| File(s) | Type | Description | Action |
|---|---|---|---|
| All_Cnu_microsatellites_combined.zip (26.36 MB) | ZIP Archive (ZIP) | Fragment analysis files (.fsa format). These files comprise a set of microsatellite loci that have been amplified by different primers. For each sample, there are 8 different PCR reactions, each with a labeled primer. They are multipexed in sets of 4, since there are 4 available dyes. So there are 2 files for each sample. These data can be analyzed to determine the microsatellite allele sizes. See site information and collection metadata for these files contained in "940678_v1_cnu-microsatellites.csv" FSA file format is used by proprietary software (Peak Scanner by Thermo Fisher and GeneMapper). They can also be used by open source tools (e.g. biopython). FSA File Structure: The FSA file contains multiple data blocks, each with specific information about the sequencing run. These include metadata (run conditions, sample name) and raw data (electropherogram peaks). Data Blocks: The data in FSA files is organized in tagged data blocks (each block contains a structured data type (e.g. an array, a sequence, etc). | Download |
| Supplemental File(s) | Type | Description | Action |
| sample_log.csv (1.32 KB) | Comma Separated Values (.csv) | This table contains a sample log for cockles collected from multiple intertidal locations in Washington State, USA. It includes a row per site along with the site_code used in the .fsa filenames. Columns (Parameters): column_name,column_description, units, data_type,format Location,"Site location description (e.g. ""Sequim Bay geoduck tubes, WA"")",unitless,String, Beach_Name,"Beach name (e.g. ""Front Beach"")",unitless,String, Code,Site Code,unitless,String,%m/%d/%Y Collection_Date,Collection date (local time zone PST/PDT),unitless,Date,%m/%d/%Y Tribe_Agency,Tribal Agency,unitless,String, GPS_Lat,Site latitude for collection,decimal degrees,Float, GPS_Lon,Site longitude for collection,decimal degrees,Float, Time,Collection time (local time zone PST/PDT),unitless,Time,%H:%M Tidal_Height,Tidal height at time of collection,feet (ft),Float, Collection_DateTime_UTC,Datetime with timezone for collection (UTC),units,Datetime,%Y-%m-%dT%H:%MZ | Download |
| 940678_v1_cnu-microsatellites.csv (28.00 KB) | Comma Separated Values (.csv) | File metadata table including collection information for all .fsa files included in "All_Cnu_microsatellites_combined.zip." Columns (Parameters): column_name,column_description, units, data_type,format filename,Fragment analysis filename (.fsa),units,String, filesize_bytes,filesize,bytes,Integer, md5sum,checksum (md5 hash) which can be used to verify intergrity of transferred files.,unitless,String, site_code,Site Code,unitless,String, Location,"Site location description (e.g. ""Sequim Bay geoduck tubes, WA"")",unitless,String, Beach_Name,"Beach name (e.g. ""Front Beach"")",unitless,String, Collection_Date,Collection date (local time zone PST/PDT),unitless,Date,%m/%d/%Y Tribe_Agency,Tribal Agency,unitless,String, GPS_Lat,Site latitude for collection,decimal degrees,Float, GPS_Lon,Site longitude for collection,decimal degrees,Float, Time,Collection time (local time zone PST/PDT),unitless,Time,%H:%M Tidal_Height,Tidal height at time of collection,feet (ft),Float, Collection_DateTime_UTC,Datetime with timezone for collection (UTC),units,Datetime,%Y-%m-%dT%H:%MZ | Download |
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