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Table 1 Datasets accessed in this study

From: Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma

Datasets

Cohort

Data type

Source

Reference

TCGA LUSC

RNAseq, WES, CNV, RPPA (Level 4 data)

GDAC Firehose, TCPA Portal

[42, 43]

TCGA LUAD

RNAseq

GDAC Firehose

[44]

NCI-MD Cohort SqCC

RNAseq

This study; Gene Expression Omnibus, GSE201221

 

UHN Cohort

Microarray

Gene Expression Omnibus, GSE50081

[20]

TCGA Pan-Cancer Cohort

RNAseq

https://gdc.cancer.gov/about-data/publications/pancanatlas with survival data from [45]

[45]

SqCC cell types from scRNAseq

scRNAseq

Loom files and Signature Matrix

[46]

Premalignant lesions

RNAseq

Gene Expression Omnibus GSE108124

[7]

Aging lung

RNAseq

Gene Expression Omnibus GSE165192

[47]

Data and signatures

Data type

Data format

Source

Reference

IPF fibrosis score

Expression Data

Manuscript

[48]

IPF fibroblast phenotypes from scRNAseq

scRNAseq

Gene Expression Omnibus

[49]

IPF cell types from scRNAseq

Signature matrix

Manuscript

[50]

Lung cancer-specific immunological cell types

Gene Signatures

Manuscript

[51]