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| Status |
Public on Feb 22, 2018 |
| Title |
Genome-wide transcriptome analysis of NIPBL iPSC and commited cardiomyoctes |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The purpose of this study was to compare the transcriptome of NIPBL patient derived iPSCs and patient-derived cardiomyocytes to healthy unaffected individuals
Methods: iPSC transcriptome profiles of three CdLS patient iPSCs harboring mutations in the NIPBL gene and cardiomyocytes derived from patient-iPSCS were generated by deep sequencing, in triplicate, using Illumina XXXXXX. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the human genome and identified XXXX transcripts in CdLS-iPSCs and XXXXXX transcripts in control-iPSCs with XXXX workflow.
Conclusion: Our data is the represents the first human developmental model for studying CdLS through pluripotent stem cells and lineage commited subtypes (cardiomyocytes). This data highlights NIPBLs role in regulating transcriptional regulation and has significant consequences on DNA nucleosome involvement as it relates to global gene expression. This work provides preliminary evidence that NIPBL is required for normal epigenetic and DNA landscape establishment during embryonic cardiomyocyte generation.
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| |
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| Overall design |
Examine transcriptome of Control and NIPBL iPSC and Cardiomyoyctes
|
| |
|
| Contributor(s) |
Mills JA, Krantz ID |
| Citation(s) |
29348408 |
| |
| Submission date |
Aug 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Adam Mills |
| E-mail(s) |
millsja@mail.med.upenn.edu
|
| Phone |
2157468432
|
| Organization name |
The University of Pennsylvania
|
| Department |
Ophthalmology
|
| Street address |
422 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (13)
|
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| Relations |
| BioProject |
PRJNA399158 |
| SRA |
SRP115907 |
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