Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE63440

GEO first seen 2015

Autophagy mediates degradation of nuclear lamina

Organism
Homo sapiens
Samples
6
Type
Genome binding/occupancy pro...
Submitted
2014-11-18

Autophagy is a catabolic membrane trafficking process involved in degradation of cellular constituents through lysosomes, which maintains cell and tissue homeostasis. While much attention has been focused on autophagic turnover of cytoplasmic materials, little is known regarding the role of autophagy in degrading nuclear components. Here we report that autophagy machinery mediates degradation of nuclear lamina in mammalian cells, a process we term laminophagy. The autophagy protein LC3 is pre...

Provenance — who produced it, who reused it

Linked to 3 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
Zhixun DouCaiyue XuGreg DonahueTakeshi ShimiJi-An PanJiajun ZhuAndre IvanovBrian C CapellAdam M DrakeParisha P ShahJoseph M CatanzaroM D RickettsTrond LamarkStephen A AdamRonen MarmorsteinWei-Xing ZongTerje JohansenRobert D GoldmanPeter D AdamsShelley L Berger
Reused by

1 further paper cites this accession but reuse could not be confirmed.

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
Homo sapiens
Instrument
NextSeq 500
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
6 / 6 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 31492936800 reported
total reads 419905824 reported
n content pct 0.012 measured
pct q20 bases 91.6 measured
pct q30 bases 84 measured
gc content pct 43.1 measured
mean read length 75 measured
mean base quality 33.3 measured
adapter content pct 3.1 measured
duplication rate pct 3.75 measured
supplementary file types BED, BW 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 84 measured ×1 70%
QC cost 12 s compute

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