Chisholm Lake sedimentary unprocessed fish metabarcoding DNA sequences
Data files
Apr 17, 2024 version files 319.22 MB
-
A01-2328_S1_L001_R1_001.fastq.gz
5.64 MB
-
A01-2328_S1_L001_R2_001.fastq.gz
5.83 MB
-
A02-2336_S9_L001_R1_001.fastq.gz
6.66 MB
-
A02-2336_S9_L001_R2_001.fastq.gz
7.18 MB
-
A03-2339_S12_L001_R1_001.fastq.gz
4.03 MB
-
A03-2339_S12_L001_R2_001.fastq.gz
4.12 MB
-
A04-2347_S20_L001_R1_001.fastq.gz
3.73 MB
-
A04-2347_S20_L001_R2_001.fastq.gz
4.13 MB
-
A05-2352_S25_L001_R1_001.fastq.gz
4.64 MB
-
A05-2352_S25_L001_R2_001.fastq.gz
5.16 MB
-
A06-2353_S26_L001_R1_001.fastq.gz
2.15 MB
-
A06-2353_S26_L001_R2_001.fastq.gz
2.48 MB
-
A07-2356_S29_L001_R1_001.fastq.gz
3.23 MB
-
A07-2356_S29_L001_R2_001.fastq.gz
3.43 MB
-
A08-2358_S31_L001_R1_001.fastq.gz
4.13 MB
-
A08-2358_S31_L001_R2_001.fastq.gz
4.28 MB
-
B01-2329_S2_L001_R1_001.fastq.gz
6.56 MB
-
B01-2329_S2_L001_R2_001.fastq.gz
6.60 MB
-
B02-2337_S10_L001_R1_001.fastq.gz
4.80 MB
-
B02-2337_S10_L001_R2_001.fastq.gz
4.93 MB
-
B03-2340_S13_L001_R1_001.fastq.gz
6.03 MB
-
B03-2340_S13_L001_R2_001.fastq.gz
6.22 MB
-
B04-2348_S21_L001_R1_001.fastq.gz
3.76 MB
-
B04-2348_S21_L001_R2_001.fastq.gz
3.68 MB
-
B06-2354_S27_L001_R1_001.fastq.gz
1.88 MB
-
B06-2354_S27_L001_R2_001.fastq.gz
1.95 MB
-
B07-2357_S30_L001_R1_001.fastq.gz
6.60 MB
-
B07-2357_S30_L001_R2_001.fastq.gz
6.63 MB
-
B08-2359_S32_L001_R1_001.fastq.gz
7.34 MB
-
B08-2359_S32_L001_R2_001.fastq.gz
7.19 MB
-
C01-2330_S3_L001_R1_001.fastq.gz
4.18 MB
-
C01-2330_S3_L001_R2_001.fastq.gz
4.25 MB
-
C02-2338_S11_L001_R1_001.fastq.gz
5.63 MB
-
C02-2338_S11_L001_R2_001.fastq.gz
5.80 MB
-
C03-2341_S14_L001_R1_001.fastq.gz
4.19 MB
-
C03-2341_S14_L001_R2_001.fastq.gz
4.53 MB
-
C04-2349_S22_L001_R1_001.fastq.gz
3.29 MB
-
C04-2349_S22_L001_R2_001.fastq.gz
3.61 MB
-
C06-2355_S28_L001_R1_001.fastq.gz
4.13 MB
-
C06-2355_S28_L001_R2_001.fastq.gz
4.52 MB
-
C08-2360_S33_L001_R1_001.fastq.gz
8.78 MB
-
C08-2360_S33_L001_R2_001.fastq.gz
9.59 MB
-
D01-2331_S4_L001_R1_001.fastq.gz
4.16 MB
-
D01-2331_S4_L001_R2_001.fastq.gz
4.61 MB
-
D03-2342_S15_L001_R1_001.fastq.gz
6.67 MB
-
D03-2342_S15_L001_R2_001.fastq.gz
7.35 MB
-
D04-2350_S23_L001_R1_001.fastq.gz
4.31 MB
-
D04-2350_S23_L001_R2_001.fastq.gz
4.59 MB
-
E01-2332_S5_L001_R1_001.fastq.gz
2.61 MB
-
E01-2332_S5_L001_R2_001.fastq.gz
3 MB
-
E03-2343_S16_L001_R1_001.fastq.gz
3.46 MB
-
E03-2343_S16_L001_R2_001.fastq.gz
3.98 MB
-
E04-2351_S24_L001_R1_001.fastq.gz
8.02 MB
-
E04-2351_S24_L001_R2_001.fastq.gz
8.70 MB
-
F01-2333_S6_L001_R1_001.fastq.gz
3.85 MB
-
F01-2333_S6_L001_R2_001.fastq.gz
4.13 MB
-
F03-2344_S17_L001_R1_001.fastq.gz
3.45 MB
-
F03-2344_S17_L001_R2_001.fastq.gz
3.97 MB
-
G01-2334_S7_L001_R1_001.fastq.gz
3.36 MB
-
G01-2334_S7_L001_R2_001.fastq.gz
3.95 MB
-
G03-2345_S18_L001_R1_001.fastq.gz
