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| Status |
Public on Sep 17, 2024 |
| Title |
Joint single-nucleus RNA sequencing and single-nucleus ATAC sequencing of neuroblastoma cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
This study was undertaken to assess transcriptional and epigenetic heterogeneity a the level of individual cells within neuroblastoma cell lines, and to compare cell lines with MYCN amplificaion to cell lines without MYCN amplification. Methods: We used 10X Genomics multiome sequencing technology to perform joint gene expression and ATAC profiling on thousands of nuclei isolated from the following human neuoblastoma cell lines: SHSY5Y, SK-N-AS, SK-N-SH, SK-N-DZ, Be-2c, and CHP134. Results: We found considerable gene expression and epigeneic heterogeneity both within and between neuroblastoma cell lines. Conclusion: Joint single-nucleus RNA sequencing and single-nucleus ATAC sequencing has demonsrated that neuroblastoma cell lines are heterogeneous, which may have implications for therapeutic strategies.
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| Overall design |
Use of 10X Genomics muliome sequencing technology (GEX + ATAC) to analyze single-cell transcriptomics and single-cell epigenetics of neuroblastoma cell lines.
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| Contributor(s) |
Goldstein AM, Guyer RA |
| Citation(s) |
39511250 |
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| Submission date |
Mar 21, 2024 |
| Last update date |
Dec 17, 2024 |
| Contact name |
Allan M Goldstein |
| E-mail(s) |
amgoldstein@partners.org
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| Phone |
617-726-0270
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| Organization name |
Massachusetts General Hospital
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| Department |
Pediatric Surgery
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| Lab |
Goldstein Lab
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| Street address |
185 Cambridge St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA1090535 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE262189_RAW.tar |
26.8 Gb |
(http)(custom) |
TAR (of CSV, H5, TBI, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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