Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera)

Heintzman PD, Elias SA, Moore K, Paszkiewicz K, Barnes I

Date Published: November 27, 2013

DOI: http://dx.doi.org/10.5061/dryad.0179t

 

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Title Reference sequences for museum-1
Downloaded 1 time
Description Reference sequences for sample museum-1. Use with file 'Alignment of merged reads for museum-1'.
Download Amara_alpina.reference_list.museum1.fasta (54.13 Kb)
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Title Reference sequences for museum-2
Description Reference sequences for sample museum-2. Use with file 'Alignment of merged reads for museum-2'.
Download Amara_alpina.reference_list.museum2.fasta (54.13 Kb)
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Title Reference sequences for modern-1
Description Reference sequences for sample modern-1. Use with file 'Alignment of merged reads for modern-1'.
Download Amara_alpina.reference_list.modern1.fasta (54.13 Kb)
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Title Reference sequences for modern-2
Description Reference sequences for sample modern-2. Use with file 'Alignment of merged reads for modern-2'.
Download Amara_alpina.reference_list.modern2.fasta (54.13 Kb)
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Title Reference sequences for ancient-1
Description Reference sequences for sample ancient-1. Use with file 'Alignment of merged reads for ancient-1'.
Download Amara_alpina.reference_list.ancient1.fasta (54.12 Kb)
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Title Reference sequences for ancient-2
Description Reference sequences for sample ancient-2. Use with file 'Alignment of merged reads for ancient-2'.
Download Amara_alpina.reference_list.ancient2.fasta (54.13 Kb)
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Title Partial COI sequence for Amara alpina
Description Example partial sequence of the cytochrome oxidase subunit 1 (COI) gene for Amara alpina
Download KF695187 (0 bytes)
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Title Partial 28S sequence for Amara alpina
Description Example partial sequence of the 28S ribosomal RNA (28S) gene for Amara alpina
Download KF695188 (0 bytes)
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Title Partial ITS1 sequence for Amara alpina
Description Example partial sequence of the internal transcribed spacer 1 (ITS1) for Amara alpina
Download KF695189 (0 bytes)
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Title Alignment of merged reads for museum-1
Description Merged reads that aligned to the reference sequences for sample museum-1. Use with file 'Reference sequences for museum-1'.
Download Amara_alpina.merged_alignment.museum1.sam (6.221 Mb)
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Title Alignment of merged reads for museum-2
Description Merged reads that aligned to the reference sequences for sample museum-2. Use with file 'Reference sequences for museum-2'.
Download Amara_alpina.merged_alignment.museum2.sam (4.135 Mb)
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Title Alignment of merged reads for modern-2
Description Merged reads that aligned to the reference sequences for sample modern-2. Use with file 'Reference sequences for modern-2'.
Download Amara_alpina.merged_alignment.modern2.sam (4.830 Mb)
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Title Alignment of merged reads for modern-1
Description Merged reads that aligned to the reference sequences for sample modern-1. Use with file 'Reference sequences for modern-1'.
Download Amara_alpina.merged_alignment.modern1.sam (5.413 Mb)
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Title Alignment of merged reads for ancient-1
Description Merged reads that aligned to the reference sequences for sample ancient-1. Use with file 'Reference sequences for ancient-1'.
Download Amara_alpina.merged_alignment.ancient1.sam (173.0 Kb)
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Title Alignment of merged reads for ancient-2
Description Merged reads that aligned to the reference sequences for sample ancient-2. Use with file 'Reference sequences for ancient-2'.
Download Amara_alpina.merged_alignment.ancient2.sam (113.8 Kb)
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Title Contig data for modern-1
Description FASTA file of all contigs considered during the metagenomic analysis of sample modern-1. Use with 'BLAST assignment data for modern-1' in MEGAN v4.70.
Download Amara_alpina.contigs.modern-1.fasta (114.0 Mb)
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Title Contig data for modern-2
Description FASTA file of all contigs considered during the metagenomic analysis of sample modern-2. Use with 'BLAST assignment data for modern-2' in MEGAN v4.70.
Download Amara_alpina.contigs.modern-2.fasta (172.3 Mb)
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Title Contig data for museum-1
Description FASTA file of all contigs considered during the metagenomic analysis of sample museum-1. Use with 'BLAST assignment data for museum-1' in MEGAN v4.70.
Download Amara_alpina.contigs.museum-1.fasta (110.5 Mb)
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Title Contig data for museum-2
Description FASTA file of all contigs considered during the metagenomic analysis of sample museum-2. Use with 'BLAST assignment data for museum-2' in MEGAN v4.70.
Download Amara_alpina.contigs.museum-2.fasta (63.03 Mb)
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Title Contig data for ancient-1
Description FASTA file of all contigs considered during the metagenomic analysis of sample ancient-1. Use with 'BLAST assignment data for ancient-1' in MEGAN v4.70.
Download Amara_alpina.contigs.ancient-1.fasta (59.22 Mb)
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Title Contig data for ancient-2
Description FASTA file of all contigs considered during the metagenomic analysis of sample ancient-2. Use with 'BLAST assignment data for ancient-2' in MEGAN v4.70.
Download Amara_alpina.contigs.ancient-2.fasta (50.55 Mb)
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Title BLAST assignment data for modern-1
Description Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample modern-1. Use with 'Contig data for modern-1' in MEGAN v4.70. See attached readme file for column headers.
Download Amara_alpina.assignments.modern-1.BLAST (9.692 Mb)
Download README.txt (315 bytes)
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Title BLAST assignment data for modern-2
Description Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample modern-2. Use with 'Contig data for modern-2' in MEGAN v4.70. See attached readme file for column headers.
Download Amara_alpina.assignments.modern-2.BLAST (33.31 Mb)
Download README.txt (315 bytes)
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Title BLAST assignment data for museum-1
Description Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample museum-1. Use with 'Contig data for museum-1' in MEGAN v4.70. See attached readme file for column headers.
Download Amara_alpina.assignments.museum-1.BLAST (25.34 Mb)
Download README.txt (315 bytes)
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Title BLAST assignment data for museum-2
Downloaded 1 time
Description Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample museum-2. Use with 'Contig data for museum-2' in MEGAN v4.70. See attached readme file for column headers.
Download Amara_alpina.assignments.museum-2.BLAST (17.35 Mb)
Download README.txt (315 bytes)
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Title BLAST assignment data for ancient-1
Downloaded 1 time
Description Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample ancient-1. Use with 'Contig data for ancient-1' in MEGAN v4.70. See attached readme file for column headers.
Download Amara_alpina.assignments.ancient-1.BLAST (96.10 Mb)
Download README.txt (315 bytes)
Details View File Details
Title BLAST assignment data for ancient-2
Downloaded 1 time
Description Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample ancient-2. Use with 'Contig data for ancient-2' in MEGAN v4.70. See attached readme file for column headers.
Download Amara_alpina.assignments.ancient-2.BLAST (113.3 Mb)
Download README.txt (315 bytes)
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When using this data, please cite the original publication:

Heintzman PD, Elias SA, Moore K, Paszkiewicz K, Barnes I (2013) Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera). Molecular Ecology Resources 14(3): 606–615. http://dx.doi.org/10.1111/1755-0998.12205

Additionally, please cite the Dryad data package:

Heintzman PD, Elias SA, Moore K, Paszkiewicz K, Barnes I (2013) Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.0179t
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