Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE128063

GEO first seen 2019

Physical and functional compartmentalization of archaeal chromosomes

Organism
Sulfolobus acidocaldarius; Saccharolobus islandicus
Samples
94
Type
Other; Genome binding/occupa...
Submitted
2019-03-08

The three-dimensional organization of chromosomes can have a profound impact on their replication and expression. The chromosomes of higher eukaryotes possess discrete compartments that are characterized by differing transcriptional activities. Contrastingly, most bacterial chromosomes have simpler organization with local domains, the boundaries of which are influenced by gene expression. Numerous studies have revealed that the higher-order architectures of bacterial and eukaryotic chromosomes a...

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
Naomichi TakemataRachel Y SamsonStephen D Bell
Reused by

Deep data QC

insufficient data to score

Standardized, field-standard QC computed by touching the data — every metric states how it was obtained

Data type / assay
ChIP-seq
Organism
Sulfolobus acidocaldarius; Saccharolobus islandicus
Instrument
Illumina Genome Analyzer IIx
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
94 / 94 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 225233968047 reported
total reads 3014036646 reported
n content pct 0.005 measured
pct q20 bases 97 measured
pct q30 bases 95.5 measured
gc content pct 36.7 measured
mean read length 42 measured
mean base quality 34.5 measured
adapter content pct 0 measured
duplication rate pct 46.61 measured
supplementary file types TXT reported
How this grade was computed

The insufficient grade is a transparent weighted average. Each metric below scored from 0–100% against the published ChIP-seq thresholds, weighted by its importance; nothing is hidden or subjective.

pct q30 bases 95.5 measured ×1 100%
QC cost 13 s compute

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