ChIP-qPCR and ChIP-seq for Epigenomic Profiling

ChIP followed by quantitative polymerase chain reaction (ChIP-qPCR) was performed as described previously (31 (link)). Antibodies specific for CTCF (Millipore 07–729) or normal rabbit IgG (Millipore 12-370) were used. qPCR was performed using SYBR Green reagents (Life Technologies) and primers listed in Supplementary Table S1B.
ChIP and deep-sequencing (ChIP-seq) data was generated according to standard protocol as described previously (20 (link)). Antibodies used were from Abcam (ab) or Millipore (mi) and specific for H3K4me1 (ab8895), H3K27ac (ab4729), H3K4me3 (mi07–473), H3K27me3 (mi07–449), H3K9me2 (ab1220), H3K9me3 (ab8898) and H3K36me3 (ab9050). H3K4me1 and H3K27ac data in Calu3 and HBE cells used here were generated previously (Calu3 (20 (link)), HBE (55 )) All data are deposited at GEO (http://www.ncbi.nlm.nih.gov/geo; GSE63400, GSE74709, GSE94726).

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Stolzenburg L.R., Yang R., Kerschner J.L., Fossum S., Xu M., Hoffmann A., Lamar K.M., Ghosh S., Wachtel S., Leir S.H, & Harris A. (2017). Regulatory dynamics of 11p13 suggest a role for EHF in modifying CF lung disease severity. Nucleic Acids Research, 45(15), 8773-8784.

Publication 2017

SYBR Green reagents ab8895 ab4729 ab1220 ab8898 ab9050

Antibodies Cells Chip Chip seq Ctcf H3k4me3 Polymerase chain reaction Primers Rabbit Sybr green

Corresponding Organization : Case Western Reserve University

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Variable analysis

independent variables

Antibodies specific for CTCF (Millipore 07–729) or normal rabbit IgG (Millipore 12-370)
Antibodies specific for H3K4me1 (ab8895), H3K27ac (ab4729), H3K4me3 (mi07–473), H3K27me3 (mi07–449), H3K9me2 (ab1220), H3K9me3 (ab8898) and H3K36me3 (ab9050)

dependent variables

ChIP-qPCR results
ChIP-seq data

control variables

SYBR Green reagents (Life Technologies)
Primers listed in Supplementary Table S1B
Standard protocol for ChIP and deep-sequencing (ChIP-seq) data generation as described previously (20 (link))

positive controls

Normal rabbit IgG (Millipore 12-370)

negative controls

None specified

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