Can anyone recommend good controls for H3K4me3 ChIP that I can use for a qPCR assay? I'm looking for a region that generally has this mark (positive control) and one that generally does not have it (negative control).
Hi Robin,
in Washington bist Du also gelandet. Ich hab gehoert, dass Du vorher bim Lars warst! Vielleicht erinerst Du Dich ja noch an einen Deiner frueheren Superviser aus Koelle....
The answers to your question will differ depending on the tissue you are interested in.
For shoot tissue, I would chose any from the respective two articles, as they turned out to be highly reproducible: The data for H3K27me3 targets were taken from (Lafos et al, 2011), the data for any other histone marks were taken from (Roudier et al, 2011).
However, our research revealed that there s no clear-cut answer from NGS data, wich might depend on the fragment sizes due to the IP. Hence, there are certain gene loci that display extended H3K4me3, but neighboring H3K27me3 in the vicinity.
When doing x-ChIP with qPCR detection you can use the data by Libault (2005) (The Arabidopsis LHP1 protein is a component of euchromatin. Planta).
As an other control, you should use H3K27me3 side by side!
Hi Dierk,
na klar kann ich mich noch erinnern. Schoen die Auxinpaste auf Helianthus Keimlinge schmieren!
Danke fuer die Literaturhinweise. Hab dank GEO ein paar Regionen gefunden, die brauchbar als Kontrollen sind.
Glueckwunsch zur Professur! Hoffe, der Umzug wird nicht zum Nervenspiel.
...bin Prof. in Vertretung!
Deswegen: Kein Umzug, auch wenn ich mich im Saarland wirklich wohlfuehle.
'Meine Jungs' forschen weiter in Tuebingen. Ich bin 1 Tag in der Woche dort.
Falls Du ne genauere Antwort willst.. gerne ueber eine meiner Institutsmails (TU/SB).
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