1 / 6

The whole genome expression array of Serpula lacrymans Array design and data analysis

The whole genome expression array of Serpula lacrymans Array design and data analysis A Kohler, E Tisserant and F Martin Experimental set-up and sample preparation N Hoegberg, A Rosling, K Ihrmark and J Stenlid . NimbleGen Serpula Expression Oligoarray.

zinnia
Download Presentation

The whole genome expression array of Serpula lacrymans Array design and data analysis

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. The whole genome expression array of Serpula lacrymans Array design and data analysis A Kohler, E Tisserant and F Martin Experimental set-up and sample preparation N Hoegberg, A Rosling, K Ihrmark and J Stenlid

  2. NimbleGen Serpula Expression Oligoarray -Serpula lacrymans S7.9 Slacrymansv1.FilteredModelsv1.transcripts - 72,000 60-mer (5 probes per gene model) Starting number of sequences: 12917 Sequences with probes: 12909 Exemplars (five identical probes for several models): 112 Sequence with no probes: 8 -BLOCK1 - contains 63947 experimental probes  -1200 randomly chosen gene models in duplicate (5960 probes) -RANDOM – contains 2130 randomly generated probes - these can be used as negative controls

  3. NimbleGen Pair-file (raw data) Oligo filter: non-specific oligos were eliminated from the file (an oligo was considered as non-specific if it shares more than 90% homology with a gene model other than the gene model it was made for) Data analysis procedure Filtered Pair-file 11803 gene models with expression data RMA normalisation (using ArraySTAR software) Filtered Norm-call-file From the random-oligos present on the array the mean expression value was calculated. The three-fold of the mean expression value of the random oligos was considered as cut-off value for « gene expression » and substracted from each value. If the expression value became negativ, it was set to 1 Cut-off corrected file Calculation of mean expressions; fold expression; Student t-test with FDR (Benjamin Hohberg) multiple testing correction (using ArraySTAR software) Result file

  4. Samples series 1

  5. Principal components analysis Goethite 30d MMN 30d FeCL2 10d FeCL2 + Goethite 10d Goethite 10d Wood 30d Wood 10d MMN 10d FeCL2 + Goethite 30d

  6. Most highly up-regulated transcripts by growth on wood compared to MMN medium

More Related