Telomere dataset used for calculating bulk and chromosome specific telomere length
Data files
Apr 05, 2024 version files 13.63 GB
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GCA_009914755.4_T2T-CHM13v2.0_genomic.TeloBPBoundaries.500kb.ends.fna
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HG002.1.NB65uq.fastq
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HG002.1.NB72uq.fastq
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HG002.1A14.NB50uq.fastq.gz
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HG002.1A14.NB68uq.fastq.gz
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HG002.1A14.NB88uq.fastq.gz
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HG002.1A15.NB68uq.fastq.gz
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HG002.1A16.NB68uq.fastq.gz
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HG002.1A16.NB88uq.fastq.gz
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HG002.1A18.NB68uq.fastq.gz
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HG002.1A21.NB68uq.fastq.gz
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HG002.1A34.NB65uq.fastq.gz
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HG002.1A34.NB72uq.fastq.gz
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HG002.1A35.NB01uq.fastq.gz
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HG002.1A35.NB50uq.fastq.gz
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HG002.2.NB01uq.fastq
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HG002.2.NB50uq.fastq
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HG002.3.NB50uq.fastq
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hg002v1.0.1_TeloBP_500Kb.fasta.gz
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InterRun1.F20.NB88.fastq.gz
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InterRun2.F22.NB50.fastq.gz
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InterRun3.F24.NB50.fastq.gz
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InterRun4.F51.NB68.fastq.gz
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InterRun5.F67.NB01.fastq.gz
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InterRun6.F68.NB01.fastq.gz
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IntraRun1.F52.NB01.fastq.gz
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IntraRun10.F52.NB68.fastq.gz
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IntraRun11.F52.NB69.fastq.gz
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IntraRun12.F52.NB70.fastq.gz
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IntraRun13.F52.NB72.fastq.gz
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IntraRun14.F52.NB88.fastq.gz
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IntraRun2.F52.NB02.fastq.gz
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IntraRun3.F52.NB15.fastq.gz
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IntraRun4.F52.NB19.fastq.gz
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IntraRun5.F52.NB20.fastq.gz
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IntraRun6.F52.NB50.fastq.gz
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IntraRun7.F52.NB65.fastq.gz
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IntraRun8.F52.NB66.fastq.gz
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IntraRun9.F52.NB67.fastq.gz
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JH100.F49.NB67.fastq.gz
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JH101.F47.NB69.fastq.gz
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JH102.F47.NB01.fastq.gz
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JH103.F48.NB15.fastq.gz
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JH104.F48.NB70.fastq.gz
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JH105.F50.NB19.fastq.gz
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JH106.F50.NB65.fastq.gz
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JH109.F53.NB68.fastq.gz
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JH110.F53.NB19.fastq.gz
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JH111.F54.NB88.fastq.gz
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JH112.F54.NB65.fastq.gz
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JH113.F38.NB67.fastq.gz
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JH114.F55.NB65.fastq.gz
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JH115.F55.NB67.fastq.gz
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JH116.F56.NB69.fastq.gz
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JH117.F56.NB70.fastq.gz
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JH118.F57.NB72.fastq.gz
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JH119.F57.NB01.fastq.gz
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JH120.F58.NB15.fastq.gz
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JH121.F58.NB19.fastq.gz
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JH122.F38.NB69.fastq.gz
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JH123.F39.NB70.fastq.gz
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JH124.F39.NB72.fastq.gz
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JH125.F59.NB01.fastq.gz
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JH126.F59.NB15.fastq.gz
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JH127.F61.NB01.fastq.gz
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JH128.F61.NB02.fastq.gz
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JH129.F61.NB50.fastq.gz
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JH130.F61.NB66.fastq.gz
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JH131.F61.NB15.fastq.gz
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JH132.F62.NB15.fastq.gz
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JH133.F62.NB01.fastq.gz
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JH134.F62.NB02.fastq.gz
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JH135.F62.NB66.fastq.gz
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JH136.F62.NB50.fastq.gz
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JH137.F64.NB01.fastq.gz
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JH138.F64.NB02.fastq.gz
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JH139.F64.NB15.fastq.gz
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JH140.F64.NB19.fastq.gz
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JH141.F65.NB20.fastq.gz
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JH142.F65.NB50.fastq.gz
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JH143.F65.NB65.fastq.gz
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JH144.F65.NB66.fastq.gz
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JH145.F66.NB67.fastq.gz
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JH146.F66.NB68.fastq.gz
