Skip to main content

Table 2 Technical information on the ChIP-on-chip and MeDIP-on-chip datasets used for the normalization approach comparison.

From: An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

Dataset number

#1

#2

#3

#4

#5

ArrayExpress ID

not registered

E-TABM-529

E-GEOD-17581

E-GEOD-24286

E-GEOD-22831

Assay type

ChIP-on-chip

ChIP-on-chip

MeDIP-on-chip

MeDIP-on-chip

MeDIP-on-chip

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

Species

Human

Mouse

Human

Mouse

Mouse

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

No of microarrays

8

11

6

8

11

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

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

Data publication date

Article publication: 15/01/2010

PMID: 19698761

08/01/2008

27/10/2010

30/09/2010

01/11/2010

  1. 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.