Sequence Read Archive: Database for High-throughput sequencing best practice 2013

統合データベース講習会 AJACS富山「次世代シーケンスデータベース Sequence Read Archive を利用する」

Transcript

1. ࣍ੈ୅γʔέϯεσʔλϕʔε 4FRVFODF
   3FBE
   "SDIJWFΛར༻͢Δ AJACS#42 TOYAMA 
   ౷߹σʔλϕʔεߨशձ
   "+"$4෋ࢁ 0
2. ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔ
   ಛ೚ٕज़ઐ໳һ
   େాୡ࿠ 5B[SP
   0IUB
   5FDI
   4QFDJBMJTU
   %BUBCBTF
   $FOUFS
   GPS
   -JGF
   4DJFODF Effective SRA - public database for high-throughput sequencing
3. ͓͜ͱΘΓ Preface A
4. /(4σʔλղੳͷνϡʔτϦΞϧ͸͋Γ·ͤΜ %#΁ͷσʔλొ࿥ͷνϡʔτϦΞϧ͸͋Γ·ͤΜ /(4ݚڀΛαϙʔτ͢Δެڞσʔλͷ͓࿩Ͱ͢ Preface σʔλղੳΛαϙʔτ͢ΔϦιʔε͸͝঺հ͠·͢ σʔλొ࿥ͷࡍʹඞཁͳ৘ใ͸͝঺հ͠·͢ ݚڀͷݱ৔Ͱ׆͔ͨ͢Ίͷެڞ%#ͷ࢖͍ํΛ͝঺հ͠·͢ A A D
5. ຊ೔ͷ಺༰ 0 Table of Contents
6. 4FRVFODF
   3FBE
   "SDIJWF
   43"ʹ͍ͭͯ %#$-4ʹ͓͚ΔऔΓ૊Έ /(4σʔλݕࡧͱར༻ͷ࣮ྫ Table of Contents ӡӦମ੍ɼϙϦγʔɼެ։͞ΕΔσʔλ ଞ%#ͱͷ౷߹ɼݕࡧػೳͷ։ൃɼ౷ܭʹΑΔ%#ͷݱঢ়ͷՄࢹԽ ঺հͨ͠αʔϏεΛར༻ͯ͠ɼաڈͷ/(4ݚڀࣄྫΛௐࠪ͢Δ n E X
7. ެڞ/(4σʔλϕʔε
   4FRVFODF
   3FBE
   "SDIJWF
   43"
   ʹ͍ͭͯ ӡӦମ੍ɼϙϦγʔɼެ։͞ΕΔσʔλ SRA: The public DB for primary NGS data n
8. ӡӦମ੍ ϙϦγʔ ެ։͞ΕΔσʔλ About SRA /$#*
   43"
   &#*
   &/"
   %%#+
   %3"͔ΒͳΔ*/4%$ʹΑͬͯ ڠಉӡӦɽہͷͲ͔͜ΒͰ΋ొ࿥ɾσʔλΞΫηε͕Մೳɽ ഑ྻσʔλͱ࣮ݧɼαϯϓϧͳͲͷৄࡉΛهड़ͨ͠ϝλσʔλɽ ഑ྻ͸H[C[΋͘͠͸ಠࣗܗࣜͰѹॖ͞Εͨ΋ͷ͕%-Մೳɽ C L J ௒ฒྻܕγʔέϯα͔ΒಘΒΕΔҰ࣍഑ྻσʔλΛड෇ɾެ։ɽ QFSTPOBMMZ
   JEFOUJGJBCMFͳσʔλ͸ผ%# EC(B1
   &(" ʹొ࿥ɽ
9. INSDC: International Nucleotide Sequence Database Collaboration http://www.insdc.org ήϊϜ৘ใͷඪ४ԽͳͲͷ৘ใ %#
   DPMMBC
   ͷϙϦγʔ
10. The INSDC Members /$#*
    43" &.#-&#*
    &/"
    
    43" %%#+
    %3" ࠷΋ड෇σʔλ਺͕ଟ͍ɽ ಠࣗѹॖϑΥʔϚοτ43"ϑΥʔϚοτͷ։ൃݩɽ ࡾౡͷҨ఻ֶݚڀॴ಺ʹ͋Δ%%#+ʹΑͬͯӡ༻͞Ε͍ͯΔɽ ඇѹॖܗࣜͰ΋σʔλΛެ։͍ͯ͠Δɽ ैདྷͷ഑ྻΞʔΧΠϒͱಉ͡ηΫγϣϯ͕։ൃɾӡ༻͍ͯ͠Δɽ ొ࿥ɾݕࡧڞʹ(6*$6*྆ํΛ૝ఆͯ͠։ൃ͞Ε͍ͯΔɽ
11. The INSDC Members /$#*
    43" &.#-&#*
