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A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

ABSTRACT: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

PROVIDER: PRJNA609182 | ENA |

REPOSITORIES: ENA

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A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Project description:Single cell genomics is essential to chart tumor ecosystems. While single cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 212,498 cells and nuclei from 39 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate, and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.

2020-05-11 | GSE140819 | GEO

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Project description:A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

| PRJNA591014 | ENA

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Project description:A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

| PRJNA609183 | ENA

Single Cell RNA Sequencing of Fresh and Frozen Human Atheroma Tissue

Project description:We conducted a comparison of scRNA-seq on four paired fresh and cryopreserved atheroma samples, two from coronary arteries and two from carotid arteries, to determine whether it is possible to obtain comparable data from frozen samples. After enzymatic digestion into single cell suspensions, we sorted CD45+ cells from half of each sample and immediately processed these using the 10X Genomics scRNA-seq workflow after collection, while the other half was frozen in liquid nitrogen. After cryopreservation for an average of 7 days, the other half of each sample was thawed and sorted identically to the fresh samples.

2022-10-31 | GSE179159 | GEO

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.

Project description: Not available

| S-EPMC7220853 | biostudies-literature

Single Nucleus Sequencing Reveals Artifactual Gene Expression and Variance in Post-Mortem Brain

Project description:Single nucleus sequencing of fresh frozen post-mortem brain

2020-12-01 | GSE157760 | GEO

array-CGH on single blastomeres from day-4 human preimplantation fresh and frozen embryos

Project description:In total, 240 single blastomeres from nine top-quality day-4 embryos frozen at day 3 of development and four fresh top-quality day-4 embryos that had one-cell biopsy on day 3 for preimplantation genetic diagnosis (PGD) were collected. Blastomeres' DNA was amplified using SurePlex DNA Amplification System (BlueGnome, Cambridge, UK) . Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome, www.cytochip.com).

2013-04-05 | GSE39518 | GEO

miRNA experiment of fresh frozen colonic biopsy samples

Project description:The aim of the present study was to perform an additional global miRNA microarray analysis of tubular and tubulovillous adenoma biopsy specimen completed with colorectal adenocarcinomas using fresh frozen tisse

2016-10-19 | GSE83924 | GEO

Whole genome bisulfite sequencing and Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis (WGBS)

Project description:We compared the global DNA methylation levels of hairless mouse epidermis using the Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulfite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of xxx,xxx CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.996) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study’s aims and the available resources in the laboratory.

2022-09-23 | GSE213747 | GEO

array-CGH on single blastomeres from day-4 human preimplantation fresh and frozen embryos

2013-04-05 | E-GEOD-39518 | biostudies-arrayexpress

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