Single Cell Allele Specific Expression and AlleleSeq

Q:
We have developed a method to perform single cell allele specific expression by labeling individual mRNA molecules with single base specificity in situ. In other words, we can differentially label and detect transcripts with a single SNP difference with our fluorescent probes.

As part of our validation, we were happy to find your published diploid genome of GM12878, and used it to design probes for various candidate genes to see what patterns of allelic imbalance we could see at a single cell level. We were hoping that you might be able to provide us with some form of quantification for the allelic imbalance (such as # of reads that aligned to the maternal versus paternal allele) for some of the genes on your list of "Genes with allele specific expression" that you published on your website, such as SKA and SUZ12. We also noted that some of the genes on the "Genes with allele specific expression" have heterozygous SNPs in them that are not on the "SNP’s resulting in allele specific behavior table" and vice versa, so we weren’t exactly sure how to interpret that difference.

I look forward to hearing from you as being able to relate our single cell measurements with the genomic measurements is an exciting prospect, and I thank you again for having made available such a useful resource.

A:
thanks for interest to AlleleSeq.
Allelic imbalances can be inferred for each SNP from NA12878_AS_SNPs.vcf file. The file has counts for ref and alt alleles. Is it what you are asking?

We also noted that some of the genes on the "Genes with allele specific expression" have heterozygous SNPs in them that are not on the "SNP’s resulting in allele specific behavior table" and vice versa, so we weren’t exactly sure how to interpret that difference.
If you point us to few such cases we would be happy to look and resolve the inconsistencies. However, my feeling is that, it is probably reflects differences in gene annotation in different databases.

Your paper sounds very cool. I would be happy to read it when it comes out or even before that (if you consider that possible).

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