We conducted single nuclei RNA-Seq of hindbrain organoids and now would like to use these data for further this analysis with the question if we could identify that certain cells belong to a particular region (nucleus) in the hindbrain. Does anyone know whether reference data for this are available in human?
Please see An anatomically comprehensive atlas of the adult human brain transcriptome | Nature (Supplemental table 2 has a nice overview of the sampled regions you might be interested in) and the recent single cell RNA-seq preprint of the whole human brain: Transcriptomic diversity of cell types across the adult human brain | bioRxiv
Thanks a lot!
Hi Rachel, Thank you very much for your answer. We checked the resources you provided us, and we see that we can search by a specific gene of interest or by gene category. However, what we would like to do is extract the list of genes identified and attributed to hindbrain regions, so that we can compare the human tissue with our transcriptomic data from human-derived organoids. Is there any way we could extract this kind of gene list? Or a different way to get this information? Thank you very much for your kind help! -Gemma
Hello @gemmagomez you can download the data here, Microarray Data Download :: Allen Brain Atlas: Human Brain and might find these posts helpful Transcriptomics (RNA-seq/microarray) data normalization - FAQ - #2 by fanikonst and Microarray Expression File
For access to data in Transcriptomic diversity of cell types across the adult human brain check out the “Data and materials availability” section.