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| Status |
Public on Nov 05, 2024 |
| Title |
Gene expression profile of patient with biallelic BRF2 mutation |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We performed single-cell RNA sequencing (scRNA-seq) on whole blood cells from a patient with biallelic BRF2 variants (c.782C>T and c.379C>T), exhibiting defective RNA polymerase III activity. The patient presented with recurrent infections, hypogammaglobulinemia, and was later diagnosed with low-grade B cell lymphoma. Our scRNA-seq analysis revealed alterations in gene expression related to BRF2-dependent Pol III transcription, particularly affecting redox genes, including GPX1 and GPX4.
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| Overall design |
Peripheral blood mononuclear cells (PBMCs) were isolated from the blood of a healthy control and a patient with biallelic BRF2 mutations and cryopreserved. Single-cell RNA sequencing (scRNA-seq) libraries were prepared using the 10X Genomics Chromium platform, and genomic DNA was extracted for demultiplexing. The scRNA-seq data was aligned to the human transcriptome (hg38) using Cell Ranger version 7.1.0, and ambient RNA contamination was removed with SoupX. Quality control included filtering cells by gene expression and mitochondrial content, followed by batch correction using Harmony. Dimensionality reduction was achieved using UMAP, and clustering was performed with the Louvain algorithm. Differential gene expression and gene set enrichment analyses were carried out to identify pathways associated with BRF2 dysfunction.
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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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| Contributor(s) |
Kwon H, Yoon S, Lee S, Jeong S, Joh C, Kim H, Kim K, Chae J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Oct 23, 2024 |
| Last update date |
Nov 05, 2024 |
| Contact name |
Haeyoon KWON |
| E-mail(s) |
hannahkwon@snu.ac.kr
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| Organization name |
Seoul National University College of Medicine
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| Street address |
103 Daehak-ro
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| City |
Seoul |
| ZIP/Postal code |
03080 |
| Country |
South Korea |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA1176549 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE280147_RAW.tar |
227.3 Mb |
(http)(custom) |
TAR (of RDS) |
| Raw data not provided for this record |
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