Transcriptomics

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Genome wide transcriptional profiling of RBMXDRGG human induced poluripotent stem cells and neural progenitor cells


ABSTRACT: Purpose: investigate Shashi XLID patient mutation (RBMX-RGG motif deletion) caused gene expression and splicing alteration during neural differentiation Methods: hiPSCs with Shashi XLID patient mutation(RBMX-DRGG) were generated by CRISPR-Cas9. hiPSCs were differentiated to NPCs using STEMdiff SMADi Neuronal Induction Kit. A patient-mutation iPS cell line (DRGG1) and a non-edited clone (CTRL) and the derived NPCs were selected for characterization by mRNA profiling. iPSC and NPC RNA samples were purified using GenElute™ Mammalian Total RNA Miniprep Kit (RTN70, Sigma Aldrich). Total RNA was assessed for quality using an Agilent Tapestation 4200, and RNA sequencing libraries were generated using TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, starting with 50 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 base pair (bp) paired-end reads (PE100) to a depth of approximately 60 million reads per sample on an Illumina HiSeq 4000. Results:Gene expression was quantified by HOMER and differential expression was analyzed by DESeq2. Comparing with CTRL, we identified 1914 and 1028 differentially expressed genes in DRGG1 iPSCs and NPCs respectively with a threshold of |FC|>1.5 and FDR<0.05. Alternative splicing analysis was carried out using rMATs , which revealed 369 and 111 altered splicing events in iPSCs and NPCs respectively.

ORGANISM(S): Homo sapiens

PROVIDER: GSE156923 | GEO | 2021/06/30

REPOSITORIES: GEO

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