sci-CAR Cell Lines

sci-CAR profiles of 5k cell line cells (HEK293T, NIH/3T3, A549) across three treatment conditions (DEX 0h, 1h and 3h)

openproblems_v1_multimodal

Info

openproblems_v1_multimodal/scicar_cell_lines
Cao et al. (2018)
205.41 MiB
02-02-2024
4739 cells × 60550 genes

Used in

No related benchmarks found.

Description

Single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment).

Preview

dataset_mod1 is an AnnData object with n_obs × n_vars = 4739 × 60550 with slots:

dataset_mod2 is an AnnData object with n_obs × n_vars = 4739 × 146713 with slots:

Reference

Dataset mod1

Name Description Type Data type Size
obs
cell_type Classification of the cell type based on its characteristics and function within the tissue or organism. vector category 4739
size_factors The size factors created by the normalisation method, if any. vector float32 4739
var
feature_name A human-readable name for the feature, usually a gene symbol. vector object 60550
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 60550
hvg_score A ranking of the features by hvg. vector float64 60550
obsm
X_svd The resulting SVD embedding. densematrix float32 4739 × 100
layers
counts Raw counts sparsematrix float32 4739 × 60550
normalized Normalised expression values sparsematrix float32 4739 × 60550
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
normalization_id Which normalization was used atomic str 1

Dataset mod2

Name Description Type Data type Size
obs
cell_type Classification of the cell type based on its characteristics and function within the tissue or organism. vector category 4739
size_factors The size factors created by the normalisation method, if any. vector float64 4739
var
feature_name A human-readable name for the feature, usually a gene symbol. vector object 146713
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 146713
hvg_score A ranking of the features by hvg. vector float64 146713
obsm
X_svd The resulting SVD embedding. densematrix float64 4739 × 100
layers
counts Raw counts sparsematrix float64 4739 × 146713
normalized Normalised expression values sparsematrix float64 4739 × 146713
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
normalization_id Which normalization was used atomic str 1

References

Cao, Junyue, Darren A. Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A. Pliner, Andrew J. Hill, Riza M. Daza, et al. 2018. “Joint Profiling of Chromatin Accessibility and Gene Expression in Thousands of Single Cells.” Science 361 (6409): 1380–85. https://doi.org/10.1126/science.aau0730.