File(s) | Type | Description | Action |
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854878_v1_raw_icwgs_sampleinfo.csv (25.53 KB) | Comma Separated Values (.csv) | Primary data file for dataset ID 854878, version 1 | Download |
Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside individuals (some individuals are represented by multiple sequence data files). The raw low-coverage genomic sequence reads are deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA376564. These data were published in Wilder et al. (2020).
The following is an excerpt of the methods used to generate these data. Full details can be found in the associated publication and supplemental material of Wilder et al. (2020).
Data generation:
Atlantic silverside muscle samples collected from Georgia (GA), New York (NY), Gulf of Maine (GoM) and Gulf of St. Lawrence (GSL) were sequenced by Therkildsen & Palumbi (2017) to a final, average depth of 1.5x across the reference transcriptome. All the samples were collected in the spring. See Therkildsen & Palumbi (2017) and Therkildsen et al. (2019) for further detail. We added 47 additional samples from Oregon Inlet, North Carolina (NC) near Cape Hatteras.
Individually barcoded sample libraries were prepared at Cornells Biotechnology Resource Center using similar methods to Therkildsen & Palumbi (2017), with a few minor modifications. Reagents from the Illumina Nextera kit (96 sample Nextera DNA Library Prep Kit) were used at 1/3 the recommended concentration in 1/10 the recommended volume (5ul instead of 50ul), with 2ng of input DNA. Individual libraries were pooled, and size-selected using a Pippin Prep to remove fragments <286 bp (150 bp insert plus 136 bp of Illumina adapters). Filtered mapped reads for the NC samples had a final average depth of 1.5x.
Sampling and analytical procedures:
Samples were collected directly from the wild as described in Hice et al. (2012).
Locations:
Five locations along the east coast of North America.
USA:Jekyll Island,Georgia 31.02 -81.43
USA:Oregon Inlet,NorthCarolina 35.77 -75.52
USA:Minas Basin,Gulf of Maine 45.2 -64.38
USA:Patchogue,NewYork 40.75 -73.00
Canada:Magdalen Island, Gulf of St. Lawrence 47.4 -61.85
Problem report:
The following samples should be excluded from analysis because of possible errors during library preparation:
JekyllIs_1223, JekyllIs_1224, MagdalenIs_911, MagdalenIs_912, MagdalenIs_913, MagdalenIs_914, MagdalenIs_915, MagdalenIs_916, MagdalenIs_917, MagdalenIs_918, Patchogue_1030
Therkildsen, N. O., Baumann, H. (2024) Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-06-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.854878.1 [access date]
Terms of Use
This dataset is licensed under Creative Commons Attribution 4.0.
If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.