Source Name	Material Type	Characteristics [specimen with known storage state]	Characteristics [cell type]	Characteristics[cell line]	Characteristics [organism]	Protocol REF	Protocol REF	Sample Name	Material Type	Characteristics[genetic modification]	Characteristics[genotype]	Comment [transfected cell line]	Protocol REF	Extract Name	Material Type	Protocol REF	Term Source REF	Labeled Extract Name	Material Type	Label	Protocol REF	Term Source REF	Assay Name	Technology Type	Array Design REF	Protocol REF	Term Source REF	Scan Name	Array Data File	Comment [ArrayExpress FTP file]	Protocol REF	Normalization Name	Derived Array Data Matrix File	Comment [Derived ArrayExpress FTP file]	Factor Value [RNA interference]	Factor Value [genotype]
sa3_shGFP-a	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34703	sa3_shGFP-a	cell	gene knock down	GFP knockdown control	CGR8-GFP_KD	P-MTAB-34706	E_sa3_shGFP-a	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shGFP-a Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shGFP-a	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shGFP-a	sa3_shGFP-a.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	GFP shRNA	GFP knockdown control
sa3_shGFP-b	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34703	sa3_shGFP-b	cell	gene knock down	GFP knockdown control	CGR8-GFP_KD	P-MTAB-34706	E_sa3_shGFP-b	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shGFP-b Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shGFP-b	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shGFP-b	sa3_shGFP-b.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	GFP shRNA	GFP knockdown control
sa3_shGFP-c	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34703	sa3_shGFP-c	cell	gene knock down	GFP knockdown control	CGR8-GFP_KD	P-MTAB-34706	E_sa3_shGFP-c	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shGFP-c Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shGFP-c	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shGFP-c	sa3_shGFP-c.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	GFP shRNA	GFP knockdown control
sa3_shKLF4seq1-a	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34704	sa3_shKLF4seq1-a	cell	gene knock down	Klf4 knockdown	CGR8-KLF4_KD	P-MTAB-34706	E_sa3_shKLF4seq1-a	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF4seq1-a Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF4seq1-a	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF4seq1-a	sa3_shKLF4seq1-a.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf4 shRNA	Klf4 knockdown
sa3_shKLF4seq1-b	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34704	sa3_shKLF4seq1-b	cell	gene knock down	Klf4 knockdown	CGR8-KLF4_KD	P-MTAB-34706	E_sa3_shKLF4seq1-b	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF4seq1-b Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF4seq1-b	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF4seq1-b	sa3_shKLF4seq1-b.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf4 shRNA	Klf4 knockdown
sa3_shKLF4seq1-c	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34704	sa3_shKLF4seq1-c	cell	gene knock down	Klf4 knockdown	CGR8-KLF4_KD	P-MTAB-34706	E_sa3_shKLF4seq1-c	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF4seq1-c Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF4seq1-c	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF4seq1-c	sa3_shKLF4seq1-c.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf4 shRNA	Klf4 knockdown
sa3_shKLF4seq2-a	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34704	sa3_shKLF4seq2-a	cell	gene knock down	Klf4 knockdown	CGR8-KLF4_KD	P-MTAB-34706	E_sa3_shKLF4seq2-a	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF4seq2-a Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF4seq2-a	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF4seq2-a	sa3_shKLF4seq2-a.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf4 shRNA	Klf4 knockdown
sa3_shKLF4seq2-b	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34704	sa3_shKLF4seq2-b	cell	gene knock down	Klf4 knockdown	CGR8-KLF4_KD	P-MTAB-34706	E_sa3_shKLF4seq2-b	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF4seq2-b Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF4seq2-b	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF4seq2-b	sa3_shKLF4seq2-b.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf4 shRNA	Klf4 knockdown
sa3_shKLF4seq2-c	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34704	sa3_shKLF4seq2-c	cell	gene knock down	Klf4 knockdown	CGR8-KLF4_KD	P-MTAB-34706	E_sa3_shKLF4seq2-c	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF4seq2-c Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF4seq2-c	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF4seq2-c	sa3_shKLF4seq2-c.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf4 shRNA	Klf4 knockdown
sa3_shKLF5seq1-a	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34705	sa3_shKLF5seq1-a	cell	gene knock down	Klf5 knockdown	CGR8-KLF5_KD	P-MTAB-34706	E_sa3_shKLF5seq1-a	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF5seq1-a Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF5seq1-a	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF5seq1-a	sa3_shKLF5seq1-a.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf5 shRNA	Klf5 knockdown
sa3_shKLF5seq1-b	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34705	sa3_shKLF5seq1-b	cell	gene knock down	Klf5 knockdown	CGR8-KLF5_KD	P-MTAB-34706	E_sa3_shKLF5seq1-b	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF5seq1-b Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF5seq1-b	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF5seq1-b	sa3_shKLF5seq1-b.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf5 shRNA	Klf5 knockdown
sa3_shKLF5seq1-c	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34705	sa3_shKLF5seq1-c	cell	gene knock down	Klf5 knockdown	CGR8-KLF5_KD	P-MTAB-34706	E_sa3_shKLF5seq1-c	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF5seq1-c Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF5seq1-c	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF5seq1-c	sa3_shKLF5seq1-c.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf5 shRNA	Klf5 knockdown
sa3_shKLF5seq2-a	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34705	sa3_shKLF5seq2-a	cell	gene knock down	Klf5 knockdown	CGR8-KLF5_KD	P-MTAB-34706	E_sa3_shKLF5seq2-a	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF5seq2-a Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF5seq2-a	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF5seq2-a	sa3_shKLF5seq2-a.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf5 shRNA	Klf5 knockdown
sa3_shKLF5seq2-b	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34705	sa3_shKLF5seq2-b	cell	gene knock down	Klf5 knockdown	CGR8-KLF5_KD	P-MTAB-34706	E_sa3_shKLF5seq2-b	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF5seq2-b Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF5seq2-b	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF5seq2-b	sa3_shKLF5seq2-b.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf5 shRNA	Klf5 knockdown
sa3_shKLF5seq2-c	cell	frozen sample	embryonic stem cell	CGR8	Mus musculus	P-MTAB-34702	P-MTAB-34705	sa3_shKLF5seq2-c	cell	gene knock down	Klf5 knockdown	CGR8-KLF5_KD	P-MTAB-34706	E_sa3_shKLF5seq2-c	total RNA	P-AFFY-2	ArrayExpress	LE_sa3_shKLF5seq2-c Biotin	synthetic DNA	biotin	P-AFFY-3	ArrayExpress	sa3_shKLF5seq2-c	array assay	A-AFFY-45	P-AFFY-6	ArrayExpress	sa3_shKLF5seq2-c	sa3_shKLF5seq2-c.CEL	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.raw.1.zip	P-MTAB-34707	RMARESULTS_INS-3.txt	RMARESULTS_INS-3mt.txt	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-1838/E-MTAB-1838.processed.1.zip	Klf5 shRNA	Klf5 knockdown