    &/"43" %%#+
    %3" ࠷΋ड෇σʔλ਺͕ଟ͍ɽ ಠࣗѹॖϑΥʔϚοτ43"ϑΥʔϚοτͷ։ൃݩɽ ࡾౡͷҨ఻ֶݚڀॴ಺ʹ͋Δ%%#+ʹΑͬͯӡ༻͞Ε͍ͯΔɽ ඇѹॖܗࣜͰ΋σʔλΛެ։͍ͯ͠Δɽ ैདྷͷ഑ྻΞʔΧΠϒͱಉ͡ηΫγϣϯ͕։ൃɾӡ༻͍ͯ͠Δɽ ొ࿥ɾݕࡧڞʹ(6*$6*྆ํΛ૝ఆͯ͠։ൃ͞Ε͍ͯΔɽ
12. NCBI SRA http://www.ncbi.nlm.nih.gov/sra ϑϦʔϫʔυݕࡧ ৄࡉݕࡧ 43"
    #-"45 ϩϯάϦʔυͷΈ 4PGUXBSF
    43"UPPMLJU
13. NCBI SRA #JPQSPKFDUͷώοτ ώοτ݅਺ &YQFSJNFOU୯Ґ λΠτϧɼγʔέϯαɼ γʔέϯεྔͳͲͷ৘ใ ώοτͨ͠ੜ෺छ Ωʔϫʔυ
    lIVNBO
    NJDSPCJPNF
    QSPKFDUz
    ͷݕࡧ݁Ռ
14. NCBI SRA ࣮ݧͷλΠτϧ MBZPVU
    BEBQUPSͳͲͷ Ϧʔυͷ৘ใ γʔέϯγϯάϥϯ͝ͱͷ ৘ใͱ%-ϦϯΫ ݕࡧ݁Ռͷτοϓώοτ
    439
15. The INSDC Members /$#*
    43" &.#-&#*
    &/"43" %%#+
    %3" ࠷΋ड෇σʔλ਺͕ଟ͍ɽ ಠࣗѹॖϑΥʔϚοτ43"ϑΥʔϚοτͷ։ൃݩɽ ࡾౡͷҨ఻ֶݚڀॴ಺ʹ͋Δ%%#+ʹΑͬͯӡ༻͞Ε͍ͯΔɽ ඇѹॖܗࣜͰ΋σʔλΛެ։͍ͯ͠Δɽ ैདྷͷ഑ྻΞʔΧΠϒͱಉ͡ηΫγϣϯ͕։ൃɾӡ༻͍ͯ͠Δɽ ొ࿥ɾݕࡧڞʹ(6*$6*྆ํΛ૝ఆͯ͠։ൃ͞Ε͍ͯΔɽ
16. EMBL-EBI ENA http://www.ebi.ac.uk/ena ৄࡉݕࡧ ϑϦʔϫʔυݕࡧ ഑ྻݕࡧ
17. EMBL-EBI ENA ֤ΧςΰϦʹ͓͚Δݕࡧ݁Ռͷ ώοτ਺ ֤ΧςΰϦͷτοϓώοτ Ωʔϫʔυ
    lIVNBO
    NJDSPCJPNF
    QSPKFDUz
    ͷݕࡧ݁Ռ
18. EMBL-EBI ENA ࣮ݧʹ͍ͭͯͷ৘ใ γʔέϯγϯάϥϯͷ৘ใɼ %-ϦϯΫ z&YQFSJNFOUzͷτοϓώοτ
    439 Ұׅ%-ɼςΩετܗࣜͰͷ දࣔɼΧϥϜͷબ୒ දࣔ͞Ε͍ͯΔ৘ใΛ ςΩετܗࣜͰ%-
19. The INSDC Members /$#*
    43" &.#-&#*
    &/"43" %%#+
    %3" ࠷΋ड෇σʔλ਺͕ଟ͍ɽ ಠࣗѹॖϑΥʔϚοτ43"ϑΥʔϚοτͷ։ൃݩɽ ࡾౡͷҨ఻ֶݚڀॴ಺ʹ͋Δ%%#+ʹΑͬͯӡ༻͞Ε͍ͯΔɽ ඇѹॖܗࣜͰ΋σʔλΛެ։͍ͯ͠Δɽ ैདྷͷ഑ྻΞʔΧΠϒͱಉ͡ηΫγϣϯ͕։ൃɾӡ༻͍ͯ͠Δɽ ొ࿥ɾݕࡧڞʹ(6*$6*྆ํΛ૝ఆͯ͠։ൃ͞Ε͍ͯΔɽ
20. DDBJ DRA αΠτ಺ݕࡧ σʔλͷݕࡧɼ σʔλͷొ࿥ɼ ಈըϚχϡΞϧ http://trace.ddbj.ac.jp/dra
21. DDBJ DRA *%ʹΑΔݕࡧɼ ϑΝηοτ ߜࠐ ݕࡧɼ ΩʔϫʔυʹΑΔݕࡧ ੜ෺छɼ࣮ݧछɼσʔλొ࿥ݩͷ ϥϯΩϯάUPQ http://trace.ddbj.ac.jp/DRASearch *%छ͝ͱͷΤϯτϦ਺
22. DDBJ DRA ૯ώοτ਺ ݕࡧ݁Ռ http://trace.ddbj.ac.jp/DRASearch ϝλσʔλͷλΠϓͱ ੜ෺छʹΑΔߜΓࠐΈ
23. DDBJ DRA ؔ࿈ΞΠςϜ΁ͷϦϯΫͱ %-ϦϯΫ ࣮ݧͷৄࡉ৘ใ ϥΠϒϥϦ࡞੡ɼ γʔέϯαɼ ϕʔείʔϧͳͲͷ৘ใ z&YQFSJNFOUzͰߜΓࠐΈˠτοϓώοτ
    439
24. DDBJ DRA /BWJHBUJPOˠ3VO
    433
    %-Ͱ͖ͳ͍΋ͷͷྫ
25. DDBJ DRA %3"4FBSDIˠ%33
