title: EBT_UA_Daphnia magna_Unique_1.9K_version1
status: Public on Sep 01 2013
contact.city: Leuven
contact.first: Mieke
contact.last: Jansen
contact.email: Mieke.Jansen@bio.kuleuven.be
contact.address: Ch. Deberiotstraat 32
contact.department: Biology
contact.country: Belgium
contact.institute: KULeuven
organism: Daphnia magna
description: 1918 out of 1924 spots from the cDNA libraries were measured.
  
  This Platform represents two batches of arrays that differ in the control spikes that are spotted. One batch has Lucidea controls, and the other batch has Stratagene controls.
manufacture_protocol: Gene expression profiles were determined based on a previously in-house made (UAntwerpen) cDNA microarray of D. magna (Soetaert et al., 2006; Soetaert et al., 2007). This existing cDNA microarray (Vandenbrouck et al., 2009) was extended with three cDNA libraries (i.e. carbaryl, predator and P. ramosa related cDNA libraries; see Orsini et al.). In brief, sequences were assessed for redundancy and consequently the unique sequences per masterset (i.e., either the three existing libraries and the three supplementary libraries) were selected i.e., 1189 unique gene fragments (Vandenbrouck et al., 2009) collected from the three cDNA libraries (life stage, moulting and energy metabolism) were supplemented with 735 unique cDNA fragments identified within the three stressor specific libraries. This last group of sequences was yielded from a collection of 1698 stressor-specific gene fragments (see Orsini et al.). After trimming those 1698 fragments by use of the program CodonCode Aligner (http://www.codoncode.com/aligner/), a group of 1372 fragments remained. Clustering and assembling those ESTs was done with TGICL (Pertea et al., 2003). Default parameters were used for clustering and assembly, which was performed with CAP3 (Huang & Madan, 1999). A total of 1924 gene fragments (1189 + 735) were spotted on amino-coated glass slides (Asper Biotech. Ltd., Estonia) in triplicate (technical spot replication) by using the Qarray Mini (Genetix Ltd., UK). Those two masterset of gene fragments were than analysed for redundant sequences and in the end only 1734 unique sequences were represented, composed of 156 clusters and 1578 singletons (using TIGR Gene Indices Clustering (TGICL), Huang & Madan, 1999; Pertea et al., 2003).