Table 3. Compilation of re-processed RNA-seq data sets for use as ground-truths in normalization.

Data set label	Experimental design	Number of genes	Number of samples	Number of good references	Spike-ins
dmelAC	2 environments × 16 strains × 2 sexes	17860	367	7	ERCC 78A, centrifuge
dmelAV	2 environments × 16 strains × 2 sexes	17860	165	15	ERCC 78A, vacuum
mpreg1a	3 brain regions × 3 post-partum stages	55493	27	14	ERCC, 1:10 dilution
mpreg1b	1 brain region × 3 post-partum stages	55493	9	15	ERCC, 1:100 dilution
mpreg2a	3 brain regions × 3 stages	55493	27	16	ERCC, 1:10 dilution
mpreg2b	1 brain region × 3 stages	55493	9	17	ERCC, 1:100 dilution
rbm1	5 organs × 4 stages × 2 sexes	32975	159	28	ERCC Mix 1
rbm2	6 organs × 4 stages × 2 sexes	32975	159	27	ERCC Mix 2
rnor1	26 chemicals	32975	64	37	ERCC Mix 1
rnor2	16 chemicals	32975	52	37	ERCC Mix 2
sarcoma	9 diseases × 2 metastatic states	58380	125	36	ERCC Mix, Life Technologies
lymphoma	4 cell lines × 3 treatments	58380	34	11	ERCC Mix 1, 1 µL to 5000 ng RNA
yfv	2 cell models × 3 infections	58380	24	21	ERCC Mix 1
xtro1m	Time series, replicated in 2 clutches	21550	145	16	ERCC Mix 1, polyA enrichment
xtro2	Time series	21550	48	28	ERCC Mix 1, RiboZero enrichment