Dataset Requests & Suggestions

Click for a searchable table with links to all ImmGen data series:

ImmGen satasets

If these data were of value to you, we would be grateful if you could mention ImmGen in the acknowledgments of publications that were enriched by these data (for example: “This work benefitted from data assembled by the ImmGen consortium”), and/or quote the primary ImmGen reference: Heng TS, et al, Immunological Genome Project Consortium. Nat Immunol. 2008 10 : 1091.

It would also be most useful if you could send us an email for our records.

For general comments and suggestions: email us at ImmGen@hms.harvard.edu

ImmGen is updating the gene/transcript reference framework used to map and assign RNAseq data. Liang Yang has performed the herculean task of re-processing all existing ULI RNAseq data against GENCODE Version M25, from the previously used M16. This update applies to data on the “RNAseq Skyline”, "Population Comparison (RNASeq)" and "MyGeneSet" databrowser pages.
In addition, Gene tables for datasets deposited at NCBI’s Gene Expression Omnibus (GSE109125, GSE122108, GSE122597) have been updated to M25, as have the raw count numbers and normalized tables found on the ImmGen Dataset page.

Please be aware of small discrepancies that may occur while comparing to previously downloaded data or figures. Changes are minimal for most genes, but M25 differs from M16 by introducing around 2400 new genes and 8000 new transcripts (for a total of 55401 total genes, of which 21859 are recognized as protein-coding). Many of them are microRNA precursors, others correspond to better distinguished members of gene families. The most significant “newcomers” are Vps28, Tmem179b, and Itprip (primarily expressed in Mast cells, Macrophages and Granulocytes, respectively).