1
GSM249012 1
GSM249013 1
GSM249014 1
GSM249014 1
GSM249015 1
GSM249015 1
GSM249016 1
GSM249016 1
GSM249017 1
GSM249017 1
GSM249018 1
GSM249018 1
GSM249019 1
GSM249019 1
GSM252509 1
GSM252509 2
GSM252780 1
GSM252780 1
GSM252780 2
GSM252780 2
GSM252781 1
GSM252781 1
GSM252781 2
GSM252781 2
GSM252782 1
GSM252782 1
GSM252782 2
GSM252782 2
GSM254805 1
GSM254805 1
GSM254805 2
GSM254805 2
GSM254806 1
GSM254806 1
GSM254806 2
GSM254806 2
GSM254807 1
GSM254807 1
GSM254807 2
GSM254807 2
GSM254930 1
GSM254930 1

		Sample Attributes		Variables	Assay
Sample_description	Sample_source_name	Organism	BioSourceProvider	BIOSOURCEPROVIDER	Label	Hybridization Name
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	Homo sapiens		not specified	Cy5	GSM245281
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	Homo sapiens		not specified	Cy5	GSM245281
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	Homo sapiens		not specified	Cy3	GSM245281
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	Homo sapiens		not specified	Cy3	GSM245281
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	Homo sapiens		not specified	Cy5	GSM245282
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	Homo sapiens		not specified	Cy5	GSM245282
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	Homo sapiens		not specified	Cy3	GSM245282
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	Homo sapiens		not specified	Cy3	GSM245282
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	Homo sapiens		not specified	Cy5	GSM245283
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	Homo sapiens		not specified	Cy5	GSM245283
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	Homo sapiens		not specified	Cy3	GSM245283
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	Homo sapiens		not specified	Cy3	GSM245283
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	Homo sapiens		not specified	Cy5	GSM245284
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	Homo sapiens		not specified	Cy5	GSM245284
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	Homo sapiens		not specified	Cy3	GSM245284
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	Homo sapiens		not specified	Cy3	GSM245284
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	Homo sapiens		not specified	Cy5	GSM245285
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	Homo sapiens		not specified	Cy5	GSM245285
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	Homo sapiens		not specified	Cy3	GSM245285
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	Homo sapiens		not specified	Cy3	GSM245285
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	Homo sapiens		not specified	Cy5	GSM245286
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	Homo sapiens		not specified	Cy5	GSM245286
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	Homo sapiens		not specified	Cy3	GSM245286
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	Homo sapiens		not specified	Cy3	GSM245286
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	Homo sapiens		not specified	Alexa 647	GSM245949
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	Homo sapiens		not specified	Alexa 555	GSM245949
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	Homo sapiens		not specified	Alexa 647	GSM245950
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	Homo sapiens		not specified	Alexa 555	GSM245950
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	Homo sapiens		not specified	Alexa 647	GSM245951
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	Homo sapiens		not specified	Alexa 555	GSM245951
Array #1	Control Spike in data	Homo sapiens		not specified	Cy5	GSM248654
Array #1	Whole Cell Extract	Homo sapiens		not specified	Cy3	GSM248654
Array #2	Spike-in Controls	Homo sapiens		not specified	Cy5	GSM248657
Array #2	Whole Cell Extract	Homo sapiens		not specified	Cy3	GSM248657
Array #3	Spike-in Control Testing	Homo sapiens		not specified	Cy5	GSM248666
Array #3	Whole Cell Extract	Homo sapiens		not specified	Cy3	GSM248666
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM248996
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM248996
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM248997
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM248997
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM248998
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM248998
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM248999
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM248999
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249000
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249000
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249001
hybridized at Dana-Farber	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249001
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249002
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249003
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249004
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249005
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249006
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249007
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249008
