ChIP on chip array cover genome or promoter regions?

Question

[adelest.ad]

Hello evrybody, On NCBI with a GSE number where I can find the information about the array used for a ChIP on chip. I try to know if the array cover all the genome or just specific regions (promoter, genes ...). Thank you

[Ian]

Could you add the GSE number?

[adelest.ad]

Hello Ian,

2 exemples of ChIP on chip -GSE54108 -GSE17733 where I'm not able to figure out if the array cover all genome or just promoter regions. Thank you for your time. Anna

Answer 1

[Ian]

The first one GSE54108 is not a ChIP-on-chip kit, it is gene expression: Agilent-026652 Whole Human Genome Microarray 4x44K v2 http://www.genomics.agilent.com/article.jsp?pageId=1516

The second would appear to be a promoter array, possibly -2.5 to 1kb from TSS: Agilent-014706 Human Promoter ChIP-on-Chip Set 244K, Microarray 1 of 2 G4489A Agilent-014707 Human Promoter ChIP-on-Chip Set 244K, Microarray 2 of 2 G4489A http://www.genomics.agilent.com/article.jsp?crumbAction=push&pageId=1488 https://www.ebi.ac.uk/arrayexpress/arrays/A-MEXP-1997/?keywords=244K+agilent&directsub=on

I hope this helps. But I would suggest contacting Agilent directly if you have further queries.

[adelest.ad]

Thank you Ian your reply help me,

In conclusion in a GEO serie (Ex: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17733) the information about the array is on his name at the session "Platforms" of the page. Have a nice day.

Answer 2

[adelest.ad]

Hello Ian,

2 exemples of ChIP on chip -GSE54108 -GSE17733 where I'm not able to figure out if the array cover all genome or just promoter regions. Thank you for your time. Anna