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Evolution of Translation Regulation in budding Yeast
Organism
Saccharomyces cerevisiae; Saccharomyces paradoxus; Saccharomyces cerevisiae x Saccharomyces paradoxus
Samples
12
Type
Expression profiling by high...
Submitted
2013-11-05
Comparison of translation efficiency in S. cerevisiae, S. paradoxus, and their F1 hybrid.
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
Charles J McManusGemma E MayPieter SpealmanAlan Shteyman
Reused by
- Long non-coding RNAs as a source of new peptides 2014 · 559 cites
- Accounting for biases in riboprofiling data indicates a major ro... 2014 · 154 cites
- riboCIRC: a comprehensive database of translatable circRNAs 2021 · 82 cites
2 further papers cite this accession but reuse could not be confirmed.
Deep data QC
100/100 · AStandardized, field-standard QC computed by touching the data — every metric states how it was obtained · evidence: measured
Data type / assay
bulk-RNA-seq
Organism
Saccharomyces paradoxus; Saccharomyces cerevisiae x Saccharomyces paradoxus; Saccharomyces cerevisiae
Instrument
Illumina HiSeq 2000
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
15 / 12 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok
yes
reported
total bases
30312704050
reported
total reads
606254081
reported
n content pct
0.002
measured
pct q20 bases
99.3
measured
pct q30 bases
97.7
measured
gc content pct
44.1
measured
mean read length
50
measured
mean base quality
38
measured
adapter content pct
0.51
measured
duplication rate pct
20.72
measured
supplementary file types
BED, BEDGRAPH, TXT
reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 100/100
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
97.7
measured
×1
100%
mean base quality
38
measured
×0.6
100%
adapter content pct
0.51
measured
×0.4
100%
duplication rate pct
20.72
measured
×0.4
100%
QC cost
9 s compute
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0