Using RNA-seq to identify suitable housekeeping genes for hypoxia studies in human adipose-derived stem cells

Table 2 Housekeeping gene candidates – selected on smallest coefficient of variance in TPM and DESeq2-normalised counts

Gene	Norm	CV calculated					L2FC	\(\underline{CV}\)	Norm CV	Norm L2FC	Arbitrary Ranking
Gene	Norm	A	B	C	D	E	L2FC			Norm L2FC	Sum	Rank
GUSB	TPM	0.19	0.37	0.11	0.04	0.27	0.01^a	0.01	1.1	1.0^a	2.1	1
GUSB	DE	0.09	0.08	0.14	0.04	0.28	0.01^a	0.01	1.1	1.0^a	2.1	1
RRP1	TPM	0.30	0.30	0.08	0.13	0.15	-0.02	0.02	1.2	2.2	3.4	2
RRP1	DE	0.08	0.08	0.09	0.10	0.16	-0.02	0.02	1.2	2.2	3.4	2
ALAS1	TPM	0.15	0.35	0.18	0.03	0.14	0.05	0.01^a	1.0^a	6.4	7.4	3
ALAS1	DE	0.11	0.08	0.06	0.06	0.14	0.05	0.01^a	1.0^a	6.4	7.4	3
POLR2B	TPM	0.12	0.33	0.27	0.06	0.38	-0.12	0.01	1.1	14.0	15.1	4
POLR2B	DE	0.13	0.05	0.12	0.05	0.38	-0.12	0.01	1.1	14.0	15.1	4
CHFR	TPM	0.24	0.15	0.23	0.13	0.12	0.12	0.01	1.2	14.3	15.5	5
CHFR	DE	0.05	0.30	0.10	0.08	0.11	0.12	0.01	1.2	14.3	15.5	5
GGA1	TPM	0.42	0.47	0.11	0.15	0.14	-0.15	0.02	1.8	17.9	19.7	6
GGA1	DE	0.20	0.16	0.13	0.15	0.14	-0.15	0.02	1.8	17.9	19.7	6
YWHAZ	TPM	0.06	0.05	0.07	0.22	0.08	0.39	0.01	1.1	47.2	48.2	7
YWHAZ	DE	0.28	0.34	0.18	0.18	0.08	0.39	0.01	1.1	47.2	48.2	7
NONO	TPM	0.06	0.06	0.11	0.09	0.14	0.46	0.02	1.2	55.2	56.4	8
NONO	DE	0.23	0.36	0.19	0.13	0.15	0.46	0.02	1.2	55.2	56.4	8

Coefficient of variance was calculated from TPM and DESeq2-normalised values with L2FC values extracted from DESeq2. The average CV was calculated from HKG with CV ≤ 0.15 (bolded), before normalising CV and L2FC to the smallest corresponding values (^a) of the 78 candidates and summed. HKG were ranked from smallest to the largest value for the sum of these four methods

ISSN: 2661-8850