    %-͕Մೳͳ΋ͷͷྫ Ϧʔυͷ৘ใ RVBMJUZʹνΣοΫ͢Δͱ QISFE
    TDPSF͕දࣔ͞ΕΔ 'BTURܗࣜͱ 43"-JUFܗࣜɼ ͦΕͧΕͷ%-ϦϯΫ '51
26. DDBJ DRA /$#*
    43"Ͱ
    z433z
    Λݕࡧˠ3FDPSE
    JT
    SFNPWFE
27. Handson ݕࡧͯ͠ΈΔ ੜ෺छɼγʔέϯαʔ໊ɼҨ఻ࢠ໊ɼ࣬ױ໊ͳͲͰݕࡧɽ "EWBODFEৄࡉݕࡧ΋࢖ͬͯΈΔɽ c ग़͖ͯͨσʔλͷৄࡉΛௐ΂Δ σʔλ͕ͲΕ͘Β͍ͷେ͖͔͞ௐ΂Δ μ΢ϯϩʔυʹͲΕ͘Β͍͕͔͔࣌ؒΓͦ͏͔ʁ ϋʔυσΟεΫͷۭ͖༰ྔʹऩ·Δ͔ʁ ώοτͨ݅͠਺͕ଟ͗͢Δগͳ͗͢Δ࣌͸ผͷݕࡧΛࢼ͢ɽ ໘നͦ͏ͳσʔλ͔Ͳ͏͔൑அͰ͖Δ৘ใΛ୳͢ɽ
28. Search Tips ͦΕͧΕ͕ಠࣗʹػೳΛ։ൃ͍ͯ͠Δ ࣮ߦͰ͖Δݕࡧͷछྨɼ݁ՌͷදࣔͳͲ͕ҟͳΔɽ *%͸ڞ௨ͳͷͰɼ࢖͍෼͚Δ͜ͱͰΑΓศརʹ୳ͤΔɽ O %-Ͱ͖ͳ͍σʔλ΋͋Δ ϝλσʔλʹهड़͞Εͳ͍৘ใ͸ݕࡧͰ͖ͳ͍ ϝλσʔλͱ͸ɼ഑ྻσʔλʹର͢Δ஫ऍσʔλͷ͜ͱɽ ࢦఆͷܗࣜʹै͍ొ࿥ऀʹΑͬͯهड़͞ΕΔɽ ༷ʑͳཧ༝Ͱొ࿥ऀʹΑͬͯऔΓԼ͛ΒΕΔͳͲͷଞʹɼ ొ࿥͞Εͨ͹͔ΓͰڞ༗͞Ε͍ͯͳ͍ͨΊݟ͔ͭΒͳ͍͜ͱ΋ɽ
29. ! ϝλσʔλ Metadata Object
30. Metadata Object Dependencies Submission Analysis Study Sample Sample Experiment Experiment Run Run Run Run ഑ྻσʔλͱڞʹొ࿥͞ΕΔϝλσʔλ͸छྨͷΦϒδΣΫτ͔Β ߏ੒͞ΕɼΦϒδΣΫτͷछྨʹԠͯ͡৘ใ͕هड़͞ΕΔ
31. Metadata Object Dependencies Submission Analysis Study Sample Sample Experiment Experiment Run Run Run Run ϝλσʔλΛొ࿥୯ҐͰ·ͱΊΔ4VCNJTTJPOΛআ͘ͱɼ جຊతͳϝλσʔλͷηοτͷؔ܎ੑ͸͜ͷΑ͏ʹͳΔ
32. Metadata Object Dependencies DRA000001 DRZ000001 DRP000001 DRS000001 DRS000001 DRX000001 DRX000002 DRR000004 DRR000003 DRR000002 DRR000001 ͦΕͧΕͷΦϒδΣΫτ͸ಠࣗͷ*%Λ͍࣋ͬͯΔɽ *%͸σʔλΛड͚෇͚ͨ%#ͱΦϒδΣΫτͷछྨΛࣔ͢ ӳࣈࣈʹଓܻ͘ͷ਺ࣈͰࣔ͞ΕΔ
33. Metadata Tips ΦϒδΣΫτɼ*%ͷؔ܎͸ෳࡶ େن໛ͳϓϩδΣΫτʹͳΔͱ3VO΍4BNQMF͕਺ඦʹ΋ͳΔɽ ·ͨɼ༷ʑͳཧ༝Ͱ ྫ֎తʹ ϧʔϧ͔Β֎Ε͍ͯΔ΋ͷ΋͋Δɽ O lͲͷ৘ใ͕Ͳ͜ʹهड़͞ΕΔ͔zΛ೺Ѳ͢Δ ొ࿥ऀʹΑͬͯϝλσʔλͷهड़ʹ͕ࠩ͋Δ ಛʹϥΠϒϥϦௐ੔ͷ߲ͳͲɽ ࿦จͳͲͷ৘ใ͕ߋ৽͞Εͯ΋Ξοϓσʔτ͞Εͳ͍৔߹΋ɽ σʔλͷొ࿥͚ͩͰͳ͘ɼݕࡧ͢Δࡍʹ΋ॏཁɽ ৄ͘͠͸
    IUUQUSBDFEECKBDKQESBNFUBEBUBIUNM
34. ·ͱΊ n Summary #1
35. Summary #1 43"͸*/4%$ϝϯόʔہʹΑͬͯӡӦ͞ΕΔ σʔλ͸ڞ༗͞ΕΔͷͰೖΓޱ͕Ͳ͜Ͱ΋ಉ͕ͩ͡ɼ ݕࡧػೳͳͲ͕ͦΕͧΕҟͳΔɽ ഑ྻσʔλͷొ࿥ɾݕࡧʹ͸ϝλσʔλ͕ॏཁ ͦΕͧΕʹ*%͕ৼΒΕొ࿥ऀ͕هड़͢Δɽ ಺༰ͱؔ܎͸ಛʹσʔλొ࿥࣌ʹ͸ཧղ͢Δඞཁ͕͋Δɽ n
