표제지
정책연구용역사업 최종결과보고서
목차
I. 연구결과 요약문 11
보고서 요약문 11
Summary 12
II. 정책연구용역사업 연구결과 13
제1장 최종 목표 13
제2장 국내외 기술 현황 25
제3장 최종 정책연구용역사업 내용 및 방법 29
제4장 최종 정책연구용역사업 결과 43
1) 연구 결과 (ChIP 실험 및 라이브러리 제작) 43
2) 연구 결과 (ChIP-Seq 정보생산) 92
제5장 연구결과 고찰 및 결론 142
제6장 연구성과 및 활용계획 143
제7장 정책연구용역사업 진행과정에서 수집한 해외과학기술정보 146
제8장 기타 중요변경사항 147
제9장 연구비 사용 내역 및 연구원 분담표 148
제10장 참고문헌 152
제11장 첨부서류 153
정책연구용역과제 변경요청 승인 내역서 155
별지 제7호 서식 : 참여연구자 변경통보서 156
별지 제15호 서식 : 정책연구용역사업 연구비 내역 변경 [요청/통보]서 158
판권기 159
Table 1. US dielectric relevant market size and forecast 27
Table 2. Quality control standards for Chromatin immunoprecipitation 35
Table 3. Quality control standards for DNA Chip 35
Table 4. Quality control standards for sequencing library 40
Table 5. ChIP-seq guidelines given by the IHEC consortium 40
Table 6. List of received cells from ordering department 44
Table 7. ChIP DNA concentration and the amount of human islet cell 140905 51
Table 8. ChIP DNA concentration and the amount of human islet cell 140912 51
Table 9. ChIP DNA concentration and the amount of human islet cell 140711 51
Table 10. ChIP DNA concentration and the amount of human islet cell 140822 51
Table 11. ChIP DNA concentration and the amount of human B cell 140805 51
Table 12. ChIP DNA concentration and amount of human islet cell 140805 51
Table 13. ChIP DNA concentration and amount of human islet cell 140819 52
Table 14. ChIP DNA concentration and amount of human CKD2-SNU-016-01-0306 52
Table 15. ChIP DNA concentration and amount of CKD2-SNU-015-01-0406 52
Table 16. ChIP DNA concentration and amount of CKD2-SNU-018-04-0306 52
Table 17. ChIP DNA concentration and amount of CKD2-SNU-022-04-0306 52
Table 18. ChIP DNA concentration and amount of CKD2-SNU-030-06-0406 52
Table 19. ChIP DNA concentration and amount of CKD2-SNU-033-03-0406 53
Table 20. ChIP DNA concentration and amount of CKD2-SNU-030-06-0306 53
Table 21. ChIP DNA concentration and amount of human 141104 PSA-NCAM 53
Table 22. ChIP DNA concentration and the amount of human pre-Adipocyte 141010 53
Table 23. ChIP DNA concentration and the amount of human pre-Adipocyte 141104 53
Table 24. ChIP DNA concentration and amount of CKD2-SNU-033-03-0306 53
Table 25. ChIP DNA concentration and the amount of human pre-Adipocyte 141027 54
Table 26. List of ChIP-seq library construction 91
Table 27. Numerical summary of the raw sequencing data 95
Table 28. Numerical summary of the sequencing data alignment 96
Table 29. The number of enriched regions to find using the peak calling program 97
Table 30. bigbed Summary 97
Table 31. Numerical summary of the raw sequencing data 103
Table 32. Numerical summary of the sequencing data alignment 104
Table 33. The number of enriched regions to find using the peak calling program 105
Table 34. bigbed Summary 105
Table 35. Numerical summary of the raw sequencing data 109
Table 36. FASTX-Toolkit using the sequence program, the number of pieces of filtered out 110
Table 37. Numerical summary of the sequencing data alignment 110
Table 38. The number of enriched regions to find using the peak calling program 111
Table 39. bigbed Summary 111
Table 40. Numerical summary of the raw sequencing data 115
Table 41. Numerical summary of the sequencing data alignment 116
Table 42. The number of enriched regions to find using the Peak calling program 117
Table 43. bigbed Summary 117
Table 44. Numerical summary of the raw sequencing data 122
Table 45. Numerical summary of the sequencing data alignment 123
Table 46. The number of enriched regions to find using the Peak calling program 124
Table 47. bigbed Summary 124
Table 48. Numerical summary of the raw sequencing data 128
Table 49. Numerical summary of the sequencing data alignment 129
Table 50. The number of enriched regions to find using the Peak calling program 130
Table 51. bigbed Summary 130
Table 52. GRCh37(hg19) version 139
Table 53. GRCh38(hg38) primary assembly with no alts (Genecode 22) 140
Table 54. ChIP-seq QC summary 141
Fig. 1. Chromatin structure and epigenetic modifications - histone modifications and transcription 16