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JH147.F66.NB69.fastq.gz
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JH148.F66.NB70.fastq.gz
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JH149.F66.NB72.fastq.gz
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JH150.F76.NB01.fastq.gz
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JH151.F76.NB50.fastq.gz
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JH152.F76.NB66.fastq.gz
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JH153.F76.NB15.fastq.gz
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JH154.F77.NB01.fastq.gz
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JH155.F77.NB66.fastq.gz
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JH156.F77.NB15.fastq.gz
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JH157.F78.NB01.fastq.gz
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JH158.F78.NB66.fastq.gz
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JH159.F78.NB50.fastq.gz
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JH160.F78.NB15.fastq.gz
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JH161.F79.NB15.fastq.gz
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JH162.F79.NB66.fastq.gz
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JH163.F77.NB50.fastq.gz
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JH164.F80.NB15.fastq.gz
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JH165.F80.NB66.fastq.gz
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JH166.F80.NB68.fastq.gz
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JH167.F80.NB01.fastq.gz
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JH169.F80.NB20.fastq.gz
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JH170.F80.NB50.fastq.gz
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JH171.F79.NB01.fastq.gz
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JH172.F79.NB50.fastq.gz
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JH173.F93.NB68.fastq.gz
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JH174.F93.NB01.fastq.gz
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JH176.F94.NB01.fastq.gz
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JH177.F94.NB68.fastq.gz
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JH178.F94.NB50.fastq.gz
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JH179.F95.NB01.fastq.gz
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JH180.F95.NB68.fastq.gz
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JH182.F96.NB50.fastq.gz
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JH183.F96.NB01.fastq.gz
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JH184.F96.NB68.fastq.gz
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JH185.F97.NB01.fastq.gz
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JH187.F98.NB50.fastq.gz
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JH189.F70.NB01.fastq.gz
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JH190.F69.NB01.fastq.gz
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JH191.F81.NB50.fastq.gz
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JH23.F89.NB20.fastq.gz
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JH27.F89.NB66.fastq.gz
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JH29.F92.NB66.fastq.gz
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JH30.F89.NB68.fastq.gz
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JH31.F89.NB50.fastq.gz
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JH32.F92.NB68.fastq.gz
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JH34.F92.NB20.fastq.gz
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JH35.F90.NB50.fastq.gz
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JH36.F90.NB66.fastq.gz
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JH37.F90.NB68.fastq.gz
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JH38.F90.NB20.fastq.gz
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JH40.F92.NB65.fastq.gz
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JH41.F92.NB70.fastq.gz
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JH42.F86.NB50.fastq.gz
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JH43.F86.NB66.fastq.gz
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JH44.F86.NB68.fastq.gz
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JH45.F86.NB20.fastq.gz
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JH46.F86.NB65.fastq.gz
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JH47.F86.NB70.fastq.gz
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JH48.F87.NB50.fastq.gz
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JH50.F87.NB66.fastq.gz
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JH52.F87.NB67.fastq.gz
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JH53.F87.NB65.fastq.gz
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JH54.F87.NB68.fastq.gz
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JH55.F87.NB70.fastq.gz
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JH56.F87.NB69.fastq.gz
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JH58.F87.NB20.fastq.gz
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JH59.F88.NB68.fastq.gz
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JH60.F88.NB20.fastq.gz
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JH61.F88.NB65.fastq.gz
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JH62.F88.NB70.fastq.gz
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JH63.F88.NB69.fastq.gz
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JH64.F88.NB72.fastq.gz
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JH65.F88.NB67.fastq.gz
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JH66.F88.NB15.fastq.gz
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JH67.F88.NB50.fastq.gz
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JH68.F88.NB66.fastq.gz
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JH69.F88.NB19.fastq.gz
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JH70.F33.NB01.fastq.gz
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JH71.F33.NB72.fastq.gz
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JH76.F40.NB01.fastq.gz
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JH76.UCSC.A24Mix3.NB88uq.fastq.gz
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JH77.F40.NB15.fastq.gz
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JH77.UCSC.A24Mix3.NB50uq.fastq.gz
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JH78.F35.NB01.fastq.gz
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JH80.F41.NB50.fastq.gz
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JH81.F41.NB65.fastq.gz