36. E %#$-4ʹ͓͚ΔऔΓ૊Έ ଞ%#ͱͷ౷߹ɼݕࡧػೳͷ։ൃɼ౷ܭʹΑΔ%#ͷݱঢ়ͷՄࢹԽ Tech Dev at DBCLS - Search and Statistics
37. ଞ%#ͱͷ౷߹ ݕࡧػೳͷ։ൃ ౷ܭʹΑΔ%#ͷݱঢ়೺Ѳ DBCLS v SRA ϝλσʔλ͚ͩͰͳ͘ɼ࿦จͳͲͷจݙ৘ใ΍ɼ ࣬ױͷ৘ใɼ͞Βʹݸผσʔλͷ഑ྻΫΦϦςΟΛܭࢉɽ ہͷػೳΛ౷߹ͭͭ͠ɼಠࣗͷػೳΛ௥Ճͨ͠ɼ ΑΓσʔλར༻ऀΛࢦ޲ͨ͠ݕࡧػೳΛ։ൃɽ ϝλσʔλΛݩʹͨ͠ొ࿥਺ͷਪҠΛެ։ɽ ͞Βʹ഑ྻ৘ใΛݩʹͨ͠%#શମͷ৘ใΛ෼ੳɽ ≠ π ¥
38. %#$-4
    43" ≠ DBCLS SRA
39. DBCLS SRA http://sra.dbcls.jp/ ొ࿥͞Ε͍ͯΔσʔλΛ ϝλσʔλผʹϦετදࣔ 43"
    *%΍ੜ෺छɼ γʔέϯαͳͲ͔Βݕࡧ
40. http://sra.dbcls.jp/ ࣮ݧछɼγʔέϯαɼ ੜ෺छ͝ͱͷϥϯΩϯά ೔෇ʹΑΔਪҠͷάϥϑ DBCLS SRA
41. http://sra.dbcls.jp/ σʔλΛจݙ৘ใ͔Β୳͢ σʔλΛ࣬ױ৘ใ͔Β୳͢ DBCLS SRA
42. จݙ৘ใͷ౷߹ ∆ DBCLS SRA Publication Search
43. ഑ྻσʔλͷ৘ใ͸࿦จͷํ͕ৄ͍͠ ഑ྻσʔλ͕࿦จΑΓલʹެ։͞ΕΔ͜ͱ΋ ϝλσʔλʹจݙ৘ใ͕௥ه͞Εͳ͍͜ͱ͕͋Δ DBCLS SRA Publication Search ݚڀͷதͰͷγʔέϯεͷҐஔ͚ͮ΋ॏཁɽ .BUFSJBMT.FUIPETʹৄ͍͠৘ใ͕͋Δ͜ͱ͕ଟ͍ɽ άϥϯτͷ੍໿ɼδϟʔφϧʹΑΔσʔλެ։ͷࢦࣔͳͲɽ େن໛ͳϓϩδΣΫτͰ͸ެ։ϙϦγʔΛઃఆ͢Δ͜ͱ΋ɽ Ұ౓ొ࿥͞Εͨޙʹϝλσʔλ͕Ξοϓσʔτ͞Εͳ͍໰୊ɽ ެ։͞Εͨσʔλͱ࿦จͷඥ෇͚Λߦ͏ඞཁ͕͋Δɽ ∆
44. %#$-4
    43"
    ˠ
    zจݙ͔Β୳͢z ࣮ݧछɼγʔέϯαɼ ੜ෺छʹΑΔߜΓࠐΈݕࡧ 43"
    *%ͱ1VC.FE
    *%ͷର Ԡද͓Αͼจݙͷ৘ใ ΧϥϜ໊ΛΫϦοΫͯ͠ ฒ΂ସ͑ DBCLS SRA Publication Search
45. ࣬ױ৘ใͷ౷߹ ® DBCLS SRA Diseases Search
46. ΫϦχΧϧγʔέϯεͷݕࡧ͸ࠔ೉ ϝλσʔλͷهड़͚ͩͰ͸ෆे෼ͳ৔߹΋ จݙ৘ใʹ෇༩͞ΕͨλάΛར༻͢Δ DBCLS SRA Diseases Search શήϊϜγʔέϯε΍ଟܕͷ৘ใͳͲ͸ɼ 43"Ͱ͸ެ։͞Εͳ͍৔߹΋ଟ͍ɽ ొ࿥ऀʹΑͬͯهड़ͷ࢓ํɼ৘ใྔʹ͕ࠩ͋ΔͨΊɼ Ұׅͯ͠ݕࡧ͢Δ͜ͱ͕೉͍͠ɽ 1VC.FEΤϯτϦʹ෇༩͞ΕΔ.F4)λʔϜΛར༻ͯ͠ɼ ࣬ױͷ৘ใΛΩʔʹͨ͠σʔλݕࡧػೳΛ։ൃɽ ®
47. %#$-4
    43"
    ˠ
    z࣬ױ͔ΒோΊΔz
    ˠ
    ස౓ผ ࣬ױλΠϓ͔Βݕࡧ ࣬ױ໊ͱొ࿥σʔλ਺ දࣔ݅਺ͷࢦఆ DBCLS SRA Diseases Search
48. %#$-4
    43"
    ˠ
    z࣬ױ͔ΒோΊΔz
    ˠ
    ࣬ױΧςΰϦผ ΫϦοΫͯ͠πϦʔΛల։ ਺ࣈΛΫϦοΫͯ͠ Ϧετදࣔ DBCLS SRA Diseases Search
49. %#$-4ಠࣗͷݕࡧػೳ S DBCLS SRA Metadata Search
50. S ΑΓϢʔβࢦ޲ͷݕࡧػೳΛఏڙ͢Δ ΑΓଟ͘ͷ৘ใΛݕࡧʹ൓өͤ͞Δ ࣗಈԽʹରԠ͢Δ DBCLS SRA Metadata Search ϝλσʔλ*%ʹΑΔ؅ཧͳͲɼϢʔβʹͱͬͯ ֮͑ͳ͚Ε͹͍͚ͳ͍஌ࣝΛͳΔ΂͘ݮΒ͢ɽ ϝλσʔλ͚ͩͰͳ͘ɼ౷߹͞Εͨଞ%#ͷ৘ใ΍ ಠࣗͷ৘ใΛऔΓೖΕͨॊೈͳݕࡧػೳΛ։ൃɽ खಈͰݕࡧΛ܁Γฦ͢ͷ͸ޮ཰͕ѱ͍ɽ ࣗಈԽͰղੳύΠϓϥΠϯ΁ͷ૊ΈࠐΈ΋Մೳʹɽ
