Rui:LabNotes/SingleCell/2011-5-17: Difference between revisions

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TATGGTTACCGCCTCCTCTTCCTTATCCACATTGCTTGTTTGTGACAACTNCCATGTTCCCGTTGCCAAGCTCTCCACTT
TATGGTTACCGCCTCCTCTTCCTTATCCACATTGCTTGTTTGTGACAACTNCCATGTTCCCGTTGCCAAGCTCTCCACTT
GAAGAAAACTTAAAAAAAAAAAAAAAAAAAAAAGGATANCCCTANANNGAGTCNNATTTAAAGCCNAATTCTGCANATNN
GAAGAAAACTTAAAAAAAAAAAAAAAAAAAAAAGGATANCCCTANANNGAGTCNNATTTAAAGCCNAATTCTGCANATNN
===DNA samples===
* 15 colonies directly for TempliPhi, roughly ~500ng/ul in 10ul PCR, 3ul sending for sequencing (M13R provided by Genewiz)
* No priming: 3
* mRNA: 11
* Potential non-coding region: 1
DNA-1:
DNA-2:
DNA-3:
DNA-4:
DNA-5:
DNA-6:
DNA-7:
DNA-8:
DNA-9:
DNA-10:
DNA-11:
DNA-12:
DNA-13:
DNA-14:
DNA-15:

Revision as of 21:18, 17 May 2011

Sequence result

Continue with lab note on 5.16.11

RNA sample Hues54

  • 15 colonies directly for TempliPhi, roughly ~500ng/ul in 10ul PCR, 3ul sending for sequencing (M13R provided by Genewiz)
  • No priming: 3
  • mRNA: 11
  • Potential non-coding region: 1


RNA-1: poor quality; first 60bp match to intergenic region with 88% >RNA-1-M13R_F01.ab1 NNNNNNANNNTGNNNNNNGCTCGGATCCNCTAGTAACGGCCGCCNGTGTGCTGGAATTCGGCTTTAATACGACTCACNNN NGGNGTATGCTTTTTTTTTTTTTTTTTTTTTTTTTCCNCNGGAANAANTGCACCTGTGTCGCCNTCCCACAGGGGAACTC GGGAGACAAAGGCGCTTTGNCNCNTCTGGGGGANCCTATCAGGACCAATTCCCATGGCGAATACCATGATATCGTCCGTN ACTGGGGGGANANTGACNTGGNTCCNAANACTGNGGNTCGGCCCGATNTTTANAAAAAAACNAACGCTAAANAAAATTGA CAATTCCAAATTAACCGGTTCCCCGTAGANCTTTCGGGGGNGGGGANCNGGGGANNNNNNNGGNCTTTCCNNCNNCCANA ANAAAAAAGAAAGGGACGGGCCGGGGAAAGGCCGGNGAAACAGGCNATAGNNCCTAGGACANTGNNNATGATNAAGACCG ACTAATGGGGGCTGCGGNCCCGTGTGTANGNGTCAGGCTGTTTCTTTTGGNANGAAGAGGGGTGGTCTTTCATANAATTC GGTGGGGGGTGGGCTCGGAGAGGGTCTACTTTGTGGAGAGNATGANGGCCAANNNANNCCNAAAGCCNAGCACNTCGGCG AAGATCAGAATCCGANNTACCNNTN

RNA-2: "poor quality"; spliced form of RPL35, 98.1% >RNA-2-M13R_F02.ab1 NNNNNNNNNNNNNNNNNNNNNCTCGGANCCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTCACT ATAGGGGTATCCTTTTTTTTTTTTTTTTTTTTTTTTGGAGCTGCTGAAACAGCTGGACGACCTGAAGGTGGAGCTGTCCN NNCTGCGCGTCGCCAAAGTGACAGGGGGNGCGGCCTCCAAGCTCTCTAAGATCCGAGTCGTCCGGAAATCCATTGCCCGT GTTCTCACAGTTATTAACCAGACTCAGAAAGAAAACCTCAGGAAATTCTACAAGGGCAAGTAGTACAAGCCCCTGGACCT GCGGCCTAAGAAGAAACGTGCCATGCNCCGCCGGCTCAATAANCACGANGANAACCTGAAAACCAAGAAGCAGCAGCGGA AGGAGCGGCTGTACCCGCTGCGGAAATACCCGGTCAAGGNCTGAGGGGCGCATTGTCAATAAAGCACAGCTGGNTGAGAA A

