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| Status |
Public on Jun 22, 2022 |
| Title |
Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification. [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: A systematic analysis of the transcriptomic profile of HGPS patient-derived fibroblasts, stratifying the analysis by comparing defined age groups to matched controls
Methods: Total mRNA, acquired from Coriell Institute for Medical Research was submitted for RNA-seq library preparation and sequencing at Genewiz. Libraries were prepared using Illumina, RNA with PolyA selection approach, and then sequenced on a HiSeq instrument using 2x150 bp sequencing.
Results: We observe that these fibroblasts carry abnormal transcriptional signatures, centering around five main functional hubs: DNA maintenance and epigenetics, bone development and homeostasis, blood vessel maturation and development, fat deposition and lipid management, and processes related to muscle growth. Stratification of patients by age revealed that a cohort of genes related to endochondral ossification and chondrogenic commitment show altered expression patterns in children aged four to seven years old, where this differentiation program starts in earnest, related to the growth of long bones. We further report changes in lamin associated domains and 3D genome organization around a cohort of genes of interest, identified in this study.
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| Overall design |
Purified mRNA from skin fibroblasts derived from HGPS patients was acquired from Coriell Insitute, at the earliest passage number available, prepared, and sequenced with PolyA selection and 2x150 bp reads.
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| Contributor(s) |
San Martin R, Das P, Sanders JT, Hill A, McCord RP |
| Citation(s) |
36579892 |
| |
| Submission date |
Jun 22, 2022 |
| Last update date |
Jan 24, 2023 |
| Contact name |
Rachel Patton McCord |
| E-mail(s) |
rmccord@utk.edu
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| Organization name |
University of Tennessee Knoxville
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| Department |
Department of Biochemistry & Cellular and Molecular Biology
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| Lab |
Rachel Patton McCord Lab
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| Street address |
1311 Cumberland Avenue
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| City |
Knoxville |
| State/province |
Tennessee |
| ZIP/Postal code |
37996 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (11)
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| This SubSeries is part of SuperSeries: |
| GSE206707 |
Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification. |
|
| Relations |
| BioProject |
PRJNA851770 |
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