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JH81.UCSC.A24Mix3.NB68uq.fastq.gz
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JH82.F42.NB67.fastq.gz
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JH82.UCSC.A24Mix4.NB50uq.fastq.gz
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JH83.F35.NB15.fastq.gz
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JH84.F36.NB19.fastq.gz
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JH85.F36.NB50.fastq.gz
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JH86.F37.NB65.fastq.gz
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JH87.F37.NB67.fastq.gz
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JH88.F42.NB69.fastq.gz
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JH88.UCSC.A24Mix4.NB88uq.fastq.gz
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JH89.F43.NB70.fastq.gz
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JH90.F43.NB69.fastq.gz
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JH91.F44.NB72.fastq.gz
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JH93.F44.NB01.fastq.gz
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JH93.UCSC.A24Mix4.NB68uq.fastq.gz
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JH94.F45.NB15.fastq.gz
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JH95.F45.NB19.fastq.gz
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JH95.UCSC.A24Mix4.NB69uq.fastq.gz
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JH96.F46.NB70.fastq.gz
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JH97.F46.NB72.fastq.gz
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JH98.F49.NB50.fastq.gz
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README.md
Apr 18, 2024 version files 13.71 GB
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GCA_009914755.4_T2T-CHM13v2.0_genomic.TeloBPBoundaries.500kb.ends.fna
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HG002.1.NB65uq.fastq
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HG002.1.NB72uq.fastq
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HG002.1A14.NB50uq.fastq.gz
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HG002.1A14.NB68uq.fastq.gz
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HG002.1A14.NB88uq.fastq.gz
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HG002.1A15.NB68uq.fastq.gz
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HG002.1A16.NB68uq.fastq.gz
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HG002.1A16.NB88uq.fastq.gz
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HG002.1A18.NB68uq.fastq.gz
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HG002.1A21.NB68uq.fastq.gz
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HG002.1A34.NB65uq.fastq.gz
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HG002.1A34.NB72uq.fastq.gz
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HG002.1A35.NB01uq.fastq.gz
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HG002.1A35.NB50uq.fastq.gz
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HG002.2.NB01uq.fastq
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HG002.2.NB50uq.fastq
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HG002.3.NB50uq.fastq
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HG002.v0.7.TeloBP.cut.BothHaplotypes.fasta
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HG002.v0.7.TeloBP.cut.MATERNAL.fasta
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HG002.v0.7.TeloBP.cut.PATERNAL.fasta
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InterRun1.F20.NB88.fastq.gz
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InterRun2.F22.NB50.fastq.gz
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InterRun3.F24.NB50.fastq.gz
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InterRun4.F51.NB68.fastq.gz
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InterRun5.F67.NB01.fastq.gz
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InterRun6.F68.NB01.fastq.gz
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IntraRun1.F52.NB01.fastq.gz
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IntraRun10.F52.NB68.fastq.gz
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IntraRun11.F52.NB69.fastq.gz
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IntraRun12.F52.NB70.fastq.gz
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IntraRun13.F52.NB72.fastq.gz
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IntraRun14.F52.NB88.fastq.gz
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IntraRun2.F52.NB02.fastq.gz
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IntraRun3.F52.NB15.fastq.gz
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IntraRun4.F52.NB19.fastq.gz
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IntraRun5.F52.NB20.fastq.gz
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IntraRun6.F52.NB50.fastq.gz
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IntraRun7.F52.NB65.fastq.gz
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IntraRun8.F52.NB66.fastq.gz
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IntraRun9.F52.NB67.fastq.gz
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JH100.F49.NB67.fastq.gz
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JH101.F47.NB69.fastq.gz
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JH102.F47.NB01.fastq.gz
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JH103.F48.NB15.fastq.gz
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JH104.F48.NB70.fastq.gz
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JH105.F50.NB19.fastq.gz
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JH106.F50.NB65.fastq.gz
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JH109.F53.NB68.fastq.gz
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JH110.F53.NB19.fastq.gz
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JH111.F54.NB88.fastq.gz
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JH112.F54.NB65.fastq.gz
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JH113.F38.NB67.fastq.gz
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JH114.F55.NB65.fastq.gz
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JH115.F55.NB67.fastq.gz
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JH116.F56.NB69.fastq.gz
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JH117.F56.NB70.fastq.gz
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JH118.F57.NB72.fastq.gz
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JH119.F57.NB01.fastq.gz
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JH120.F58.NB15.fastq.gz
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JH121.F58.NB19.fastq.gz
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JH122.F38.NB69.fastq.gz
