Tissue specific mRNA expression dataset in human and mouse

Question

[Shicheng Guo]

Dear All,

I am trying to calculate/estimate tissue specific mRNA expression in human and mouse and trying to get these 6 dataset. Anyone to share how to download these files? These 6 files have been used in this paper: https://academic.oup.com/bib/article/18/2/205/2562739#supplementary-data

EncodeCshlAdult8wksEnsV68RNAseqGene.txt
Mus_musculus_RNA-Seq_RPKM_GSE30352_Tissues.txt
Mus_musculus_probesets_GSE9954_A-AFFY-45_gcRMA_TissuesBgee.txt
ArrayExpressHumanAdultEnsV69RNAseq.txt
Homo_sapiens_RNA-Seq_RPKM_GSE30352_Tissues.txt
Homo_sapiens_probesets_GSE2361_A-AFFY-33_gcRMA_TissuesBgee.txt

I have contacted the authors, but didn't received response yet.

Thanks
Shicheng

Answer 1

[BioinfGuru]

Awesome, years ago I wrote my thesis on the use of Tau to calculate tissue specificity, enjoy!

The supplementary materials in the paper is not helpful, you have to go to the original papers that produced the data.

It states in the "Material and Methods" section.

"We used the following RNA-seq data: 27 human tissues (E-MTAB-1733) from Fagerberg et al. [46] downloaded from their Supplementary Materials , 22 mouse tissues (GSE36025) from the ENCODE project [47, 48] as used in Kryuchkova-Mostacci and Robinson-Rechavi [20] and 8 human tissues and 6 mouse tissues from Brawand et al. [49], as processed in the Bgee database [50]."

Note: The "supplementary material" mentioned in the paragraph is a link to this paper's supplementary material, it is not the supplementary material from the Fagerberg paper.

Go to the references section to get to those papers mentioned, you will find directions to the data in those papers. If memory serves me, I think you will be looking for links to a SRA archive. eg. SRAxxxxxxxx