SRX999220 GSM1661107 SRP057391 SRS913423 GSM1661107 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661107 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661107 gds 301661107 GEO Accession GSM1661107 SRX999221 GSM1661108 SRP057391 SRS913422 GSM1661108 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661108 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661108 gds 301661108 GEO Accession GSM1661108 SRX999222 GSM1661109 SRP057391 SRS913421 GSM1661109 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661109 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661109 gds 301661109 GEO Accession GSM1661109 SRX999223 GSM1661110 SRP057391 SRS913419 GSM1661110 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661110 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661110 gds 301661110 GEO Accession GSM1661110 SRX999224 GSM1661111 SRP057391 SRS913420 GSM1661111 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661111 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661111 gds 301661111 GEO Accession GSM1661111 SRX999225 GSM1661112 SRP057391 SRS913416 GSM1661112 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661112 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661112 gds 301661112 GEO Accession GSM1661112 SRX999226 GSM1661113 SRP057391 SRS913417 GSM1661113 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661113 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661113 gds 301661113 GEO Accession GSM1661113 SRX999227 GSM1661114 SRP057391 SRS913418 GSM1661114 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661114 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661114 gds 301661114 GEO Accession GSM1661114 SRX999228 GSM1661115 SRP057391 SRS913415 GSM1661115 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661115 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661115 gds 301661115 GEO Accession GSM1661115 SRX999229 GSM1661116 SRP057391 SRS913414 GSM1661116 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661116 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661116 gds 301661116 GEO Accession GSM1661116 SRX999230 GSM1661117 SRP057391 SRS913412 GSM1661117 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661117 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661117 gds 301661117 GEO Accession GSM1661117 SRX999231 GSM1661118 SRP057391 SRS913413 GSM1661118 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661118 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661118 gds 301661118 GEO Accession GSM1661118 SRX999232 GSM1661119 SRP057391 SRS913411 GSM1661119 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661119 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661119 gds 301661119 GEO Accession GSM1661119 SRX999233 GSM1661120 SRP057391 SRS913410 GSM1661120 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661120 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661120 gds 301661120 GEO Accession GSM1661120 SRX999234 GSM1661121 SRP057391 SRS913409 GSM1661121 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661121 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661121 gds 301661121 GEO Accession GSM1661121 SRX999235 GSM1661122 SRP057391 SRS913408 GSM1661122 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661122 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661122 gds 301661122 GEO Accession GSM1661122 SRX999236 GSM1661123 SRP057391 SRS913407 GSM1661123 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661123 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661123 gds 301661123 GEO Accession GSM1661123 SRX999237 GSM1661124 SRP057391 SRS913406 GSM1661124 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661124 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661124 gds 301661124 GEO Accession GSM1661124 SRX999238 GSM1661125 SRP057391 SRS913405 GSM1661125 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661125 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661125 gds 301661125 GEO Accession GSM1661125 SRX999239 GSM1661126 SRP057391 SRS913404 GSM1661126 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661126 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661126 gds 301661126 GEO Accession GSM1661126 SRX999240 GSM1661127 SRP057391 SRS913403 GSM1661127 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661127 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661127 gds 301661127 GEO Accession GSM1661127 SRX999241 GSM1661128 SRP057391 SRS913402 GSM1661128 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661128 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661128 gds 301661128 GEO Accession GSM1661128 SRX999242 GSM1661129 SRP057391 SRS913401 GSM1661129 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661129 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661129 gds 301661129 GEO Accession GSM1661129 SRX999243 GSM1661130 SRP057391 SRS913400 GSM1661130 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661130 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661130 gds 301661130 GEO Accession GSM1661130 SRX999244 GSM1661131 SRP057391 SRS913399 GSM1661131 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661131 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661131 gds 301661131 GEO Accession GSM1661131 SRX999245 GSM1661132 SRP057391 SRS913398 GSM1661132 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661132 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661132 gds 301661132 GEO Accession GSM1661132 SRX999246 GSM1661133 SRP057391 SRS913397 GSM1661133 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661133 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661133 gds 301661133 GEO Accession GSM1661133 SRX999247 GSM1661134 SRP057391 SRS913396 GSM1661134 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661134 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661134 gds 301661134 GEO Accession GSM1661134 SRX999248 GSM1661135 SRP057391 SRS913395 GSM1661135 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661135 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661135 gds 301661135 GEO Accession GSM1661135 SRX999249 GSM1661136 SRP057391 SRS913394 GSM1661136 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661136 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661136 gds 301661136 GEO Accession GSM1661136 SRX999250 GSM1661137 SRP057391 SRS913393 GSM1661137 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661137 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661137 gds 301661137 GEO Accession GSM1661137 SRX999251 GSM1661138 SRP057391 SRS913392 GSM1661138 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661138 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661138 gds 301661138 GEO Accession GSM1661138 SRX999252 GSM1661139 SRP057391 SRS913390 GSM1661139 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661139 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661139 gds 301661139 GEO Accession GSM1661139 SRX999253 GSM1661140 SRP057391 SRS913391 GSM1661140 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661140 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661140 gds 301661140 GEO Accession GSM1661140 SRX999254 GSM1661141 SRP057391 SRS913389 GSM1661141 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661141 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661141 gds 301661141 GEO Accession GSM1661141 SRX999255 GSM1661142 SRP057391 SRS913388 GSM1661142 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661142 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661142 gds 301661142 GEO Accession GSM1661142 SRX999256 GSM1661143 SRP057391 SRS913387 GSM1661143 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661143 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661143 gds 301661143 GEO Accession GSM1661143 SRX999257 GSM1661144 SRP057391 SRS913386 GSM1661144 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661144 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661144 gds 301661144 GEO Accession GSM1661144 SRX999258 GSM1661145 SRP057391 SRS913385 GSM1661145 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661145 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661145 gds 301661145 GEO Accession GSM1661145 SRX999259 GSM1661146 SRP057391 SRS913384 GSM1661146 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661146 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661146 gds 301661146 GEO Accession GSM1661146 SRX999260 GSM1661147 SRP057391 SRS913383 GSM1661147 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661147 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661147 gds 301661147 GEO Accession GSM1661147 SRX999261 GSM1661148 SRP057391 SRS913382 GSM1661148 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661148 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661148 gds 301661148 GEO Accession GSM1661148 SRX999262 GSM1661149 SRP057391 SRS913381 GSM1661149 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661149 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661149 gds 301661149 GEO Accession GSM1661149 SRX999263 GSM1661150 SRP057391 SRS913380 GSM1661150 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661150 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661150 gds 301661150 GEO Accession GSM1661150 SRX999264 GSM1661151 SRP057391 SRS913377 GSM1661151 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661151 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661151 gds 301661151 GEO Accession GSM1661151 SRX999265 GSM1661152 SRP057391 SRS913378 GSM1661152 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661152 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661152 gds 301661152 GEO Accession GSM1661152 SRX999266 GSM1661153 SRP057391 SRS913379 GSM1661153 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661153 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661153 gds 301661153 GEO Accession GSM1661153 SRX999267 GSM1661154 SRP057391 SRS913375 GSM1661154 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661154 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661154 gds 301661154 GEO Accession GSM1661154 SRX999268 GSM1661155 SRP057391 SRS913374 GSM1661155 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661155 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661155 gds 301661155 GEO Accession GSM1661155 SRX999269 GSM1661156 SRP057391 SRS913373 GSM1661156 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661156 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661156 gds 301661156 GEO Accession GSM1661156 SRX999270 GSM1661157 SRP057391 SRS913376 GSM1661157 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661157 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661157 gds 301661157 GEO Accession GSM1661157 SRX999271 GSM1661158 SRP057391 SRS913372 GSM1661158 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661158 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661158 gds 301661158 GEO Accession GSM1661158 SRX999272 GSM1661159 SRP057391 SRS913370 GSM1661159 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661159 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661159 gds 301661159 GEO Accession GSM1661159 SRX999273 GSM1661160 SRP057391 SRS913371 GSM1661160 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661160 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661160 gds 301661160 GEO Accession GSM1661160 SRX999274 GSM1661161 SRP057391 SRS913369 GSM1661161 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661161 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661161 gds 301661161 GEO Accession GSM1661161 SRX999275 GSM1661162 SRP057391 SRS913367 GSM1661162 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661162 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661162 gds 301661162 GEO Accession GSM1661162 SRX999276 GSM1661163 SRP057391 SRS913368 GSM1661163 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661163 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661163 gds 301661163 GEO Accession GSM1661163 SRX999277 GSM1661164 SRP057391 SRS913366 GSM1661164 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661164 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661164 gds 301661164 GEO Accession GSM1661164 SRX999278 GSM1661165 SRP057391 SRS913365 GSM1661165 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661165 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661165 gds 301661165 GEO Accession GSM1661165 SRX999279 GSM1661166 SRP057391 SRS913364 GSM1661166 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661166 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661166 gds 301661166 GEO Accession GSM1661166 SRX999280 GSM1661167 SRP057391 SRS913362 GSM1661167 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661167 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661167 gds 301661167 GEO Accession GSM1661167 SRX999281 GSM1661168 SRP057391 SRS913363 GSM1661168 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661168 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661168 gds 301661168 GEO Accession GSM1661168 SRX999282 