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JH123.F39.NB70.fastq.gz
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JH124.F39.NB72.fastq.gz
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JH125.F59.NB01.fastq.gz
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JH126.F59.NB15.fastq.gz
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JH127.F61.NB01.fastq.gz
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JH128.F61.NB02.fastq.gz
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JH129.F61.NB50.fastq.gz
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JH130.F61.NB66.fastq.gz
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JH131.F61.NB15.fastq.gz
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JH132.F62.NB15.fastq.gz
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JH133.F62.NB01.fastq.gz
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JH134.F62.NB02.fastq.gz
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JH135.F62.NB66.fastq.gz
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JH136.F62.NB50.fastq.gz
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JH137.F64.NB01.fastq.gz
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JH138.F64.NB02.fastq.gz
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JH139.F64.NB15.fastq.gz
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JH140.F64.NB19.fastq.gz
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JH141.F65.NB20.fastq.gz
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JH142.F65.NB50.fastq.gz
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JH143.F65.NB65.fastq.gz
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JH144.F65.NB66.fastq.gz
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JH145.F66.NB67.fastq.gz
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JH146.F66.NB68.fastq.gz
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JH147.F66.NB69.fastq.gz
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JH148.F66.NB70.fastq.gz
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JH149.F66.NB72.fastq.gz
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JH150.F76.NB01.fastq.gz
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JH151.F76.NB50.fastq.gz
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JH152.F76.NB66.fastq.gz
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JH153.F76.NB15.fastq.gz
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JH154.F77.NB01.fastq.gz
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JH155.F77.NB66.fastq.gz
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JH156.F77.NB15.fastq.gz
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JH157.F78.NB01.fastq.gz
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JH158.F78.NB66.fastq.gz
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JH159.F78.NB50.fastq.gz
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JH160.F78.NB15.fastq.gz
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JH161.F79.NB15.fastq.gz
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JH162.F79.NB66.fastq.gz
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JH163.F77.NB50.fastq.gz
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JH164.F80.NB15.fastq.gz
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JH165.F80.NB66.fastq.gz
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JH166.F80.NB68.fastq.gz
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JH167.F80.NB01.fastq.gz
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JH169.F80.NB20.fastq.gz
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JH170.F80.NB50.fastq.gz
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JH171.F79.NB01.fastq.gz
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JH172.F79.NB50.fastq.gz
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JH173.F93.NB68.fastq.gz
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JH174.F93.NB01.fastq.gz
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JH176.F94.NB01.fastq.gz
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JH177.F94.NB68.fastq.gz
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JH178.F94.NB50.fastq.gz
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JH179.F95.NB01.fastq.gz
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JH180.F95.NB68.fastq.gz
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JH182.F96.NB50.fastq.gz
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JH183.F96.NB01.fastq.gz
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JH184.F96.NB68.fastq.gz
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JH185.F97.NB01.fastq.gz
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JH187.F98.NB50.fastq.gz
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JH189.F70.NB01.fastq.gz
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JH190.F69.NB01.fastq.gz
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JH191.F81.NB50.fastq.gz
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JH23.F89.NB20.fastq.gz
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JH27.F89.NB66.fastq.gz
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JH29.F92.NB66.fastq.gz
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JH30.F89.NB68.fastq.gz
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JH31.F89.NB50.fastq.gz
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JH32.F92.NB68.fastq.gz
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JH34.F92.NB20.fastq.gz
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JH35.F90.NB50.fastq.gz
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JH36.F90.NB66.fastq.gz
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JH37.F90.NB68.fastq.gz
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JH38.F90.NB20.fastq.gz
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JH40.F92.NB65.fastq.gz
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JH41.F92.NB70.fastq.gz
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JH42.F86.NB50.fastq.gz
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JH43.F86.NB66.fastq.gz
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JH44.F86.NB68.fastq.gz
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JH45.F86.NB20.fastq.gz
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JH46.F86.NB65.fastq.gz
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JH47.F86.NB70.fastq.gz
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JH48.F87.NB50.fastq.gz
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JH50.F87.NB66.fastq.gz
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JH52.F87.NB67.fastq.gz
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JH53.F87.NB65.fastq.gz
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JH54.F87.NB68.fastq.gz
