Dataset Information

A High-Resolution Stereo-seq Spatial Transcriptomic Dataset of the Bovine Liver

ABSTRACT: Spatial transcriptomics preserves molecular and morphological context, enabling direct mapping of gene expression across tissue architecture. Here, we present a high-resolution spatial transcriptomic dataset of bovine liver generated with Stereo-seq (SpaTial Enhanced REsolution Omics-sequencing). Tissue sections from Holstein cattle were processed on DNA nanoball arrays, sequenced, and processed through an established Stereo-seq analysis workflow (SAW) and downstream toolkits (Stereopy, SingleR, and Seurat). The dataset includes raw FASTQ files, processed spatial gene-expression matrices, spot-level metadata. Quality control and validation demonstrate high tissue integrity, reproducible spatial expression patterns, and recovery of canonical hepatic zonation markers. Data are provided with full metadata and analysis scripts to facilitate reuse for comparative biology, livestock genomics, and algorithm development.

ORGANISM(S): Bos taurus

PROVIDER: GSE315416 | GEO | 2026/09/17

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other
	GSE315416_RAW.tar	Raw
	filelist.txt	Txt

Items per page:

1 - 3 of 3

Similar Datasets

Project description:To glean an appreciation of the holistic genetic activity in the gastrulating mouse embryo, we performed a genome-wide spatial transcriptome analysis (Stereo-seq), using a low-cell number sequencing protocol on laser microdissected samples of epiblast cells with retained positional address. The 3D transcriptome reveals that (i) the epiblast is partitioned into transcription domains corresponding to regions of epiblast where cells are endowed specifically with ectoderm and mesendoderm potency, (ii) novel lineage markers are identified as genes expressed in epiblast domains populated by cells displaying different lineage fates, (iii) functionally related gene regulatory circuitry and signaling pathways are acting in concert in the transcriptional domains, and (iv) the spatial information provides reference zipcodes for mapping the prospective address of cell samples from different embryos and stem cell lines. The quantified expression data can also be visualized as â3D digitized whole mount in situ hybridizationâ of all the expressed transcripts in the epiblast. (i) By using laser-microdissection, we carried out transcriptome profiling on embryo sections at a high resolution of ~20 cells per sample with the spatial information preserved. We then constructed a comprehensive spatial transcriptome map in the mid-gastrulation embryo that is visualized in a 3D embryonic model based on the sequencing data. Embryo position (A/L/P/R) and section (1-11) descriptors: A stands for laser capture microdissected samples from the anterior epiblast of the embryo; P for posterior; L for the left lateral epiblast of the embryo; R for the right lateral. The section is collected from distal to proximal, and the section 1 to 11 is the cryosection order, covering the whole embryonic part of a late mid-streak embryo. Section 1 is the most distal section and 11 is the most proximal section. (ii) Additional samples are RNA-seq data of 70 single cells from E7.0 mouse embryo. These 70 samples were randomly picked from the anterior or posterior embryonic half.

Dataset Information

A High-Resolution Stereo-seq Spatial Transcriptomic Dataset of the Bovine Liver

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets