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| Status |
Public on Nov 14, 2023 |
| Title |
Mouse_551628_PONS - Pmot-Psat post_10Xv3 [L8TX_201113_01_G06] |
| Sample type |
SRA |
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| Source name |
PONS - Pmot-Psat post
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| Organism |
Mus musculus |
| Characteristics |
tissue: PONS - Pmot-Psat post
genotype: Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt
treatment: Light
age: 62 days
donor id: 551628
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| Extracted molecule |
total RNA |
| Extraction protocol |
Allen Institute for Brain Science. Mouse Whole Cell Tissue Processing for 10x Genomics Platform V.9. Protocols.io, doi:dx.doi.org/10.17504/protocols.io.q26g7b52klwz/v9 (2022)
Allen Institute for Brain Science. 10Xv2 RNASeq Sample Processing. Protocols.io, doi:dx.doi.org/10.17504/protocols.io.bq68mzhw (2021); Allen Institute for Brain Science. 10Xv3.1 Genomics Sample Processing V.2. Protocols.io, doi:dx.doi.org/10.17504/protocols.io.dm6gpwd8jlzp/v2 (2022).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
WMB_Cell type annotation.xlsx
WMB_sample_metadata.csv
WMB.umap.2d.csv
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| Data processing |
10x libraries were sequenced on the Illumina NovaSeq6000, and sequencing reads were aligned to the mouse reference transcriptome (M21, GRCm38.p6) using the 10x Genomics CellRanger pipeline (version 6.1.1) with default parameters.
To remove low quality cells, cells were first classified into broad cell classes after mapping to an existing, preliminary version of the taxonomy, and cell quality was assessed based on gene detection, qc score, and doublet score. The qc score was calculated by summing the log transformed expression of a set of genes whose expression level is decreased significantly in poor quality cells. These are housekeeping genes that are strongly expressed in nearly all cells with a very tight co-expression pattern that is anti-correlated with the nucleus localized gene Malat1. Out of the 62 QC genes chosen, 30 are annotated as mitochondrial inner membrane category based on GO ontology cellular component, although they are not located on the mitochondrial chromosome. We used this qc score to quantify the integrity of cytoplasmic mRNA content, which tended to show bimodal distribution. Cells at the low end were very similar to single nuclei, which we removed for downstream analysis. Doublets were identified using a modified version of the DoubletFinder algorithm and removed when doublet score > 0.3. Thresholds were tailored to different cell classes. For example, for neurons (excluding granule cells) we used gene counts cutoff of 2,000 and qc score cutoff of 200.
Assembly: M21, GRCm38.p6
Supplementary files format and content: Text file containing information for location viewing and loading associated data
Supplementary files format and content: Excel file containing cell type annotations
Supplementary files format and content: Comma-separated values file containing cell-level metadata
Supplementary files format and content: Comma-separated values file containing UMAP coordinates for all QC-passed cells
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| Submission date |
Oct 31, 2023 |
| Last update date |
Nov 14, 2023 |
| Contact name |
Cindy van Velthoven |
| E-mail(s) |
cindy.vanvelthoven@alleninstitute.org
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| Phone |
+12065487000
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| Organization name |
Allen Institute
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| Street address |
615 Westlake Ave N
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE246717 |
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain |
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| Relations |
| BioSample |
SAMN37926969 |
| SRA |
SRX22232103 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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