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| Status |
Public on Dec 05, 2023 |
| Title |
Transcriptonal and epigenetic profiling of neuroblastoma cells based on CD49b expression |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
This study was undertaken to assess heterogeneity within neuroblastoma cell populations, and to assess whether the integrin CD49b can distinguish different neuroblastoma phenotypes. Methods: We performed bulk RNA sequencing on Neuro-2a and SH-SY5Y neuroblastoma cells sorted based on CD49b expression, and CUT&RUN for H3K4me1 and H3K27ac on Neuro-2a cells sorted based on CD49b expression. Results: We find that CD49b expression identifies transcriptionally distinct neuroblastoma cell populations. High CD49b expression marks cells expressing mesenchymal genes, while lack of CD49 denotes cells expression neuronal genes. CUT&RUN analysis shows that CD49b distinguishes cells with distinct enhancer and super enhancer profiles. Conclusion: RNA sequencing and CUT&RUN demonstrate that neuroblastoma cell lines include heterogeneous populations.
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| Overall design |
Use of bulk RNA sequencing and CUT&RUN technologies to analyze transcription and enhancer status of neuroblastoma cell lines.
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| Contributor(s) |
Goldstein AM |
| Citation(s) |
38095019 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 DK119210 |
Characterizing neurogenic progenitors in the adult intestine |
MASSACHUSETTS GENERAL HOSPITAL |
ALLAN M GOLDSTEIN |
| F32 DK121440 |
Transcription factors mediate postnatal neurogenesis from enteric glial cells |
MASSACHUSETTS GENERAL HOSPITAL |
Richard A Guyer |
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| |
| Submission date |
Jul 05, 2022 |
| Last update date |
Feb 09, 2024 |
| Contact name |
Allan M Goldstein |
| E-mail(s) |
amgoldstein@partners.org
|
| Phone |
617-726-0270
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Pediatric Surgery
|
| Lab |
Goldstein Lab
|
| Street address |
185 Cambridge St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (26)
|
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| Relations |
| BioProject |
PRJNA855951 |
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