Fused in sarcoma regulates DNA replication timing and progression

Scripts and resource data for figures:

• Fig. 3 and Sup. Fig. 5C to E: GSEA anlysis of FUS RNA-Seq
  • Rmd file.
  • MSigDB for biological processing(c5.bp.v6.2.symbols.gmt).
  • raw data of res_WTvsKO_shrunken_tb_entrez.csv.
  • raw data of normalized_counts.csv.
  • raw data of ann.sample.csv.
  • raw data of FUS_Seq_SSIV_All.csv.
• Fig. 5C-5E: Analysis of Chromatin loading proteins
  • raw data
• Fig. 6A and Sup. Fig. 6: Analysis of FUS MS/MS data
  • Rmd file.
  • MSigDB for biological processing(c5.bp.v6.2.symbols.gmt).
  • raw data of AllResultsOfQuantification_FUS.csv.
  • raw data of PSMs_FUS.csv.
• Fig. 6E: Quantification results of PLA_FUS
  • Rmd file.
  • CellProfiler pipeline(PLA_Nuclear.cppipe).
  • raw data of POLD1_U2OS_CSK_Nuclei.csv.
  • raw data of POLD1_Clone110_CSK_Nuclei.csv.
  • raw data of PCNA_U2OS_CSK_Nuclei.csv.
  • raw data of PCNA_Clone110_CSK_Nuclei.csv.
  • raw data of FEN1_U2OS_CSK_Nuclei.csv.
  • raw data of FEN1_Clone110_CSK_Nuclei.csv.
• Fig. 7: FUS regulates DNA replication timing in U-2 OS cells
  • Rmd file.
  • raw data of 7B.
  • raw data of 7D.
• Fig. 8, 9 and Sup. Fig. 8: Analysis of FUS replication timing
  • Code for QC, mapping and log2(S/G1): RT_FUS.sh.
  • RT signal Normalization and smoothing: normalization_smoothing.R.
  • RT plot of Fig. 8 and Sup. Fig. 8A to D.
    • Rmd file: Fig_RT_Plots20190102.Rmd.
    • Raw data of smoothing data: all_sample_r1_r2_smooth.txt.
  • RT domain plots for Fig. 9A to C.
    • Rmd file: Fig_RT_domain_plots.Rmd.
    • Raw data of segway results:
      • U2OS, FUS^+/+
      • Clone110, FUS^-/-
      • FUS/Clonee110, FUS^-/-:FUS
  • RT enrich plots for Fig. 9E and Sup. Fig. 8E to G(R2).
    • Rmd file: Fig_RT_domain_plots.Rmd.
    • RT enrich plots of R1
      • Rmd file: Fig_RT_domain_plotsR1.Rmd.
    • Raw data FADs and RT signal files:
      • FAD-E.bed
      • FAD-M.bed
      • FAD-L.bed
      • U2OS-RT-R1.bedGraph, FUS^+/+
      • Clone110-RT-R1.bedGraph, FUS^-/-
      • FUS/Clonee110-RT-R1.bedGraph, FUS^-/-:FUS
      • U2OS-RT-R2.bedGraph, FUS^+/+
      • Clone110-RT-R2.bedGraph, FUS^-/-
      • FUS/Clonee110-RT-R2.bedGraph, FUS^-/-:FUS
  • RT domain identification:
    • code file: RDsIdentifybySegway.sh.
    • hg38.chrom.sizes.txt: hg38.chrom.sizes.txt.
    • RT signal files used are same as Raw data FADs and RT signal files.
  • Code for FAD GO enrichment analysis in Fig 9H and I:
    • code file: FUS_RT_groupcompare_GOEnrich.R.
    • input file: ERD_MRD_LRD_ENTREID.txt.
  • RT signal enrichment in gene regions in Fig. 9F and G, and Sup. Fig. 8H to J:
    • code file for FUS regulated gene bed file: FUS_gene_bed.sh.
    • code file for RT enrichment analysis: RT_Signal_EnrichPlots.sh.
    • code file for Transcription enrichment analysis: Transcription_Signal_EnrichPlots.sh.
    • RT signal files used are same as "Raw data FADs and RT signal files".
    • RT bed files:
      • FADs: refer to "Raw data FADs and RT signal files"
      • RDs:
        • U2OS_ERD.bed
        • U2OS_MRD.bed
        • U2OS_LRD.bed
        • Clone110_ERD.bed
        • Clone110_MRD.bed
        • Clone110_LRD.bed
        • FUSClone110_ERD.bed
        • FUSClone110_MRD.bed
        • FUSClone110_LRD.bed
• Fig. 9D: Doughnut Pie chart of FADs coverage
  • Rmd file.
  • raw data of 9D.
• Sup. Fig. 1: IRIF of 53BP1 in FUS knockout cells
  • Rmd file
  • raw data
    • R1
    • R2
    • R3
    • CellProfiler Setting
• Sup. Fig. 2: IRIF of BRCA1 in FUS knockout cells
  • Rmd file
  • raw data
    • R1
    • R2
    • R3
    • CellProfiler Setting
• Sup. Fig. 5A and B: RNA SEQ analysis of FUS
  • Rmd file.
  • Count Matrix by FeatureCounts.
  • Normalized RNA-seq counts by DESeq2.
  • FUS specific regulated genes.
  • DEG list of WT and KO cells.
  • DEG list of WT and RE cells.
  • DEG list of RE and KO cells.