Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE142425

GEO first seen 2019

Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development

Organism
Mus musculus
Samples
4
Type
Expression profiling by high...
Submitted
2019-12-20

The coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular...

Provenance — who produced it, who reused it

Linked to 6 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
Natalie H KellyNguyen P HuynhFarshid Guilak
Reused by

5 further papers cite this accession but reuse could not be confirmed.

Deep data QC

94/100 · A

Standardized, 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
Illumina NovaSeq 6000
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
8 / 4 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 193756181073 reported
total reads 2129188803 reported
n content pct 0.002 measured
pct q20 bases 97 measured
pct q30 bases 94 measured
gc content pct 47.4 measured
mean read length 91 measured
mean base quality 35.9 measured
adapter content pct 0.01 measured
duplication rate pct 47.18 measured
supplementary file types MTX, TSV reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 94/100

The A 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 94 measured ×1 100%
mean base quality 35.9 measured ×0.6 100%
adapter content pct 0.01 measured ×0.4 100%
duplication rate pct 47.18 measured ×0.4 62%
QC cost 25 s compute

measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0