Dataset: Single Nucleotide Polymorphism
Deployment: Lab_Stanford_HMS_Palumbi

Single Nucleotide Polymorphism (SNP)

Principal Investigator:

Stephen R. Palumbi (Stanford University - Hopkins, Stanford-HMS)

Project Coordinator:

Kristen Milligan (Oregon State University, OSU)

Contact:

Stephen R. Palumbi (Stanford University)

BCO-DMO Data Manager:

Stephen R. Gegg (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

OCEAN ACIDIFICATION - Category 1: COLLABORATIVE RESEARCH: Acclimation and adaptation to ocean acidification of key ecosystem components in the California Current System (OMEGAS-MaS)

Current State:

Final no updates expected

Version:

26 November 2013

Version Date:

2013-11-26

Data URL:

https://www.bco-dmo.org/dataset-deployment/472396/data

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Description

Single Nucleotide Polymorphism for each of the Strongylocentrotus purpuratus genes from the GLEAN3 genome build.

Data structure: Fractions are allele frequency values. Location, Day samples (D1 or D7), and CO2 level (385 or 1000) are listed.

Data are for each of the S. purpuratus genes from the GLEAN3 genome build.

Parameter Names/Definitions:
GLEAN ID: ID code
POS: base position
Random trails larger than observed value (running record): no units
Sample ID code format: State_Site_Tidal Height_:
OR: Oregon
FC: Fogarty Creek Site
ST: Strawberry Hill
BD: Bodega Bay
NC: Northern California
VD: Van Damme
CC: Central California
SH: Sand Hill Bluff
TP: Terrace Point
SB: Santa Barbara region
AL: Alegria

Resulting Publications:
2013. Pespeni, M. E. Sanford, B. Gaylord, T. M. Hill, J. D. Hosfelt, H. Jaris, M. LaVigne, E. Lenz, A. D. Russell, M. K. Young, S. R. Palumbi. Evolutionary change during experimental ocean acidification. Published online before print April 8, 2013, http://dx.doi.org/10.1073/pnas.1220673110

Pespeni MH, Barney BT, Palumbi SR (2012) Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin. Evolution 67(7): 1901–1914. doi:10.1111/evo.12036

Methods & Sampling

Dataset acquisition description

See resulting publications and http://sfg.stanford.edu/

Data Processing Description

Dataset Processing Description

filtered by: minimum 10 reads, <.1 diff day 1- 7, >5% minor allele

See: resulting publications and http://sfg.stanford.edu/

BCO-DMO Processing Notes
Original file: "larval SNPs for NSF-palumbi.xlsx" contributed by Kristen Milligan
- Approx Lat/Lon of Hopkins Marine Station/Palumbi Lab appended to enable data discovery in MapServer
- Parameter names edited to conform to BCO-DMO parameter naming conventions

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1041222	NSF Division of Ocean Sciences

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Lab_Id	Lab Id – Lab identifier where experiments were conducted	text	laboratory
Lat	Approximate Latitude Position of Lab; South is negative	decimal degrees	lat
Lon	Approximate Longitude Position of Lab; West is negative	decimal degrees	lon
GLEAN_ID	ID code	text	no_bcodmo_term
POS	Base Position	dimensionless	no_bcodmo_term
Random_Trails	Random trails larger than observed value (running record)	dimensionless	no_bcodmo_term
OR_FC_L_D1_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
OR_FC_L_D7_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
OR_FC_L_D1_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
OR_FC_L_D7_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
OR_ST_H_D1_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
OR_ST_H_D7_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
OR_ST_H_D1_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
OR_ST_H_D7_1002_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
NC_BD_L_D1_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
NC_BD_L_D7_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
NC_BD_L_D1_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
NC_BD_L_D7_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
NC_VD_H_D1_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
NC_VD_H_D7_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
NC_VD_H_D1_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
NC_VD_H_D7_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
CC_SH_H_D1_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
CC_SH_H_D7_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
CC_SH_H_D1_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
CC_SH_H_D7_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
CC_TP_L_D1_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
CC_TP_L_D7_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
CC_TP_L_D1_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
CC_TP_L_D7_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
SB_AL_L_D1_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
SB_AL_L_D7_0385_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
SB_AL_L_D1_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term
SB_AL_L_D7_1000_af	Allele frequency values for Sample Id: Location (State and Site); Day Sample (D1 or D7); CO2 Level (385 or 1000 in ppm)<br>See Metadata Dataset Description for key to State and Site	text	no_bcodmo_term

Database

Contribute Data

Dataset: Single Nucleotide Polymorphism
Deployment: Lab_Stanford_HMS_Palumbi

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Single Nucleotide PolymorphismDeployment: Lab_Stanford_HMS_Palumbi

Dataset acquisition description

Dataset Processing Description

Dataset: Single Nucleotide Polymorphism
Deployment: Lab_Stanford_HMS_Palumbi