MERFISH - Human Cortex 4

Info

zenodo_spatial/merfish/human_cortex_4
Fang et al. (2022)
11.07 MiB
23-09-2024
3970 cells × 3511 genes

Quick links

Source

Used in

• Spatially Variable Genes
  

DATASET ID

zenodo_spatial/merfish/human_cortex_4

REFERENCE

Fang et al. (2022)

SIZE

11.07 MiB

CREATED

23-09-2024

DIMENSIONS

3970 × 3511

Description

Spatially resolved profiling of human cerebral cortex (middle temopral gyrus) replicate 3 using multiplexed error-robust fluorescence in situ hybridization (MERFISH) (4000 gene panel).

Preview

dataset is an AnnData object with n_obs × n_vars = 3970 × 3511 with slots:

• var: feature_name
  
• layers: counts
  
• uns: dataset_description, dataset_id, dataset_name, dataset_organism, dataset_reference, dataset_summary, dataset_url

Reference

Name	Description	Type	Data type	Size
var
feature_name	A human-readable name for the feature, usually a gene symbol.	vector	object	3511
layers
counts	Raw counts	densematrix	float32	3970 × 3511
uns
dataset_description	Long description of the dataset.	atomic	str	1
dataset_id	A unique identifier for the dataset. This is different from the obs.dataset_id field, which is the identifier for the dataset from which the cell data is derived.	atomic	str	1
dataset_name	A human-readable name for the dataset.	atomic	str	1
dataset_organism	The organism of the sample in the dataset.	atomic	str	1
dataset_reference	Bibtex reference of the paper in which the dataset was published.	atomic	str	1
dataset_summary	Short description of the dataset.	atomic	str	1
dataset_url	Link to the original source of the dataset.	atomic	str	1

Slot crossref data

dataset.layers['counts']

In R: dataset$layers[["counts"]]

Type: densematrix, data type: float32, shape: 3970 × 3511

Raw counts

dataset.uns['dataset_description']

In R: dataset$uns[["dataset_description"]]

Type: atomic, data type: str, shape: 1

Long description of the dataset.

dataset.uns['dataset_id']

In R: dataset$uns[["dataset_id"]]

Type: atomic, data type: str, shape: 1

A unique identifier for the dataset. This is different from the obs.dataset_id field, which is the identifier for the dataset from which the cell data is derived.

dataset.uns['dataset_name']

In R: dataset$uns[["dataset_name"]]

Type: atomic, data type: str, shape: 1

A human-readable name for the dataset.

dataset.uns['dataset_organism']

In R: dataset$uns[["dataset_organism"]]

Type: atomic, data type: str, shape: 1

The organism of the sample in the dataset.

dataset.uns['dataset_reference']

In R: dataset$uns[["dataset_reference"]]

Type: atomic, data type: str, shape: 1

Bibtex reference of the paper in which the dataset was published.

dataset.uns['dataset_summary']

In R: dataset$uns[["dataset_summary"]]

Type: atomic, data type: str, shape: 1

Short description of the dataset.

dataset.uns['dataset_url']

In R: dataset$uns[["dataset_url"]]

Type: atomic, data type: str, shape: 1

Link to the original source of the dataset.

dataset.var['feature_name']

In R: dataset$var[["feature_name"]]

Type: vector, data type: object, shape: 3511

A human-readable name for the feature, usually a gene symbol.

References

Fang, Rongxin, Chenglong Xia, Jennie L. Close, Meng Zhang, Jiang He, Zhengkai Huang, Aaron R. Halpern, et al. 2022. “Conservation and Divergence of Cortical Cell Organization in Human and Mouse Revealed by MERFISH.” Science 377 (6601): 56–62. https://doi.org/10.1126/science.abm1741.