RNA-3: "poor quality; spliced form of BQBP1, 98.4% >RNA-3-M13R_F03.ab1 NNNNNNNNNNNNNNNNNNNNNNCTNNNNATCCNCTAGTAACGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTCA CTNNNGGGGGANCCTTTTTTTTTTTTTTTTTTTTTTTTTCCCNNGANANGNTCTGNCAGGGATCGAGAGCGTGGNTATGA CAAGGTAGACAGANAGAGAGAGCGANNGNNNNAACGGGATCGGGACCGCGGGTATGANAAGGCAGACCGGGAANAGGGCA AAGAAGGGCGCCCCCATCGCCGGGAGGAGCNGNCTCCCTATCCCAAGAGCNAGAAGGCAGTAAGCCGAAAGGATGAAGAG TTANACCCCNTGGACCCTAGCTCATACNCNNACGCCCCCCGGGGCNGTNGNCAACAGGANTCCCCAAGNGGAATGAGGCN AAAAN

RNA-4: PQ; MTF1, 98.6% >RNA-4-M13R_F04.ab1 NNNNNNNNNNNNNNNNNNNNNTCGGATCCNCTAGTAACGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTCACTA NAGGGGNNNCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAGCCGACAAGCAGAGACTCCTTCAGACCCTCAAAC AGAAACATTAAGTGCCATGGATGTGTNAGAGTTTCTNTCCCTCCAGAGCCTGGACACCCCGTCCAATCTGATTCCCATTG AAGCACTACTGCAGGGGGAGGAGGAGATGGGCCTCACCAGCAGCTTCTCCAAGTNAAGGGCCCATGTGTGCTCCCCTCTG GGAAAAGCGGGTGAGCAGGAGGCATGAGGTACAATGCCTGCCATCATGGGTCAAAAATTTGAAGGATGAAAAAATCTACT GTTTGAAATCCTCACCTTTTAGACGTATTTTTTTTATTCAN

RNA-5: PQ; SNX9, 99.5% >RNA-5-M13R_F05.ab1 NNNNNNNNNNNNNNNNNCNNANNNNNNNNNCACNANTAACGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTCAC TATANNGNGNGNNTTTTTTTTTTTTTTTTTTTTTTTAACAGGNNCNNGNNACACCGTCAGCTCGAACTCAACACTGGCAG CCACCGTCTCACCCCTGCGGAGGAGCGCTCCCGTCTCCCACAGGTGCCTTACCGCGTTCCCTCCCGCTGCTTTCATTTTT CTGACCTAATAATTACGGGAAANGGAAAGTCTGGGCCANCANCNATAAAATGACACCAAAAATAAGTANANGANATCGAA T

RNA-6: no priming

RNA-7:PQ; CR594125, 94.6% >RNA-7-M13R_F07.ab1 NNNNNNNNNNNNTGNNNNNAGCTCGNATNNNNTAGTAACGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTCACT ANNGGGGNNNCCNTTTTTTTTTTTTTTTTTTTTTTTTTTGCTTCCCCGTGGTTTAATATGAACAGAGTTGAATATGACAT TGTCTGACAAAAGAATGAACAATTTGCTGAATAAAAGCCCCAAGTCAGGATATATACACAGAAGAAATGGAGCCTCAGAG TCTCAGCACTTGTGCNCAATGAAAGGAGAAATCTTTAAAAAAAAAAATCTGTAACAGAGGATAAAAATCAAAAGGCAGCA AGGACACCGACACTGGNGAGGTGGGAAAGGGGCTNNTCANCTACCAGCATGGGCTCNNCNGCTAGAGAGCTAACCNATNT CAAGGATTTTCAACNCTGAGGTGGGTTCCANNTCCCCTGNN