51. ։ൃऀ޲͚৘ใɼαϙʔτ༻ πΠολʔΞΧ΢ϯτ ϑϦʔϫʔυݕࡧ http://sra.dbcls.jp/search DBCLS SRA Metadata Search ߜΓࠐΈݕࡧ
52. ৚݅ʹ֘౰͢Δσʔλʹ ରͯ͠ϑϦʔϫʔυݕࡧ ৚݅ʹ֘౰͢Δ σʔλΛશͯදࣔ DBCLS SRA Metadata Search ֤৚݅ʹ֘౰͢Δ σʔλͷׂ߹ ߜΓࠐΈݕࡧ
    .VT
    NVTDVMVT
    
    5SBOTDSJQUPNF
    
    *MMVNJOB
    .J4FR
53. ΧϥϜ໊ΛΫϦοΫͯ͠ ฒ΂ସ͑ ΩʔϫʔυͰΞΠςϜΛ ߜΓࠐΉ DBCLS SRA Metadata Search ώοτͨ͠σʔλͷ৘ใɽ ੨͍ߦ͸࿦จ৘ใ෇͖ ݕࡧ݁Ռ
54. ϓϩδΣΫτͷ֓ཁ ࿦จͷ֓ཁͱཁࢫ DBCLS SRA Metadata Search 1VC.FE
    1.$΁ͷϦϯΫ 431ΛΫϦοΫͨ݁͠Ռ
55. DBCLS SRA Metadata Search 431ΛΫϦοΫͨ݁͠Ռ ΫϦοΫͯ͠ల։ .BUFSJBMT
    BOE
    .FUIPET 3FTVMUT
56. DBCLS SRA Metadata Search 431ΛΫϦοΫͨ݁͠Ռ ςʔϒϧΛUTW
    KTPOܗࣜͰදࣔ ฒ΂ସ͑ͱߜΓࠐΈ μ΢ϯϩʔυϦϯΫ 3VO
    4BNQMFͷ৘ใ
57. DBCLS SRA Metadata Search 431ΛΫϦοΫͨ݁͠Ռ ςʔϒϧΛUTW
    KTPOܗࣜͰදࣔ ฒ΂ସ͑ͱߜΓࠐΈ શମͰͷࠩ෼ΛϋΠϥΠτ
58. DBCLS SRA Metadata Search 3VOͷΫΦϦςΟ৘ใ
    433 Ϧʔυ਺ɼϦʔυ௕ɼ ($ͳͲͷ৘ใ ֤Ϟδϡʔϧͷ݁ՌΛ ΫϦοΫ֦ͯ͠େ
59. S ݕࡧΛՄࢹԽ͢Δ ࿦จ৘ใ΋ؚΊͨΩʔϫʔυݕࡧ Ϧʔυͷ৘ใΛ%-લʹ֬ೝ͢Δ DBCLS SRA Metadata Search ͳͥݕࡧ݁Ռ͕ଟ͍গͳ͍ͷ͔ɼ શମʹ͓͚Δׂ߹Λݟͯ൑அͰ͖Δɽ ͳΔ΂͘ଟ͘ͷؔ࿈͢Δσʔλ͕ݕࡧͰ ώοτ͢ΔΑ͏ʹݕࡧର৅Λ֦େ͍ͯ͠Δɽ μ΢ϯϩʔυʹ͸௕͍࣌ؒΛཁ͢Δ͜ͱ΋ɽ ࣮֬ʹ࢖͑Δσʔλ͚ͩΛબͿͨΊͷ৘ใΛఏڙɽ
60. ·ͱΊ E Summary #2
61. Summary #2 %#$-4
    43"͸43"ͷػೳ֦ுͰ͋Δ σʔλొ࿥͸ड͚෇͚ͣɼ43"ͷঢ়گΛ೺Ѳ͢ΔͨΊͷ৘ใ΍ ΑΓσʔλΛ୳͠΍͍͢ݕࡧػೳΛఏڙ͍ͯ͠Δɽ ഑ྻσʔλͷొ࿥ɾݕࡧʹ͸ϝλσʔλ͕ॏཁ ͦΕͧΕʹ*%͕ৼΒΕొ࿥ऀ͕هड़͢Δɽ ಺༰ͱؔ܎ੑ͸ಛʹσʔλొ࿥࣌ʹ͸ཧղ͢Δඞཁ͕͋Δɽ E
62. X /(4σʔλݕࡧͱར༻ͷ࣮ྫ ঺հͨ͠αʔϏεΛར༻ͯ͠ɼաڈͷ/(4ݚڀࣄྫΛௐࠪ͢Δ Search published NGS data and project
63. X ஈ֊ผɾެڞσʔλͷར༻ྫ Use cases of Public data
64. X ͜Ε͔Βߦ͏γʔέϯε ࠓਐߦ͍ͯ͠Δγʔέϯε ׬ྃͨ͠γʔέϯε Use cases of Public data ྨࣅϓϩδΣΫτͱσʔλͷ৘ใΛݩʹɼ γʔέϯγϯάͷσβΠϯͱγϛϡϨʔγϣϯΛߦ͏ɽ ಉ͡ੜ෺छɾγʔέϯαͷσʔλΛݩʹɼ γʔέϯγϯάͷΫΦϦςΟͷධՁΛߦ͏ɽ ۙԑछɾྨࣅϓϩδΣΫτͷσʔλΛ௥Ճͯ͠ɼ ղੳͷਫ਼౓޲্ʹ໾ཱͯΔɽ
65. σʔλͷݕࡧɾར༻Ͱඞཁͳ͜ͱ ∑ Practical search tips
66. ∑ ࣮ݧछ͕ٻΊΔϦʔυεϖοΫΛ೺Ѳ͢Δ γʔέϯαͷϦʔυεϖοΫΛ೺Ѳ͢Δ Practical search tips ήϊϜϦγʔέϯεɼ3/"4FR
