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| Status |
Public on May 02, 2022 |
| Title |
A CRISPR-engineered Isogenic Model Reveals Altered Neuronal Phenotypes of the 22q11.2 A-B Syndromic Deletion |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The 22q11.2 deletion syndrome (22q11.2DS) is the most common copy number variant (CNV)-associated syndrome, leading to congenital, cognitive, and neuropsychiatric anomalies in patients. The clinical presentation of the disease phenotypes is variable, posing significant challenges for prognosis of inheritance risk and clinical outcomes for the CNV carriers. ~85% of patients and almost all available human-centered models of this condition reflect the ~2.7 Mb “A-D” deletion at this locus. Leveraging a CRISPR/Cas9-based engineering strategy and induced pluripotent stems cells, we generated novel isogenic models for the smaller, commonly inherited 1.5 Mb “A-B” deletion found in ~5-10% of 22q11.2DS patients. The bulk RNA-seq data included here reflects paired-end 100 bp sequencing of iPSC-derived neuronal progenitor cells and excitatory neurons. These data reflect three independent clones either carrying the designed 22q11.2 deletion or control comparators (2 clones nucleofected with same sgRNA but with no deletion generated; 1 clone derived from the parental Cas9-expressing iPSC line). We anticipate that these novel, isogenic models will carry significant utility for the study of 22q11.2 deletion syndrome.
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| Overall design |
RNA sequencing of iPS derived NPCs and neurons (control and those harboring CRISPR engineered 22qAB deletions) in biological triplicates to study RNA level changes in control vs deletion NPCs and neurons and also across stages
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| Contributor(s) |
Paranjape NP, Lin Y, Flores-Ramirez Q, Sarin V, Johnson AB, Chu J, Paredes M, Wiita AP |
| Citation(s) |
37169815 |
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| Submission date |
Apr 05, 2022 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Arun P Wiita |
| Organization name |
University of California San Francisco
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| Street address |
185 Berry St, Ste 290/Rm 2410
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| City |
San Francisco |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94107 |
| Country |
USA |
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| Platforms (1) |
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| Samples (12)
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| GSM6022362 |
Neuron, deletion, 1 |
| GSM6022363 |
Neuron, deletion, 2 |
| GSM6022364 |
Neuron, deletion, 3 |
| GSM6022365 |
Neuronal Progenitor Cell, control, 1 |
| GSM6022366 |
Neuronal Progenitor Cell, control, 2 |
| GSM6022367 |
Neuronal Progenitor Cell, control, 3 |
| GSM6022368 |
Neuronal Progenitor Cell, deletion, 1 |
| GSM6022369 |
Neuronal Progenitor Cell, deletion, 2 |
| GSM6022370 |
Neuronal Progenitor Cell, deletion, 3 |
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| Relations |
| BioProject |
PRJNA823698 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE200225_DESeq2-NPC-deletion-vs-control.csv.gz |
488.0 Kb |
(ftp)(http) |
CSV |
| GSE200225_DESeq2-neuron-deletion-vs-control.csv.gz |
565.8 Kb |
(ftp)(http) |
CSV |
| GSE200225_Paranjape_et_al_processed_read_counts_NPC_neurons_BGI_RNAseq.xlsx |
4.7 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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