Fig. 2. Domestic diabetes status 16
Fig. 3. Epigenetics research on diabetes per year 17
Fig. 4. Transcriptional regulation by the Set7 lysine methyltransferase in hyperglycemia-induced... 17
Fig. 5. International consortium 20
Fig. 6. Production of diabetes-related histone modification profiles 20
Fig. 7. Project workflow process 22
Fig. 8. Epigenome global market 27
Fig. 9. Epigenome global market distribution 28
Fig. 10. Disease-specific epigenome global market 28
Fig. 11. Role and vision of the IHEC 30
Fig. 12. Schematic workflow of the procedure 31
Fig. 13. A guideline given by the IHEC consortium suggests to map the following 6... 31
Fig. 14. Diabetes-related target cells 33
Fig. 15. Experimental procedure of ChIP-seq 33
Fig. 16. Instrument used for quality control 35
Fig. 17. Workflow diagram for sequencing library creation process 38
Fig. 18. Process of DNA sequencing library purification using the HiAccuBead 38
Fig. 19. Workflow diagram for next-generation sequencing analysis 40
Fig. 20. Sequencing data analysis and quality control regulation 42
Fig. 21. Chromatin size check I 47
Fig. 22. Chromatin size check II 48
Fig. 23. ChIP DNA QC results of human islet cell 140905 56
Fig. 24. ChIP DNA QC results of human islet cell 140912 56
Fig. 25. ChIP DNA QC results of human pre-Adipocyte 140711 57
Fig. 26. ChIP DNA QC results of human islet cell 140822 57
Fig. 27. ChIP DNA QC results of human B cell 140805 58
Fig. 28. ChIP DNA QC results of human islet cell 140805 58
Fig. 29. ChIP DNA QC results of human islet cell 140819 59
Fig. 30. ChIP DNA QC results of human CKD2-SNU-016-01-0306 59
Fig. 31. ChIP DNA QC results of human CKD2-SNU-015-01-0406 60
Fig. 32. ChIP DNA QC results of human CKD2-SNU-018-04-0306 60
Fig. 33. ChIP DNA QC results of human CKD2-SNU-022-04-0306 60
Fig. 34. ChIP DNA QC results of human CKD2-SNU-030-06-0406 61
Fig. 35. ChIP DNA QC results of human CKD2-SNU-033-03-0406 61
Fig. 36. ChIP DNA QC results of human CKD2-SNU-030-06-0306 61
Fig. 37. ChIP DNA QC results of human 141104 PSA-NCAM 62
Fig. 38. ChIP DNA QC results of human pre-Adipocyte 141010 62
Fig. 39. ChIP DNA QC results of human pre-Adipocyte 141104 62
Fig. 40. ChIP DNA QC results of human CKD2-SNU-033-03-0306 63
Fig. 41. ChIP DNA QC results of human pre-Adipocyte 141027 63
Fig. 42. Conventional ChIP PCR result of human islet cell 140905 65
Fig. 43. Conventional ChIP PCR result of human islet cell 140912 65
Fig. 44. Conventional ChIP PCR result of human preAdipocyte 140711 65
Fig. 45. Conventional ChIP PCR result of human islet cell 140822 66
Fig. 46. Conventional ChIP PCR result of human B cell 140805 66
Fig. 47. Conventional ChIP PCR result of human islet cell 140805 66
Fig. 48. Example of primer validation result (primers for... 67
Fig. 49. ChIP qPCR result of human islet cell 140905 70
Fig. 50. ChIP qPCR result of human islet cell 140912 70
Fig. 51. ChIP qPCR result of human pre-Adipocyte 140711 70
Fig. 52. ChIP qPCR result of human islet cell 140822 71
Fig. 53. ChIP qPCR result of human B cell 140805 71
Fig. 54. ChIP qPCR result of human islet cell 140805 71
Fig. 55. ChIP qPCR result of human islet cell 140819 72
Fig. 56. ChIP qPCR result of human CKD2-SNU-016-01-0306 72
Fig. 57. ChIP qPCR result of human CKD2-SNU-015-01-0406 72
Fig. 58. ChIP qPCR result of human CKD2-SNU-018-04-0306 73
Fig. 59. ChIP qPCR result of human CKD2-SNU-022-04-0306 73
Fig. 60. ChIP qPCR result of human CKD2-SNU-030-06-0406 73
Fig. 61. ChIP qPCR result of human CKD2-SNU-033-03-0406 74
Fig. 62. ChIP qPCR result of human CKD2-SNU-030-06-0306 74
Fig. 63. ChIP qPCR result of human 141104 PSA-NCAM 74
Fig. 64. ChIP qPCR result of human pre-Adipocyte 141010 75
Fig. 65. ChIP qPCR result of human pre-Adipocyte 141104 75
Fig. 66. ChIP qPCR result of human CKD2-SNU-033-03-0306 75
Fig. 67. ChIP qPCR result of human pre-Adipocyte 141027 76
Fig. 68. ChIP-sequencing library QC result of human islet 140905 80
Fig. 69. ChIP-sequencing library QC result of human islet 140912 80
