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The effect of freezing delay of cell-type specific transcriptome responses in human brain via snRNA-seq

In other analysis in the current manuscript, we find a similar gene signature (to dissociation based artifacts in mouse and human tissue) is present in post-mortem microglia and astrocytes, across all snRNA-seq datasets analyzed, although it is highly variable between subjects. ​ Using acutely-resected neurosurgical tissue, we performed single-nucleus RNA-seq and reveal that a similar signature can be detected in microglia following prolonged exposure to room temperature. Tissue handling and methods details, as well as sequencing and analysis details) can be found in the methods section of related manuscript (Marsh et al., 2022). Together, these results suggest that the presence of this signature in post-mortem brain samples may be the result of a combination of acute pre-mortem (agonal state, cause of death, comorbidities, etc.) and post-mortem (post-mortem interval (PMI), storage time, RNA quality, etc.) variables and may not represent normally present cell state.

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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001002494 Transcriptome Analysis

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00005791462 bam 42.9 GB
EGAF00005791463 bam 39.5 GB
EGAF00005791464 bam 50.9 GB
EGAF00005791465 bam 29.6 GB
EGAF00005791472 tsv.gz 53.8 kB
EGAF00005791473 mtx.gz 89.0 MB
EGAF00005791474 mtx.gz 122.7 MB
EGAF00005791475 tsv.gz 304.9 kB
EGAF00005791476 tsv.gz 36.0 kB
EGAF00005791477 tsv.gz 304.9 kB
EGAF00005791478 tsv.gz 43.7 kB
EGAF00005791479 tsv.gz 304.9 kB
EGAF00005791480 tsv.gz 304.9 kB
EGAF00005791481 mtx.gz 94.1 MB
EGAF00005791482 tsv.gz 33.0 kB
EGAF00005791483 mtx.gz 72.9 MB
16 Files (163.3 GB)