GSE57872

Single cell RNA-seq of primary human glioblastomas

Organism

Homo sapiens

Samples

875

Type

Expression profiling by high...

Submitted

2014-05-21

We report transcriptomes from 430 single glioblastoma cells isolated from 5 individual tumors and 102 single cells from gliomasphere cells lines generated using SMART-seq. In addition, we report population RNA-seq from the five tumors as well as RNA-seq from cell lines derived from 3 tumors (MGH26, MGH28, MGH31) cultured under serum free (GSC) and differentiated (DGC) conditions. This dataset highlights intratumoral heterogeneity with regards to the expression of de novo derived transcriptional...

Provenance — who produced it, who reused it

Linked to 23 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

Patel AnoopTirosh Itay

Single-cell RNA-seq highlights intratumoral heterogeneity in pri... 2014

Reused by

A general and flexible method for signal extraction from single-... 2018 · 837 cites
Linking transcriptional and genetic tumor heterogeneity through... 2018 · 265 cites
The linker histone H1.0 generates epigenetic and functional intr... 2016 · 201 cites
Quantification of cell identity from single-cell gene expression... 2015 · 170 cites
Chromatin landscapes reveal developmentally encoded transcriptio... 2019 · 142 cites
Linnorm: improved statistical analysis for single cell RNA-seq e... 2017 · 134 cites
Detecting heterogeneity in single-cell RNA-Seq data by non-negat... 2017 · 97 cites
Using single nucleotide variations in single-cell RNA-seq to ide... 2018 · 88 cites
Glioblastoma cell populations with distinct oncogenic programs r... 2021 · 78 cites

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

Deep data QC

96/100 · 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

Instrument

Illumina HiSeq 2500

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

875 / 875 runs

Completeness

100%

Metrics (value · how obtained)

checksum ok yes reported

total bases 172891833250 reported

total reads 2791556522 reported

n content pct 0.006 measured

pct q20 bases 99.2 measured

pct q30 bases 98.1 measured

gc content pct 46.9 measured

mean read length 25 measured

mean base quality 38 measured

adapter content pct 0 measured

duplication rate pct 41.88 measured

supplementary file types TXT reported

How this grade was computed

Weighted mean of 4 scored metric(s) → 96/100

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 98.1 measured ×1 100%

mean base quality 38 measured ×0.6 100%

adapter content pct 0 measured ×0.4 100%

duplication rate pct 41.88 measured ×0.4 74%

QC cost 21 s compute

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