Fig. 70. ChIP-sequencing library QC result of human pre-Adipocyte 140711 81
Fig. 71. ChIP-sequencing library QC result of human islet 140822 81
Fig. 72. ChIP-sequencing library QC result of human B cell 140805 82
Fig. 73. ChIP-sequencing library QC result of human islet 140805 82
Fig. 74. ChIP-sequencing library QC result of human islet 140819 83
Fig. 75. ChIP-sequencing library QC result of human CKD2-SNU-016-01-0306 83
Fig. 76. ChIP-sequencing library QC result of human CKD2-SNU-015-01-0406 84
Fig. 77. ChIP-sequencing library QC result of human CKD2-SNU-018-04-0306 84
Fig. 78. ChIP-sequencing library QC result of human CKD2-SNU-022-04-0306 85
Fig. 79. ChIP-sequencing library QC result of human CKD2-SNU-030-06-0406 85
Fig. 80. ChIP-sequencing library QC result of Human CKD2-SNU-033-03-0406 86
Fig. 81. ChIP-sequencing library QC result of Human CKD2-SNU-030-06-0306 86
Fig. 82. ChIP-sequencing library QC result of Human 141104 PSA-NCAM 87
Fig. 83. ChIP-sequencing library QC result of Human pre-Adipocyte 141010 87
Fig. 84. ChIP-sequencing library QC result of Human pre-Adipocyte 141104 88
Fig. 85. ChIP-sequencing library QC result of Human CKD2-033-03-0306 88
Fig. 86. ChIP-sequencing library QC result of Human pre-Adipocyte 141027 89
Fig. 87. Flow chart of ChIP-seq data analysis 93
Fig. 88. Box plot showing the length of the sequence-specific quality score distribution 95
Fig. 89. A line graph showing the level of redundancy sequence 96
Fig. 90. Visualization of the area near the ACTB gene 98
Fig. 91. Visualization of the gene regions near ROR1 gene 98
Fig. 92. Visualization of the area near the GAPDH gene 99
Fig. 93. Visualization of the gene regions near IRX4 99
Fig. 94. Genomic distribution of ChIP-seq signal 100
Fig. 95. Box plot showing the length of the sequence-specific quality score... 103
Fig. 96. A line graph showing the level of redundancy sequence 104
Fig. 97. Visualization of the area near the ACTB gene 106
Fig. 98. Visualization of the gene regions near ROR1 gene 106
Fig. 99. Visualization of the area near the GAPDH gene 107
Fig. 100. Visualization of the gene regions near IRX4 gene 107
Fig. 101. Genomic distribution of ChIP-seq signal 108
Fig. 102. Box plot showing the length of the sequence-specific quality score distribution 109
Fig. 103. A line graph showing the level of redundancy sequence 109
Fig. 104. Visualization of the area near the ACTB gene 111
Fig. 105. Visualization of the gene regions near ROR1 gene 112
Fig. 106. Visualization of the area near the GAPDH gene 112
Fig. 107. Visualization of the gene regions near IRX4 gene 112
Fig. 108. Genomic distribution of ChIP-seq signal 113
Fig. 109. Box plot showing the length of the sequence-specific quality score distribution 115
Fig. 110. A line graph showing the level of redundancy sequence 116
Fig. 111. Visualization of the area near the ACTB gene 118
Fig. 112. Visualization of the gene regions near ROR1 gene 118
Fig. 113. Visualization of the area near the GAPDH gene 119
Fig. 114. Visualization of the gene regions near IRX4 gene 119
Fig. 115. Genomic distribution of ChIP-seq signal 120
Fig. 116. Box plot showing the length of the sequence-specific quality score distribution 122
Fig. 117. A line graph showing the level of redundancy sequence 123
Fig. 118. Visualization of the area near the ACTB gene 124
Fig. 119. Visualization of the gene regions near ROR1 gene 125
Fig. 120. Visualization of the area near the GAPDH gene 125
Fig. 121. Visualization of the gene regions near IRX4 gene 126
Fig. 122. Genomic distribution of ChIP-seq signal 126
Fig. 123. Box plot showing the length of the sequence-specific quality score... 128
Fig. 124. A line graph showing the level of redundancy sequence 129
Fig. 125. Visualization of the area near the ACTB gene 130
Fig. 126. Visualization of the gene regions near ROR1 gene 131
Fig. 127. Visualization of the area near the GAPDH gene 131
Fig. 128. Visualization of the gene regions near IRX4 gene 132
Fig. 129. Genomic distribution of ChIP-seq signal 132