NCBI accession numbers and associated metadata for raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals from 1998-01-01 to 2007-12-31 (NCEI Accession 0277716)
This dataset contains biological and survey - biological data collected at Poquott Beach during deployment Palumbi_silversides in the Bay of Fundy, Gulf of St. Lawrence, New York Bight, and North Atlantic Ocean from 1998-01-01 to 2007-12-31. These data include species. The instruments used to collect these data include Automated DNA Sequencer. These data were collected by Stephen R. Palumbi of Stanford University - Hopkins as part of the "High resolution genome changes during evolution in a classic fisheries experiment (Fishery Genome Changes)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2022-03-18.
The following is the text of the dataset description provided by BCO-DMO:
Accession numbers for raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals
Dataset Description:
Raw low-coverage genomic sequence reads: 1190 files with raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals (some individuals are represented by multiple sequence data files) are deposited in the NCBI Sequence Read Archive (SRA) with accession numbers SRS2001281- SRS2003099 associated with BioProject PRJNA376564 and BioSamples SAMN06436077 - SAMN06436952.
The following is the text of the dataset description provided by BCO-DMO:
Accession numbers for raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals
Dataset Description:
Raw low-coverage genomic sequence reads: 1190 files with raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals (some individuals are represented by multiple sequence data files) are deposited in the NCBI Sequence Read Archive (SRA) with accession numbers SRS2001281- SRS2003099 associated with BioProject PRJNA376564 and BioSamples SAMN06436077 - SAMN06436952.
Dataset Citation
- Cite as: Palumbi, Stephen R. (2023). NCBI accession numbers and associated metadata for raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals from 1998-01-01 to 2007-12-31 (NCEI Accession 0277716). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277716. Accessed [date].
Dataset Identifiers
ISO 19115-2 Metadata
gov.noaa.nodc:0277716
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Ordering Instructions | Contact NCEI for other distribution options and instructions. |
Distributor |
NOAA National Centers for Environmental Information +1-301-713-3277 NCEI.Info@noaa.gov |
Dataset Point of Contact |
NOAA National Centers for Environmental Information ncei.info@noaa.gov |
Time Period | 1998-01-01 to 2007-12-31 |
Spatial Bounding Box Coordinates |
West: -81.43
East: -61.85
South: 31.02
North: 47.4
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Dataset Progress Status | Complete - production of the data has been completed Historical archive - data has been stored in an offline storage facility |
Data Update Frequency | As needed |
Supplemental Information | Acquisition Description: Species: Atlantic silverside ( Menidia menidia) Source: From laboratory breeding experiment or wild caught at one of four locations along the east coast of North America. Library preparation method: Modified version of Illumina Nextera sample preparation kit. Sequencing instrument: Illumina HiSeq 2000 Read type: Paired-end 125 bp Sequencing strategy: Whole genome sequencing The sequence data were prepared as described in Therkildsen & Palumbi (2017). The tissue samples used for sequencing had been stored in minus 20 degrees C freezer for 8-17 years prior to DNA extraction. We used the Qiagen DNeasy Blood and Tissue kit to extract DNA from muscle tissue and evaluated the degradation level of each extract through 1.5% agarose gel electrophoresis. Only samples that showed clear high molecular weight bands and limited smearing were retained for library preparation. To ensure DNA integrity in the retained samples, we removed fragments shorter than ~1000 bp from each extract using Agencourt AMPure XP beads in a 0.4:1 AMPure to sample ratio and eluted the DNA in 10 mM Tris-Cl, pH 8.5. We measured DNA concentrations with a Quant-iT high-sensitivity assay (Invitrogen) and prepared a separate barcoded library for each individual with Illumina’s Nextera kit according to the protocol described in Therkildsen and Palumbi (2017). Briefly, the tagmentation reaction, which simultaneously fragments the DNA and incorporates partial adapters, was carried out in a 2.5 ul volume with 1.6–7.9 ng of input DNA for each library. We then used a two-step PCR procedure with a total of 12 cycles (8 + 4) to add the remaining Illumina adapter sequence with dual index barcodes and amplify the libraries. The PCR was conducted with the KAPA Library Amplification Kit and the Illumina Nextera index kit with primers N501– N508 + S511 and N701–N712 + N714. As a final step, we purified and size-selected the amplification products with Agencourt AMPure XP beads and quantified the concentration of the final libraries with the Invitrogen Quant-iT high-sensitivity assay. We also examined the fragment size distribution of multiple libraries from each plate on an Agilent Bioanalyzer instrument. We combined equimolar amounts of 56–76 libraries into separate pools for sequencing across 13.5 lanes of paired-end 125-bp reads on an Illumina HiSeq 2000 (v4 chemistry) at the University of Utah’s Bioinformatics Core Facility. To even out the data yield among samples, we repooled libraries that initially had obtained the lowest read output for supplementary sequencing in 4.5 additional HiSeq lanes. |
Purpose | This dataset is available to the public for a wide variety of uses including scientific research and analysis. |
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Data Center keywords | NODC COLLECTING INSTITUTION NAMES THESAURUS NODC SUBMITTING INSTITUTION NAMES THESAURUS Global Change Master Directory (GCMD) Data Center Keywords |
Platform keywords | BCO-DMO Platform Names |
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Last Modified: 2024-05-31T18:50:46Z
For questions about the information on this page, please email: ncei.info@noaa.gov
For questions about the information on this page, please email: ncei.info@noaa.gov