Chip-Chip peaks calling

Question

[marina-orlova]

Hi

I am new to ChIP-ChIP analysis. Can you please help me to understand which files from this experement are control samples and which ones are treatment? (the organism is D.melanogaster)

Link to the data: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1283/samples/?s_sortby=col_39&s_sortorder=ascending

[roy.granit]

Have you read the experiment description?

Genomewide mapping of D. melanogaster Lame duck protein binding at 6-8hrs after egg laying. Two different rabbit antibodies were used to precipitate the Lmd protein isoform in biological replicates. Additionally a rabbit preimmune-serum was used as a control. The enriched DNA was hybridized to high density Affymetrix GeneChip Drosophila Tiling 1.0R array.

Answer 1

[Ian]

The preimmune sample are the controls (this is sera taken from the animals before challenge with the antigen).

The description from http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1283/samples/?s_sortby=col_39&s_sortorder=ascending says:

Two different rabbit antibodies were used to precipitate the Lmd protein isoform in biological replicates. Additionally a rabbit preimmune-serum was used as a control.

I hope this helps.