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RNA-Seq of frozen human brain tissue

ABSTRACT: RNA-Seq of frozen human brain tissue

PROVIDER: PRJEB31537 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3196920_1.fastq.gz	Fastqsanger.gz
	ERR3196920_2.fastq.gz	Fastqsanger.gz
	ERR3196921_1.fastq.gz	Fastqsanger.gz
	ERR3196921_2.fastq.gz	Fastqsanger.gz
	ERR3196922_1.fastq.gz	Fastqsanger.gz

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RNA-Seq of frozen human brain tissue

Project description:These are three technical replicates RNA-Seq for frozen human brain tissue. They are generated for comparison with single cell RNA sequencing data that generated by the same sample and provided elsewhere.

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Genome-wide Expression Assay Comparison Across Frozen and Fixed Postmortem Brain Tissue Samples

Project description:Comparison between in vitro transcription- and cDNA-mediated annealing, selection and ligation (DASL)-based assays on brain-specific reference RNA, and postmortem frozen and formalin fixed brain tissue from autistic and control cases. Investigation of data preprocessing techniques for DASL-assayed RNA samples from frozen brain tissue. IVT- and DASL-based expression assays were performed on 10 reference RNA samples (brain and pooled artificially degraded at 0, 10, 30, and 60 min), 4 formalin-fixed tissue-extracted RNA samples with replicates, and 57 frozen tissue-extracted RNA samples with replicates. A subset of the 57 (N=33 samples) from frozen brain tissue assayed using the DASL-based platform were then used to test different dataset preprocessing strategies implemented in the lumi package in R/Bioconductor. The data from frozen-tissue extracted DASL-processed RNA samples passing exclusion criteria were log2 transformed and normalized using quantile normalisation with lumi in R (quantile-normalized data available as a supplementary file linked to the Series record).

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Single Cell RNA Sequencing of Fresh and Frozen Human Atheroma Tissue

Project description:Single Cell RNA Sequencing of Fresh and Frozen Human Atheroma Tissue

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Isolated nuclei from frozen tissue are the superior source for single cell RNA-seq compared with whole cells

Project description:The isolation of intact single cells from frozen tissue is a challenge due to the mechanical and physical stress inflicted upon the cell during the freeze-thaw process. Ruptured cells release ambient RNA into the cell suspension, which can become encapsulated into droplets during droplet based single cell RNA-seq library preparation methods. The presence of ambient RNA in droplets has been suggested to impact data quality, however there have been limited reports on single cell RNA-seq data from frozen tissue. Here, we compare the results of single cell RNA-seq derived from disaggregated cells from frozen brain tissue with single nuclei RNA-seq derived from purified nuclei of identical tissue using the 10X Genomics Chromium 3’ gene expression assay. Our results indicated that presence of ambient RNA in the cell suspension resulted in single cell RNA-seq data with a 25-fold lower gene count, a 5-fold lower UMI count per cell and a 2-fold lower fraction of reads per cell compared with single nuclei RNA-seq data. Cell clustering with the single cell RNA-seq data was unable to resolve the heterogeneity of brain cell types. Our conclusion is that nuclei from frozen tissue are the superior substrate for single cell transcriptome analysis.

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Proteomic Characterization of Post-Mortem Human Brain Tissue Following Ultracentrifugation-based Subcellular Fractionation

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