Arnold CD*, Zabidi MA*, Pagani M, Rath M, Schernhuber K, Kazmar T, Stark A. Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution. Nature Biotech, 2016 Dec 26. Pubmed 28024147.

• Tracks on the UCSC Genome Browser

• Raw sequencing data (also on GEO (GSE78886)

  Genome-wide STAP-seq

  zfh1 S2 STAP-seq replicate 1, paired-end read 1 [1.1G]
  zfh1 S2 STAP-seq replicate 1, paired-end read 2 [1.2G]
  zfh1 S2 STAP-seq replicate 2, paired-end read 1 [1.1G]
  zfh1 S2 STAP-seq replicate 2, paired-end read 2 [1.2G]

  ctrl S2 STAP-seq replicate 1, paired-end read 1 [889M]
  ctrl S2 STAP-seq replicate 1, paired-end read 2 [1.2G]
  ctrl S2 STAP-seq replicate 2, paired-end read 1 [833M]
  ctrl S2 STAP-seq replicate 2, paired-end read 2 [1.1G]

  Genome-wide experimentally defined zfh1 TSSs or eTSS [440K]
  zfh1 and ctrl raw tag counts, and enhancer-responsiveness of +1 positions of eTSS [679K]

  subthreshold positions 4 zfh1 tag counts[43K]
  subthreshold positions 3 zfh1 tag counts[156K]
  subthreshold positions 2 zfh1 tag counts[1.3M]
  random positions[337K]

  Focused BAC STAP-seq S2

  zfh1 S2 STAP-seq replicate 1, paired-end read 1 [37M]
  zfh1 S2 STAP-seq replicate 1, paired-end read 2 [42M]
  zfh1 S2 STAP-seq replicate 2, paired-end read 1 [207M]
  zfh1 S2 STAP-seq replicate 2, paired-end read 2 [216M]
  zfh1 S2 STAP-seq replicate 3, paired-end read 1 [193M]
  zfh1 S2 STAP-seq replicate 3, paired-end read 2 [203M]

  ctrl S2 STAP-seq replicate 1, paired-end read 1 [20M]
  ctrl S2 STAP-seq replicate 1, paired-end read 2 [27M]

  Focused BAC experimentally defined zfh1 TSSs or eTSS [13K]

  sgl S2 STAP-seq replicate 1, paired-end read 1 [45M]
  sgl S2 STAP-seq replicate 1, paired-end read 2 [51M]
  sgl S2 STAP-seq replicate 2, paired-end read 1 [109M]
  sgl S2 STAP-seq replicate 2, paired-end read 2 [116M]

  ham S2 STAP-seq replicate 1, paired-end read 1 [27M]
  ham S2 STAP-seq replicate 1, paired-end read 2 [33M]
  ham S2 STAP-seq replicate 2, paired-end read 1 [76M]
  ham S2 STAP-seq replicate 2, paired-end read 2 [84M]

  ncm S2 STAP-seq replicate 1, paired-end read 1 [27M]
  ncm S2 STAP-seq replicate 1, paired-end read 2 [30M]
  ncm S2 STAP-seq replicate 2, paired-end read 1 [173M]
  ncm S2 STAP-seq replicate 2, paired-end read 2 [176M]

  ssp3 S2 STAP-seq replicate 1, paired-end read 1 [29M]
  ssp3 S2 STAP-seq replicate 1, paired-end read 2 [51M]
  ssp3 S2 STAP-seq replicate 2, paired-end read 1 [86M]
  ssp3 S2 STAP-seq replicate 2, paired-end read 2 [87M]

  Focused BAC STAP-seq OSC

  tj OSC STAP-seq replicate 1, paired-end read 1 [244M]
  tj OSC STAP-seq replicate 1, paired-end read 2 [251M]
  tj OSC STAP-seq replicate 2, paired-end read 1 [4M]
  tj OSC STAP-seq replicate 2, paired-end read 2 [4M]

­

STAP-seq screening and luciferase validation vectors
STAP-seq zfh1 (sbd|gbk)
STAP-seq ctrl (sbd|gbk)
STAP-seq ham (sbd|gbk)
STAP-seq ncm (sbd|gbk)
STAP-seq ssp3 (sbd|gbk)
STAP-seq tj (sbd|gbk)
STAP-seq spike-in eve (sbd|gbk)
STAP-seq spike-in CG32369 (sbd|gbk)
STAP-seq spike-in ush-1 (sbd|gbk)
STAP-seq spike-in ush-2 (sbd|gbk)