Continuing the discussion from Evaluation datasets etc:
Thanks to @javh for the list of publically available HTS data. Most of these are sequenced from mRNA, so are unlikely to capture the nonproductive repertoire.
However, some used gDNA, allowing the nonproductive repertoire to be captured as well:
- Boyd, S. D. et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci. Transl. Med. 1, 12ra23 (2009). SRA Accession: SRP001460
- Jiang,N. et al. (2013) Lineage structure of the human antibody repertoire in response to influenza vaccination. Sci. Transl. Med., 5, 171ra19. SRA Accession: SRA058972
- Ohm-Laursen and Barington (2007) Analysis of 6912 unselected somatic hypermutations in human VDJ rearrangements reveals lack of strand specificity and correlation between phase II substitution rates and distance to the nearest 3’ activation-induced cytidine deaminase target. J Immunol. 178(7):4322-34. EMBL AM076988–AM083316
However, the first two use VH-internal primers (FR1 or FR2) and the last only looks at a single V gene (VH3-23). There’s also a really nice paper looking directly at the nonproductive allele in mice:
Any one aware of other data sets?