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Table 1 Samples included in the study

From: Transcriptome instability as a molecular pan-cancer characteristic of carcinomas

Tissue

Samples

Histology

Other sample characteristics

GEO accession number

Literature references

Breast cancer

84

-

Hormone receptor status: HER2-positive (n = 35); ER/PR-positive (n = 25); ER/PR/HER2-negative (n = 24)

GSE16534

[45]

Cervical cancer

28

Squamous cell carcinoma (n = 19); adenocarcinoma (n = 9)

-

GSE27388

[44]

Colorectal cancer series I

26

Adenocarcinoma

-

GSE16534

[45]

Colorectal cancer series II

101a

Adenocarcinoma

Stage: Stage I (n = 28); stage II (n = 34); stage III (n = 26); stage IV (n = 13)

GSE24550 (n = 55); GSE29638 (n = 46)

[20, 49]

MSI-status: MSI-high (n = 21); MSS/MSI-low (n = 77); NA (n = 3)

Gastric cancer

25

Adenocarcinoma

Stage: Stage I (n = 8); stage II (n = 4); stage III (n = 5); stage IV (n = 8)

GSE13195

-

Lung cancer series I

20

Non-small-cell lung adenocarcinoma

Stage: Stage I (n = 12); stage II (n = 3); stage III (n = 5)

GSE12236

[48]

Lung cancer series II

43

Non-small-cell lung adenocarcinoma (n = 21) and squamous cell carcinoma (n = 22)

-

GSE16534

[45]

Neuroblastoma

47

-

Stage: stage I (n = 10); stage IV (n = 37)

GSE27608

[43]

Prostate cancer series I

131

Adenocarcinoma Gleason grade: Grade 5 (n = 1); grade 6 (n = 77); grade 7 (n = 42), grade 8 (n = 7); grade 9 (n = 4)

Pathologic T stage: stage 2 (n = 85); stage 3 (n = 40); stage 4 (n = 6)

GSE21034

[47]

Prostate cancer series II

50a

Gleason grade: Grade 5 (n = 2); grade 6 (n = 15); grade 7 (n = 32); grade 9 (n = 1)

Pathologic T stage: stage 2 (n = 26), stage 3 (n = 24)

GSE42954

[46]

Normal colonic mucosa

21a

 

19 samples corresponding to tumors from GSE24550 and GSE29638

GSE42690 (n = 19); GSE29638 (n = 2)

[20, 49]

Normal lung

20

 

Corresponding to tumors from GSE12236

GSE12236

[48]

Normal prostate

29

 

Corresponding to tumors from GSE21034

GSE21034

[47]

Normal stomach

23b

 

Corresponding to tumors from GSE13195

GSE13195

-

  1. aPatient samples analyzed in-house bTwo samples from the GEO entry (GSM333256 and GSM333270) were excluded due to failure of reading the raw data files. Abbreviations: GEO Gene Expression Omnibus, MSI microsatellite instability, MSS microsatellite stable, NA not available T tumor.