CS202210140_266
LLC_265 (CS202210140_266)
Hierarchy: CS202210140_485 > CS202210140_266
PURL: https://purl.brain-bican.org/taxonomy/CS202210140/CS202210140_neurons/CS202210140_266
Labelset: Cluster (Rank: 1)
Parent Cell Set: LAMP5-LHX6 and Chandelier (CS202210140_485)
Cell Ontology Term: chandelier cell (CL:4023083)
Rationale: Based on Annotaton transfer from MTG + markers: UNC5B, RORA, TRPS1, and NFIB from Bakken et. al 2021 motor cortex paper Note that these genes are also expressed in LAMP5-LHX6 cells. Added FOXG1 to limit this annotation to the telencephalon, and GAD1 to limit to GABAergic cells. ChC cells in our data did not express GAD2. Add CA8 based on the human data. Removed PVALB, some chandelier cells in our human data are PVALB negative
| Marker Genes |
|---|
| FOXG1 |
| GAD1 |
| UNC5B |
| RORA |
| TRPS1 |
| NFIB |
| CA8 |
| PLEKHH2 |
Transferred annotations:
| Transferred cell label | Source taxonomy | Source node accession | Algorithm name | Comment |
|---|---|---|---|---|
| Chandelier | https://purl.brain-bican.org/taxonomy/AIT_MTG/AIT_MTG.json | CrossArea_subclass:149f7d8007 | We performed PCA (50 components) on our full dataset, trained a random forest classifier (scikit-learn, class_ weight=‘balanced’, max_depth=50) on the MTG labels, and then predicted labels for all cells. We labeled each cluster with the mode of its constituent cells if two conditions were met: more than 0.8 of predicted labels matched the mode, and the mean probability of these pre- dictions was greater than 0.8. |
Author annotation fields:
| Author annotation | Value |
|---|---|
| Cluster ID | 265 |
| Class auto_annotation | NEUR |
| Neurotransmitter auto_annotation | GABA |
| Neuropeptide auto_annotation | CBLN CCK CHGA CHGB CRH IGF NAMPT NPPC NUCB NXPH PTHLH SCG TAC UBL VGF proSAAS |
| Subtype auto_annotation | CHAND |
| Transferred MTG Label | Chandelier |
| Top three regions | Cerebral cortex: 72.8%, Amygdala: 17.1%, Hippocampus: 5.1% |
| Top three dissections | Human MEC: 6.1%, Human M1C: 4.8%, Human BL: 4.2% |
| Top Enriched Genes | AC046195.2, LINC00943, PCDH18, COL15A1, PTHLH, C1QL1, LINC01837, NOG, CA8, PLEKHH2 |
| Number of cells | 4251.0 |
| DoubletFinder score | 0.050070837 |
| Total UMI | 19015.92425 |
| Fraction unspliced | 0.691003555 |
| Fraction mitochondrial | 0.007942596 |
| H19.30.002 | 1474.0 |
| H19.30.001 | 1446.0 |
| H18.30.002 | 1274.0 |
| H18.30.001 | 57.0 |
| Fraction cells from top donor | 0.346741943 |
| Number of donors | 4.0 |
| subcluster_id | None |