Muerdter F*, Boryń ŁM*, Woodfin AR**, Neumayr C**, Rath M, Zabidi MA, Pagani M, Haberle V, Kazmar T, Catarino RR, Schernhuber K, Arnold CD, Stark A. Resolving systematic errors in widely-used enhancer activity assays in human cells enables genome-wide functional enhancer characterization. Nature Methods, 2018 February 15(2):141-149

** This manuscript resolves ORI-initiation and type-I-interferon response for enhancer-activity assays in human cells and publishes a novel genome-wide STARR-seq protocol

• Tracks on the UCSC Genome Browser

• Raw sequencing data also on GEO GSE100432

  Genome-wide STARR-seq HeLaS3

  STARR-seq inhibitor treated HeLaS3 ORI CP genomewide replicate 1, paired-end read 1 [1.5G]
  STARR-seq inhibitor treated HeLaS3 ORI CP genomewide replicate 1, paired-end read 2 [1.5G]
  STARR-seq inhibitor treated HeLaS3 ORI CP genomewide replicate 2, paired-end read 1 [1.5G]
  STARR-seq inhibitor treated HeLaS3 ORI CP genomewide replicate 2, paired-end read 2 [1.5G]

  STARR-seq non treated HeLaS3 ORI CP genomewide replicate 1, paired-end read 1 [2.2G]
  STARR-seq non treated HeLaS3 ORI CP genomewide replicate 1, paired-end read 2 [2.1G]
  STARR-seq non treated HeLaS3 ORI CP genomewide replicate 2, paired-end read 1 [2.0G]
  STARR-seq non treated HeLaS3 ORI CP genomewide replicate 2, paired-end read 2 [1.9G]

  Genome-wide input

  ORI CP genomewide input replicate 1, paired-end read 1 [3.3G]
  ORI CP genomewide input replicate 1, paired-end read 2 [3.4G]
  ORI CP genomewide input replicate 2, paired-end read 1 [4.1G]
  ORI CP genomewide input replicate 2, paired-end read 2 [4.2G]

  Genome-wide STARR-seq peaks files

  Note: headers included
  STARR-seq inhibitor treated vs non treated HeLaS3 ORI CP genomewide differential peaks [1.2M]
  STARR-seq inhibitor treated HeLaS3 ORI CP genomewide peaks with corrected enrichment cut off of 4 [1.2M]
  STARR-seq inhibitor treated HeLaS3 ORI CP genomewide short listed regions enrichment cut off of 3 [7.6M]
  STARR-seq non treated HeLaS3 ORI CP genomewide peaks with corrected enrichment cut off of 4 [1.2M]

  Focused BAC STARR-seq HeLaS3

  STARR-seq ORI CP HeLaS3 inhibitor treated bac, single-end [75M]
  STARR-seq ORI CP HeLaS3 non treated bac, single-end [51M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq non treated bac, single-end [71M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking control, paired-end read 1 [51M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking control, paired-end read 2 [51M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking construct 1, paired-end read 1 [54M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking construct 1, paired-end read 2 [53M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking construct 2, paired-end read 1 [119M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking construct 2, paired-end read 2 [118M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking construct 3, paired-end read 1 [67M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking construct 3, paired-end read 2 [66M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking construct 4, paired-end read 1 [63M]
  STARR-seq SCP1 CP HeLaS3 STARR-seq blocking construct 4, paired-end read 2 [62M]
  STARR-seq mCP HeLaS3 core promoter comparison bac, single-end [53M]
  STARR-seq OCT4 HeLaS3 core promoter comparison bac, single-end [170M]
  STARR-seq SCP1 HeLaS3 core promoter comparison bac, single-end [38M]
  STARR-seq SULT1C2 HeLaS3 core promoter comparison bac, single-end [26M]
  STARR-seq TFF2 HeLaS3 core promoter comparison bac, single-end [117M]

  Focused BAC STARR-seq HCT116

  STARR-seq ORI CP HCT116 inhibitor treated bac, single-end [31M]
  STARR-seq ORI CP HCT116 non treated bac, single-end [23M]
  STARR-seq SCP1 CP HCT116 STARR-seq non treated bac, single-end [15M]

  Focused BAC input

  ORI CP bac input, paired-end read 1 [5.6G]
  ORI CP bac input, paired-end read 2 [5.6G]
  SCP1 CP bac input, paired-end read 1 [7.1G]
  SCP1 CP bac input, paired-end read 2 [7.2G]

  Focused STAP-seq processed STARR-seq HeLaS3

  STAP-seq processed STARR-seq mCP HeLaS3 bac, paried-end read 1 [64M]
  STAP-seq processed STARR-seq mCP HeLaS3 bac, paried-end read 2 [74M]
  STAP-seq processed STARR-seq OCT4 CP HeLaS3 bac, paried-end read 1 [55M]
  STAP-seq processed STARR-seq OCT4 CP HeLaS3 bac, paried-end read 2 [63M]
  STAP-seq processed STARR-seq SCP1 CP HeLaS3 bac, paried-end read 1 [66M]
  STAP-seq processed STARR-seq SCP1 CP HeLaS3 bac, paried-end read 2 [78M]
  STAP-seq processed STARR-seq SULT1C2 CP HeLaS3 bac, paried-end read 1 [1.7M]
  STAP-seq processed STARR-seq SULT1C2 CP HeLaS3 bac, paried-end read 2 [1.9M]
  STAP-seq processed STARR-seq TFF2 CP HeLaS3 bac, paried-end read 1 [69M]
  STAP-seq processed STARR-seq TFF2 CP HeLaS3 bac, paried-end read 2 [80M]

  Supplementary Protocols

  Human STARR-seq Library Preparation Protocol [546K]
  Human STARR-seq Protocol [730K]
  qPCR Reporter Assay Protocol [522K]
  qPCR ISG Expression Assay Protocol [530K]

  STARR-seq screening and luciferase validation vectors will be available on ADDgene