Corpus 1,273 assessed · 1,174 scored · 643 reproduced ≥75 · 169 flagged ·∅ 74.1/100
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GSE102843

GEO first seen 2017

CG-dinucleotide suppression enables antiviral defense targeting non-self RNA

Organism
Human immunodeficiency virus 1
Samples
2
Type
Other
Submitted
2017-08-21

Vertebrate genomes exhibit marked CG-suppression, that is lower than expected numbers of 5’-CG-3’ dinucleotides1. This feature is likely due to C-to-T mutations that have accumulated over hundreds of millions of years, driven by CG-specific DNA methyl transferases and spontaneous methyl-cytosine deamination. Remarkably, many RNA viruses of vertebrates that are not substrates for DNA methyl transferases mimic the CG-suppression of their hosts2-4. This striking property of viral genomes is unexpla...

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
Matthew A TakataPaul D Bieniasz

Deep data QC

metadata only · no data-level QC for this type

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

Data type / assay
RNA-protein
Organism
Human immunodeficiency virus 1
Instrument
Illumina HiSeq 2000
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
2 / 2 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 190936707 reported
total reads 3743857 reported
supplementary file types XLS reported
QC cost 17 s compute

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