RNA-8: spliced NUCKS1, 99.7% >RNA-8-M13R_F08.ab1 NNNNNNNNNNNNNNNNNNNNNNTCGGNNCCNCTAGTNNCGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTCACT ATAGGGGTATCCTTTTTTTTTTTTTTTTTTTTTTTTCGAACTGCCATAGTCACTATCGTCATCATCTTCCATTAGGAAAT CTTCATCGCTGCCGGAATTCTCCTGGAATGGTGCCTCATCCTCCTCTTCTTGTTCTTCCTCACTGCCCACATCTTCCATG AGCATCTCTCTCTGTTTAGAAGCTGCTTTCGATGCCGCCTGCCGTTGTTGGCGCACATTTTTATGATCTTCTTTTTCATC TTCACTATCCTCTGCTGAGTGAGAATCATCCTTCTTGGTCTTCACATCTTTGTCTTCTGAGTCCTCACTATCTTCCTGTG AATTCTTTCCAGATCGCCTCTTATTTTTAGCTTCTCGGGGAGATGATCGAATTTTCTTAGTGGGAGGGCCCGAATCTCTT CCATAATCTTCATCTGCNTCATCAGATTCCTGAAACTGTGAGTAATCAACAACCTTCCTATTTCTGACAGGCCGCGACAT GTTCGCTGTCGAAACAGGACCGAGTCGAGAAGCCAAAGACCAGGACCCCCCCTACCCCGCGCGCTCGGCGCCCCACCCAA AANNNANNNAAANANAAAAGGGATACCCCTATNNNNNNTCGTATTNAAGCCNNNNNNNNGCAAGATATCCATCACACTGG NCGGCCGCTCGAGCATGCATCTAGAGGGNCCCAATTTCNCCCCTAT

RNA-9: no priming

RNA-10: spliced EST, 99.0% >RNA-10-M13R_F10.ab1 NNNNNNNNNNNNGNNNNNNNNNNNNCNNNNNNNCTAGTAACGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTCA CTATNGGGGTATCCTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTCCTAGCTCATCCTGGCTCAAAAAGCACCCCCACTGA GCACCTTGCGACCCCCACTCCTGCCCGCCAGAGAACAAACCCCCTTTGACTGTAATTTTCCTTTACCTACCCAAATCCTA TAAAACAGCTCCACCCCTATCTCCCTTCACTGACTCTCTTTTCGGACTCGGCCCCCCTGCACCCAGGTGAAATAAACAGC CATGTTGCTCACACAAAGCCTGTTTGGTGATCTCTTCACATGGATGCACATGAAATTTGGTGCTGTGACTCAAATCGGGG GACCTCCCTTGGGAGATCAATCCCCTGTACTCCTGTTCTTTGCTCCATGACAAAGATCCACCTATGACCTCAGGTCCTCA GACCAACCANCCCAAGGAACATCTCACCGATTGTAAATCAGGTGAAGTATGAAGTTATGAGGAGAAAGGAACAGAGGACA ACCACACAGAGAAAGTGTAGCTTTATCTACTAGAGCTGAAGACATTCAAATTTATGATCCAACAATTCTACTCTGAAGTG CAGTGGTGNATATACTGCAACAATGTGTACTCATGTGCCCTGAGAACTANNNNTGAAAAAAACCTTACAGCAATATGCNT AATANNNNNNAAAAAAAAAAAAAAAAAAAANGGGATNCCCCCTATNGNNGNNTCNNNNTTAAAGCCAAATTCTGGCNGAN ANTNCNTCANN

