Source Name	Characteristics [Organism]	Term Source REF	Term Accession Number	Characteristics [CellLine]	Term Source REF	Term Accession Number	Protocol REF	Protocol REF	Sample Name	Protocol REF	Parameter Value [Amplification]	Parameter Value [Extracted product]	Extract Name	Material Type	Protocol REF	Parameter Value [Amplification]	Parameter Value [Label used]	Labeled Extract Name	Label	Material Type	Protocol REF	Parameter Value [Chamber type]	Parameter Value [Quantity of label target used]	Unit [MassUnit]	Parameter Value [temperature]	Unit [TemperatureUnit]	Hybridization Name	Array Design REF	Protocol REF	Factor Value [RNAi]	Scan Name	Array Data File	Comment [ArrayExpress FTP file]
VCP knockdown 1 fourth replicate	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	VCP knockdown 1 fourth replicate	P-MEXP-30004	none	total RNA	E_VCP knockdown 1 fourth replicate	total_RNA	P-MEXP-30608	none	Cy3	L_VCP knockdown 1 fourth replicate_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 1 fourth replicate	A-BASE-3	P-MEXP-30610	VCP-1 siRNA	H_VCP knockdown 1 fourth replicate	VCP_kd_1_fourth_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for VCP kd 1	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	  	  	Control for VCP kd 1	P-MEXP-30004	none	total RNA	E_Control for VCP kd 1	total_RNA	P-MEXP-30609	none	Cy5	L_Control for VCP kd 1_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 1 fourth replicate	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_VCP knockdown 1 fourth replicate	VCP_kd_1_fourth_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for VCP kd 2	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	  	  	Control for VCP kd 2	P-MEXP-30004	none	total RNA	E_Control for VCP kd 2	total_RNA	P-MEXP-30608	none	Cy3	L_Control for VCP kd 2_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 2 second replicate	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_VCP knockdown 2 second replicate	VCP_kd_2_second_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
VCP knockdown 2 second replicate	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	VCP knockdown 2 second replicate	P-MEXP-30004	none	total RNA	E_VCP knockdown 2 second replicate	total_RNA	P-MEXP-30609	none	Cy5	L_VCP knockdown 2 second replicate_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 2 second replicate	A-BASE-3	P-MEXP-30610	VCP-2 siRNA	H_VCP knockdown 2 second replicate	VCP_kd_2_second_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
VCP knockdown 1 third replicate	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	VCP knockdown 1 third replicate	P-MEXP-30004	none	total RNA	E_VCP knockdown 1 third replicate	total_RNA	P-MEXP-30609	none	Cy5	L_VCP knockdown 1 third replicate_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 1 third replicate	A-BASE-3	P-MEXP-30610	VCP-1 siRNA	H_VCP knockdown 1 third replicate	VCP_kd_1_third_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for VCP kd 1	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	  	  	Control for VCP kd 1	P-MEXP-30004	none	total RNA	E_Control for VCP kd 1	total_RNA	P-MEXP-30608	none	Cy3	L_Control for VCP kd 1_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 1 third replicate	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_VCP knockdown 1 third replicate	VCP_kd_1_third_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
VCP knockdown 2 third replicate	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	VCP knockdown 2 third replicate	P-MEXP-30004	none	total RNA	E_VCP knockdown 2 third replicate	total_RNA	P-MEXP-30608	none	Cy3	L_VCP knockdown 2 third replicate_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 2 third replicate	A-BASE-3	P-MEXP-30610	VCP-2 siRNA	H_VCP knockdown 2 third replicate	VCP_kd_2_third_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for VCP kd 2	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	  	  	Control for VCP kd 2	P-MEXP-30004	none	total RNA	E_Control for VCP kd 2	total_RNA	P-MEXP-30609	none	Cy5	L_Control for VCP kd 2_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 2 third replicate	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_VCP knockdown 2 third replicate	VCP_kd_2_third_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for Control i.e. mock knockdown	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	  	  	  	  	  	Control for Control i.e. mock knockdown	P-MEXP-30004	none	total RNA	E_Control for Control i.e. mock knockdow	total_RNA	P-MEXP-30609	none	Cy5	L_Control for Control i.e. mock kd_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_Control 1	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_Control 1	Control_first_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control 1	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	Control 1	P-MEXP-30004	none	total RNA	E_Mock 1	total_RNA	P-MEXP-30608	none	Cy3	L_Mock Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_Control 1	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_Control 1	Control_first_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