    $I*14FRͳͲɼ ࣮ݧͷछྨʹΑͬͯඞཁͳϦʔυ௕ɼϦʔυ਺͸ҟͳΔɽ ͦΕͧΕͷγʔέϯα͔ΒಘΒΕΔϦʔυͷεϖοΫ͸ɼ ࢼༀͷΞοϓσʔτ౳ʹΑͬͯ΋มΘΔͷͰ஫ҙ͕ඞཁɽ ੜ෺छͱ࣮ݧछʹԠͯ͡γʔέϯαΛબ୒͢Δ ެڞ%#͔ΒྨࣅͷϓϩδΣΫτΛݕࡧ͢ΔͨΊʹ΋ɼ ήϊϜαΠζͱ࣮ݧछʹԠͨ͡Ϧʔυͷ৘ใ͕ॏཁ
67. Required read spec by application application / ࣮ݧछ total bases / ૯Ԙج਺ read length / Ϧʔυ௕ read number (M) / Ϧʔυ਺ ώτήϊϜϦγʔέϯε 90-150Gb 2x100 900-1500 λʔήοτϦγʔέϯε <1Gb 2x100 10 exome sequence 5~7Gb 2x100 70 RNA-Seq 5Gb 2x100 50 TSS-Seq 1Gb 1x50 20 small RNA 0.35Gb 1x35 >10 ඍੜ෺ήϊϜ >150Mb 2x100 >1.5 ਅ֩ੜ෺ήϊϜ >4Gb 2x100 >40 Bisulfite-Seq 90-150Gb 2x100 900-1500 ChIP-Seq >6Gb 1x100 60 ࡉ๔޻ֶผ࡭
    ࣍ੈ୅γʔέϯαʔ໨తผΞυόϯετϝιου
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    ର৅ͷήϊϜαΠζͳͲͰ਺ࣈ͕มΘΔ͜ͱ͕͋Γ·͢ɽ·ͨɼطʹ৘ใ͕ݹ͘ͳ͍ͬͯΔՄೳੑ΋͋Γ·͢
68. Required read spec by application ४උಋೖ ώτήϊϜղੳ Ҩ఻ࢠൃݱ੍ޚղੳ ৽نήϊϜ഑ྻܾఆ ΤϐδΣωςΟΫεղੳ ϝλήϊϜղੳ ήϊϜߏ଄ղੳ σʔλղੳπʔϧˍอଘ ౷߹ղੳ એ఻Ͱ͕͢པ·Ε͍ͯΔΘ͚Ͱ΋ചΕΔͱ๻ʹ͓͕ۚೖΔΘ͚Ͱ΋͋Γ·ͤΜ
69. Read spec, still improving ࢼༀ΍ιϑτ΢ΣΞͷ޲্ʹΑΓಉ͡γʔέϯαͰ΋ Ϧʔυ਺Ϧʔυ௕͕සൟʹมΘΔ
    ྫ
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    .J4FR
70. ྫ
    Ϛ΢εͷҨ఻ࢠൃݱͷݚڀྫΛ୳͢ ∑ Example survey: mouse brain transcriptome
71. Example survey: mouse brain transcriptome ੜ෺छͱ࣮ݧछΛࢦఆ TVCNJU
    DPOEJUJPOΛԡ͢ http://sra.dbcls.jp/search γʔέϯα͸ۭཝͷ··
72. ϓϩδΣΫτ͕֘౰ http://sra.dbcls.jp/search/filter?species=Mus %20musculus&type=Transcriptome&instrument= ΩʔϫʔυʹzCSBJOzΛ ೖྗͯ͠zTFBSDIzΛԡ͢ Example survey: mouse brain transcriptome
73. ϓϩδΣΫτ͕֘౰ http://sra.dbcls.jp/search/search?species=Mus %20musculus&type=Transcriptome&instrument=&search_query=brain 4UVEZ
    5JUMFͷԼͷೖྗཝʹ lCSBJOzͱೖྗͯ͠ߜΓࠐΈ Example survey: mouse brain transcriptome
74. ϓϩδΣΫτΛ৽͍͠ॱ ʹฒ΂ΔͨΊ4UVEZ
