Vascular fate in misidentified pluripotent-derived blood-brain-barrier endothelial cells rescued by transcriptional reprogramming.

UID: 10775

Description: Summary from the GEO: "A single-cell suspension was loaded into the Bio-Rad ddSEQ Single-Cell Isolator on which cells were isolated, lysed and barcoded in droplets. Droplets were then disrupted and cDNA was pooled for second strand synthesis. Libraries were generated with direct tagmentation followed by 3’ enrichment and sample indexing using Illumina Nextera library prep kit. Pooled libraries were sequenced on the Illumina NextSeq500 sequencer. Sequencing data were primarily analyzed using the SureCell RNA Single-Cell App in Illumina BaseSpace Sequence Hub."

Overall design from the GEO: "Cell samples were harvested from in vitro culture conditions and sequenced using Illumina NextSeq500."

Subject of Study

Subject(s)

Access via GEO
CSV files of expression profiling by high throughput sequencing
Accession #: GSE138025

Access via SRA
RNA sequencing of 28 samples.
Accession #: SRP223288

Access via BioProject
Additional information about the overall inititative.
Accession #: PRJNA574184
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files.
Associated Publications: Lu T, Houghton S, Magdeldin T, et al. Pluripotent stem cell-derived epithelium misidentified as brain microvascular endothelium requires ETS factors to acquire vascular fate. Proceedings of the National Academy of Sciences of the United States of America. 2021; 118(8):e2016950118.
Data Type: Genomic
Equipment Used: Illumina NextSeq 550
Sequencing and array capabilities for transcriptome, targeted resequencing and genotype sequencing
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): CSV, SRA, TAR
Data Tool(s): RNA Seq
Dataset Size: 897.4 MB (TAR of CSV), 231.1 Gb (SRA)

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