Table 1.
Glioblastoma Datasets Used in This Article
| Data type | Dataset | Accession(s) | Samples (used in this study) | Platform | Reference |
|---|---|---|---|---|---|
| Bulk | Stead | EGAD00001009806 (https://ega-archive.org/datasets/EGAD00001009806) | 64 bulk tumor samples from 32 matched primary and recurrent pairs | Illumina NGS paired-end stranded total RNA | Tanner et al6 |
| Additional stead | Unpublished and available from the corresponding author via data access agreement | 42 bulk tumor samples from 21 matched primary and recurrent pairs | Illumina NGS paired-end stranded total RNA | Unpublished | |
| GLASS | The GLASS Consortium (https://www.synapse.org/#!Synapse:syn31121291) | 46 bulk tumor samples from 23 matched primary and recurrent pairs | Illumina HiSeq 4000 stranded paired-end mRNA | Varn et al26 | |
| Nam | EGAD00001001424 (https://ega-archive.org/datasets/EGAD00001001424) | 70 bulk tumor samples from 35 matched primary and recurrent pairs | Illumina HiSeq 2000 unstranded paired-end mRNA | Kim et al21 | |
| Kim | PRJNA580196 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA580196) | 26 bulk tumor samples from 13 matched primary and recurrent pairs | Illumina NextSeq 500 paired-end stranded total RNA | Kim et al24 | |
| DFKZ | EGAD00001004564 (https://ega-archive.org/datasets/EGAD00001004564) | 32 bulk tumor samples from 16 matched primary and recurrent pairs | Illumina HiSeq 2000 paired-end stranded total RNA | Körber et al23 | |
| Rabadan | EGAD00001002143 (https://ega-archive.org/datasets/EGAD00001002143) | 16 bulk tumor samples from 8 matched primary and recurrent pairs | Illumina TruSeq stranded paired-end total (14), mRNA (2) | Wang et al22 | |
| Diaz | EGAS00001004524 (https://ega-archive.org/studies/EGAS00001004524) | 8 bulk tumor samples from 4 matched primary and recurrent pairs | Illumina NovaSeq paired-end unstranded mRNA | Wang et al25 | |
| EORTC | EGAD00001007860 (https://ega-archive.org/datasets/EGAD00001007860) | 260 bulk tumor samples from 130 matched primary and recurrent pairs | Illumina NovaSeq stranded paired-end total RNA | Hoogstrate et al27 | |
| TCGA | TCGAbiolinks R package28 | 144 bulk tumor samples | Illumina HiSeq 4000 stranded paired-end mRNA | Ceccarelli et al29 | |
| CGGA | http://www.cgga.org.cn/download.jsp | 109 bulk tumor samples | Illumina HiSeq 2000, 2500, or 4000 paired-end total RNA | Zhao et al31 | |
| Single-cell | Wang | GSE174554 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174554) | 245 952 single-nuclei from 57 samples including 22 matched primary and recurrent pairs | 10X Genomics, Illumina NovaSeq 6000 | Wang et al11 |
| Neftel | GSE131928 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131928) | 16 201 single-cells from 9 patients | 10X Genomics Chromium 3’ single-cell | Neftel et al5 | |
| GBmap | https://cellxgene.cziscience.com/collections/999f2a15-3d7e-440b-96ae-2c806799c08c | 890892 single-cells and 244 785 single-nuclei from 240 patients across 26 studies | Various | Ruiz-Moreno et al32 |