Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2020 Oct 19;10:17597. doi: 10.1038/s41598-020-74483-1

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Mapping of the TCGA poly-A cohort to FFPE ribo-deplete samples. Comparison of transcript bias between the two cohorts reveals (Ai) strong 3′ bias in TCGA poly-A data (the biggest point density is leaning in the y = x direction, to the right of the x = 0 line) and (Aii) slight 5′ bias in FFPE ribo-deplete data (the biggest point density is leaning slightly to the left of the x = 0 line). In parts (Ai) and (Aii), the dashed red line shows the position on the x-axis where the transcript bias is 0. (Aiii) When graphed together, TCGA transcripts have a clear 3′ bias compared to the same transcripts in the FFPE cohort. (B) PCA projection of the first 2 principal components of combined FFPE and TCGA cohorts before (i) and after (ii) mapping of TCGA into FFPE RNA-Seq space is represented. (C) Shown is a t-SNE projection of the FFPE and TCGA cohorts after the mapping method is applied to TCGA; samples are colored by the cancer type. (D) The same t-SNE projection as in (C) is shown, but now colored by sample cohort. FFPE samples are yellow, TCGA samples are blue. TCGA and FFPE cohorts mix across cancer type groupings.