Deep analysis of cellular transcriptomes – LongSAGE versus classic MPSS

doi:10.1186/1471-2164-8-333

BMC Genomics
Volume 8

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Sreenu VB
Vuong MT
Abidi SHI
Sutton JK
Rowland-Jones SL
Davis SJ
Evans EJ

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Sutton JK
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Methodology article

Deep analysis of cellular transcriptomes – LongSAGE versus classic MPSS

Lawrence Hene^* , Vattipally B Sreenu^* , Mai T Vuong , S Hussain I Abidi , Julian K Sutton , Sarah L Rowland-Jones , Simon J Davis and Edward J Evans

Nuffield Department of Clinical Medicine and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, The University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK

author email corresponding author email* Contributed equally

BMC Genomics 2007, 8:333doi:10.1186/1471-2164-8-333


Published:	24 September 2007

Additional files

Additional file 1:

Effect of tag length on frequency of matches to the genome and transcriptome. Additional figure showing a histogram of the frequencies of every tag found in the Ensembl genome and transcriptome for various combinations of tagging enzyme and tag length.

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Additional file 2:

Number of transcriptional loci identified. Additional table showing the number of different active transcriptional loci identified in the same cell sample by either SAGE or MPSS according the method described in the text when various alternative parameters are used.

Format: PDF Size: 72KB Download file

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Additional file 3:

Comparisons of tag abundance distributions for LongSAGE tags from the activated CD4⁺T-cell library matching UTBS transcripts according to whether the transcripts are also detected by MPSS. Additional figure comparing the apparent frequency distributions of transcripts from known genes according to whether their corresponding tags were found by SAGE and MPSS or exclusively by one of these techniques in order to demonstrate that transcripts detected only by SAGE did not represent a fixed level of genomic contamination.

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Additional file 4:

Novel loci of transcription identified by combining LongSAGE and MPSS. Additional table listing all the pairs of SAGE and MPSS tags found close together in genomic regions with no previously annotated transcriptional locus nearby.

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