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JH55.F87.NB70.fastq.gz
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JH56.F87.NB69.fastq.gz
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JH58.F87.NB20.fastq.gz
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JH59.F88.NB68.fastq.gz
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JH60.F88.NB20.fastq.gz
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JH61.F88.NB65.fastq.gz
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JH62.F88.NB70.fastq.gz
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JH63.F88.NB69.fastq.gz
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JH64.F88.NB72.fastq.gz
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JH65.F88.NB67.fastq.gz
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JH66.F88.NB15.fastq.gz
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JH67.F88.NB50.fastq.gz
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JH68.F88.NB66.fastq.gz
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JH69.F88.NB19.fastq.gz
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JH70.F33.NB01.fastq.gz
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JH71.F33.NB72.fastq.gz
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JH76.F40.NB01.fastq.gz
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JH76.UCSC.A24Mix3.NB88uq.fastq.gz
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JH77.F40.NB15.fastq.gz
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JH77.UCSC.A24Mix3.NB50uq.fastq.gz
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JH78.F35.NB01.fastq.gz
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JH80.F41.NB50.fastq.gz
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JH81.F41.NB65.fastq.gz
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JH81.UCSC.A24Mix3.NB68uq.fastq.gz
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JH82.F42.NB67.fastq.gz
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JH82.UCSC.A24Mix4.NB50uq.fastq.gz
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JH83.F35.NB15.fastq.gz
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JH84.F36.NB19.fastq.gz
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JH85.F36.NB50.fastq.gz
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JH86.F37.NB65.fastq.gz
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JH87.F37.NB67.fastq.gz
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JH88.F42.NB69.fastq.gz
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JH88.UCSC.A24Mix4.NB88uq.fastq.gz
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JH89.F43.NB70.fastq.gz
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JH90.F43.NB69.fastq.gz
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JH91.F44.NB72.fastq.gz
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JH93.F44.NB01.fastq.gz
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JH93.UCSC.A24Mix4.NB68uq.fastq.gz
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JH94.F45.NB15.fastq.gz
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JH95.F45.NB19.fastq.gz
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JH95.UCSC.A24Mix4.NB69uq.fastq.gz
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JH96.F46.NB70.fastq.gz
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JH97.F46.NB72.fastq.gz
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JH98.F49.NB50.fastq.gz
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README.md
Apr 18, 2024 version files 13.71 GB
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GCA_009914755.4_T2T-CHM13v2.0_genomic.TeloBPBoundaries.500kb.ends.fna
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HG002.1.NB65uq.fastq
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HG002.1.NB72uq.fastq
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HG002.1A14.NB50uq.fastq.gz
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HG002.1A14.NB68uq.fastq.gz
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HG002.1A14.NB88uq.fastq.gz
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HG002.1A15.NB68uq.fastq.gz
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HG002.1A16.NB68uq.fastq.gz
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HG002.1A16.NB88uq.fastq.gz
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HG002.1A18.NB68uq.fastq.gz
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HG002.1A21.NB68uq.fastq.gz
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HG002.1A34.NB65uq.fastq.gz
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HG002.1A34.NB72uq.fastq.gz
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HG002.1A35.NB01uq.fastq.gz
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HG002.1A35.NB50uq.fastq.gz
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HG002.2.NB01uq.fastq
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HG002.2.NB50uq.fastq
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HG002.3.NB50uq.fastq
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HG002.v0.7.TeloBP.cut.BothHaplotypes.fasta
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HG002.v0.7.TeloBP.cut.MATERNAL.fasta
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HG002.v0.7.TeloBP.cut.PATERNAL.fasta
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InterRun1.F20.NB88.fastq.gz
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InterRun2.F22.NB50.fastq.gz
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InterRun3.F24.NB50.fastq.gz
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InterRun4.F51.NB68.fastq.gz
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InterRun5.F67.NB01.fastq.gz
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README.md
Abstract
Short telomeres cause age-related disease and long telomeres predispose to cancer; however, the mechanisms regulating telomere length are unclear. To probe these mechanisms, we developed a nanopore sequencing method, Telomere Profiling, that identified mean telomere length to similar a Southern and to the clinical FlowFISH assay. We mapped telomere reads to specific chromosome ends and, strikingly, could identify chromosome end-specific lengths that differed by more than 6kb. We measured chromosome end-specific telomere lengths for 147 individuals and found that specific chromosome ends were consistently shorter or longer. This rank order of specific chromosome end telomere lengths was also found in newborn cord blood, suggesting telomere length is determined at birth. The average telomere length at birth was ~8kb +/- 250 bp, shorter than previously estimated. Understanding the mechanisms regulating length will allow deeper insights into telomere biology that can lead to new approaches to disease.
