Question: How do I use the Feature Barcode whitelist?
Answer: The Feature Barcode whitelist lists 10,000 Feature Barcode Sequences recommended when designing oligonucleotides for custom antibody conjugations. They are distinct from the 10x cell barcode whitelist.
Here are the first ten lines of the Feature Barcode whitelist:
AAGGCAGACGGTGCA
GGCTGCGCACCGCCT
TAGTTGACATGCCAT
GACGCGCGTTGTCAT
CGTCCTAGGACATAT
CTCCAGCTCGAGCTC
GGACGCAACTTAAGA
AGCGAACCGCCGCTG
GTGCAAGAGTTGGCG
GAAGAAGCGTTATTC
You can find the full Feature Barcode whitelist file (.txt) here: https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-cell-surface-protein-labeling-for-single-cell-rna-sequencing-protocols
To design a custom conjugate oligonucleotide, use a sequence from the Feature Barcode whitelist (15 nt; pink sequence). This sequence should be flanked by a 10nt region of diversity and a 9nt region of diversity. (When ordering custom DNA oligos, the regions of diversity can be specified by requesting a string of N's.) The oligonucleotide must also contain an amine group at 5'-end (5' amine-modified; IDT code /5AmMC12/).
Note: When ordering, ensure that Tris buffers are NOT used for resuspension as they are not compatible with conjugation.
See the 10x Demonstrated Protocol 'Cell Surface Labeling for Single Cell RNA Sequencing Protocols for guidance on antibody-oligonucleotide conjugation.'
Products: Single Cell Gene Expression, Single Cell Immune Profiling, Fixed RNA Profiling Gene Expression