GSE107122
GSE GEODevelopmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling
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Summary
Adult neural stem cells (NSCs) derive from embryonic precursors, but little is known about how or when this occurs. We have addressed this issue using single cell RNAseq at multiple developmental timepoints to analyze the embryonic murine cortex, one source of adult forebrain NSCs. We computationally identify all major cortical cell types, including the embryonic radial precursors (RPs) that generate adult NSCs. We define the initial emergence of RPs from neuroepithelial stem cells at E11.5. We show that by E13.5 these RPs express a transcriptional identity that is maintained and reinforced throughout their transition to a non-proliferative state between E15.5 and E17.5. These slowly-proliferating late embryonic RPs share a core transcriptional phenotype with quiescent adult forebrain NSCs. Together, these findings support a model where cortical RPs maintain a core transcriptional identity from embryogenesis through to adulthood, and where the transition to a quiescent adult NSC occurs during late neurogenesis.
Overall Design
We applied the high-throughput single-cell mRNA sequencing technique, Drop-seq, to the embryonic mouse cortex. 2000-5000 single cells from wildtype CD1 embryos of gestational ages E11.5, E13.5, E15.5 and E17.5 were characterized.
Analysis (4 steps)
View Data Processing- FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/) with settings as described in the Drop-seq Alignment Cookbook (version 1.2 Jan2016, http://mccarrolllab.com/dropseq/)
- The number of cell barcodes per embryonic age was identified by calculating the cumulative fraction of reads attributable to each individual cell barcode and arranging these in decreasing order.
- 2000 Barcodes were selected at E11.5, E13.5 and E17.5 and 5000 Barcodes at E15.5
- Two batches data collected from E15.5 embryos (Batch1 and Batch2) were combined together.
Supplementary Files (3)
GEO Samples (5)
Dataset Citations (1)
SRA Experiments (5) and Runs (7)
Total: 36687 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR6307231 | 158943493 | 13192309919 | 6184.46 | E115_R1.fastq.gz, E115_R2.fastq.gz, SRR6307231, SRR6307231.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR6307232 | 173739327 | 12161752890 | 5391.19 | E135_R1.fastq.gz, E135_R2.fastq.gz, SRR6307232, SRR6307232.sralite | SRA |
Sample attributes
Original files (1)
Sample attributes
Original files (1)
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR6307237 | 190861671 | 15841518693 | 7427.53 | E175_R1.fastq.gz, E175_R2.fastq.gz, SRR6307237, SRR6307237.sralite | SRA |
Linked Publications (1)
Data Files (7)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | E115_R1.fastq.gz | RNA-Seq | 6.0 GB | link | |||
| — | E135_R1.fastq.gz | RNA-Seq | 5.3 GB | link | |||
| — | E155_Batch1_Run1_R1.fastq.gz | RNA-Seq | 2.5 GB | link | |||
| — | E155_Batch1_Run2_R1.fastq.gz | RNA-Seq | 3.7 GB | link | |||
| — | E155_Batch2_Run1_R1.fastq.gz | RNA-Seq | 2.5 GB | link | |||
| — | E155_Batch2_Run2_R1.fastq.gz | RNA-Seq | 8.6 GB | link | |||
| — | E175_R1.fastq.gz | RNA-Seq | 7.3 GB | link |