Table 1 Summary of bulk RNA-seq datasets involved in GepLiver.

From: GepLiver: an integrative liver expression atlas spanning developmental stages and liver disease phases

Dataset	Source	Reference	Selection	Layout
GepLiver-bulk-01	GTEx	GTEx⁵	PolyA	Paired
GepLiver-bulk-02	GSE114150	Xiao, S. et al.⁴⁴	rRNA-d	Paired
GepLiver-bulk-03	GSE128102	Touboul, T. et al.⁴⁵	rRNA-d, PolyA	Paired
GepLiver-bulk-04	GSE78569	ENCODE⁴⁶	rRNA-d	Paired
GepLiver-bulk-05	GSE126848	Suppli, M. P. et al.⁴⁷	PolyA	Single
GepLiver-bulk-06	GSE130970	Hoang, S. A. et al.⁴⁸	PolyA	Paired
GepLiver-bulk-07	GSE135251	Govaere, O. et al.⁷	PolyA	Paired
GepLiver-bulk-08	GSE162694	Pantano, L. et al.⁴⁹	rRNA-d	Single
GepLiver-bulk-09	GSE167523	Kozumi, K. et al.⁵⁰	PolyA	Single
GepLiver-bulk-10	GSE142530	Massey, V. et al.⁵¹	rRNA-d	Paired
GepLiver-bulk-11	GSE143318	Hyun, J. et al.⁵²	rRNA-d	Single
GepLiver-bulk-12	GSE155907⁵³	N/A	rRNA-d	Paired
GepLiver-bulk-13	E-MTAB-6863	Ramnath, D. et al.⁵⁴	rRNA-d	Single
GepLiver-bulk-14	GSE112221	Hlady, R. A. et al.⁵⁵	PolyA	Paired
GepLiver-bulk-15	GSE144269	Candia, J. et al.⁵⁶	rRNA-d	Single
GepLiver-bulk-16	GSE84346	Boldanova, T. et al.⁵⁷	PolyA	Single
GepLiver-bulk-17	GSE94660	Yoo, S. et al.⁵⁸	PolyA	Paired
GepLiver-bulk-19	TCGA	TCGA⁴	PolyA	Paired
GepLiver-bulk-20	GSE114564	Kim, S. S. et al.⁵⁹	rRNA-d	Paired
GepLiver-bulk-21	GSE124535	Jiang, Y. et al.⁴²	PolyA	Paired
GepLiver-bulk-22	GSE140462	Hall, Z. et al.⁶⁰	rRNA-d	Single
GepLiver-bulk-23	GSE148355	Yoon, S. H. et al.¹²	rRNA-d	Paired
GepLiver-bulk-24	GSE77314	Liu, G. et al.⁶¹	PolyA	Paired
GepLiver-bulk-25	GSE77509	Yang, Y. et al.⁶²	rRNA-d	Paired
GepLiver-bulk-26	TCGA	TCGA⁶³	PolyA	Paired
GepLiver-bulk-27	GSE107943	Ahn, K. S. et al.⁶⁴	PolyA	Paired
GepLiver-bulk-28	GSE119336⁶⁵	N/A	PolyA	Paired
GepLiver-bulk-29	GSE162396	Kim, H. D. et al.⁶⁶	PolyA	Single
GepLiver-bulk-30	GSE63420	Sia, D. et al.⁶⁷	PolyA	Single
GepLiver-bulk-31	Fudan-ICC	Dong, L. et al.⁶⁸	PolyA	Paired
GepLiver-bulk-32	GSE104766	Hooks, K. B. et al.⁶⁹	PolyA	Paired
GepLiver-bulk-33	GSE133039	Carrillo-Reixach, J. et al.⁷⁰	PolyA	Paired
GepLiver-bulk-34	GSE151347	Wagner, A. E. et al.⁷¹	PolyA	Paired
GepLiver-bulk-35	GSE81928	Valanejad, L. et al.⁷²	PolyA	Paired
GepLiver-bulk-36	GSE89775	Ranganathan, S. et al.⁷³	PolyA	Paired
GepLiver-bulk-38	CCLE	CCLE⁷⁴	PolyA	Paired
GepLiver-bulk-39	GSE108348	Darbellay, F. et al.⁷⁵	PolyA	Single
GepLiver-bulk-40	GSE109345	van Koppen, A. et al.⁷⁶	PolyA	Single
GepLiver-bulk-41	GSE165752	Broadfield, L. A. et al.⁷⁷	PolyA	Single
GepLiver-bulk-42	GSE162876	Loft, A. et al.⁷⁸	PolyA	Paired
GepLiver-bulk-43	GSE166353	Sun, L. et al.⁷⁹	rRNA-d	Paired
GepLiver-bulk-44	GSE48052	Lee, S. M. et al.⁸⁰	PolyA	Single
GepLiver-bulk-45	GSE95424	Kan, F. et al.⁸¹	PolyA	Paired
GepLiver-bulk-46	GSE166868	Holland, C. H. et al.⁸²	rRNA-d	Paired
GepLiver-bulk-47	GSE148379	Molina-Sánchez, P. et al.⁶	PolyA	Paired
GepLiver-bulk-48	GSE153077⁸³	N/A	PolyA	Single
GepLiver-bulk-49	GSE90497	Shalapour, S. et al.⁸⁴	PolyA	Single
GepLiver-bulk-50	GSE99010	Tsuchida, T. et al.⁸⁵	PolyA	Paired
GepLiver-bulk-51	PRJNA488497	Dow, M. et al.⁸⁶	PolyA	Single
GepLiver-bulk-52	GSE141511	Di-Luoffo, M. et al.⁸⁷	rRNA-d	Paired
GepLiver-bulk-53	GSE150504	Cristinziano, G. et al.⁸⁸	PolyA	Paired
GepLiver-bulk-54	GSE87578	Wang, H. et al.⁸⁹	PolyA	Single
GepLiver-bulk-55	GSE156545	Wang, H. et al.⁹⁰	PolyA	Paired

For each bulk RNA-seq dataset included in GepLiver, the data source, related publication, library selection method and layout were provided in the table. PolyA: PolyA-selected; rRNA-d: rRNA-depleted; Paired: Paired-end; Single: Single-end.

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Table 1 Summary of bulk RNA-seq datasets involved in GepLiver.

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