RNA-11: PQ, CMTM3, 97.5% >RNA-11-M13R_F11.ab1 NNNNNNNNNNNNNNNNNNNANCNNNGATCCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGGCTTATACGACTCACTAT AGGGGTANCCTTTTTTTTTTTTTTTTTTTTTTTTTGTCAGTCTGGCTTAATTCATTATGGCTTTTTTTCAGGGTAAGAAA TTCACACCCAAGAGAATAAGGCTACAAATGCTCCAAACATGGGTCCAGAACTCCGGCTCTTTTGTGAGGCCTAGAGTCAC AAAAAATGCCATCTGTTAAAAAGCTGCCTTTGCATAAAAAAATATAAAAAGTTACAAAATTCCATCAAAGACAGATACAC AGTATAAATCGTTAGGTGAACACAGAAAGCTGGTCTCATCTCCTGCAGTGGCCCATAAACCTGCCCTGANGTCTGGAAAT TCACTGTCCTGAGGGTCCAGGAACTCCTGCCTGCTGGCTGGGCTCTAGGAAGAAGGAGGGTTTGGCTGGGCCTGCCCAGC TCCCCATGACACTGTCACTGTGATGCCACTGTTGTACCCTCTGTCTTCTGGACCAGTCAGTCTATGAGCTCTTCTTTGAA ACAGTCGTAGACCCAGAATGGTCATCTCACCCCCAGAANACATGGTTTCCAAGGGTGGGAGGTGTTAGTTATGGGTGCCG AGCCCCACTTCCTGGGCGACAAGGCAAAAGGTCAATTTCCCCCTGCTTCAAGAATGAAGAGGGAACTGAAAAAAAAAAAA AAAAAAAAAAAAAAGGATACCCCTAANANTGAGTCNTATTAAANCCGAATTCTGCAANAATCCATNACNANTGGNGGCNG CTCGAANNNGCATTTAGAGGGNCCCNATNTCGCCCCTATANTGAGGTCNNAATANNAANTCACTGGCCCNTCNTTTTAAC AACNNTCNNTGNANNGGGAAAAACCCTGGCNGTTANCCCAATNTTNANTCGCCCTTGNAAGCANNNNCCCCCCTTTTNCC AGNCTGGGNGTAATAACCGAAAAGNNCCCNCANCNNNNCGCCCNTTCCCNANAGTTGCGCNACCNGANANNGNNAATGGG NCNGCNCCCNGNNNNCGGCGNNNTTATANNNNNGNNNNNNNNGN

RNA-12: PQ, HN1, 98.9% >RNA-12-M13R_F12.ab1 NNNNNNNNNNNNNNGNNNNNNNNNNTCGGANCCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTC ACTNNNAGGNGATNNTTTTTTTTTTTTTTTTTTTTTTTTTTTACNNGTCCTAAACTACTAAACCTGCATTAAAAATTTCG GTTGGGGCGACCTCGGANCAAAACCCAACCTCCGANCAGTACNTGCTAAGACTTCACCAGTCAAAGCGAACTACTATACT CAATTGATCCAATAACTTGNCCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATTCTATTCTAGAGTCCATATCAAC AATAGGGTTTACGACCTCNATGTTGGATCAGGACATCCCAATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT AAAGTCCTACGTGATCTGAGTTCAGACCGGAGNAATCCNNGTCGGTTTNTATCTACTTCAAATTCCTCCCTGTACGAAAG GACAAGAGAAATAAGGNCTACTTCACATAGNGCCTTCCCCCGTAAATGANATCATCTCAACTTAGTATNNTACCCACACC C

