Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE106220

GEO first seen 2018

Ten-eleven translocation proteins modulate the response to environmental stress in mice

Organism
Mus musculus
Samples
22
Type
Expression profiling by high...
Submitted
2017-10-26

5-hydroxymethylcytosine (5hmC) is enriched in brain and has been recognized as an important DNA modification. However, the roles of 5hmC and its “writers”, Ten-eleven translocation (Tet) proteins, in stress-induced response have yet to be elucidated. Here, we show that chronic restraint stress (CRS) induced the depression-like behavior in mice and resulted in a 5hmC reduction in prefrontal cortex (PFC). Interestingly, we found that the loss of Tet1 (Tet1 KO) led to the resistance to CRS while th...

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
Ying ChengPeng Jin
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
Mus musculus
Instrument
Illumina HiSeq 2000
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
22 / 22 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 35170010954 reported
total reads 556153504 reported
n content pct 0.002 measured
pct q20 bases 98.2 measured
pct q30 bases 94.5 measured
gc content pct 44.5 measured
mean read length 51 measured
mean base quality 36.8 measured
adapter content pct 0.08 measured
duplication rate pct 18.58 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 94.5 measured ×1 100%
QC cost 22 s compute

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