aptamers: Sequence data for the Somalogic SOMAscan assay

In readat: Functionality to Read and Manipulate SomaLogic ADAT files

Description

Sequence data for the SOMAmers in the 1129 and 1310 panels of the Somalogic SOMAscan assay.

Format

A data frame with the following columns.

AptamerId

Character, primary key. The identifier of the aptamer sequence identified using SELEX. It consists of an SomaLogic SeqId truncated at the underscore, to remove its sequence version number.

SomaId

Character. The SomaLogic identifier for the protein target. For the 1129 and 1310 assays, there is a one-to-one correspondence between SeqId and SomaId, but in theory there is a many-to-one correspondence.

Target

Character. The name of the protein target, from the protein standard supplier, sometimes with additional annotation by SomaLogic.

TargetFullName

Character. The name of the protein target, from UniProt.

UniProt

List of character vectors. UniProt IDs for the protein target.

EntrezGeneID

List of character vectors. Entrez Gene IDs for the gene associated with protein target.

EntrezGeneSymbol

List of character vectors. Entrez Gene symbols for the gene associated with protein target.

Organism

Either "Human" or the name of a virus.

Units

Should always be RFU, short for Relative Fluorescence Units.

Type

The protein standard source for the original SELEX performed for the sequence. "Protein" refers to human protein; a few sequences used rat protein standard sources in the SELEX.

PlasmaDilution

What dilution factor is used in plasma?

SerumDilution

What dilution factor is used in serum?

IsIn1129Panel

Is the aptamer in the 1129 panel of the SOMAscan assay?

IsIn1310Panel

Is the aptamer in the 1310 panel of the SOMAscan assay?

References

The SOMAmers in the SomaLogic SOMAscan 1310 assay can be found in this PDF: http://www.somalogic.com/somalogic/media/Assets/PDFs/SSM-045-REV-1-SOMAscan-Assay-1-3k-Content.pdf Those from the 1129 assay can be found here: http://www.somalogic.com/somalogic/media/Assets/PDFs/SSM-011-Rev-11-SOMAscan-Assay-%28V1-1k%29-Content.pdf

Examples

head(aptamers)

Example output

  AptamerId   SomaId                    Target
1   4829-43 SL001737                 STRATIFIN
2   3804-66 SL007403                      DMP1
3   3814-63 SL007423                  IL-11 RA
4  14156-33 SL004815 14-3-3 protein beta/alpha
5   7625-27 SL008071      14-3-3 protein theta
6    5858-6 SL005688 14-3-3 protein zeta/delta
                         TargetFullName UniProt EntrezGeneID EntrezGeneSymbol
1                  14-3-3 protein sigma  P31947         2810              SFN
2 Dentin matrix acidic phosphoprotein 1  Q13316         1758             DMP1
3 Interleukin-11 receptor subunit alpha  Q14626         3590           IL11RA
4             14-3-3 protein beta/alpha  P31946         7529            YWHAB
5                  14-3-3 protein theta  P27348        10971            YWHAQ
6             14-3-3 protein zeta/delta  P63104         7534            YWHAZ
  Organism Units    Type PlasmaDilution SerumDilution IsIn1310Panel
1    Human   RFU Protein             40            40          TRUE
2    Human   RFU Protein             40            40         FALSE
3    Human   RFU Protein             40            40         FALSE
4    Human   RFU Protein              1             1          TRUE
5    Human   RFU Protein              1             1          TRUE
6    Human   RFU Protein              1             1          TRUE
  IsIn1129Panel
1          TRUE
2          TRUE
3          TRUE
4         FALSE
5         FALSE
6         FALSE

readat documentation built on Oct. 31, 2019, 8:19 a.m.