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249009
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249010
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249011
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249012
hybridized at Affymetrix	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249013
Spike-in rep1	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249014
Spike-in rep1	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249014
Spike-in rep2	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249015
Spike-in rep2	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249015
Spike-in rep3	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249016
Spike-in rep3	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249016
Control rep1	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249017
Control rep1	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249017
Control rep2	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249018
Control rep2	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249018
Control rep3	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249019
Control rep3	Human genomic DNA	Homo sapiens		not specified	biotin	GSM249019
Array #4	Spike-in Control	Homo sapiens		not specified	Cy5	GSM252509
Array #4	Whole Cell Extract	Homo sapiens		not specified	Cy3	GSM252509
Red Channel: "ENCODE spike", 5 ug	ENCODE Spike, Undiluted	Homo sapiens		not specified	Cy5	GSM252780
Red Channel: "ENCODE spike", 5 ug	ENCODE Spike, Undiluted	Homo sapiens		not specified	Cy5	GSM252780
Green Channel: "ENCODE control", 5 ug	Control for ENCODE Spike	Homo sapiens		not specified	Cy3	GSM252780
Green Channel: "ENCODE control", 5 ug	Control for ENCODE Spike	Homo sapiens		not specified	Cy3	GSM252780
Green Channel: "ENCODE control", 5 ug	ENCODE Spike, Undiluted	Homo sapiens		not specified	Cy5	GSM252781
Green Channel: "ENCODE control", 5 ug	ENCODE Spike, Undiluted	Homo sapiens		not specified	Cy5	GSM252781
Green Channel: "ENCODE control", 5 ug	Control for ENCODE Spike	Homo sapiens		not specified	Cy3	GSM252781
Green Channel: "ENCODE control", 5 ug	Control for ENCODE Spike	Homo sapiens		not specified	Cy3	GSM252781
Red Channel: "ENCODE spike", 5 ug	ENCODE Spike, Undiluted	Homo sapiens		not specified	Cy5	GSM252782
Red Channel: "ENCODE spike", 5 ug	ENCODE Spike, Undiluted	Homo sapiens		not specified	Cy5	GSM252782
Green Channel: "ENCODE control", 5 ug	Control for ENCODE Spike	Homo sapiens		not specified	Cy3	GSM252782
Green Channel: "ENCODE control", 5 ug	Control for ENCODE Spike	Homo sapiens		not specified	Cy3	GSM252782
see www.nimblegen.com for array protocol information	DNA plus artificial spike-in DNA. Source of DNA: Roche commercial DNA.	Homo sapiens	Generated by lab	Generated by lab	Cy5	GSM254805
see www.nimblegen.com for array protocol information	DNA plus artificial spike-in DNA. Source of DNA: Roche commercial DNA.	Homo sapiens	Generated by lab	Generated by lab	Cy5	GSM254805
see www.nimblegen.com for array protocol information	DNA without spikein (background DNA). Source of DNA: Roche commercial DNA.	Homo sapiens	artificial	artificial	Cy3	GSM254805
see www.nimblegen.com for array protocol information	DNA without spikein (background DNA). Source of DNA: Roche commercial DNA.	Homo sapiens	artificial	artificial	Cy3	GSM254805
see www.nimblegen.com for array protocol information	DNA plus artificial spike-in DNA. Source of DNA: Roche commercial DNA.	Homo sapiens	Generated by lab	Generated by lab	Cy5	GSM254806
see www.nimblegen.com for array protocol information	DNA plus artificial spike-in DNA. Source of DNA: Roche commercial DNA.	Homo sapiens	Generated by lab	Generated by lab	Cy5	GSM254806
see www.nimblegen.com for array protocol information	DNA without spikein (background DNA). Source of DNA: Roche commercial DNA.	Homo sapiens	artificial	artificial	Cy3	GSM254806
see www.nimblegen.com for array protocol information	DNA without spikein (background DNA). Source of DNA: Roche commercial DNA.	Homo sapiens	artificial	artificial	Cy3	GSM254806
see www.nimblegen.com for array protocol information	DNA plus artificial spike-in DNA. Source of DNA: Roche commercial DNA.	Homo sapiens	Generated by lab	Generated by lab	Cy5	GSM254807
see www.nimblegen.com for array protocol information	DNA plus artificial spike-in DNA. Source of DNA: Roche commercial DNA.	Homo sapiens	Generated by lab	Generated by lab	Cy5	GSM254807
see www.nimblegen.com for array protocol information	DNA without spikein (background DNA). Source of DNA: Roche commercial DNA.	Homo sapiens	artificial	artificial	Cy3	GSM254807
see www.nimblegen.com for array protocol information	DNA without spikein (background DNA). Source of DNA: Roche commercial DNA.	Homo sapiens	artificial	artificial	Cy3	GSM254807
all array processing by NimbleGen, Inc. See www.nimblegen.com for details	DNA with artificial spike-in, non-amplified. Source of DNA: Roche commercial DNA.	Homo sapiens		not specified	Cy5	GSM254930
all array processing by NimbleGen, Inc. See www.nimblegen.com for details	DNA with artificial spike-in, non-amplified. Source of DNA: Roche commercial DNA.	Homo sapiens		not specified	Cy5	GSM254930

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