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| Status |
Public on Jun 02, 2023 |
| Title |
PS19, replicate 3, snRNAseq |
| Sample type |
SRA |
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| Source name |
hippocampus
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| Organism |
Mus musculus |
| Characteristics |
Sex: female
tissue: hippocampus
strain: C57BL/6
age: 9 months old
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| Extracted molecule |
total RNA |
| Extraction protocol |
For snRNA-seq, single nucleus suspensions were isolated from about 50mg frozen mouse hippocampus following 10x genomics recommendation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting were made using CellRanger
removing ambient RNA by decountX
removing doublets by DoubletFinder
cell cluster umap analysis by Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Nov 25, 2022 |
| Last update date |
Jun 02, 2023 |
| Contact name |
chuangye Qi |
| E-mail(s) |
qicy2019@gmail.com
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| Organization name |
Baylor College of Medicine
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| Department |
Huffington Center
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| Street address |
One plaza
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| City |
HOUSTON |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE218728 |
TFEB-vacuolar ATPase signaling regulates lysosomal activity and immune response in tauopathy |
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| Relations |
| BioSample |
SAMN31871948 |
| SRA |
SRX18378220 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6755763_PS19_3_barcodes.tsv.gz |
37.7 Kb |
(ftp)(http) |
TSV |
| GSM6755763_PS19_3_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM6755763_PS19_3_matrix.mtx.gz |
62.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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