Table 2 List of gene targets and corresponding assays for quantifying materials.

From: An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

Organism	Gene	Accession no.	Oligonucleotide Name	Sequence (5′–3′)	Amplicon size (bp)	References
A. baumannii	ompA	KJ363323	ompA_F	CATGGAACTTCGTGTGATTCTTTG	111	O’Sullivan et al. (2014)¹⁴
			ompA_R	GCAGTAGCGTTAGGGTATTCAGATAAT
			ompA_MGB	[6FAM] AAATCAAACATCAAAGACC [MGBNFQ]
E. coli	uidA	AE014075	uidA_F	GCCCGCTTCGAAACCAAT	120	O’Sullivan et al. (2014)¹⁴
			uidA_R	TCGCATTACCCTTACGCTGAA
			uidA_HP	[6FAM] TCCATGTTCATCTGCCCAGTCGAGC [BHQ1]
E. faecalis	groES	AF335185	groES_F	TTACTGTGTCACCAATTTTTACTTCCA	96	O’Sullivan et al. (2014)¹⁴
			groES_R	AACCACAAACAGGTGAAGTTATCG
			groES_HP	[6FAM] TGCCATTTTCAAGCACACGACCTTCA [BHQ1]
E. faecium	ddl	U39790,	ddl_F	ACGTAGCATTCTATGATTATGAAGC	124	Naserpour Farivar et al. (2014)⁴³
			ddl_R	CATCGTGTAAGCTAACTTCG
			ddl_P	[6FAM] CAGATTCCAGCCGAAGTGCC [BHQ1]
H. influenzae	hin	P26093	Hin_F	CCGGGTGCGGTAGAATTTAATAA	91	Garcha et al. (2012)⁴⁴
			Hin_R	CTGATTTTTCAGTGCTGTCTTTGC
			Hin_HP	[6FAM]ACAGCCACAACGGTAAAGTGTTCTACG [BHQ1]
K. pneumoniae	khe	AF293352	Khe_F	GATGAAACGACCTGATTGCATTC	77	Hartman et al. (2009)⁴⁵
			Khe_R	CCGGGCTGTCGGGATAAG
			Khe_HP	[6FAM] CGCGAACTGGAAGGGCCCG [BHQ1]
M. catarrhalis	mor	U69982	Mor_F	GTGAGTGCCGCTTTTACAACC	72	Greiner et al. (2003)⁴⁶
			Mor_R	TGTATCGCCTGCCAAGACAA
			Mor_HP	[6FAM] TGCTTTTGCAGCTGTTAGCCAGCCTAA [BHQ1]
M. tuberculosis	rpo_B	AL123456	RPOB_FW1	CAAAACAGCCGCTAGTCCTAGTC	84	Devonshire et al. (2015)⁴⁷
			RPOB_RV1	AAGGAGACCCGGTTTGGC
			RPOB_P1	[6FAM]AGTCGCCCGCAAAGTTCCTCGAA[NFQ]
N. meningitidis	ctrA	AM4210808	CtrA_F	GCCGTTTGTTGGCGATATTT	150	O’Sullivan et al. (2014)¹⁴
			CtrA_R	GCACGAATCACCGACACATT
			CtrA_HP	[6FAM]CGGTGGTCGGTAAAACGCCTGG [BHQ1]
P. aeruginosa	regA	EU342000	regA_F	TGCTGGTGGCACAGGACAT	65	Lee et al. (2006)⁴⁸
			regA_R	TTGTTGGTGCAGTTCCTCATTG
			regA_MGB	[6FAM] CAGATGCTTTGCCTCAA [MGBNFQ]
S. agalactiae	sip	HQ878436	sip_F	ATCCTGAGACAACACTGACA	78	O’Sullivan et al. (2014)¹⁴
			sip-R	TTGCTGGTGTTTCTATTTTCA
			sip-HP	[6FAM] ATCAGAAGAGTCATACTGCCACTTC [BHQ1]
S. aureus	coA	AB436985	coA_F	GTAGATTGGGCAATTACATTTTGGAGG	117	O’Sullivan et al. (2014)¹⁴
			coA_R	CGCATCTGCTTTGTTATCCCATGTA
			coA-HP	[6FAM] TAGGCGCATTAGCAGTTGCATC [BHQ1]
S. enterica	ttr	AE006468	ttr_F	CGGCGATGCGTATCACTTT	61	This study
			ttr_R	TTGGACACAGTGCGGTATCC
			ttr_P	[FAM] CATCGGCATTAACCCGGGCG [BHQ1]
S. epidermidis	femA_SE	U23713	F femA-SE	TGCCTTTACAGATAGCATGCCA	172	Francois et al. (2003)⁴⁹
			R femA-SE	AGTAAGTAAGCAAGCTGCAATGACC
			P femA-SE	TCATTTCACGCAAACTGTTGGCCACTATG
S. pneumoniae	lytA	HG531769	LytA_F	ACGCAATCTAGCAGATGAAGC	101	Harris et al. (2008)⁵⁰
			LytA_R	TGTTTGGTTGGTTATTCGTGC
			LytA_HP	[6FAM] TTTGCCGAAAACGCTTGATACAGGG [BHQ1]
S. pyogenes	csrR	JX414161	csrR_F	TGGATGTGGTTGCAGGTTTAGAC	79	O’Sullivan et al. (2014)¹⁴
			csrR_R	CGGGCAAGTAGTTCTTCAATGG
			csrR_HP	[6FAM] CGGTGCAGACGACTATATTGTTAAACC [BHQ1]

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Table 2 List of gene targets and corresponding assays for quantifying materials.

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