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Evaluation of protein artifacts in tissue cryopreservation

ABSTRACT: This dataset presents proteomic analyses validating the spatial proteomics technology, NicheProt. NicheProt is a 3D optical microscopy–guided, photobleaching-mediated cell barcoding approach for isolating intact cell types from defined microanatomical niches. Here, we evaluate whether tissue cryopreservation introduces protein artifacts by comparing proteomic profiles of mouse spleens processed immediately after fixation with those cryopreserved in 100% D-fructose at −80 °C prior to extraction. Our results demonstrate that D-fructose–based cryopreservation preserves protein integrity without introducing significant artifacts.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Spleen, Lymphocyte

SUBMITTER: Steve Seung-Young Lee

LAB HEAD: Steve Seung-Young

PROVIDER: PXD075811 | Pride | 2026-03-19

REPOSITORIES: pride

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			Action	DRS
	CE3_2024Jul31_05_P24-095_CS4.raw	Raw
	CE3_2024Jul31_07_P24-095_CS5.raw	Raw
	CE3_2024Jul31_09_P24-095_CS6.raw	Raw
	CE3_2024Jul31_11_P24-095_CS7.raw	Raw
	CE3_2024Jun03_UIC_P24035_CS2.mzML	Mzml

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Project description:Studies on embryo cryopreservation efficiency had been focused mainly on technical and embryo factors. While structural damages can be easily evaluated, physiological damages only can be estimated by analyzing their in vitro and in vivo development to later stages. In order to determine how cryopreservation process affect embryo pre-implantory development, a transcriptional microarray study has been performed comparing gene expression of 6 days old rabbit embryos, previously vitrified or frozen and transferred into recipients rabbit females, to their in vivo counterparts. For each experimental group, control, vitrified and frozen late blastocysts, total RNA was extracted from 3 pools of approximately 10 embryos and labeled with Cy3 or Cy5 dyes. Then, six competitive hybridizations were carried out including two dye-swaps to compensate dye-bias. A specifically microarray designed to study rabbit gene expression profiling, the Rabbit 44K oligonucleotide array (Agilent Technologies), was used in this study. Identification of differentially expressed transcripts from 6 day old blastocysts was achieved using the Limma algorithm, and functional annotation was performed by Blast2GO software. Compared to 6 day old in vivo derived embryos, viable vitrified embryos only present 3 differentially expressed genes, in contrast to frozen viable embryos with 24 genes upregulated and 46 genes downregulated. These results reveal that effects of cryopreservation still remain in late blastocyst pre-implantatory gene expression, and potential damage and alterations produced by vitrification and slow-freezing procedures are differentially resolved after 3 days of in vivo development. Transcriptional microarray study that compares gene expression of viable 6 day old rabbit embryos, previosly vitrified or frozen and tranferred into recipient rabbit females, to their in vivo counterparts. Experiment 1: Control embryos vs. Vitrified embryos and Experiment 2: Control embryos vs. Frozen embryos. Biological replicates used: 3 replicates for control embryos, 3 replicates for vitrified embryos and 3 replicates for frozen embryos.

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Evaluation of protein artifacts in tissue cryopreservation

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