Is PanCan data microarray or rna-seq

Question

[survive]

Hi, I would like to use the PanCanAtlas dataset, the expression data (EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv) from the download page appears to be rna-seq data. But in some old papers which also use the PanCanAtlas dataset, they refer to these data as microarrays.

I am wondering if PanCanAtlas run their samples (previously ran as microarray) again with rna-seq, or only part of the data is rna-seq data?

Answer 1

[ATpoint]

Illumina HiSeq is a sequencing machine / platform, so RNA-seq, not array.

[solarchan7]

Hi, so this paper uses the TCGA dataset and in the supplementary information, it mentions the TCGAOVARIAN dataset uses the GPL4685 which is [U133AAofAv2] Affymetrix GeneChip HT-HG_U133A Early Access Array and it's array?

thank you.

[GenoMax]

This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be this dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28299

[survive]

So both arrays and rna-seq have been performed on the same samples?