Specifications/Details:

Specifications/Details: The coding sequence selected for the mouse exome probe pool design includes 203,225 exonic regions, including microRNAs, and collectively comprises over 54.3 Mb of target sequence (C57BL/6J, NCBI37/mm9). The design was based on a unified, Mouse Genome Database-curated gene set, consisting of non-redundant gene predictions from the National Center for Biotechnology Information (NCBI), Ensembl and The Vertebrate Genome Annotation (VEGA) database. The gene list is available at . To manage the size of the probe pool and to avoid non-uniquely mappable regions, we excluded olfactory receptors and pseudogenes from the target sequence. In cases where an exon contained both UTR and coding sequence, the UTR sequence was included in the design.

Specifications/Details: A total of 391199 CDS features (76.5 Mbp) were used as the starting point for the design. CDS features on scaffolds were ignored for this design. CDS regions were merged, padded to a minimum size of 100 bp, and merged again to produce a final set of 322428 target regions, covering 70.95 Mbp. Variable length oligonucleotide probes (50-120 nt) were generated for the entire genome at an interval spacing of 5 bp. A frequency table of 15-mers was generated for the entire genome, using both strands, and those probes with an average 15-mer frequency greater than 100 were considered repetitive and removed from consideration. Uniqueness in the genome was assessed using SSAHA (v3.2), using a word-length of 12, minimum match length of 38 bp, a maximum gap of 5 and a maximum number of insertion/deletions of 5. Probes were selected by tiling across the target regions at an average probe spacing of 25 bp, restricting selection to only completely unique probes with an average 15-mer frequency score of 25 or less. The selected probes extend beyond the boundary of the initial target region by 35- to 50-bp to ensure adequate sequence coverage on the edges of the exons. A total of 223890 out of the initial 322428 target regions (69.4%) are covered by the design. The final capture probe set covers 40.4 Mbp of genomic sequence, and 35.2 Mbp (49.7%) of the final set of CDS target regions. Using an offset of 100 bp from each capture probe, 52.3 Mbp (73.8%) of the target regions should be covered in a typical experiment.

Specifications/Details: Relayout 100407_HG19_454_BB_cap_HX3 to remove customer specific name, and to change to SeqCap EZ

Specifications/Details:

Specifications/Details:

Specifications/Details: HX1 - RN34 promoter design. Promoter regions tiled 6500 bp upstream of TSS, 1500 bp downstream of TSS. miRNA regions tiled 20000 bp upstream, 1000 bp downstream. CpG islands expanded to 700 bp. Gene sets are RefSeq and Ensembl genes from UCSC. Regions tiled at int65win35max10.

Specifications/Details: Human HG19 DNA methylation array covering the 5' ends of transcripts (promoters), 3' ends of transcripts, and CpG islands and their "shores." using UCSC for RefSeq Genes, MGC genes, and CpG islands as source data. Design consists of 50-75mers probe sequences using up to 5 close matches with a mean probe spacing of 99bps, median probe spacing of 100bps, n= 4,120,234. Methylation controls (positive, negative and nonCG) were added to the design. Further details about regions: Reflat file (version March 29 2011) and MGC file (version March 23rd 2011) and CpG (version April 27 2009) were downloaded from UCSC on March 31st 2011 TSS and TES regions were expanded in both directions by 7KB while CpG were expanded by 3KB.

Specifications/Details: 1:2 design of 21645 genes/ests from D. ananassae provided by Brian Oliver NIH/NIDDK with 9 probes/gene. Each gene replicated 2x. Design includes random GC probes.

Specifications/Details: 60mer expression design from flybase annotation 4.2.1. Ten probes per target for 19,178 genes. 359 probes truncated at 148 cycles. Random probes included.

Specifications/Details: 1:2 design of 17364 genes/ests from D. mojavensis provided by Brian Oliver NIH/NIDDK with 11 probes/gene. Each gene replicated 2x. Design includes random GC probes.

Specifications/Details: 1:2 design of 15844 genes/ests from D. pseudoobscura provided by Brian Oliver NIH/NIDDK with 12 probes/gene. Each gene replicated 2x. Design includes random GC probes.

Specifications/Details: 1:2 design of 17017 genes/ests from D. simulans provided by Brian Oliver NIH/NIDDK with 11 probes/gene. Each gene replicated 2x. Design includes random GC probes.

Specifications/Details: 1:2 design of 21229 genes/ests from D. yakuba provided by Brian Oliver NIH/NIDDK with 9 probes/gene. Each gene replicated 2x. Design includes random GC probes.

Specifications/Details: 1:2 expression design of 13691 genes provided by customer with 9 probes/gene. Each probe replicated 3x on chip. Design includes random GC probes. Probes truncated at 148 cycles.

Specifications/Details: Resequencing design for various consensus sequences for swine flu influenza, provided by GIS.