GSE34448

RNA Subcellular CAGE Localization from ENCODE/RIKEN

Organism

Homo sapiens

Samples

78

Type

Expression profiling by high...

Submitted

2011-12-14

This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Piero Carninci mailto:«email»). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:«email»). This track shows 5' cap analysis gene expression (CAGE) tags and clusters in RNA extracts (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=rnaExtract) from different sub-cellular localizations (http://hgwdev.cse.ucsc.edu/cgi-bin/hg...

Provenance — who produced it, who reused it

Linked to 7 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

Timo LassmannPhil KapranovHazuki TakahashiYoshihide HayashizakiCarrie DavisTom GingerasPiero Carninci

Landscape of transcription in human cells 2012

Reused by

Modeling gene expression using chromatin features in various cel... 2012 · 295 cites

5 further papers cite this accession but reuse could not be confirmed.

Deep data QC

71/100 · C

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

Data type / assay

bulk-RNA-seq

Organism

Homo sapiens

Metrics (value · how obtained)

n content pct 0.012 measured

pct q20 bases 100 measured

pct q30 bases 100 measured

gc content pct 58.7 measured

mean read length 36 measured

mean base quality 30 measured

adapter content pct 0 measured

duplication rate pct 64.39 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 71/100

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

pct q30 bases 100 measured ×1 100%

mean base quality 30 measured ×0.6 33%

adapter content pct 0 measured ×0.4 100%

duplication rate pct 64.39 measured ×0.4 24%

QC cost 41 s compute

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