Dataset details
| Technique | seqFISH |
|---|---|
| Title | In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus |
| PMID | 27764670 |
| Description | SeqFISH was used to identify unique transcriptional states by quantifying and clustering up to 249 genes in 16,958 cells to examine whether the hippocampus is organized into transcriptionally distinct subregions. |
| Source | brain sections (hippocampus) from C57BL/6 with Ai6Cre-reporter (uncrossed) female mice aged 50-80 days |
| Species | mouse |
| No. genes | 249 genes |
| No. cells | 16,958 cells |
| Resolution | single molecule |
| Data normalization | - |
| Data availability | Raw data can be found in the Supplemental Information. |
Spatially variable (SV) genes
SV genes identified by SpatialDE (Q-value<0.05)
| ID | Gene | Species | Tissue | Field of view | P-value | Q-value |
|---|---|---|---|---|---|---|
| ID | Gene | Species | Tissue | Field of view | P-value | Q-value |
SV genes identified by trendsceek (Q-value<0.05)
| ID | Gene | Species | Tissue | Field of view | Q-value(Emark) | Q-value(Vmark) | Q-value(MarkCorr) | Q-value(MarkVario) |
|---|---|---|---|---|---|---|---|---|
| ID | Gene | Species | Tissue | Field of view | Q-value(Emark) | Q-value(Vmark) | Q-value(MarkCorr) | Q-value(MarkVario) |