Small region subset of Xenium spatial transcriptomics data

Source: R/data_transcriptomics.R

A subset of Xenium spatial transcriptomics data containing molecules from a small region (x between 3700-4200 and y between 5000-5500) for demonstration purposes. This data is derived from the SubcellularSpatialData package's mouse brain dataset.

data(tx_small_region)

Format

A data frame containing single-molecule spatial transcriptomics data with the following columns:

sample_id

Sample identifier for the Xenium dataset

cell

Cell identifier, NA for molecules not assigned to cells

gene

Gene name

genetype

Type of gene (e.g., "Gene")

x

x-coordinate of the molecule

y

y-coordinate of the molecule

counts

Count value for the transcript (typically 1 for single-molecule data)

region

Anatomical region annotation (e.g., "CA1")

technology

Technology platform used ("Xenium")

level

Hierarchical level of annotation (e.g., "Level9")

Level0

Root level annotation ("root")

Level1

First level annotation (e.g., "grey")

Level2

Second level annotation (e.g., "CH")

Level3

Third level annotation (e.g., "CTX")

Level4

Fourth level annotation (e.g., "CTXpl")

Level5

Fifth level annotation (e.g., "HPF")

Level6

Sixth level annotation (e.g., "HIP")

Level7

Seventh level annotation

Level8

Eighth level annotation (e.g., "CA")

Level9

Ninth level annotation (e.g., "CA1")

Level10

Tenth level annotation

Level11

Eleventh level annotation

transcript_id

Unique identifier for the transcript

overlaps_nucleus

Boolean (0/1) indicating if molecule overlaps with nucleus

z_location

z-coordinate of the molecule

qv

Quality value score

Source

Data derived from SubcellularSpatialData package (EH8230 in ExperimentHub), filtered to a small region for demonstration purposes. Original data from Xenium V1 FF Mouse Brain MultiSection.