RNA-13: no priming

RNA-14: PQ, spliced TVC (truncated?) 87.6% >RNA-14-M13R_G02.ab1 NNNNNNNNNNNNNNNNNNNNNNTCGGNNNNNCTAGTAACGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTCACT ATAGGGGTATCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAAAGTACTGTGCTTTTATTAAAAAACAAAACAAAACAA AAAAAATACAATCAGGTACTGTCCAGACANGTTTGGGAAGGGAAAATCTCTTTTAAAGTCCTCAGTTTTCATCATCACCA TCACCATTATTATATTAATAATATTAATGTCCTTGAAATTTAAACAATATCACTTTTCTGGCTTCAGTTGTAGGAAATGT ACAAAACATCGAGGGTGGGGGTGGGGCAAGGGGTAACTTCCAATGACACAAGTTTCATCTTTGTGACCTCAACCAATAAC AATTGNACAGCTTTGTGTAAAACACAGCTGGCTCGGAGAATGACCATGTCCCCTGTATGGCCAGCTTGCCCCTCTCCCAT TCCCAGAGCCACCCAAGAGAAGTAAAATTCATGGTGTTGCTGTCACTAGGAGACTTTGCTCAATCGAACAAAAAAGTAGA AACTTGTAGACTGTTGTCTTTGGTGCAAAGGAAGTCGTTGCAGAGGGGCCTACCTCAGTGCCTCAGTGATCCGTGTGGTC TGCTTGGACGCCCATCAAATGCCCAAGGAGAGCTTCNNTGTNNNNNNTGGNTGTGTCGATGCTTTGGNAAAAATCCTTTC TTTTCTCTGGGGCCCCATTCCCTCTCTCACCNAATTATCCCTGGAATTTATGCCCNGCTTACGCCTGCCNTTCNANATTT CGGGAAGTTGCTGGGTNCTCAANTTTCANCTCACAAACTGGANTTGAGTACTCATGGCCCNTTNCAANNGGNAANCNAGT NTAANGCCCCTGACTGTNNATTATNGNNCCATATCTGCCCCATCAGGNNNCNCGATGACANTTCNNNAAAAAAAAAAAAA AAANNANAANAAAAANNGTNACCCCCTANNNNNAGTCTANTTTAAAGCCCNAATTCTCNGCNAAATANNNNTNNNNNNNG CNN

RNA-15: spliced and truncated PCNA, 88.4% >RNA-15-M13R_G03.ab1 NNNNNNNNNNNNNNNNNNNNNNGNNTCGGANCCNCTAGTAACGGCCGCCAGTGTGCTGGAATTCGGCTTTAATACGACTC ACTANNNGGGNTCCTTTTTTTTTTTTTTTTTTTTTTTTACTTTNAAANTTGTTAACTTTATTTAAATTGTACAATATTTC TTAAACTGCATTTAGCGTCAAGATCNNNNNNGAGAATCACCAGTATTTGTAAAGCAGAAACATTCATGTTAACAAAACTA GTTTTTACTTTGGAGCTTATTCTTTAAGCAAATTATGGAGAATGGAGAGAAAAGAAAGTAGGTTATTTACAGAAGATATC TACATATTTTATTTTAATATTTAAGAATACTCAGGTACAAACTTGGTGACAGAAAAGACCTCAGGACACGCTGGCATCTC AGGAGCAATCTTCAAAGGTTTAGTTTTCTCAATTTCTAGCAATGCCTAAGATGCTTCCTCATCTTCAATCTTGGGAGCCA AATAATACTTTAAGTGTCCCATGTCAGCAATTTTATACTCTACAACAAGGGGCACATCTGCAGACATACTGAGTGTTACT GTTGNAGACAGTGGAGTGGCTTTTGTGAAAAAGTTCAGGTACCTCANAGCAAACGTTAGGTGAACAGGCTCATTCATCTC TATGGTTACCGCCTCCTCTTCCTTATCCACATTGCTTGTTTGTGACAACTNCCATGTTCCCGTTGCCAAGCTCTCCACTT GAAGAAAACTTAAAAAAAAAAAAAAAAAAAAAAGGATANCCCTANANNGAGTCNNATTTAAAGCCNAATTCTGCANATNN


DNA samples

  • 15 colonies directly for TempliPhi, roughly ~500ng/ul in 10ul PCR, 3ul sending for sequencing (M13R provided by Genewiz)
  • No priming: 3
  • mRNA: 11
  • Potential non-coding region: 1

DNA-1:

DNA-2:

DNA-3:

DNA-4:

DNA-5:

DNA-6:

DNA-7:

DNA-8:

DNA-9:

DNA-10:

DNA-11:

DNA-12:

DNA-13:

DNA-14:

DNA-15: