title: Chicken mRNA MPSS signatures
status: Public on Sep 20 2006
contact.city: Seoul
contact.first: heebal
contact.last: kim
contact.email: heebal@snu.ac.kr
contact.address: San 56-1 Sillim-dong Gwanak-gu
contact.country: South Korea
contact.institute: Seoul National University
organism: Gallus gallus
description: The generation of MPSS datasets in the gonad and PGCs samples was performed by Takara Biotechnology Cooperation (Shiga, Japan).
  Annotation Classe Table:
  Virtual Signature Class mRNA Orientation Poly-Adenylation Features Position
  Class   PASa    PATb    Strand                         Position
  1     yes     yes     Forward                        The first one 5’ to the PAS and PAT
  2     yes     no      Forward                        The first one 5’to the PAS
  3     no      yes     Forward                        The first one 5’ to the PAT
  4     no      no      Forward                        The most 3’ signature of the sequence
  5     yes/no  yes/no  Forward                        Not the most 3’ signature of the sequence
  11     yes     yes     Reverse complement             The first one 5’ to the PAS and PAT
  12     yes     no      Reverse complement             The first one 5’to the PAS
  13     no      yes     Reverse complement             The first one 5’ to the PAT
  14     no      no      Reverse complement             The most 3’ signature of the reverse complement strand of the cDNA sequence
  15     yes/no  yes/no  Reverse complement             Not the most 3’ signature of the reverse complement strand of the cDNA sequence
  22     yes     no      unknown                        The first one 5’ to the polyA signal
  23     no      yes     unknown                        The first one 5’ to the polyA tail
  24     no      no      unknown                        The most 3’ signature of the sequence
  25     yes/no  yes/no  unknown                        Not the most 3’ signature of the sequence
  1000    NA      NA      Forward or reverse complement  The signature has only chromosome matches
  0     NA      NA      Forward or reverse complement  The signature matches more than 100 chromosome loci
manufacture_protocol: Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J and Corcoran K. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630–634, 2000.
  Brenner S, Williams SR, Vermaas EH, Storck T, Moon K, McCollum C, Mao JI, Luo S, Kirchner JJ, Eletr S, DuBridge RB, Burcham T and Albrecht G. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci U S A 97(4):1665-70, 2000.
  Ruan Y, Le Ber P, Ng HH and Liu ET. Interrogating the transcriptome. Trends Biotechnol 22(1): 23-30, 2004.