Matt:LabNotes/2014-6-4

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Agi26k0gap Probes for use in Mouse Brain Tissue?[edit]

  • Hosuk was wondering if we could use the Agi26k0gap probeset in the mouse brain tissue sections he has generated rolonies in
    • This would allow us to test second rolony generation in fixed tissue without using human brain tissue

Procedure[edit]

  • Download Mus Musculus mRNA sequences from Biomart
    • Filter: Genes - protein coding only
  • Build bowtie2 index
 bowtie2-build Mus_proteincoding_mart_export.fa Mus_proteincoding
 bowtie2 -x Mus_proteincoding -f Dec2012_targetseq.fa > Targetseq_alignto_MusRNA.sam &
   13127 (100.00%) were unpaired; of these:
     12038 (91.70%) aligned 0 times
     643 (4.90%) aligned exactly 1 time
     446 (3.40%) aligned >1 times
 8.30% overall alignment rate

Conclusion[edit]

  • Only 8% of padlock probes would hybridize (and this doesn't even account for small number of mismatches) so Agi26k probes should not be used in mouse tissue