Data from: Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

 

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Title FASTA file of CAP3 assembly
Downloaded 33 times
Description Assembly in fasta format of white-footed mouse 454 cDNA libraries from in and around New York City (NYC) using the CAP3 assembler with default setting.
Download Assembly_P.leucopus_CAP3_12APRIL2013.fasta (18.61 Mb)
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Title FASTA file of Newbler cDNA assembly
Downloaded 16 times
Description Assembly in fasta format of white-footed mouse 454 cDNA sequence reads from in and around New York City (NYC) using the Newbler assembly program with the cDNA option.
Download Assembly_P.leucopus_NewblercDNA_05NOV2012.fasta (14.54 Mb)
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Title FASTA file of Newbler genome assembly
Downloaded 13 times
Description Assembly in fasta format of white-footed mouse 454 cDNA sequence reads from in and around New York City (NYC) using the Newbler assembly program with the large genome option.
Download Assembly_P.leucopus_NewblerGenome_15APRIL2...fasta (13.97 Mb)
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Title Sequence alignment file (SAM) of 454 reads from Central Park population
Downloaded 23 times
Description Sequence alignment file of fastq files from Central Park 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.
Download SequenceAlignment_P.leucopus_CentralPark_...12.sam (41.35 Mb)
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Title Sequence alignment file (SAM) of 454 reads from Flushing Meadows population
Downloaded 21 times
Description Sequence alignment file (SAM) of fastq files from Flushing Meadows 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.
Download SequenceAlignment_P.leucopus_FlushingMead...12.sam (76.32 Mb)
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Title Sequence alignment file (SAM) of 454 reads from Harriman State Park population
Downloaded 13 times
Description Sequence alignment file (SAM) of fastq files from Harriman State Park 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.
Download SequenceAlignment_P.leucopus_HarrimanPark...12.sam (79.53 Mb)
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Title Sequence alignment file (SAM) of 454 reads from New York Botanical Garden population
Downloaded 20 times
Description Sequence alignment file (SAM) of fastq files from New York Botanical Garden 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.
Download SequenceAlignment_P.leucopus_NewYorkBotan...12.sam (50.00 Mb)
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Title Sequence alignment file (SAM) of 454 reads from Ridgewood Reservoir population
Downloaded 11 times
Description Sequence alignment file (SAM) of fastq files from Ridgewood Reservoir sequencing. Fastq Files were aligned to Newbler cDNA assembly.
Download SequenceAlignment_P.leucopus_RidgewoodRes...12.sam (49.33 Mb)
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Title BLAST and gene ontology annotations for white-footed mouse cDNA sequences
Downloaded 19 times
Description Output file from software program BLAST2GO. Must be opened in BLAST2GO. Contains full BLAST and GO annotations for Newber assembly of all Peromyscus leucopus 454 sequences
Download Annotations_P.leucopus_01MAY2012.dat (31.44 Mb)
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Title VCF (variant call format) file of SNPs identified in NYC white-footed mice
Downloaded 17 times
Description Variant call format file of SNPs generated using the SAMTOOLS mpileup function. All populations were used to make probabilistic SNP calls.
Download SNP_P.leucopus_CP_FM_NYBG_RR_HP_07DEC2012.vcf (6.492 Mb)
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Title Results of Ka / Ks calculations for each white-footed mouse population pair
Downloaded 76 times
Description Excel spreadsheet of results from KAKS_Calculator. Each population pair was compared and the 10 comparisons are displayed in separate tabs.
Download KAKS_P.leucopus_26FEB2013.xls (1.070 Mb)
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When using this data, please cite the original publication:

Harris SE, Munshi-South J, Obergfell C, O'Neill R (2013) Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area. PLoS ONE 8(8): e74938. http://dx.doi.org/10.1371/journal.pone.0074938

Additionally, please cite the Dryad data package:

Harris SE, Munshi-South J, Obergfell C, O'Neill R (2013) Data from: Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r8ns3
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