README: Telomere Profiling Dataset: Telomere dataset used for calculating bulk and chromosome specific telomere lengths
https://doi.org/10.5061/dryad.dz08kps5d
The dataset includes demultiplexed raw telomere reads that were used for measuring telomere length across a wide population, telomere reads from the HG002 cell line, as well as custom CHM13 and HG002 reference genomes with truncated telomere sequences which were used for mapping reads.
Description of the data and file structure
1) Data files types are described in the table below.
Data Type | File Name | Description | Additional info |
---|---|---|---|
Telomere reads from individual donors. | JHIDXX.FXX.NBXX.fastq | JHID=individual donor number, F=experiment number, NB=barcode used | Each file contains telomere reads (fastq) from a single donor. Age of donor can be found in Table S2 of manuscript. Barcode sequence can be found in Table S3. The dataset includes telomere sequences from 132 individual donors and 15 donors diagnosed with short telomere syndromes. JH173-JH191 represent samples from short telomere syndrome patients. |
Intra-assay variance data. | IntraRunXX.F52.NBXX.fastq | 14 total files reflecting a single source sample ligated and prepared using different barcodes and sequenced on a single flow cell. | Barcode sequence can be found in Table S3. |
Inter-assay variance data. | InterRunXX.F20.NBXX.fastq | 6 data files reflecting single source material which was sequenced on 6 different flow cells. | Barcode sequence can be found in Table S3. |
Inter lab variance data. | JHXX.UCSC.A24MixX.NBXX.fastq, or JHIDXX.FXX.NBXX.fastq | 14 data files reflecting samples prepared and sequenced by different people at UCSC or Johns Hopkins. UCSC file names include: JHID=individual donor ID number, UCSC marker, Mix=experiment number, NB=barcode. Samples sequenced at Hopkins include JHID=individual donor ID number. F=experiment number, NB=barcode number | Barcode sequence can be found in Table S3. |
Customized reference genomes with removed telomeres used for mappings | 1) HG002.v0.7.TeloBP.cut.XXX.fasta ; 2) GCA_009914755.4_T2T-CHM13v2.0_genomic.TeloBPBoundaries.500kb.ends.fna | The last 500kb of subtelomere sequence from chromosome arms of the HG002 or CHM13 genomes were used to create a customized reference for telomere length measurements using mapping software. Telomeres were removed using the TeloBP algorithm. For HG002 three reference genomes are included for Only Paternal haplotype (denoted Paternal), Only Maternal alleles (denoted Maternal), or both combined in a single file (denoted Both). | TeloBP algorithm can be found at GitHub.com/GreiderLab |
HG002 sequenced telomeres | HG002.1AXX.NBXX.fastq.gz | Telomeres sequenced from HG002 cell line. A=experiment number. NB=barcode. | Alignment based pipeline for calculating telomere length of HG002 dataset can be found at GitHub.com/GreiderLab |
Methods
Telomeres were isolated and measured using telomere profiling protocol with Oxford Nanopore's MinION instrument and basecalled using ONT's guppy basecaller.