Hello,
I'm currently investigating the microglia population based on the recent Cell paper titled "Human microglial state dynamics in Alzheimer's disease progression," with the DOI: https://doi.org/10.1016/j.cell.2023.08.037.
In the paper, the authors mentioned that they analyzed 174,420 immune cells. However, upon reviewing the "Gene Expression (snRNAseq - 10x) processed" folder under this link: https://www.synapse.org/#!Synapse:syn52293442, I noticed that the 'Immune cell' RDS file only contains 83,889 cells, which is inconsistent with the paper. I understand that the paper involved pooling data from multiple brain regions for analysis. My next question is whether the "Immune cell" RDS file contains data from other brain regions, or if I need to extract immune cells from the files in the 'Gene Expression (snRNAseq - 10x) processed, multi-region' folder.
Additionally, if the "Immune cell" RDS file doesn't include data from multiple regions, could you please specify the brain regions that are represented in this file?
I would greatly appreciate your assistance in clarifying this matter.
Thank you,
Wenqiang
Created by Wenqiang Fan fanwq907 Thank you so much for the additional information! I've taken a look at some of this data, and the files in "Gene Expression (snRNAseq - 10x) processed" either do not go with this paper, or are from PFC only. There are not enough unique projids for the full dataset and not enough microglial clusters.
I looked at the other folder for multi-region data, and this is _probably_ the data they used for non-PFC regions, however from the paper I think they loaded it all, filtered down to microglial cells, and did their own clustering, without putting their microglia-specific data on Synapse. There is a file in this folder that has cell type assignments (syn52408579), but it only has data for 48 individuals (which matches what the paper used for other non-PFC brain regions) and not enough microglia clusters, so I don't think this is what you need either.
I noticed in the paper that they linked to https://compbio.mit.edu/microglia_states/ for "count matrices, metadata and supplementary data in this study", but when I follow the link it says I don't have permission to access that page. I think at this point you will need to contact the authors of the paper and ask them for access to that page and/or ask them for the filtered data and metadata directly. I would hope that their metadata contains the batch information you need as well.
I hope that helps,
Jaclyn Hello once more, @jaclynbeck
I have another question concerning the same subject ID associated with different batches. For instance, take ROSMAP-85806 from PFC, which has two distinct batches: SM_190312Tsa and PFC. However, both batches are linked to the same project ID in the metadata of the SeuratObject. This presents a challenge because I cannot differentiate between cells from different batches, given that they share the same project ID. Do you have any suggestions for resolving this issue? Batch information is crucial, as it is needed for batch effect correction and data integration.
Thanks,
Wenqiang Hello,
Sure, here is the link for the datasets: https://www.synapse.org/#!Synapse:syn52293442.
I am refering to the two folders: "Gene Expression (snRNAseq - 10x) processed" and "Gene Expression (snRNAseq - 10x) processed, multi-region".
Thanks,
Wenqiang Hello,
Can you please provide the Synapse IDs or links to the folders you are referencing, to help me find the data?
Thanks,
Jaclyn