Additional file 1 of Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA
Creators: name: Hisano, Osamu
name: Ito, Takashi
name: Miura, Fumihito
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 1: Figures S1-S18, Tables S1-2, S6-11, Supplementary methods, Supplementary Information. Figure S1. – Short single-stranded DNA in cell-free blood fractions. Figure S2. – The membranous fraction of the plasma does not contain cfDNA. Figure S3. – TACS-T4 scheme for the library preparation from ssDNA. Figure S4. – The size distributions of cfDNA fragments in the libraries prepared with different pretreatments reflect different forms of DNA. Figure S5. – Two major clusters of cfDNA were consistently detected with the three ssDNA-adapted library preparation methods. Figure S6. – Locations of the C3D peaks are well conserved among individuals. Figure S7. – C3D is enriched in the regulatory regions of genes. Figure S8. – The short single-stranded cfDNA detected by other studies is enriched in the open chromatin regions and TFBS. Figure S9. – The colocalization of C3D peaks with TFBS. Figure S10. – The colocalization of short single-stranded cfDNA with TFBS based on the literature. Figure S11. – The colocalization of C3Don and C3Doff reads and short single-stranded cfDNA with the open chromatin regions and TFBS based on the literature. Figure S12. – The base composition of C3D peaks was highly biased. Figure S13. – The antisense strand of G4-Seq reads well localize on the C3D peaks. Figure S14. – Colocalization analysis of the G4 structure with short single-stranded cfDNA in the literature as well as C3Don and C3Doff reads. Figure S15. – Enriched C3D reads on the G4 structure with different library preparation methods. Figure S16. – C3D peaks without antisense G4 structures are less enriched in the regulatory regions. Figure S17. – Colocalization of C3D peaks and repetitive sequences. Figure S18. – The antisense strands of G4 motifs are enriched at the 5′-end of C3D peaks. Table S1. – Summary of the library preparations and sequencing methods Table S2. – The number of reads and peaks calculated from two publicly available single-stranded cfDNA datasets Table S6. – Numbers of uniquely mapped reads and multiply mapped reads TableS7. – Blood samples used in the current study Table S8. – Oligonucleotides used in the current study Table S9. – Indexing sequences Table S10. – Sources of publicly available data used in the current study Table S11. – Files of the ENCODE datasets downloaded from the UCSC Table Browser Information S1. – Nucleotide sequence of a gene encoding codon-optimized TS2126 RNA ligase with a Strep-Tag. Information S2. – Nucleotide sequence of a gene encoding codon-optimized human aprataxin. Information S3. – Flowcharts for bioinformatic analyses.