Supplementary Table 1: The accession number, number of samples and related study title of data used in this study that obtained from different experiments (~116 billion reads).

Accession number

Samples

Title

GSE130401

21

The hippo pathway effector protein YAP modulated resistance to trametinib neuroblastomas with hyperactivated RAS pathway signalling

GSE137290

21

Distinct mechanisms of acquired resistance to oncogenic kinase inhibition in cancer cells revealed using a single-step, high-dose selection scheme

GSE135902

40

The Transcriptome Of Cmml Monocytes Is Highly Inflammatory And Reflects Leukemia-Specific And Age-Related Alterations

GSE124326

480

Whole blood transcriptome analysis in bipolar disorder reveals strong lithium effect

GSE120597

50

Genetic Abnormalities in Large to Giant Congenital Nevi: Beyond NRAS mutations

GSE139250

51

Exploring the impact of chonic hypoxia on the expression of DNA repair gene in Glioblastoma and Medulloblastoma cells.

GSE129705

128

RNA-sequencing of whole blood samples from biologic naïve rheumatoid arthritis patients initiating anti-TNF treatment

GSE115046

110

Massively parallel characterization of regulatory dynamics during neural induction

GSE139181

33

Transcriptomics analysis of trimester-specific full-term placentas from three Zika virus-infected women

GSE130289

139

Dynamics of Trophoblast Differentiation in Peri-implantation Stage Human Embryos

GSE118912

32

Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations

GSE105160

197

RNASeq of mouse, human, and non-human primate primary dermal fibroblasts to poly(I:C) transfection

GSE138988

24

Transcriptome-wide comparison of stress granules and P-bodies reveals that translation plays a major role in RNA partitioning

GSE138853

30

Impact of transcriptional mutagenesis on p53 transactivation

GSE137392

60

MITF regulates SCD and fatty acid saturation to control melanoma phenotypic state.

GSE137391

24

Transcriptomics profiling of some commonly used cell lines at the base-line culture condition

GSE137390

36

Lineage-restricted regulation of SCD and fatty acid saturation by MITF controls melanoma phenotypic plasticity

GSE116698

76

Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation.

GSE112855

45

Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [RNA-seq]

GSE138730

32

Altered m6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection

GSE124685

84

mRNA Sequencing to identify transcriptional changes in early and late stages of lung in human Idiopathic Pulmonary Fibrosis

GSE94690

40

eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5’UTR

GSE138485

46

Retrospective gene expression analysis of human RNA samples from Hepatocellular Carcinoma in relation with survival

GSE130751

63

Non-oncogene addiction to SIRT3 plays a critical role in lymphomagenesis

GSE127696

78

Transcriptomic profile of cystic fibrosis airway epithelial cells undergoing repair

GSE133151

74

Clonal selection confers distinct evolutionary trajectories in BRAF-driven cancers

GSE125873

31

RNA-Seq of blood in preterm infants with Bronchopulmonary dysplasia.