Chromatin Immunoprecipitation and ChIP-qPCR

Chromatin immunoprecipitation (ChIP) and ChIP-qPCR are performed as described previously [18 (link), 67 (link)]. Infected RBCs were cross-linked with 1% formaldehyde (Catalogue number- 28908, THERMO Scientific) for 10 min, lysed and sonicated. ChIP samples were reverse-crosslinked and DNA was purified using a Qiaquick column (Qiagen). Target sites obtained from ChIP-seq analysis were further validated by quantitative PCR using Power SYBR Green Master Mix (Applied Biosystems).

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Ubhe S., Rawat M., Verma S., Anamika K, & Karmodiya K. (2017). Genome-wide identification of novel intergenic enhancer-like elements: implications in the regulation of transcription in Plasmodium falciparum. BMC Genomics, 18, 656.

Publication 2017

formaldehyde Qiaquick column Power SYBR Green Master Mix

Chromatin immunoprecipitation Formaldehyde Rbcs Sybr green

Corresponding Organization :

Other organizations : Indian Institute of Science Education and Research Pune, Persistent Systems (India)

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Variable analysis

independent variables

Chromatin immunoprecipitation (ChIP)

dependent variables

Target sites obtained from ChIP-seq analysis
Quantitative PCR results using Power SYBR Green Master Mix

control variables

Infected RBCs were cross-linked with 1% formaldehyde (Catalogue number- 28908, THERMO Scientific) for 10 min
Cells were lysed and sonicated
ChIP samples were reverse-crosslinked and DNA was purified using a Qiaquick column (Qiagen)

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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