Mitochondrial encoded genes

Question

Mitochondrial encoded genes

jmzvillarreal opened this issue 5 years ago · 10 comments

Hi,
I am reanalyzing the datasets from bladder (Smartseq and 10X), I usually use the % of mitochondrial genes as a metric of cell QC and I find that there are no mt-genes in both datasets... Why is that ? I tried to find out in the methods but I could not...
Thanks in advance !
Jaime.

Answer 1 · 2019-06-29T18:37:44.000Z

Hi @jmzvillarreal, the reference we used didn't have mitochondrial genes so they are not part of the objects. Best, Angela

Answer 2 · 2019-09-10T14:59:46.000Z

Hi @aopisco , why did you exclude mitochondrial genes from your reference ?
Thanks!

Answer 3 · 2019-09-11T08:16:44.000Z

@jmzvillarreal no, the reference did not contain them and we did not realize it until recently. We have realigned the data though, if you're interested in unprocessed gene counts tables?

Answer 4 · 2020-03-06T23:26:29.000Z

@jmzvillarreal no, the reference did not contain them and we did not realize it until recently. We have realigned the data though, if you're interested in unprocessed gene counts tables?

That would be helpful, please!
Thank you!

Answer 5 · 2020-03-06T23:46:22.000Z

all available here: https://s3.console.aws.amazon.com/s3/buckets/czb-tabula-muris-senis/?region=us-west-2

for h5ad: s3://czb-tabula-muris-senis/Data-to-reproduce-figures/mutation-analysis-objs/adata_genecode_counts_for_gatk_with_metadata_and_embeddings.h5ad

Answer 6 · 2021-02-08T15:15:12.000Z

Many thanks for your great work and the AWS link.

I am also interested in getting count tables with mt-gene counts. So far I tried tabula-muris-senis-droplet-official-raw-obj.h5ad which seems more complete but it has not stored mt-genes.

Could you point me to the right directory? Is there a merged file of all FACS tissues? It would be great to have that information for proper scaling.

Answer 7 · 2022-04-07T05:04:54.000Z

I noticed that the data in this file does not contain integer values, so I guess it has been processed (normalized? rescaled to range 0 to 10?) in some way.
s3://czb-tabula-muris-senis/Data-to-reproduce-figures/mutation-analysis-objs/adata_genecode_counts_for_gatk_with_metadata_and_embeddings.h5ad

I wonder if there is also a file available with the original raw count data?

Answer 8 · 2022-04-26T06:45:09.000Z

I've realigned the 10X fastq data (Marrow, 1m) to the reference mouse genome (with mtDNA). There is no mtDNA in any of the cells. I am guessing the mtDNA was not part of the original sequencing library used to amplify the scRNA seq data in the first place. Can someone confirm it for me please. Thanks

Answer 9 · 2022-04-26T18:59:34.000Z

correct, mt genes were not part of the original alignment gtf

Answer 10 · 2022-08-22T06:42:56.000Z

@alexisvdb did you end up finding an original raw count matrix with mtDNA? perhaps i misunderstood but it seems like the file s3://czb-tabula-muris-senis/Data-to-reproduce-figures/mutation-analysis-objs/adata_genecode_counts_for_gatk_with_metadata_and_embeddings.h5ad that @aopisco suggested has been normalized and scaled. is there a raw counts matrix? thanks!