Dataset Information

Evaluation of protein artifacts in the NicheProt workflow

ABSTRACT: This dataset contains proteomic analyses that validate the spatial proteomics technology, NicheProt. NicheProt is a 3D optical microscopy–guided, photobleaching-mediated cell barcoding approach designed to isolate intact cell types from specific microanatomical niches. We evaluate the proteomic profiles of samples processed using the multi-step NicheProt workflow and demonstrate that it does not introduce detectable protein artifacts.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Spleen, Lymphocyte

SUBMITTER: Steve Seung-Young Lee

LAB HEAD: Steve Seung-Young

PROVIDER: PXD075769 | Pride | 2026-03-19

REPOSITORIES: pride

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Dataset's files

Source:

			Action	DRS
	CE3_2024Oct08_05_P24-162_ES1-ES6.mzML	Mzml
	CE3_2024Oct08_05_P24-162_ES1-ES6.mzid	Mzid
	CE3_2024Oct08_05_P24-162_ES1.raw	Raw
	CE3_2024Oct08_07_P24-162_ES4.raw	Raw
	CE3_2024Oct08_09_P24-162_ES2.raw	Raw

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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.

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Evaluation of protein artifacts in the NicheProt workflow

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