Table 1.

Selection of targets and MiSeq verification of knockouts.

Cell line	Target	Protein name	Uniprot	Rationale	Location	Frameshift
6xKO	BGN	Biglycan	G3HSX8	A	Secreted	+1
	TIMP1	Metalloproteinase inhibitor 1	G3IBH0	A/C	Secreted	−5/−2/+1
	LGALS3BP	Galectin-3-binding protein	G3H3E4	A/C	Membrane	+33
	NID1.1	Nidogen-1	G3HWE4	A/C	Membrane/matrix	+1
	NID1.2	Nidogen-1	G3I3U5	A/C	Membrane/matrix	+1
	CTSD	Cathepsin D	G3I4W7	A/C/Q	Lysosome	−8
11xKO	Aga	N(4)-(Beta-N-acetylglucosaminyl)-l-asparaginase	G3HGM6	A	Secreted	−40
	Erp29	Endoplasmic reticulum resident protein 29	G3H284	A	ER	−1
	Gpr56	G-protein coupled receptor 56	G3I3K5	A/C	Membrane	+1
	Tinagl1	Tubulointerstitial nephritis antigen-like	G3H1W4	A/C	Secreted	+1
	Lgmn	Legumain	G3I1H5	A/C/Q	Lysosome	+1
14xKO	Yeats2	YEATS domain-containing protein 2	G3I3I8	A	Nucleus	+1
	Sparc	SPARC	G3H584	A/C	Secreted	−5
	Lpl	Lipoprotein lipase	G3H6V7	A/C/Q	Membrane/secreted	+1

The target names, full protein names, UniProt identifiers, rationale for deletion, subcellular location, and indel size are indicated. Source data are provided as a Source Data file.

A abundance, C copurifying, Q quality.