Corpus 1,273 assessed · 1,174 scored · 643 reproduced ≥75 · 169 flagged ·∅ 74.1/100
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GSE118519

GEO first seen 2020

Functional cooperation of glycine synthase-reductase pathway with Wood-Ljungdahl pathway for autotrophic growth of Clostridium drakei

Organism
Clostridium drakei
Samples
4
Type
Expression profiling by high...
Submitted
2018-08-14

The Wood-Ljungdahl pathway in acetogens converts C1 compounds, such as CO2 and CO, into acetyl-CoA. Similarly, the glycine synthase pathway assimilates C1 compounds into glycine. Partial glycine synthase genes are widely conserved in the Wood-Ljungdahl pathway gene cluster but functional relationship between the pathways in autotrophic condition remains unknown. To comprehend, we assembled Clostridium drakei genome (5.7-Mbp) with intact glycine synthase pathway and constructed a genome-scale met...

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
Yoseb SongJongoh ShinSangrak JinGyu-Min LeeJin-Soo LeeSeul-Gi KangJung-Kul LeeDong-Rip KimEun-Yeol LeeSuhyung ChoSun-Chang KimDonghyuk KimByung-Kwan Cho
Reused by

1 further paper cites this accession but reuse could not be confirmed.

Deep data QC

83/100 · B

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
Clostridium drakei
Metrics (value · how obtained)
n content pct 0.003 measured
pct q20 bases 99.7 measured
pct q30 bases 98.7 measured
gc content pct 37.1 measured
mean read length 134 measured
mean base quality 37.5 measured
adapter content pct 0.34 measured
duplication rate pct 75.13 measured
How this grade was computed
Weighted mean of 4 scored metric(s) → 83/100

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.

pct q30 bases 98.7 measured ×1 100%
mean base quality 37.5 measured ×0.6 100%
adapter content pct 0.34 measured ×0.4 100%
duplication rate pct 75.13 measured ×0.4 0%
QC cost 25 s compute

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