Journal: bioRxiv

Article Title: Cellf-Deception: Human microglia clone 3 (HMC3) cells exhibit more astrocyte-like than microglia-like gene expression

doi: 10.1101/2025.08.04.665415

Figure Lengend Snippet: (A) PubMed search results for “(HMC3) AND (microglia)” show sharply increasing numbers of publications since 2020, with 57 articles in 2023, 81 in 2024 and 46 so far in 2025 as of July 12. (B) Principal components were recalculated using brain cell types from Quiroga, 2022 (GSE181153). We observed an unexpected clustering of the HMC3 microglial cell line with the U-87 astrocyte cell line (red and pink clusters). Note: Adapted from Synthetic amyloid beta does not induce a robust transcriptional response in innate immune cell culture systems , I. Y. Quiroga, 2022, http://creativecommons.org/licenses/by/4.0/ .

Article Snippet: While the paper states that the HMC3 cells were purchased from the Korean Cell Line Bank, the organization confirmed in direct communication that they do not offer this cell line.

Techniques: Cell Culture

Journal: bioRxiv

Article Title: Cellf-Deception: Human microglia clone 3 (HMC3) cells exhibit more astrocyte-like than microglia-like gene expression

doi: 10.1101/2025.08.04.665415

Figure Lengend Snippet: (A) A dataset of the HMC3 cell lines generated by Quiroga et al. was run through the classifier. A barplot presents an assorted composition of cell prediction scores, identifying most closely with astrocytes. (B) Again, an expression dataset of iMG cells was classified by our Random Forest prediction, and rule activation scores are presented in a boxplot. (C) The same scores are presented for the classification of U87 cells generated by Gupta et al.

Article Snippet: While the paper states that the HMC3 cells were purchased from the Korean Cell Line Bank, the organization confirmed in direct communication that they do not offer this cell line.

Techniques: Generated, Expressing, Activation Assay

Journal: bioRxiv

Article Title: Cellf-Deception: Human microglia clone 3 (HMC3) cells exhibit more astrocyte-like than microglia-like gene expression

doi: 10.1101/2025.08.04.665415

Figure Lengend Snippet: Two additional datasets of the HMC3 cell lines run through the classifier present an assorted composition of cell prediction scores, and identify most closely with astrocytes. (C) An expression dataset of monocytes and microglia (fetal and adult) cells was collected from human tissue and analyzed by our primary cell classifier, which shows clear distinctions between microglia from monocytic cells. Sample names provided by the manuscript, and indicators in the sample name indicate the origin of the cells collected: 5 classic monocytes, 3 fetal mic roglial samples, and 3 adult mic roglial collections.

Article Snippet: While the paper states that the HMC3 cells were purchased from the Korean Cell Line Bank, the organization confirmed in direct communication that they do not offer this cell line.

Techniques: Expressing

Journal: bioRxiv

Article Title: Cellf-Deception: Human microglia clone 3 (HMC3) cells exhibit more astrocyte-like than microglia-like gene expression

doi: 10.1101/2025.08.04.665415

Figure Lengend Snippet: 7 panels from 5 studies show how the DepMap classifier assigns predictions to many different data types in the exact same manner as - . (A) HMC3 lines from Quiroga et al., (B) U87s from Gupta et al., (C) iMG (induced microglial lines) from Quiroga et al., (D) HMC3 lines from Chai et al., (E) HMC3 lines from Armanville et al., and ( F) iMG (induced microglial line), monocytes, fetal microglia, and adult microglia samples from Abud et al.

Article Snippet: While the paper states that the HMC3 cells were purchased from the Korean Cell Line Bank, the organization confirmed in direct communication that they do not offer this cell line.

Techniques:

Journal: bioRxiv

Article Title: Cellf-Deception: Human microglia clone 3 (HMC3) cells exhibit more astrocyte-like than microglia-like gene expression

doi: 10.1101/2025.08.04.665415

Figure Lengend Snippet: Bar charts for the three HMC3 studies show the percentage of RNA sequencing kmers that match with the Rat transcriptomic reference (Rattus norvegicus) or the Human transcriptomic reference (homo sapiens). The x-axis indicates the percentage of k-mers that are unique to Rat, Human, Both, Neither, or are Ambiguous. More samples are present in the Armenville study than previous analyses because we did not restrict to HMC3-lines.

Article Snippet: While the paper states that the HMC3 cells were purchased from the Korean Cell Line Bank, the organization confirmed in direct communication that they do not offer this cell line.

Techniques: RNA Sequencing