    *%Λ ΫϦοΫ ͜ͷϓϩδΣΫτͷσʔλΛ ݟͯΈ·͢ http://sra.dbcls.jp/search/search?species=Mus %20musculus&type=Transcriptome&instrument=&search_query=brain Example survey: mouse brain transcriptome
75. ϓϩδΣΫτͷ֓ཁ http://sra.dbcls.jp/search/view/SRP011204 ϓϩδΣΫτͰߦΘΕͨ γʔέϯεͷ֓ཁ Example survey: mouse brain transcriptome
76. Ϧʔυ਺
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    SFQMJDBUFT Example survey: mouse brain transcriptome
77. λΠτϧʹ͋ͬͨ(&0
    *% l(4&zͰݕࡧ http://www.ncbi.nlm.nih.gov/geo/ Example survey: mouse brain transcriptome
78. SFQMJDBUFTͰͨ͠ http://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSE36232 Example survey: mouse brain transcriptome
79. (&0Ͱ͸࿦จͷ৘ใ͕ Ξοϓσʔτ͞Ε͍ͯΔ http://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSE36232 ͦΕͧΕͷαϯϓϧͷ ৄ͍͠৘ใ $POUSPMͷ৘ใΛݟΔͨΊ (&0
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    *%ΛΫϦοΫ Example survey: mouse brain transcriptome
80. 4BNQMF
    $IBSBDUFSJTUJDT http://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSM884353 4BNQMFॲཧͷϓϩτίϧ Example survey: mouse brain transcriptome
81. 43"ͷ&YQFSJNFOU
    *% http://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSM884353 4BNQMFͷؔ܎ΛݟΔͨΊ #JPTBNQMF
    *%ΛΫϦοΫ Example survey: mouse brain transcriptome
82. ରԠ͢Δ43"
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    *% http://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSM884353 43"ϑΥʔϚοτͷ ഑ྻσʔλͷ%-ϦϯΫ Example survey: mouse brain transcriptome
83. (&0ͷϖʔδʹ໭ͬͯ ࿦จͷϦϯΫΛΫϦοΫ http://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSE36232 Example survey: mouse brain transcriptome
84. ͔ͤͬ͘ͳͷͰ 1VC3FBEFSͰશจΛ֬ೝ http://www.ncbi.nlm.nih.gov/pubmed/22563483 Example survey: mouse brain transcriptome