GSM1661169 SRP057391 SRS913361 GSM1661169 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661169 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661169 gds 301661169 GEO Accession GSM1661169 SRX999283 GSM1661170 SRP057391 SRS913360 GSM1661170 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661170 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661170 gds 301661170 GEO Accession GSM1661170 SRX999284 GSM1661171 SRP057391 SRS913358 GSM1661171 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661171 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661171 gds 301661171 GEO Accession GSM1661171 SRX999285 GSM1661172 SRP057391 SRS913359 GSM1661172 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. NextSeq 500 GEO Sample GSM1661172 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661172 gds 301661172 GEO Accession GSM1661172 SRX999286 GSM1661173 SRP057391 SRS913357 GSM1661173 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. NextSeq 500 GEO Sample GSM1661173 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661173 gds 301661173 GEO Accession GSM1661173 SRX999287 GSM1661174 SRP057391 SRS913356 GSM1661174 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661174 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661174 gds 301661174 GEO Accession GSM1661174 SRX999288 GSM1661175 SRP057391 SRS913355 GSM1661175 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. NextSeq 500 GEO Sample GSM1661175 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661175 gds 301661175 GEO Accession GSM1661175 SRX999289 GSM1661176 SRP057391 SRS913354 GSM1661176 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. NextSeq 500 GEO Sample GSM1661176 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661176 gds 301661176 GEO Accession GSM1661176 SRX999290 GSM1661177 SRP057391 SRS913353 GSM1661177 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. NextSeq 500 GEO Sample GSM1661177 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661177 gds 301661177 GEO Accession GSM1661177 SRX999291 GSM1661178 SRP057391 SRS913351 GSM1661178 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. NextSeq 500 GEO Sample GSM1661178 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661178 gds 301661178 GEO Accession GSM1661178 SRX999292 GSM1661179 SRP057391 SRS913352 GSM1661179 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. NextSeq 500 GEO Sample GSM1661179 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661179 gds 301661179 GEO Accession GSM1661179 SRX999293 GSM1661180 SRP057391 SRS913350 GSM1661180 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. NextSeq 500 GEO Sample GSM1661180 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661180 gds 301661180 GEO Accession GSM1661180 SRX999294 GSM1661181 SRP057391 SRS913348 GSM1661181 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. NextSeq 500 GEO Sample GSM1661181 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661181 gds 301661181 GEO Accession GSM1661181 SRX999295 GSM1661182 SRP057391 SRS913347 GSM1661182 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661182 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661182 gds 301661182 GEO Accession GSM1661182 SRX999296 GSM1661183 SRP057391 SRS913345 GSM1661183 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661183 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661183 gds 301661183 GEO Accession GSM1661183 SRX999297 GSM1661184 SRP057391 SRS913346 GSM1661184 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661184 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661184 gds 301661184 GEO Accession GSM1661184 SRX999298 GSM1661185 SRP057391 SRS913344 GSM1661185 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661185 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661185 gds 301661185 GEO Accession GSM1661185 SRX999299 GSM1661186 SRP057391 SRS913343 GSM1661186 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661186 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661186 gds 301661186 GEO Accession GSM1661186 SRX999300 GSM1661187 SRP057391 SRS913349 GSM1661187 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661187 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661187 gds 301661187 GEO Accession GSM1661187 SRX999301 GSM1661188 SRP057391 SRS913341 GSM1661188 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661188 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661188 gds 301661188 GEO Accession GSM1661188 SRX999302 GSM1661189 SRP057391 SRS913338 GSM1661189 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661189 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661189 gds 301661189 GEO Accession GSM1661189 SRX999303 GSM1661190 SRP057391 SRS913340 GSM1661190 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661190 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661190 gds 301661190 GEO Accession GSM1661190 SRX999304 GSM1661191 SRP057391 SRS913339 GSM1661191 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661191 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661191 gds 301661191 GEO Accession GSM1661191 SRX999305 GSM1661192 SRP057391 SRS913335 GSM1661192 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661192 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661192 gds 301661192 GEO Accession GSM1661192 SRX999306 GSM1661193 SRP057391 SRS913336 GSM1661193 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661193 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661193 gds 301661193 GEO Accession GSM1661193 SRX999307 GSM1661194 SRP057391 SRS913337 GSM1661194 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661194 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661194 gds 301661194 GEO Accession GSM1661194 SRX999308 GSM1661195 SRP057391 SRS913334 GSM1661195 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661195 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661195 gds 301661195 GEO Accession GSM1661195 SRX999309 GSM1661196 SRP057391 SRS913333 GSM1661196 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661196 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661196 gds 301661196 GEO Accession GSM1661196 SRX999310 GSM1661197 SRP057391 SRS913332 GSM1661197 OTHER GENOMIC other DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis. Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers. Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads. Illumina HiSeq 2000 GEO Sample GSM1661197 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1661197 gds 301661197 GEO Accession GSM1661197