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

. 2022 Dec 20;3(12):1534–1552. doi: 10.1038/s43018-022-00475-x

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

© The Author(s) 2022

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Extended Data Fig. 3 — a) Comparison of PN, MES and monocytic-lineage cell marker genes between primary and recurrent bulk RNA-seq of patient-matched GBM longitudinal specimens, N = 30 tumors. A one-sided paired T-test was used to assess significance. Boxplots in panels A-B and D are defined as follows, lower/upper whiskers: smallest/largest observation ≥/≤ the lower/upper hinge −/+ 1.5 times the interquartile range (IQR); lower/upper hinge: 25^th/75^th percentile; center: 50^th percentile. b) Boxplots of RNA velocities for MES hallmark genes CD44, CHI3L1 computed over PN neoplastic cells from recurrent GBM cases, N = 37,428 cells. A one-sided signed Wilcoxon rank-sum test was used to assess significance. c) (Left) A heatmap representation of the pseudotime inference shown in Fig. 3d, e is shown above. Gene ontology terms from WikiPathway.org that are over-represented (FDR < 0.05) based on genes that correlate with pseudotime, is shown below. (Right) RNA velocity and expression for MKI67 in MES neoplastic cells from recurrent GBMs, visualized in PCA space. d) The fractions of total spliced and unspliced mRNAs, compared between cycling and quiescent MES cells from recurrent cases using a two-sided Wilcoxon rank-sum test, p = 0.0551, N = 10,456 cells. e) RNA velocity and expression for CDK6, TLK1, and RRM2 in MES neoplastic cells from recurrent GBMs, visualized in PCA space, N = 10,456 cells. f) (Left) The DNA-damage response pathway adapted from Wikipathway.org. (Right) The response to IR pathway adapted from Wikipathway.org. Genes correlating with cell-cycle re-entry by MES cells at recurrence are annotated in green. g) Read-density and heatmap plots summarizing reads mapping to primary- and recurrent-specific scATAC-seq peaks respectively, from N = 10,981 cells. h) Over-represented transcription factor motifs in primary- and recurrent-specific scATAC-seq peaks, from N = 10,981 cells. i) (left) A comparison of genotypes between each of the patient-derived cell lines and the tumor specimens from which they were derived, performed via UCSF500 clinical genotyping. (right) Expression levels via RNA-seq of the patient-derived cell lines for PN and MES markers and genes targeted in in vitro assays.