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Hi everyone,
I have RNA-seq data from a fluorescently activated cell sorted (FACS) population. Unfortunately, this cell type (call it A) is very difficult to isolate alone and other cell types (call them C) can be sorted along with it. After looking at cell type-specific gene/transcript expression, we found that C cell type-specific transcripts were expressed, suggesting contamination.
We submitted a manuscript and reviewers are asking for a quantification of the level of contamination of the C cell type. Can anyone recommend a way to do this?
Extra details:
1. No spike-in control was used when generating the RNA-seq data
2. There are no publicly available RNA-seq datasets for either A or C cell type...though I might be able to gain access to a private dataset.
3. Microarray data is available for the C cell type.
4. Genes/transcripts that are commonly thought of as specifically expressed in each cell type have been highly expressed in microarray data from FACS A cell types in past publications.
5. Microarray data from Cell type A that has been isolated by hand (single-cell) does not show high expression of C cell type specific genes.
I think it is clear that contamination exists, but I am not sure how to begin quantifying the level of contamination.
Thanks for any help!
C
I have RNA-seq data from a fluorescently activated cell sorted (FACS) population. Unfortunately, this cell type (call it A) is very difficult to isolate alone and other cell types (call them C) can be sorted along with it. After looking at cell type-specific gene/transcript expression, we found that C cell type-specific transcripts were expressed, suggesting contamination.
We submitted a manuscript and reviewers are asking for a quantification of the level of contamination of the C cell type. Can anyone recommend a way to do this?
Extra details:
1. No spike-in control was used when generating the RNA-seq data
2. There are no publicly available RNA-seq datasets for either A or C cell type...though I might be able to gain access to a private dataset.
3. Microarray data is available for the C cell type.
4. Genes/transcripts that are commonly thought of as specifically expressed in each cell type have been highly expressed in microarray data from FACS A cell types in past publications.
5. Microarray data from Cell type A that has been isolated by hand (single-cell) does not show high expression of C cell type specific genes.
I think it is clear that contamination exists, but I am not sure how to begin quantifying the level of contamination.
Thanks for any help!
C