BioMicroCenter:ChIP

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HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY

The BioMicro Center now supports preparation of Chromatin IP samples. Basics about Chromatin IP can be found at [1]

DIAGENODE IP-STAR

The BioMicro Center hosts a Diagenode IP-Star automated ChIP system.

Sonicated chromatin will undergo IP on the IPstar. RNase A, Proteinase K, Phenol Chloroform extraction and purification will be performed off of the instrument and submitted for QC on the Bioanalyzer. These ChIP samples may be picked up for qPCR or sent directly to SPRI for library construction and sequencing (options are listed on submission forms). Users will be contacted if ChIP samples fail QC. These samples will not be submitted to SPRI-works but will be charged for the IP.

Marson A, et al. Cell 2008

ChIP-seq

Chromatin Immunoprecipitation Sequencing (ChIP-Seq) combines ChIP with DNA sequencing, allowing researchers to identify the binding sites of DNA-associated proteins. It can be used as a more cost effective and higher quality alternative to whole genome microarray hybridization. You can find more information about Illumina's ChIP-Seq protocols and kits here. ChIP-Seq samples are typically run as 36nt or 40nt single-end runs on the GAIIx or HiSeq, respectively.



ChIP Seq Literature

  1. Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, Guenther MG, Johnston WK, Wernig M, Newman J, Calabrese JM, Dennis LM, Volkert TL, Gupta S, Love J, Hannett N, Sharp PA, Bartel DP, Jaenisch R, and Young RA. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell. 2008 Aug 8;134(3):521-33. DOI:10.1016/j.cell.2008.07.020 | PubMed ID:18692474 | HubMed [Paper1]
  2. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, and Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug;4(8):651-7. DOI:10.1038/nmeth1068 | PubMed ID:17558387 | HubMed [Paper2]
All Medline abstracts: PubMed | HubMed