3.71 MB
-
G03-2345_S18_L001_R2_001.fastq.gz
4.19 MB
-
H01-2335_S8_L001_R1_001.fastq.gz
7.09 MB
-
H01-2335_S8_L001_R2_001.fastq.gz
7.37 MB
-
H03-2346_S19_L001_R1_001.fastq.gz
2.46 MB
-
H03-2346_S19_L001_R2_001.fastq.gz
2.75 MB
-
README.md
1.58 KB
Abstract
We sequenced amplicons targeting a segment of the 12S ribosomal DNA gene in vertebrates from DNA pools isolated from sections of a sediment core from Chisholm Lake in interior Alaska. The primary aim of this sequencing effort was to add to our understanding of the evolution of fish faunas in Beringian regions impacted by glacial cycles. This dataset consists of unprocessed output from amplicon paired end short read sequencing on an Illumina sequencing by synthesis platform. Analyses of these sequences are being incorporated into a broader effort to examine post-glacial Beringian biotas and ecologies.
README: Chisholm Lake sedimentary unprocessed fish metabarcoding DNA sequences
https://doi.org/10.5061/dryad.08kprr58x
Description of the data and file structure
The dataset consists of 50 paired-end sequencing read files compressed by gzip. The sequence data is in FASTQ format as produced by an Illumina MiSeq instrument used for sequencing the libraries described below. Paired reads are in separate files denoted as R1 and R2.
Data was derived from the following sources:
- Samples of sediment from a core from Chisholm Lake (64.3017° N, 146.6890° W) in Alaska.
- Nucleic acids were isolated from subsamples of the core at regular depth intervals
- Sedimentary DNA was used as template for amplification using a primer pair targeting a segment of the 12S ribosomal RNA coding gene in fish mitochondrial genomes. The primer pair sequences were designed, validated and published by Miya et al. (2015; https://doi.org/10.1098/rsos.150088)
- Libraries for sequencing on Illumina short read platforms were assembled for each sample amplification and subsequently pooled for sequencing
- Libraries were sequenced on a MiSeq instrument
Sharing/Access information
These sequences are being used in analyses to validate a sedimentary DNA metabarcoding approach to study temporal changes of fauna and flora around aquatic habitats at high latitudes. They are available here and are free to share and re-use. At this point, the dataset is not associated with a published manuscript.
Methods
DNA was isolated from sections from a lake bottom sediment core. DNA isolates were used as PCR templates using the reagents described in the MiFish metabarcoding protocols of Miya et al. (2015). Amplicons were then used to prepare libraries suitable for sequencing on Illumina platforms. All libraries generated from core sections and section replicates were uniquely indexed then pooled together and sequenced on a MiSeq instrument.