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| Status |
Public on Sep 28, 2020 |
| Title |
NC16 |
| Sample type |
SRA |
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| Source name |
prefrontal cortex snRNAseq
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| Organism |
Homo sapiens |
| Characteristics |
tissue: prefrontal cortex
diagnosis: healthy control
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Alignment is done by cellranger to hg38 pre-mRNA reference
Downstream differential analysis and subcluster analysis is done by Seurat
Genome_build: hg38
Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
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| Submission date |
Sep 11, 2020 |
| Last update date |
Sep 28, 2020 |
| Contact name |
Nancy Ip |
| E-mail(s) |
[email protected]
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| Organization name |
Hong Kong University of Science and Technology
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| Street address |
Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
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| City |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE157827 |
Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer's disease |
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| Relations |
| BioSample |
SAMN16100308 |
| SRA |
SRX9106602 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4775579_NC16_barcodes.tsv.gz |
32.5 Kb |
(ftp)(http) |
TSV |
| GSM4775579_NC16_features.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM4775579_NC16_matrix.mtx.gz |
13.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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