85. /BWJHBUJPOΛΫϦοΫ .BUFSJBMT.FUIPETΛ ΫϦοΫ http://www.ncbi.nlm.nih.gov/pmc/articles/ PMC3341364/?report=reader Example survey: mouse brain transcriptome
86. σʔλղੳʹ͍ͭͯ ར༻ͨ͠πʔϧͳͲ http://www.ncbi.nlm.nih.gov/pmc/articles/ PMC3341364/?report=reader ϥΠϒϥϦௐ੔ͱ γʔέϯγϯάʹ͍ͭͯ Example survey: mouse brain transcriptome
87. ∑ ৚݅ʹ߹͏σʔλͷϦʔυͷ৘ใΛಘΔ ϥΠϒϥϦௐ੔΍σʔλղੳͷ৘ใΛಘΔ ৚݅ʹ߹ͬͨσʔλΛμ΢ϯϩʔυ Practical search tips Ϧʔυͷ௕͞ɼϦʔυ਺ɼαϯϓϧͷ৘ใͳͲɽ ར༻໨తʹ߹͍ͬͯΔ͔ɼσʔλͷ਺͸े෼͔ɽ 43"ʹهࡌ͕͋Δ͜ͱ͸ଟ͘ͳ͍ɽ ࿦จ΍(&0ͳͲ֎෦%#ͷ৘ใΛ୧Δ͜ͱͰಘΒΕΔ͜ͱ΋ɽ σʔλʹΑͬͯ͸%-ɼϑΝΠϧల։ʹඇৗʹ͕͔͔࣌ؒΔɽ %%#+
    '51ͰGBTURΛ%-ɼ΋͘͠͸%%#+ύΠϓϥΠϯΛར༻ɽ
88. σʔλͷ֬ೝͱμ΢ϯϩʔυ ∑ Quality check and download
89. Read quality check ϦʔυͷҐஔ͝ͱͷ ΫΦϦςΟΛνΣοΫ http://sra.dbcls.jp/search/view/SRR426841 ($ͳͲ΋νΣοΫ
90. Data download via FTP l'51zΛΫϦοΫ http://sra.dbcls.jp/search/view/SRP011204 %#ܗࣜΛબ୒͢Δͱ '51αΠτ͕։͘
91. Data download via FTP http://trace.ddbj.nig.ac.jp/DRASearch/run?acc=SRR426841 '"45243"-JUF ͲͪΒ͔ͷܗࣜΛΫϦοΫ
92. '51αΠτʹήετͰϩάΠϯ C[ܗࣜͰѹॖ͞ΕͨGBTURϑΝΠϧʹΞΫηεͰ͖·͢ Data download via FTP
93. ύΠϓϥΠϯΛར༻͢Δ ∑ DDBJ Read Annotation Pipeline
94. DDBJ Read Annotation Pipeline ϩάΠϯޙɼ l*NQPSU
    QVCMJD
    %3"zΛ ΫϦοΫ https://p.ddbj.nig.ac.jp/
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    *%Λೖྗͯ͠ σʔλΛύΠϓϥΠϯʹ௥Ճ
95. ·ͱΊ Summary #3 X
96. X Summary #3 จݙ΍Ϧʔυ৘ใΛ׆༻ͯ͠ඞཁͳ৘ใΛಘΔ Ϧʔυͷ৘ใ΍ϥΠϒϥϦௐ੔ɾղੳͳͲͷ৘ใ͕ඞཁɽ Ͳ͏ͯ͠΋৘ใ͕ݟ͔ͭΒͳ͍࣌͸ఘΊΔͷ΋େࣄɽ ެڞͷղੳύΠϓϥΠϯΛ͏·͘ར༻͢Δ ڊେͳσʔλ͸%-ʹ͕͔͔࣌ؒΓɼ)%%༰ྔ΋ѹഭ͢Δɽ %%#+ύΠϓϥΠϯΛ׆༻͢Δ͜ͱͰίετΛԼ͛ΒΕΔɽ
97. ΦϯϥΠϯͰඞཁͳ৘ใΛ୳͢ Œ Online Reference
98. IUUQHJUIVCDPNJOVUBOPTSB@NFUBEBUB@UPPMLJUXJLJ 43"
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99. ࣭ٙԠ౴ Thank you for your attention ¿ ·ͨ͸࣭໰͸
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