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Single-Cell Analysis of Sensory Experience Regulated Gene Expression in Mouse Visual Cortex
Single-cell (inDrops) analysis of primary visual cortex in visually stimulated mice
Provenance — who produced it, who reused it
Linked to 17 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.
Deposited / produced by
Sinisa HrvatinDaniel R HochbaumM A NagyBernardo L SabatiniMichael E Greenberg
Reused by
- Shared and distinct transcriptomic cell types across neocortical... 2018 · 1,968 cites
- Confronting false discoveries in single-cell differential expres... 2021 · 980 cites
- Identifying gene expression programs of cell-type identity and c... 2019 · 610 cites
- Fast interpolation-based t-SNE for improved visualization of sin... 2019 · 594 cites
- Cell type prioritization in single-cell data 2020 · 268 cites
- scClassify: sample size estimation and multiscale classification... 2020 · 165 cites
9 further papers cite this accession but reuse could not be confirmed.
Deep data QC
20/100 · FStandardized, field-standard QC computed by touching the data — every metric states how it was obtained · evidence: measured
Data type / assay
bulk-RNA-seq
Organism
Mus musculus
Instrument
NextSeq 500
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
40 / 40 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok
yes
reported
total bases
439258548158
reported
total reads
5177850613
reported
n content pct
31.004
measured
pct q20 bases
65.4
measured
pct q30 bases
63.8
measured
gc content pct
27
measured
mean read length
35
measured
mean base quality
23.9
measured
adapter content pct
0.21
measured
duplication rate pct
67.29
measured
supplementary file types
CSV, TXT
reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 20/100
The F 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.
pct q30 bases
63.8
measured
×1
0%
mean base quality
23.9
measured
×0.6
0%
adapter content pct
0.21
measured
×0.4
100%
duplication rate pct
67.29
measured
×0.4
17%
QC cost
28 s compute
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0