title: NimbleGene-P.tetrauerlia-variousSETs-50mer-v1
status: Public on Aug 01 2009
contact.city: Villerubanne
contact.first: Jean-François
contact.last: Gout
contact.email: gout@biomserv.univ-lyon1.fr
contact.address: 43 Bld du 11 Novembre 1918
contact.country: France
contact.institute: Laboratoire Biométrie et Biologie Evolutive
contact.phone: +33  (0) 4 72 44 62 97
organism: Paramecium tetraurelia
description: The grid of features is 768x1024 (X, Y). It consists of 11 different SETs as described below.
  SET01 : Probes that match annotated transcripts. Each transcript has 6 probes (3 on the forward strand and 3 on the reverse strand).
  SET02 : Probes for complete tilling of 4 scaffolds : SCAFFOLD_106, SCAFFOLD_142, SCAFFOLD_164, SCAFFOLD_96. The probes cover both strands of the 4 scaffolds with a 25 nucleotides overlap.
  SET03 : Probes designed specifically to distinguish spliced and unspliced transcripts from the 4 scaffolds described in SET02. For each annotated intron, one probe covers the genomic sequence, centered on the middle of the intron (since introns in P. tetraurelia are between 20 and 30 nt length these probes contain the full sequence of the intron and a few bases from the surronding exons) while an other probe covers the spliced version of the transcript, centered on the exon-exon junction site.
  SET04 : Probes that match 219 annotated tRNAs. Each tRNAs has 4 probes (2 on the forward and 2 on the reverse strand).
  SET05 : Probes that match 3 non-codgin RNAs of particular interrest : AB059619, MS2B and PTU45433. Each ncRNA is fully tilled by the probes on both strands.
  SET06 : Probes that match the rDNA.
  SET07 : Probes designed specifically to study retention and expression of known IESs in paramecium (see Duret & al. Genome Res. 2008; 18(4):585-96 for more informations about IESs).
  SET08 : Probes that match 74 known transposons. Each transposons is fully coverd by tilling on both strands.
  SET09 : Tilling of both strands for 51Gmic gene.
  SET10 : Probes that match the mitochondrial genome (both strands)
  SET11 : Probes designed to distinguish spliced and unspliced transcripts from 6137 annotated genes confirmed by EST alignment. The protocol is the same than described for SET03.
  RANDOM : random probes.
manufacture_protocol: In situ oligonucleotide synthesis as described in www.nimblegen.com