Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Quantification of contamination from cell types within same species in RNA-seq data

    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

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-13-2024, 08:58 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-12-2024, 02:20 PM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-07-2024, 06:58 AM
0 responses
184 views
0 likes
Last Post seqadmin  
Working...
X