Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE100373

GEO first seen 2018

The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity

Organism
Escherichia coli
Samples
4
Type
Expression profiling by high...
Submitted
2017-06-22

Ribosome biogenesis is a complex and intricate process involving multiple factors. A plethora of auxiliary proteins assist the correct assembly of rRNA and ribosomal proteins into mature ribosomes. Defects in this process cause dysfunctional ribosomes which may alter protein synthesis and impair cell fitness. Despite its importance, yet we are lacking mechanistic details of ribosome biogenesis. Here we show that the widely-conserved RNA chaperone Hfq, which is an important post-transcriptional r...

Provenance — who produced it, who reused it

Linked to 1 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
José M AndradeRicardo F Dos SantosIrina ChelyshevaZoya IgnatovaCecília M Arraiano
Reused by

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
Escherichia coli
Instrument
Illumina HiSeq 2000
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
4 / 4 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 7397817036 reported
total reads 145055236 reported
n content pct 0.005 measured
pct q20 bases 99.1 measured
pct q30 bases 97.4 measured
gc content pct 56.2 measured
mean read length 51 measured
mean base quality 38.4 measured
adapter content pct 0 measured
duplication rate pct 86.97 measured
supplementary file types TAB reported
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 97.4 measured ×1 100%
mean base quality 38.4 measured ×0.6 100%
adapter content pct 0 measured ×0.4 100%
duplication rate pct 86.97 measured ×0.4 0%
QC cost 36 s compute

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