Table 2 |
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Technical information on the ChIP-on-chip and MeDIP-on-chip datasets used for the normalization approach comparison. |
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Dataset number |
#1 |
#2 |
#3 |
#4 |
#5 |
|
|
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ArrayExpress ID |
not registered |
E-TABM-529 |
E-GEOD-17581 |
E-GEOD-24286 |
E-GEOD-22831 |
|
|
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|
Assay type |
ChIP-on-chip |
ChIP-on-chip |
MeDIP-on-chip |
MeDIP-on-chip |
MeDIP-on-chip |
|
|
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|
Microarray ID |
NimbleGen Human HGS17 minimal promoter |
NimbleGen Mouse Tiling 2006-07-17 MM8Tiling Set17 |
NimbleGen Homo sapiens 385 K CGH array |
NimbleGen mouse 385 K Refseq and miRNA promoter tiling (2-array set) |
NimbleGen Nimblegen HD2 MM8 promoter deluxe array |
|
|
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|
Species |
Human |
Mouse |
Human |
Mouse |
Mouse |
|
|
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|
Investigation |
Identification of ER-α target genes in breast cancer cells |
Identification of histone modification profiles in WT and Kcnq1ot1 |
Methylome analysis of congenital ectopic thyroids |
Mecp2-dependent regulation of MicroRNAs in Rett Syndrome |
DNA methylation analysis in E3.5 blastocysts, E6.5 epiblasts and E9.5 whole embryos |
|
|
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|
No of microarrays |
8 |
11 |
6 |
8 |
11 |
|
|
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|
Microarray content |
3 stimulated by 17beta-estradiol 1 pool of the 3 stimulated 3 untreated 1 pool of the 3 untreated |
2 Kcnq1ot1 9 wild type Tissues are placenta or liver |
3 orthotopic thyroid 3 congenital ectopic thyroid |
2 KO using Mecp2 4 wild type using Mecp2 2 wild type using 5-methylcytosine |
2 E3.5 blastocysts 3 E6.5 epiblasts 3 E9.5 whole embryos 3 Control pooled unamplified MeDIPs in E9.5 embryos |
|
|
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Microarrays used for this study |
3: 2 stimulated + the pool of stimulated |
4: H3K27me3 in wild-type placenta |
6: all |
8: all |
8: all except the pooled controls |
|
|
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Data publication date |
Article publication: 15/01/2010 PMID: 19698761 |
08/01/2008 |
27/10/2010 |
30/09/2010 |
01/11/2010 |
|
|
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|
Table 2 contains all relevant the technical information of the ChIP-on-chip and MeDIP-on-chip datasets used for the normalization approach comparison, including the dataset number as used herein, the ArrayExpress ID, the assay type, the microarray ID, species, the total number of microarrays in the dataset, the experimental content of the microarrays, a specification of the subset of microarrays used for the analyses, and the publication date of the dataset on ArrayExpress. |
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Adriaens et al. BMC Genomics 2012 13:42 doi:10.1186/1471-2164-13-42 |
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