Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE100266

GEO first seen 2017

The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin Remodeling Complexes

Organism
Homo sapiens
Samples
32
Type
Genome binding/occupancy pro...
Submitted
2017-06-20

BET proteins commonly activate cellular gene expression, yet inhibiting their recruitment paradoxically reactivates latent HIV-1 transcription. Here we identify the short isoform of BET family member BRD4 (BRD4S) as a novel corepressor of HIV-1 transcription. We found that BRD4S was enriched in chromatin fractions of latently infected T cells and was more rapidly displaced from chromatin upon BET inhibition than the long isoform. BET inhibition induced marked nucleosome remodeling at the latent...

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
Melanie OttRyan J Conrad
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
ATAC-seq
Organism
Homo sapiens
Instrument
Illumina HiSeq 2500
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
32 / 32 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 295714641140 reported
total reads 1467227915 reported
n content pct 0.007 measured
pct q20 bases 95.1 measured
pct q30 bases 90.8 measured
gc content pct 47.4 measured
mean read length 101 measured
mean base quality 35.5 measured
adapter content pct 0.31 measured
duplication rate pct 2.01 measured
supplementary file types WIG, XLSX reported
How this grade was computed

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

pct q30 bases 90.8 measured ×1 100%
QC cost 35 s compute

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