Corpus 1,280 assessed · 1,181 scored · 646 reproduced ≥75 · 170 flagged ·∅ 74/100
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GSE40243

GEO first seen 2014

Hydroxymethylation at gene regulatory regions directs stem cell commitment during erythropoiesis

Organism
Homo sapiens
Samples
12
Type
Expression profiling by high...
Submitted
2012-08-20

CD34 positive hematopoietic stem cells were differentiated into erythroid lineage. Next generation sequencing (NGS) of 5hmC affinity pulldown and RNAseq were performed in four time point of different stages of erythroid differentiation.

Provenance — who produced it, who reused it

Linked to 2 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
Jozef MadzoHui LiuAlex RodriguezAparna VasanthakumarSriram SundaravelDonne D CacesTim LooneyLi ZhangJanet B LeporeAlan H ShihChun-Xiao SongYiting YuRobert GrossmanBrigitte RaumannAmit K VermaChuan HeRoss L LevineDon LavelleBruce T LahnAmittha WickremaLucy A Godley
Reused by

Deep data QC

100/100 · A

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 0.037 measured
pct q20 bases 96.6 measured
pct q30 bases 91.5 measured
gc content pct 47.4 measured
mean read length 50 measured
mean base quality 35.9 measured
adapter content pct 0.6 measured
duplication rate pct 13.48 measured
How this grade was computed
Weighted mean of 4 scored metric(s) → 100/100

The A 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 91.5 measured ×1 100%
mean base quality 35.9 measured ×0.6 100%
adapter content pct 0.6 measured ×0.4 100%
duplication rate pct 13.48 measured ×0.4 100%
QC cost 26 s compute

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