Corpus 1,277 assessed · 1,178 scored · 644 reproduced ≥75 · 170 flagged ·∅ 74/100
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GSE107230

GEO first seen 2018

Patient-iPSC-derived kidney organoids show functional validation of a ciliopathic renal phenotype

Organism
Homo sapiens
Samples
6
Type
Expression profiling by high...
Submitted
2017-11-21

Purpose: A proof of concept study examining the disease modelling capabilities of patient iPSC derived kidney organoids. Methods: A proband was diagnosed by genome sequencing with compound heterozygous IFT140 mutations. A one-step reprogramming/gene-editing protocol of proband fibroblasts was used to derive both uncorrected patient and isogenic gene-corrected induced pluripotent stem cells (iPSC) which were differentiated to kidney organoids. Organoids were examined by immunofluorescence. Additi...

Provenance — who produced it, who reused it

Linked to 2 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
Andrew LonsdaleThomas Forbes
Reused by

Deep data QC

96/100 · 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
Homo sapiens
Metrics (value · how obtained)
n content pct 0.066 measured
pct q20 bases 97.7 measured
pct q30 bases 96.7 measured
gc content pct 45.5 measured
mean read length 75.5 measured
mean base quality 34.9 measured
adapter content pct 0 measured
duplication rate pct 41.94 measured
How this grade was computed
Weighted mean of 4 scored metric(s) → 96/100

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 96.7 measured ×1 100%
mean base quality 34.9 measured ×0.6 100%
adapter content pct 0 measured ×0.4 100%
duplication rate pct 41.94 measured ×0.4 74%
QC cost 28 s compute

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