Transcription Factor Binding Site Prediction and ChIP Analysis

Binding sites for transcription factors were predicted using the matrix60 (link), and the Regulatory Sequence Analysis Tools portal (http://rsat.ulb.ac.be/rsat/, last accessed March 15, 2015). Testis samples (20 mg) from dmrt1bY:GFP transgenic fish and GFP antibody (Upstate) were used for in vivo chromatin immunoprecipitation (ChIP) by using the EpiQuik Tissue Chromatin Immunoprecipitation kit (Epigentek)16 (link)61 (link). After tissue disaggregation and cell re-suspension, DNA was sheared by sonication (9 pulses of 10s with an amplitude of 10%)16 (link). ChIP procedure and analysis of DNA enrichment by real-time PCR were as described16 (link)62 (link).

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Zhang X., Guan G., Li M., Zhu F., Liu Q., Naruse K., Herpin A., Nagahama Y., Li J, & Hong Y. (2016). Autosomal gsdf acts as a male sex initiator in the fish medaka. Scientific Reports, 6, 19738.

Publication 2016

EpiQuik Tissue Chromatin Immunoprecipitation kit

Antibody Binding sites Cell Chromatin immunoprecipitation Fish Pulses Real time pcr Sequence analysis Testis Tissue Transcription factors Transgenic

Corresponding Organization :

Other organizations : National University of Singapore, Shanghai Ocean University, National Institute for Basic Biology, Fish Physiology and Genomics Institute, Ehime University

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Variable analysis

independent variables

Binding sites for transcription factors predicted using the matrix60 and the Regulatory Sequence Analysis Tools portal

dependent variables

DNA enrichment by real-time PCR

control variables

Testis samples (20 mg) from dmrt1bY:GFP transgenic fish
GFP antibody (Upstate)

controls

Positive control: Not explicitly mentioned.
Negative control: Not explicitly mentioned.

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