Adult mouse cortical cell taxonomy by single cell transcriptomics
Nervous systems are composed of numerous cell types, but the extent of cell type diversity is poorly understood. Here, we construct a cellular taxonomy of one cortical region, primary visual cortex, in adult mice based on single cell RNA-sequencing. We identify 49 transcriptomic cell types including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types.
Provenance — who produced it, who reused it
Linked to 31 papers in the literature. Roles are inferred factual signals (who deposited the data vs who reused it), with counts — never a judgement about any author.
- Chromatin Potential Identified by Shared Single-Cell Profiling o... 2020 · 1,205 cites
- Massively parallel single-nucleus RNA-seq with DroNc-seq 2017 · 1,191 cites
- SPOTlight: seeded NMF regression to deconvolute spatial transcri... 2021 · 753 cites
- Identifying gene expression programs of cell-type identity and c... 2019 · 610 cites
- Brain Cell Type Specific Gene Expression and Co-expression Netwo... 2018 · 547 cites
- Single-cell transcriptomic analysis of mouse neocortical develop... 2019 · 319 cites
- Identification of spatially associated subpopulations by combini... 2018 · 293 cites
- Knowledge-graph-based cell-cell communication inference for spat... 2022 · 212 cites
- scClassify: sample size estimation and multiscale classification... 2020 · 165 cites
- Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with... 2017 · 160 cites
- Mapping the transcriptional diversity of genetically and anatomi... 2019 · 96 cites
- Exploiting single-cell expression to characterize co-expression... 2016 · 94 cites
- Benchmark and Parameter Sensitivity Analysis of Single-Cell RNA... 2019 · 86 cites
- Significant Evolutionary Constraints on Neuron Cells Revealed by... 2020 · 81 cites
- Genome-Wide Analysis of Differential Gene Expression and Splicin... 2019 · 78 cites
15 further papers cite this accession but reuse could not be confirmed.
Deep data QC
87/100 · BStandardized, field-standard QC computed by touching the data — every metric states how it was obtained · evidence: measured
Mus musculus bulk RNA-seq. Grade B (87/100) with strong base quality (89% Q30, 35.3 mean BQ) but moderate read duplication (58.98%). Q30 is marginally below the 90% benchmark, and duplication suggests library prep stress; together these warrant careful scrutiny of abundance estimates. Suitable for expression profiling with validation.
The B grade is a transparent weighted average. Each metric below scored from 0–100% against the published bulk-RNA-seq thresholds, weighted by its importance; nothing is hidden or subjective.
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0
Scientific quality
Based on hands-on reproduction of the papers that use this dataset. A reproducible paper that stands on this data is positive evidence; a flagged one is a prompt to look closer — never a verdict on the dataset itself without the evidence.