Analysed expression data spreadsheet

[Diana-star-code]

Hello, as a biologist, I do not have the possibility to analyse the raw data by myself and this often delays my work. Since "single cell portal" essentially displays the analysed data already, would it be possible to download the analysed data excel file, containing Log2(TP10K+1) for each gene across all cell types collected?
Another issue I was wondering about is what is your recommended cutoff for setting the background expression level of a gene?

[jlchang]

Dear @Diana-star-code,

You are correct that our portal displays analyzed data. Each study owner uploads files of expression data, metadata and cluster information. It sounds like the data you seek would be the expression files. While we recommend some variant of log2(TPM +1) for expression data, the expression matrix units are determined by the study owner.

When you are looking at the EXPLORE option, do you see a greyed out Download option? If yes, then you may want to consider creating/using a gmail account to access the portal. Once logged in, you should be able to access the Download option and download expression matrix files. Would this satisfy your request for access to analyzed data?

As for a cutoff setting for background gene expression levels, the portal does not have a recommended cutoff.

Please let us know if you have additional questions about portal functionality.

[Diana-star-code]

Hi Jean and thank you for your quick response. I am registered with a gmail account and I tried to access the processed files which contain the following data per cell type and across all cell types: gene name (not a serial number), log2 gene copy number. But I have to say that in some cases it is not clear at all.

I am now specifically interested in downloading the data from "Study: Single Cell Comparison: PBMC data" I would love to know which file exactly I should download that contains all the processed read numbers and gene names/symbol across all cell types.

Thank you in advanced,

Diana

[jlchang]

@Diana-star-code,

The expression matrix file used for visualization of that study is a sparse gene-barcode matrix.

The sparse matrix itself is the "gene_sorted-expression.txt" file. The Study Owners provide a text description of the file as: PBMC expression data (log counts per 10K)

The gene index file for the sparse matrix is the "genes.txt" file and the barcode (cell) index is the "barcodes.txt" file.

Information about the cell type for each cell can be found in the "meta.txt" file.

The file "README_PBMC.docx" also describes additional files that were uploaded which provide raw read count and raw UMI count data.

Best Regards,

Jean

[jlchang]

Hi @Diana-star-code,

Does the information shared above help clarify which files you are seeking?

Regards,

Jean

[jlchang]

@Diana-star-code,

I hope the data shared previously helped you identify the files you need. I'm closing this issue due to inactivity. Please reach out if you have additional questions.

Regards,

Jean