Sentence examples for mouse reference sequence from inspiring English sources

The script findmotifs.pl was used with the mouse reference sequence and the default settings of 400 bp upstream and 100 bp downstream of the transcriptional start site and a length of approximately 8 bp.

Microarrays were manufactured in-house using the long oligonucleotide (70-mer) of the Mouse Genome Oligo Set Version 2 (Operon) which contains the 16,463 unique genes designed from representative sequences of the UniGene Database Build Mm. 102 (February 2002) and the mouse Reference sequence (RefSeq) Database.

aThe Otop1 locus actually resides in two loci in these hominoid species (with respect to the mouse reference sequence; see text for details).

bThe Ush1g-Otop2-Otop3 locus is duplicated in teleost fish (with respect to the mouse reference sequence; see text for details).

Before being finally stored, the methylomes from assemblies other than the University of California, Santa Cruz (UCSC) July 2007 mouse reference sequence (mm9, NCBI build 37) were converted into mm9 by the LiftOver tool from UCSC (30).

The following database versions were used in all analyses: Mouse UniGene build #136 (March 26 , 2004, mouse SAGEmap (April 3, 2004) corresponding to the mouse UniGene #136, LocusLink (April 3, 2004), mouse genome assembly NCBI build 32 (November 2003), mouse Reference Sequence collection (April 3, 2004) and Gene Ontology database (July, 2004).

We downloaded the human and mouse reference sequences hg19 and mm10, respectively, from the UCSC Table Browser [ 16, 17].

For the RNA-Seq data in Date Set 4, we apply SeqMap [ 28] with two mismatches and map all sequencing reads to the mouse reference sequences (mm9, NCBI, Build 37) and download gene annotations from the RefSeq mouse mRNA database(mm9, NCBI, Build 37) We apply PDEGEM to three sub-datasets in Data Set 1 and compared their R2 with that of mseq.

We obtained expected NspI and StyI restriction fragment lengths from the mouse genome reference sequence (NCBI mouse genome Build 37).

Sequencing data were mapped to mouse reference genome sequence (mm9) and SNVs were called using VarScan software (min-coverage 10, min-reads 2, min-avq-qual 20, min-var-freq 0.20, P value 0.99) [31].

Importantly, this is a lower bound estimate because the C57BL/6J (B6) strain, used for the mouse genome reference sequence (NCBI m37, Apr 2007), is the only mouse strain sequenced in its entirety.