VCP knockdown 2 first replicate	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	VCP knockdown 2 first replicate	P-MEXP-30004	none	total RNA	E_VCP knockdown 2 first replicate	total_RNA	P-MEXP-30608	none	Cy3	L_VCP knockdown 2 first replicate_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 2 first replicate	A-BASE-3	P-MEXP-30610	VCP-2 siRNA	H_VCP knockdown 2 first replicate	VCP_kd_2_first_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for VCP kd 2	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	  	  	Control for VCP kd 2	P-MEXP-30004	none	total RNA	E_Control for VCP kd 2	total_RNA	P-MEXP-30609	none	Cy5	L_Control for VCP kd 2_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 2 first replicate	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_VCP knockdown 2 first replicate	VCP_kd_2_first_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control 4	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	Control 4	P-MEXP-30004	none	total RNA	E_Mock 4	total_RNA	P-MEXP-30609	none	Cy5	L_Mock_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_Control 4	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_Control 4	Control_fourth_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for Control i.e. mock knockdown	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	  	  	  	  	  	Control for Control i.e. mock knockdown	P-MEXP-30004	none	total RNA	E_Control for Control i.e. mock knockdow	total_RNA	P-MEXP-30608	none	Cy3	L_Control for Control i.e. mock kd_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_Control 4	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_Control 4	Control_fourth_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control 3	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	Control 3	P-MEXP-30004	none	total RNA	E_Mock_3	total_RNA	P-MEXP-30608	none	Cy3	L_Mock_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_Control 3	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_Control 3	Control_third_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for Control i.e. mock knockdown	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	  	  	  	  	  	Control for Control i.e. mock knockdown	P-MEXP-30004	none	total RNA	E_Control for Control i.e. mock knockdow	total_RNA	P-MEXP-30609	none	Cy5	L_Control for Control i.e. mock kd_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_Control 3	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_Control 3	Control_third_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for Control i.e. mock knockdown	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	  	  	  	  	  	Control for Control i.e. mock knockdown	P-MEXP-30004	none	total RNA	E_Control for Control i.e. mock knockdow	total_RNA	P-MEXP-30608	none	Cy3	L_Control for Control i.e. mock kd_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_Control 2	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_Control 2	Control_second_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control 2	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	Control 2	P-MEXP-30004	none	total RNA	E_Mock 2	total_RNA	P-MEXP-30609	none	Cy5	L_Mock Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_Control 2	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_Control 2	Control_second_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
VCP knockdown 1 second replicate	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	VCP knockdown 1 second replicate	P-MEXP-30004	none	total RNA	E_VCP knockdown 1 second replicate	total_RNA	P-MEXP-30608	none	Cy3	L_VCP knockdown 1 second replicate_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 1 second replicate	A-BASE-3	P-MEXP-30610	VCP-1 siRNA	H_VCP knockdown 1 second replicate	VCP_kd_1_second_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for VCP kd 1	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	  	  	Control for VCP kd 1	P-MEXP-30004	none	total RNA	E_Control for VCP kd 1	total_RNA	P-MEXP-30609	none	Cy5	L_Control for VCP kd 1_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 1 second replicate	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_VCP knockdown 1 second replicate	VCP_kd_1_second_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for VCP kd 2	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	  	  	Control for VCP kd 2	P-MEXP-30004	none	total RNA	E_Control for VCP kd 2	total_RNA	P-MEXP-30608	none	Cy3	L_Control for VCP kd 2_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 2 fourth replicate	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_VCP knockdown 2 fourth replicate	VCP_kd_2_fourth_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
VCP knockdown 2 fourth replicate	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	VCP knockdown 2 fourth replicate	P-MEXP-30004	none	total RNA	E_VCP knockdown 2 fourth replicate	total_RNA	P-MEXP-30609	none	Cy5	L_VCP knockdown 2 fourth replicate_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 2 fourth replicate	A-BASE-3	P-MEXP-30610	VCP-2 siRNA	H_VCP knockdown 2 fourth replicate	VCP_kd_2_fourth_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
VCP knockdown 1 first replicate	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	P-MEXP-30646	P-MEXP-30645	VCP knockdown 1 first replicate	P-MEXP-30004	none	total RNA	E_VCP knockdown 1 first replicate	total_RNA	P-MEXP-30609	none	Cy5	L_VCP knockdown 1 first replicate_Cy5	Cy5	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 1 first replicate	A-BASE-3	P-MEXP-30610	VCP-1 siRNA	H_VCP knockdown 1 first replicate	VCP_kd_1_first_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip
Control for VCP kd 1	Homo sapiens	EFO	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9606	HeLa	EFO	EFO_0001185	  	  	Control for VCP kd 1	P-MEXP-30004	none	total RNA	E_Control for VCP kd 1	total_RNA	P-MEXP-30608	none	Cy3	L_Control for VCP kd 1_Cy3	Cy3	total_RNA	P-MEXP-30006	other	100	ug	-40	degree_C	H_VCP knockdown 1 first replicate	A-BASE-3	P-MEXP-30610	EGFP siRNA	H_VCP knockdown 1 first replicate	VCP_kd_1_first_replicate.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-817/E-MEXP-817.raw.1.zip